Query gi|254780788|ref|YP_003065201.1| transcription elongation factor NusA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 526
No_of_seqs 242 out of 1121
Neff 5.2
Searched_HMMs 39220
Date Sun May 29 18:46:27 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780788.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09202 nusA transcription el 100.0 0 0 1079.2 48.4 427 5-506 2-428 (428)
2 PRK12329 nusA transcription el 100.0 0 0 997.0 43.1 406 6-411 6-448 (457)
3 PRK12327 nusA transcription el 100.0 0 0 977.3 42.7 351 5-355 1-352 (353)
4 PRK12328 nusA transcription el 100.0 0 0 975.5 43.0 349 7-355 2-357 (375)
5 TIGR01953 NusA transcription t 100.0 0 0 983.3 37.2 339 8-346 1-366 (366)
6 COG0195 NusA Transcription elo 100.0 0 0 425.9 17.6 182 160-347 1-183 (190)
7 pfam08529 NusA_N NusA N-termin 100.0 8E-31 2E-35 245.8 14.5 122 8-129 1-122 (122)
8 PRK08406 transcription elongat 99.9 8E-26 2E-30 209.0 6.0 94 250-344 44-139 (142)
9 cd04455 S1_NusA S1_NusA: N-uti 99.8 7E-19 1.8E-23 158.0 8.6 67 136-202 1-67 (67)
10 cd02134 NusA_KH NusA_K homolog 99.7 9.6E-17 2.4E-21 142.3 4.8 60 283-342 1-61 (61)
11 TIGR01954 nusA_Cterm_rpt trans 99.1 5.1E-11 1.3E-15 100.2 4.5 50 368-417 1-52 (52)
12 PRK00087 4-hydroxy-3-methylbut 98.8 7.7E-07 2E-11 69.5 14.4 72 137-210 303-381 (670)
13 PRK07899 rpsA 30S ribosomal pr 98.6 1E-06 2.6E-11 68.6 11.5 270 23-342 18-347 (484)
14 TIGR01954 nusA_Cterm_rpt trans 98.6 6.1E-08 1.6E-12 77.6 4.8 50 443-511 1-52 (52)
15 PRK07400 30S ribosomal protein 98.6 2.3E-06 5.9E-11 66.0 12.8 64 137-203 117-183 (314)
16 cd05687 S1_RPS1_repeat_ec1_hs1 98.5 5.7E-07 1.4E-11 70.5 8.2 63 139-203 1-70 (70)
17 PRK06299 rpsA 30S ribosomal pr 98.5 8.6E-06 2.2E-10 61.8 13.0 64 138-203 104-171 (556)
18 PRK13806 rpsA 30S ribosomal pr 98.4 1.2E-06 3E-11 68.1 7.7 124 73-201 140-273 (489)
19 pfam00575 S1 S1 RNA binding do 98.4 1.9E-06 4.8E-11 66.7 7.9 65 136-202 2-73 (74)
20 PRK06299 rpsA 30S ribosomal pr 98.4 2E-06 5E-11 66.5 7.8 109 88-202 143-259 (556)
21 PRK07899 rpsA 30S ribosomal pr 98.4 2.5E-06 6.4E-11 65.7 8.1 123 73-202 147-276 (484)
22 PRK06676 rpsA 30S ribosomal pr 98.3 6E-06 1.5E-10 63.0 9.4 188 89-312 61-260 (390)
23 PRK13806 rpsA 30S ribosomal pr 98.3 2.9E-05 7.4E-10 58.0 12.0 115 75-204 57-182 (489)
24 PRK00087 4-hydroxy-3-methylbut 98.2 1.9E-05 4.9E-10 59.2 9.9 160 73-259 326-502 (670)
25 PRK07400 30S ribosomal protein 98.2 1.3E-05 3.4E-10 60.4 8.5 78 130-209 21-107 (314)
26 PRK12269 bifunctional cytidyla 98.1 2E-05 5.2E-10 59.1 8.1 68 135-208 318-386 (863)
27 TIGR00717 rpsA ribosomal prote 98.1 3.3E-05 8.4E-10 57.5 9.1 174 69-269 39-234 (534)
28 smart00316 S1 Ribosomal protei 98.1 2.8E-05 7.2E-10 58.0 8.6 64 137-202 1-71 (72)
29 cd05691 S1_RPS1_repeat_ec6 S1_ 98.1 2.9E-05 7.5E-10 57.9 8.5 62 139-202 1-69 (73)
30 cd04461 S1_Rrp5_repeat_hs8_sc7 98.0 2.8E-05 7.3E-10 58.0 8.1 67 131-201 9-82 (83)
31 COG0539 RpsA Ribosomal protein 98.0 5.1E-05 1.3E-09 56.1 9.1 112 79-201 134-259 (541)
32 PRK06676 rpsA 30S ribosomal pr 98.0 7E-05 1.8E-09 55.1 9.5 73 126-202 182-260 (390)
33 PRK08059 general stress protei 97.9 5.7E-05 1.5E-09 55.8 7.6 65 137-203 5-76 (119)
34 cd05697 S1_Rrp5_repeat_hs5 S1_ 97.9 7.9E-05 2E-09 54.7 8.1 61 139-201 1-68 (69)
35 TIGR00717 rpsA ribosomal prote 97.9 0.00016 4E-09 52.5 9.6 152 41-201 101-269 (534)
36 COG0539 RpsA Ribosomal protein 97.9 0.00056 1.4E-08 48.5 12.4 122 75-205 45-174 (541)
37 cd02409 KH-II KH-II (K homolo 97.9 2.2E-05 5.6E-10 58.8 5.1 58 284-341 1-67 (68)
38 cd05698 S1_Rrp5_repeat_hs6_sc5 97.9 7.7E-05 2E-09 54.8 7.9 62 139-202 1-69 (70)
39 TIGR02236 recomb_radA DNA repa 97.9 3.1E-05 8E-10 57.7 5.7 56 363-418 3-58 (333)
40 cd05688 S1_RPS1_repeat_ec3 S1_ 97.8 7.5E-05 1.9E-09 54.9 6.8 58 138-195 1-64 (68)
41 cd05685 S1_Tex S1_Tex: The C-t 97.8 0.00012 3E-09 53.4 7.6 61 139-201 1-68 (68)
42 cd04465 S1_RPS1_repeat_ec2_hs2 97.8 0.00019 4.9E-09 51.9 8.2 62 139-203 1-67 (67)
43 cd04452 S1_IF2_alpha S1_IF2_al 97.8 0.00016 4.2E-09 52.4 7.8 65 136-202 1-74 (76)
44 PRK07252 hypothetical protein; 97.7 0.00019 4.9E-09 51.9 7.5 66 137-204 2-74 (120)
45 cd04472 S1_PNPase S1_PNPase: P 97.7 0.00017 4.3E-09 52.3 7.0 61 139-202 1-68 (68)
46 TIGR02236 recomb_radA DNA repa 97.7 4.3E-05 1.1E-09 56.7 3.9 58 436-510 1-58 (333)
47 cd05708 S1_Rrp5_repeat_sc12 S1 97.7 0.00019 4.8E-09 52.0 7.2 66 137-204 1-74 (77)
48 PRK12269 bifunctional cytidyla 97.6 0.00043 1.1E-08 49.3 8.0 124 69-204 339-474 (863)
49 PRK07956 ligA NAD-dependent DN 97.5 0.00061 1.6E-08 48.2 8.1 99 363-474 448-549 (668)
50 cd05692 S1_RPS1_repeat_hs4 S1_ 97.4 0.00082 2.1E-08 47.3 7.7 61 139-202 1-68 (69)
51 PRK04301 radA DNA repair and r 97.4 0.00033 8.3E-09 50.2 5.3 56 362-417 9-64 (318)
52 PRK03987 translation initiatio 97.4 0.002 5.2E-08 44.4 9.3 75 136-210 6-89 (262)
53 cd00164 S1_like S1_like: Ribos 97.4 0.00087 2.2E-08 47.1 7.3 58 142-201 1-65 (65)
54 cd05706 S1_Rrp5_repeat_sc10 S1 97.3 0.0021 5.3E-08 44.3 8.7 63 137-201 2-71 (73)
55 cd05690 S1_RPS1_repeat_ec5 S1_ 97.3 0.0013 3.2E-08 45.9 7.3 56 139-194 1-64 (69)
56 PRK08406 transcription elongat 97.3 0.00064 1.6E-08 48.1 5.4 70 278-347 4-75 (142)
57 cd05689 S1_RPS1_repeat_ec4 S1_ 97.2 0.0017 4.4E-08 44.9 7.5 59 137-195 2-68 (72)
58 cd05707 S1_Rrp5_repeat_sc11 S1 97.2 0.0021 5.3E-08 44.3 7.3 61 139-201 1-68 (68)
59 PRK05807 hypothetical protein; 97.2 0.0019 5E-08 44.5 7.2 64 137-203 4-73 (136)
60 PRK01172 ski2-like helicase; P 97.2 0.018 4.6E-07 37.4 12.1 107 387-510 548-670 (674)
61 PRK01172 ski2-like helicase; P 97.1 0.0015 3.8E-08 45.4 5.8 57 362-418 614-670 (674)
62 cd05694 S1_Rrp5_repeat_hs2_sc2 97.0 0.0041 1E-07 42.1 7.6 64 137-200 3-68 (74)
63 PRK08582 hypothetical protein; 97.0 0.0039 1E-07 42.3 7.2 63 137-202 4-73 (139)
64 PRK04301 radA DNA repair and r 96.9 0.0027 6.9E-08 43.4 5.8 22 14-35 40-61 (318)
65 cd04471 S1_RNase_R S1_RNase_R: 96.9 0.0071 1.8E-07 40.4 7.9 58 138-195 1-77 (83)
66 cd05684 S1_DHX8_helicase S1_DH 96.7 0.0091 2.3E-07 39.6 7.5 61 139-203 1-72 (79)
67 PRK09202 nusA transcription el 96.7 0.0016 4.2E-08 45.1 3.5 170 178-414 255-428 (428)
68 PTZ00035 Rad51; Provisional 96.7 0.0031 7.8E-08 43.1 4.9 56 362-417 34-92 (350)
69 cd04473 S1_RecJ_like S1_RecJ_l 96.7 0.0083 2.1E-07 39.9 7.1 56 137-194 15-71 (77)
70 cd04460 S1_RpoE S1_RpoE: RpoE, 96.7 0.0083 2.1E-07 39.9 7.0 68 140-207 1-88 (99)
71 PTZ00162 RNA polymerase II sub 96.7 0.011 2.7E-07 39.1 7.5 72 134-205 77-164 (170)
72 PRK08563 DNA-directed RNA poly 96.6 0.0085 2.2E-07 39.8 6.7 74 134-207 77-170 (182)
73 PRK00254 ski2-like helicase; P 96.5 0.0039 1E-07 42.3 4.3 105 387-508 578-700 (717)
74 COG1095 RPB7 DNA-directed RNA 96.4 0.0086 2.2E-07 39.8 5.7 73 134-207 77-170 (183)
75 COG1093 SUI2 Translation initi 96.4 0.026 6.6E-07 36.3 8.1 71 136-206 9-88 (269)
76 PRK05054 exoribonuclease II; P 96.4 0.047 1.2E-06 34.4 9.1 65 142-206 86-158 (644)
77 PRK08097 ligB NAD-dependent DN 96.3 0.024 6.1E-07 36.5 7.6 116 363-518 429-547 (563)
78 TIGR00575 dnlj DNA ligase, NAD 96.2 0.06 1.5E-06 33.6 9.2 285 128-504 315-663 (706)
79 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 96.2 0.022 5.6E-07 36.8 6.8 59 134-192 2-71 (86)
80 cd05703 S1_Rrp5_repeat_hs12_sc 96.2 0.042 1.1E-06 34.7 8.1 63 139-203 1-72 (73)
81 PRK04163 exosome complex RNA-b 96.1 0.025 6.2E-07 36.4 6.8 63 132-194 56-129 (232)
82 cd04454 S1_Rrp4_like S1_Rrp4_l 96.1 0.016 4.1E-07 37.8 5.8 70 134-206 2-78 (82)
83 cd04453 S1_RNase_E S1_RNase_E: 96.1 0.03 7.5E-07 35.8 6.8 66 135-200 4-81 (88)
84 PRK11642 exoribonuclease R; Pr 95.9 0.17 4.2E-06 30.3 10.6 25 14-38 38-62 (813)
85 cd02134 NusA_KH NusA_K homolog 95.9 0.0067 1.7E-07 40.6 2.9 58 205-277 2-61 (61)
86 TIGR02063 RNase_R ribonuclease 95.9 0.087 2.2E-06 32.4 8.6 93 105-197 637-750 (755)
87 COG2996 Predicted RNA-bindinin 95.9 0.017 4.5E-07 37.5 5.0 106 78-193 101-209 (287)
88 PTZ00248 eukaryotic translatio 95.8 0.043 1.1E-06 34.6 6.9 82 129-210 8-98 (324)
89 TIGR00575 dnlj DNA ligase, NAD 95.8 0.076 1.9E-06 32.8 8.0 118 363-517 455-589 (706)
90 PRK11824 polynucleotide phosph 95.8 0.11 2.7E-06 31.8 8.7 61 282-342 514-590 (694)
91 PRK13766 Hef nuclease; Provisi 95.8 0.019 4.7E-07 37.3 4.8 46 365-411 711-756 (764)
92 PRK11712 ribonuclease G; Provi 95.7 0.057 1.5E-06 33.7 7.0 181 136-323 36-282 (489)
93 PRK00254 ski2-like helicase; P 95.6 0.21 5.4E-06 29.5 11.9 53 362-414 646-698 (717)
94 PRK06418 transcription elongat 95.5 0.23 5.8E-06 29.3 12.3 135 199-342 28-165 (167)
95 pfam10246 MRP-S35 Mitochondria 95.5 0.029 7.5E-07 35.8 5.1 66 128-194 13-79 (105)
96 COG0272 Lig NAD-dependent DNA 95.5 0.099 2.5E-06 32.0 7.6 49 362-411 510-561 (667)
97 cd05791 S1_CSL4 S1_CSL4: CSL4, 95.4 0.1 2.6E-06 31.8 7.6 70 135-207 3-89 (92)
98 cd05693 S1_Rrp5_repeat_hs1_sc1 95.4 0.1 2.6E-06 31.8 7.6 66 137-202 2-94 (100)
99 smart00322 KH K homology RNA-b 95.4 0.017 4.2E-07 37.7 3.4 41 305-345 2-42 (69)
100 TIGR03491 RecB family nuclease 95.3 0.042 1.1E-06 34.7 5.1 58 362-419 209-266 (457)
101 cd05686 S1_pNO40 S1_pNO40: pNO 95.2 0.072 1.8E-06 33.0 6.2 64 137-203 2-73 (73)
102 PRK02362 ski2-like helicase; P 95.0 0.34 8.6E-06 28.1 11.0 100 388-507 589-705 (736)
103 PRK07956 ligA NAD-dependent DN 94.9 0.14 3.5E-06 30.9 7.1 51 360-411 508-561 (668)
104 COG1097 RRP4 RNA-binding prote 94.9 0.12 3.1E-06 31.4 6.6 63 132-194 58-131 (239)
105 TIGR03591 polynuc_phos polyrib 94.8 0.18 4.6E-06 30.1 7.4 62 281-342 510-587 (684)
106 KOG1070 consensus 94.8 0.15 3.9E-06 30.6 6.9 91 136-226 1160-1261(1710)
107 PRK02362 ski2-like helicase; P 94.5 0.072 1.8E-06 33.0 4.8 49 362-412 654-702 (736)
108 cd05705 S1_Rrp5_repeat_hs14 S1 94.4 0.35 9E-06 27.9 8.0 59 137-195 2-70 (74)
109 PRK08609 hypothetical protein; 94.4 0.32 8.3E-06 28.2 7.8 33 311-343 243-281 (570)
110 COG2183 Tex Transcriptional ac 94.2 0.17 4.3E-06 30.3 6.1 162 229-411 333-527 (780)
111 cd05702 S1_Rrp5_repeat_hs11_sc 94.1 0.29 7.3E-06 28.6 7.1 55 139-193 1-64 (70)
112 cd02410 archeal_CPSF_KH The ar 94.0 0.19 4.9E-06 29.8 6.0 100 238-346 10-116 (145)
113 smart00483 POLXc DNA polymeras 93.9 0.15 3.7E-06 30.7 5.3 12 7-18 4-15 (334)
114 cd05704 S1_Rrp5_repeat_hs13 S1 93.9 0.31 8E-06 28.3 6.9 61 137-201 2-70 (72)
115 PRK09521 exosome complex RNA-b 93.8 0.15 3.9E-06 30.6 5.2 68 135-207 61-146 (187)
116 pfam10447 EXOSC1 Exosome compo 93.8 0.35 9.1E-06 27.9 7.1 53 136-188 2-71 (72)
117 cd00141 NT_POLXc Nucleotidyltr 93.8 0.28 7.2E-06 28.6 6.5 34 311-344 237-276 (307)
118 COG1855 ATPase (PilT family) [ 93.7 0.35 9E-06 27.9 6.8 299 19-349 178-529 (604)
119 cd05695 S1_Rrp5_repeat_hs3 S1_ 93.6 0.63 1.6E-05 26.1 8.3 61 139-201 1-66 (66)
120 PRK12704 phosphodiesterase; Pr 93.5 0.64 1.6E-05 26.0 8.9 150 284-470 126-289 (455)
121 PRK10811 rne ribonuclease E; R 93.4 0.24 6.1E-06 29.1 5.7 162 136-303 36-260 (1063)
122 PRK12766 50S ribosomal protein 93.2 0.1 2.6E-06 31.9 3.5 53 359-411 9-61 (238)
123 PTZ00035 Rad51; Provisional 93.0 0.26 6.7E-06 28.9 5.3 51 441-508 41-91 (350)
124 PRK12705 hypothetical protein; 93.0 0.63 1.6E-05 26.1 7.3 168 260-470 137-318 (485)
125 COG0272 Lig NAD-dependent DNA 93.0 0.77 2E-05 25.4 8.2 99 363-474 448-549 (667)
126 PRK13764 ATPase; Provisional 92.8 0.21 5.4E-06 29.5 4.7 150 186-348 344-526 (605)
127 pfam03118 RNA_pol_A_CTD Bacter 92.6 0.19 4.9E-06 29.9 4.2 55 358-412 5-59 (62)
128 KOG3409 consensus 92.6 0.46 1.2E-05 27.1 6.1 75 128-205 58-149 (193)
129 COG2251 Predicted nuclease (Re 92.6 0.15 3.8E-06 30.7 3.6 71 367-441 232-302 (474)
130 KOG2193 consensus 92.5 0.18 4.7E-06 30.0 4.0 40 303-342 408-447 (584)
131 TIGR03319 YmdA_YtgF conserved 92.4 0.92 2.3E-05 24.9 8.5 129 308-470 206-348 (514)
132 KOG3298 consensus 92.3 0.39 1E-05 27.6 5.5 63 133-195 76-155 (170)
133 COG2996 Predicted RNA-bindinin 92.2 0.7 1.8E-05 25.7 6.7 113 78-212 31-147 (287)
134 COG1185 Pnp Polyribonucleotide 92.2 0.95 2.4E-05 24.7 8.2 67 396-463 507-578 (692)
135 COG1530 CafA Ribonucleases G a 92.0 0.33 8.5E-06 28.1 4.8 64 136-199 35-111 (487)
136 cd02396 PCBP_like_KH K homolog 92.0 0.18 4.6E-06 30.1 3.4 39 307-345 1-39 (65)
137 TIGR02239 recomb_RAD51 DNA rep 91.8 1.1 2.7E-05 24.4 7.6 90 365-458 6-95 (317)
138 TIGR03491 RecB family nuclease 91.7 0.31 8E-06 28.3 4.4 31 436-466 208-238 (457)
139 TIGR03675 arCOG00543 arCOG0178 91.5 0.72 1.8E-05 25.6 6.1 161 37-215 73-274 (630)
140 KOG2190 consensus 91.4 1.2 3E-05 24.1 7.5 100 248-347 264-379 (485)
141 COG1096 Predicted RNA-binding 91.2 0.54 1.4E-05 26.6 5.2 57 134-190 60-133 (188)
142 cd03586 Pol_IV_kappa Pol_IV_ka 91.1 1.2 3.1E-05 23.9 7.5 36 437-472 174-209 (337)
143 PRK00558 uvrC excinuclease ABC 89.9 0.93 2.4E-05 24.8 5.4 50 362-412 556-605 (609)
144 pfam02889 Sec63 Sec63 Brl doma 89.4 1.1 2.7E-05 24.4 5.5 42 433-474 146-187 (309)
145 TIGR01009 rpsC_bact ribosomal 89.3 1.2 2.9E-05 24.1 5.6 59 283-341 40-107 (217)
146 PRK05182 DNA-directed RNA poly 89.2 0.66 1.7E-05 25.9 4.3 54 358-411 242-295 (306)
147 smart00322 KH K homology RNA-b 88.5 0.62 1.6E-05 26.1 3.8 40 236-281 4-43 (69)
148 cd05790 S1_Rrp40 S1_Rrp40: Rrp 88.0 1.7 4.4E-05 22.8 5.8 68 134-204 2-75 (86)
149 KOG4078 consensus 87.6 0.93 2.4E-05 24.8 4.2 75 116-194 64-138 (173)
150 pfam00013 KH_1 KH domain. KH m 87.3 0.67 1.7E-05 25.9 3.3 34 308-341 2-35 (57)
151 CHL00013 rpoA RNA polymerase a 87.3 1.2 3E-05 24.0 4.6 32 88-120 24-55 (333)
152 pfam00730 HhH-GPD HhH-GPD supe 87.2 2.3 5.8E-05 21.9 6.5 78 372-452 17-98 (144)
153 PRK07220 DNA topoisomerase I; 86.9 1.6 4.1E-05 23.1 5.0 39 435-473 686-724 (740)
154 COG0092 RpsC Ribosomal protein 86.7 1.2 2.9E-05 24.1 4.2 57 282-338 27-87 (233)
155 pfam00313 CSD 'Cold-shock' DNA 86.5 1.7 4.3E-05 22.9 5.0 54 142-198 1-60 (66)
156 PRK00468 hypothetical protein; 86.3 1.2 3.1E-05 24.0 4.2 49 282-330 3-54 (75)
157 cd00105 KH-I K homology RNA-bi 86.1 0.78 2E-05 25.4 3.1 39 308-346 2-40 (64)
158 smart00611 SEC63 Domain of unk 86.1 1.8 4.7E-05 22.6 5.0 41 434-474 150-190 (312)
159 cd02411 archeal_30S_S3_KH K ho 85.8 1.1 2.7E-05 24.4 3.7 46 284-329 16-61 (85)
160 TIGR01952 nusA_arch NusA famil 85.7 0.73 1.9E-05 25.6 2.8 96 247-343 40-139 (143)
161 COG1782 Predicted metal-depend 84.7 3 7.6E-05 21.1 10.6 37 30-67 73-110 (637)
162 PRK00106 hypothetical protein; 84.5 3 7.7E-05 21.0 8.8 151 283-470 205-369 (535)
163 pfam08292 RNA_pol_Rbc25 RNA po 84.0 2.8 7.1E-05 21.3 5.2 55 137-191 2-76 (120)
164 PRK02821 hypothetical protein; 84.0 2.1 5.3E-05 22.2 4.5 49 282-330 4-55 (77)
165 LOAD_cold consensus 83.9 3.2 8.2E-05 20.9 5.7 54 141-197 1-60 (67)
166 COG0122 AlkA 3-methyladenine D 83.8 2.8 7.1E-05 21.3 5.1 87 378-465 141-233 (285)
167 PRK07758 hypothetical protein; 83.8 1.9 4.9E-05 22.5 4.2 40 372-411 46-85 (95)
168 PRK13482 DNA integrity scannin 83.5 2.6 6.5E-05 21.6 4.8 55 358-413 285-339 (352)
169 TIGR00448 rpoE DNA-directed RN 83.3 2.8 7.1E-05 21.3 4.9 74 133-206 76-174 (184)
170 COG1948 MUS81 ERCC4-type nucle 83.3 2.4 6.2E-05 21.7 4.6 55 362-417 184-238 (254)
171 PRK10354 major cold shock prot 83.1 3.4 8.8E-05 20.6 5.6 56 140-198 3-64 (70)
172 TIGR00596 rad1 DNA repair prot 82.9 1.3 3.3E-05 23.7 3.1 44 431-474 875-920 (939)
173 KOG0950 consensus 82.9 2.9 7.3E-05 21.2 4.8 38 436-473 895-932 (1008)
174 PRK01064 hypothetical protein; 82.8 2.2 5.6E-05 22.1 4.2 48 282-329 3-53 (78)
175 PRK02794 DNA polymerase IV; Pr 82.5 3.2 8.1E-05 20.9 4.9 12 79-90 89-100 (417)
176 TIGR02062 RNase_B exoribonucle 81.9 1.6 4E-05 23.1 3.2 128 201-342 207-362 (664)
177 TIGR02027 rpoA DNA-directed RN 80.9 2 5.2E-05 22.3 3.5 31 443-473 268-298 (324)
178 pfam04994 TfoX_C TfoX C-termin 80.9 2.1 5.5E-05 22.1 3.6 35 437-471 1-35 (77)
179 PRK01216 DNA polymerase IV; Va 80.7 3.4 8.5E-05 20.7 4.6 48 364-413 182-229 (351)
180 PRK03103 DNA polymerase IV; Re 80.6 3.9 1E-04 20.2 4.9 34 367-400 189-222 (410)
181 PRK02406 DNA polymerase IV; Va 80.6 3.6 9.1E-05 20.5 4.7 49 364-415 184-232 (355)
182 KOG1676 consensus 80.6 2 5.2E-05 22.3 3.4 105 231-344 224-356 (600)
183 PRK03352 DNA polymerase IV; Va 80.3 4.3 0.00011 20.0 5.6 34 367-400 184-217 (345)
184 PTZ00084 40S ribosomal protein 79.9 3.6 9.1E-05 20.5 4.5 50 283-332 21-70 (220)
185 COG1107 Archaea-specific RecJ- 79.7 3.9 0.0001 20.2 4.6 58 137-194 121-179 (715)
186 cd04462 S1_RNAPII_Rpb7 S1_RNAP 79.4 4.3 0.00011 19.9 4.7 44 138-181 1-44 (88)
187 cd02414 jag_KH jag_K homology 79.2 2.8 7.1E-05 21.3 3.7 44 297-340 15-58 (77)
188 cd02393 PNPase_KH Polynucleoti 79.0 2.4 6.2E-05 21.7 3.4 35 308-342 4-38 (61)
189 PRK12278 50S ribosomal protein 78.4 2.2 5.6E-05 22.1 3.0 44 431-474 149-192 (216)
190 cd00424 Pol_Y Y-family of DNA 78.3 3.8 9.8E-05 20.3 4.2 38 436-473 174-211 (341)
191 COG1796 POL4 DNA polymerase IV 78.2 4.9 0.00013 19.5 5.6 70 394-467 54-126 (326)
192 cd02394 vigilin_like_KH K homo 78.0 2 5E-05 22.4 2.7 37 308-344 2-38 (62)
193 smart00478 ENDO3c endonuclease 77.6 5.1 0.00013 19.4 5.2 78 372-456 13-93 (149)
194 COG1098 VacB Predicted RNA bin 75.7 5.7 0.00015 19.0 5.6 57 136-192 3-66 (129)
195 PRK04191 rps3p 30S ribosomal p 75.3 5.8 0.00015 19.0 4.6 46 284-329 18-63 (225)
196 TIGR02238 recomb_DMC1 meiotic 75.1 5.9 0.00015 18.9 4.9 133 365-507 6-170 (314)
197 PRK09507 cspE cold shock prote 74.7 6 0.00015 18.8 5.5 55 141-198 3-63 (69)
198 KOG2916 consensus 74.5 6.1 0.00016 18.8 4.5 164 130-296 8-209 (304)
199 pfam11731 Cdd1 Pathogenicity l 74.5 3.4 8.6E-05 20.7 3.1 42 435-476 12-53 (92)
200 KOG1856 consensus 74.2 6.2 0.00016 18.8 4.8 149 109-290 542-718 (1299)
201 cd01700 Pol_V Pol V was discov 74.1 4.7 0.00012 19.6 3.7 37 365-401 180-216 (344)
202 COG3743 Uncharacterized conser 74.0 3.7 9.4E-05 20.4 3.2 41 433-473 65-105 (133)
203 PRK00024 radC DNA repair prote 73.9 5.6 0.00014 19.1 4.1 41 370-411 44-84 (224)
204 PRK10702 endonuclease III; Pro 73.8 6.3 0.00016 18.7 4.8 76 371-453 49-127 (211)
205 TIGR01259 comE comEA protein; 73.5 3 7.8E-05 21.0 2.7 58 385-454 64-121 (124)
206 KOG3013 consensus 73.5 1.7 4.2E-05 23.0 1.3 62 129-190 76-154 (301)
207 PRK01810 DNA polymerase IV; Va 72.8 4.6 0.00012 19.7 3.4 34 367-400 186-219 (410)
208 PRK03348 DNA polymerase IV; Pr 72.8 2.8 7.1E-05 21.3 2.3 45 367-413 186-230 (456)
209 PRK03858 DNA polymerase IV; Va 72.7 4.9 0.00013 19.5 3.6 32 367-398 180-211 (398)
210 pfam07650 KH_2 KH domain. 72.0 3.1 8E-05 20.9 2.4 31 308-338 2-32 (55)
211 pfam10391 DNA_pol_lambd_f Fing 71.7 4 0.0001 20.2 2.9 27 361-387 3-29 (52)
212 cd00056 ENDO3c endonuclease II 70.9 7.3 0.00019 18.2 5.9 82 372-457 21-105 (158)
213 TIGR00757 RNaseEG ribonuclease 70.3 2.5 6.5E-05 21.6 1.7 44 134-177 23-70 (464)
214 cd02412 30S_S3_KH K homology R 69.3 7.1 0.00018 18.3 3.8 46 284-329 39-84 (109)
215 PRK04203 rpl1P 50S ribosomal p 68.6 7 0.00018 18.4 3.6 41 22-62 3-46 (216)
216 cd03468 Pol_Y_like Pol_Y_like: 68.1 8.3 0.00021 17.8 4.6 52 360-414 167-218 (330)
217 COG1837 Predicted RNA-binding 67.0 7 0.00018 18.4 3.3 49 282-330 3-54 (76)
218 COG0557 VacB Exoribonuclease R 66.8 8.8 0.00022 17.6 11.0 85 88-192 102-190 (706)
219 KOG2534 consensus 66.0 9.1 0.00023 17.5 4.7 40 4-44 10-49 (353)
220 TIGR03665 arCOG04150 arCOG0415 64.9 4.8 0.00012 19.6 2.2 23 319-341 102-124 (172)
221 COG0322 UvrC Nuclease subunit 64.3 9.7 0.00025 17.3 5.0 99 182-286 291-428 (581)
222 COG0202 RpoA DNA-directed RNA 63.9 2.7 6.9E-05 21.4 0.8 107 312-418 185-302 (317)
223 PRK12311 rpsB 30S ribosomal pr 63.4 7.9 0.0002 18.0 3.1 46 429-474 263-308 (332)
224 COG0177 Nth Predicted EndoIII- 62.4 11 0.00027 17.1 5.4 68 378-451 55-125 (211)
225 PRK03609 umuC DNA polymerase V 62.1 7.9 0.0002 18.0 2.9 38 364-401 183-220 (422)
226 COG0295 Cdd Cytidine deaminase 61.6 7.1 0.00018 18.4 2.5 46 229-282 65-111 (134)
227 KOG2191 consensus 61.4 11 0.00028 17.0 7.2 36 306-341 244-279 (402)
228 cd01701 Pol_zeta Pol_zeta, a m 60.7 11 0.00029 16.9 4.4 159 229-414 94-277 (405)
229 smart00357 CSP Cold shock prot 58.0 12 0.00032 16.6 5.5 54 143-197 1-57 (64)
230 PRK10917 ATP-dependent DNA hel 57.8 11 0.00028 16.9 3.0 65 94-158 306-387 (677)
231 KOG3127 consensus 57.2 1.4 3.7E-05 23.4 -1.6 48 229-283 73-122 (230)
232 KOG1918 consensus 57.1 6.3 0.00016 18.7 1.7 84 379-463 108-198 (254)
233 pfam00633 HHH Helix-hairpin-he 57.1 6.1 0.00016 18.8 1.6 28 384-411 2-29 (30)
234 PRK00310 rpsC 30S ribosomal pr 56.8 13 0.00033 16.4 4.2 46 284-329 40-85 (233)
235 TIGR02851 spore_V_T stage V sp 56.6 9.3 0.00024 17.5 2.5 48 143-205 3-50 (184)
236 PRK01250 inorganic pyrophospha 56.6 6.2 0.00016 18.8 1.5 75 216-299 12-93 (176)
237 KOG2841 consensus 56.3 12 0.00031 16.6 3.0 45 366-411 201-245 (254)
238 COG1623 Predicted nucleic-acid 56.1 13 0.00034 16.3 3.3 138 248-411 205-343 (349)
239 COG1555 ComEA DNA uptake prote 55.1 14 0.00035 16.2 4.8 60 383-454 87-146 (149)
240 KOG1433 consensus 52.7 7.2 0.00018 18.3 1.4 58 360-417 24-81 (326)
241 cd05696 S1_Rrp5_repeat_hs4 S1_ 51.4 16 0.0004 15.8 6.7 56 139-194 1-65 (71)
242 TIGR01008 rpsC_E_A ribosomal p 50.8 16 0.00041 15.8 5.3 56 207-271 14-69 (204)
243 PRK09890 cold shock protein Cs 50.5 16 0.00041 15.7 6.5 55 140-197 3-63 (70)
244 COG1847 Jag Predicted RNA-bind 49.3 9.2 0.00023 17.5 1.5 73 286-360 73-154 (208)
245 COG2106 Uncharacterized conser 49.0 17 0.00043 15.6 4.4 48 135-189 102-150 (272)
246 PRK10880 adenine DNA glycosyla 48.2 17 0.00044 15.5 6.7 68 379-452 57-126 (350)
247 TIGR01083 nth endonuclease III 46.6 18 0.00047 15.3 4.7 67 379-451 54-123 (192)
248 cd01703 Pol_iota Pol iota is m 45.7 19 0.00048 15.2 4.0 93 318-417 172-266 (394)
249 COG0335 RplS Ribosomal protein 45.5 19 0.00048 15.2 3.8 15 176-190 21-35 (115)
250 KOG1004 consensus 45.3 19 0.00049 15.2 5.6 84 130-213 57-163 (230)
251 KOG0187 consensus 44.7 16 0.00041 15.7 2.1 55 337-391 67-121 (134)
252 PRK00296 minE cell division to 44.0 20 0.00051 15.0 5.1 55 16-70 26-82 (85)
253 cd00501 Peptidase_C15 Pyroglut 42.4 8.8 0.00022 17.6 0.5 56 262-318 117-175 (194)
254 pfam00719 Pyrophosphatase Inor 41.7 16 0.00041 15.7 1.8 64 233-300 8-77 (156)
255 pfam02738 Ald_Xan_dh_C2 Molybd 41.7 22 0.00055 14.8 3.7 15 49-64 52-66 (543)
256 KOG4384 consensus 41.7 22 0.00055 14.8 5.5 95 321-417 173-275 (361)
257 pfam05557 MAD Mitotic checkpoi 41.6 13 0.00034 16.3 1.3 17 331-347 640-656 (722)
258 TIGR02544 III_secr_YscJ type I 41.5 14 0.00036 16.2 1.4 20 130-149 119-138 (203)
259 CHL00162 thiG thiamin biosynth 41.3 20 0.00052 15.0 2.2 11 139-149 41-51 (267)
260 TIGR00426 TIGR00426 competence 40.9 22 0.00056 14.7 3.6 54 386-451 10-64 (70)
261 cd02395 SF1_like-KH Splicing f 40.7 22 0.00057 14.7 3.5 33 317-349 17-49 (120)
262 TIGR00118 acolac_lg acetolacta 40.4 14 0.00035 16.2 1.2 63 54-140 293-373 (593)
263 KOG2279 consensus 39.2 15 0.00039 15.9 1.3 36 308-343 298-333 (608)
264 KOG3297 consensus 39.0 24 0.0006 14.5 5.9 123 20-190 11-134 (202)
265 KOG3853 consensus 38.9 24 0.0006 14.5 2.4 71 194-275 228-304 (350)
266 KOG2767 consensus 37.7 25 0.00063 14.4 3.6 71 442-523 327-397 (400)
267 pfam01470 Peptidase_C15 Pyrogl 37.1 20 0.0005 15.1 1.6 67 249-316 97-173 (203)
268 PRK13913 3-methyladenine DNA g 35.9 26 0.00067 14.2 7.6 68 382-451 67-137 (218)
269 PTZ00225 60S ribosomal protein 35.8 26 0.00067 14.2 2.9 33 21-53 3-35 (214)
270 pfam00833 Ribosomal_S17e Ribos 35.7 20 0.0005 15.1 1.4 46 339-384 69-114 (122)
271 TIGR00643 recG ATP-dependent D 35.2 23 0.00059 14.6 1.7 33 117-149 569-602 (721)
272 PRK13910 DNA glycosylase MutY; 34.2 28 0.00071 14.0 6.8 16 197-212 199-214 (290)
273 PRK00378 nucleoid-associated p 33.5 28 0.00073 13.9 3.3 156 259-423 60-236 (334)
274 TIGR01077 L13_A_E ribosomal pr 33.1 26 0.00067 14.2 1.7 15 105-119 9-23 (144)
275 cd01702 Pol_eta Pol eta is mem 33.0 29 0.00074 13.8 3.6 48 367-414 189-237 (358)
276 KOG0438 consensus 32.9 29 0.00074 13.8 3.7 34 226-259 105-139 (312)
277 pfam11694 DUF3290 Protein of u 32.8 22 0.00057 14.6 1.3 64 7-72 79-142 (149)
278 PRK13453 F0F1 ATP synthase sub 32.8 29 0.00075 13.8 4.1 16 406-421 112-127 (173)
279 COG0389 DinP Nucleotidyltransf 32.5 29 0.00075 13.8 3.0 39 436-474 177-215 (354)
280 TIGR02660 nifV_homocitr homoci 31.4 30 0.00076 13.8 1.8 63 371-459 27-89 (369)
281 PRK13763 putative RNA-processi 31.2 31 0.00079 13.6 3.1 38 308-345 6-43 (185)
282 PRK00642 inorganic pyrophospha 30.9 29 0.00074 13.8 1.6 22 397-418 184-206 (212)
283 KOG2093 consensus 30.8 31 0.0008 13.6 8.5 137 319-473 421-587 (1016)
284 PRK05578 cytidine deaminase; V 30.4 32 0.00081 13.5 4.0 30 245-282 80-109 (132)
285 COG4776 Rnb Exoribonuclease II 30.3 32 0.00081 13.5 4.0 90 199-305 201-293 (645)
286 PRK10929 hypothetical protein; 30.3 32 0.00082 13.5 6.7 36 4-39 23-58 (1109)
287 cd05701 S1_Rrp5_repeat_hs10 S1 30.0 32 0.00082 13.5 4.2 56 143-198 5-68 (69)
288 PRK13193 pyrrolidone-carboxyla 29.8 21 0.00053 14.9 0.7 116 179-313 33-166 (201)
289 PRK13194 pyrrolidone-carboxyla 29.6 20 0.00051 15.0 0.6 52 261-313 116-168 (204)
290 COG2003 RadC DNA repair protei 29.0 33 0.00085 13.4 4.5 40 379-418 52-94 (224)
291 PRK11281 potassium efflux prot 28.8 34 0.00086 13.3 6.7 33 5-37 35-69 (1107)
292 cd00412 pyrophosphatase Inorga 28.5 34 0.00087 13.3 2.2 67 233-303 11-85 (155)
293 TIGR02701 shell_carb_anhy carb 28.3 34 0.00086 13.3 1.6 112 49-192 263-389 (463)
294 PRK09970 xanthine dehydrogenas 28.2 34 0.00088 13.3 3.8 27 231-260 338-365 (762)
295 PRK10737 FKBP-type peptidyl-pr 27.8 35 0.00089 13.2 2.2 70 89-160 50-123 (196)
296 cd01296 Imidazolone-5PH Imidaz 27.5 35 0.0009 13.2 3.0 13 206-218 159-171 (371)
297 COG1529 CoxL Aerobic-type carb 27.4 36 0.00091 13.2 3.7 17 196-212 197-213 (731)
298 TIGR03194 4hydrxCoA_A 4-hydrox 27.2 36 0.00091 13.2 3.7 28 232-262 323-351 (746)
299 cd02413 40S_S3_KH K homology R 27.2 36 0.00092 13.2 5.5 54 208-270 7-60 (81)
300 pfam09953 DUF2187 Uncharacteri 27.1 36 0.00092 13.1 2.2 18 142-159 16-33 (57)
301 TIGR02704 carboxysome_B carbox 26.8 36 0.00093 13.1 2.0 32 226-257 10-47 (80)
302 KOG0196 consensus 25.8 38 0.00097 13.0 1.9 25 449-473 940-964 (996)
303 KOG1921 consensus 25.8 38 0.00097 13.0 6.5 75 371-453 98-177 (286)
304 KOG3873 consensus 24.5 35 0.00089 13.2 1.1 32 252-283 225-258 (422)
305 PRK13680 hypothetical protein; 24.3 28 0.00073 13.9 0.6 45 239-286 23-69 (121)
306 pfam03459 TOBE TOBE domain. Th 24.3 40 0.001 12.8 5.4 48 139-189 4-57 (61)
307 PRK09618 flgD flagellar basal 24.2 40 0.001 12.8 3.2 31 136-166 102-135 (146)
308 TIGR02592 cas_Cas5h CRISPR-ass 24.2 24 0.00062 14.4 0.3 64 327-390 114-181 (268)
309 pfam08414 NADPH_Ox Respiratory 24.1 19 0.0005 15.1 -0.2 16 450-465 34-49 (96)
310 TIGR01522 ATPase-IIA2_Ca calci 23.9 37 0.00095 13.0 1.2 34 155-189 121-156 (856)
311 TIGR00350 lytR_cpsA_psr cell e 23.6 41 0.0011 12.7 2.5 21 103-125 160-180 (182)
312 PRK13197 pyrrolidone-carboxyla 23.6 27 0.00068 14.1 0.4 103 204-314 49-170 (215)
313 PRK10676 DNA-binding transcrip 23.5 42 0.0011 12.7 5.1 97 141-245 130-236 (262)
314 TIGR03196 pucD xanthine dehydr 23.3 42 0.0011 12.7 3.7 22 161-182 258-279 (768)
315 pfam03293 Pox_RNA_pol Poxvirus 23.1 42 0.0011 12.6 6.0 64 137-200 80-155 (160)
316 pfam07431 DUF1512 Protein of u 23.0 42 0.0011 12.6 1.3 63 239-326 220-282 (356)
317 PRK07352 F0F1 ATP synthase sub 23.0 43 0.0011 12.6 4.0 12 407-418 114-125 (174)
318 COG1094 Predicted RNA-binding 22.8 43 0.0011 12.6 4.2 40 307-346 9-48 (194)
319 TIGR02885 spore_sigF RNA polym 22.7 43 0.0011 12.6 1.8 23 19-41 33-55 (231)
320 CHL00127 rpl11 ribosomal prote 21.5 42 0.0011 12.6 1.1 35 238-272 10-45 (140)
321 pfam01330 RuvA_N RuvA N termin 21.3 46 0.0012 12.4 6.3 50 141-193 4-55 (61)
322 cd04458 CSP_CDS Cold-Shock Pro 21.1 46 0.0012 12.4 6.2 53 142-197 1-59 (65)
323 pfam09883 DUF2110 Uncharacteri 21.1 46 0.0012 12.4 5.2 36 138-173 75-110 (226)
324 pfam00029 Connexin Connexin. 21.1 25 0.00063 14.4 -0.2 17 278-294 42-58 (107)
325 COG3264 Small-conductance mech 20.9 47 0.0012 12.3 7.1 85 136-235 661-753 (835)
326 COG1255 Uncharacterized protei 20.9 47 0.0012 12.3 1.3 66 10-80 2-68 (129)
327 PRK13460 F0F1 ATP synthase sub 20.9 47 0.0012 12.3 3.8 15 406-420 110-124 (173)
328 TIGR02888 spore_YlmC_YmxH spor 20.7 47 0.0012 12.3 1.9 46 41-90 17-70 (76)
329 TIGR01578 MiaB-like-B MiaB-lik 20.5 47 0.0012 12.3 2.9 161 70-246 309-479 (487)
330 TIGR01204 bioW 6-carboxyhexano 20.5 33 0.00085 13.4 0.3 38 19-57 11-49 (238)
331 PRK00591 prfA peptide chain re 20.3 45 0.0011 12.5 1.0 25 299-330 217-241 (360)
332 COG1460 Uncharacterized protei 20.2 48 0.0012 12.2 5.7 87 393-502 19-105 (114)
333 PRK00140 rplK 50S ribosomal pr 20.1 47 0.0012 12.3 1.0 63 238-316 10-75 (142)
No 1
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=100.00 E-value=0 Score=1079.23 Aligned_cols=427 Identities=55% Similarity=0.923 Sum_probs=418.2
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHH
Q ss_conf 88999999999986239999999999999999999613687453599974998839999998851767787532348999
Q gi|254780788|r 5 NRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVA 84 (526)
Q Consensus 5 ~~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A 84 (526)
++.+++.+++++|+||||+++.+++|+++||.+||||+||++.+++|.||++||++++|+.|.||+++++|..||+|++|
T Consensus 2 m~~e~l~~i~~la~EK~I~~e~v~~aie~Al~~A~kK~~~~~~~i~V~Id~~tG~i~v~~~~~VVe~v~d~~~eI~L~~A 81 (428)
T PRK09202 2 MSKELLLAIEAVAREKGIDREVIIEALEEALATAYKKKYGPEANVRVEIDRKTGDIEVFRRWEVVEEVEDPAKEISLEDA 81 (428)
T ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEECCCCCCCCCEEEHHHH
T ss_conf 74999999999998759699999999999999998442499676799998889819999999853787787647459999
Q ss_pred HHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEE
Q ss_conf 86288986473799850845620799999999999999999988779999852083899999840576389995793587
Q gi|254780788|r 85 RDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGV 164 (526)
Q Consensus 85 ~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~ 164 (526)
++++|++++||++.++++|.+|||+|||+|||+|.||+|++||+.+|++|++|+|+||+|+|+|+++++++||||++||+
T Consensus 82 ~~~~p~~~iGd~i~~~i~~~~fgRiaaq~AkQvi~QkireaEr~~i~~ef~~r~Geiv~G~V~r~~~~~i~Vdlg~~ea~ 161 (428)
T PRK09202 82 RKIDPDAEVGDYIEEEIEPIDFGRIAAQAAKQVIVQKIREAERERVYEEYKDRVGEIITGTVKRVERGNIIVDLGRAEAI 161 (428)
T ss_pred HHHCCCCCCCCEEEEECCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCEEEEECCEEEE
T ss_conf 86589875186688865834258899999999999999999999999999873298899999997278389997882575
Q ss_pred EEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEEC
Q ss_conf 44787488751152766999997611358702898715988999999997667775580878566316775034999940
Q gi|254780788|r 165 IRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSS 244 (526)
Q Consensus 165 Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~ 244 (526)
||+++|||||+|++|||+||||.+|+.++|||||+||||||+||++||++|||||++|+|+||+|||+||+||||||+|+
T Consensus 162 Lp~~e~ip~E~~~~Gdrik~~i~~V~~~~kg~qi~lSRt~p~~v~~Lfe~EVPEI~dG~IeIk~iaRepG~RtKiAV~s~ 241 (428)
T PRK09202 162 LPRDEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIAEGLIEIKAIARDPGSRAKIAVKSN 241 (428)
T ss_pred CCHHHCCCCCCCCCCCEEEEEEEEHHCCCCCCEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCEEEEEECC
T ss_conf 64787699866799987999872021258985799954878999999986456853882999986136787237999725
Q ss_pred CCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCC
Q ss_conf 89988127655488621788998627782679955987899999762866542489875678799998534221102544
Q gi|254780788|r 245 DSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRR 324 (526)
Q Consensus 245 d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~ 324 (526)
|++||||||||||||||||+|++||+|||||||+||+||++||+|||+||+|.+|++|++++++.|+||++||||||||+
T Consensus 242 d~~iDpVGAcVG~rGsRI~~I~~EL~gEkIDIi~~s~d~~~fi~nAlsPA~v~~V~ide~~~~~~VvV~d~qlSlAIGk~ 321 (428)
T PRK09202 242 DKRIDPVGACVGMRGSRIQAISNELNGEKIDIILWSDDPAQFIINALSPAEVSSIVVDEDKHSMDVVVPDDQLSLAIGKN 321 (428)
T ss_pred CCCCCCCEEEECCCCCCHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCCCEEEEECCCCCEEEEEECCCCHHHHHCCC
T ss_conf 99978513777788642999998746776899967888899999817942121899727788899998865224775778
Q ss_pred HHHHHHHHHHHCCEEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHH
Q ss_conf 27899999861674578552200110100122100011122588846788887732111477750588887765305889
Q gi|254780788|r 325 GQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEE 404 (526)
Q Consensus 325 GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee 404 (526)
||||||||+||||+|||+|++++.++++.++....+.|++.+++++.+++.
T Consensus 322 GqNvrLAs~Ltgw~IdI~s~~~~~e~~~~e~~~~~~~f~~~~~~~e~~~~~----------------------------- 372 (428)
T PRK09202 322 GQNVRLASKLTGWKIDIMTEEEASEKQQAEFARLIDLFMEALDVDEDIAQL----------------------------- 372 (428)
T ss_pred CEEHHHHHHHHCCEEEEEEHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH-----------------------------
T ss_conf 685999999779869995589999987778888999877752622888887-----------------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCC
Q ss_conf 99999999999999999998987754284356640779998999999987984788965326775212312344432112
Q gi|254780788|r 405 TAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKF 484 (526)
Q Consensus 405 ~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~ 484 (526)
.++|.+++|++++++..|.++|+.|++|||+++.|||.++.
T Consensus 373 -----------------------------~~~l~~~~~~~~~~~~~l~~~g~~~~edl~~~~~del~~~~---------- 413 (428)
T PRK09202 373 -----------------------------ADDLLNLEGLDPELAFKLAEKGVKTLEDLAELAVDELIDIE---------- 413 (428)
T ss_pred -----------------------------HHHHHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHCC----------
T ss_conf -----------------------------77786456999999999998699879999657988896377----------
Q ss_pred CCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 4533435889999999999841
Q gi|254780788|r 485 DGFLSSLGTPKDQVESMIIHAR 506 (526)
Q Consensus 485 ~gil~~~~l~~~~A~~lIM~AR 506 (526)
++++++|+.|||.||
T Consensus 414 -------~~~~e~a~~li~~ar 428 (428)
T PRK09202 414 -------GLDEEEAGELIMAAR 428 (428)
T ss_pred -------CCCHHHHHHHHHHCC
T ss_conf -------989999999998419
No 2
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=100.00 E-value=0 Score=997.00 Aligned_cols=406 Identities=34% Similarity=0.530 Sum_probs=382.1
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHC-----------CCCC--CCEEEEECCCCCEEEEEEEEEEECCC
Q ss_conf 8999999999986239999999999999999999613-----------6874--53599974998839999998851767
Q gi|254780788|r 6 RLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSL-----------YGTM--SDIRVEINPETGDISLFRLLEVVEEV 72 (526)
Q Consensus 6 ~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~-----------~~~~--~~i~V~iD~~tG~i~i~~~~~VVedv 72 (526)
--.|..++++||+||||+++.+++|||+||++||||. |+.+ .+++|.||++||+|.+|+.|.||+++
T Consensus 6 ~~~L~~vIe~vs~EKgI~ke~I~eAlE~AL~sAykK~~~~~~~~~~~~~~e~~~~n~~V~ID~~tG~~~v~~~k~VVeev 85 (457)
T PRK12329 6 LPGLNNLIEDISEEKNLPKQAVEAALREALLKGYERYRRTLYLGSEDPFDEDYFSNFDVELDLEEEGFRVLATKIIVEEV 85 (457)
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEECCC
T ss_conf 36599999999860298989999999999999986410443333223345455450799998889968999999985267
Q ss_pred CCCCCEECHHHHHHHCCCCCCCCEEEEECCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC
Q ss_conf 7875323489998628898647379985084--56207999999999999999999887799998520838999998405
Q gi|254780788|r 73 ENYTCQISLKVARDRDPSIDIGGVVSDPLPP--MDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE 150 (526)
Q Consensus 73 ed~~~eI~l~~A~~~~~~~~iGD~i~~~i~~--~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e 150 (526)
+|+..||+|++|++++|++++||.+..+++| .+|||||||+|||+|.||||++||+++|++|++|+|+||+|+|+|++
T Consensus 86 ed~~~EIsL~eA~ei~p~~eiGD~i~~ev~pe~~dFGRIAAqtAKQvI~QKIREaER~~I~eef~~k~GeIVtG~V~Rve 165 (457)
T PRK12329 86 ENEDHQIALAEVQQVADDAQLGDTVVLDVTPEKEDFGRMAAIQTKQVLAQKLRDQQRKMIQEEFADLEDPVLTARVLRFE 165 (457)
T ss_pred CCCCCCCCHHHHHHHCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEE
T ss_conf 68765414999986588885698799953865246367999999999999999999999999998555967999999981
Q ss_pred CCEEEEEECC------CEEEEEHHHCCCCCCCCCCCEEEEEEEEECCC-CCEEEEEEECCCHHHHHHHHHHHHHHHHCCE
Q ss_conf 7638999579------35874478748875115276699999761135-8702898715988999999997667775580
Q gi|254780788|r 151 YGNVIVDLGN------SDGVIRRDETISRENLRPGDRVKSYIYDVRRE-QRGPQVLLSRTHPQFMVKLFHMEVPEIYNGI 223 (526)
Q Consensus 151 ~~~iiVdlg~------~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~-~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ 223 (526)
+++++|++|+ +||+||+++|||+|+|++|||+||||++|+.+ .|||||+||||||+||++||++|||||++|+
T Consensus 166 ~~~viv~l~~~lG~~~~EAiLP~~EqIP~E~yr~Gdrira~i~~V~~~~~kGpqIiLSRt~p~fv~kLFe~EVPEI~dG~ 245 (457)
T PRK12329 166 RQSVIMAVSSGFGRPEVEAELPKREQLPNDNYRANATFKVFLKEVSEGPRRGPQLFVSRANAGLVVYLFENEVPEIEEGV 245 (457)
T ss_pred CCCEEEEECCCCCCCCEEEEECHHHCCCCCCCCCCCEEEEEEEEEECCCCCCCEEEEECCCHHHHHHHHHHHCHHHHCCC
T ss_conf 69779996477776423697278886999878999989999999764678885699954877999999986455863894
Q ss_pred EEEEEEECCC-------CCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCC
Q ss_conf 8785663167-------750349999408998812765548862178899862778267995598789999976286654
Q gi|254780788|r 224 VQVKAVSRDP-------GSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIV 296 (526)
Q Consensus 224 ieIk~iaR~p-------G~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v 296 (526)
|+||+|||+| |+||||||+|+|++||||||||||||+|||+|++||+|||||||+||+||++||+|||+||+|
T Consensus 246 VeIk~iARep~~~~r~~G~RtKIAV~S~d~~iDPVGaCVG~rG~RIq~I~~EL~gEkIDii~ws~d~~~~i~nALsPA~v 325 (457)
T PRK12329 246 VRIVAVAREANPPSRAVGPRTKIAVDTLERDVDPVGACIGARGSRIQQVVNELRGEKIDVIRWSPDPATYIANSLSPARV 325 (457)
T ss_pred EEEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCCC
T ss_conf 89999984488777788650389998069997731478889974299999885796389997578789999984396535
Q ss_pred CEE-EECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHH-------CCCCCCCCCCCCCCCC
Q ss_conf 248-98756787999985342211025442789999986167457855220011010-------0122100011122588
Q gi|254780788|r 297 TKV-VLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQ-------KDFNERTQFFMQAINV 368 (526)
Q Consensus 297 ~~v-~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~-------~e~~~~~~~f~e~LdV 368 (526)
.+| ++|++++++.|+||++||||||||+||||||||+||||+|||+|++++.+... .+..+..+.|.+.++.
T Consensus 326 ~~v~~~d~~~~~~~V~V~~dqLslAIGk~GqNvrLAa~Ltgw~IdIks~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~ 405 (457)
T PRK12329 326 DEVRLVDPEGQHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDSAEYDQEAEDAQVAELISQREEEEALQREAEL 405 (457)
T ss_pred CEEEEECCCCCEEEEEECCCCCHHHHCCCCCHHHHHHHHHCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 17999858888799998854103762798757999999779878856689988877888765667888778888776533
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 8467888877321114777505888877653058899999999
Q gi|254780788|r 369 DEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 369 DE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
++..++.|+.+||+++++++|++.+++..++|||++...-...
T Consensus 406 ~~~~~~~~~~e~~~~~~e~~~~~~~e~~~~~~~de~~~~~~~~ 448 (457)
T PRK12329 406 RLEAEQAERAEEDARLRELYPLPEDEEEEEEEEDEDELEDEDD 448 (457)
T ss_pred HHHHHHHHHHCCCCCCHHCCCCCHHHHHHHCCCCCCCCCCCCC
T ss_conf 1568988875453320011157837766301444310013320
No 3
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=100.00 E-value=0 Score=977.30 Aligned_cols=351 Identities=43% Similarity=0.735 Sum_probs=344.6
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHH
Q ss_conf 88999999999986239999999999999999999613687453599974998839999998851767787532348999
Q gi|254780788|r 5 NRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVA 84 (526)
Q Consensus 5 ~~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A 84 (526)
++.|||.+++++|+||||+++.+++|+|+||.+||+|+||++.+++|.||++||++++|+.|.||++++|+..||+|++|
T Consensus 1 M~kell~al~~la~EK~I~~e~v~~aie~Al~~A~kK~~~~~~~i~V~iD~~tG~i~v~~~~~Vveev~d~~~eI~L~eA 80 (353)
T PRK12327 1 MSKEFLEALRALEEEKGISKDVLIEAIEAALLSAYKKNYGQAQNVRVEFDEKTGEVKVYAQKEVVDEVFDSRLEISLEDA 80 (353)
T ss_pred CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEECCCCCCCCCEEEHHHH
T ss_conf 97899999999998749799999999999999998542399776799997899869999999836887687547777665
Q ss_pred HHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEE
Q ss_conf 86288986473799850845620799999999999999999988779999852083899999840576389995793587
Q gi|254780788|r 85 RDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGV 164 (526)
Q Consensus 85 ~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~ 164 (526)
++++|++++||++.++++|.+|||+|||+|||+|.||||++||+++|++|++|+|+||+|+|+|+++++++||||++||+
T Consensus 81 k~~~~~~~vGD~i~~~i~~~~fgRiAaq~AKQvi~QkireaEr~~i~~ey~~r~GeiV~G~V~r~~~~~~~Vdlg~~ea~ 160 (353)
T PRK12327 81 LAINPAYELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREVIYNEFKEREGDIVTGTVQRDDNRFVYVNLGKIEAV 160 (353)
T ss_pred HHCCCCCCCCCEEEEECCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCEEEEECCEEEE
T ss_conf 52477651386589964835459899999999999999999999999999874396699999997588589997882464
Q ss_pred EEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEEC
Q ss_conf 44787488751152766999997611358702898715988999999997667775580878566316775034999940
Q gi|254780788|r 165 IRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSS 244 (526)
Q Consensus 165 Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~ 244 (526)
||+++|||||+|++|||+||||.+|+.++|||||+||||||+||++||++|||||++|+|+||+|||+||+||||||+|+
T Consensus 161 LP~~eqip~E~~~~Gdrika~i~~V~~~~kgp~I~lSRt~p~~v~~Lfe~EVPEI~dG~VeIk~iaRepG~RtKvAV~s~ 240 (353)
T PRK12327 161 LPPAEQIPGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTHPGLVKRLFELEVPEIYDGTVEIVSIAREAGDRTKIAVRSN 240 (353)
T ss_pred CCHHHCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEECCCHHHHHHHHHHHCHHHHCCEEEEEEEECCCCCCEEEEEEEC
T ss_conf 68798699877799997999999999759974799964988999999986366863882999996016787148999925
Q ss_pred CCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEE-CCCCCEEEEEECCCCCCCCCCC
Q ss_conf 899881276554886217889986277826799559878999997628665424898-7567879999853422110254
Q gi|254780788|r 245 DSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVL-DEDVGRIEVIVPKEQLSLAIGR 323 (526)
Q Consensus 245 d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~-de~~~~~~v~v~~~qls~AIGk 323 (526)
|++||||||||||||+|||+|++||+|||||||+||+||++||+|||+||+|.+|.+ |++++++.|+||++||||||||
T Consensus 241 d~~iDpvGAcVG~~G~RI~~I~~EL~gEkIDii~~s~d~~~fi~nALsPA~v~~V~i~de~~k~~~ViV~~~qlslAIGk 320 (353)
T PRK12327 241 NPNVDAIGACVGPKGQRVQNIVNELKGEKIDIIDWSEDPAEFIANALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGK 320 (353)
T ss_pred CCCCCCCEEEECCCCCHHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCCEEEEEEECCCCCEEEEEECCHHHHHHHCC
T ss_conf 99988405888799725999998747777889967898899999737976103899975878669999881041576279
Q ss_pred CHHHHHHHHHHHCCEEEEEECCCHHHHHHCCC
Q ss_conf 42789999986167457855220011010012
Q gi|254780788|r 324 RGQNVRLASQLTGWTIDIITEEEDSINRQKDF 355 (526)
Q Consensus 324 ~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~ 355 (526)
+||||||||+||||+|||+|++++.++..++.
T Consensus 321 ~GqNvrLAs~Ltgw~IdI~s~~~~~e~~~e~~ 352 (353)
T PRK12327 321 EGQNARLAAKLTGWKIDIKSESEAEELGIEEE 352 (353)
T ss_pred CCCHHHHHHHHHCCEEEEEEHHHHHHHCCHHC
T ss_conf 97749999997799799856889767364101
No 4
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=100.00 E-value=0 Score=975.52 Aligned_cols=349 Identities=33% Similarity=0.548 Sum_probs=341.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECC-----CCCCCCEECH
Q ss_conf 99999999998623999999999999999999961368745359997499883999999885176-----7787532348
Q gi|254780788|r 7 LELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEE-----VENYTCQISL 81 (526)
Q Consensus 7 ~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVed-----ved~~~eI~l 81 (526)
.|||.+++++|+||||+++.+++|+++||.+||||+||++.+++|.||++||++.+|+.|.||++ ++++..+|+|
T Consensus 2 ~Ell~~i~~la~EKgI~~e~i~~aie~Al~~A~kK~~g~~~~i~V~id~~tG~i~i~~~~~VVed~de~~~~d~~~eIsL 81 (375)
T PRK12328 2 EKISDIIESIAYEKGLPKEMVSEAVKEALINTAKRELGPLYEYEVVIDPKNKTLKLYQKIEVVADDDERLINDPEKFISL 81 (375)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEEECCCCCCCCCCCCCEECH
T ss_conf 58999999999775969999999999999999734049835679999889985999999999768864454685443029
Q ss_pred HHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCC-CEEEEEECC
Q ss_conf 9998628898647379985084562079999999999999999998877999985208389999984057-638999579
Q gi|254780788|r 82 KVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEY-GNVIVDLGN 160 (526)
Q Consensus 82 ~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~-~~iiVdlg~ 160 (526)
++|++++|++++||++.++++|.+|||+|||+|||+|.||+|++||+++|++|++|+|+||+|+|+|+++ ++++||||+
T Consensus 82 ~eA~~~~~~~~iGd~i~~~i~~~~FgRiAaq~AKQvi~QkireaEr~~i~~efk~r~GeiV~G~V~r~~~~~~~~vdlg~ 161 (375)
T PRK12328 82 SKAKEMDPDVEIGDELSYELSLENMGRTAANTLFKELEYHIQRLLEDSIFEKYKEKVGSVVFGTVVRVDNEENTFIEIDE 161 (375)
T ss_pred HHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCEEEECCC
T ss_conf 99987489984178899842844541899999999999999999999999999864294899999999658848997398
Q ss_pred CEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC-EEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEE
Q ss_conf 3587447874887511527669999976113587-028987159889999999976677755808785663167750349
Q gi|254780788|r 161 SDGVIRRDETISRENLRPGDRVKSYIYDVRREQR-GPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKL 239 (526)
Q Consensus 161 ~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r-gpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKI 239 (526)
+||+||+++|||+|+|++||||||||.+|+.+++ ||||+||||||+||++||++|||||+||+|+||+|||+||+||||
T Consensus 162 ~ea~Lp~~eqip~E~y~~Gdrik~~i~~V~~~~~~gpqI~lSRt~p~fv~~LFe~EVPEI~dG~VeIk~IaRepG~RtKI 241 (375)
T PRK12328 162 IRAILPMKNRIKGEKFKVGDVVKAVLRRVKIDKKNGIKLELSRTSPKFLEALLELEVPEIKDGEVIIIHCARIPGERAKV 241 (375)
T ss_pred CEEEECHHHCCCCCCCCCCCEEEEEEEEEECCCCCCCEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCEEE
T ss_conf 17980277638865589998699999998727899958999679889999999988899848968999985378874069
Q ss_pred EEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCC
Q ss_conf 99940899881276554886217889986277826799559878999997628665424898756787999985342211
Q gi|254780788|r 240 AVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSL 319 (526)
Q Consensus 240 AV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~ 319 (526)
||+|+|++||||||||||||+|||+|++||+|||||||+||+||++||+|||+||+|.+|.+|++.+++.|+||++||||
T Consensus 242 AV~S~d~~iDpVGAcVG~kG~RI~~I~~EL~gEkIDii~~s~d~~~fi~nALsPA~V~~V~i~e~~~~a~viV~~~qlSl 321 (375)
T PRK12328 242 ALFSNSANIDPVGATVGVKGVRINAVSKELNGENIDCIEYSNIPEIFIARALAPAIILSVKIEKIPKKAIVTLPSEQKSK 321 (375)
T ss_pred EEEECCCCCCCEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCHHHHHHHCCCCCCCEEEEEECCCCEEEEEECCHHHHH
T ss_conf 99925998674047888886309999998579627899778888999986378553018999568887999988014337
Q ss_pred CCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCC
Q ss_conf 025442789999986167457855220011010012
Q gi|254780788|r 320 AIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDF 355 (526)
Q Consensus 320 AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~ 355 (526)
||||+||||||||+||||+|||+|++++.++++.+.
T Consensus 322 AIGk~GqNvrLAskLtgw~IDI~s~~~~~e~~~~~~ 357 (375)
T PRK12328 322 AIGKNGINIRLASMLTGYEIELNEIGSVKENASNES 357 (375)
T ss_pred HHCCCCCHHHHHHHHHCCEEEEEEHHHHHHHHHHHH
T ss_conf 626998719999997798799867788778876343
No 5
>TIGR01953 NusA transcription termination factor NusA; InterPro: IPR010213 This entry describes NusA, or N utilisation substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents a region of NusA shared by all bacterial forms, and includes the S1 (IPR003029 from INTERPRO) and KH RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this entry, with two repeats of 50-residue domain rich in acidic amino acids.; GO: 0003723 RNA binding, 0030528 transcription regulator activity.
Probab=100.00 E-value=0 Score=983.31 Aligned_cols=339 Identities=53% Similarity=0.875 Sum_probs=333.5
Q ss_pred HHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHCCCCC---CCEEEEECCCCCEEEEEEEEEEE--CCCCCCCC----
Q ss_conf 9999999998623999-99999999999999996136874---53599974998839999998851--76778753----
Q gi|254780788|r 8 ELLQIADAVAYEKSID-RDVVLSVMADSIQKAARSLYGTM---SDIRVEINPETGDISLFRLLEVV--EEVENYTC---- 77 (526)
Q Consensus 8 ell~vie~va~EK~I~-~e~i~~aie~Al~~a~kK~~~~~---~~i~V~iD~~tG~i~i~~~~~VV--edved~~~---- 77 (526)
+++++++++|+||||+ .+.|+.+||+||.+||||+|+.+ .|++|.||++||++++|+.|.|| |+++|+.+
T Consensus 1 ~~~~~~~~~a~~K~i~i~e~v~~~~e~Al~~Aykk~~~~~~~~~n~~v~id~~~G~~~v~~~~~vV~de~v~d~~~~~~~ 80 (366)
T TIGR01953 1 ELLAAIEALAEEKGISIIETVIEAIEEALEQAYKKTFGSDTNAENVEVNIDRKTGEIEVYRRKEVVEDEEVEDPSLDYSL 80 (366)
T ss_pred CHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCCCC
T ss_conf 95798999998708722699999999999999997368777642179998288655999985540345231064335351
Q ss_pred ----EECHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEE--CCC
Q ss_conf ----23489998628898647379985084562079999999999999999998877999985208389999984--057
Q gi|254780788|r 78 ----QISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKR--VEY 151 (526)
Q Consensus 78 ----eI~l~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r--~e~ 151 (526)
||+|++|++++|++++||++..|+++.+|||+|||+|||+|.||+||+||+.+|++|++++|+||+|+|+| +++
T Consensus 81 dd~leI~L~~A~~~~p~~~iGd~~~~~~~~~~FgR~a~~~a~Q~~~Qk~re~e~~~~~~ef~~~~g~~i~g~V~r~d~~~ 160 (366)
T TIGR01953 81 DDMLEISLEDAREIDPDVQIGDEVKKEINPENFGRIAAQAAKQVITQKIREAERERVYDEFKSKVGEIISGTVKRVDVNK 160 (366)
T ss_pred HHHEECCHHHHHHCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEEEEEECC
T ss_conf 14135220785210779621537887427666447899999999988889999876776643331808999999975257
Q ss_pred CE----EEEEE-CCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCE--EEEEEECCCHHHHHHHHHHHHHHHHCCEE
Q ss_conf 63----89995-7935874478748875115276699999761135870--28987159889999999976677755808
Q gi|254780788|r 152 GN----VIVDL-GNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRG--PQVLLSRTHPQFMVKLFHMEVPEIYNGIV 224 (526)
Q Consensus 152 ~~----iiVdl-g~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rg--pqi~lSRt~p~~l~~Lf~~EVPEI~~G~i 224 (526)
++ ++|+| |+++|+||+++|||+|+|++|||||+||++|+++++| |||+||||||+||++||++|||||+||+|
T Consensus 161 ~~~~~g~~v~l~g~~e~~lp~~e~iP~E~~~~Gd~i~~~~~eV~~~~~g~~~~i~lSRt~p~fl~~Ll~~EvPEI~dG~v 240 (366)
T TIGR01953 161 EGNETGLIVELAGKTEAILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGGLPQIILSRTHPEFLKELLKLEVPEIADGIV 240 (366)
T ss_pred CCCCCEEEEEECCCEEEECCHHHCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHCCCCEEECCEE
T ss_conf 87521079998575025213533788875235888999999999868896689999708979999998616965417819
Q ss_pred EEEEEECCCCCEEEEEEEE-CCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEE-EEC
Q ss_conf 7856631677503499994-08998812765548862178899862778267995598789999976286654248-987
Q gi|254780788|r 225 QVKAVSRDPGSRAKLAVFS-SDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV-VLD 302 (526)
Q Consensus 225 eIk~iaR~pG~RsKIAV~s-~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v-~~d 302 (526)
+||+|||+||+||||||+| ||++||||||||||||+|||+|++||+|||||||.||+||++||.|||+||+|.+| ++|
T Consensus 241 eIk~iAR~pG~R~KiAV~SH~d~~iDPvGAcvG~~G~Ri~~i~~EL~gEkIDii~y~~d~~~Fi~nAL~PA~V~~v~i~d 320 (366)
T TIGR01953 241 EIKKIAREPGSRTKIAVESHNDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAEVISVEILD 320 (366)
T ss_pred EEEEEECCCCCCCEEEEEEECCCCCCEEEEEECCCCCCHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCEECEEEEEE
T ss_conf 99999817887613578850789987046588898865433388747871789836888799999741863121148985
Q ss_pred CCC--CEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCC
Q ss_conf 567--87999985342211025442789999986167457855220
Q gi|254780788|r 303 EDV--GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346 (526)
Q Consensus 303 e~~--~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~ 346 (526)
+|+ |++.|+||++|||+||||+||||||||+||||+|||+|.++
T Consensus 321 ~d~~~~~a~v~V~~~QlslAIGK~GqNvRLAs~Ltgw~Idv~~~~~ 366 (366)
T TIGR01953 321 EDKRDKSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWKIDVKTESQ 366 (366)
T ss_pred CCCCCCEEEEEECCCCCCHHCCCCCCCHHHHHHHCCCEEEEEECCC
T ss_conf 3778837999857557750113356338877512263122212379
No 6
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=100.00 E-value=0 Score=425.88 Aligned_cols=182 Identities=55% Similarity=0.878 Sum_probs=177.2
Q ss_pred CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEE
Q ss_conf 93587447874887511527669999976113587028987159889999999976677755808785663167750349
Q gi|254780788|r 160 NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKL 239 (526)
Q Consensus 160 ~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKI 239 (526)
+++|+||+++|+|+|+|++|||+++|+++|+++.+| |+++|||||.|+.+||++|||||++|+++|++++|+| |+
T Consensus 1 ~~~~~l~~~~~~~~e~~~~g~ri~~~~~~v~~~~~g-~~~~srt~~~~~~~L~~~evpEi~~g~i~ik~i~rd~--r~-- 75 (190)
T COG0195 1 KVEAILPKREQIPGENFKVGDRIRALLYEVQKEAKG-QIELSRTIPELLEKLFEIEVPEIGDGVIEIKCVARDP--RA-- 75 (190)
T ss_pred CCEEECCHHHCCCCCCCCCCCEEEEEEEEEEECCCC-CEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEEEECC--CC--
T ss_conf 941671554538886443476799998255405766-5999824678999999851430047857999998267--55--
Q ss_pred EEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECC-CCCEEEEEECCCCCC
Q ss_conf 9994089988127655488621788998627782679955987899999762866542489875-678799998534221
Q gi|254780788|r 240 AVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDE-DVGRIEVIVPKEQLS 318 (526)
Q Consensus 240 AV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de-~~~~~~v~v~~~qls 318 (526)
||.|++.++||+|||||++|+|||+|++||| ||||||.||+||++||.|||+||+|.+|.+++ +++.+.|+||++|+|
T Consensus 76 av~~~~~~~d~vG~~iG~~G~rvk~i~~eLg-ekIdVVe~s~d~~~fI~nal~Pa~v~~V~~~~~d~~~~~v~V~~~~~~ 154 (190)
T COG0195 76 AVVSNVVKIDPVGACIGKRGSRVKAVSEELG-EKIDVVEWSEDPAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLS 154 (190)
T ss_pred CEEEEECCCCCHHHHCCCCCHHHHHHHHHHC-CCEEEEEECCCHHHHHHHHCCCCEEEEEEEEECCCCEEEEEECHHHHH
T ss_conf 0399615768445421777628999999868-954899906999999998608354778999957981899998989974
Q ss_pred CCCCCCHHHHHHHHHHHCCEEEEEECCCH
Q ss_conf 10254427899999861674578552200
Q gi|254780788|r 319 LAIGRRGQNVRLASQLTGWTIDIITEEED 347 (526)
Q Consensus 319 ~AIGk~GqNvrLas~Ltg~~idi~~~~~~ 347 (526)
+||||+|||+|||++||||++||++..+.
T Consensus 155 ~aIGk~G~Nvrla~~Ltg~~i~I~~~~~~ 183 (190)
T COG0195 155 LAIGKGGQNVRLASQLTGWEIDIETISEA 183 (190)
T ss_pred HCCCCCCHHHHHHHHHHCCEEEEEEHHHH
T ss_conf 44686658899999986887777762111
No 7
>pfam08529 NusA_N NusA N-terminal domain. This domain represents the RNA polymerase binding domain of NusA.
Probab=99.97 E-value=8e-31 Score=245.79 Aligned_cols=122 Identities=48% Similarity=0.782 Sum_probs=119.4
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHHHHH
Q ss_conf 99999999986239999999999999999999613687453599974998839999998851767787532348999862
Q gi|254780788|r 8 ELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDR 87 (526)
Q Consensus 8 ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A~~~ 87 (526)
+|+.+++++|+||||+++.+++++++||.+||+|+||.+.+++|.||++||++.+|+.|.||++++|+..+|+|++|+++
T Consensus 1 eil~~i~~la~EK~i~~e~v~~aie~al~~a~kk~~~~~~~~~V~id~~tG~i~v~~~~~VVe~~~d~~~eI~L~~A~~~ 80 (122)
T pfam08529 1 ELLEAIDAIAREKGIDKEVLIEAIEEALLSAYKKKYGEDENVRVEIDRETGEIEVYRRKEVVEEVEDPDTEISLEEAKEI 80 (122)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCEEEEEEEEEECCCCCCCCCEEEHHHHHHH
T ss_conf 97999999998709899999999999999999873399676799996789839999999815666798667657878741
Q ss_pred CCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 889864737998508456207999999999999999999887
Q gi|254780788|r 88 DPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDR 129 (526)
Q Consensus 88 ~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~ 129 (526)
+|++++||++..+++|.+|||+|||+|||+|+||+|++||++
T Consensus 81 ~~~~~iGd~i~~~i~~~~fgRiaaq~akQ~i~qklre~Er~~ 122 (122)
T pfam08529 81 DPDAEIGDEIEEEVTPKDFGRIAAQTAKQVIIQKIREAERER 122 (122)
T ss_pred CCCCEECCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 788703562668417677488999999999999999998159
No 8
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=99.92 E-value=8e-26 Score=209.02 Aligned_cols=94 Identities=31% Similarity=0.467 Sum_probs=86.6
Q ss_pred CEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECC--CCCEEEEEECCCCCCCCCCCCHHH
Q ss_conf 127655488621788998627782679955987899999762866542489875--678799998534221102544278
Q gi|254780788|r 250 PVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDE--DVGRIEVIVPKEQLSLAIGRRGQN 327 (526)
Q Consensus 250 pVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de--~~~~~~v~v~~~qls~AIGk~GqN 327 (526)
-+|+|||.+|+||+.+.+.| |+|||||+||+||.+||.|||+||+|.+|.+.+ +.+.+.|.||++|+|+||||+|||
T Consensus 44 ~mG~AIGk~G~~Ik~l~~~l-gkkIdiVe~seDp~~FI~N~l~Pa~V~~V~i~~~~~~~~a~V~V~~~~~~lAIGK~G~N 122 (142)
T PRK08406 44 DMGLAIGKGGENVKRLKEKL-GKDIELVEYSEDPEEFIKNLLAPAKVKSVKISEKNGKKVAYVTVAPEDKGIAIGKNGKN 122 (142)
T ss_pred HHHHHHCCCCCHHHHHHHHH-CCCEEEEECCCCHHHHHHHCCCCCEEEEEEEECCCCCEEEEEEECHHHHHHHHCCCCCC
T ss_conf 68897587960799999985-89458996478999999870693256799998279968999996856520433757644
Q ss_pred HHHHHHHHCCEEEEEEC
Q ss_conf 99999861674578552
Q gi|254780788|r 328 VRLASQLTGWTIDIITE 344 (526)
Q Consensus 328 vrLas~Ltg~~idi~~~ 344 (526)
+|||++|++|++||.+.
T Consensus 123 i~lA~~L~~r~~dI~~i 139 (142)
T PRK08406 123 IKRAKDLAKRHFDIDDI 139 (142)
T ss_pred HHHHHHHHHHHCCCEEE
T ss_conf 99999987534697079
No 9
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=99.78 E-value=7e-19 Score=158.01 Aligned_cols=67 Identities=52% Similarity=1.003 Sum_probs=65.9
Q ss_pred HHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 5208389999984057638999579358744787488751152766999997611358702898715
Q gi|254780788|r 136 DKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
+|+|+||+|+|+|+++++++||||++||+||++||||+|+|++||||||||.+|+.++|||||+|||
T Consensus 1 ~k~geiv~G~V~r~~~~~v~vdlg~~eailp~~eqip~E~~~~Gdrik~~i~~V~~~~kgp~i~lSR 67 (67)
T cd04455 1 DREGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCCEEEEEEEEEECCCEEEEECCCEEECCHHHCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEEC
T ss_conf 9878889999999808979999899489737899578866399998999999987469988899839
No 10
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=99.65 E-value=9.6e-17 Score=142.31 Aligned_cols=60 Identities=55% Similarity=0.783 Sum_probs=56.0
Q ss_pred HHHHHHHHCCCCCCCEEEECC-CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf 899999762866542489875-678799998534221102544278999998616745785
Q gi|254780788|r 283 SATFVINALRPAIVTKVVLDE-DVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII 342 (526)
Q Consensus 283 ~~~fi~nAl~PA~v~~v~~de-~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~ 342 (526)
|++||.|||+||+|.+|.+++ ..+.+.|+|+++|+|+||||+||||||||+||||+|||+
T Consensus 1 p~~fi~nal~Pa~v~~V~i~~~~~~~~~V~V~~~~~~~AIGk~G~Nvrla~~l~g~~IdI~ 61 (61)
T cd02134 1 PAEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDIV 61 (61)
T ss_pred CHHHHHHHCCCCEEEEEEECCCCCCEEEEEECHHHHHHHHCCCCEEHHHHHHHHCCEEEEC
T ss_conf 9789986369875579884478773799998857843876678670999999779877649
No 11
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214 NusA, or N utilisation substance protein A, is a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents an acidic 50-residue region found in two copies toward the C terminus of most proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic ; GO: 0030528 transcription regulator activity.
Probab=99.13 E-value=5.1e-11 Score=100.20 Aligned_cols=50 Identities=60% Similarity=0.837 Sum_probs=48.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCHHHHHH--HHCCCHHHHHHHHHHHHHHH
Q ss_conf 884678888773211147775058888776--53058899999999999999
Q gi|254780788|r 368 VDEIIAHLLVAEGFADVEELACVKISEIAS--IEGFDEETAVEIQGRAREYL 417 (526)
Q Consensus 368 VDE~iA~~LV~eGf~SiEeIa~a~~eeL~~--IeGfdee~a~eL~~rA~~~L 417 (526)
||+.+|+.||.+||+|+|+|||+|+++|++ |+|||+|+|.+|+.||++++
T Consensus 1 ~~e~~a~~Lv~eGf~t~EdlAy~~~~EL~~fGIeG~~Ee~A~~L~~~Ar~~~ 52 (52)
T TIGR01954 1 IDEEIAQLLVEEGFTTVEDLAYVPVDELLSFGIEGLDEETAKELINRARNAL 52 (52)
T ss_pred CCHHHHHHHHHHCCCHHHHHHCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHC
T ss_conf 9578899999736731788750455668863589988788999999987529
No 12
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.76 E-value=7.7e-07 Score=69.54 Aligned_cols=72 Identities=31% Similarity=0.509 Sum_probs=37.4
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHH
Q ss_conf 20838999998405763899957-935874478748------87511527669999976113587028987159889999
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMV 209 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~ 209 (526)
+.|+||.|+|.+++.+.++||+| +.||++|++|.. +.+.|++||.+++||..++.... +++|||.-....+
T Consensus 303 ~~G~iV~G~Vv~v~~~~v~VDiG~KseG~Ip~~E~~~~~~~~~~~~~kvGDei~v~V~k~ed~~G--~i~LS~kka~~~~ 380 (670)
T PRK00087 303 RRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLEELTKDEDSSLKESVKVGDEIEVKVLKLENEDG--YVVLSKKEADREK 380 (670)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCCEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCC--CEEEEHHHHHHHH
T ss_conf 78987999999993898999836784368889993667677733457999989999999868998--2998889999888
Q ss_pred H
Q ss_conf 9
Q gi|254780788|r 210 K 210 (526)
Q Consensus 210 ~ 210 (526)
.
T Consensus 381 ~ 381 (670)
T PRK00087 381 A 381 (670)
T ss_pred H
T ss_conf 7
No 13
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.61 E-value=1e-06 Score=68.59 Aligned_cols=270 Identities=19% Similarity=0.252 Sum_probs=142.7
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCE---EEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHHH---HHCC--CCCCC
Q ss_conf 999999999999999996136874535---999749988399999988517677875323489998---6288--98647
Q gi|254780788|r 23 DRDVVLSVMADSIQKAARSLYGTMSDI---RVEINPETGDISLFRLLEVVEEVENYTCQISLKVAR---DRDP--SIDIG 94 (526)
Q Consensus 23 ~~e~i~~aie~Al~~a~kK~~~~~~~i---~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A~---~~~~--~~~iG 94 (526)
+.+.+..+++.++ |+|....-+ .+.|+.+. .+|+=-.....-|++.+.. ..++ .+++|
T Consensus 18 S~edf~~~le~s~-----k~~~eGdIV~GtVv~I~~d~---------VlVDIG~KsEGiIP~~E~s~~~d~d~~e~vkvG 83 (484)
T PRK07899 18 SAEDFLAAIDKTI-----KYFNDGDIVEGTVVKVDRDE---------VLLDIGYKTEGVIPSRELSIKHDVDPNEVVSVG 83 (484)
T ss_pred CHHHHHHHHHHHH-----HCCCCCCEEEEEEEEEECCE---------EEEEECCCEEEEEEHHHHCCCCCCCCCCCCCCC
T ss_conf 9999999888787-----35889988999999997898---------999826870478799994667577845457899
Q ss_pred CEEEEECCH-H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCC-
Q ss_conf 379985084-5-6207999999999999999999887799998520838999998405763899957935874478748-
Q gi|254780788|r 95 GVVSDPLPP-M-DFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETI- 171 (526)
Q Consensus 95 D~i~~~i~~-~-~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~i- 171 (526)
|.++.-+.. . .-|++....-|- ++.+ -.+.+-..|. .|++|+|+|...-+|.++||+ ++.|+||.++.-
T Consensus 84 DeIeV~Vi~~ed~eG~vvLSkkkA---~~~k--~W~~Leea~e--~~~vVeGkV~~~vKGGliVdi-GvraFlP~Sqid~ 155 (484)
T PRK07899 84 DEVEALVLTKEDKEGRLILSKKRA---QYER--AWGTIEKLKE--KDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEM 155 (484)
T ss_pred CEEEEEEEEEECCCCCEEEEHHHH---HHHH--HHHHHHHHHH--CCCEEEEEEEEEECCCEEEEC-CCEEEEECCCCCC
T ss_conf 999999998737887499888997---6567--8999999975--798699999999667099982-6579986422565
Q ss_pred -CCCCCC--CCCEEEEEEEEECCCCCEEEEEEECCCH------HHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEE
Q ss_conf -875115--2766999997611358702898715988------9999999976677755808785663167750349999
Q gi|254780788|r 172 -SRENLR--PGDRVKSYIYDVRREQRGPQVLLSRTHP------QFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVF 242 (526)
Q Consensus 172 -p~E~~~--~Gdrika~i~~V~~~~rgpqi~lSRt~p------~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~ 242 (526)
|-+++. .|..+++.|.++++..+ .|+|||..- .--.++|+ .+..|.|-== -|
T Consensus 156 r~v~dl~~~vGk~l~~kIieid~~r~--nIVlSRRa~LEee~~~~r~e~l~----~L~~G~vveG------------~V- 216 (484)
T PRK07899 156 RRVRDLQPYIGQEIEAKIIELDKNRN--NVVLSRRAWLEQTQSEVRSEFLN----QLQKGQVRKG------------VV- 216 (484)
T ss_pred CCCCCHHHHCCCEEEEEEEEECCCCC--CEEEEHHHHHHHHHHHHHHHHHH----HCCCCCEEEE------------EE-
T ss_conf 10478388779879999999757668--06501999999999889999997----4778987999------------99-
Q ss_pred ECCCCCCCEEEEECCCC------------HHHHHHHHHH-CCCCEEEEE----------------CCCCHHHHHHHHCCC
Q ss_conf 40899881276554886------------2178899862-778267995----------------598789999976286
Q gi|254780788|r 243 SSDSSIDPVGACVGMRG------------SRVQAVVTEL-RDEKIDIVV----------------WSPDSATFVINALRP 293 (526)
Q Consensus 243 s~d~~iDpVGAcVG~rG------------sRiq~I~~EL-~gEkIDii~----------------ws~d~~~fi~nAl~P 293 (526)
.+|-+-||.|-..| .||+..+.-| -|.++.+.. -.+||=.-+..-+.+
T Consensus 217 ---k~It~fGAFVDLGGVDGLvHiSEiSW~Rv~~Psev~~vGd~V~VkVl~iD~Ek~RISLslKql~~dPW~~~~~k~~v 293 (484)
T PRK07899 217 ---SSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGDEVTVEVLDVDLDRERVSLSLKATQEDPWQVFARTHAI 293 (484)
T ss_pred ---EEECCCEEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHCCC
T ss_conf ---98216468999557237898134035677998995779987999998774767889886254778838989864899
Q ss_pred CCC-----CEEEE----CCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHH--CCEEEEE
Q ss_conf 654-----24898----7567879999853422110254427899999861--6745785
Q gi|254780788|r 294 AIV-----TKVVL----DEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLT--GWTIDII 342 (526)
Q Consensus 294 A~v-----~~v~~----de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Lt--g~~idi~ 342 (526)
..+ .++.- -+=..-++=.|.=.+|| .+ +++-.+... |=.+.++
T Consensus 294 G~vv~GkV~~l~~fGAFVel~~GIEGLVHISElS---~~---~v~~P~dvv~~GdeV~vk 347 (484)
T PRK07899 294 GQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELA---ER---HVEVPEQVVSVGDEVMVK 347 (484)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCC---CC---CCCCHHHHCCCCCEEEEE
T ss_conf 8989999998726605999369967667877645---64---447988847799889999
No 14
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214 NusA, or N utilisation substance protein A, is a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents an acidic 50-residue region found in two copies toward the C terminus of most proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic ; GO: 0030528 transcription regulator activity.
Probab=98.60 E-value=6.1e-08 Score=77.62 Aligned_cols=50 Identities=38% Similarity=0.507 Sum_probs=47.8
Q ss_pred CCHHHHHHHHHCCCCCHHHHHHCCHHHHCC--CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 998999999987984788965326775212--312344432112453343588999999999984122578
Q gi|254780788|r 443 IDSKIKVALGENGIKTMEDLAGCSVDDLLG--WSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGW 511 (526)
Q Consensus 443 l~~~~~~~L~e~gIktleDlAels~dEL~~--~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~gW 511 (526)
|+..|+..|++.|+.|+||||++++|||++ |. |++++.|.+|||.||.+ |
T Consensus 1 ~~e~~a~~Lv~eGf~t~EdlAy~~~~EL~~fGIe-----------------G~~Ee~A~~L~~~Ar~~--~ 52 (52)
T TIGR01954 1 IDEEIAQLLVEEGFTTVEDLAYVPVDELLSFGIE-----------------GLDEETAKELINRARNA--L 52 (52)
T ss_pred CCHHHHHHHHHHCCCHHHHHHCCCHHHHHHHCCC-----------------CCCHHHHHHHHHHHHHH--C
T ss_conf 9578899999736731788750455668863589-----------------98878899999998752--9
No 15
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.59 E-value=2.3e-06 Score=66.00 Aligned_cols=64 Identities=20% Similarity=0.339 Sum_probs=37.9
Q ss_pred HCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCC---CCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 208389999984057638999579358744787488---7511527669999976113587028987159
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETIS---RENLRPGDRVKSYIYDVRREQRGPQVLLSRT 203 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip---~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt 203 (526)
..|++|+|+|....+|.++|++++.+|+||.++.-. .+.| +|+.+++-+.+++...+ .|+|||.
T Consensus 117 ~~~~~V~gkV~~~~kgG~~V~i~gl~gFiP~Sqls~~~~~~~~-vG~~~~~kIieid~~~~--rivlS~r 183 (314)
T PRK07400 117 KEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEEL-VGEELPLKFLEVDEERN--RLVLSHR 183 (314)
T ss_pred HCCCEEEEEEEEEECCCEEEEECCEEEEEEHHHCCCCCCCHHH-CCCEEEEEEEEEECCCC--CEEEEEE
T ss_conf 2598799999999638489997686568552451635563210-69768899999715668--2489983
No 16
>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=98.53 E-value=5.7e-07 Score=70.49 Aligned_cols=63 Identities=37% Similarity=0.671 Sum_probs=57.2
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 838999998405763899957-935874478748------87511527669999976113587028987159
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRT 203 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt 203 (526)
|++|+|+|.+++...++||+| +.+|++|.+|.. |.+.|++||.+.|+|..++.+.+ ++.|||-
T Consensus 1 G~iV~G~V~~i~~~gv~Vdig~k~eG~ip~~E~s~~~~~~~~~~~~vGd~i~~~V~~~d~~~g--~i~LS~k 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEG--NVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCCEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCC--EEEEECC
T ss_conf 998999999997886999968985026899994533238974712699999999999999999--7998509
No 17
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.46 E-value=8.6e-06 Score=61.83 Aligned_cols=64 Identities=19% Similarity=0.357 Sum_probs=35.8
Q ss_pred CCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC--C--CCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 083899999840576389995793587447874887--5--11527669999976113587028987159
Q gi|254780788|r 138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR--E--NLRPGDRVKSYIYDVRREQRGPQVLLSRT 203 (526)
Q Consensus 138 ~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~--E--~~~~Gdrika~i~~V~~~~rgpqi~lSRt 203 (526)
.|+.|+|+|....+|.++|+++++.|+||.++.-.+ + ..-.|..+++.|.++++..+ .|++||.
T Consensus 104 ~~~~v~g~i~~~vKGG~~V~i~gv~aFlP~Sq~d~~~v~d~~~~vG~~l~~kIi~~d~~~~--~iVvSrr 171 (556)
T PRK06299 104 NGEIVEGVINGKVKGGFTVDLNGVRAFLPGSQVDVRPVRDTDPLEGKELEFKVIKLDKKRN--NIVVSRR 171 (556)
T ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCEEEEEEEEEECCCC--EEEEEHH
T ss_conf 8987999999997780999988989997858825755566176579669999999752358--0897328
No 18
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.42 E-value=1.2e-06 Score=68.12 Aligned_cols=124 Identities=22% Similarity=0.333 Sum_probs=68.7
Q ss_pred CCCCCEECHHHHHHHCCCCCCCCEEEEECCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCC
Q ss_conf 787532348999862889864737998508456-2079999999999999999998877999985208389999984057
Q gi|254780788|r 73 ENYTCQISLKVARDRDPSIDIGGVVSDPLPPMD-FGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEY 151 (526)
Q Consensus 73 ed~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~~-fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~ 151 (526)
+-|..|+.+.. -.+++--+|..+...+--.+ -+|...-+ +-.+.+.-++..|+..++.+ ++|+++.|+|+++..
T Consensus 140 FlP~Sqid~r~--v~d~~~~vGk~~~~~Iikid~~~~nIVvS-RR~lLe~e~~~~~~~~~~~l--~~G~vv~G~V~~i~~ 214 (489)
T PRK13806 140 FCPVSQIDLHQ--VEDPESFVGQTFQFLITRVEQNGRNIVVS-RRALLEREQAESLATFLEGV--KEGDVLEGTVTRLAP 214 (489)
T ss_pred EEEHHHCCCCC--CCCHHHHCCCEEEEEEEEECCCCCEEEEE-HHHHHHHHHHHHHHHHHHHH--CCCCEECEEEEEECC
T ss_conf 42316604666--67858967965899999970568707866-89988888777899999861--148800429999757
Q ss_pred CEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCC--EEEEEEE
Q ss_conf 63899957-935874478748------87511527669999976113587--0289871
Q gi|254780788|r 152 GNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQR--GPQVLLS 201 (526)
Q Consensus 152 ~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~r--gpqi~lS 201 (526)
-.++|||| +++|++|.+|+. |.+.|++||.|++.|.++.++++ ++.|-||
T Consensus 215 ~GaFVdl~~GvdGllHiSeiSw~rv~~p~~~~~vGd~v~vkVl~id~e~~~~~~risLs 273 (489)
T PRK13806 215 FGAFVEIAPGVEGMVHISELSWSRVQQADEAVSVGDRVRVKVLGIGEAPKGKGLRISLS 273 (489)
T ss_pred CEEEEEECCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECCCCCCCEEEEEE
T ss_conf 53899937980799983555865668888945169889999999864456665069860
No 19
>pfam00575 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Probab=98.38 E-value=1.9e-06 Score=66.66 Aligned_cols=65 Identities=35% Similarity=0.590 Sum_probs=60.0
Q ss_pred HHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 520838999998405763899957-935874478748------8751152766999997611358702898715
Q gi|254780788|r 136 DKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
.++|+++.|+|.++++..++|+|+ +.+|++|.+++. |.+.|++||+++|.|.+++.+.+ ++.||+
T Consensus 2 ~~~G~iv~G~V~~i~~~G~fV~l~~~~~g~v~~s~ls~~~~~~~~~~~~~G~~v~~~V~~vd~~~~--~i~lS~ 73 (74)
T pfam00575 2 PEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVDKERG--RIILSI 73 (74)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHHHCCCCEEEEEEEEEECCCC--EEEEEE
T ss_conf 889999999999998775999978997999984461365556776830599999999999999999--999983
No 20
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.37 E-value=2e-06 Score=66.54 Aligned_cols=109 Identities=24% Similarity=0.389 Sum_probs=81.2
Q ss_pred CCCCCCCCEEEEECCHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEE
Q ss_conf 889864737998508456--207999999999999999999887799998520838999998405763899957935874
Q gi|254780788|r 88 DPSIDIGGVVSDPLPPMD--FGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVI 165 (526)
Q Consensus 88 ~~~~~iGD~i~~~i~~~~--fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~L 165 (526)
+++.=+|..+...+--.+ -+++ .-+ +..+.+.-++.+++..++.++ +|+++.|+|+++..-.++||||+++|++
T Consensus 143 d~~~~vG~~l~~kIi~~d~~~~~i-VvS-rr~~lee~~~~~~~~~~~~l~--~G~vv~G~V~~i~~~GaFVdlggvdGll 218 (556)
T PRK06299 143 DTDPLEGKELEFKVIKLDKKRNNI-VVS-RRAVLEEERAEEREELLENLE--EGQVVEGVVKNITDYGAFVDLGGVDGLL 218 (556)
T ss_pred CHHHHCCCEEEEEEEEEECCCCEE-EEE-HHHHHHHHHHHHHHHHHHHCC--CCCEEEEEEEEEECCCEEEEECCEEEEE
T ss_conf 617657966999999975235808-973-289888888888999998524--7972789999970575899958958999
Q ss_pred EHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 478748------8751152766999997611358702898715
Q gi|254780788|r 166 RRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 166 p~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
|.+++. |.+.|++||.+++.|.+++.+.+ +|-||-
T Consensus 219 hiseiSw~rv~~p~~~~~~G~~v~vkVl~id~e~~--risLsl 259 (556)
T PRK06299 219 HITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKK--RVSLGL 259 (556)
T ss_pred EHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCC--EEEEEE
T ss_conf 85671556669989926689889999998826563--899997
No 21
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.36 E-value=2.5e-06 Score=65.74 Aligned_cols=123 Identities=22% Similarity=0.296 Sum_probs=87.8
Q ss_pred CCCCCEECHHHHHHHCCCCCCCCEEEEECCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCC
Q ss_conf 78753234899986288986473799850845620-79999999999999999998877999985208389999984057
Q gi|254780788|r 73 ENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFG-RVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEY 151 (526)
Q Consensus 73 ed~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~~fg-RiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~ 151 (526)
+-|..++.+.-.+ |.+.-+|..+...+--.+-. |...-+ +..+.+.-++..|+..++.+ .+|+++.|+|+++..
T Consensus 147 FlP~Sqid~r~v~--dl~~~vGk~l~~kIieid~~r~nIVlS-RRa~LEee~~~~r~e~l~~L--~~G~vveG~Vk~It~ 221 (484)
T PRK07899 147 FLPASLVEMRRVR--DLQPYIGQEIEAKIIELDKNRNNVVLS-RRAWLEQTQSEVRSEFLNQL--QKGQVRKGVVSSIVN 221 (484)
T ss_pred EEECCCCCCCCCC--CHHHHCCCEEEEEEEEECCCCCCEEEE-HHHHHHHHHHHHHHHHHHHC--CCCCEEEEEEEEECC
T ss_conf 9864225651047--838877987999999975766806501-99999999988999999747--789879999998216
Q ss_pred CEEEEEECCCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 6389995793587447874------88751152766999997611358702898715
Q gi|254780788|r 152 GNVIVDLGNSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 152 ~~iiVdlg~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
-..+||||+++|+++-+++ -|.|.|++||.|+++|.++.++.. .|-||.
T Consensus 222 fGAFVDLGGVDGLvHiSEiSW~Rv~~Psev~~vGd~V~VkVl~iD~Ek~--RISLsl 276 (484)
T PRK07899 222 FGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGDEVTVEVLDVDLDRE--RVSLSL 276 (484)
T ss_pred CEEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCC--EEEEEE
T ss_conf 4689995572378981340356779989957799879999987747678--898862
No 22
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.33 E-value=6e-06 Score=62.97 Aligned_cols=188 Identities=21% Similarity=0.314 Sum_probs=101.1
Q ss_pred CCCCCCCEEEEECCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEEE
Q ss_conf 8986473799850845--62079999999999999999998877999985208389999984057638999579358744
Q gi|254780788|r 89 PSIDIGGVVSDPLPPM--DFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIR 166 (526)
Q Consensus 89 ~~~~iGD~i~~~i~~~--~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp 166 (526)
.-.++||.++..+-.. +-+++.. +.|+. -.....+.+.+.| ..|+++.|+|.++.++.++|++++..|+||
T Consensus 61 ~~~kvGd~V~~~Vl~~~~~~~~l~L-S~kk~----~~~~~w~~~~~~~--~~g~~v~g~V~~~~kgG~~V~~~gv~gFlP 133 (390)
T PRK06676 61 DVVKVGDTLEVYVLKVEDGEGNYLL-SKRRL----EARKAWDKLEEKF--EEGEVVEVKVTEVVKGGLVVDVGGVRGFIP 133 (390)
T ss_pred HCCCCCCEEEEEEEEEECCCCEEEE-EHHHH----HHCHHHHHHHHHH--HCCCEEEEEEEEEECCCEEEEECCCEEEEE
T ss_conf 2469989999999999889973999-96792----2010088888765--379779999999955859999768168775
Q ss_pred HHHCCCC-----CCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEE
Q ss_conf 7874887-----51152766999997611358702898715988999999997667775580878566316775034999
Q gi|254780788|r 167 RDETISR-----ENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAV 241 (526)
Q Consensus 167 ~~e~ip~-----E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV 241 (526)
.++.-.. ..| .|+.++|.|.++....+ .|+|||-. ++..--.....++.+ .-.||.--+-.|
T Consensus 134 ~S~ls~~~~~~~~~~-vGq~v~~kVi~vd~~~~--~ivlS~K~--~l~~~~~~~~~~~~~--------~l~~Gdvv~G~V 200 (390)
T PRK06676 134 ASLISTRFVEDLSDF-KGKTLDVKIIELDPEKN--RVILSRRA--VVEEERAEKKKELLS--------SLKEGDVVEGKV 200 (390)
T ss_pred HHHCCCCCCCCCHHH-CCEEEEEEEEEEECCCC--CEEECCHH--HHHHHHHHHHHHHHH--------HCCCCCEEEEEE
T ss_conf 487256445770554-37169999999853788--28970324--546667665766776--------346898478999
Q ss_pred EECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECC--CCHHHHHHHHCCCCCCCEEE---ECCCCCEEEEEE
Q ss_conf 940899881276554886217889986277826799559--87899999762866542489---875678799998
Q gi|254780788|r 242 FSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWS--PDSATFVINALRPAIVTKVV---LDEDVGRIEVIV 312 (526)
Q Consensus 242 ~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws--~d~~~fi~nAl~PA~v~~v~---~de~~~~~~v~v 312 (526)
. +|.+-|+-|-..| |.+.+ .+.=+-|+ .+|.. -+.+.+-.++. +|.+++++.+-.
T Consensus 201 ~----~i~~~G~FV~lgg--v~glv------h~sels~~~~~~~~~----~~k~G~~v~~~Vl~id~~~~ri~Lsl 260 (390)
T PRK06676 201 A----RLTDFGAFVDIGG--VDGLV------HISELSHERVNKPSE----VVSVGQEVEVKVLSIDEETERISLSL 260 (390)
T ss_pred E----EEECCCEEEECCC--EEEEE------EECCCCHHHHCCHHH----HHCCCCEEEEEEEEEECCCCEEEEEE
T ss_conf 9----9945636998077--67999------961057333359888----30479757999999946788999998
No 23
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.28 E-value=2.9e-05 Score=57.95 Aligned_cols=115 Identities=14% Similarity=0.098 Sum_probs=77.7
Q ss_pred CCCEECHHHHHHHCC--CCCCCCEEEEECCHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEE
Q ss_conf 753234899986288--9864737998508456-----207999999999999999999887799998520838999998
Q gi|254780788|r 75 YTCQISLKVARDRDP--SIDIGGVVSDPLPPMD-----FGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVK 147 (526)
Q Consensus 75 ~~~eI~l~~A~~~~~--~~~iGD~i~~~i~~~~-----fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~ 147 (526)
...-|++.+-...+. .+++||.++.-+...+ ++|-.++ +. ..+.+.+.|. .|+.|.|.|.
T Consensus 57 sEG~Ip~~E~~d~~~~~~~kvGD~Iev~V~~~~dgei~LSr~~~~---~~--------~~~~l~ea~e--~~~~V~g~I~ 123 (489)
T PRK13806 57 VDGVIDRRELEDAEGNLPYAVGDRLDLYVVAVNGGEIRLSKAMGG---QG--------GAAVLEEARD--NGVPVEGKVT 123 (489)
T ss_pred EEEEEEHHHHCCCCCCCCCCCCCEEEEEEEEECCCCEEEEHHHHH---HH--------HHHHHHHHHH--CCCEEEEEEE
T ss_conf 289958999257557756589989999999964981899889988---87--------8999999975--8986999999
Q ss_pred ECCCCEEEEEECCCEEEEEHHHCCCC--CC--CCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf 40576389995793587447874887--51--15276699999761135870289871598
Q gi|254780788|r 148 RVEYGNVIVDLGNSDGVIRRDETISR--EN--LRPGDRVKSYIYDVRREQRGPQVLLSRTH 204 (526)
Q Consensus 148 r~e~~~iiVdlg~~ea~Lp~~e~ip~--E~--~~~Gdrika~i~~V~~~~rgpqi~lSRt~ 204 (526)
..-+|.++|+++++.|+||.++.-.+ +. .-.|..+++.|.++++..+ .|++||-.
T Consensus 124 ~~vKGG~~V~i~Gv~aFlP~Sqid~r~v~d~~~~vGk~~~~~Iikid~~~~--nIVvSRR~ 182 (489)
T PRK13806 124 GTCKGGFNVEVLRRRAFCPVSQIDLHQVEDPESFVGQTFQFLITRVEQNGR--NIVVSRRA 182 (489)
T ss_pred EEECCCEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCEEEEEEEEECCCCC--EEEEEHHH
T ss_conf 998675999989977642316604666678589679658999999705687--07866899
No 24
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.21 E-value=1.9e-05 Score=59.24 Aligned_cols=160 Identities=21% Similarity=0.310 Sum_probs=101.4
Q ss_pred CCCCCEECHHHHH-----HHCCCCCCCCEEEEECCH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEE
Q ss_conf 7875323489998-----628898647379985084--562079999999999999999998877999985208389999
Q gi|254780788|r 73 ENYTCQISLKVAR-----DRDPSIDIGGVVSDPLPP--MDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGT 145 (526)
Q Consensus 73 ed~~~eI~l~~A~-----~~~~~~~iGD~i~~~i~~--~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~ 145 (526)
.-...-|++++-. ...+.+++||.++.-+.. ...|++....-|- .+....+.+.+.|.. |++|+|+
T Consensus 326 ~KseG~Ip~~E~~~~~~~~~~~~~kvGDei~v~V~k~ed~~G~i~LS~kka-----~~~~~w~~l~~a~e~--~e~V~g~ 398 (670)
T PRK00087 326 YKSEGVIPLEELTKDEDSSLKESVKVGDEIEVKVLKLENEDGYVVLSKKEA-----DREKAWKELEEAFEN--GETVKGK 398 (670)
T ss_pred CCCCEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCEEEEHHHH-----HHHHHHHHHHHHHHC--CCEEEEE
T ss_conf 784368889993667677733457999989999999868998299888999-----988879999999868--9869999
Q ss_pred EEECCCCEEEEEECCCEEEEEHHHCCCC--CC--CCCCCEEEEEEEEECCCCCEEEEEEECCCH------HHHHHHHHHH
Q ss_conf 9840576389995793587447874887--51--152766999997611358702898715988------9999999976
Q gi|254780788|r 146 VKRVEYGNVIVDLGNSDGVIRRDETISR--EN--LRPGDRVKSYIYDVRREQRGPQVLLSRTHP------QFMVKLFHME 215 (526)
Q Consensus 146 V~r~e~~~iiVdlg~~ea~Lp~~e~ip~--E~--~~~Gdrika~i~~V~~~~rgpqi~lSRt~p------~~l~~Lf~~E 215 (526)
|....+|.++|+++++.|+||.++.-.+ +. --.|..+++.|.+++...|.+.+++||..- .--.++|+
T Consensus 399 V~~~vKGG~~V~i~gi~~FiP~Sq~~~~~~~d~~~~vG~~~~~kIie~d~~k~r~niV~Srr~vlee~~~~~k~~~~~-- 476 (670)
T PRK00087 399 VKEVVKGGLLVDYGGVRAFLPASHVELGYVEDLSAYKGQELEVKIIEFDKKRKKTKVVLSRKALLKEEKEKQKEETWN-- 476 (670)
T ss_pred EEEEECCCEEEEECCEEEEECHHHCCCCCCCCHHHHCCCEEEEEEEEECCCCCCCCEEEECHHHHHHHHHHHHHHHHH--
T ss_conf 999985859999899899802276156656772787697489999998444576748978099999889999999997--
Q ss_pred HHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCC
Q ss_conf 67775580878566316775034999940899881276554886
Q gi|254780788|r 216 VPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRG 259 (526)
Q Consensus 216 VPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rG 259 (526)
.+..|.+ +.+ -| .+|.|-||.|...|
T Consensus 477 --~l~~G~~-v~G-----------~V----~~i~~~GaFvdlgG 502 (670)
T PRK00087 477 --SLEEGDV-VEG-----------EV----KRLTDFGAFVDIGG 502 (670)
T ss_pred --HCCCCCE-EEE-----------EE----EEEECCCEEEEECC
T ss_conf --4889988-999-----------99----99973407999779
No 25
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.18 E-value=1.3e-05 Score=60.44 Aligned_cols=78 Identities=26% Similarity=0.401 Sum_probs=64.1
Q ss_pred HHHHH--HHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 79999--8520838999998405763899957-93587447874------887511527669999976113587028987
Q gi|254780788|r 130 QYLEF--KDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLL 200 (526)
Q Consensus 130 i~~ef--~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~l 200 (526)
++++| .-+.|++|.|+|..++.+.++||+| +++|++|.+|. -|.+.+..||.+.++|..++.+.. ++.|
T Consensus 21 lLe~~~~~~k~GdiVeG~V~~I~~~~v~VdiG~k~eG~i~~~E~s~~~~~~~~e~~~vGd~iev~V~~~~~~~g--~i~L 98 (314)
T PRK07400 21 LLDKYDYHFKPGDIVNGTVFSLEPKGALIDIGAKTAAFMPLQEMSINRVEGPSEVLQPGETREFFILSEENEDG--QLTL 98 (314)
T ss_pred HHHHHHCCCCCCCEEEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCCCCCCCCCCEEEEEEEEEECCCC--CEEE
T ss_conf 99875236999998999999997998999977980799999993666568943013589769999999856889--6899
Q ss_pred ECCCHHHHH
Q ss_conf 159889999
Q gi|254780788|r 201 SRTHPQFMV 209 (526)
Q Consensus 201 SRt~p~~l~ 209 (526)
|+.-.....
T Consensus 99 S~k~~~~~~ 107 (314)
T PRK07400 99 SIRRIEYMR 107 (314)
T ss_pred EECHHHHHH
T ss_conf 860432120
No 26
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.10 E-value=2e-05 Score=59.07 Aligned_cols=68 Identities=34% Similarity=0.565 Sum_probs=34.2
Q ss_pred HHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHH
Q ss_conf 8520838999998405763899957-9358744787488751152766999997611358702898715988999
Q gi|254780788|r 135 KDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFM 208 (526)
Q Consensus 135 ~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l 208 (526)
..+.|+||+|+|-+++.++++||.| +.||.+|.+|- ...-++||.+.+||..++. .|++ |||.-..-+
T Consensus 318 ~~~~G~vi~g~Vv~i~~d~V~vdvG~KsEg~ip~~eF--~~~~~vGD~v~V~ie~~e~--~~~~--LSr~kA~r~ 386 (863)
T PRK12269 318 APEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEF--EAPPKAGDGVRVYVERVTP--YGPE--LSKTKADRL 386 (863)
T ss_pred CCCCCCEEEEEEEEEECCEEEEECCCCCCCCCCHHHC--CCCCCCCCEEEEEEEEECC--CCCE--ECHHHHHHH
T ss_conf 7998625899999995897999647744553269992--7788999999999999708--8975--618999878
No 27
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 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 of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=98.09 E-value=3.3e-05 Score=57.53 Aligned_cols=174 Identities=22% Similarity=0.265 Sum_probs=112.2
Q ss_pred ECCCCCCCCEECHHHHHHHC--CCCCCCCEEEEECCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE
Q ss_conf 17677875323489998628--8986473799850845--6207999999999999999999887799998520838999
Q gi|254780788|r 69 VEEVENYTCQISLKVARDRD--PSIDIGGVVSDPLPPM--DFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISG 144 (526)
Q Consensus 69 Vedved~~~eI~l~~A~~~~--~~~~iGD~i~~~i~~~--~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G 144 (526)
|+=---...-|++++-.... -.++.||.|...|+-. .+|+-.-..-|+ ||.+ ..++-+-..+.|++|.|
T Consensus 39 VDvG~KsEg~ip~~Ef~~~~G~l~~~~Gd~v~V~l~~~~~~~g~~~LS~~ka---~r~~----~~~~l~~~~~~~~~V~G 111 (534)
T TIGR00717 39 VDVGLKSEGRIPVEEFLDAQGELEIQVGDEVEVYLDRVEDRIGETVLSREKA---QRKE----AWIKLEKAYEEGSIVEG 111 (534)
T ss_pred EEEECCCCCCCCHHHCCCCCCCCEEECCCEEEEEEEEECCCCCCCEEECCHH---HHHH----HHHHHHHHHHCCCEEEE
T ss_conf 9831563123417682688884000058879999984428999702304525---7888----99999998616984567
Q ss_pred EEEECC--CCEEEEEEC-CCEEEEEHHHCCCC----CCCCCCCEEEEEEEEECCCC--CE-EEEEEECCC------HHHH
Q ss_conf 998405--763899957-93587447874887----51152766999997611358--70-289871598------8999
Q gi|254780788|r 145 TVKRVE--YGNVIVDLG-NSDGVIRRDETISR----ENLRPGDRVKSYIYDVRREQ--RG-PQVLLSRTH------PQFM 208 (526)
Q Consensus 145 ~V~r~e--~~~iiVdlg-~~ea~Lp~~e~ip~----E~~~~Gdrika~i~~V~~~~--rg-pqi~lSRt~------p~~l 208 (526)
.+.|-. +|.++|||+ +++|+||.++-=-+ ..--.|-+.+++|..++... || ++|++||-. ..-.
T Consensus 112 ~I~~kvekKGGf~Vdl~aGv~AFLP~Sq~d~k~~~~~~~~~g~~~~f~i~k~d~~rqhrGn~nivvSRr~~lE~~~~~~r 191 (534)
T TIGR00717 112 KIVGKVEKKGGFIVDLEAGVEAFLPGSQVDVKKIKDLDSLIGKTLKFKIIKLDKKRQHRGNNNIVVSRRAYLEEERSQAR 191 (534)
T ss_pred EEEEEEECCCCEEEECCCCEEEECCCCCCCCCCCCCCCCCCCCEEEEEEEEECCHHCCCCCCCEEEEEEEEECHHHHHHH
T ss_conf 98776605657799923681786164604662666403034307789999863100125799769941001042568889
Q ss_pred HHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEE--EEECCCCHHHHHHHHHH
Q ss_conf 99999766777558087856631677503499994089988127--65548862178899862
Q gi|254780788|r 209 VKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVG--ACVGMRGSRVQAVVTEL 269 (526)
Q Consensus 209 ~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVG--AcVG~rGsRiq~I~~EL 269 (526)
..||+. | .+|.+-+=-|+ +|+|-| |-|=..|.+==-=.+++
T Consensus 192 ~e~le~----l------------~~g~~v~GvVk----~iT~fGGv~Fvdlgg~dGLLH~~d~ 234 (534)
T TIGR00717 192 EELLEK----L------------KEGEVVKGVVK----NITDFGGVAFVDLGGVDGLLHITDM 234 (534)
T ss_pred HHHHHH----C------------CCCCEEEEEEE----EECCCCCEEEEECCCEEECCCHHHC
T ss_conf 888761----5------------55857610888----8889874999981643320350121
No 28
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.09 E-value=2.8e-05 Score=58.03 Aligned_cols=64 Identities=34% Similarity=0.562 Sum_probs=58.4
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCC------CCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 20838999998405763899957-93587447874887------51152766999997611358702898715
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISR------ENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~------E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
+.|+++.|+|.++..+.++|+++ +.+|++|..++.+. +.|++||.++|.|.++....+ ++.||+
T Consensus 1 ~~G~iv~g~V~~v~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~--~i~ls~ 71 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKG--RIILSL 71 (72)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECCCC--EEEEEE
T ss_conf 99989999999997873999976998999980750555547846836389899999999999999--999985
No 29
>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=98.07 E-value=2.9e-05 Score=57.89 Aligned_cols=62 Identities=34% Similarity=0.576 Sum_probs=56.3
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 838999998405763899957-935874478748------8751152766999997611358702898715
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
|++|+|+|.++....++|+|+ +.+|++|.+|.. |.+.|+.||.|+|.|.+++...| +|.||.
T Consensus 1 G~iV~G~V~~i~~~G~fV~l~~~v~G~ih~sels~~~~~~~~~~~~vGd~v~akIi~iD~~~~--ri~LSi 69 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNR--KISLSI 69 (73)
T ss_pred CCEEEEEEEEEECCCEEEEECCCCEEEEEHHHCCCCHHHCHHHCCCCCCEEEEEEEEEECCCC--EEEEEE
T ss_conf 999999999997786899928996999998997821132925438999999999999978899--998674
No 30
>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=98.05 E-value=2.8e-05 Score=58.00 Aligned_cols=67 Identities=21% Similarity=0.352 Sum_probs=58.3
Q ss_pred HHHHHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 99998520838999998405763899957-93587447874------8875115276699999761135870289871
Q gi|254780788|r 131 YLEFKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 131 ~~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS 201 (526)
|+++ ++|.+++|+|+++....++|+++ +.+|++|.++. -|.+.|++|+.++|.|.+|+.+.+ +|.||
T Consensus 9 ~~~l--k~G~iv~G~V~~i~~~G~FV~l~~~v~Glv~~s~ls~~~~~~~~~~~~vGq~V~~~V~~iD~e~~--ri~LS 82 (83)
T cd04461 9 FSDL--KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQ--RFLLS 82 (83)
T ss_pred HHHC--CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEEEE
T ss_conf 7787--99999999999992781999956994899899996864226989945599999999999958988--78875
No 31
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.03 E-value=5.1e-05 Score=56.14 Aligned_cols=112 Identities=28% Similarity=0.352 Sum_probs=67.7
Q ss_pred ECHHHHHHHC-CCCCCCCEEEEEC---CH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC
Q ss_conf 3489998628-8986473799850---84----56207999999999999999999887799998520838999998405
Q gi|254780788|r 79 ISLKVARDRD-PSIDIGGVVSDPL---PP----MDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE 150 (526)
Q Consensus 79 I~l~~A~~~~-~~~~iGD~i~~~i---~~----~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e 150 (526)
.|+.+.+.++ .+.-+|-++...+ +. ...+|.++..+ =+..+|+..++.. .+|+++.|+|+++.
T Consensus 134 ~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~-------~~~~~r~e~~~~l--~~G~vV~G~V~~It 204 (541)
T COG0539 134 GSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEE-------ERSEQREELLNKL--EVGEVVEGVVKNIT 204 (541)
T ss_pred HHHHCCCCCCCCCCCCCCEEEEEEEEECCCCCCEEEEHHHHHHH-------HHHHHHHHHHHCC--CCCCEEEEEEEEEE
T ss_conf 78715452346523478658999999853348478771777667-------7888799997247--88766999999861
Q ss_pred CCEEEEEECCCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 76389995793587447874------8875115276699999761135870289871
Q gi|254780788|r 151 YGNVIVDLGNSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 151 ~~~iiVdlg~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS 201 (526)
.-+++||||+++|+||.+++ -|.+.|++||.|++.|.+++.+.+ .|-||
T Consensus 205 ~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~--RVsLS 259 (541)
T COG0539 205 DYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERG--RVSLS 259 (541)
T ss_pred CCCEEEEECCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCC--EEEEE
T ss_conf 57479992571668864760655558989953569889999999726788--69999
No 32
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.01 E-value=7e-05 Score=55.11 Aligned_cols=73 Identities=23% Similarity=0.412 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 988779999852083899999840576389995793587447874------88751152766999997611358702898
Q gi|254780788|r 126 ERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVL 199 (526)
Q Consensus 126 Er~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~ 199 (526)
.++..++.| ++|+++.|+|.++....++|+||+++|+++.++. -|.+.|++||.+++.|.+++.+.+ +|.
T Consensus 182 ~~~~~~~~l--~~Gdvv~G~V~~i~~~G~FV~lggv~glvh~sels~~~~~~~~~~~k~G~~v~~~Vl~id~~~~--ri~ 257 (390)
T PRK06676 182 KKKELLSSL--KEGDVVEGKVARLTDFGAFVDIGGVDGLVHISELSHERVNKPSEVVSVGQEVEVKVLSIDEETE--RIS 257 (390)
T ss_pred HHHHHHHHC--CCCCEEEEEEEEEECCCEEEECCCEEEEEEECCCCHHHHCCHHHHHCCCCEEEEEEEEEECCCC--EEE
T ss_conf 576677634--6898478999999456369980776799996105733335988830479757999999946788--999
Q ss_pred EEC
Q ss_conf 715
Q gi|254780788|r 200 LSR 202 (526)
Q Consensus 200 lSR 202 (526)
||.
T Consensus 258 Lsl 260 (390)
T PRK06676 258 LSL 260 (390)
T ss_pred EEE
T ss_conf 998
No 33
>PRK08059 general stress protein 13; Validated
Probab=97.91 E-value=5.7e-05 Score=55.77 Aligned_cols=65 Identities=26% Similarity=0.433 Sum_probs=58.0
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 20838999998405763899957-935874478748------87511527669999976113587028987159
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRT 203 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt 203 (526)
++|+++.|+|.++..-+++|+++ +.+|++|.+|.- |.+.|++||.|+|-|.+++.+.+ .|-||.-
T Consensus 5 kvGdiv~G~V~~I~~fG~FV~l~~gv~GLihiSEls~~~v~~~~~~~~vGd~V~vkVi~iD~e~~--ri~LSlK 76 (119)
T PRK08059 5 EVGVVVTGKVTGIQDYGAFVALDEETQGLVHISEITHGFVKDIHDFLKVGDEVKVKVLSVDEEHG--KISLSIR 76 (119)
T ss_pred CCCCEEEEEEEEEECEEEEEEEECCCEEEEEHHHHCCCCCCCHHHHHCCCCEEEEEEEEEECCCC--EEEEECC
T ss_conf 99999999999997404899994395378887882456667999970589989999999989999--9987503
No 34
>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=97.90 E-value=7.9e-05 Score=54.74 Aligned_cols=61 Identities=21% Similarity=0.537 Sum_probs=54.9
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 838999998405763899957-93587447874------8875115276699999761135870289871
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS 201 (526)
|+++.|+|+++..-.++|+|+ +++|++|.+++ -|.+.|++||.++|.|.+|+.+.+ +|.||
T Consensus 1 G~iv~G~V~~i~~fG~fV~l~~~i~Glv~~s~lsd~~v~~p~~~fk~G~~Vk~rVl~vD~~~~--ri~LS 68 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERK--RLVLT 68 (69)
T ss_pred CCEEEEEEEEECCCEEEEEECCCEEEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCC--EEEEE
T ss_conf 999999999973842799957990699878990865206988908999999999999948879--98865
No 35
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 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 of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein S1 contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities . Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=97.89 E-value=0.00016 Score=52.51 Aligned_cols=152 Identities=20% Similarity=0.253 Sum_probs=96.2
Q ss_pred HCCCCCCCEEEEECCCC---CEEEEEEEEEEECCCCCCCCEECHHHHHHHCC-CCCCCCEEEEECCHHHHHH-----HHH
Q ss_conf 13687453599974998---83999999885176778753234899986288-9864737998508456207-----999
Q gi|254780788|r 41 SLYGTMSDIRVEINPET---GDISLFRLLEVVEEVENYTCQISLKVARDRDP-SIDIGGVVSDPLPPMDFGR-----VAV 111 (526)
Q Consensus 41 K~~~~~~~i~V~iD~~t---G~i~i~~~~~VVedved~~~eI~l~~A~~~~~-~~~iGD~i~~~i~~~~fgR-----iaA 111 (526)
+.|-..+.+.-.|.+++ |-|.+=. .---...+-+|..+.|+++. .--+|=..++.+-..|-.| -..
T Consensus 101 ~~~~~~~~V~G~I~~kvekKGGf~Vdl-----~aGv~AFLP~Sq~d~k~~~~~~~~~g~~~~f~i~k~d~~rqhrGn~ni 175 (534)
T TIGR00717 101 KAYEEGSIVEGKIVGKVEKKGGFIVDL-----EAGVEAFLPGSQVDVKKIKDLDSLIGKTLKFKIIKLDKKRQHRGNNNI 175 (534)
T ss_pred HHHHCCCEEEEEEEEEEECCCCEEEEC-----CCCEEEECCCCCCCCCCCCCCCCCCCCEEEEEEEEECCHHCCCCCCCE
T ss_conf 986169845679877660565779992-----368178616460466266640303430778999986310012579976
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCE--EEEEECCCEEEEEHHHC------CCCCCCCCCCEEE
Q ss_conf 999999999999999887799998520838999998405763--89995793587447874------8875115276699
Q gi|254780788|r 112 QSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGN--VIVDLGNSDGVIRRDET------ISRENLRPGDRVK 183 (526)
Q Consensus 112 q~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~--iiVdlg~~ea~Lp~~e~------ip~E~~~~Gdrik 183 (526)
-.-|..++.--|..+|+..++.- ..|+-+.|+|+.++.-. ++||||+++|+||..++ -|.|.+..||.|+
T Consensus 176 vvSRr~~lE~~~~~~r~e~le~l--~~g~~v~GvVk~iT~fGGv~Fvdlgg~dGLLH~~d~sWkr~~~P~e~~~~G~~~~ 253 (534)
T TIGR00717 176 VVSRRAYLEEERSQAREELLEKL--KEGEVVKGVVKNITDFGGVAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVK 253 (534)
T ss_pred EEEEEEEECHHHHHHHHHHHHHC--CCCCEEEEEEEEECCCCCEEEEECCCEEECCCHHHCCCCCCCCCHHHCCCCCEEE
T ss_conf 99410010425688898887615--5585761088888898749999816433203501214788788346400798899
Q ss_pred EEEEEECCCCCEEEEEEE
Q ss_conf 999761135870289871
Q gi|254780788|r 184 SYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 184 a~i~~V~~~~rgpqi~lS 201 (526)
+-+..++.+.+ .|.||
T Consensus 254 Vkv~~~D~~~~--Ri~Ls 269 (534)
T TIGR00717 254 VKVIKFDKEKK--RISLS 269 (534)
T ss_pred EEEEEECCCCC--EEEEE
T ss_conf 99996526576--07787
No 36
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.89 E-value=0.00056 Score=48.46 Aligned_cols=122 Identities=19% Similarity=0.298 Sum_probs=83.0
Q ss_pred CCCEECHHHHHHHCCC--CCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HCCCEEEEEEEECC
Q ss_conf 7532348999862889--8647379985084562079999999999999999998877999985--20838999998405
Q gi|254780788|r 75 YTCQISLKVARDRDPS--IDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKD--KVGEIISGTVKRVE 150 (526)
Q Consensus 75 ~~~eI~l~~A~~~~~~--~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~--r~Geiv~G~V~r~e 150 (526)
...-|++++-...... +++||.+..-+...+.+.- + +.-..|.+++.+.+..-.+ ..|++|.|.|...-
T Consensus 45 seg~ip~~E~~~~~~~~~~~~gd~v~v~v~~~e~~~g------~-~~lS~~k~~~~~~w~~l~~~~e~~~~V~~~v~~~v 117 (541)
T COG0539 45 SEGVIPISEFSNEPVEDVVQVGDEVEVLVLRVEDGEG------E-LVLSRRKAERERAWEKLEEAFENGEIVEGKITGKV 117 (541)
T ss_pred CCCEEEHHHCCCCCCCCEECCCCEEEEEEEEEECCCC------E-EEEEHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEE
T ss_conf 1557688980566655131589889999999836886------0-88617788877778999988745983899999884
Q ss_pred CCEEEEEECCCEEEEEHHHCCCC----CCCCCCCEEEEEEEEECCCCCEEEEEEECCCH
Q ss_conf 76389995793587447874887----51152766999997611358702898715988
Q gi|254780788|r 151 YGNVIVDLGNSDGVIRRDETISR----ENLRPGDRVKSYIYDVRREQRGPQVLLSRTHP 205 (526)
Q Consensus 151 ~~~iiVdlg~~ea~Lp~~e~ip~----E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p 205 (526)
+|.++||+++..|+||.+..--+ -.-..|..+.+.+.++++..+ .+++||-.-
T Consensus 118 KGG~~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n--~vv~SrR~~ 174 (541)
T COG0539 118 KGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRN--NVVLSRRAV 174 (541)
T ss_pred CCCEEEEECCEEEECCHHHHCCCCCCCCCCCCCCEEEEEEEEECCCCC--CEEEEHHHH
T ss_conf 484899987878865578715452346523478658999999853348--478771777
No 37
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=97.89 E-value=2.2e-05 Score=58.84 Aligned_cols=58 Identities=31% Similarity=0.487 Sum_probs=50.5
Q ss_pred HHHHHHHCCCCCCCEEEECCC--CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHC-------CEEEE
Q ss_conf 999997628665424898756--78799998534221102544278999998616-------74578
Q gi|254780788|r 284 ATFVINALRPAIVTKVVLDED--VGRIEVIVPKEQLSLAIGRRGQNVRLASQLTG-------WTIDI 341 (526)
Q Consensus 284 ~~fi~nAl~PA~v~~v~~de~--~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg-------~~idi 341 (526)
.+|+.+.|.||.+.+|.+... .....+++...|.+++|||+|+|+++...|++ |.||+
T Consensus 1 ~~~l~~~l~~~~~~~V~i~~~~~~~~~~i~~~~~~~g~~IGk~G~~l~~l~~ll~~~~~~~~~~i~v 67 (68)
T cd02409 1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKRVKIDV 67 (68)
T ss_pred CHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCCCEEECCCCHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 9578745565685569999779967999998777996489888363999999999982899843853
No 38
>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=97.89 E-value=7.7e-05 Score=54.82 Aligned_cols=62 Identities=31% Similarity=0.449 Sum_probs=56.0
Q ss_pred CCEEEEEEEECCCCEEEEEE-CCCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 83899999840576389995-7935874478748------8751152766999997611358702898715
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDL-GNSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdl-g~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
|.++.|+|.++.....+|++ ++.+|++|.+|.- |.+.|++|+.++|.|.+|+.+.+ ++.||.
T Consensus 1 G~vv~G~V~~i~~~G~fV~~~~~i~Glvp~seis~~~v~~p~~~f~~Gq~V~v~Vl~vd~~~~--ri~LS~ 69 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQ--RLLLSC 69 (70)
T ss_pred CCEEEEEEEEEECCCEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEEEEC
T ss_conf 999999999998171899948996999898992832028989937799999999999808999--999971
No 39
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=97.87 E-value=3.1e-05 Score=57.70 Aligned_cols=56 Identities=27% Similarity=0.335 Sum_probs=51.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 12258884678888773211147775058888776530588999999999999999
Q gi|254780788|r 363 MQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLE 418 (526)
Q Consensus 363 ~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~ 418 (526)
-+-.+|...+|+.|.++||.|++.||.|++.||+.+.|+.+..|.++++.|++++.
T Consensus 3 edLPGVGp~TA~KL~EaGy~t~~~iA~A~~~EL~~~~gI~E~~A~kiI~AAR~a~~ 58 (333)
T TIGR02236 3 EDLPGVGPATAEKLREAGYDTLEAIAVASPKELSEIAGIGEGTAAKIIQAARKAAD 58 (333)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHHHHC
T ss_conf 65789757688998861078899984458579532037877789999999999846
No 40
>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=97.81 E-value=7.5e-05 Score=54.89 Aligned_cols=58 Identities=28% Similarity=0.517 Sum_probs=53.1
Q ss_pred CCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf 0838999998405763899957935874478748------875115276699999761135870
Q gi|254780788|r 138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRG 195 (526)
Q Consensus 138 ~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rg 195 (526)
+|+++.|+|+++..-.++|++++.+|++|.+|.. |++.|++||.++|.|.+++.+.+-
T Consensus 1 eG~iv~g~V~~i~~fG~FV~l~gi~Glihisels~~~~~~~~~~~k~Gd~v~~kVi~iD~~k~r 64 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKR 64 (68)
T ss_pred CCCEEEEEEEEEECCEEEEEECCEEEEEECHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCE
T ss_conf 9999999999995638899979989999843646666689889147999999999999999798
No 41
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=97.80 E-value=0.00012 Score=53.42 Aligned_cols=61 Identities=26% Similarity=0.440 Sum_probs=54.8
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 838999998405763899957-93587447874------8875115276699999761135870289871
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS 201 (526)
|+++.|+|+++..-.++|+|+ +.+|++|.++. -|.+.|++||.++|.|.+|+.+.+ +|-||
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~~~~~GLvhisels~~~~~~~~~~~~vGd~v~~kVi~id~e~~--ri~LS 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERG--RISLS 68 (68)
T ss_pred CCEEEEEEEEEECEEEEEEECCCCEEEEECHHHCCCCCCCHHHCCCCCCEEEEEEEEEECCCC--EEECC
T ss_conf 999999999996528999914997899981897678767986857999999999999989999--88779
No 42
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.76 E-value=0.00019 Score=51.88 Aligned_cols=62 Identities=29% Similarity=0.495 Sum_probs=53.8
Q ss_pred CCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC-----CCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 83899999840576389995793587447874887-----511527669999976113587028987159
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR-----ENLRPGDRVKSYIYDVRREQRGPQVLLSRT 203 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~-----E~~~~Gdrika~i~~V~~~~rgpqi~lSRt 203 (526)
|++|+|+|....+|.++|++++.+|+||.++.-.. +.| .|..+++.|.++++..+ .+++||-
T Consensus 1 g~~v~g~I~~~~kGG~~v~~~gv~~FiP~Sq~~~~~~~~~~~~-vG~~i~~~Ii~~d~~~~--~ivvSrk 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEY-VGKELKFKIIEIDRERN--NIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCCEEEEECCEEEEEECHHCCCCCCCCHHHH-CCCEEEEEEEEEECCCC--EEEEECC
T ss_conf 9999999999985719999999999988025255456896897-89989999999927889--9999879
No 43
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=97.76 E-value=0.00016 Score=52.42 Aligned_cols=65 Identities=26% Similarity=0.295 Sum_probs=56.9
Q ss_pred HHCCCEEEEEEEECCCCEEEEEEC---CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 520838999998405763899957---935874478748------8751152766999997611358702898715
Q gi|254780788|r 136 DKVGEIISGTVKRVEYGNVIVDLG---NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~~iiVdlg---~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
+.+|+++.|+|.++..-.++|+|+ +.+|++|-+|.- |.+.|++||+++|.+.+|+.+.+ +|-||+
T Consensus 1 Pe~G~iv~G~V~~i~~~GafV~l~e~~g~eGlihiSEis~~~v~~~~d~~~~G~~v~~kVi~vD~~k~--~i~LS~ 74 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKG--YIDLSK 74 (76)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEEEEE
T ss_conf 98899999999999734699997336991999997996845115999955899999999999978999--998223
No 44
>PRK07252 hypothetical protein; Provisional
Probab=97.70 E-value=0.00019 Score=51.89 Aligned_cols=66 Identities=23% Similarity=0.358 Sum_probs=57.2
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf 20838999998405763899957-935874478748------875115276699999761135870289871598
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRTH 204 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~ 204 (526)
++|+++.|+|.++..-.++|+|+ +++|+++-+|.- |.+.|++||.|+|.|.+|+.+.+ +|-||.-.
T Consensus 2 kvGdiv~G~V~~I~~fGaFV~l~~gv~GLiHISEis~~~v~~~~~~~kvGd~V~vkVi~ID~e~~--rIsLSiK~ 74 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGNEVLVQVIDIDEYTK--KASLSMRT 74 (120)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEECCHHH
T ss_conf 88889999999997545799957995788886660102004999947899999999999868999--88613633
No 45
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=97.69 E-value=0.00017 Score=52.32 Aligned_cols=61 Identities=28% Similarity=0.444 Sum_probs=52.9
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 838999998405763899957-93587447874------88751152766999997611358702898715
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
|+++.|+|.++..-.++|+|+ +.+|+++-+|. -|.+.|++||.++|.+.+++... .|-|||
T Consensus 1 G~iv~G~V~~i~~fG~FV~l~~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD~~~---ri~LSr 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRG---RISLSR 68 (68)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCC---CCCCCC
T ss_conf 99999999999732999995799624888689345654698890789999999999999999---720529
No 46
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=97.69 E-value=4.3e-05 Score=56.71 Aligned_cols=58 Identities=26% Similarity=0.361 Sum_probs=53.6
Q ss_pred HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 664077999899999998798478896532677521231234443211245334358899999999998412257
Q gi|254780788|r 436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMG 510 (526)
Q Consensus 436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~g 510 (526)
+|.+|||+.+.++.+|-++|..|++.+|--|..||..+. ++++..|.++|+.||+-++
T Consensus 1 ~ledLPGVGp~TA~KL~EaGy~t~~~iA~A~~~EL~~~~-----------------gI~E~~A~kiI~AAR~a~~ 58 (333)
T TIGR02236 1 DLEDLPGVGPATAEKLREAGYDTLEAIAVASPKELSEIA-----------------GIGEGTAAKIIQAARKAAD 58 (333)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC-----------------CCCHHHHHHHHHHHHHHHC
T ss_conf 966578975768899886107889998445857953203-----------------7877789999999999846
No 47
>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=97.69 E-value=0.00019 Score=51.99 Aligned_cols=66 Identities=33% Similarity=0.575 Sum_probs=57.1
Q ss_pred HCCCEEEEEEEECCCCEEEEEE-C-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf 2083899999840576389995-7-93587447874------8875115276699999761135870289871598
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDL-G-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTH 204 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdl-g-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~ 204 (526)
++|+++.|+|.++..-.++|++ | +.+|+++.+|. -|.+.|++||.++|.|.+++.+.+ +|-||.-.
T Consensus 1 kVG~~v~G~V~~i~~fG~FV~l~g~~i~GLvHiSels~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~--rI~LSiKa 74 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKK--RISLGLKA 74 (77)
T ss_pred CCCCEEEEEEEEEECEEEEEEECCCCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCC--EEEEEEEC
T ss_conf 998999999999964178999678980799887881756568988916899999999999989999--99989841
No 48
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.60 E-value=0.00043 Score=49.35 Aligned_cols=124 Identities=15% Similarity=0.211 Sum_probs=78.4
Q ss_pred ECCCCCCCCEECHHHHHHHCCCCCCCCEEEEECCHH-HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEE
Q ss_conf 176778753234899986288986473799850845-62-0799999999999999999988779999852083899999
Q gi|254780788|r 69 VEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPM-DF-GRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTV 146 (526)
Q Consensus 69 Vedved~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~-~f-gRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V 146 (526)
|+-......-|++++- ....++||.+..-++.. ++ |+.+-.-||+.- -...+-.. -..|++|+|+|
T Consensus 339 vdvG~KsEg~ip~~eF---~~~~~vGD~v~V~ie~~e~~~~~LSr~kA~r~~-------~w~~le~a--~~~~~~v~G~i 406 (863)
T PRK12269 339 VDIGGKSEGRVPVEEF---EAPPKAGDGVRVYVERVTPYGPELSKTKADRLG-------LKVKLRDA--ERDGTPVEGRI 406 (863)
T ss_pred EECCCCCCCCCCHHHC---CCCCCCCCEEEEEEEEECCCCCEECHHHHHHHH-------HHHHHHHH--HHCCCEEEEEE
T ss_conf 9647744553269992---778899999999999970889756189998789-------99999999--75699079999
Q ss_pred EECC--CCEEEEEEC-CCEEEEEHHHC----CCCCCCCCCCEEEEEEEEECCC--CCE-EEEEEECCC
Q ss_conf 8405--763899957-93587447874----8875115276699999761135--870-289871598
Q gi|254780788|r 147 KRVE--YGNVIVDLG-NSDGVIRRDET----ISRENLRPGDRVKSYIYDVRRE--QRG-PQVLLSRTH 204 (526)
Q Consensus 147 ~r~e--~~~iiVdlg-~~ea~Lp~~e~----ip~E~~~~Gdrika~i~~V~~~--~rg-pqi~lSRt~ 204 (526)
.|+. +|.+.|||| ++.|+||-++- ++.-.+-.|....+.+..+... .|| ..|++||..
T Consensus 407 ~~~~~vkgG~~Vdl~~gv~AFLPgSqvd~rpv~d~~~~~g~~~~f~iik~~~~~~~r~~~NiVvSRra 474 (863)
T PRK12269 407 VRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQSKQHRGNDNIVINRRR 474 (863)
T ss_pred EECCCCCCCEEEECCCCCEEECCHHHCCCEECCCCHHHCCCCCCEEEEEEEHHHHCCCCCCEEEECHH
T ss_conf 74461045379985889678676656471136886321588741599995313312677888997679
No 49
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.53 E-value=0.00061 Score=48.21 Aligned_cols=99 Identities=21% Similarity=0.314 Sum_probs=69.6
Q ss_pred CCCCCCCHHHHHHHHHHHH-HHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH--C
Q ss_conf 1225888467888877321-114777505888877653058899999999999999999999898775428435664--0
Q gi|254780788|r 363 MQAINVDEIIAHLLVAEGF-ADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELC--S 439 (526)
Q Consensus 363 ~e~LdVDE~iA~~LV~eGf-~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~--~ 439 (526)
|+.-++.+.+.+.|++.|| .++.+|.....++|..++||.+..|..|.+.-.. . +......=|. .
T Consensus 448 mdI~GlG~~~i~~L~~~g~i~~~~Diy~L~~~~L~~l~gfgeKsa~nLl~aIe~---------S---K~~~l~r~L~ALG 515 (668)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHTPADLFKLTEEDLLQLEGFGEKSAQNLLDAIEK---------S---KETPLARFLYALG 515 (668)
T ss_pred CCCCCCCHHHHHHHHHCCCCCCHHHHHCCCHHHHHCCCCHHHHHHHHHHHHHHH---------H---CCCCHHHHHHHCC
T ss_conf 164665999999998768766589997288545402123556699999999998---------5---4775888998627
Q ss_pred CCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf 77999899999998798478896532677521231
Q gi|254780788|r 440 IPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS 474 (526)
Q Consensus 440 l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~ 474 (526)
++++....+-.|+.+ .+|++.|...+.++|..+.
T Consensus 516 I~~VG~~~Ak~La~~-f~sl~~l~~as~e~L~~I~ 549 (668)
T PRK07956 516 IRHVGEKAAKALARH-FGSLEALEAASEEELAAVE 549 (668)
T ss_pred CCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHCCC
T ss_conf 864129999999999-6689999708999985768
No 50
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.44 E-value=0.00082 Score=47.26 Aligned_cols=61 Identities=30% Similarity=0.543 Sum_probs=53.1
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 838999998405763899957-93587447874------88751152766999997611358702898715
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
|+++.|+|.++..-.++|+++ +.+|+++-+|. -|.+.|++||.+++.+.+++. +| .|-||+
T Consensus 1 G~vv~G~V~~I~~fGaFV~l~~g~~GL~HiSeis~~~v~~~~~~~~~Gd~v~vkVi~id~--~~-ri~LS~ 68 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA--RG-RISLSI 68 (69)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECC--CC-CEEECC
T ss_conf 999999999998538999968998899996983456557988917899999999999999--99-668015
No 51
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.40 E-value=0.00033 Score=50.22 Aligned_cols=56 Identities=32% Similarity=0.395 Sum_probs=51.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 11225888467888877321114777505888877653058899999999999999
Q gi|254780788|r 362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL 417 (526)
Q Consensus 362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L 417 (526)
+.+-.+|....++.|-++||.|+++++++++.+|.++.|+++..|.+++..|++.+
T Consensus 9 l~~lpGv~~~~~~kL~~aG~~tv~~l~~~~~~~L~~~~gis~~~a~ki~~~a~~~~ 64 (318)
T PRK04301 9 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEIAGISESTAAKIIEAAREAL 64 (318)
T ss_pred CCCCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf 45589989999999998699549998748999999850999999999999999853
No 52
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=97.39 E-value=0.002 Score=44.39 Aligned_cols=75 Identities=25% Similarity=0.354 Sum_probs=62.5
Q ss_pred HHCCCEEEEEEEECCCCEEEEEE---CCCEEEEEHHHCCC------CCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHH
Q ss_conf 52083899999840576389995---79358744787488------7511527669999976113587028987159889
Q gi|254780788|r 136 DKVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDETIS------RENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQ 206 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~~iiVdl---g~~ea~Lp~~e~ip------~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~ 206 (526)
+.+|++|.|+|.++..-..+|+| |+.+|++|-+|..+ ++.+++|+++.|.|..|+.+.+.--+-+-|.+|+
T Consensus 6 Pe~g~~v~~~V~~i~~~Ga~v~l~ey~~~eG~i~isEis~~~v~~i~d~~k~G~~v~~kVi~vd~~kg~IdLS~k~Vs~~ 85 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVCKVIRVDPKKGHIDLSLKRVNEH 85 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCCCEEEEHHHCCHHHHHCHHHHCCCCCEEEEEEEEECCCCCEEEEECCCCCHH
T ss_conf 99998899999999566799993565993167887983467751999851589889999998838788787110449989
Q ss_pred HHHH
Q ss_conf 9999
Q gi|254780788|r 207 FMVK 210 (526)
Q Consensus 207 ~l~~ 210 (526)
=.++
T Consensus 86 e~~~ 89 (262)
T PRK03987 86 QRRE 89 (262)
T ss_pred HHHH
T ss_conf 9999
No 53
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=97.38 E-value=0.00087 Score=47.07 Aligned_cols=58 Identities=26% Similarity=0.426 Sum_probs=50.1
Q ss_pred EEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 999998405763899957-935874478748------875115276699999761135870289871
Q gi|254780788|r 142 ISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 142 v~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lS 201 (526)
+.|+|.++....++|+++ +.+|++|.++.. |.+.|++||.++|.+.+++...+ .+.||
T Consensus 1 v~G~V~~i~~~G~fV~~~~~~~gli~~s~~s~~~~~~~~~~~~~G~~V~~~Vi~vd~~~~--~i~LS 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG--RISLS 65 (65)
T ss_pred CEEEEEEEECCEEEEEECCCEEEEEEHHHHCCCCCCCHHHEECCCCEEEEEEEEEECCCC--EEECC
T ss_conf 989999997845999989871788988891676535951098599999999999989999--89769
No 54
>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=97.33 E-value=0.0021 Score=44.29 Aligned_cols=63 Identities=27% Similarity=0.432 Sum_probs=56.7
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 20838999998405763899957-93587447874------8875115276699999761135870289871
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS 201 (526)
++|.++.|.|.++....++|+|| +.+|.....|. -|.+.|+.||.++|-+.+|..+.| +|-||
T Consensus 2 kvG~~l~G~Vt~V~~~g~fV~L~~~~~Glvhisel~dd~~~~~~~~~~~g~~V~v~Vl~VD~~~k--rI~LS 71 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNK--KIALS 71 (73)
T ss_pred CCCCEEEEEEEEECCCEEEEEECCCCEEEEEHHHHCCCCCCCCHHHCCCCCEEEEEEEEEECCCC--EEEEE
T ss_conf 88989999999988887999908994799998993046013817516899999999999988899--89886
No 55
>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=97.30 E-value=0.0013 Score=45.89 Aligned_cols=56 Identities=21% Similarity=0.452 Sum_probs=50.8
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC-------CCCCCCCCCEEEEEEEEECCCCC
Q ss_conf 838999998405763899957-935874478748-------87511527669999976113587
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI-------SRENLRPGDRVKSYIYDVRREQR 194 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i-------p~E~~~~Gdrika~i~~V~~~~r 194 (526)
|+++.|+|.++..-.++|+|. +.+|+++.+|+. |.+.|+.||.++|.|.+++.+.+
T Consensus 1 G~~v~G~V~~i~~fG~FV~l~~gieGLvHiselsw~~~~~~~~~~~~~Gd~V~vkVl~iD~e~~ 64 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERE 64 (69)
T ss_pred CCEEEEEEEEECCCEEEEEECCCCEEEEEHHHHCCCCCCCCHHHCCCCCCEEEEEEEEEECCCC
T ss_conf 9999999999913189999769965999948824566667976825899999999999979868
No 56
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.26 E-value=0.00064 Score=48.06 Aligned_cols=70 Identities=26% Similarity=0.490 Sum_probs=56.7
Q ss_pred ECCCCHHHHHH--HHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCH
Q ss_conf 55987899999--76286654248987567879999853422110254427899999861674578552200
Q gi|254780788|r 278 VWSPDSATFVI--NALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEED 347 (526)
Q Consensus 278 ~ws~d~~~fi~--nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~ 347 (526)
..+.+.-.|+. ..+.-|.+...++|++..+..-+|++.++.+||||+|.|++-.+.+.|-+|||.-.++.
T Consensus 4 ~l~~e~~ryi~lFe~~T~~~~~DCi~d~~~~riiFvV~~g~mG~AIGk~G~~Ik~l~~~lgkkIdiVe~seD 75 (142)
T PRK08406 4 KLTTEEIRYIALFESITGATVRDCIIDEEYDRIIFVVKEGDMGLAIGKGGENVKRLKEKLGKDIELVEYSED 75 (142)
T ss_pred EECHHHHHHHHHHHHHHCCCEEEEEECCCCCEEEEEECCCHHHHHHCCCCCHHHHHHHHHCCCEEEEECCCC
T ss_conf 988899999999999879972356870899889999876768897587960799999985894589964789
No 57
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.24 E-value=0.0017 Score=44.92 Aligned_cols=59 Identities=22% Similarity=0.357 Sum_probs=52.5
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC-------CCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf 20838999998405763899957-935874478748-------875115276699999761135870
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI-------SRENLRPGDRVKSYIYDVRREQRG 195 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i-------p~E~~~~Gdrika~i~~V~~~~rg 195 (526)
.+|.+++|+|.++..-.++|+|+ +.+|+++-+|+- |.+.|++||.+++.|.+++.+.|-
T Consensus 2 ~~G~~v~G~V~~It~fG~FV~i~~g~eGLvHiSelsw~~~~~~p~~~~~~Gd~v~vkIl~iD~e~~r 68 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRR 68 (72)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCE
T ss_conf 8899999999899476239996699389999766316546679636038999999999999599799
No 58
>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=97.17 E-value=0.0021 Score=44.28 Aligned_cols=61 Identities=25% Similarity=0.464 Sum_probs=53.5
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 838999998405763899957-935874478748------875115276699999761135870289871
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lS 201 (526)
|+++.|+|+++..-.++|+|| +.+|++|-++.. |.+.|++|+.+++-|.+++.+.+ +|-||
T Consensus 1 G~~v~G~V~~i~~~G~FV~l~~~~~glVhiselsd~fVkd~~~~f~vGq~V~~kV~~iD~~~~--ri~LS 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNG--RIEMT 68 (68)
T ss_pred CCEEEEEEEEECCCCEEEEECCCCEEEEEHHHHCHHHHCCHHHHCCCCCEEEEEEEEEECCCC--EEECC
T ss_conf 999899999803640799917996799995991723564998917999999999999828758--67359
No 59
>PRK05807 hypothetical protein; Provisional
Probab=97.17 E-value=0.0019 Score=44.52 Aligned_cols=64 Identities=27% Similarity=0.455 Sum_probs=54.9
Q ss_pred HCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 20838999998405763899957935874478748------87511527669999976113587028987159
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRT 203 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt 203 (526)
.+|+++.|+|.++..-..+|+|++.+|+++-+|.- +.+.|+.||.|+|.|..|.. +| .|-||.-
T Consensus 4 evG~iv~G~V~~I~~fGaFV~l~g~~GLvHISEis~~~Vk~i~d~lk~Gd~V~vkVl~iD~--~g-kI~LSiK 73 (136)
T PRK05807 4 EAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD--NG-KISLSIK 73 (136)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECC--CC-CCEEEHH
T ss_conf 5788999999999724479997892768985670776436999967899999999999899--99-8143322
No 60
>PRK01172 ski2-like helicase; Provisional
Probab=97.17 E-value=0.018 Score=37.38 Aligned_cols=107 Identities=16% Similarity=0.161 Sum_probs=73.8
Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHCCHHHH---HHCCCCCCHHHHHH
Q ss_conf 75058888776530588999999999999999-------------999998987754284356---64077999899999
Q gi|254780788|r 387 LACVKISEIASIEGFDEETAVEIQGRAREYLE-------------GIDITLQKKIRELGVSEE---LCSIPGIDSKIKVA 450 (526)
Q Consensus 387 Ia~a~~eeL~~IeGfdee~a~eL~~rA~~~L~-------------~~~~~~~e~~~e~~~~e~---L~~l~gl~~~~~~~ 450 (526)
+..++...+.+--|++.-....+.+.|.-+.- ......-..+-..|+.++ |+.++|+...-+-+
T Consensus 548 i~E~~~~~I~~~y~v~~G~lq~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~l~~Rl~~Gv~~eLl~L~~I~gigr~RAR~ 627 (674)
T PRK01172 548 ISEASMQKITDTYGIAPGDVQARASSADWISYSLARLSSIYKPEMRRKLEILNIRIKEGIREDLIDLVLIPKVGRVRARR 627 (674)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHH
T ss_conf 73899999999869894899999999999999999999861199999999999999819868889771889999899999
Q ss_pred HHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 998798478896532677521231234443211245334358899999999998412257
Q gi|254780788|r 451 LGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMG 510 (526)
Q Consensus 451 L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~g 510 (526)
|-++||+|++|+|..+.++|..+. +++..-|.++|=.||.=++
T Consensus 628 Ly~aG~~s~~dia~a~~~~L~~i~-----------------g~~~~~A~~Ii~~A~~l~~ 670 (674)
T PRK01172 628 LYDAGFKTVDDIARSSPERIKKIY-----------------GFSDTLANAIVNRAMKISS 670 (674)
T ss_pred HHHCCCCCHHHHHHCCHHHHHHCC-----------------CCCHHHHHHHHHHHHHHHH
T ss_conf 998699999999709998987641-----------------9899999999999997775
No 61
>PRK01172 ski2-like helicase; Provisional
Probab=97.07 E-value=0.0015 Score=45.36 Aligned_cols=57 Identities=26% Similarity=0.335 Sum_probs=50.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 112258884678888773211147775058888776530588999999999999999
Q gi|254780788|r 362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLE 418 (526)
Q Consensus 362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~ 418 (526)
|+...+|....|..|+.+||+|+++||.+++++|.+|.|+....|..+++.|+..+.
T Consensus 614 L~~I~gigr~RAR~Ly~aG~~s~~dia~a~~~~L~~i~g~~~~~A~~Ii~~A~~l~~ 670 (674)
T PRK01172 614 LVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRAMKISS 670 (674)
T ss_pred HCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf 718899998999999986999999997099989876419899999999999997775
No 62
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.02 E-value=0.0041 Score=42.13 Aligned_cols=64 Identities=22% Similarity=0.352 Sum_probs=55.3
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC--CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 20838999998405763899957--93587447874887511527669999976113587028987
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG--NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLL 200 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg--~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~l 200 (526)
..|-+++|.|+.+|-..+++|+| +..|+||+++.-+...+++|.-+-|.|..|+...|-.++-.
T Consensus 3 ~~g~~l~a~V~SvEDHGyild~Gi~~~~gFl~~k~~~~~~~l~~G~v~~c~V~~v~~~g~vv~ls~ 68 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKDDGRVVSLSA 68 (74)
T ss_pred CCCCEEEEEEEEEECCEEEEECCCCCCEEEEEHHHCCCCCCCCCCCEEEEEEEEEECCCEEEEEEC
T ss_conf 678299999856714418998477772667301334755633488789999999928960999966
No 63
>PRK08582 hypothetical protein; Provisional
Probab=96.98 E-value=0.0039 Score=42.27 Aligned_cols=63 Identities=24% Similarity=0.390 Sum_probs=54.0
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC------CCCCCCCCCEEEEEEEEECCCCCEEEEEEEC
Q ss_conf 20838999998405763899957-935874478748------8751152766999997611358702898715
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI------SRENLRPGDRVKSYIYDVRREQRGPQVLLSR 202 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSR 202 (526)
.+|+++.|+|.++..-.++|+|+ +.+|+++-+|.- +.+.|++||.|+|-|.+|..+. .|-||-
T Consensus 4 evG~iv~G~V~~I~~fGaFV~l~~g~~GLvHISeis~~~V~~i~d~lkvGd~V~vKVi~id~~g---KI~LSi 73 (139)
T PRK08582 4 EVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLSVGDEVEVKVLNVEDDG---KIGLSI 73 (139)
T ss_pred CCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCC---CEEEEH
T ss_conf 4787999999899641789995699667887366256656899995789999999999888999---705165
No 64
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=96.89 E-value=0.0027 Score=43.44 Aligned_cols=22 Identities=5% Similarity=0.099 Sum_probs=13.3
Q ss_pred HHHHHHCCCCHHHHHHHHHHHH
Q ss_conf 9998623999999999999999
Q gi|254780788|r 14 DAVAYEKSIDRDVVLSVMADSI 35 (526)
Q Consensus 14 e~va~EK~I~~e~i~~aie~Al 35 (526)
..+++.+||+...+..+++.|-
T Consensus 40 ~~L~~~~gis~~~a~ki~~~a~ 61 (318)
T PRK04301 40 KELSEIAGISESTAAKIIEAAR 61 (318)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9999850999999999999999
No 65
>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=96.88 E-value=0.0071 Score=40.37 Aligned_cols=58 Identities=26% Similarity=0.402 Sum_probs=50.2
Q ss_pred CCCEEEEEEEECCCCEEEEEEC--CCEEEEEHHHCC-----------------CCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf 0838999998405763899957--935874478748-----------------875115276699999761135870
Q gi|254780788|r 138 VGEIISGTVKRVEYGNVIVDLG--NSDGVIRRDETI-----------------SRENLRPGDRVKSYIYDVRREQRG 195 (526)
Q Consensus 138 ~Geiv~G~V~r~e~~~iiVdlg--~~ea~Lp~~e~i-----------------p~E~~~~Gdrika~i~~V~~~~rg 195 (526)
+|+...|+|..+..-.++|.|. .+||++|.++.- ++..|+.||++++-|.+|....+.
T Consensus 1 IG~~f~g~I~~v~~~GiFV~l~~~~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~~~lGd~v~V~i~~vd~~~~~ 77 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRK 77 (83)
T ss_pred CCCEEEEEEEEEEEEEEEEEEECCCEEEEEECCCCCCCCEEECCCCEEEECCCCCCEEECCCEEEEEEEEEECCCCE
T ss_conf 99999999998983069999828873999982214567224474021898134775997899999999999430398
No 66
>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=96.73 E-value=0.0091 Score=39.59 Aligned_cols=61 Identities=20% Similarity=0.369 Sum_probs=50.4
Q ss_pred CCEEEEEEEECCCCEEEEEEC----CCEEEEEHHHCC-------CCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 838999998405763899957----935874478748-------87511527669999976113587028987159
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG----NSDGVIRRDETI-------SRENLRPGDRVKSYIYDVRREQRGPQVLLSRT 203 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg----~~ea~Lp~~e~i-------p~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt 203 (526)
|+++.|+|+++..-..+|+|. +.+|++.-+|.- |.+.|++||++++-|.++++. .|-||+.
T Consensus 1 G~i~~G~V~~i~~fGaFV~l~~~~~~~~GLvHiSeis~~~~~~~~~~~~~~G~~V~vkVi~id~~----ki~LS~K 72 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNG----KISLSMK 72 (79)
T ss_pred CCEEEEEEEEEEEEEEEEEEECCCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEECC----EEEEEEE
T ss_conf 99999999899753399999678898067899568157555589889367999999999998699----8887226
No 67
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.71 E-value=0.0016 Score=45.07 Aligned_cols=170 Identities=26% Similarity=0.405 Sum_probs=96.9
Q ss_pred CCCEEEEEEEEECCCCCEEEE---EEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCC-EEEEEEEECCCCCCCEEE
Q ss_conf 276699999761135870289---8715988999999997667775580878566316775-034999940899881276
Q gi|254780788|r 178 PGDRVKSYIYDVRREQRGPQV---LLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGS-RAKLAVFSSDSSIDPVGA 253 (526)
Q Consensus 178 ~Gdrika~i~~V~~~~rgpqi---~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~-RsKIAV~s~d~~iDpVGA 253 (526)
.|.||++++.+ -+|=.| .-|--...|+..-+. | -++.+|-=++-. ++.|.| .|. -.--
T Consensus 255 rGsRI~~I~~E----L~gEkIDIi~~s~d~~~fi~nAls---P------A~v~~V~ide~~~~~~VvV--~d~---qlSl 316 (428)
T PRK09202 255 RGSRIQAISNE----LNGEKIDIILWSDDPAQFIINALS---P------AEVSSIVVDEDKHSMDVVV--PDD---QLSL 316 (428)
T ss_pred CCCCHHHHHHH----HCCCEEEEEECCCCHHHHHHHHCC---C------CCCEEEEECCCCCEEEEEE--CCC---CHHH
T ss_conf 86429999987----467768999678888999998179---4------2121899727788899998--865---2247
Q ss_pred EECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHH
Q ss_conf 55488621788998627782679955987899999762866542489875678799998534221102544278999998
Q gi|254780788|r 254 CVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQ 333 (526)
Q Consensus 254 cVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~ 333 (526)
.+|-+|.-|+-- ..|-|=+|||...++--..-.. ...+.. .
T Consensus 317 AIGk~GqNvrLA-s~Ltgw~IdI~s~~~~~e~~~~-------------------------------------e~~~~~-~ 357 (428)
T PRK09202 317 AIGKNGQNVRLA-SKLTGWKIDIMTEEEASEKQQA-------------------------------------EFARLI-D 357 (428)
T ss_pred HHCCCCEEHHHH-HHHHCCEEEEEEHHHHHHHHHH-------------------------------------HHHHHH-H
T ss_conf 757786859999-9977986999558999998777-------------------------------------888899-9
Q ss_pred HHCCEEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 61674578552200110100122100011122588846788887732111477750588887765305889999999999
Q gi|254780788|r 334 LTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRA 413 (526)
Q Consensus 334 Ltg~~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA 413 (526)
+..-.+++ .+ .+....+.+....++++..+..|+.+||.|+++++.++.++|..++|++++.+.+|...|
T Consensus 358 ~f~~~~~~---~e-------~~~~~~~~l~~~~~~~~~~~~~l~~~g~~~~edl~~~~~del~~~~~~~~e~a~~li~~a 427 (428)
T PRK09202 358 LFMEALDV---DE-------DIAQLADDLLNLEGLDPELAFKLAEKGVKTLEDLAELAVDELIDIEGLDEEEAGELIMAA 427 (428)
T ss_pred HHHHHCCC---HH-------HHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHC
T ss_conf 87775262---28-------888877778645699999999999869987999965798889637798999999999841
Q ss_pred H
Q ss_conf 9
Q gi|254780788|r 414 R 414 (526)
Q Consensus 414 ~ 414 (526)
+
T Consensus 428 r 428 (428)
T PRK09202 428 R 428 (428)
T ss_pred C
T ss_conf 9
No 68
>PTZ00035 Rad51; Provisional
Probab=96.70 E-value=0.0031 Score=43.05 Aligned_cols=56 Identities=20% Similarity=0.307 Sum_probs=50.9
Q ss_pred CCCCC---CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 11225---888467888877321114777505888877653058899999999999999
Q gi|254780788|r 362 FMQAI---NVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL 417 (526)
Q Consensus 362 f~e~L---dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L 417 (526)
.++.| +|...-.+.|-++||.|++.|++++..+|..|.||.+-.|++|++.|+..+
T Consensus 34 ~i~~l~~~Gi~~~di~kl~~aG~~tv~~v~~~~~k~L~~ikgise~k~~Ki~~~a~k~~ 92 (350)
T PTZ00035 34 KIEQLLAKGFVKRDLELLKEGGLQTVECVAYAPMRTLCAIKGISEQKAEKLKKACKELC 92 (350)
T ss_pred CHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHC
T ss_conf 29999877999899999998491248999850999897737946999999999999755
No 69
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=96.70 E-value=0.0083 Score=39.89 Aligned_cols=56 Identities=29% Similarity=0.472 Sum_probs=49.1
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf 20838999998405763899957-93587447874887511527669999976113587
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQR 194 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r 194 (526)
.+|++..|+|.++..=.++|+|+ +.+|.+..++..+ .|++||.+.+-+.+++...|
T Consensus 15 evG~~y~G~V~~v~~fGaFV~l~~~~~GLiHiS~l~~--~~~vGD~V~VkV~~I~~~Gk 71 (77)
T cd04473 15 EVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLR--DYEVGDEVIVQVTDIPENGN 71 (77)
T ss_pred CCCCEEEEEEEEEEECCEEEECCCCCEEEEEEHHCCC--CCCCCCEEEEEEEEECCCCC
T ss_conf 2399999999889662889992699879689316668--78999999999999999997
No 70
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=96.69 E-value=0.0083 Score=39.87 Aligned_cols=68 Identities=25% Similarity=0.411 Sum_probs=56.9
Q ss_pred CEEEEEEEECCCCEEEEEECCCEEEEEHHHC-----------------CCCCCCCCCCEEEEEEEEECCCC---CEEEEE
Q ss_conf 3899999840576389995793587447874-----------------88751152766999997611358---702898
Q gi|254780788|r 140 EIISGTVKRVEYGNVIVDLGNSDGVIRRDET-----------------ISRENLRPGDRVKSYIYDVRREQ---RGPQVL 199 (526)
Q Consensus 140 eiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~-----------------ip~E~~~~Gdrika~i~~V~~~~---rgpqi~ 199 (526)
|++.|+|..+..-.++|.||.+||+++-+++ =.+..|+.||++++-|..|..+. ..+.|-
T Consensus 1 Ev~eG~Vs~Vt~fG~FV~L~~ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V~~~~r~i~~~~Ig 80 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG 80 (99)
T ss_pred CEEEEEEEEEEECCEEEEECCCEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEEECCCCCCCCCEEE
T ss_conf 97999999588256699932810689936757843998124468985127869847999999999980620676764665
Q ss_pred EECCCHHH
Q ss_conf 71598899
Q gi|254780788|r 200 LSRTHPQF 207 (526)
Q Consensus 200 lSRt~p~~ 207 (526)
||.-.|.+
T Consensus 81 Ltmrqp~l 88 (99)
T cd04460 81 LTMRQPGL 88 (99)
T ss_pred ECCCCCCC
T ss_conf 02247889
No 71
>PTZ00162 RNA polymerase II subunit 7; Provisional
Probab=96.67 E-value=0.011 Score=39.07 Aligned_cols=72 Identities=14% Similarity=0.193 Sum_probs=56.0
Q ss_pred HHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC----------------CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 9852083899999840576389995793587447874887----------------511527669999976113587028
Q gi|254780788|r 134 FKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR----------------ENLRPGDRVKSYIYDVRREQRGPQ 197 (526)
Q Consensus 134 f~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~----------------E~~~~Gdrika~i~~V~~~~rgpq 197 (526)
|+.-.||++.|.|..+..-.+++++|..+++++++..-+. ...+.||++|+-|..++.+.+..+
T Consensus 77 fkP~~~EVvdg~V~~v~~~G~fv~~GPl~~fv~~s~i~~d~~yd~~~~~~~~~~~~~~i~kgd~VR~rIvg~~~~~~~~~ 156 (170)
T PTZ00162 77 FKPFKDEVLDAIVTDVNKLGFFAQAGPLKIFVSRTAIPPNFVYDSDSAYPCFSDGTISIKPQSEVRLRLQGIRYDNSNLF 156 (170)
T ss_pred EECCCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHCCCCCEECCCCCCCEECCCCCEECCCCEEEEEEEEEEECCCCCE
T ss_conf 93367989999999996407999912808998989999864897899860482788388889999999999873556746
Q ss_pred EEEECCCH
Q ss_conf 98715988
Q gi|254780788|r 198 VLLSRTHP 205 (526)
Q Consensus 198 i~lSRt~p 205 (526)
.+.|-..|
T Consensus 157 aigtm~~d 164 (170)
T PTZ00162 157 AIATINSD 164 (170)
T ss_pred EEEEECCC
T ss_conf 99996687
No 72
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=96.62 E-value=0.0085 Score=39.80 Aligned_cols=74 Identities=28% Similarity=0.485 Sum_probs=61.3
Q ss_pred HHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC-----------------CCCCCCCEEEEEEEEEC---CCC
Q ss_conf 9852083899999840576389995793587447874887-----------------51152766999997611---358
Q gi|254780788|r 134 FKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR-----------------ENLRPGDRVKSYIYDVR---REQ 193 (526)
Q Consensus 134 f~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~-----------------E~~~~Gdrika~i~~V~---~~~ 193 (526)
|+.-.||++.|.|..+..-.++|.+|-.++++.+++..+- -.|+.||.||+=|..+. .++
T Consensus 77 frPf~~EVv~g~V~~~~~~G~fv~~Gp~d~~vh~sqi~dd~~~fD~~~~~~ig~~s~~~i~~Gd~VR~RIv~vs~~~~~~ 156 (182)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDEKNGALIGKESKRTLKVGDVVRARIVAVSLNEREP 156 (182)
T ss_pred EECCCCCEEEEEEEEEECCEEEEEEECCCEEEEHHHCCCCCCEECCCCCEEEEECCCEEECCCCEEEEEEEEEECCCCCC
T ss_conf 94136848999999996676999984661176099947776238365651999068649828998999999977188887
Q ss_pred CEEEEEEECCCHHH
Q ss_conf 70289871598899
Q gi|254780788|r 194 RGPQVLLSRTHPQF 207 (526)
Q Consensus 194 rgpqi~lSRt~p~~ 207 (526)
+++.|-|+...|.|
T Consensus 157 ~~~kIglTmrq~gL 170 (182)
T PRK08563 157 RDSKIGLTMRQPGL 170 (182)
T ss_pred CCCEEEEEECCCCC
T ss_conf 76626689538887
No 73
>PRK00254 ski2-like helicase; Provisional
Probab=96.50 E-value=0.0039 Score=42.25 Aligned_cols=105 Identities=22% Similarity=0.246 Sum_probs=73.9
Q ss_pred HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH-------H--------HHHHHHHHHHCCHHHH---HHCCCCCCHHHH
Q ss_conf 750588887765305889999999999999999-------9--------9998987754284356---640779998999
Q gi|254780788|r 387 LACVKISEIASIEGFDEETAVEIQGRAREYLEG-------I--------DITLQKKIRELGVSEE---LCSIPGIDSKIK 448 (526)
Q Consensus 387 Ia~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~-------~--------~~~~~e~~~e~~~~e~---L~~l~gl~~~~~ 448 (526)
+...+..++.+--|++.-.+..+++.|.-+.-. . ....-...-..|+.++ |+.++|+...-+
T Consensus 578 i~E~~~~~I~~ky~v~~G~lq~l~~~a~~~a~~~~~~~~~l~~~~~~~~~l~~l~~Rl~~Gv~~ELl~L~~I~gvgr~RA 657 (717)
T PRK00254 578 INEVPEGEIVEKYNVEPGDIYRIVETAEWLVYSLKEIAKVLEASQDVVDYLETLRLRVKHGIREELIPLMELPMIGRKRA 657 (717)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHCCCCCCCHHHH
T ss_conf 55999999999879697899999999999999999999983851889999999999998099765683564899898999
Q ss_pred HHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 999987984788965326775212312344432112453343588999999999984122
Q gi|254780788|r 449 VALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYK 508 (526)
Q Consensus 449 ~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~ 508 (526)
-+|-++||+|++|+|.....+|..+. ++...-|++++-.++..
T Consensus 658 R~Ly~aGi~s~~~ia~A~p~~l~~i~-----------------g~g~~~a~~i~~~~~~~ 700 (717)
T PRK00254 658 RALYNAGFRDLEDIMNAKPSELLAVE-----------------GIGAKIVEGIFKHLGKE 700 (717)
T ss_pred HHHHHCCCCCHHHHHCCCHHHEECCC-----------------CCCHHHHHHHHHHHCCE
T ss_conf 99998699999999659999903023-----------------72789999999983864
No 74
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=96.43 E-value=0.0086 Score=39.77 Aligned_cols=73 Identities=29% Similarity=0.464 Sum_probs=59.3
Q ss_pred HHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCCC------------------CCCCCCEEEEEEEEECCCCC-
Q ss_conf 98520838999998405763899957935874478748875------------------11527669999976113587-
Q gi|254780788|r 134 FKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRE------------------NLRPGDRVKSYIYDVRREQR- 194 (526)
Q Consensus 134 f~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E------------------~~~~Gdrika~i~~V~~~~r- 194 (526)
|+...||+|.|.|.++..-.++|.+|-.++++|.++ |+.+ .++.||+|||=|..+....+
T Consensus 77 fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sq-i~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~ 155 (183)
T COG1095 77 FKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQ-IMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR 155 (183)
T ss_pred EEECCCCEEEEEEEEEEECCEEEEECCCCCCCCHHH-CCCCCCCCCCCCCEEEECCCCEEEECCCEEEEEEEEEECCCCC
T ss_conf 970356389999999961446999636222113866-6575325275554124036515884198899999996146776
Q ss_pred --EEEEEEECCCHHH
Q ss_conf --0289871598899
Q gi|254780788|r 195 --GPQVLLSRTHPQF 207 (526)
Q Consensus 195 --gpqi~lSRt~p~~ 207 (526)
...|.++...|.+
T Consensus 156 ~~~~~I~lTmrq~~L 170 (183)
T COG1095 156 PRESKIGLTMRQPGL 170 (183)
T ss_pred CCCCEEEEEECCCCC
T ss_conf 542169999536667
No 75
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.42 E-value=0.026 Score=36.27 Aligned_cols=71 Identities=27% Similarity=0.388 Sum_probs=58.5
Q ss_pred HHCCCEEEEEEEECCCCEEEEEE---CCCEEEEEHHHCCCC------CCCCCCCEEEEEEEEECCCCCEEEEEEECCCHH
Q ss_conf 52083899999840576389995---793587447874887------511527669999976113587028987159889
Q gi|254780788|r 136 DKVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDETISR------ENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQ 206 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~~iiVdl---g~~ea~Lp~~e~ip~------E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~ 206 (526)
+.+||||.|+|+++..-+.+|.| ++.||++|-+|...| ...|.|.++-|-+..|++..+---+-|+|..++
T Consensus 9 PeeGEiVv~tV~~V~~~GA~v~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~ 88 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEH 88 (269)
T ss_pred CCCCCEEEEEEEEEECCCCEEEEECCCCEEEEEEHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEHHHCCHH
T ss_conf 98886899999986046427984205996226778998778998899986169869999988868777476254338787
No 76
>PRK05054 exoribonuclease II; Provisional
Probab=96.36 E-value=0.047 Score=34.35 Aligned_cols=65 Identities=15% Similarity=0.121 Sum_probs=30.4
Q ss_pred EEEEEEECCCCE-EEEEECCCEEEEEH-HHCCCCCCCCCCCEEEEEEEEECC-CCCEE-----EEEEECCCHH
Q ss_conf 999998405763-89995793587447-874887511527669999976113-58702-----8987159889
Q gi|254780788|r 142 ISGTVKRVEYGN-VIVDLGNSDGVIRR-DETISRENLRPGDRVKSYIYDVRR-EQRGP-----QVLLSRTHPQ 206 (526)
Q Consensus 142 v~G~V~r~e~~~-iiVdlg~~ea~Lp~-~e~ip~E~~~~Gdrika~i~~V~~-~~rgp-----qi~lSRt~p~ 206 (526)
+.|++++..... ++-|..+..-.+|. ...-.....+.||.+.|-|..--. ..++| +++-+...|.
T Consensus 86 ~vG~~~~~~~~~~v~Pd~~~~~~~i~~~~~~~~~~~~~~gd~V~v~i~~~P~~~~~~~~g~i~~vlG~~~d~~ 158 (644)
T PRK05054 86 FVGRVQKKDDRLSIVPDHPLLKDAIPCRAAKGLNHEFKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHF 158 (644)
T ss_pred EEEEEEEECCEEEEEECCCCCCCCEECCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEEEECCCCCCC
T ss_conf 9999999898799997897776765514765555567899899999987888888886379999978789871
No 77
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=96.34 E-value=0.024 Score=36.50 Aligned_cols=116 Identities=13% Similarity=0.206 Sum_probs=81.1
Q ss_pred CCCCCCCHHHHHHHHHHHH-HHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCC-
Q ss_conf 1225888467888877321-11477750588887765305889999999999999999999989877542843566407-
Q gi|254780788|r 363 MQAINVDEIIAHLLVAEGF-ADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSI- 440 (526)
Q Consensus 363 ~e~LdVDE~iA~~LV~eGf-~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l- 440 (526)
|+.-++.+.+.+.|++.|+ .++-++...+.++|.+++||.+..+..|.+ +++.. +......=|..|
T Consensus 429 mdI~GLGek~i~~L~~~gli~~~~Dly~L~~~~L~~l~g~geKsa~nLl~---------aIe~S---K~~~l~r~l~aLG 496 (563)
T PRK08097 429 LGLDGIGEGTWRALHQTGRFEHLFSWLALTPEQLANTPGIGKARAAQLWH---------QFNLA---RQQPFTRWLKALG 496 (563)
T ss_pred CCCCCCCHHHHHHHHHCCCCCCHHHHHHCCHHHHHCCCCHHHHHHHHHHH---------HHHHH---CCCCHHHHHHHCC
T ss_conf 58567699999999975888997997508999985589857899999999---------99997---2899999999869
Q ss_pred -CCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf -799989999999879847889653267752123123444321124533435889999999999841225788800024
Q gi|254780788|r 441 -PGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVA 518 (526)
Q Consensus 441 -~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~gWf~~e~~~ 518 (526)
++.....+..|+ .+.++|+..+.+||..+. ++...-|.+|. . ||.++.+.
T Consensus 497 I~~vG~~~a~~l~----~~~~~L~~as~e~l~~i~-----------------gIG~~~A~si~-----~--fF~~~~n~ 547 (563)
T PRK08097 497 IPLTQAALNASLD----RSWQQLLSRTEQQWQQLP-----------------GIGEGRARQLI-----A--FFDHPQVQ 547 (563)
T ss_pred CCCHHHHHHHHHH----CCHHHHHCCCHHHHHCCC-----------------CCCHHHHHHHH-----H--HHCCHHHH
T ss_conf 9508999999986----199999739998995579-----------------84899999999-----9--98598899
No 78
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=96.24 E-value=0.06 Score=33.59 Aligned_cols=285 Identities=19% Similarity=0.271 Sum_probs=136.3
Q ss_pred HHHHHHHHHHCC-CEEEEEEEECCC-CEE-----E--EEECCC---EEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf 877999985208-389999984057-638-----9--995793---5874478748875115276699999761135870
Q gi|254780788|r 128 DRQYLEFKDKVG-EIISGTVKRVEY-GNV-----I--VDLGNS---DGVIRRDETISRENLRPGDRVKSYIYDVRREQRG 195 (526)
Q Consensus 128 ~~i~~ef~~r~G-eiv~G~V~r~e~-~~i-----i--Vdlg~~---ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rg 195 (526)
=.|-=+|..+.. ..+.+++-+|-| |-| . |.++|+ .|-|-..+.|..=..|+||+|-+. ..|
T Consensus 315 WAiAYKFpa~e~~T~L~dv~~qVGRTG~iTPvA~LePV~vaG~~Vs~ATLHN~D~I~~kdiriGD~Vvv~-------kAG 387 (706)
T TIGR00575 315 WAIAYKFPAEEAQTKLLDVVVQVGRTGAITPVAKLEPVFVAGTTVSRATLHNEDEIEEKDIRIGDTVVVR-------KAG 387 (706)
T ss_pred HHHCCCCCCCCCCEEEEEEEEEECCEEEECCEEEECCEEECCEEEEEEEECCHHHHHCCCCCCCCEEEEE-------ECC
T ss_conf 0102366743010089878998465677600367565587207862344016002420276658889998-------448
Q ss_pred EEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEE
Q ss_conf 28987159889999999976677755808785663167750349999408998812765548862178899862778267
Q gi|254780788|r 196 PQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKID 275 (526)
Q Consensus 196 pqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkID 275 (526)
= | ||+| |.+..=.| ||+...+-.=++=| +| | =.
T Consensus 388 d-V-----------------IP~v----v~v~~~~R-~~~~~~~~~P~~CP------~C----~--------------s~ 420 (706)
T TIGR00575 388 D-V-----------------IPKV----VEVLLEKR-TGEERPIKFPTHCP------SC----G--------------SP 420 (706)
T ss_pred C-C-----------------CHHH----HHCCCCCC-CCCCCEEECCCCCC------CC----C--------------CE
T ss_conf 6-2-----------------5355----41023578-88887034287188------88----8--------------33
Q ss_pred EEECCCCHHHHHHH-HCCCCCCCEEEE-CCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEE-----EEEECC--C
Q ss_conf 99559878999997-628665424898-75678799998534221102544278999998616745-----785522--0
Q gi|254780788|r 276 IVVWSPDSATFVIN-ALRPAIVTKVVL-DEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTI-----DIITEE--E 346 (526)
Q Consensus 276 ii~ws~d~~~fi~n-Al~PA~v~~v~~-de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~i-----di~~~~--~ 346 (526)
++..-+....|-.| -.-||....-+. --..+.|+| .|-.-++..+|---++ |+++-. .
T Consensus 421 lv~~~~e~~~rC~Ng~~Cpa~~~e~i~hFaSr~AmdI-------------~GLG~~~I~~LfE~~Lv~~~~DLY~L~~k~ 487 (706)
T TIGR00575 421 LVRIEEEVDIRCTNGLNCPAQLVERIKHFASRNAMDI-------------DGLGEKVIEQLFEEKLVRSVADLYALKEKL 487 (706)
T ss_pred EECCCCCEEEECCCCCCCHHHHHHHEEEEEEECCCCC-------------CCCCHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf 1115787216538876653676511023454110332-------------222389999998726667856665778899
Q ss_pred HHHHHHCC-CC----------------CCCCCCCCCCC---CCHHHHHHHHHHHHHHHHHHHHCCHH-----------HH
Q ss_conf 01101001-22----------------10001112258---88467888877321114777505888-----------87
Q gi|254780788|r 347 DSINRQKD-FN----------------ERTQFFMQAIN---VDEIIAHLLVAEGFADVEELACVKIS-----------EI 395 (526)
Q Consensus 347 ~~~~~~~e-~~----------------~~~~~f~e~Ld---VDE~iA~~LV~eGf~SiEeIa~a~~e-----------eL 395 (526)
..=.+-+- |. .-...|.-+|+ |.+..|..|+..+. |++.+..|+.| +|
T Consensus 488 ~~Ll~le~~~g~~sa~nLl~aIe~sK~~pl~RlL~aLGIr~VG~~~A~~La~~f~-tl~~L~~A~~e~~~~~~~f~~s~L 566 (706)
T TIGR00575 488 EDLLELEGKFGEKSAQNLLSAIEKSKKKPLARLLFALGIRHVGEVTAKLLAKHFG-TLDKLKAASLETLESIYQFDRSEL 566 (706)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC-CHHHHHHCCHHHHHHHHHHCCHHH
T ss_conf 9987064035568899999999985210489999862860357999999998558-868998508216778875160556
Q ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH-HCCCCCCHHHHHHHHHCCCCCHH----------HHHH
Q ss_conf 765305889999999999999999999989877542843566-40779998999999987984788----------9653
Q gi|254780788|r 396 ASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEEL-CSIPGIDSKIKVALGENGIKTME----------DLAG 464 (526)
Q Consensus 396 ~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L-~~l~gl~~~~~~~L~e~gIktle----------DlAe 464 (526)
++++|+.+.+|..|.+- +.. ...+ + -+.-|.+.+..|-+.|+.+.+ ...+
T Consensus 567 ~~~~g~G~~vA~~~~~~---------------F~~---~~~~~~-qPYRta~~~~~L~~~gv~~~~~D~~~~LL~~~~~~ 627 (706)
T TIGR00575 567 LSVEGVGPKVAESIVNF---------------FHD---PNNLSL-QPYRTAELIEKLEELGVNMESEDEFCRLLDQALKE 627 (706)
T ss_pred HHCCCCHHHHHHHHHHH---------------HHC---CCCCCC-CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 41014027899999998---------------712---000135-60468999999988316310113578777642011
Q ss_pred CCHHHHCC-CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 26775212-31234443211245334358899999999998
Q gi|254780788|r 465 CSVDDLLG-WSENKGGNIEKFDGFLSSLGTPKDQVESMIIH 504 (526)
Q Consensus 465 ls~dEL~~-~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~ 504 (526)
..-.++.+ + ..||..=+-|-|+. ||+++|.++|-.
T Consensus 628 ~~~~~~~~~~---~~GK~fVlTG~L~~--~sR~~a~~~~~~ 663 (706)
T TIGR00575 628 KVEAELAGSP---LAGKTFVLTGTLSQ--MSRDEAKELLEA 663 (706)
T ss_pred HCCCCCCCCC---CCCCEEEEECCCCC--CCHHHHHHHHHH
T ss_conf 0010005752---02776899515688--888999999998
No 79
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=96.21 E-value=0.022 Score=36.78 Aligned_cols=59 Identities=25% Similarity=0.423 Sum_probs=51.5
Q ss_pred HHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCC-C---------CCCCCCCCEEEEEEEEECCC
Q ss_conf 98520838999998405763899957-935874478748-8---------75115276699999761135
Q gi|254780788|r 134 FKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETI-S---------RENLRPGDRVKSYIYDVRRE 192 (526)
Q Consensus 134 f~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~i-p---------~E~~~~Gdrika~i~~V~~~ 192 (526)
|..+.|++|.|.|..+....+.||+| ...|+||-++.. | ++.|..||-|-|=|.+|...
T Consensus 2 Y~P~~GD~ViG~V~~i~~~~w~vdi~s~~~a~L~ls~v~~~~~~~d~~~mr~~l~iGDli~a~V~~v~~~ 71 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD 71 (86)
T ss_pred CCCCCCCEEEEEEEEEECCCEEEECCCCEEEEEEHHHCCCCCCCHHHHHHHHHCCCCCEEEEEEEEECCC
T ss_conf 8798899999999998088189974996077987454467776314677886566898999999998899
No 80
>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=96.18 E-value=0.042 Score=34.68 Aligned_cols=63 Identities=21% Similarity=0.302 Sum_probs=54.7
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC--------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 838999998405763899957-93587447874--------887511527669999976113587028987159
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET--------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSRT 203 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~--------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt 203 (526)
|+.++|.|.++.++.+.|.+. .+.|.+|.-+. -|-.+|.+|..++|.+..|+.+.+ .+.||.+
T Consensus 1 G~~v~gfV~n~~~~~~wv~iSp~V~gri~~l~lSdd~s~l~~~e~~FpvG~avk~~V~~vD~e~~--~l~LS~r 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHK--LLRLSAR 72 (73)
T ss_pred CCEEEEEEEECCCCEEEEEECCCEEEEEEHHHHCCCHHHHCCHHHHCCCCCEEEEEEEEECCCCC--EEEEEEC
T ss_conf 98799999972598499998888189997054268856853888729998459999999828778--8999803
No 81
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.14 E-value=0.025 Score=36.43 Aligned_cols=63 Identities=22% Similarity=0.384 Sum_probs=52.1
Q ss_pred HHHHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCC----------CCCCCCCCEEEEEEEEECCCCC
Q ss_conf 9998520838999998405763899957-9358744787488----------7511527669999976113587
Q gi|254780788|r 132 LEFKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETIS----------RENLRPGDRVKSYIYDVRREQR 194 (526)
Q Consensus 132 ~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip----------~E~~~~Gdrika~i~~V~~~~r 194 (526)
..|..+.|++|-|.|..+....+.||+| ...|+||-.+... +..|.+||-|-|=|..|..+..
T Consensus 56 grY~P~~GD~VIG~V~~v~~~~W~VDI~s~~~a~L~~s~~~~r~~~~~~~~mr~~l~~GDlI~ArV~~v~~~~~ 129 (232)
T PRK04163 56 GKYIPKKGDLVIGKVTDVGFSGWEVDINSPYKAILPVSEVLGRPVDVESTDLRKYLDIGDYIIAKVKDVDETKD 129 (232)
T ss_pred CCCCCCCCCEEEEEEEEECCCEEEEECCCCCEEEECHHHCCCCCCCCCHHHHHHHCCCCCEEEEEEEEECCCCC
T ss_conf 51058769989999998318717998699605585244456655556435677517889889999999668997
No 82
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=96.13 E-value=0.016 Score=37.78 Aligned_cols=70 Identities=23% Similarity=0.378 Sum_probs=54.7
Q ss_pred HHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHH------HCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHH
Q ss_conf 98520838999998405763899957-935874478------74887511527669999976113587028987159889
Q gi|254780788|r 134 FKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRD------ETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQ 206 (526)
Q Consensus 134 f~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~------e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~ 206 (526)
|..++|++|.|.|.++....+.||++ ...|.||-. +.--++.|++||-|.|-+..+..... +.||..+++
T Consensus 2 Y~P~vGDvVigrV~~v~~~~w~vdI~~~~~a~l~~~~~~~~D~~~m~~~f~~GDlI~A~V~~~~~~~~---~~L~T~~~~ 78 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMN---VLLTTADNE 78 (82)
T ss_pred CCCCCCCEEEEEEEEECCCEEEEEECCCEEEEEEEHHCCCCCHHHHHHHCCCCCEEEEEEEEECCCCC---EEEEECCCC
T ss_conf 87989999999999970781899968632889730216773066798745877689999999769997---899956655
No 83
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=96.05 E-value=0.03 Score=35.83 Aligned_cols=66 Identities=23% Similarity=0.443 Sum_probs=52.0
Q ss_pred HHHCCCEEEEEEEECCCC--EEEEEEC-CCEEEEEHHHCC---------CCCCCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 852083899999840576--3899957-935874478748---------87511527669999976113587028987
Q gi|254780788|r 135 KDKVGEIISGTVKRVEYG--NVIVDLG-NSDGVIRRDETI---------SRENLRPGDRVKSYIYDVRREQRGPQVLL 200 (526)
Q Consensus 135 ~~r~Geiv~G~V~r~e~~--~iiVdlg-~~ea~Lp~~e~i---------p~E~~~~Gdrika~i~~V~~~~rgpqi~l 200 (526)
+..+|+|..|.|.++..+ ..+||+| +-.|+||.++.. ..+.++.||.|-+=|..=-...|||.+.-
T Consensus 4 ~~~vGnIY~GkV~~v~p~i~AAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~l~~G~~ilVQV~Ke~~~~Kgp~lT~ 81 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT 81 (88)
T ss_pred CCCCCCEEEEEEEEECCCCCEEEEECCCCCCEEEECHHCCHHHHCCCCCHHHHCCCCCEEEEEEEECCCCCCCCEEEE
T ss_conf 561124899999886668748999658986899990345723513578877837799999999976687997860884
No 84
>PRK11642 exoribonuclease R; Provisional
Probab=95.92 E-value=0.17 Score=30.33 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=13.2
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf 9998623999999999999999999
Q gi|254780788|r 14 DAVAYEKSIDRDVVLSVMADSIQKA 38 (526)
Q Consensus 14 e~va~EK~I~~e~i~~aie~Al~~a 38 (526)
..+++.=+|..+.-++++...|...
T Consensus 38 ~el~~~~~l~~~~~~~~L~~~L~~l 62 (813)
T PRK11642 38 EELAVELNIEGEEQLEALRRRLRAM 62 (813)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 9999981999889999999999999
No 85
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.90 E-value=0.0067 Score=40.57 Aligned_cols=58 Identities=31% Similarity=0.446 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHHCCEEEEEEEECCCC--CEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEE
Q ss_conf 899999999766777558087856631677--5034999940899881276554886217889986277826799
Q gi|254780788|r 205 PQFMVKLFHMEVPEIYNGIVQVKAVSRDPG--SRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIV 277 (526)
Q Consensus 205 p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG--~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii 277 (526)
.+|+..+|.-+ ++.++...+. .+++|.|.. |+.|.|+|.+|.+|+..++.++ .+|||+
T Consensus 2 ~~fi~nal~Pa---------~v~~V~i~~~~~~~~~V~V~~-----~~~~~AIGk~G~Nvrla~~l~g-~~IdI~ 61 (61)
T cd02134 2 AEFIRNALSPA---------KVTSVTVLDDEEKRARVVVPD-----DQLGLAIGKGGQNVRLASKLLG-EKIDIV 61 (61)
T ss_pred HHHHHHHCCCC---------EEEEEEECCCCCCEEEEEECH-----HHHHHHHCCCCEEHHHHHHHHC-CEEEEC
T ss_conf 78998636987---------557988447877379999885-----7843876678670999999779-877649
No 86
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=95.89 E-value=0.087 Score=32.37 Aligned_cols=93 Identities=20% Similarity=0.273 Sum_probs=67.7
Q ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEC--CCEEEEEHH------------
Q ss_conf 62079999999999--99999999887799998520838999998405763899957--935874478------------
Q gi|254780788|r 105 DFGRVAVQSAKQVI--IQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLG--NSDGVIRRD------------ 168 (526)
Q Consensus 105 ~fgRiaAq~AKQvI--~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg--~~ea~Lp~~------------ 168 (526)
.+.-++.++-++-. ..-=||+..-...+-..+|+|+.-.|+|.-|++=+++|.|. .+||..|-+
T Consensus 637 ~l~~~~~h~S~~ERrA~~AERd~~d~kkaeyM~~~iG~~f~G~Is~VT~FG~FVeL~~~~ieGLVhI~~L~dDYY~Fd~~ 716 (755)
T TIGR02063 637 KLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEK 716 (755)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEEEEEECCCEEEEEEECCCCCCCCCEECCC
T ss_conf 89999986112112155312779999999999850796887799756620138973674111026327898856307522
Q ss_pred -HCCCCC----CCCCCCEEEEEEEEECCCCCEEE
Q ss_conf -748875----11527669999976113587028
Q gi|254780788|r 169 -ETISRE----NLRPGDRVKSYIYDVRREQRGPQ 197 (526)
Q Consensus 169 -e~ip~E----~~~~Gdrika~i~~V~~~~rgpq 197 (526)
..+-|+ .||.||+|++-|.+|+...|.--
T Consensus 717 ~~~L~G~R~gk~frLGD~v~V~V~~ad~~~~~id 750 (755)
T TIGR02063 717 GLALVGERTGKVFRLGDRVKVRVVKADLDTGKID 750 (755)
T ss_pred CCEEEEECCCCEEECCCEEEEEEEEECCCCCEEE
T ss_conf 0788643268737248748999999610336698
No 87
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=95.86 E-value=0.017 Score=37.50 Aligned_cols=106 Identities=19% Similarity=0.223 Sum_probs=72.7
Q ss_pred EECHHHHHHHCCC--CCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-CCEE
Q ss_conf 2348999862889--864737998508456207999999999999999999887799998520838999998405-7638
Q gi|254780788|r 78 QISLKVARDRDPS--IDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE-YGNV 154 (526)
Q Consensus 78 eI~l~~A~~~~~~--~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e-~~~i 154 (526)
-+++++-... ++ .++||.+...+.-..=|||.+..|.+-+.+++-. ..+.+..++.+.|+|.|.. -|..
T Consensus 101 ~vp~~elp~~-~~~wpq~Gd~l~v~l~~Dkk~Ri~g~~a~~~~l~~l~~-------~~~~~l~nq~v~~tVYr~~~~G~f 172 (287)
T COG2996 101 LVPLDELPTL-KSLWPQKGDKLLVYLYVDKKGRIWGTLAIEKILENLAT-------PAYNNLKNQEVDATVYRLLESGTF 172 (287)
T ss_pred EEEHHHCCCC-CCCCCCCCCEEEEEEEECCCCCEEEEECCHHHHHHCCC-------CCCHHHHCCEEEEEEEEEECCCEE
T ss_conf 6162536443-12377879899999998567847777331557876177-------211145437610599998214239
Q ss_pred EEEECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCC
Q ss_conf 999579358744787488751152766999997611358
Q gi|254780788|r 155 IVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQ 193 (526)
Q Consensus 155 iVdlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~ 193 (526)
.+-=++--|+++++|.- ..+|.|+|+.++|..|+.+.
T Consensus 173 v~~e~~~~GfIh~sEr~--~~prlG~~l~~rVi~~reDg 209 (287)
T COG2996 173 VITENGYLGFIHKSERF--AEPRLGERLTARVIGVREDG 209 (287)
T ss_pred EEECCCEEEEECCHHHC--CCCCCCCEEEEEEEEECCCC
T ss_conf 99718768998606600--66667755788999982487
No 88
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional
Probab=95.82 E-value=0.043 Score=34.60 Aligned_cols=82 Identities=21% Similarity=0.276 Sum_probs=64.9
Q ss_pred HHHHHHHHHCCCEEEEEEEECCCCEEEEEE---CCCEEEEEHHHCCCC------CCCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 779999852083899999840576389995---793587447874887------51152766999997611358702898
Q gi|254780788|r 129 RQYLEFKDKVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDETISR------ENLRPGDRVKSYIYDVRREQRGPQVL 199 (526)
Q Consensus 129 ~i~~ef~~r~Geiv~G~V~r~e~~~iiVdl---g~~ea~Lp~~e~ip~------E~~~~Gdrika~i~~V~~~~rgpqi~ 199 (526)
+.|+.=-+.+|++|.++|+++..-..||.| ++.||++|.+|..++ ...|+|...-|.|..|..+..---+-
T Consensus 8 RfYe~~~Pe~~e~V~~~V~~i~~~gayV~LlEY~~~egmI~~sEls~rrir~I~k~ikvG~~~v~~VlRVD~~KGyIDLS 87 (324)
T PTZ00248 8 RFYENKYPEENDLVMVKVNRIEEMGVYVSLLEYDDIEGMILLSELSKRRIRSINKLVKVGRHEVVLVLRVDKDKGYIDLS 87 (324)
T ss_pred CCCCCCCCCCCCEEEEEEEEEECCEEEEEEEEECCCCCEEEHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCEECH
T ss_conf 02355699988889999999802568999840088222146888637888637887106877899999985877824441
Q ss_pred EECCCHHHHHH
Q ss_conf 71598899999
Q gi|254780788|r 200 LSRTHPQFMVK 210 (526)
Q Consensus 200 lSRt~p~~l~~ 210 (526)
+.|.+|+=..+
T Consensus 88 ~rrVs~ed~~k 98 (324)
T PTZ00248 88 KRRVTPEDIIK 98 (324)
T ss_pred HHCCCHHHHHH
T ss_conf 50299889999
No 89
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=95.79 E-value=0.076 Score=32.80 Aligned_cols=118 Identities=21% Similarity=0.326 Sum_probs=89.4
Q ss_pred CCCCCCCHHHHHHHHHHHH-HHHHHHHHCC--HHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf 1225888467888877321-1147775058--888776530-58899999999999999999999898775428435664
Q gi|254780788|r 363 MQAINVDEIIAHLLVAEGF-ADVEELACVK--ISEIASIEG-FDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELC 438 (526)
Q Consensus 363 ~e~LdVDE~iA~~LV~eGf-~SiEeIa~a~--~eeL~~IeG-fdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~ 438 (526)
|+.=++.+.+++.|+++|+ .|+-|+.... .++|+.++| |.+..|..|.+ +++ +-+....+-=|.
T Consensus 455 mdI~GLG~~~I~~LfE~~Lv~~~~DLY~L~~k~~~Ll~le~~~g~~sa~nLl~---------aIe---~sK~~pl~RlL~ 522 (706)
T TIGR00575 455 MDIDGLGEKVIEQLFEEKLVRSVADLYALKEKLEDLLELEGKFGEKSAQNLLS---------AIE---KSKKKPLARLLF 522 (706)
T ss_pred CCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH---------HHH---HHHHHHHHHHHH
T ss_conf 33222238999999872666785666577889999870640355688999999---------999---852104899998
Q ss_pred --CCCCCCHHHHHHHHHCCCCCHHHHHHCCHH-----------HHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf --077999899999998798478896532677-----------5212312344432112453343588999999999984
Q gi|254780788|r 439 --SIPGIDSKIKVALGENGIKTMEDLAGCSVD-----------DLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHA 505 (526)
Q Consensus 439 --~l~gl~~~~~~~L~e~gIktleDlAels~d-----------EL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~A 505 (526)
.++++...++-.|+.+.= |+|.|...|.| +|+.+. ++...-|.+++-
T Consensus 523 aLGIr~VG~~~A~~La~~f~-tl~~L~~A~~e~~~~~~~f~~s~L~~~~-----------------g~G~~vA~~~~~-- 582 (706)
T TIGR00575 523 ALGIRHVGEVTAKLLAKHFG-TLDKLKAASLETLESIYQFDRSELLSVE-----------------GVGPKVAESIVN-- 582 (706)
T ss_pred HCCCHHHHHHHHHHHHHHCC-CHHHHHHCCHHHHHHHHHHCCHHHHHCC-----------------CCHHHHHHHHHH--
T ss_conf 62860357999999998558-8689985082167788751605564101-----------------402789999999--
Q ss_pred CCCCCCCCCCCC
Q ss_conf 122578880002
Q gi|254780788|r 506 RYKMGWIEKEKV 517 (526)
Q Consensus 506 R~~~gWf~~e~~ 517 (526)
||..+.+
T Consensus 583 -----~F~~~~~ 589 (706)
T TIGR00575 583 -----FFHDPNN 589 (706)
T ss_pred -----HHHCCCC
T ss_conf -----8712000
No 90
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.79 E-value=0.11 Score=31.77 Aligned_cols=61 Identities=20% Similarity=0.239 Sum_probs=43.7
Q ss_pred CHHHHHHHHCCCCCCCEE--------EE-------CCCC-CEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf 789999976286654248--------98-------7567-8799998534221102544278999998616745785
Q gi|254780788|r 282 DSATFVINALRPAIVTKV--------VL-------DEDV-GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII 342 (526)
Q Consensus 282 d~~~fi~nAl~PA~v~~v--------~~-------de~~-~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~ 342 (526)
=+.+.+..||.-|+.-+. .+ .+.. +...+-+|.+.....||.+|.|+|--..-||-+|||-
T Consensus 514 i~~~il~~Al~qA~~gR~~IL~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~gGk~Ik~i~e~tg~~Idi~ 590 (694)
T PRK11824 514 ITREIMEEALEQAKEGRLHILGKMNEAISEPRTELSPYAPRIETIKIDPDKIRDVIGPGGKTIREITEETGAKIDIE 590 (694)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECHHHHHHEECCCHHHHHHHHHHHCCEEEEE
T ss_conf 69899999999999999999999987366654333568987999997879866506863388999999889889996
No 91
>PRK13766 Hef nuclease; Provisional
Probab=95.78 E-value=0.019 Score=37.31 Aligned_cols=46 Identities=28% Similarity=0.456 Sum_probs=32.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 25888467888877321114777505888877653058899999999
Q gi|254780788|r 365 AINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
-.+|....|..|... |.|++.|+.|+.++|.+++|+.+.+|.+|+.
T Consensus 711 ~pgvg~~~a~~ll~~-fgsi~~i~~a~~~eL~~v~giG~~~A~~i~~ 756 (764)
T PRK13766 711 LPDVGPVLARNLLDH-FGSVENVMTASEEELKAVEGIGEKTAKKIRE 756 (764)
T ss_pred CCCCCHHHHHHHHHH-CCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH
T ss_conf 899999999999997-1999999659999995474969999999999
No 92
>PRK11712 ribonuclease G; Provisional
Probab=95.67 E-value=0.057 Score=33.72 Aligned_cols=181 Identities=16% Similarity=0.227 Sum_probs=111.1
Q ss_pred HHCCCEEEEEEEECCCC--EEEEEEC-CCEEEEEHHHCCCC------------------CCCCCCCEEEEEEEEECCCCC
Q ss_conf 52083899999840576--3899957-93587447874887------------------511527669999976113587
Q gi|254780788|r 136 DKVGEIISGTVKRVEYG--NVIVDLG-NSDGVIRRDETISR------------------ENLRPGDRVKSYIYDVRREQR 194 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~--~iiVdlg-~~ea~Lp~~e~ip~------------------E~~~~Gdrika~i~~V~~~~r 194 (526)
..+|.|..|.|.++.+| ..+||+| +-.|+||.++..|. +-+++|+.|-+=|..=...+|
T Consensus 36 ~~vGnIY~G~V~~V~pgl~AAFVdiG~~k~gFL~~~di~~~~~~~~~~~~~~~~~~~I~~~l~~Gq~ilVQV~Ke~~~~K 115 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTK 115 (489)
T ss_pred CCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEHHHCCCCHHCCCCCCCCCCCCCCHHHHCCCCCEEEEEEEECCCCCC
T ss_conf 76676699999430688776999847987428785543852111333223566646767746799989999962687898
Q ss_pred EEEEE--------------------EECCC-----HHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECC----
Q ss_conf 02898--------------------71598-----89999999976677755808785663167750349999408----
Q gi|254780788|r 195 GPQVL--------------------LSRTH-----PQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSD---- 245 (526)
Q Consensus 195 gpqi~--------------------lSRt~-----p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d---- 245 (526)
||.+. +||.- -.-++.++..-.|+-+ | +-|+..|-.... .....|
T Consensus 116 Ga~lT~~isl~GRylVl~P~~~~igiSrkI~~~~eR~rLk~i~~~~~~~~~-G-~IiRT~a~~~~~----e~l~~d~~~L 189 (489)
T PRK11712 116 GARLTTDITLPSRYLVFMPGASHVGVSQRIESEEERERLKKIVAPYCDEQG-G-FIIRTAAEGVGE----EELAQDAAFL 189 (489)
T ss_pred CCCEEEEEEECCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC-C-EEEECHHHCCCH----HHHHHHHHHH
T ss_conf 876751255453269995389987643167987899999998885388888-6-698413202999----9999999999
Q ss_pred ----------CCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHH-----HHHHCCCCCCCEEEECCCC-CEEE
Q ss_conf ----------99881276554886217889986277826799559878999-----9976286654248987567-8799
Q gi|254780788|r 246 ----------SSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATF-----VINALRPAIVTKVVLDEDV-GRIE 309 (526)
Q Consensus 246 ----------~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~f-----i~nAl~PA~v~~v~~de~~-~~~~ 309 (526)
..--+--+|+-.-.+-+..+++.+-++.++-|.-+ |+..| ......|.-..+|....+. .-++
T Consensus 190 ~~~W~~I~~~~~~~~~p~ll~~e~~~~~r~lRD~~~~~~~~I~vD-~~~~~~~~~~~~~~~~p~~~~~v~~y~~~~plF~ 268 (489)
T PRK11712 190 KRVWTKVMERKKRPQTRYQLYGELALAQRVLRDFVGAELDRIRVD-SRLTYEELKEFTSEYIPELTDKLEHYSGRQPIFD 268 (489)
T ss_pred HHHHHHHHHHHHCCCCCCEEECCCHHHHHHHHHHCCCCCCEEEEC-CHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHH
T ss_conf 999999999985499961464272389999998447765278857-8899999999998759410011343268621776
Q ss_pred EEECCCCCCCCCCC
Q ss_conf 99853422110254
Q gi|254780788|r 310 VIVPKEQLSLAIGR 323 (526)
Q Consensus 310 v~v~~~qls~AIGk 323 (526)
.+=-+.|+..|..|
T Consensus 269 ~y~ie~~I~~~l~~ 282 (489)
T PRK11712 269 LYDVENEIQRALER 282 (489)
T ss_pred HCCHHHHHHHHHCC
T ss_conf 42899999997168
No 93
>PRK00254 ski2-like helicase; Provisional
Probab=95.63 E-value=0.21 Score=29.53 Aligned_cols=53 Identities=25% Similarity=0.328 Sum_probs=47.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 11225888467888877321114777505888877653058899999999999
Q gi|254780788|r 362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAR 414 (526)
Q Consensus 362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~ 414 (526)
++...+|.-..|..|+.+||+|+++||.+++++|..|.||.+.+|..|.+-+.
T Consensus 646 L~~I~gvgr~RAR~Ly~aGi~s~~~ia~A~p~~l~~i~g~g~~~a~~i~~~~~ 698 (717)
T PRK00254 646 LMELPMIGRKRARALYNAGFRDLEDIMNAKPSELLAVEGIGAKIVEGIFKHLG 698 (717)
T ss_pred HCCCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHEECCCCCCHHHHHHHHHHHC
T ss_conf 56489989899999998699999999659999903023727899999999838
No 94
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=95.54 E-value=0.23 Score=29.32 Aligned_cols=135 Identities=19% Similarity=0.148 Sum_probs=98.8
Q ss_pred EEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEE
Q ss_conf 87159889999999976677755808785663167750349999408998812765548862178899862778267995
Q gi|254780788|r 199 LLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVV 278 (526)
Q Consensus 199 ~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ 278 (526)
.++-.+-+.++.|+++|= .....-++-++ |.+.|.--=+.|.+.| . .-+|..|.=.++.+++| |.|+-||.
T Consensus 28 ~v~~~dV~v~~~L~kL~e-~~~l~~~~y~k-a~ev~~lvIi~~~~~~--~----~~i~k~~ki~k~Ls~~l-g~kVrVvE 98 (167)
T PRK06418 28 EVTELDVEVSKALLKLTQ-FIGLSDVEYKK-AYEVDDLVILLVGSGD--R----IPIGKGGKIEKALSRAL-GKRVRVVE 98 (167)
T ss_pred CEEEEHHHHHHHHHHHHH-HCCCCCEEEEE-EEEECCEEEEEECCCC--C----CCHHHHHHHHHHHHHHH-CCCEEEEE
T ss_conf 545306799999998875-05755338999-9998999999984788--5----43578899999999986-89279997
Q ss_pred CCCCHHHHHHHHCCCCCCCEEEE--CCCC-CEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf 59878999997628665424898--7567-8799998534221102544278999998616745785
Q gi|254780788|r 279 WSPDSATFVINALRPAIVTKVVL--DEDV-GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII 342 (526)
Q Consensus 279 ws~d~~~fi~nAl~PA~v~~v~~--de~~-~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~ 342 (526)
+.+|..+|+.--++||.+..|.. -++. ....|.|+-.....-=++.-+=.++-|++||-++-|.
T Consensus 99 ~~~dik~li~qLl~PArvlgVNtvwlPdG~~~~~v~V~~rd~rrlp~~~e~le~ils~i~g~~vkI~ 165 (167)
T PRK06418 99 KTSDIKKLAVQLLSPARVLGVNTVWLPDGTTEYVVRIPSRDRRRLPAKPEVLESILSQITGTEVKVR 165 (167)
T ss_pred CCCCHHHHHHHHHCCHHHCEEEEEECCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHCCCEEEE
T ss_conf 3675889999972525131278899189958999996377402279998999999999649955899
No 95
>pfam10246 MRP-S35 Mitochondrial ribosomal protein MRP-S35. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. that are highly conserved from worms to humans. The structure has previously been referred to as MRP-S18 but the current numbering fits the preferred nomenclature from these authors.
Probab=95.52 E-value=0.029 Score=35.85 Aligned_cols=66 Identities=20% Similarity=0.460 Sum_probs=53.7
Q ss_pred HHHHHHHHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf 87799998520838999998405763899957-93587447874887511527669999976113587
Q gi|254780788|r 128 DRQYLEFKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQR 194 (526)
Q Consensus 128 ~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r 194 (526)
..-+-..-+-.|.++.|+|..+-.+.+|||.| +--++.++- ..++|.|+.|.|++.-+++-+-+.|
T Consensus 13 ~S~fi~lG~~~gk~v~G~I~hvv~dDLYIDfG~KFhcVc~rP-~~~~~~y~~G~rV~lrLkdlELt~~ 79 (105)
T pfam10246 13 NSKFVQLGDAEGKLVIGKIFHIVEDDLYIDFGGKFHCVCKRP-AVNGEKYQRGSRVRLRLKDLELTSR 79 (105)
T ss_pred CCCHHHCCCCCCCEEEEEEEEEECCCEEEEECCEEEEEECCC-CCCHHHCCCCCEEEEEECCHHHHHH
T ss_conf 591210578557788999999706725998377167887376-6471005778889999668756445
No 96
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=95.49 E-value=0.099 Score=31.98 Aligned_cols=49 Identities=35% Similarity=0.425 Sum_probs=28.8
Q ss_pred CCCCCC---CCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 112258---88467888877321114777505888877653058899999999
Q gi|254780788|r 362 FMQAIN---VDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 362 f~e~Ld---VDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
|.-+|+ |.+..|..|.. .|.|++.+..++.++|..++|+.+..|..+.+
T Consensus 510 ~l~aLGIr~VG~~~Ak~La~-~f~sl~~l~~a~~e~l~~i~giG~~vA~si~~ 561 (667)
T COG0272 510 FLYALGIRHVGETTAKSLAR-HFGTLEALLAASEEELASIPGIGEVVARSIIE 561 (667)
T ss_pred HHHHCCCCHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHCCCHHHHHHHHHHH
T ss_conf 99987971140899999998-76029999842999995066612899999999
No 97
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=95.43 E-value=0.1 Score=31.82 Aligned_cols=70 Identities=29% Similarity=0.478 Sum_probs=52.8
Q ss_pred HHHCCCEEEEEEEECCCCEEEEEE---C------CCEEEEEHHHCCCC--------CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 852083899999840576389995---7------93587447874887--------511527669999976113587028
Q gi|254780788|r 135 KDKVGEIISGTVKRVEYGNVIVDL---G------NSDGVIRRDETISR--------ENLRPGDRVKSYIYDVRREQRGPQ 197 (526)
Q Consensus 135 ~~r~Geiv~G~V~r~e~~~iiVdl---g------~~ea~Lp~~e~ip~--------E~~~~Gdrika~i~~V~~~~rgpq 197 (526)
-.++|.+|+|.|.|+......+++ + ...|++.+.+.-+. +.|||||-|||-+...-. +.+
T Consensus 3 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~l~~~f~g~Ir~~dVr~te~d~v~m~~~FrpGDIVrA~Vislgd---~~~ 79 (92)
T cd05791 3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD---ASS 79 (92)
T ss_pred CCCCCCEEEEEEEEECCCEEEEEEEEECCEECCCEEEEEEEHHHCCCCCCCCEEHHHCCCCCCEEEEEEEECCC---CCE
T ss_conf 68899999999999711378999999999983762578879244343555304341354999899999997478---724
Q ss_pred EEEECCCHHH
Q ss_conf 9871598899
Q gi|254780788|r 198 VLLSRTHPQF 207 (526)
Q Consensus 198 i~lSRt~p~~ 207 (526)
..||-+.++|
T Consensus 80 y~LSTa~neL 89 (92)
T cd05791 80 YYLSTAENEL 89 (92)
T ss_pred EEEEECCCCC
T ss_conf 9998537876
No 98
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: 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 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=95.43 E-value=0.1 Score=31.82 Aligned_cols=66 Identities=17% Similarity=0.314 Sum_probs=53.0
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCC-------------------------CCCCCCCCEEEEEEEEEC
Q ss_conf 20838999998405763899957-9358744787488-------------------------751152766999997611
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETIS-------------------------RENLRPGDRVKSYIYDVR 190 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip-------------------------~E~~~~Gdrika~i~~V~ 190 (526)
..|-++.|.|+.+..-.+.|-|. +.-|+.|..+... .+-|++|+.+||+|..+.
T Consensus 2 ~~G~lvLG~V~~I~~~~l~isLP~~L~G~V~it~ISd~~t~~le~~~~~~~~~~~~~e~~~L~~lF~vGq~vr~~V~s~~ 81 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD 81 (100)
T ss_pred CCCCEEEEEEEEECCCCEEEECCCCCEEEEEHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCCCCCEEEEEEEECC
T ss_conf 88989999998984663899858985899887885299999999987300236763234587884768989999999845
Q ss_pred CCCCE-EEEEEEC
Q ss_conf 35870-2898715
Q gi|254780788|r 191 REQRG-PQVLLSR 202 (526)
Q Consensus 191 ~~~rg-pqi~lSR 202 (526)
...+| ..|.||-
T Consensus 82 ~~~~~~krI~LSl 94 (100)
T cd05693 82 KSKSGKKRIELSL 94 (100)
T ss_pred CCCCCCEEEEEEC
T ss_conf 8877854899982
No 99
>smart00322 KH K homology RNA-binding domain.
Probab=95.39 E-value=0.017 Score=37.68 Aligned_cols=41 Identities=32% Similarity=0.558 Sum_probs=36.6
Q ss_pred CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECC
Q ss_conf 78799998534221102544278999998616745785522
Q gi|254780788|r 305 VGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEE 345 (526)
Q Consensus 305 ~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~ 345 (526)
.....+.||.+.....||++|.|++...+.|||+|++....
T Consensus 2 ~~~~~i~vp~~~~g~iIG~~G~~i~~i~~~~~~~I~i~~~~ 42 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG 42 (69)
T ss_pred CEEEEEEECHHHCCEEECCCCCCHHHHHHHHCCEEEECCCC
T ss_conf 87999998978768549999845799999728889977999
No 100
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=95.25 E-value=0.042 Score=34.69 Aligned_cols=58 Identities=21% Similarity=0.238 Sum_probs=51.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 1122588846788887732111477750588887765305889999999999999999
Q gi|254780788|r 362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEG 419 (526)
Q Consensus 362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~ 419 (526)
+....+|...-.+.|.+.|++|++++|.++++.|....++..+.+..|+..|+..+..
T Consensus 209 LslVagi~~~q~~~L~~~GI~Ti~~LA~~~~~~l~~~~~~~~~~~~~l~~qA~a~~~~ 266 (457)
T TIGR03491 209 LSLVPGIGPSRYRLLQELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQARAQLEG 266 (457)
T ss_pred HHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 7660599999999999859987999862994330356663669999999999984379
No 101
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=95.23 E-value=0.072 Score=33.00 Aligned_cols=64 Identities=17% Similarity=0.248 Sum_probs=50.6
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC--CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCCEEEEEEECC
Q ss_conf 20838999998405763899957--93587447874------887511527669999976113587028987159
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG--NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQRGPQVLLSRT 203 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg--~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt 203 (526)
.+|+++.|+|.++..-..+|++. +.+|++--+|+ -|.+.++.||.+++-+.+++... .+-||-|
T Consensus 2 evg~i~~G~V~~i~~fGAFV~i~g~~~~GLvHiSeis~~rv~~~~dvv~vGd~V~Vkvi~id~~~---ki~LSls 73 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD---KMKLSLS 73 (73)
T ss_pred CCCCEEEEEEEEEEECCEEEEECCCCCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEECCCC---CEEEECC
T ss_conf 78869999998997532399908988435599560541202899995579999999999886899---8898419
No 102
>PRK02362 ski2-like helicase; Provisional
Probab=94.96 E-value=0.34 Score=28.07 Aligned_cols=100 Identities=19% Similarity=0.133 Sum_probs=65.7
Q ss_pred HHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHCCHHHH---HHCCCCCCHHHHHH
Q ss_conf 50588887765305889999999999999999--------------99998987754284356---64077999899999
Q gi|254780788|r 388 ACVKISEIASIEGFDEETAVEIQGRAREYLEG--------------IDITLQKKIRELGVSEE---LCSIPGIDSKIKVA 450 (526)
Q Consensus 388 a~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~--------------~~~~~~e~~~e~~~~e~---L~~l~gl~~~~~~~ 450 (526)
...+..++..--|++.-....+++.|.-++-. ...... .+=..|+.++ |+.++|+...-+-+
T Consensus 589 ~E~~~~~I~~ky~v~~G~l~~l~~~a~~~~~~~~~~~~~l~~~~~~~l~~l~-~Rl~~Gv~~ELl~L~~I~gvgr~RAR~ 667 (736)
T PRK02362 589 DEVSEDRICERYGVGPGDIRGKVETAEWLMHAAERLAGELDLKCTREARELE-KRVHYGVREELLDLVGLRGIGRVRARR 667 (736)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHCCCCHHHHHHCCCCCCCHHHHHH
T ss_conf 0798999999879892899999999999999999999986668999999999-999859877689770889999899999
Q ss_pred HHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC
Q ss_conf 998798478896532677521231234443211245334358899999999998412
Q gi|254780788|r 451 LGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARY 507 (526)
Q Consensus 451 L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~ 507 (526)
|-++||+|++|||.....+|..+ +.+.-|.+++..+..
T Consensus 668 Ly~aGi~s~~dla~A~p~~l~~i-------------------lg~~~a~~i~~~~~~ 705 (736)
T PRK02362 668 LYNAGITSRADLRAADKEVVAAI-------------------LGPKIAERVLEQLGR 705 (736)
T ss_pred HHHCCCCCHHHHHHCCHHHHHHH-------------------HHHHHHHHHHHHHCC
T ss_conf 99879999999970999999999-------------------777899999998388
No 103
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.95 E-value=0.14 Score=30.88 Aligned_cols=51 Identities=31% Similarity=0.457 Sum_probs=44.0
Q ss_pred CCCCCCCCC---CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 011122588---8467888877321114777505888877653058899999999
Q gi|254780788|r 360 QFFMQAINV---DEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 360 ~~f~e~LdV---DE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
..|.-+|+| .+..|..|... |.|++.+..++.++|.+|+||.+.+|..|.+
T Consensus 508 ~r~L~ALGI~~VG~~~Ak~La~~-f~sl~~l~~as~e~L~~I~giG~~~A~si~~ 561 (668)
T PRK07956 508 ARFLYALGIRHVGEKAAKALARH-FGSLEALEAASEEELAAVEGIGEEVAQSIVE 561 (668)
T ss_pred HHHHHHCCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH
T ss_conf 88998627864129999999999-6689999708999985768844999999999
No 104
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=94.89 E-value=0.12 Score=31.36 Aligned_cols=63 Identities=24% Similarity=0.337 Sum_probs=53.4
Q ss_pred HHHHHHCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHHC----------CCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf 99985208389999984057638999579-3587447874----------887511527669999976113587
Q gi|254780788|r 132 LEFKDKVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDET----------ISRENLRPGDRVKSYIYDVRREQR 194 (526)
Q Consensus 132 ~ef~~r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e~----------ip~E~~~~Gdrika~i~~V~~~~r 194 (526)
..|...+|++|-|.|.-+...++.||+|. .-|+||-++. =.+..|++||-+-|-|.+|.++..
T Consensus 58 g~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~ 131 (239)
T COG1097 58 GRYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGE 131 (239)
T ss_pred CCCCCCCCCEEEEEEEEECCCCEEEECCCCCCEEEEHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCC
T ss_conf 75248889999999999715633897289532374266620022554223452226768789999997267775
No 105
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=94.84 E-value=0.18 Score=30.06 Aligned_cols=62 Identities=23% Similarity=0.251 Sum_probs=45.4
Q ss_pred CCHHHHHHHHCCCCCCCEE--------EECCC--------CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf 8789999976286654248--------98756--------78799998534221102544278999998616745785
Q gi|254780788|r 281 PDSATFVINALRPAIVTKV--------VLDED--------VGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII 342 (526)
Q Consensus 281 ~d~~~fi~nAl~PA~v~~v--------~~de~--------~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~ 342 (526)
-=+.+.+..||.-|+.-+. .+.+- -+...+-+|.+.....||.+|.|+|--..-||-+|||-
T Consensus 510 Gi~~~il~~Al~qA~~~R~~IL~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~gGk~Ik~i~~~tg~~I~i~ 587 (684)
T TIGR03591 510 GITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE 587 (684)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECHHHHHHEECCCCHHHHHHHHHHCCEEEEE
T ss_conf 978999999999999999999999997352543344578875799997878866507875288989999889889985
No 106
>KOG1070 consensus
Probab=94.80 E-value=0.15 Score=30.60 Aligned_cols=91 Identities=20% Similarity=0.295 Sum_probs=69.1
Q ss_pred HHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEH------HHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEC----CC
Q ss_conf 520838999998405763899957-93587447------87488751152766999997611358702898715----98
Q gi|254780788|r 136 DKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRR------DETISRENLRPGDRVKSYIYDVRREQRGPQVLLSR----TH 204 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~------~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSR----t~ 204 (526)
-++|++++|.|.-+....+++-|+ +++|+.|- -+-.+.-.|.+|+.+.+-++.|+..++--.+.|-- -.
T Consensus 1160 lk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~ 1239 (1710)
T KOG1070 1160 LKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDT 1239 (1710)
T ss_pred CCCCCEEEEEEEEECCCCEEEEECCCEEEEEECCCCCCCHHHHHHCCCCCCCEEEEEEEEEECCCCEEEEEEECCCCCCC
T ss_conf 25576468899970377489997156289998345664023222113885444315899852368628999852666884
Q ss_pred HHHHHHHHHHHHHHHHCCEEEE
Q ss_conf 8999999997667775580878
Q gi|254780788|r 205 PQFMVKLFHMEVPEIYNGIVQV 226 (526)
Q Consensus 205 p~~l~~Lf~~EVPEI~~G~ieI 226 (526)
+..++-+=.+-+-+-++|+|+-
T Consensus 1240 ~~~~~~~~~l~~gd~~~g~v~~ 1261 (1710)
T KOG1070 1240 VKLLKDSKDLKKGDREDGTVEV 1261 (1710)
T ss_pred HHHHHHHHHHHCCCCCCCEEEE
T ss_conf 4443455664226300434999
No 107
>PRK02362 ski2-like helicase; Provisional
Probab=94.55 E-value=0.072 Score=32.98 Aligned_cols=49 Identities=14% Similarity=0.227 Sum_probs=40.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 112258884678888773211147775058888776530588999999999
Q gi|254780788|r 362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGR 412 (526)
Q Consensus 362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~r 412 (526)
++...+|...-|..|+.+||+|+++||.|+++.|..| +.+.+|+.+.+-
T Consensus 654 L~~I~gvgr~RAR~Ly~aGi~s~~dla~A~p~~l~~i--lg~~~a~~i~~~ 702 (736)
T PRK02362 654 LVGLRGIGRVRARRLYNAGITSRADLRAADKEVVAAI--LGPKIAERVLEQ 702 (736)
T ss_pred HCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH--HHHHHHHHHHHH
T ss_conf 7088999989999999879999999970999999999--777899999998
No 108
>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=94.38 E-value=0.35 Score=27.92 Aligned_cols=59 Identities=20% Similarity=0.276 Sum_probs=48.9
Q ss_pred HCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHHC---CCC------CCCCCCCEEEEEEEEECCCCCE
Q ss_conf 208389999984057638999579-3587447874---887------5115276699999761135870
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDET---ISR------ENLRPGDRVKSYIYDVRREQRG 195 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e~---ip~------E~~~~Gdrika~i~~V~~~~rg 195 (526)
+.|+++.|.|+.+....++|.|++ +.|.....+. .+. ..|..|.-+++-+..|+.+.+-
T Consensus 2 keGq~vRGyVk~v~~~GvFv~Ls~~v~grv~~~nls~~~v~dp~~~~~~fp~GkLv~~kVlsvd~~~~~ 70 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNL 70 (74)
T ss_pred CCCCEEEEEEEECCCCCEEEEECCCEEEEEEEECCCHHHHCCHHHHHCCCCCCCEEEEEEEEECCCCCE
T ss_conf 988798999998268739999568748999970036212068268861489998999999998677684
No 109
>PRK08609 hypothetical protein; Provisional
Probab=94.36 E-value=0.32 Score=28.18 Aligned_cols=33 Identities=24% Similarity=0.414 Sum_probs=16.4
Q ss_pred EECCCCCCCCC----CCCHHHHHHHH--HHHCCEEEEEE
Q ss_conf 98534221102----54427899999--86167457855
Q gi|254780788|r 311 IVPKEQLSLAI----GRRGQNVRLAS--QLTGWTIDIIT 343 (526)
Q Consensus 311 ~v~~~qls~AI----Gk~GqNvrLas--~Ltg~~idi~~ 343 (526)
+||+++...|+ |.+-.|++|-. .=-||+++=+.
T Consensus 243 vv~~~~fg~aLlyFTGSk~hNi~lR~~A~~kG~~LnEyG 281 (570)
T PRK08609 243 LVEPEAFATTLHHFTGSKDHNVRMRQLAKARGEKISEYG 281 (570)
T ss_pred EECHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 808899899999976669999999999997488503024
No 110
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=94.24 E-value=0.17 Score=30.30 Aligned_cols=162 Identities=21% Similarity=0.278 Sum_probs=76.6
Q ss_pred EECCCCCEE--EEEEEECCCCCCCEEEEECCC--C--HHHHHH-HHHHCCCCEEEEE-----CCCCHHHHHHH---HCCC
Q ss_conf 631677503--499994089988127655488--6--217889-9862778267995-----59878999997---6286
Q gi|254780788|r 229 VSRDPGSRA--KLAVFSSDSSIDPVGACVGMR--G--SRVQAV-VTELRDEKIDIVV-----WSPDSATFVIN---ALRP 293 (526)
Q Consensus 229 iaR~pG~Rs--KIAV~s~d~~iDpVGAcVG~r--G--sRiq~I-~~EL~gEkIDii~-----ws~d~~~fi~n---Al~P 293 (526)
..=+||.|+ |+||.-.-...=-...|+-.. + .--++- .+=+...++..|- -|....+|+.. .+.+
T Consensus 333 lglDPg~rtG~k~Avvd~tGk~l~~~~Iyp~~p~~~~~~~~~~l~~l~~~~~Ve~iaIGngTaSrete~fv~~vl~~~~~ 412 (780)
T COG2183 333 LGLDPGFRTGCKVAVVDDTGKLLDTATIYPHPPVNQSDKAEATLKDLIRKYKVELIAIGNGTASRETEKFVADVLKELPK 412 (780)
T ss_pred EECCCCCCCCCEEEEECCCCCEECEEEEECCCCCCCHHHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHHCCC
T ss_conf 20487630130799983788555316997279754157899999999998371079873687655479999999984667
Q ss_pred CCCCEEEECCCCCEEE-------EEECCCCCC----CCCCCCHHHHHHHHHHHCCEEEEEE--CCCHHH-----HHHCCC
Q ss_conf 6542489875678799-------998534221----1025442789999986167457855--220011-----010012
Q gi|254780788|r 294 AIVTKVVLDEDVGRIE-------VIVPKEQLS----LAIGRRGQNVRLASQLTGWTIDIIT--EEEDSI-----NRQKDF 355 (526)
Q Consensus 294 A~v~~v~~de~~~~~~-------v~v~~~qls----~AIGk~GqNvrLas~Ltg~~idi~~--~~~~~~-----~~~~e~ 355 (526)
-.+..|++.|+.-+.. --.|+-+.+ .+|+|+=|+-. ++|. +||-+| ..++.- +-....
T Consensus 413 ~~~~~viVsEagAsvYsaSe~A~~EFPdL~v~~r~aVSIaRrlqdPL--aElv--kIdpKSiGVgqyQHdv~q~~L~~~L 488 (780)
T COG2183 413 EKVLKVIVSEAGASVYSASERAAEEFPDLDVSLRGAVSIARRLQDPL--AELV--KIDPKSIGVGQYQHDVSQKKLAESL 488 (780)
T ss_pred CCCCEEEECCCCCCHHCCCHHHHHHCCCCCHHHHHHHHHHHHHCCHH--HHHH--HCCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf 89867997265310213448899877999666776877988620647--6876--1475314555321468878999999
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 21000111225888467888877321114777505888877653058899999999
Q gi|254780788|r 356 NERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 356 ~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
.......++..+||... |+..-|..+-|+..-.|..+..
T Consensus 489 d~vved~VN~VGVdvNt-----------------Asa~lL~~VsGL~kt~A~nIv~ 527 (780)
T COG2183 489 DAVVEDCVNAVGVDVNT-----------------ASASLLSYVSGLNKTLAKNIVA 527 (780)
T ss_pred HHHHHHHHCCCCCCCCC-----------------CCHHHHHHHHHHCHHHHHHHHH
T ss_conf 99999873102611342-----------------7899998774025667899999
No 111
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=94.14 E-value=0.29 Score=28.59 Aligned_cols=55 Identities=22% Similarity=0.371 Sum_probs=48.0
Q ss_pred CCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHC--------CCCCCCCCCCEEEEEEEEECCCC
Q ss_conf 838999998405763899957-93587447874--------88751152766999997611358
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDET--------ISRENLRPGDRVKSYIYDVRREQ 193 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~--------ip~E~~~~Gdrika~i~~V~~~~ 193 (526)
|+++.|+|+.+..-.+.|.|+ +..|.+.-+|. -|...|+.||.|+|-|.-++...
T Consensus 1 G~vv~g~V~sik~~~l~V~L~d~~~GrVhiSei~D~~~~~k~P~~~~k~Gq~V~~rViG~~d~k 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCCCCCCCCCHHHHCCCCCEEEEEEEEEECCC
T ss_conf 9779999999946708999689957789845521355555694685689999999999765462
No 112
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=94.02 E-value=0.19 Score=29.85 Aligned_cols=100 Identities=30% Similarity=0.570 Sum_probs=72.5
Q ss_pred EEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEE-----EECCCCHHHHHHHHCCC--CCCCEEEECCCCCEEEE
Q ss_conf 499994089988127655488621788998627782679-----95598789999976286--65424898756787999
Q gi|254780788|r 238 KLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDI-----VVWSPDSATFVINALRP--AIVTKVVLDEDVGRIEV 310 (526)
Q Consensus 238 KIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDi-----i~ws~d~~~fi~nAl~P--A~v~~v~~de~~~~~~v 310 (526)
-|++|+.||+. +.-.|.=|+.+.+.|.- ||=| ++-+++-+.=+++.+-| |.+..+..|+... +|
T Consensus 10 ~ivIYt~~p~~------f~~~~~li~~iAk~ikK-RIviRpdpsil~~~e~a~~~I~~ivPeeA~i~~i~FD~~~g--EV 80 (145)
T cd02410 10 ELVVYTKNPEL------FAEDGDLVKDLAKDLRK-RIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTG--EV 80 (145)
T ss_pred EEEEEECCHHH------HCCCCHHHHHHHHHHHC-EEEECCCHHHCCCHHHHHHHHHHHCCCCCCCEEEEECCCCC--EE
T ss_conf 28999799799------72674099999998720-27973880341899999999998589646844689748885--79
Q ss_pred EECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCC
Q ss_conf 985342211025442789999986167457855220
Q gi|254780788|r 311 IVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346 (526)
Q Consensus 311 ~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~ 346 (526)
+..-+.=.++|||+|.|.+--..=|||...|....-
T Consensus 81 ~Iea~kPg~viGk~g~~l~eI~~~tGW~p~v~RtPp 116 (145)
T cd02410 81 IIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred EEEECCCEEEECCCCHHHHHHHHHHCCEEEEEECCC
T ss_conf 999779777972761679999997398157886599
No 113
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=93.91 E-value=0.15 Score=30.72 Aligned_cols=12 Identities=8% Similarity=0.138 Sum_probs=4.8
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999986
Q gi|254780788|r 7 LELLQIADAVAY 18 (526)
Q Consensus 7 ~ell~vie~va~ 18 (526)
.++..+++.+|.
T Consensus 4 ~~i~~~L~~la~ 15 (334)
T smart00483 4 RGIIDALEILAE 15 (334)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999999
No 114
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=93.87 E-value=0.31 Score=28.30 Aligned_cols=61 Identities=23% Similarity=0.361 Sum_probs=45.9
Q ss_pred HCCCEEEEEEEECCCC-EEEEEEC-CCEEEEE------HHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 2083899999840576-3899957-9358744------78748875115276699999761135870289871
Q gi|254780788|r 137 KVGEIISGTVKRVEYG-NVIVDLG-NSDGVIR------RDETISRENLRPGDRVKSYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~-~iiVdlg-~~ea~Lp------~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lS 201 (526)
..|.++.|.|.++..+ .++|.|+ +.-|..- ...-.|-|.|++|+-+||+|.. .++..+.||
T Consensus 2 ~~G~i~~G~V~kV~p~~Gl~Vqlp~g~~G~V~itdl~D~y~~~Pl~~f~~~qiVrc~VLs----~~~g~~~LS 70 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS----KKDGKYQLS 70 (72)
T ss_pred CCCCEEEEEEEEECCCCCEEEECCCCCEEEEEEEEECCCCCCCCHHHCCCCCEEEEEEEE----CCCCEEEEE
T ss_conf 887474039999728985699848996668999971474544967765789789999995----369989987
No 115
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=93.83 E-value=0.15 Score=30.62 Aligned_cols=68 Identities=21% Similarity=0.278 Sum_probs=44.7
Q ss_pred HHHCCCEEEEEEEECCCCEEEEEECC------------CEEEEEHHHCCC------CCCCCCCCEEEEEEEEECCCCCEE
Q ss_conf 85208389999984057638999579------------358744787488------751152766999997611358702
Q gi|254780788|r 135 KDKVGEIISGTVKRVEYGNVIVDLGN------------SDGVIRRDETIS------RENLRPGDRVKSYIYDVRREQRGP 196 (526)
Q Consensus 135 ~~r~Geiv~G~V~r~e~~~iiVdlg~------------~ea~Lp~~e~ip------~E~~~~Gdrika~i~~V~~~~rgp 196 (526)
..++|++|+|.|.++......|.+-. ..|.+..++.-. .+.||+||-|||-|.... +
T Consensus 61 ~p~vGdiVig~V~~v~~~~a~v~I~~v~g~~~~~l~~~~~g~i~i~~v~~~~~~~~~d~fr~gDIVrAkVis~~-----~ 135 (187)
T PRK09521 61 LLKKGDIVYGRVVDVKEQRALVRIVSIEGRGNRELATSKLGGIHISQVSDGYVEDLTDAFKIGDIVRAKVISTT-----D 135 (187)
T ss_pred CCCCCCEEEEEEEEECCCEEEEEEEEECCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHCCCCCEEEEEEEECC-----C
T ss_conf 88989999999999547679999999868688625654488888543786674526752487868999997359-----8
Q ss_pred EEEEECCCHHH
Q ss_conf 89871598899
Q gi|254780788|r 197 QVLLSRTHPQF 207 (526)
Q Consensus 197 qi~lSRt~p~~ 207 (526)
++.||-..|+|
T Consensus 136 ~~~Lst~~~eL 146 (187)
T PRK09521 136 PIQLSTKGKDL 146 (187)
T ss_pred CEEEEECCCCC
T ss_conf 46999538884
No 116
>pfam10447 EXOSC1 Exosome component EXOSC1/CSL4. This family of proteins are components of the exosome 3'-5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions.
Probab=93.83 E-value=0.35 Score=27.89 Aligned_cols=53 Identities=32% Similarity=0.595 Sum_probs=41.7
Q ss_pred HHCCCEEEEEEEECCCCEEEEEE---C------CCEEEEEHHHCCCCC--------CCCCCCEEEEEEEE
Q ss_conf 52083899999840576389995---7------935874478748875--------11527669999976
Q gi|254780788|r 136 DKVGEIISGTVKRVEYGNVIVDL---G------NSDGVIRRDETISRE--------NLRPGDRVKSYIYD 188 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~~iiVdl---g------~~ea~Lp~~e~ip~E--------~~~~Gdrika~i~~ 188 (526)
.++|.+|++.|.|+......+++ | .-.|++.+.+.=+.| .|||||-|+|-+..
T Consensus 2 P~vGdiV~arVtrv~~~~a~~~Il~v~~~~l~~~f~G~IR~~DVRate~Dkv~~~~~FrPGDiVrA~ViS 71 (72)
T pfam10447 2 PKVGDIVLARVTRVTPRQAYCEILAVGGTALKETFKGIIRKQDVRATEKDRVKIYECFRPGDIVRAKVIS 71 (72)
T ss_pred CCCCCEEEEEEEEECHHEEEEEEEEECCEECCCCEEEEEEHHHCCCCCCCEEEHHHCCCCCCEEEEEEEE
T ss_conf 9899999999999750157999999999987885558989476665641018384683999899999962
No 117
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=93.77 E-value=0.28 Score=28.60 Aligned_cols=34 Identities=24% Similarity=0.377 Sum_probs=17.3
Q ss_pred EECCCCCCCCC----CCCHHHHHH--HHHHHCCEEEEEEC
Q ss_conf 98534221102----544278999--99861674578552
Q gi|254780788|r 311 IVPKEQLSLAI----GRRGQNVRL--ASQLTGWTIDIITE 344 (526)
Q Consensus 311 ~v~~~qls~AI----Gk~GqNvrL--as~Ltg~~idi~~~ 344 (526)
+||.++...|. |.+--|+.| -++=-||+++=++-
T Consensus 237 ~~~~~~~~~aLl~fTGS~~fn~~lR~~A~~kG~~Lne~GL 276 (307)
T cd00141 237 VVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGL 276 (307)
T ss_pred ECCHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 8389999999998447699999999999985996542017
No 118
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=93.66 E-value=0.35 Score=27.92 Aligned_cols=299 Identities=22% Similarity=0.292 Sum_probs=147.7
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEE--CCCCCCCCEECHHHH--HHHCCCCCCC
Q ss_conf 239999999999999999999613687453599974998839999998851--767787532348999--8628898647
Q gi|254780788|r 19 EKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVV--EEVENYTCQISLKVA--RDRDPSIDIG 94 (526)
Q Consensus 19 EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VV--edved~~~eI~l~~A--~~~~~~~~iG 94 (526)
+|-++++.+-....+-+..|.+- .+-.++|++.--.+--++...+| .-......||+...- +.--.++.+.
T Consensus 178 d~pl~~~ele~ia~eIi~~a~~~-----~~sfIEi~r~GatVvQlrn~RIvIarPPfSd~~EITavRPvvk~~ledY~L~ 252 (604)
T COG1855 178 DKPLTREELEEIAREIIERAKRD-----PDSFIEIDRPGATVVQLRNYRIVIARPPFSDRWEITAVRPVVKLSLEDYGLS 252 (604)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHC-----CCCEEEEECCCCEEEEECCEEEEEECCCCCCCEEEEEEEEEEEEEHHHCCCC
T ss_conf 76688999999999999987528-----6764898069966998435799994599877628999713699605542879
Q ss_pred CEEEEECCHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCC-CE------------EEEEE
Q ss_conf 37998508456207---9999999999999999998877999985208389999984057-63------------89995
Q gi|254780788|r 95 GVVSDPLPPMDFGR---VAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEY-GN------------VIVDL 158 (526)
Q Consensus 95 D~i~~~i~~~~fgR---iaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~-~~------------iiVdl 158 (526)
|.+.+-+....=|= -+-.+-|..|.|- ..+|-...|.|| |-++. ++ ..-++
T Consensus 253 dkl~eRL~eraeGILIAG~PGaGKsTFaqA---------lAefy~~~GkiV----KTmEsPRDl~v~~eITQYs~l~g~m 319 (604)
T COG1855 253 DKLKERLEERAEGILIAGAPGAGKSTFAQA---------LAEFYASQGKIV----KTMESPRDLQVSPEITQYSPLEGDM 319 (604)
T ss_pred HHHHHHHHHHHCCEEEECCCCCCHHHHHHH---------HHHHHHHCCCEE----EECCCCCCCCCCHHHHHCCCCCCCH
T ss_conf 899999886416469956999974689999---------999998669688----6324751356886663206445645
Q ss_pred CCCEEE--E-EHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCH-----HHHHHHHHHHHHHHHCCEEEEEEEE
Q ss_conf 793587--4-4787488751152766999997611358702898715988-----9999999976677755808785663
Q gi|254780788|r 159 GNSDGV--I-RRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHP-----QFMVKLFHMEVPEIYNGIVQVKAVS 230 (526)
Q Consensus 159 g~~ea~--L-p~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p-----~~l~~Lf~~EVPEI~~G~ieIk~ia 230 (526)
+.+--+ | .++..|-.|- |.-+-++.| .+.+.-.-|--=++--|.| .|+.+.=--=+|-|-|-+|=|+
T Consensus 320 e~t~DiLLLvRPDYTIyDEm-R~t~DF~vy-aDmRLAGVGMVGVVHATrpIDAiQR~igRVELG~IPqIvDTVIfI~--- 394 (604)
T COG1855 320 EKTADILLLVRPDYTIYDEM-RKTEDFQVY-ADLRLAGVGMVGVVHATRPIDAIQRFIGRVELGMIPQIVDTVIFIK--- 394 (604)
T ss_pred HHHCCEEEEECCCCEEHHHH-HCCCCEEEE-EEEECCCCCEEEEEECCCHHHHHHHHHCCEEECCCCCCEEEEEEEE---
T ss_conf 55233799965884510334-156661676-6500115754768961780589998644063146641226899981---
Q ss_pred CCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHH--------HHHHH------CCCCEEEEECCCCH--------HHHH-
Q ss_conf 1677503499994089988127655488621788--------99862------77826799559878--------9999-
Q gi|254780788|r 231 RDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQA--------VVTEL------RDEKIDIVVWSPDS--------ATFV- 287 (526)
Q Consensus 231 R~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~--------I~~EL------~gEkIDii~ws~d~--------~~fi- 287 (526)
.|.-+||-..|.--.+ --||+-.-.-. ++.+| -||.+=+++-.... ..-|
T Consensus 395 --~G~V~kVy~ls~tVKV-----P~Gm~EeDLARPVIeVrDfeTg~~eYEIYtfGEqvvVvPv~~~~~~~~~~~a~~~i~ 467 (604)
T COG1855 395 --DGEVAKVYELSYTVKV-----PTGMTEEDLARPVIEVRDFETGELEYEIYTFGEQVVVVPVKEEEESPALKLAEEEIE 467 (604)
T ss_pred --CCEEEEEEEEEEEEEC-----CCCCCHHHHCCCEEEEEECCCCCEEEEEEECCCEEEEEECCCCCCCCHHHHHHHHHH
T ss_conf --8818899999999976-----788786771585389765036854689997164799997568777726677999999
Q ss_pred --HHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHH
Q ss_conf --97628665424898756787999985342211025442789999986167457855220011
Q gi|254780788|r 288 --INALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSI 349 (526)
Q Consensus 288 --~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~ 349 (526)
++.+.|. -..|.+ ...+++.|.||+..++..|||+|+|+.=-.+-.|.+|+++..++..+
T Consensus 468 ~~i~r~~p~-~~eVe~-~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~~~~ 529 (604)
T COG1855 468 REIKRYLPG-DVEVEV-VGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEE 529 (604)
T ss_pred HHHHHHCCC-CCEEEE-ECCCEEEEEECHHHHHHHHHCCCCHHHHHHHHHCCEEEEEECCCCCC
T ss_conf 999974799-825999-61871799948788567761055318999987498068888665666
No 119
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=93.60 E-value=0.63 Score=26.08 Aligned_cols=61 Identities=23% Similarity=0.342 Sum_probs=46.5
Q ss_pred CCEEEEEEEECCCCEEEEEE-CCCEEEEEHHHCCC----CCCCCCCCEEEEEEEEECCCCCEEEEEEE
Q ss_conf 83899999840576389995-79358744787488----75115276699999761135870289871
Q gi|254780788|r 139 GEIISGTVKRVEYGNVIVDL-GNSDGVIRRDETIS----RENLRPGDRVKSYIYDVRREQRGPQVLLS 201 (526)
Q Consensus 139 Geiv~G~V~r~e~~~iiVdl-g~~ea~Lp~~e~ip----~E~~~~Gdrika~i~~V~~~~rgpqi~lS 201 (526)
|-+|.+.|+++-.+.+++.+ +--.|..-.-+.-| ...|++|+++||-|.-|...+| +|-||
T Consensus 1 GmlV~a~V~kV~~~Gl~~~fl~~F~G~Vd~~HL~~~~~~~~~Y~~~~~v~ArIL~Vdp~tK--~V~Ls 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTK--VVGLS 66 (66)
T ss_pred CCEEEEEEEEECCCCEEEEEECCEEEEEEHHHCCCCCCCCCCCCCCCEEEEEEEEECCCCC--EEECC
T ss_conf 9559999999817948999651289998876768776870004679889999999988747--88539
No 120
>PRK12704 phosphodiesterase; Provisional
Probab=93.52 E-value=0.64 Score=25.99 Aligned_cols=150 Identities=20% Similarity=0.284 Sum_probs=94.2
Q ss_pred HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCC-CCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCCCCCCCCC
Q ss_conf 999997628665424898756787999985342-2110254427899999861674578552200110100122100011
Q gi|254780788|r 284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQ-LSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFF 362 (526)
Q Consensus 284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~q-ls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~~~~~~~f 362 (526)
...+..|++---..-+ -+...-.|-.|.+. .-.-|||.|.|+|---.+||-.|-|-...+.
T Consensus 126 r~Ii~~AIQR~A~e~~---~E~tvsvV~LPsdemKGRIIGREGRNIRa~E~~TGVDlIIDDtPe~--------------- 187 (455)
T PRK12704 126 KEILAQAIQRCAAEHA---AENTVSVVNLPNDEMKGRIIGREGRNIRTLETLTGVDIIIDDTPEA--------------- 187 (455)
T ss_pred HHHHHHHHHHHCCCCC---CHHEEEEEECCCHHHHCCCCCCCCCHHHHHHHHHCCEEEECCCCCE---------------
T ss_conf 9999999986364300---1310466854856764640077752399999986964897599983---------------
Q ss_pred CCCCCCCHHHHHHHHHHHHHHH-HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCC
Q ss_conf 1225888467888877321114-777505888877653058899999999999999999999898775428435664077
Q gi|254780788|r 363 MQAINVDEIIAHLLVAEGFADV-EELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIP 441 (526)
Q Consensus 363 ~e~LdVDE~iA~~LV~eGf~Si-EeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~ 441 (526)
.+-.||+.+ -+||....+.|..=.-+.+..++++.++|+.-+...-.+..+..- .+ +.+.
T Consensus 188 -------------V~lS~FDpvRREiAr~aLe~Li~DGRIhPaRIEe~v~k~~~ei~~~i~~~Ge~a~-----~e-lgi~ 248 (455)
T PRK12704 188 -------------VILSGFDPIRREIARLALEKLVEDGRIHPARIEEMVEKVRKEVDEEIREEGEQAV-----FE-LGIH 248 (455)
T ss_pred -------------EEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HH-CCCC
T ss_conf -------------7885687788999999999998848958899999999999999999999999999-----98-0999
Q ss_pred CCCHHHHHHHHHCCCCC------------HHHHHHCCHHHH
Q ss_conf 99989999999879847------------889653267752
Q gi|254780788|r 442 GIDSKIKVALGENGIKT------------MEDLAGCSVDDL 470 (526)
Q Consensus 442 gl~~~~~~~L~e~gIkt------------leDlAels~dEL 470 (526)
||.++++-.|+.=...| +-.||++-..||
T Consensus 249 ~l~peli~~lGrLkyRtSygQNvL~Hs~Eva~lag~~A~el 289 (455)
T PRK12704 249 GLHPELIKLIGRLKYRTSYGQNVLQHSREVAHLAGLMAAEL 289 (455)
T ss_pred CCCHHHHHHHHHEECCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99979999986310202040479999999999999999982
No 121
>PRK10811 rne ribonuclease E; Reviewed
Probab=93.44 E-value=0.24 Score=29.14 Aligned_cols=162 Identities=22% Similarity=0.326 Sum_probs=97.8
Q ss_pred HHCCCEEEEEEEECCCC--EEEEEEC-CCEEEEEHHHCCCC---------------CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 52083899999840576--3899957-93587447874887---------------511527669999976113587028
Q gi|254780788|r 136 DKVGEIISGTVKRVEYG--NVIVDLG-NSDGVIRRDETISR---------------ENLRPGDRVKSYIYDVRREQRGPQ 197 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~--~iiVdlg-~~ea~Lp~~e~ip~---------------E~~~~Gdrika~i~~V~~~~rgpq 197 (526)
.+.|.|--|.|.|+..+ -.+||+| .-.||||-++..+. +.++.|+.|-+=|..=...+|||.
T Consensus 36 q~kgNIYKGkV~rVePgLqAAFVDiG~eR~GFLp~kEI~~ey~~~~~~~~grp~I~dvLkeGQeILVQV~KEp~GtKGAr 115 (1063)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAA 115 (1063)
T ss_pred CCCCCCEEEEEEEECCCCEEEEEECCCCCCCCCCHHHCCHHHCCCCCCCCCCCCHHHHCCCCCEEEEEEEECCCCCCCCC
T ss_conf 34054268999785688605777238975542168882865426553435687878836799989999966787897836
Q ss_pred EE---------------------EECCCH-----HHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECC------
Q ss_conf 98---------------------715988-----9999999976677755808785663167750349999408------
Q gi|254780788|r 198 VL---------------------LSRTHP-----QFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSD------ 245 (526)
Q Consensus 198 i~---------------------lSRt~p-----~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d------ 245 (526)
+. +||--. .|-.-|-.+++|+ .-|+ |.|-+|.-....-...|
T Consensus 116 LTT~ISLaGRYLVLMPn~~~~gGISRKIe~eER~rLkeiL~~L~~Pe-g~Gl-----IVRTAa~g~s~eeL~~Dl~~Ll~ 189 (1063)
T PRK10811 116 LTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPE-GMGL-----IVRTAGVGKSAEALQWDLSFRLK 189 (1063)
T ss_pred EEEEEEECCEEEEECCCCCCCCCEECCCCCHHHHHHHHHHHHCCCCC-CCEE-----EEECCCCCCCHHHHHHHHHHHHH
T ss_conf 64215434201898248987761514789078999999997135788-8269-----99757689999999999999999
Q ss_pred --------CCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCC-HHHHHH---HHC-CCCCCCEEEECC
Q ss_conf --------9988127655488621788998627782679955987-899999---762-866542489875
Q gi|254780788|r 246 --------SSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPD-SATFVI---NAL-RPAIVTKVVLDE 303 (526)
Q Consensus 246 --------~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d-~~~fi~---nAl-~PA~v~~v~~de 303 (526)
..--|--.|+-.-+.-+..+++.+-++.|+-|.-++. ..+++. ..+ .|-...+|....
T Consensus 190 ~W~~I~k~~~~~~AP~LIyqE~~li~R~iRD~l~~di~eIiVDd~e~ye~ak~~i~~l~~P~~~~kVklY~ 260 (1063)
T PRK10811 190 HWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYT 260 (1063)
T ss_pred HHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCCCCEEEEC
T ss_conf 99999999735899868753754899999986217778899969999999999999744733337458857
No 122
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=93.25 E-value=0.1 Score=31.90 Aligned_cols=53 Identities=25% Similarity=0.350 Sum_probs=45.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 00111225888467888877321114777505888877653058899999999
Q gi|254780788|r 359 TQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 359 ~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
.+.|.+.-+|.+.-|+.|-.+||.|++++..++.++|+.+.|+..-+|..|+.
T Consensus 9 ~~~l~disgvg~~~a~~l~~ag~e~~~d~~~a~q~~l~~~~gignalaarika 61 (238)
T PRK12766 9 YEELTDISGVGPSKAESLREAGFESVEDVRAADQSELADVDGIGNALAARIKA 61 (238)
T ss_pred HHHHHCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 67764123668003678887040128989764277664201313899998741
No 123
>PTZ00035 Rad51; Provisional
Probab=93.00 E-value=0.26 Score=28.86 Aligned_cols=51 Identities=20% Similarity=0.223 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 79998999999987984788965326775212312344432112453343588999999999984122
Q gi|254780788|r 441 PGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYK 508 (526)
Q Consensus 441 ~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~ 508 (526)
.|++...+.+|.++|+.|++-+|-.+.-+|+.+- ++|+..|++|+..||+-
T Consensus 41 ~Gi~~~di~kl~~aG~~tv~~v~~~~~k~L~~ik-----------------gise~k~~Ki~~~a~k~ 91 (350)
T PTZ00035 41 KGFVKRDLELLKEGGLQTVECVAYAPMRTLCAIK-----------------GISEQKAEKLKKACKEL 91 (350)
T ss_pred CCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHCC-----------------CCCHHHHHHHHHHHHHH
T ss_conf 7999899999998491248999850999897737-----------------94699999999999975
No 124
>PRK12705 hypothetical protein; Provisional
Probab=92.99 E-value=0.63 Score=26.08 Aligned_cols=168 Identities=20% Similarity=0.240 Sum_probs=98.5
Q ss_pred HHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCC-CCCCCCCCHHHHHHHHHHHCCE
Q ss_conf 217889986277826799559878999997628665424898756787999985342-2110254427899999861674
Q gi|254780788|r 260 SRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQ-LSLAIGRRGQNVRLASQLTGWT 338 (526)
Q Consensus 260 sRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~q-ls~AIGk~GqNvrLas~Ltg~~ 338 (526)
.+|+.+-.+..-+ .+......+..|++-.-...+ .|.+ ...|-.|.+. --.-|||.|.|+|.--.|||-.
T Consensus 137 ~~ik~~e~eak~~------a~~~Ar~Ii~~AiqR~a~d~~--~E~t-vsvV~LPsdemKGRIIGREGRNIRa~E~~TGVD 207 (485)
T PRK12705 137 QRIAKIEEEANLE------AERTAQYILVFTMQRIAEDTI--ANIS-VSNVLLPSESMKGKIIGREGRNKRAFEELTGVD 207 (485)
T ss_pred HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHH--HHHC-CCCEECCCHHHHCCCCCCCCCCHHHHHHHHCCE
T ss_conf 9999999999988------999999999999988434677--7751-320245877873730487765299999987955
Q ss_pred EEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH-HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 5785522001101001221000111225888467888877321114-777505888877653058899999999999999
Q gi|254780788|r 339 IDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADV-EELACVKISEIASIEGFDEETAVEIQGRAREYL 417 (526)
Q Consensus 339 idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~Si-EeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L 417 (526)
+=| ++.... .+-.||+.+ .++|....+.|..=.-+....++++..+|+..+
T Consensus 208 lII--DDtPe~--------------------------VvlS~FdPiRREiAr~aLe~Li~DGRIhPaRIEe~v~ka~~e~ 259 (485)
T PRK12705 208 LII--DDTPEA--------------------------VVISSFNPIRREIARITLEKLLLDGRIDPARIEEYVQKANEEF 259 (485)
T ss_pred EEE--CCCCCE--------------------------EEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf 897--499985--------------------------8885797789999999999999848918899999999999999
Q ss_pred HHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHCCCCC------------HHHHHHCCHHHH
Q ss_conf 99999989877542843566407799989999999879847------------889653267752
Q gi|254780788|r 418 EGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKT------------MEDLAGCSVDDL 470 (526)
Q Consensus 418 ~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~gIkt------------leDlAels~dEL 470 (526)
...-.+..+.. -.+ +.+.||.++++-.|+.=...| +-.||++-..||
T Consensus 260 ~~~i~e~Ge~a-----~~e-lgi~~l~pelikllGrLkyRtSyGQNvL~HSiEvA~lag~mA~El 318 (485)
T PRK12705 260 EQKCYEIGKEV-----LEE-LGIFDLSPGLVRLLGRLYFRTSYGQNVLSHSLEVAFLAAILAALI 318 (485)
T ss_pred HHHHHHHHHHH-----HHH-CCCCCCCHHHHHHHHCEECCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999-----998-099999978999986010002340579999999999999999983
No 125
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=92.96 E-value=0.77 Score=25.40 Aligned_cols=99 Identities=21% Similarity=0.323 Sum_probs=72.2
Q ss_pred CCCCCCCHHHHHHHHHHH-HHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH--C
Q ss_conf 122588846788887732-1114777505888877653058899999999999999999999898775428435664--0
Q gi|254780788|r 363 MQAINVDEIIAHLLVAEG-FADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELC--S 439 (526)
Q Consensus 363 ~e~LdVDE~iA~~LV~eG-f~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~--~ 439 (526)
|+.-++.+.+.+.|++.| +.++-++.+...++|+.+++|.+..+..|.+. .+..++-...-=|. .
T Consensus 448 mdI~GLG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l~~~~~ks~~nLl~a------------Ie~sK~~~l~r~l~aLG 515 (667)
T COG0272 448 LDIDGLGEKIIEQLFEKGLIKDIADLYTLTEEDLLSLEGFGEKSAENLLNA------------IEKSKKQPLARFLYALG 515 (667)
T ss_pred CCCCCCCHHHHHHHHHCCCCCCHHHHHHCCHHHHHHCCCHHHHHHHHHHHH------------HHHHCCCCHHHHHHHCC
T ss_conf 577776799999999737537879877378988841622446579999999------------99860498999999879
Q ss_pred CCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf 77999899999998798478896532677521231
Q gi|254780788|r 440 IPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS 474 (526)
Q Consensus 440 l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~ 474 (526)
++++.+.++..|+. ...|++.|-..+.++|..+.
T Consensus 516 Ir~VG~~~Ak~La~-~f~sl~~l~~a~~e~l~~i~ 549 (667)
T COG0272 516 IRHVGETTAKSLAR-HFGTLEALLAASEEELASIP 549 (667)
T ss_pred CCHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHCC
T ss_conf 71140899999998-76029999842999995066
No 126
>PRK13764 ATPase; Provisional
Probab=92.83 E-value=0.21 Score=29.54 Aligned_cols=150 Identities=21% Similarity=0.273 Sum_probs=85.6
Q ss_pred EEEECCCCCEEEEEEECCCH-----HHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCH
Q ss_conf 97611358702898715988-----9999999976677755808785663167750349999408998812765548862
Q gi|254780788|r 186 IYDVRREQRGPQVLLSRTHP-----QFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGS 260 (526)
Q Consensus 186 i~~V~~~~rgpqi~lSRt~p-----~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGs 260 (526)
..+.+...-|--=++--|+| .|+-+.=--=+|-|-|-+|=|++ |.=+||--.+-- |..--||+-.
T Consensus 344 faD~RlaGvGmvGvvHA~~~iDAiQRfigRVELG~IPqivDTVIfI~~-----G~v~kVy~l~~t-----VKvP~Gm~e~ 413 (605)
T PRK13764 344 FADMRLAGVGMVGVVHATSPIDAIQRFIGRVELGMIPQIVDTVIFIKD-----GEVAKVYDLEFT-----VKVPTGMKEE 413 (605)
T ss_pred EEHHHHCCCCEEEEEECCCHHHHHHHHHCCCHHCCCCHHEEEEEEEEC-----CEEEEEEEEEEE-----EECCCCCCHH
T ss_conf 010100057447688528878999987330110564214048999807-----848899998888-----8578998845
Q ss_pred H-HHH-------HHHHH------CCCCEEEEECCC-----CH---------HHHHHHHCCCCCCCEEEECCCCCEEEEEE
Q ss_conf 1-788-------99862------778267995598-----78---------99999762866542489875678799998
Q gi|254780788|r 261 R-VQA-------VVTEL------RDEKIDIVVWSP-----DS---------ATFVINALRPAIVTKVVLDEDVGRIEVIV 312 (526)
Q Consensus 261 R-iq~-------I~~EL------~gEkIDii~ws~-----d~---------~~fi~nAl~PA~v~~v~~de~~~~~~v~v 312 (526)
- .+. .++++ -||.+=+++-.. .| ...+.+-+. . -..|.+. ..+++.|.|
T Consensus 414 DLARPVI~V~Df~t~~~eyEIYtfGeq~vVvPv~~~~~~~~~~~~~a~~~i~~~i~r~~~-~-~~eV~~~-~d~~avv~v 490 (605)
T PRK13764 414 DLARPVIEVKDFETGEPEYEIYTFGEQTVVVPVKREEEEKSPVWKLAEEEIEREIKRYLK-G-PVEVEVI-SDNKAVVYV 490 (605)
T ss_pred HCCCCEEEEEECCCCCEEEEEEEECCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCC-C-CCEEEEE-CCCEEEEEE
T ss_conf 514864998762789888999983877999987888766575889999999999987468-9-8349996-498689997
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCHH
Q ss_conf 534221102544278999998616745785522001
Q gi|254780788|r 313 PKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS 348 (526)
Q Consensus 313 ~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~ 348 (526)
|+...+.+|||+|.|+.=--+-.|.+|||...++..
T Consensus 491 ~~~~i~~~igK~g~~i~~ie~~lgi~IdV~~~~e~~ 526 (605)
T PRK13764 491 PEKDIPAVIGKGGKNISKIEKKLGIDIDVRPLSEEE 526 (605)
T ss_pred CCCCCHHHHCCCCCCHHHHHHHHCCCEEEEECCCCC
T ss_conf 645313665559747999998648835765766566
No 127
>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.
Probab=92.60 E-value=0.19 Score=29.86 Aligned_cols=55 Identities=15% Similarity=0.229 Sum_probs=43.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 0001112258884678888773211147775058888776530588999999999
Q gi|254780788|r 358 RTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGR 412 (526)
Q Consensus 358 ~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~r 412 (526)
.....++.|+++--....|-.+|+.|+.++...+.++|.++++|......|+++.
T Consensus 5 ~l~~~I~~L~LS~R~~N~Lk~~~I~tv~dL~~~s~~dLl~i~N~G~kSl~EI~~~ 59 (62)
T pfam03118 5 LLSIPIEELELSVRSYNCLKRAGINTVGDLLSKSEEDLLKIKNFGKKSLEEIKEK 59 (62)
T ss_pred HHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
T ss_conf 8639899816868999999894996799998589999974889868579999999
No 128
>KOG3409 consensus
Probab=92.58 E-value=0.46 Score=27.07 Aligned_cols=75 Identities=28% Similarity=0.497 Sum_probs=53.0
Q ss_pred HHHHHHHHHHCCCEEEEEEEECCCCEEEEEE---C------CCEEEEEHHHCCCCC--------CCCCCCEEEEEEEEEC
Q ss_conf 8779999852083899999840576389995---7------935874478748875--------1152766999997611
Q gi|254780788|r 128 DRQYLEFKDKVGEIISGTVKRVEYGNVIVDL---G------NSDGVIRRDETISRE--------NLRPGDRVKSYIYDVR 190 (526)
Q Consensus 128 ~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdl---g------~~ea~Lp~~e~ip~E--------~~~~Gdrika~i~~V~ 190 (526)
+..+++-....|.||++.|.|+.-.+.-+++ | .-.|+|++.+.=+.| .|||||-|+|-+.+-.
T Consensus 58 ~~~~~~~LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~ 137 (193)
T KOG3409 58 KQLFNELLPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLG 137 (193)
T ss_pred CCCHHHCCCCCCCEEEEEEEEECCCEEEEEEEEECCEEHHHHHCCEEEHHHCCCCCCCHHHHHHCCCCCCEEEEEEEECC
T ss_conf 65143307765767999987624413567899986797001121143354356444011216343698868888885147
Q ss_pred CCCCEEEEEEECCCH
Q ss_conf 358702898715988
Q gi|254780788|r 191 REQRGPQVLLSRTHP 205 (526)
Q Consensus 191 ~~~rgpqi~lSRt~p 205 (526)
-|..-+|+-+..
T Consensus 138 ---~~~~y~LTtAen 149 (193)
T KOG3409 138 ---DGSNYLLTTAEN 149 (193)
T ss_pred ---CCCCEEEEEECC
T ss_conf ---787279987516
No 129
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=92.56 E-value=0.15 Score=30.68 Aligned_cols=71 Identities=18% Similarity=0.162 Sum_probs=56.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCC
Q ss_conf 888467888877321114777505888877653058899999999999999999999898775428435664077
Q gi|254780788|r 367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIP 441 (526)
Q Consensus 367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~ 441 (526)
||...-...|-..|++|++++|.++...+....|+..+.+..++-.|+...+....... -+.+.+...+++
T Consensus 232 Gi~~~r~~~l~~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~~~e~~~~~~~----P~~P~e~~fD~E 302 (474)
T COG2251 232 GITPSRYDVLEEVGITTIEDLADASLPILELVAGALTALAAQLVLQARARVEGRPLMEI----PLFPVELYFDFE 302 (474)
T ss_pred CCCHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEECC----CCCCCCCEEECC
T ss_conf 99878899999738223999975255402566546777789999999852468850126----899754534102
No 130
>KOG2193 consensus
Probab=92.54 E-value=0.18 Score=29.99 Aligned_cols=40 Identities=23% Similarity=0.563 Sum_probs=30.8
Q ss_pred CCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf 5678799998534221102544278999998616745785
Q gi|254780788|r 303 EDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII 342 (526)
Q Consensus 303 e~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~ 342 (526)
.+.....+.+|+.-.---||++|||++-.++.+|-.|-|-
T Consensus 408 pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIa 447 (584)
T KOG2193 408 PEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIA 447 (584)
T ss_pred CCHHHEEEECCHHHHHHHHCCCCHHHHHHHHHCCCEEEEC
T ss_conf 0212201444088888887124221899987427603435
No 131
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=92.38 E-value=0.92 Score=24.86 Aligned_cols=129 Identities=22% Similarity=0.302 Sum_probs=84.1
Q ss_pred EEEEECCCC-CCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH-H
Q ss_conf 999985342-21102544278999998616745785522001101001221000111225888467888877321114-7
Q gi|254780788|r 308 IEVIVPKEQ-LSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADV-E 385 (526)
Q Consensus 308 ~~v~v~~~q-ls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~Si-E 385 (526)
-.|-.|.+. --.-|||.|.|+|---.+||-.+-|-...+. .+-.||+.+ -
T Consensus 206 svV~LPsdemKGRIIGrEGRNIRa~E~~TGVDlIIDDtPe~----------------------------V~lS~FdpvRR 257 (514)
T TIGR03319 206 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEA----------------------------VILSGFDPVRR 257 (514)
T ss_pred EEEECCCHHHHCCCCCCCCCHHHHHHHHHCCEEEECCCCCE----------------------------EEEECCCHHHH
T ss_conf 66863977875501086752399999986974898599985----------------------------88867886889
Q ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHCCCCC-------
Q ss_conf 7750588887765305889999999999999999999989877542843566407799989999999879847-------
Q gi|254780788|r 386 ELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKT------- 458 (526)
Q Consensus 386 eIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~gIkt------- 458 (526)
+||....+.|..=.-+.+..++++..+|+.-+...-.+..+..- .=+.+.||.++++-.|+.=...|
T Consensus 258 EiAr~aLe~Li~DGRIhP~rIEe~v~k~~~e~~~~i~~~Ge~a~------~elgi~~~~peli~~lGrlkyRtSygQNvL 331 (514)
T TIGR03319 258 EIARMALEKLIQDGRIHPARIEEMVEKATKEVDNAIREEGEQAA------FDLGVHGLHPELIKLLGRLKFRTSYGQNVL 331 (514)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHCCCCCCHHHHHHHHHEEHHHHCCHHHH
T ss_conf 99999999998749948899999999999999999999999999------981999999789999875000102405899
Q ss_pred -----HHHHHHCCHHHH
Q ss_conf -----889653267752
Q gi|254780788|r 459 -----MEDLAGCSVDDL 470 (526)
Q Consensus 459 -----leDlAels~dEL 470 (526)
+-.||++-..||
T Consensus 332 ~Hs~Eva~lag~~A~El 348 (514)
T TIGR03319 332 QHSIEVAHLAGIMAAEL 348 (514)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 99999999999999983
No 132
>KOG3298 consensus
Probab=92.28 E-value=0.39 Score=27.56 Aligned_cols=63 Identities=25% Similarity=0.305 Sum_probs=47.1
Q ss_pred HHHHHCCCEEEEEEEECCCCEEEEEECCCEEEE------EHHHCCCCCC-----------CCCCCEEEEEEEEECCCCCE
Q ss_conf 998520838999998405763899957935874------4787488751-----------15276699999761135870
Q gi|254780788|r 133 EFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVI------RRDETISREN-----------LRPGDRVKSYIYDVRREQRG 195 (526)
Q Consensus 133 ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~L------p~~e~ip~E~-----------~~~Gdrika~i~~V~~~~rg 195 (526)
-|+.-.||||.|+|.++.+-.++++.|-.+-+. |--+-+|+|+ .+.|++||.-|..++-..+-
T Consensus 76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~~ 155 (170)
T KOG3298 76 TFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDETE 155 (170)
T ss_pred EEEECCCCEEEEEEEEEEEEEEEEECCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEEEEEEEEE
T ss_conf 97404776888999998424489960566753232527987421789999852266432455076899999999970156
No 133
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=92.24 E-value=0.7 Score=25.71 Aligned_cols=113 Identities=19% Similarity=0.227 Sum_probs=78.9
Q ss_pred EECHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECC-CCEEEE
Q ss_conf 2348999862889864737998508456207999999999999999999887799998520838999998405-763899
Q gi|254780788|r 78 QISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVE-YGNVIV 156 (526)
Q Consensus 78 eI~l~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e-~~~iiV 156 (526)
.+.|...-....+.++||++..-+=...=+|.+|++-.. +-.+|+--.+.|-.+. +-.+++
T Consensus 31 ~ilL~k~~~~~~e~evGdev~vFiY~D~~~rl~aTt~~p------------------~~tvg~~g~~~Vv~v~~~lGaFl 92 (287)
T COG2996 31 TILLPKSEPEEDELEVGDEVTVFIYVDSEDRLIATTREP------------------KATVGEYGWLKVVEVNKDLGAFL 92 (287)
T ss_pred EEECCCCCCCCCCCCCCCEEEEEEEECCCCCEEHEEECC------------------EEEECCEEEEEEEEECCCCCEEE
T ss_conf 786256677678511376899999988877630101041------------------37405323799998737751589
Q ss_pred EEC-CCEEEEEHHHCCCCCC--CCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHH
Q ss_conf 957-9358744787488751--1527669999976113587028987159889999999
Q gi|254780788|r 157 DLG-NSDGVIRRDETISREN--LRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLF 212 (526)
Q Consensus 157 dlg-~~ea~Lp~~e~ip~E~--~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf 212 (526)
|.| .-+.++|-+++-+-.. .++||++-+|++-=++. | |.-.-...+.+..|+
T Consensus 93 D~Gl~KDl~vp~~elp~~~~~wpq~Gd~l~v~l~~Dkk~-R---i~g~~a~~~~l~~l~ 147 (287)
T COG2996 93 DWGLPKDLLVPLDELPTLKSLWPQKGDKLLVYLYVDKKG-R---IWGTLAIEKILENLA 147 (287)
T ss_pred ECCCCCCEEEEHHHCCCCCCCCCCCCCEEEEEEEECCCC-C---EEEEECCHHHHHHCC
T ss_conf 659870036162536443123778798999999985678-4---777733155787617
No 134
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=92.23 E-value=0.95 Score=24.74 Aligned_cols=67 Identities=22% Similarity=0.215 Sum_probs=36.2
Q ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCHH-HHHHCCCCCCHHHHHHHHHCCCCCHHHHH
Q ss_conf 76530588999999999999999999998987754----2843-56640779998999999987984788965
Q gi|254780788|r 396 ASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRE----LGVS-EELCSIPGIDSKIKVALGENGIKTMEDLA 463 (526)
Q Consensus 396 ~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e----~~~~-e~L~~l~gl~~~~~~~L~e~gIktleDlA 463 (526)
.+|.|++.++...-..-|+.+-......+++...+ ++.- ..+..+ -++++-+....-+|=++...+-
T Consensus 507 iKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~-~i~~dKI~dvIG~gGk~I~~I~ 578 (692)
T COG1185 507 IKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETI-KIDPDKIRDVIGPGGKTIKAIT 578 (692)
T ss_pred EEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE-CCCHHHHHHCCCCCCCCHHHHH
T ss_conf 66458889999999987999999999999998751143442458724996-1388887632188632034655
No 135
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=92.04 E-value=0.33 Score=28.11 Aligned_cols=64 Identities=27% Similarity=0.435 Sum_probs=53.0
Q ss_pred HHCCCEEEEEEEECCCC--EEEEEECC-CEEEEEHHHCCC----------CCCCCCCCEEEEEEEEECCCCCEEEEE
Q ss_conf 52083899999840576--38999579-358744787488----------751152766999997611358702898
Q gi|254780788|r 136 DKVGEIISGTVKRVEYG--NVIVDLGN-SDGVIRRDETIS----------RENLRPGDRVKSYIYDVRREQRGPQVL 199 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~--~iiVdlg~-~ea~Lp~~e~ip----------~E~~~~Gdrika~i~~V~~~~rgpqi~ 199 (526)
...|.|..|.|.|++++ ..+||+|. -.|+|+-++..| .+.++.|+.+-+-+.......+|+++.
T Consensus 35 ~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT 111 (487)
T COG1530 35 QIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLT 111 (487)
T ss_pred EEECCCEEEEECCCCCCCHHHEEECCCCCCCEEEECCCCHHHHHCCCCCCEEEECCCCEEEEEEEEECCCCCCCCCE
T ss_conf 63067168886231766322205516876606884105534420002350055417862899998625766034212
No 136
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=91.99 E-value=0.18 Score=30.07 Aligned_cols=39 Identities=23% Similarity=0.406 Sum_probs=34.9
Q ss_pred EEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECC
Q ss_conf 799998534221102544278999998616745785522
Q gi|254780788|r 307 RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEE 345 (526)
Q Consensus 307 ~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~ 345 (526)
++.+.||..+...-|||+|.|+|--.+-||-+|.|....
T Consensus 1 t~rilvP~~~vG~vIGk~G~~I~~i~~~sga~I~i~~~~ 39 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSV 39 (65)
T ss_pred CEEEEEEHHHEEEEECCCCHHHHHHHHHHCCEEEECCCC
T ss_conf 989998746722899799878999999849889999889
No 137
>TIGR02239 recomb_RAD51 DNA repair protein RAD51; InterPro: IPR011941 Homologous recombination is an evolutionarily conserved mechanism for the repair of double-strand breaks in DNA and the generation of genetic diversity. The primary function of homologous recombination in mitotic cells is to repair double-strand breaks or single-strand gaps that form as a result of replication fork collapse, from processing of spontaneous damage, and from exposure to DNA-damaging agents. During meiosis, homologous recombination is essential to establish a physical connection between homologous chromosomes to ensure their correct disjunction at the first meiotic division. In addition, the high frequency of meiotic recombination contributes to diversity by creating new linkage arrangements between genes, or parts of genes . The central step of homologous recombination is synapsis, the process of bringing together the two homologous strands. Rad51, a eukaryotic homologue of the prokaryotic recombinase RecA, mediates this process in eukaryotes . Firstly a single-stranded DNA tail is coated by ATP-bound Rad51 to yield a nucleoprotein filament. This filament then searches for a homologous sequence within double-stranded DNA, and catalyses the exchange of strands between the single-stranded and double-stranded DNA substrates. The original broken end of the resulting branched DNA is now aligned with an appropriate matching sequence in an intact duplex, and is further processed by other enzymes . Rad51 contains an N-terminal alpha-helical DNA binding domain not found in RecA, and a RecA-like C-terminal ATPase domain , . The active form of this protein is a long helical filament where the catalytically active unit is a homodimer . ; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair.
Probab=91.80 E-value=1.1 Score=24.40 Aligned_cols=90 Identities=22% Similarity=0.171 Sum_probs=66.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCC
Q ss_conf 25888467888877321114777505888877653058899999999999999999999898775428435664077999
Q gi|254780788|r 365 AINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGID 444 (526)
Q Consensus 365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~ 444 (526)
.-+|...-...|.+.||.+++.++|.+...|..|.|+.+..++.+...|...+-..-....+ -.....++..+. -.
T Consensus 6 ~~g~~~~d~~~l~~~g~~~~~~~a~~~~k~l~~~~G~~~~k~~~~~~~~~~lv~~gf~~a~~---~~~~r~~~~~~~-~G 81 (317)
T TIGR02239 6 EKGIAAADIKKLKEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEAAKLVPLGFTTATE---LHKKRKEVIQLT-TG 81 (317)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHEECC-CC
T ss_conf 30542788999986136789998876555565424730778999999988776543677999---998776541210-35
Q ss_pred HHHHHHHHHCCCCC
Q ss_conf 89999999879847
Q gi|254780788|r 445 SKIKVALGENGIKT 458 (526)
Q Consensus 445 ~~~~~~L~e~gIkt 458 (526)
...+..|-..||-|
T Consensus 82 s~~ld~~l~GG~e~ 95 (317)
T TIGR02239 82 SKELDKLLEGGIET 95 (317)
T ss_pred HHHHHHHHCCCCCC
T ss_conf 06899986087554
No 138
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=91.69 E-value=0.31 Score=28.29 Aligned_cols=31 Identities=42% Similarity=0.569 Sum_probs=11.6
Q ss_pred HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCC
Q ss_conf 6640779998999999987984788965326
Q gi|254780788|r 436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCS 466 (526)
Q Consensus 436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels 466 (526)
+|..+.||+.....+|.+.||.|+++||.+.
T Consensus 208 ~LslVagi~~~q~~~L~~~GI~Ti~~LA~~~ 238 (457)
T TIGR03491 208 HLSLVPGIGPSRYRLLQELGIHTLEDLAAAD 238 (457)
T ss_pred CHHHHCCCCHHHHHHHHHCCCCCHHHHHCCC
T ss_conf 9766059999999999985998799986299
No 139
>TIGR03675 arCOG00543 arCOG01782 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=91.47 E-value=0.72 Score=25.62 Aligned_cols=161 Identities=12% Similarity=0.164 Sum_probs=75.9
Q ss_pred HHHHHCCCCCCCE-EEEECCCCCEEEEEEEE--EEECCCCCCCCEECHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 9996136874535-99974998839999998--85176778753234899986288986473799850845620799999
Q gi|254780788|r 37 KAARSLYGTMSDI-RVEINPETGDISLFRLL--EVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQS 113 (526)
Q Consensus 37 ~a~kK~~~~~~~i-~V~iD~~tG~i~i~~~~--~VVedved~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~ 113 (526)
...++-.+.++.+ .+.||+.+|++.+...+ .|+-.--. .+ +++. .+.|=.....=.|.-.++. .+.
T Consensus 73 ~~i~~~vp~~a~i~~~~fd~~~~ev~i~~~kpg~~~g~~g~-----~~---~~i~--~~~gw~~~v~r~p~~~s~~-~~~ 141 (630)
T TIGR03675 73 EKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGS-----TL---REIT--AETGWTPKVVRTPPIESKT-IKN 141 (630)
T ss_pred HHHHHHCCCCCCCEEEEECCCCCEEEEEECCCEEEECCCCH-----HH---HHHH--HHHCCEEEEEECCCCCHHH-HHH
T ss_conf 99997589535841589748972799997796367647516-----79---9999--9749746888659997078-999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCC-EEE-------------------EEEEECCCCEEEEEECC-----CEEEEEHH
Q ss_conf 999999999999988779999852083-899-------------------99984057638999579-----35874478
Q gi|254780788|r 114 AKQVIIQKVREAERDRQYLEFKDKVGE-IIS-------------------GTVKRVEYGNVIVDLGN-----SDGVIRRD 168 (526)
Q Consensus 114 AKQvI~QkireaEr~~i~~ef~~r~Ge-iv~-------------------G~V~r~e~~~iiVdlg~-----~ea~Lp~~ 168 (526)
.++.+.+- ..||..+...+-.++.. .+. +...+.....+.+|-|= ...-+|.-
T Consensus 142 ir~~~~~~--~~~r~~~l~~~g~~i~r~~~~~~~~vrit~LG~~~eVGRSc~l~~~~~~~illDcG~~~~~~~~~~~P~~ 219 (630)
T TIGR03675 142 IREYLRSE--SEERKEFLRKLGRRIHRDPIFKDRWVRVTALGGFREVGRSALLLSTPESRILLDCGVNVGANGDNAYPYL 219 (630)
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCCC
T ss_conf 99999970--7999999999888746897688974999834676702645899963981799988888777775458865
Q ss_pred HCCCCCCCCCCCEEEEEEEE-------------ECCCCCEEEEEEECCCHHHHHHHHHHH
Q ss_conf 74887511527669999976-------------113587028987159889999999976
Q gi|254780788|r 169 ETISRENLRPGDRVKSYIYD-------------VRREQRGPQVLLSRTHPQFMVKLFHME 215 (526)
Q Consensus 169 e~ip~E~~~~Gdrika~i~~-------------V~~~~rgpqi~lSRt~p~~l~~Lf~~E 215 (526)
+ +|. |. =+.|.|++.. ++..-+|| |+.+...-+++.-|+.--
T Consensus 220 d-~~e--~~-~~~IDAVvlTHAHLDH~G~LP~L~k~Gf~Gp-Iy~T~pT~dL~~llL~D~ 274 (630)
T TIGR03675 220 D-VPE--FQ-LDELDAVVITHAHLDHSGLVPLLFKYGYDGP-VYCTPPTRDLMTLLQLDY 274 (630)
T ss_pred C-CCC--CC-CCCCCEEEEECCCCCCCCCCCHHHHCCCCCC-EEECHHHHHHHHHHHHHH
T ss_conf 6-777--98-0118589983353212563218876488898-886545999999999989
No 140
>KOG2190 consensus
Probab=91.40 E-value=1.2 Score=24.11 Aligned_cols=100 Identities=23% Similarity=0.340 Sum_probs=63.5
Q ss_pred CCCEEEEECCCCHHHHHHHHHHCCCC------EE---EEECCCCHH---HHHHHHC--CCCCCCEEEECC--CCCEEEEE
Q ss_conf 88127655488621788998627782------67---995598789---9999762--866542489875--67879999
Q gi|254780788|r 248 IDPVGACVGMRGSRVQAVVTELRDEK------ID---IVVWSPDSA---TFVINAL--RPAIVTKVVLDE--DVGRIEVI 311 (526)
Q Consensus 248 iDpVGAcVG~rGsRiq~I~~EL~gEk------ID---ii~ws~d~~---~fi~nAl--~PA~v~~v~~de--~~~~~~v~ 311 (526)
.|-+|+|+|..|+++.++-++.+-=. -| .+.-.+.|. -.-.+|+ .+........+. -.-+....
T Consensus 264 ~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~ 343 (485)
T KOG2190 264 SDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLL 343 (485)
T ss_pred HHHCEEEECCCCCCHHHHHHCCCCCEEECCCCCCCEEEECCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCEEEEEEC
T ss_conf 22202551588851065664037745732666763465035458643221003556421221245556665522212321
Q ss_pred ECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCH
Q ss_conf 853422110254427899999861674578552200
Q gi|254780788|r 312 VPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEED 347 (526)
Q Consensus 312 v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~~ 347 (526)
||.+..---|||+|-++-=--++||-.|-|...++.
T Consensus 344 vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~ 379 (485)
T KOG2190 344 VPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV 379 (485)
T ss_pred CCCCCCCEEECCCCCCHHHHHHHCCCCEEECCCCCC
T ss_conf 570000013256653057898732883697256666
No 141
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=91.22 E-value=0.54 Score=26.57 Aligned_cols=57 Identities=21% Similarity=0.254 Sum_probs=38.2
Q ss_pred HHHHCCCEEEEEEEECCCCEEEEEECCC-----------EEEEEHHHC------CCCCCCCCCCEEEEEEEEEC
Q ss_conf 9852083899999840576389995793-----------587447874------88751152766999997611
Q gi|254780788|r 134 FKDKVGEIISGTVKRVEYGNVIVDLGNS-----------DGVIRRDET------ISRENLRPGDRVKSYIYDVR 190 (526)
Q Consensus 134 f~~r~Geiv~G~V~r~e~~~iiVdlg~~-----------ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~ 190 (526)
...+.|.+|.|.|.++...-+.|.+-.+ .|.++-++. --.+.|++||-|||++...-
T Consensus 60 ~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~ 133 (188)
T COG1096 60 PLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG 133 (188)
T ss_pred CCCCCCCEEEEEEEECCCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEECC
T ss_conf 76898879999995326608999999994333367887402589782023111020134464617999998617
No 142
>cd03586 Pol_IV_kappa Pol_IV_kappa, a member of the Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases. Originally called the DinB family, they belong to the recently described Y-family of DNA polymerases. Pol IV is mostly found in bacteria and archaea. Although the structure of Pol IV is similar to that of Pol eta, it shows markedly differenct efficiencies and fidelities in bypassing various DNA lesions. All Pol IV-like polymerases studied to date are able to b
Probab=91.11 E-value=1.2 Score=23.92 Aligned_cols=36 Identities=31% Similarity=0.350 Sum_probs=18.0
Q ss_pred HHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCC
Q ss_conf 640779998999999987984788965326775212
Q gi|254780788|r 437 LCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLG 472 (526)
Q Consensus 437 L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~ 472 (526)
+.+++|+...+...|...||+|..||+.++.+.|..
T Consensus 174 v~~l~GIG~~~~~~L~~~gI~t~~dl~~~~~~~l~~ 209 (337)
T cd03586 174 VRKIWGIGKVTAEKLNRLGIRTIGDLAAADLELLKK 209 (337)
T ss_pred CHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHH
T ss_conf 302078468999999980896899986499999987
No 143
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=89.87 E-value=0.93 Score=24.83 Aligned_cols=50 Identities=14% Similarity=0.248 Sum_probs=34.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 112258884678888773211147775058888776530588999999999
Q gi|254780788|r 362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGR 412 (526)
Q Consensus 362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~r 412 (526)
|-+.-||.+.....|... |.|++.|..|+.++|.+++|+...+|..+.+.
T Consensus 556 Ld~I~GIG~kr~~~Ll~~-Fgs~~~i~~As~eeL~~v~Gi~~~~A~~I~~~ 605 (609)
T PRK00558 556 LDDIPGIGPKRRKALLKH-FGSLKAIKEASVEELAKVPGISKKLAEKIYEA 605 (609)
T ss_pred CCCCCCCCHHHHHHHHHH-CCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
T ss_conf 647899799999999997-07999997389999964899899999999999
No 144
>pfam02889 Sec63 Sec63 Brl domain. This domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum translocons.
Probab=89.40 E-value=1.1 Score=24.35 Aligned_cols=42 Identities=24% Similarity=0.355 Sum_probs=37.7
Q ss_pred HHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf 435664077999899999998798478896532677521231
Q gi|254780788|r 433 VSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS 474 (526)
Q Consensus 433 ~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~ 474 (526)
.+..|+.|++++++.+.+|.++|+.|+++|.+++.+|+.++.
T Consensus 146 ~~~pL~Qlp~~~~~~i~~l~~~~i~sl~~l~~~~~~el~~ll 187 (309)
T pfam02889 146 SDSPLRQLPHIPPEVIKKLEKKGISSLEDLMDLDPEELGELL 187 (309)
T ss_pred CCCHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHH
T ss_conf 998545179999999999997799989999609999999997
No 145
>TIGR01009 rpsC_bact ribosomal protein S3; InterPro: IPR005704 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 of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein S3 is one of the proteins from the small ribosomal subunit. This family describes the bacterial type of ribosomal protein S3 and also and many chloroplast forms. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=89.30 E-value=1.2 Score=24.12 Aligned_cols=59 Identities=19% Similarity=0.430 Sum_probs=50.3
Q ss_pred HHHHHHHHCC--CCCCCEEEECCCCCE-EEEEECCCCCCCCCCCCHHHHH----HHHHHHC--CEEEE
Q ss_conf 8999997628--665424898756787-9999853422110254427899----9998616--74578
Q gi|254780788|r 283 SATFVINALR--PAIVTKVVLDEDVGR-IEVIVPKEQLSLAIGRRGQNVR----LASQLTG--WTIDI 341 (526)
Q Consensus 283 ~~~fi~nAl~--PA~v~~v~~de~~~~-~~v~v~~~qls~AIGk~GqNvr----Las~Ltg--~~idi 341 (526)
...|+.+-|+ -|.|+.|.+--...+ +.|.+.--+=-+.|||+|+||- .-.+||| -+++|
T Consensus 40 IR~~i~k~l~~~~a~iS~veIeR~~~~~v~V~IhtArPg~vIGkkG~~iE~l~~~l~k~~~~~k~v~i 107 (217)
T TIGR01009 40 IRNLIKKELKKKNAGISDVEIERTADKKVRVTIHTARPGIVIGKKGSEIEKLKKALQKLTGSVKEVQI 107 (217)
T ss_pred HHHHHHHHCCCCCCCCCEEEEEECCCCEEEEEEEECCCCEEECCCCCHHHHHHHHHHHHHCCEEEEEE
T ss_conf 99987321133543313279981699788999982788658857884589999999988478358999
No 146
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=89.19 E-value=0.66 Score=25.93 Aligned_cols=54 Identities=11% Similarity=0.103 Sum_probs=27.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 000111225888467888877321114777505888877653058899999999
Q gi|254780788|r 358 RTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 358 ~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
....-++.|++.--...-|-.+|+.|+.++..-+.++|+++..|...-++|+.+
T Consensus 242 ~l~~~IeeLeLSvRs~NcLk~a~I~tI~dLv~~se~dLl~ikNfGkKSl~EI~~ 295 (306)
T PRK05182 242 ILLRPIEELELSVRSYNCLKRAGINTIGDLVQRTEEELLKTPNLGKKSLEEIKE 295 (306)
T ss_pred HHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCCCCHHHHHH
T ss_conf 644969881386888755878599369998747999996189976203999999
No 147
>smart00322 KH K homology RNA-binding domain.
Probab=88.52 E-value=0.62 Score=26.09 Aligned_cols=40 Identities=28% Similarity=0.356 Sum_probs=32.3
Q ss_pred EEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCC
Q ss_conf 0349999408998812765548862178899862778267995598
Q gi|254780788|r 236 RAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSP 281 (526)
Q Consensus 236 RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~ 281 (526)
+.+|.|.+ +.+|..+|.+|++|+.+.++. |-+|++....+
T Consensus 4 ~~~i~vp~-----~~~g~iIG~~G~~i~~i~~~~-~~~I~i~~~~~ 43 (69)
T smart00322 4 TIEVLIPA-----DKVGLIIGKGGSTIKKIEEET-GVKIDIPEDGS 43 (69)
T ss_pred EEEEEECH-----HHCCEEECCCCCCHHHHHHHH-CCEEEECCCCC
T ss_conf 99999897-----876854999984579999972-88899779999
No 148
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=88.03 E-value=1.7 Score=22.83 Aligned_cols=68 Identities=22% Similarity=0.234 Sum_probs=49.3
Q ss_pred HHHHCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHH-----CCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCC
Q ss_conf 985208389999984057638999579-358744787-----48875115276699999761135870289871598
Q gi|254780788|r 134 FKDKVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDE-----TISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTH 204 (526)
Q Consensus 134 f~~r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e-----~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~ 204 (526)
|....|++|.|+|.+...+++.||+|. ..|.||.-- .=.+-++++||-|-|-|....++ -...||..+
T Consensus 2 YiP~~gD~VIGiV~~~~~d~y~vdi~~~~~a~L~~laFegATKknrP~L~~GdlVYaRV~~a~~~---~e~EL~Cvd 75 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRD---MEPELSCVD 75 (86)
T ss_pred CCCCCCCEEEEEEEEECCCEEEEECCCCCCEEECCCEECCCCCCCCCCCCCCCEEEEEEEECCCC---CCEEEEEEC
T ss_conf 62889998999994432766899767986648500101787655688788788999999874899---970489888
No 149
>KOG4078 consensus
Probab=87.63 E-value=0.93 Score=24.83 Aligned_cols=75 Identities=17% Similarity=0.383 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf 9999999999988779999852083899999840576389995793587447874887511527669999976113587
Q gi|254780788|r 116 QVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQR 194 (526)
Q Consensus 116 QvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r 194 (526)
|.+..-+| ..-+-..-+-.|.+|.|.+-.+-.+++|+|.|.---..-++--..+|.|+.|.|++--+.+.+...|
T Consensus 64 qsFASlLR----nSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n~e~Y~~GaRVrlRl~DlELs~r 138 (173)
T KOG4078 64 QSFASLLR----NSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALNGEAYQKGARVRLRLIDLELSER 138 (173)
T ss_pred HHHHHHHH----CCCCCCCCCCCCCEEEEEEEEEECCCEEEECCCEEEEEECCCCCCHHHHHCCCEEEEEECCHHHHHH
T ss_conf 56999970----5840115576785887652011044238961874888873767587775057669999727667666
No 150
>pfam00013 KH_1 KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Q4R966.1/333-392;
Probab=87.29 E-value=0.67 Score=25.87 Aligned_cols=34 Identities=29% Similarity=0.516 Sum_probs=31.9
Q ss_pred EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEE
Q ss_conf 9999853422110254427899999861674578
Q gi|254780788|r 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDI 341 (526)
Q Consensus 308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi 341 (526)
..+.||.+....-||++|.|++--.+.||-+|++
T Consensus 2 ~~v~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i 35 (57)
T pfam00013 2 EEILIPSSLVGRIIGKGGSNIKEIREETGAKIRI 35 (57)
T ss_pred EEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEE
T ss_conf 8999875542068998964769999973999996
No 151
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=87.27 E-value=1.2 Score=24.02 Aligned_cols=32 Identities=9% Similarity=0.161 Sum_probs=20.3
Q ss_pred CCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf 889864737998508456207999999999999
Q gi|254780788|r 88 DPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQ 120 (526)
Q Consensus 88 ~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~Q 120 (526)
++....|-++-.|+++ .||---..+-|.++.-
T Consensus 24 ~~~~~YgrF~~~Ple~-G~g~TlGNaLRRvLLs 55 (333)
T CHL00013 24 SKRLYYGRFILSPLMK-GQADTIGIALRRALLG 55 (333)
T ss_pred CCCCEEEEEEECCCCC-CCHHHHHHHHHHHHHH
T ss_conf 6876278999705888-7421467889888774
No 152
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Probab=87.15 E-value=2.3 Score=21.94 Aligned_cols=78 Identities=28% Similarity=0.273 Sum_probs=53.3
Q ss_pred HHHHHHH-HHHHHHHHHHHCCHHHHHHH---HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHH
Q ss_conf 7888877-32111477750588887765---3058899999999999999999999898775428435664077999899
Q gi|254780788|r 372 IAHLLVA-EGFADVEELACVKISEIASI---EGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKI 447 (526)
Q Consensus 372 iA~~LV~-eGf~SiEeIa~a~~eeL~~I---eGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~ 447 (526)
+.+.|.. -||-|.++++.++.++|.++ -||..-.+.-|++-|+.+...... .........+.|+.++|+.+..
T Consensus 17 i~~rl~~~~~~pt~~~l~~~~~~~l~~~i~~~G~~~~Ka~~I~~~a~~~~~~~~~---~~~~~~~~~~~L~~l~GIG~~t 93 (144)
T pfam00730 17 ITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKELARILVEGYLG---LVPLDLEELEALLALPGVGRWT 93 (144)
T ss_pred HHHHHHHHHCCCCHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC---CCCCCHHHHHHHHCCCCCCHHH
T ss_conf 9999999828989999985999999999870897699999999999888986289---7886115699986088976999
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780788|r 448 KVALG 452 (526)
Q Consensus 448 ~~~L~ 452 (526)
+....
T Consensus 94 a~~~l 98 (144)
T pfam00730 94 AEAVL 98 (144)
T ss_pred HHHHH
T ss_conf 99999
No 153
>PRK07220 DNA topoisomerase I; Validated
Probab=86.85 E-value=1.6 Score=23.07 Aligned_cols=39 Identities=28% Similarity=0.314 Sum_probs=29.5
Q ss_pred HHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf 566407799989999999879847889653267752123
Q gi|254780788|r 435 EELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW 473 (526)
Q Consensus 435 e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~ 473 (526)
+.|.+++||+...+.+|...||.|+++|++.--++|..-
T Consensus 686 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 724 (740)
T PRK07220 686 KSIKDIEGVGKATAGKLEEAGITTVEALAEADPIELAKA 724 (740)
T ss_pred CHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH
T ss_conf 201215565889999999768875999851898999987
No 154
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=86.68 E-value=1.2 Score=24.12 Aligned_cols=57 Identities=21% Similarity=0.317 Sum_probs=46.5
Q ss_pred CHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHH----HHHHHCCE
Q ss_conf 7899999762866542489875678799998534221102544278999----99861674
Q gi|254780788|r 282 DSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL----ASQLTGWT 338 (526)
Q Consensus 282 d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrL----as~Ltg~~ 338 (526)
-..+|+..-|+-|.+..|.+--....+.|++--..-.+.|||+|.|++. ..+++|-+
T Consensus 27 kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~ 87 (233)
T COG0092 27 KIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE 87 (233)
T ss_pred HHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCCEECCCCCCHHHHHHHHHHHHCCC
T ss_conf 9999999998757845489996698439999957983157579710999999999984999
No 155
>pfam00313 CSD 'Cold-shock' DNA-binding domain.
Probab=86.48 E-value=1.7 Score=22.90 Aligned_cols=54 Identities=26% Similarity=0.414 Sum_probs=37.0
Q ss_pred EEEEEEECC--CCE--EEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 999998405--763--89995793587447874887--5115276699999761135870289
Q gi|254780788|r 142 ISGTVKRVE--YGN--VIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQV 198 (526)
Q Consensus 142 v~G~V~r~e--~~~--iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpqi 198 (526)
++|+|+.++ +|+ |.-+-|.-+-++-.+..-.. ..+++|++|.+- +...+||||-
T Consensus 1 ~tG~VK~f~~~kGfGFI~~~~~~~DiFvH~s~l~~~~~~~L~~G~~V~f~---v~~~~kG~~A 60 (66)
T pfam00313 1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQRVEFD---IVEGTKGPQA 60 (66)
T ss_pred CCEEEEEEECCCCEEEEEECCCCCEEEEEHHHHCCCCCCCCCCCCEEEEE---EEECCCCCEE
T ss_conf 94899999599996999978998469999268121478617999999999---9979998663
No 156
>PRK00468 hypothetical protein; Provisional
Probab=86.34 E-value=1.2 Score=23.96 Aligned_cols=49 Identities=22% Similarity=0.311 Sum_probs=35.1
Q ss_pred CHHHHHHHHCC--CCCCCEE-EECCCCCEEEEEECCCCCCCCCCCCHHHHHH
Q ss_conf 78999997628--6654248-9875678799998534221102544278999
Q gi|254780788|r 282 DSATFVINALR--PAIVTKV-VLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL 330 (526)
Q Consensus 282 d~~~fi~nAl~--PA~v~~v-~~de~~~~~~v~v~~~qls~AIGk~GqNvrL 330 (526)
+..+||+.+|- |-+|.=- .-++..-.+++.|.++++-..|||+|..++=
T Consensus 3 ~Lve~iv~~LVd~Pd~V~V~~~~~~~~~~~~l~V~~~D~GkVIGk~GrtakA 54 (75)
T PRK00468 3 ELVETIAKALVDNPDAVQVNEIEGEQSIILELKVAPEDMGKVIGKQGRIAKA 54 (75)
T ss_pred HHHHHHHHHHCCCCCEEEEEEEECCCEEEEEEEECHHHCCCEECCCCHHHHH
T ss_conf 8999999984899883899999679879999999935586466778714999
No 157
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=86.15 E-value=0.78 Score=25.36 Aligned_cols=39 Identities=26% Similarity=0.381 Sum_probs=34.2
Q ss_pred EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCC
Q ss_conf 999985342211025442789999986167457855220
Q gi|254780788|r 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346 (526)
Q Consensus 308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~ 346 (526)
..+.||.......||++|.|++--.+-||-+|.|.....
T Consensus 2 ~~i~ip~~~~g~vIG~~G~~I~~I~~~~~~~I~i~~~~~ 40 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS 40 (64)
T ss_pred EEEEECHHHCCEEECCCCCHHHHHHHHCCCEEEECCCCC
T ss_conf 899973665426799898134799997598999888899
No 158
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=86.06 E-value=1.8 Score=22.63 Aligned_cols=41 Identities=17% Similarity=0.211 Sum_probs=37.3
Q ss_pred HHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf 35664077999899999998798478896532677521231
Q gi|254780788|r 434 SEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS 474 (526)
Q Consensus 434 ~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~ 474 (526)
+..|+.|++++++.+..|.+.++.++++|.+++.+|+.++.
T Consensus 150 ~~pL~Qlp~~~~~~~~~l~~~~i~~l~~l~~~~~~e~~~ll 190 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGELL 190 (312)
T ss_pred CCCHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHH
T ss_conf 99012489999999999996699989999738999999997
No 159
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.82 E-value=1.1 Score=24.43 Aligned_cols=46 Identities=20% Similarity=0.275 Sum_probs=25.6
Q ss_pred HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf 9999976286654248987567879999853422110254427899
Q gi|254780788|r 284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR 329 (526)
Q Consensus 284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvr 329 (526)
.+|+..-|+-|-+++|.+.-......|++--..--+.|||+|++++
T Consensus 16 reyl~k~l~~Ag~s~ieIeRtp~~~~I~I~t~rPG~VIGr~G~~I~ 61 (85)
T cd02411 16 DEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIR 61 (85)
T ss_pred HHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCCHHHH
T ss_conf 9999998886786559999889966999997899847778866599
No 160
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal; InterPro: IPR010212 This entry represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains and is most closely related to the central region bacterial NusA, a transcription termination factor named for its interaction with phage lambda protein N in Escherichia coli. The proteins required for antitermination by N include NusA, NusB, NusE (ribosomal protein S10), and NusG. This system, on the whole, appears not to be present in the archaea..
Probab=85.71 E-value=0.73 Score=25.60 Aligned_cols=96 Identities=32% Similarity=0.473 Sum_probs=78.7
Q ss_pred CCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHH--HCCCCCCCEEEECC--CCCEEEEEECCCCCCCCCC
Q ss_conf 9881276554886217889986277826799559878999997--62866542489875--6787999985342211025
Q gi|254780788|r 247 SIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVIN--ALRPAIVTKVVLDE--DVGRIEVIVPKEQLSLAIG 322 (526)
Q Consensus 247 ~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~n--Al~PA~v~~v~~de--~~~~~~v~v~~~qls~AIG 322 (526)
.....|...|..|..+... ..+.+-.+.++.++.++..|+.| .++|+.+..+.+.+ ......+.+.......+||
T Consensus 40 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 (143)
T TIGR01952 40 KAGEMGAAIGKGGLNVKRL-EELIGKSIELIEYSEDLEEFVANILALAPAAVKNVTVSESNGSKVAYVEVSPRDKGIAIG 118 (143)
T ss_pred CCCCCCCCCCCCCCCHHHH-HHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEECCCCCCEEEECCCCCCCCCCCC
T ss_conf 2222111113332100001-110122000011211001222100000000000000001234300110012111110012
Q ss_pred CCHHHHHHHHHHHCCEEEEEE
Q ss_conf 442789999986167457855
Q gi|254780788|r 323 RRGQNVRLASQLTGWTIDIIT 343 (526)
Q Consensus 323 k~GqNvrLas~Ltg~~idi~~ 343 (526)
+.|.|...+..+.....++..
T Consensus 119 ~~~~~~~~~~~~~~~~~~~~~ 139 (143)
T TIGR01952 119 KGGKNIERAKELAKRHLDIDD 139 (143)
T ss_pred CCCCCCHHHHHHHHHCCCCCC
T ss_conf 343210012222210012222
No 161
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=84.71 E-value=3 Score=21.10 Aligned_cols=37 Identities=8% Similarity=0.083 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHCCCCCCCE-EEEECCCCCEEEEEEEEE
Q ss_conf 99999999996136874535-999749988399999988
Q gi|254780788|r 30 VMADSIQKAARSLYGTMSDI-RVEINPETGDISLFRLLE 67 (526)
Q Consensus 30 aie~Al~~a~kK~~~~~~~i-~V~iD~~tG~i~i~~~~~ 67 (526)
.-+.|... .++-...++.+ .+.+|.+||++-++..+-
T Consensus 73 ~~e~A~~~-I~eivP~ea~i~~i~Fd~~tGEViIea~KP 110 (637)
T COG1782 73 PPEEARKI-ILEIVPEEAGITDIYFDDDTGEVIIEAKKP 110 (637)
T ss_pred CHHHHHHH-HHHHCCCCCCCEEEEECCCCCEEEEEECCC
T ss_conf 98999999-997486213703678618874499995589
No 162
>PRK00106 hypothetical protein; Provisional
Probab=84.52 E-value=3 Score=21.05 Aligned_cols=151 Identities=21% Similarity=0.282 Sum_probs=90.4
Q ss_pred HHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCC-CCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCCCCCCCC
Q ss_conf 8999997628665424898756787999985342-211025442789999986167457855220011010012210001
Q gi|254780788|r 283 SATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQ-LSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQF 361 (526)
Q Consensus 283 ~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~q-ls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~~~~~~~ 361 (526)
....+..|++-.-..-+ .| ...-.|-.|++. --.-|||.|.|+|---.+||-.|=|-...+.
T Consensus 205 Ar~Ii~~AiqR~a~d~~--~E-~tvsvV~Lp~demKGRIIGREGRNIRa~E~~TGVDlIIDDTPe~-------------- 267 (535)
T PRK00106 205 AKDLLAQAMQRLAGEYV--TE-QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEV-------------- 267 (535)
T ss_pred HHHHHHHHHHHCCCCCC--CH-HCEEEEECCCHHHHCCCCCCCCCCHHHHHHHHCCEEEECCCCCE--------------
T ss_conf 99999999975163210--12-10356855977875520087754199999975964898599985--------------
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHH-HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCC
Q ss_conf 11225888467888877321114-77750588887765305889999999999999999999989877542843566407
Q gi|254780788|r 362 FMQAINVDEIIAHLLVAEGFADV-EELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSI 440 (526)
Q Consensus 362 f~e~LdVDE~iA~~LV~eGf~Si-EeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l 440 (526)
.+-.||+.+ .+||....+.|..=.-+.+..++++..+++.-+...-.+..+.. -.+ +.+
T Consensus 268 --------------V~lS~FDpvRREiAr~aLe~Li~DGRIhPaRIEe~v~k~~~e~~~~i~e~Ge~a-----~~e-lgi 327 (535)
T PRK00106 268 --------------VVLSGFDPIRREIARMTLESLIKDGRIHPARIEELVEKNRLEMDNRIREYGEAA-----AYE-IGA 327 (535)
T ss_pred --------------EEEECCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHH-CCC
T ss_conf --------------788679878999999999999981892888899999999999999999999999-----998-099
Q ss_pred CCCCHHHHHHHHHCCCCC------------HHHHHHCCHHHH
Q ss_conf 799989999999879847------------889653267752
Q gi|254780788|r 441 PGIDSKIKVALGENGIKT------------MEDLAGCSVDDL 470 (526)
Q Consensus 441 ~gl~~~~~~~L~e~gIkt------------leDlAels~dEL 470 (526)
.||.++++-.|+.=...| +-.||++-..||
T Consensus 328 ~~lhpelik~lGrLkyRtSygQNvL~HS~Eva~lag~mA~El 369 (535)
T PRK00106 328 PNLHPDLIKIMGRLQFRTSYGQNVLRHSVEVGKLAGILAGEL 369 (535)
T ss_pred CCCCHHHHHHHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999978999987600010240589999999999999999983
No 163
>pfam08292 RNA_pol_Rbc25 RNA polymerase III subunit Rpc25. Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III.
Probab=84.03 E-value=2.8 Score=21.32 Aligned_cols=55 Identities=25% Similarity=0.286 Sum_probs=41.8
Q ss_pred HCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHHCCCCCC-------------------CCCCCEEEEEEEEECC
Q ss_conf 208389999984057638999579-358744787488751-------------------1527669999976113
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISREN-------------------LRPGDRVKSYIYDVRR 191 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e~ip~E~-------------------~~~Gdrika~i~~V~~ 191 (526)
-+|||++|+|+.-++..+.|.||= -+-++|...+-..-. |..|+.||+-|.++.-
T Consensus 2 F~gEIl~G~I~s~~~eGi~vslgFFdDI~IP~~~L~~ps~fd~~eq~WvW~~d~~~~l~~d~~e~IRFRV~~~~f 76 (120)
T pfam08292 2 FVGEIITGKIKSSTAEGIKVSLGFFDDIFIPPDLLPEPSEFDEEEQAWVWEYDEETELYFDVGEEIRFRVESEIF 76 (120)
T ss_pred CCCCEEEEEEEECCCCCEEEEEECCCEEEECHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCCEEEEEEEEEEE
T ss_conf 876589999940587847997102420689989978866307334679924898640103689969999988798
No 164
>PRK02821 hypothetical protein; Provisional
Probab=83.98 E-value=2.1 Score=22.24 Aligned_cols=49 Identities=24% Similarity=0.361 Sum_probs=35.0
Q ss_pred CHHHHHHHHCC--CCCCCE-EEECCCCCEEEEEECCCCCCCCCCCCHHHHHH
Q ss_conf 78999997628--665424-89875678799998534221102544278999
Q gi|254780788|r 282 DSATFVINALR--PAIVTK-VVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL 330 (526)
Q Consensus 282 d~~~fi~nAl~--PA~v~~-v~~de~~~~~~v~v~~~qls~AIGk~GqNvrL 330 (526)
+..+|++.+|- |-.|.= ..-++.....++-|.++++-..|||+|..++-
T Consensus 4 elve~ivk~LVd~Pd~V~V~~~e~~~~~~~el~V~~eD~GkVIGk~Grta~A 55 (77)
T PRK02821 4 DAVEHLVRGIVDNPDDVRVDSVTNRRGRTLEVRVHPDDLGKVIGRGGRTATA 55 (77)
T ss_pred HHHHHHHHHCCCCCCEEEEEEEECCCEEEEEEEECHHHCCCEECCCCHHHHH
T ss_conf 9999999874799882799999789827999999934474454778677999
No 165
>LOAD_cold consensus
Probab=83.88 E-value=3.2 Score=20.86 Aligned_cols=54 Identities=26% Similarity=0.429 Sum_probs=38.1
Q ss_pred EEEEEEEECC--CC--EEEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 8999998405--76--389995793587447874887--511527669999976113587028
Q gi|254780788|r 141 IISGTVKRVE--YG--NVIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQ 197 (526)
Q Consensus 141 iv~G~V~r~e--~~--~iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpq 197 (526)
+++|+|+..+ +| +|..|-|+-+-++-.+..-.. ..++.|++|.+-+.+ ..||||
T Consensus 1 M~~G~VK~f~~~kGfGFI~~~~g~~DvFvH~s~l~~~~~~~l~~G~~V~f~~~~---~~kG~~ 60 (67)
T LOAD_cold 1 MVKGTVKWFNVKKGFGFITPEDGGEDVFVHQSAIQGDGFRSLTEGQEVEFDIVE---GPKGPQ 60 (67)
T ss_pred CCCEEEEEEECCCCCEEEEECCCCCEEEEEHHHHCCCCCCCCCCCCEEEEEEEE---CCCCCE
T ss_conf 998699999899994788757998218999478140478647999999999998---999967
No 166
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=83.82 E-value=2.8 Score=21.31 Aligned_cols=87 Identities=25% Similarity=0.295 Sum_probs=62.6
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHCCCCCCHHHH-----HHH
Q ss_conf 7321114777505888877653058899999999999999999-9998987754284356640779998999-----999
Q gi|254780788|r 378 AEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGI-DITLQKKIRELGVSEELCSIPGIDSKIK-----VAL 451 (526)
Q Consensus 378 ~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~-~~~~~e~~~e~~~~e~L~~l~gl~~~~~-----~~L 451 (526)
-..|-|.|.++.++.+.|... |+..-.++-|+.-|+.+...+ .............-+.|+.+.|+.+-.+ ..|
T Consensus 141 ~~~fptpe~l~~~~~~~l~~~-g~s~~Ka~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~l 219 (285)
T COG0122 141 YHSFPTPEQLAAADEEALRRC-GLSGRKAEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGL 219 (285)
T ss_pred CCCCCCHHHHHHCCHHHHHHH-CCCHHHHHHHHHHHHHHHCCCCCHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHC
T ss_conf 667989999984799999883-7857789999999999985996567662588999999987378867999999999816
Q ss_pred HHCCCCCHHHHHHC
Q ss_conf 98798478896532
Q gi|254780788|r 452 GENGIKTMEDLAGC 465 (526)
Q Consensus 452 ~e~gIktleDlAel 465 (526)
+..++-..+|++=.
T Consensus 220 gr~dvfP~~D~~lr 233 (285)
T COG0122 220 GRPDVFPADDLGLR 233 (285)
T ss_pred CCCCCCCCHHHHHH
T ss_conf 88986771559999
No 167
>PRK07758 hypothetical protein; Provisional
Probab=83.75 E-value=1.9 Score=22.49 Aligned_cols=40 Identities=23% Similarity=0.303 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 7888877321114777505888877653058899999999
Q gi|254780788|r 372 IAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 372 iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
--..|+++|++|+++++..+..+|+++-||.......|++
T Consensus 46 ARRAL~~~GI~TLedLskytEkELL~LHGmGP~ai~~L~~ 85 (95)
T PRK07758 46 ARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRK 85 (95)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 8999998281149999885199999984868888999999
No 168
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=83.48 E-value=2.6 Score=21.60 Aligned_cols=55 Identities=18% Similarity=0.279 Sum_probs=45.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 00011122588846788887732111477750588887765305889999999999
Q gi|254780788|r 358 RTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRA 413 (526)
Q Consensus 358 ~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA 413 (526)
.+-.+....-+...+++.||.. |.++..+..|+.++|.+++|+.+-.|..+++.-
T Consensus 285 GYR~L~kiprlp~~vie~lV~~-Fg~L~~ll~As~eeL~~VeGIGe~RAr~IregL 339 (352)
T PRK13482 285 GYRILAKIPRLPSAVIENLVKH-FGTLQGLLEASIEDLDDVEGIGEVRARAIREGL 339 (352)
T ss_pred HHHHHCCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 5888605999999999999998-527999986899888656796799999999999
No 169
>TIGR00448 rpoE DNA-directed RNA polymerase; InterPro: IPR004519 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to Escherichia coli RpoE.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription, 0005634 nucleus.
Probab=83.26 E-value=2.8 Score=21.34 Aligned_cols=74 Identities=31% Similarity=0.519 Sum_probs=54.5
Q ss_pred HHHHHCCCEEEEEEEECCCCEEEEE-ECCCEEEEEHH-------------HC-CC---CC---CCCCCCEEEEEEEEEC-
Q ss_conf 9985208389999984057638999-57935874478-------------74-88---75---1152766999997611-
Q gi|254780788|r 133 EFKDKVGEIISGTVKRVEYGNVIVD-LGNSDGVIRRD-------------ET-IS---RE---NLRPGDRVKSYIYDVR- 190 (526)
Q Consensus 133 ef~~r~Geiv~G~V~r~e~~~iiVd-lg~~ea~Lp~~-------------e~-ip---~E---~~~~Gdrika~i~~V~- 190 (526)
-|+...+|||+|-|..+.--..+|- ||-.++++-.+ .. |- +| .|..||.|||=|....
T Consensus 76 ~FkP~l~EiVeGev~~~~efG~fV~LlGp~D~l~h~sq~~ddy~~YdPk~~~liGPmD~Etk~~ld~gd~vRaRIv~~sl 155 (184)
T TIGR00448 76 VFKPELGEIVEGEVIEIVEFGAFVSLLGPFDGLLHVSQVLDDYVVYDPKESALIGPMDKETKKVLDVGDKVRARIVALSL 155 (184)
T ss_pred EECCCCEEEEEEEEEEEEECCCEEEEECCCCCEEEEEEEEECCEEECCCCCCEECCCCHHCCCEEECCCEEEEEEEEEEE
T ss_conf 96035216786589989852742675223132344100113563662656604567401217351016756678888764
Q ss_pred --CCC-CEEEEEEECCCHH
Q ss_conf --358-7028987159889
Q gi|254780788|r 191 --REQ-RGPQVLLSRTHPQ 206 (526)
Q Consensus 191 --~~~-rgpqi~lSRt~p~ 206 (526)
+.+ +|..+-|..-.|-
T Consensus 156 k~~~pk~~~k~~LtmRqp~ 174 (184)
T TIGR00448 156 KDRRPKEGSKIGLTMRQPL 174 (184)
T ss_pred CCCCCCCCCEEEEECCCCC
T ss_conf 0413788851100115731
No 170
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=83.26 E-value=2.4 Score=21.75 Aligned_cols=55 Identities=22% Similarity=0.283 Sum_probs=44.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 11225888467888877321114777505888877653058899999999999999
Q gi|254780788|r 362 FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL 417 (526)
Q Consensus 362 f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L 417 (526)
+..-.+|....|.-|.. -|.|++.+..++.++|..++|++++.|.+|+.--....
T Consensus 184 l~s~pgig~~~a~~ll~-~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~~ 238 (254)
T COG1948 184 LESIPGIGPKLAERLLK-KFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTEY 238 (254)
T ss_pred HHCCCCCCHHHHHHHHH-HHCCHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHCHH
T ss_conf 97089964899999999-85688877655999997744846889999999983444
No 171
>PRK10354 major cold shock protein; Provisional
Probab=83.08 E-value=3.4 Score=20.63 Aligned_cols=56 Identities=21% Similarity=0.343 Sum_probs=38.4
Q ss_pred CEEEEEEEECC--CC--EEEEEECCCEEEEEHHHCC--CCCCCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 38999998405--76--3899957935874478748--875115276699999761135870289
Q gi|254780788|r 140 EIISGTVKRVE--YG--NVIVDLGNSDGVIRRDETI--SRENLRPGDRVKSYIYDVRREQRGPQV 198 (526)
Q Consensus 140 eiv~G~V~r~e--~~--~iiVdlg~~ea~Lp~~e~i--p~E~~~~Gdrika~i~~V~~~~rgpqi 198 (526)
+-++|+|+-++ +| +|.-|-|.-+-++-.+..- .-..+..|+||.+ ++....||||-
T Consensus 3 ~~~tG~VKwFn~~KGyGFI~~d~g~~DvFvH~s~l~~~g~~~L~~Gq~V~f---~~~~g~kG~~A 64 (70)
T PRK10354 3 GKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSF---TIESGAKGPAA 64 (70)
T ss_pred CCEEEEEEEEECCCCEEEEECCCCCCEEEEEHHHHCCCCCCCCCCCCEEEE---EEEECCCCCEE
T ss_conf 750799998709998599842799842999858917048972599999999---99979998620
No 172
>TIGR00596 rad1 DNA repair protein (rad1); InterPro: IPR006167 All proteins in this family, for which functions are known, are components in a multiprotein endonuclease complex, usually made up of Rad1 and Rad10 homologues. This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologues of these genes, but the function of the Archaeal proteins is not known, so are not included in this family.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity, 0006281 DNA repair.
Probab=82.94 E-value=1.3 Score=23.73 Aligned_cols=44 Identities=27% Similarity=0.379 Sum_probs=39.5
Q ss_pred CCHHHH--HHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf 284356--64077999899999998798478896532677521231
Q gi|254780788|r 431 LGVSEE--LCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS 474 (526)
Q Consensus 431 ~~~~e~--L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~ 474 (526)
.++.+= |+.+||++.....-|-.+|++++..|+.+|.+||-++.
T Consensus 875 ~~~~dfkrLl~~PGV~~kN~rnl~~~G~k~~~el~~~S~~El~eL~ 920 (939)
T TIGR00596 875 SGPQDFKRLLKLPGVTKKNIRNLLKKGVKSIRELAKLSQEELEELI 920 (939)
T ss_pred CCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 5158999855789856023455554315559999998799999750
No 173
>KOG0950 consensus
Probab=82.93 E-value=2.9 Score=21.24 Aligned_cols=38 Identities=16% Similarity=0.297 Sum_probs=27.7
Q ss_pred HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf 66407799989999999879847889653267752123
Q gi|254780788|r 436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW 473 (526)
Q Consensus 436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~ 473 (526)
+|+.++++..+-+.+|-..|.+|+-++|.-...+|.-.
T Consensus 895 ~Lmrv~~~~~~RAr~lf~Agf~tv~~iA~a~p~klvke 932 (1008)
T KOG0950 895 PLMRVPDVKAERARQLFKAGFTSVGSIANATPEKLVKE 932 (1008)
T ss_pred HHHCCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHH
T ss_conf 45257436789999999844533588855882778987
No 174
>PRK01064 hypothetical protein; Provisional
Probab=82.83 E-value=2.2 Score=22.06 Aligned_cols=48 Identities=21% Similarity=0.364 Sum_probs=34.6
Q ss_pred CHHHHHHHHCC--CCCCCE-EEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf 78999997628--665424-8987567879999853422110254427899
Q gi|254780788|r 282 DSATFVINALR--PAIVTK-VVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR 329 (526)
Q Consensus 282 d~~~fi~nAl~--PA~v~~-v~~de~~~~~~v~v~~~qls~AIGk~GqNvr 329 (526)
+.-+||+.+|- |-+|.= ..-.+..-...+-|.++++-..|||+|.+++
T Consensus 3 eLve~ivk~LVd~Pd~V~V~~~~~~~~~~~~l~V~~~D~GkVIGk~Grtak 53 (78)
T PRK01064 3 EFLAYIVKNLVDRPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIK 53 (78)
T ss_pred HHHHHHHHHHCCCCCEEEEEEEECCCEEEEEEEECCCCCCCEECCCCHHHH
T ss_conf 899999998579987389999947987999999990018558788874699
No 175
>PRK02794 DNA polymerase IV; Provisional
Probab=82.49 E-value=3.2 Score=20.92 Aligned_cols=12 Identities=17% Similarity=0.116 Sum_probs=5.9
Q ss_pred ECHHHHHHHCCC
Q ss_conf 348999862889
Q gi|254780788|r 79 ISLKVARDRDPS 90 (526)
Q Consensus 79 I~l~~A~~~~~~ 90 (526)
+++.+|+++-|+
T Consensus 89 mp~~~A~~lcP~ 100 (417)
T PRK02794 89 MPMFKALKLCPD 100 (417)
T ss_pred CCHHHHHHHCCC
T ss_conf 929999987899
No 176
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=81.94 E-value=1.6 Score=23.13 Aligned_cols=128 Identities=19% Similarity=0.287 Sum_probs=80.3
Q ss_pred ECCCHHHHHHHHHHHHHH--HHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEE
Q ss_conf 159889999999976677--755808785663167750349999408998812765548862178899862778267995
Q gi|254780788|r 201 SRTHPQFMVKLFHMEVPE--IYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVV 278 (526)
Q Consensus 201 SRt~p~~l~~Lf~~EVPE--I~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ 278 (526)
|-+..+|=-.||-.++|. -.++.==|.||| ||- |--+.++.+| +-.|.++=++=|=|=+|=..|
T Consensus 207 ~~sT~DmDDALy~~~l~~nstq~~l~L~vAIA-DPT-----AYI~~~s~ld--------~~A~~R~FTnYLPGfNiPMLP 272 (664)
T TIGR02062 207 SESTKDMDDALYIEELPNNSTQGDLKLIVAIA-DPT-----AYIAEGSKLD--------KEAKKRGFTNYLPGFNIPMLP 272 (664)
T ss_pred CCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEE-CCC-----CCCCCCCHHH--------HHHHHHCCCCCCCCCCCCCCC
T ss_conf 88864423589998600555578837999971-884-----3268865789--------999870872468778898887
Q ss_pred C--CCCHHHHHHHHCCCCCCCEEEECCCCC-----EEEE-------EECCCCCCCCCCCC------------HHHHHHHH
Q ss_conf 5--987899999762866542489875678-----7999-------98534221102544------------27899999
Q gi|254780788|r 279 W--SPDSATFVINALRPAIVTKVVLDEDVG-----RIEV-------IVPKEQLSLAIGRR------------GQNVRLAS 332 (526)
Q Consensus 279 w--s~d~~~fi~nAl~PA~v~~v~~de~~~-----~~~v-------~v~~~qls~AIGk~------------GqNvrLas 332 (526)
= |||.--+..|-.=||=+..|.++-+.. .+.. -..=|+.|==+=++ -|-|||-.
T Consensus 273 R~LSdeLCSL~~ne~RP~L~C~it~~~dG~I~~~i~Ff~A~i~SkAkL~Yd~VSDwLE~~~~e~WqPE~~~ia~qv~~L~ 352 (664)
T TIGR02062 273 RELSDELCSLIANEVRPVLACSITISKDGNITDKIEFFAAYIKSKAKLVYDKVSDWLEKASSEAWQPESEEIAQQVRLLH 352 (664)
T ss_pred HHHHHHHHCCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEEEEEEEEECCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 42368872464356785789999970684122586179988862345401211123205878667887678999999999
Q ss_pred HHHCCEEEEE
Q ss_conf 8616745785
Q gi|254780788|r 333 QLTGWTIDII 342 (526)
Q Consensus 333 ~Ltg~~idi~ 342 (526)
++|.-+|+=.
T Consensus 353 ~~~~~R~~WR 362 (664)
T TIGR02062 353 QFCQARIEWR 362 (664)
T ss_pred HHHHHHHHHH
T ss_conf 9988764132
No 177
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit; InterPro: IPR011773 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins , .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription DNA-dependent.
Probab=80.95 E-value=2 Score=22.34 Aligned_cols=31 Identities=26% Similarity=0.359 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf 9989999999879847889653267752123
Q gi|254780788|r 443 IDSKIKVALGENGIKTMEDLAGCSVDDLLGW 473 (526)
Q Consensus 443 l~~~~~~~L~e~gIktleDlAels~dEL~~~ 473 (526)
||-.-..+|...||.|+-||..+|-.||+.+
T Consensus 268 LSVRs~NCLk~~gI~t~geL~~~~e~eLl~i 298 (324)
T TIGR02027 268 LSVRSYNCLKRAGIHTLGELVSKSEEELLKI 298 (324)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC
T ss_conf 5489886464603541788886038988417
No 178
>pfam04994 TfoX_C TfoX C-terminal domain. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found associated with pfam00383 in a cytidine and deoxycytidylate deaminase family protein from Neisseria meningitidis serogroup B. It is also found as an isolated domain in some proteins suggesting this is an autonomous domain.
Probab=80.88 E-value=2.1 Score=22.14 Aligned_cols=35 Identities=29% Similarity=0.433 Sum_probs=31.0
Q ss_pred HHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHC
Q ss_conf 64077999899999998798478896532677521
Q gi|254780788|r 437 LCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLL 471 (526)
Q Consensus 437 L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~ 471 (526)
|.+|+.|++.+...|.+-||.|.+||-.+...+-.
T Consensus 1 l~dLpNlg~~~er~L~~vGI~t~~~L~~~Ga~~ay 35 (77)
T pfam04994 1 LKDLPNLGLKLERMLKKAGIHTVEDLRELGAVEAY 35 (77)
T ss_pred CCCCCCCCHHHHHHHHHCCCCCHHHHHHHCHHHHH
T ss_conf 98788989999999999499989999981899999
No 179
>PRK01216 DNA polymerase IV; Validated
Probab=80.74 E-value=3.4 Score=20.73 Aligned_cols=48 Identities=17% Similarity=0.270 Sum_probs=32.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 22588846788887732111477750588887765305889999999999
Q gi|254780788|r 364 QAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRA 413 (526)
Q Consensus 364 e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA 413 (526)
+-.+|....++.|-..|+.|+.+++..+.+.|..+.| .-....|...|
T Consensus 182 ~i~GIG~~t~~~L~~~GI~ti~dL~~~~~~~L~~~fG--~~~~~~l~~~a 229 (351)
T PRK01216 182 DVPGIGKVLSERLNELGINKLRDILSKSFNKLKSIIG--EAKANYLYSLA 229 (351)
T ss_pred EECCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHC--HHHHHHHHHHH
T ss_conf 8548579999999985996899975299999999977--79999999983
No 180
>PRK03103 DNA polymerase IV; Reviewed
Probab=80.61 E-value=3.9 Score=20.23 Aligned_cols=34 Identities=21% Similarity=0.294 Sum_probs=14.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHC
Q ss_conf 8884678888773211147775058888776530
Q gi|254780788|r 367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEG 400 (526)
Q Consensus 367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeG 400 (526)
+|...++..|-..|+.|+.+++.++.+.|....|
T Consensus 189 GIG~~~~~kL~~~GI~t~~dL~~~~~~~l~~~fG 222 (410)
T PRK03103 189 GVGRRMEHHLRRMGISTIGQLAQTPLERLKKRWG 222 (410)
T ss_pred CCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHC
T ss_conf 8788999999985897499986599999999839
No 181
>PRK02406 DNA polymerase IV; Validated
Probab=80.61 E-value=3.6 Score=20.51 Aligned_cols=49 Identities=20% Similarity=0.215 Sum_probs=37.4
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 2258884678888773211147775058888776530588999999999999
Q gi|254780788|r 364 QAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRARE 415 (526)
Q Consensus 364 e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~ 415 (526)
+--+|....++.|-..|+.|+.+++..+...|....| .....|...|+-
T Consensus 184 ~l~GIG~~~~~~L~~~GI~ti~DL~~~~~~~L~~~fG---~~g~~l~~~a~G 232 (355)
T PRK02406 184 KIPGVGKVTAEKLHALGIRTCADLQKWDLATLLRRFG---KFGRRLYERARG 232 (355)
T ss_pred CCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHC---HHHHHHHHHHCC
T ss_conf 0588588999999982981799976099999999979---899999999659
No 182
>KOG1676 consensus
Probab=80.55 E-value=2 Score=22.33 Aligned_cols=105 Identities=22% Similarity=0.324 Sum_probs=70.9
Q ss_pred CCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEE-----------
Q ss_conf 167750349999408998812765548862178899862778267995598789999976286654248-----------
Q gi|254780788|r 231 RDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV----------- 299 (526)
Q Consensus 231 R~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v----------- 299 (526)
+.+|--+.+-|.--. --||+.+|--|.-|+.+.+|- |-||-+.+=++ | ..++-||.|...
T Consensus 224 ~~~g~~~~~~V~VPr---~~VG~IIGkgGE~IKklq~et-G~KIQfkpDd~-p----~speR~~~IiG~~d~ie~Aa~lI 294 (600)
T KOG1676 224 VRGGGSATREVKVPR---SKVGIIIGKGGEMIKKLQNET-GAKIQFKPDDD-P----SSPERPAQIIGTVDQIEHAAELI 294 (600)
T ss_pred CCCCCCCEEEEECCC---CCEEEEEECCCHHHHHHHHCC-CCEEEEECCCC-C----CCCCCEEEEECCHHHHHHHHHHH
T ss_conf 676654136885456---523468704716788876335-74268623888-8----87544256526799999999999
Q ss_pred --EEC--CCCC-------------EEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEEC
Q ss_conf --987--5678-------------79999853422110254427899999861674578552
Q gi|254780788|r 300 --VLD--EDVG-------------RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITE 344 (526)
Q Consensus 300 --~~d--e~~~-------------~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~ 344 (526)
+|. +... .|...||.+..-|.|||+|.|+|=-.+=+|-++..--.
T Consensus 295 ~eii~~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~ 356 (600)
T KOG1676 295 NEIIAEAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ 356 (600)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCC
T ss_conf 99999986047777677875410158896451000445478863001110367751365678
No 183
>PRK03352 DNA polymerase IV; Validated
Probab=80.33 E-value=4.3 Score=19.96 Aligned_cols=34 Identities=26% Similarity=0.298 Sum_probs=18.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHC
Q ss_conf 8884678888773211147775058888776530
Q gi|254780788|r 367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEG 400 (526)
Q Consensus 367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeG 400 (526)
+|....++.|-..|+.|+.+++.++...|....|
T Consensus 184 GIG~~~~~kL~~~GI~Ti~DL~~~~~~~L~~~fG 217 (345)
T PRK03352 184 GVGPKTAKKLAALGITTVADLAATDPAVLTATFG 217 (345)
T ss_pred CCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHC
T ss_conf 8289999999975997199986699999999978
No 184
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=79.89 E-value=3.6 Score=20.52 Aligned_cols=50 Identities=20% Similarity=0.264 Sum_probs=33.8
Q ss_pred HHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHH
Q ss_conf 89999976286654248987567879999853422110254427899999
Q gi|254780788|r 283 SATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLAS 332 (526)
Q Consensus 283 ~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas 332 (526)
..+|+...|+-|-+++|.+.-......|++--..--+.|||+|++++--.
T Consensus 21 ire~l~k~L~~AG~s~ieIert~~~~~I~I~tarPG~VIGrkG~~I~~L~ 70 (220)
T PTZ00084 21 LNEFLSRELADDGYAGVELRVTPVRTEIIIRATKTREVLGEKGRRIRELT 70 (220)
T ss_pred HHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCCHHHHHHH
T ss_conf 99999988886787759999889847999996898558868854699999
No 185
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=79.65 E-value=3.9 Score=20.21 Aligned_cols=58 Identities=31% Similarity=0.455 Sum_probs=44.6
Q ss_pred HCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf 20838999998405763899957-93587447874887511527669999976113587
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRPGDRVKSYIYDVRREQR 194 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~r 194 (526)
+.|++-.|+|.|++.-.++|+|+ .+-|.|-++++..-..|.+||.+-+-+..|+...+
T Consensus 121 e~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~~~~~vgdeiiV~v~~vr~~~g 179 (715)
T COG1107 121 EAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDVRPEKG 179 (715)
T ss_pred CCCEEEECCCCCHHHHCCEEECCHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCC
T ss_conf 46405403102143406524337354334440124788777878748998421577777
No 186
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=79.39 E-value=4.3 Score=19.95 Aligned_cols=44 Identities=20% Similarity=0.291 Sum_probs=34.3
Q ss_pred CCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCCCCCCCCCE
Q ss_conf 08389999984057638999579358744787488751152766
Q gi|254780788|r 138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDR 181 (526)
Q Consensus 138 ~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E~~~~Gdr 181 (526)
.||++-|+|.++.+-.++.+.|....+..+..+-|.=.|.++..
T Consensus 1 KGEVvDavVt~Vnk~G~Fa~~GPl~~fvS~~~ip~d~~f~~~~~ 44 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNAS 44 (88)
T ss_pred CCCEEEEEEEEECCEEEEEEECCEEEEEECCCCCCCEEECCCCC
T ss_conf 99579999999834789998047589999111899709989999
No 187
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.17 E-value=2.8 Score=21.31 Aligned_cols=44 Identities=23% Similarity=0.469 Sum_probs=31.9
Q ss_pred CEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEE
Q ss_conf 24898756787999985342211025442789999986167457
Q gi|254780788|r 297 TKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTID 340 (526)
Q Consensus 297 ~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~id 340 (526)
.+|.+.++...+.+-+.-+++++.|||+|+...=--.|+.--++
T Consensus 15 ~~v~~~~~~~~~~~~i~g~~~~~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 15 ADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEEECCEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 79999997998999994498774166898647999999999997
No 188
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=79.05 E-value=2.4 Score=21.75 Aligned_cols=35 Identities=26% Similarity=0.416 Sum_probs=31.0
Q ss_pred EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
Q ss_conf 99998534221102544278999998616745785
Q gi|254780788|r 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII 342 (526)
Q Consensus 308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~ 342 (526)
..+-+|.+.....||++|.|+|=-..-||-+|||-
T Consensus 4 ~~~~I~~dkIg~vIGpGGk~Ik~I~e~tg~~I~I~ 38 (61)
T cd02393 4 ETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIE 38 (61)
T ss_pred EEEEECHHHHHHHCCCCCHHHHHHHHHHCCEEEEC
T ss_conf 99996989987644886089999999889889983
No 189
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=78.37 E-value=2.2 Score=22.09 Aligned_cols=44 Identities=25% Similarity=0.472 Sum_probs=33.5
Q ss_pred CCHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf 28435664077999899999998798478896532677521231
Q gi|254780788|r 431 LGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS 474 (526)
Q Consensus 431 ~~~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~ 474 (526)
.+-.+||..+.|+.+.+..+|.+.||.|.+.+|.++-+++..+.
T Consensus 149 ~g~aDDLk~I~GIGP~~e~~Ln~~GI~~F~QIA~~t~~dia~id 192 (216)
T PRK12278 149 AGEADDLTKITGVGPALAKKLNEAGITTFAQIAALTDEDIAAID 192 (216)
T ss_pred CCCCCCCCEECCCCHHHHHHHHHHCCCHHHHHHCCCHHHHHHHH
T ss_conf 78996543602658899999998187239998559999999987
No 190
>cd00424 Pol_Y Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=78.27 E-value=3.8 Score=20.30 Aligned_cols=38 Identities=37% Similarity=0.388 Sum_probs=28.9
Q ss_pred HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf 66407799989999999879847889653267752123
Q gi|254780788|r 436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW 473 (526)
Q Consensus 436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~ 473 (526)
.+.+++|+...+...|.+.||.|.-||+.+..++|...
T Consensus 174 pv~~l~GIG~~~~~~L~~~gi~ti~dl~~~~~~~l~~~ 211 (341)
T cd00424 174 PLSDIPGIGSVTASRLEALGIIRKCDLLALQPDQLLAS 211 (341)
T ss_pred CHHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH
T ss_conf 87887487889999999849935999871899999999
No 191
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=78.16 E-value=4.9 Score=19.49 Aligned_cols=70 Identities=24% Similarity=0.343 Sum_probs=30.9
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHCCCCCCHHHHHHHH-HCCCCCHHHHHHCCH
Q ss_conf 87765305889999999999999999999989877542--843566407799989999999-879847889653267
Q gi|254780788|r 394 EIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIREL--GVSEELCSIPGIDSKIKVALG-ENGIKTMEDLAGCSV 467 (526)
Q Consensus 394 eL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~--~~~e~L~~l~gl~~~~~~~L~-e~gIktleDlAels~ 467 (526)
-+..++|+..-+|..|..- +.+-....-+.++.. ..-.+|+.++|+.+.-+..|- +-||+++++|-+-+-
T Consensus 54 ~~t~l~gIGk~ia~~I~e~----l~tG~~~~le~lk~~~P~gl~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~ 126 (326)
T COG1796 54 RLTELPGIGKGIAEKISEY----LDTGEVKKLEALKKEVPEGLEPLLKVPGLGPKKIVSLYKELGIKDLEELQEALE 126 (326)
T ss_pred CCCCCCCCCHHHHHHHHHH----HHCCCCHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 1477887568899999999----972860789999885795558786077989288999999978664999999998
No 192
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=78.04 E-value=2 Score=22.45 Aligned_cols=37 Identities=32% Similarity=0.464 Sum_probs=32.0
Q ss_pred EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEEC
Q ss_conf 9999853422110254427899999861674578552
Q gi|254780788|r 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITE 344 (526)
Q Consensus 308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~ 344 (526)
..+-||....+.-||++|.|++---.-||-+|++-..
T Consensus 2 ~~i~vp~~~h~~iIG~~G~~i~~i~~~~~~~I~~P~~ 38 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP 38 (62)
T ss_pred CEEEECHHHCCCEECCCCCCHHHHHHHHCCEEEECCC
T ss_conf 4899897881975889997399999985979995899
No 193
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=77.64 E-value=5.1 Score=19.39 Aligned_cols=78 Identities=26% Similarity=0.284 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHH---HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHH
Q ss_conf 788887732111477750588887765---30588999999999999999999998987754284356640779998999
Q gi|254780788|r 372 IAHLLVAEGFADVEELACVKISEIASI---EGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIK 448 (526)
Q Consensus 372 iA~~LV~eGf~SiEeIa~a~~eeL~~I---eGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~ 448 (526)
....|. ..|-|+++++.++.++|.+. -||-.-.+..|++-|+....... . .-....++|+.|+|+.+.++
T Consensus 13 ~~~~l~-~~~pt~~~l~~a~~~~l~~~i~~~g~~~~ka~~i~~~a~~i~~~~~----~--~~p~~~~~L~~lpGVG~~tA 85 (149)
T smart00478 13 ATERLF-EKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILVEEYG----G--EVPDDREELLKLPGVGRKTA 85 (149)
T ss_pred HHHHHH-HHCCCHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC----C--CCCCHHHHHHCCCCCCHHHH
T ss_conf 999999-9885999998689999999999868899999999999999998665----5--58855999875898659999
Q ss_pred HHHHHCCC
Q ss_conf 99998798
Q gi|254780788|r 449 VALGENGI 456 (526)
Q Consensus 449 ~~L~e~gI 456 (526)
......+-
T Consensus 86 ~~vl~~~~ 93 (149)
T smart00478 86 NAVLSFAL 93 (149)
T ss_pred HHHHHHHC
T ss_conf 99999987
No 194
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=75.73 E-value=5.7 Score=19.03 Aligned_cols=57 Identities=23% Similarity=0.418 Sum_probs=46.9
Q ss_pred HHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEHHHCCCC------CCCCCCCEEEEEEEEECCC
Q ss_conf 520838999998405763899957-93587447874887------5115276699999761135
Q gi|254780788|r 136 DKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISR------ENLRPGDRVKSYIYDVRRE 192 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~~e~ip~------E~~~~Gdrika~i~~V~~~ 192 (526)
-++|+++.|.|-.+..-..+|+|. +..|++--+|.-.+ +.+++||.|.+=|.++...
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~ 66 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDEN 66 (129)
T ss_pred CCCCCEEEEEEEEEEECCEEEEECCCCCCEEEEHHHHHHHHHHHHHHHCCCCEEEEEEEEECCC
T ss_conf 5346467888975674334898239973148835754436773998842788799999721468
No 195
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=75.28 E-value=5.8 Score=18.95 Aligned_cols=46 Identities=17% Similarity=0.294 Sum_probs=24.8
Q ss_pred HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf 9999976286654248987567879999853422110254427899
Q gi|254780788|r 284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR 329 (526)
Q Consensus 284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvr 329 (526)
.+|+..-|.-|-+.+|.+.-......|++--..--+.|||+|++++
T Consensus 18 reyl~k~l~~Agis~IeIeRt~~~~~I~I~tarPG~vIGr~G~~i~ 63 (225)
T PRK04191 18 DEYLAKELERAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKTIR 63 (225)
T ss_pred HHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCHHHHH
T ss_conf 9999987776785459999868946999994898515557837799
No 196
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1; InterPro: IPR011940 This entry describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (IPR011938 from INTERPRO) and RadB (IPR011939 from INTERPRO) and bacterial RecA. It has been characterised for human as a recombinase active only in meiosis .; GO: 0003677 DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0007131 meiotic recombination, 0005634 nucleus.
Probab=75.13 E-value=5.9 Score=18.92 Aligned_cols=133 Identities=19% Similarity=0.236 Sum_probs=83.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCC
Q ss_conf 25888467888877321114777505888877653058899999999999999999999898775428435664077999
Q gi|254780788|r 365 AINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGID 444 (526)
Q Consensus 365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~ 444 (526)
..+|.-.-...|-..|+.|+..|.......|..|.|+.|-.+++|.+.|.......=....+..+ .......+. -.
T Consensus 6 ~~GIn~~Di~KLk~~g~~T~~~~~~~T~r~L~~iKGlSEaKVdKi~EaA~K~~~~~f~ta~~~~~---~R~~V~~i~-TG 81 (314)
T TIGR02238 6 AHGINAADIKKLKSAGICTVNGVIMTTKRELLKIKGLSEAKVDKIKEAASKIINVGFITAVEILD---KRKKVLKIS-TG 81 (314)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHH---HCCEEEEEE-CC
T ss_conf 43887889999886368999999998888874037851677999999998764146640578874---062467762-31
Q ss_pred HHHHHHHHHCCCCCHHHHHHCCHHHHCC-------------------------------CC-CCCCCCCCCCCCCCCCCC
Q ss_conf 8999999987984788965326775212-------------------------------31-234443211245334358
Q gi|254780788|r 445 SKIKVALGENGIKTMEDLAGCSVDDLLG-------------------------------WS-ENKGGNIEKFDGFLSSLG 492 (526)
Q Consensus 445 ~~~~~~L~e~gIktleDlAels~dEL~~-------------------------------~~-~~~~~~~~~~~gil~~~~ 492 (526)
...+..+-=.||.|. |+-|+.| |. .+--.-+.+...|-+.|+
T Consensus 82 s~~~d~~LGGGi~s~------~ITE~fGEfR~GKTQl~HTL~VtaQLP~~~~g~~GKv~yIDTEgTFRPdri~~IAerf~ 155 (314)
T TIGR02238 82 SKALDKILGGGIESM------SITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGEGKVAYIDTEGTFRPDRIKAIAERFG 155 (314)
T ss_pred HHHHHHHCCCCEEEE------EHEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHCC
T ss_conf 588743407870000------00000045567714655566553206312579984289981788858178998875407
Q ss_pred CCHHHHHHHHHHHCC
Q ss_conf 899999999998412
Q gi|254780788|r 493 TPKDQVESMIIHARY 507 (526)
Q Consensus 493 l~~~~A~~lIM~AR~ 507 (526)
++.+.+=.=|+-||+
T Consensus 156 ~D~~~~L~Ni~yaRA 170 (314)
T TIGR02238 156 VDGEAVLDNILYARA 170 (314)
T ss_pred CCHHHHHHHHHHHHH
T ss_conf 898899988898875
No 197
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=74.67 E-value=6 Score=18.84 Aligned_cols=55 Identities=24% Similarity=0.401 Sum_probs=38.0
Q ss_pred EEEEEEEECC--CC--EEEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 8999998405--76--389995793587447874887--5115276699999761135870289
Q gi|254780788|r 141 IISGTVKRVE--YG--NVIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQV 198 (526)
Q Consensus 141 iv~G~V~r~e--~~--~iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpqi 198 (526)
-++|+|+-++ +| +|.-+-|+-+-++..+..... ..++.|++|.+ ++....||||-
T Consensus 3 ~i~G~VKwF~~~kGyGFI~~~dG~~DvFvH~s~i~~~g~~~L~~Gq~V~f---~v~~~~kG~~A 63 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEF---EITNGAKGPSA 63 (69)
T ss_pred CEEEEEEEEECCCCEEEEECCCCCCCEEEEHHHCCCCCCCCCCCCCEEEE---EEEECCCCCEE
T ss_conf 47889999839998799970799832999907705257861699999999---99969999851
No 198
>KOG2916 consensus
Probab=74.54 E-value=6.1 Score=18.82 Aligned_cols=164 Identities=20% Similarity=0.261 Sum_probs=94.6
Q ss_pred HHHHHHHHCCCEEEEEEEECCCCEEEEEE---CCCEEEEEHHHCCCCC------CCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 79999852083899999840576389995---7935874478748875------11527669999976113587028987
Q gi|254780788|r 130 QYLEFKDKVGEIISGTVKRVEYGNVIVDL---GNSDGVIRRDETISRE------NLRPGDRVKSYIYDVRREQRGPQVLL 200 (526)
Q Consensus 130 i~~ef~~r~Geiv~G~V~r~e~~~iiVdl---g~~ea~Lp~~e~ip~E------~~~~Gdrika~i~~V~~~~rgpqi~l 200 (526)
.|+.--+.++++|.+.|+.+---+.+|.| |+.||++.-+|...+- ..|+|-.=-+.+..|.++..---+--
T Consensus 8 ~ye~kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSk 87 (304)
T KOG2916 8 FYENKYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSK 87 (304)
T ss_pred HHHCCCCCCCCEEEEEEEEEHHCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCEECHH
T ss_conf 01015997532799875370206216762102781111003577788889899998407753489999717787066213
Q ss_pred ECCCHHHH--------------------HHHHHHHHHHHHCCEEEEEEEECCCCC---EEEEEEEECCCCCCCEEEEECC
Q ss_conf 15988999--------------------999997667775580878566316775---0349999408998812765548
Q gi|254780788|r 201 SRTHPQFM--------------------VKLFHMEVPEIYNGIVQVKAVSRDPGS---RAKLAVFSSDSSIDPVGACVGM 257 (526)
Q Consensus 201 SRt~p~~l--------------------~~Lf~~EVPEI~~G~ieIk~iaR~pG~---RsKIAV~s~d~~iDpVGAcVG~ 257 (526)
+|.+|+=+ .+-|..++-|.|.-+== .--|.-|+ --|++| +++.-.|+.---=+.
T Consensus 88 rrVs~ed~~kC~Er~~ksK~v~sIlrhvAe~~g~~LeeLY~~igW--~~~rk~g~aYdaFK~~v-td~tV~d~l~~~~~v 164 (304)
T KOG2916 88 RRVSPEDKEKCEERFAKSKLVYSILRHVAEKLGYELEELYQRIGW--PLERKYGHAYDAFKIAV-TDPTVLDELDLSEEV 164 (304)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCC--CHHHHHCHHHHHHHHHC-CCCCCCCCCCCCHHH
T ss_conf 138877889999988776789999999999949839999998377--43666360999998862-684302666777789
Q ss_pred CCHHHHHHHHHHCC------CCEEEEECCCCHHHHHHHHCCCCCC
Q ss_conf 86217889986277------8267995598789999976286654
Q gi|254780788|r 258 RGSRVQAVVTELRD------EKIDIVVWSPDSATFVINALRPAIV 296 (526)
Q Consensus 258 rGsRiq~I~~EL~g------EkIDii~ws~d~~~fi~nAl~PA~v 296 (526)
+-.=.+.|.+.|.- --|++..|+-+-.--|..||.-|.-
T Consensus 165 k~~Llk~Irrrltpq~vKIRADIEv~Cf~yeGI~aIK~alk~a~~ 209 (304)
T KOG2916 165 KEVLLKNIRRRLTPQTVKIRADIEVSCFGYEGIDAIKAALKAALN 209 (304)
T ss_pred HHHHHHHHHHHCCCCCEEEEEEEEEEECCCCCHHHHHHHHHHHHH
T ss_conf 999999998754886557873258986065679999999998872
No 199
>pfam11731 Cdd1 Pathogenicity locus. Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=74.50 E-value=3.4 Score=20.72 Aligned_cols=42 Identities=26% Similarity=0.276 Sum_probs=31.3
Q ss_pred HHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCC
Q ss_conf 566407799989999999879847889653267752123123
Q gi|254780788|r 435 EELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSEN 476 (526)
Q Consensus 435 e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~ 476 (526)
.+|.+|+++.+.++.-|..=||.+.++|++..-+||..-...
T Consensus 12 ~~L~~lPnIG~a~a~DL~~LGi~~~~~L~g~dp~elY~~lc~ 53 (92)
T pfam11731 12 KELTDLPNIGKATAKDLRLLGINSPAQLAGRDPLELYERLCE 53 (92)
T ss_pred HHHHCCCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHH
T ss_conf 987418974699999999918998999917999999999999
No 200
>KOG1856 consensus
Probab=74.21 E-value=6.2 Score=18.76 Aligned_cols=149 Identities=15% Similarity=0.160 Sum_probs=69.4
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCEEEEEE-EECCCCEEEE-EECCCEEEEEHHHCCCCCCCCCC--CEEE
Q ss_conf 999999999999-99999988779999852083899999-8405763899-95793587447874887511527--6699
Q gi|254780788|r 109 VAVQSAKQVIIQ-KVREAERDRQYLEFKDKVGEIISGTV-KRVEYGNVIV-DLGNSDGVIRRDETISRENLRPG--DRVK 183 (526)
Q Consensus 109 iaAq~AKQvI~Q-kireaEr~~i~~ef~~r~Geiv~G~V-~r~e~~~iiV-dlg~~ea~Lp~~e~ip~E~~~~G--drik 183 (526)
-+.+.|-|.+++ -+...-|..+-.+++.+++....+.. .+...+-+.= |-+.-+.-.|+ .+-+=.|.++ +-+.
T Consensus 542 ~~v~~A~~k~~~~~m~~elr~~L~~rak~~v~k~c~~kl~~~ls~apy~p~~~~~~d~~~p~--rvl~~~~~~~~~~a~f 619 (1299)
T KOG1856 542 EIVNSAVQKFFKPDMVKELRSTLTSRAKKRVAKVCRVKLYSKLSQAPYRPDDDTFEDEKIPK--RVLAVCGGTERSDAIF 619 (1299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC--EEEEECCCCCCCCEEE
T ss_conf 99999999997888899999999999999999999999997612377678888743445551--4787415888875179
Q ss_pred EEEEEECCCC----CEEEEEEECCC------HHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEE
Q ss_conf 9997611358----70289871598------8999999997667775580878566316775034999940899881276
Q gi|254780788|r 184 SYIYDVRREQ----RGPQVLLSRTH------PQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGA 253 (526)
Q Consensus 184 a~i~~V~~~~----rgpqi~lSRt~------p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGA 253 (526)
|.+.+..-+. |-+-+..-++. ++....+|..= |....| -
T Consensus 620 ~v~vn~~Gd~vD~lrl~~~~kr~~~~n~~~r~~k~~d~f~kF-------------------------I~~~kP------~ 668 (1299)
T KOG1856 620 CVLVNFEGDLVDYLRLVDITKRKTLVNDEERKKKFQDLFKKF-------------------------IEKKKP------H 668 (1299)
T ss_pred EEEECCCCCEEEEEECCCHHHHHHCCCHHHHHHHHHHHHHHH-------------------------HHHCCC------C
T ss_conf 999767776244565153033320232034366689999999-------------------------984399------8
Q ss_pred EECCCCH---------HHHHHHHHH----CCCCEEEEECCCCHHHHHHHH
Q ss_conf 5548862---------178899862----778267995598789999976
Q gi|254780788|r 254 CVGMRGS---------RVQAVVTEL----RDEKIDIVVWSPDSATFVINA 290 (526)
Q Consensus 254 cVG~rGs---------Riq~I~~EL----~gEkIDii~ws~d~~~fi~nA 290 (526)
|||.-|. +|+-++.+| ++.-|++|.-++..|..-.|+
T Consensus 669 vi~v~g~~r~~q~~~~~I~~~v~el~~~~~~~~ipv~~vd~ela~lY~nS 718 (1299)
T KOG1856 669 VIGVSGENRLKQKIYEAIRQLVHELLISDQGHPIPVIYVDNELARLYQNS 718 (1299)
T ss_pred EEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCHHHHHHHHH
T ss_conf 89962777126779999999998435312479865240361888999860
No 201
>cd01700 Pol_V Pol V was discovered in Escherichia coli as Umuc and UmuD proteins induced by UV. This branch of DNA polymerases is mostly found in bacteria. Pol V enables DNA replication to bypass covalently linked cys-sin T-T photo-dimers and 6-4 T-T or T-C photoproducts, which would otherwise stall the DNA replication fork.
Probab=74.08 E-value=4.7 Score=19.64 Aligned_cols=37 Identities=16% Similarity=0.084 Sum_probs=30.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCC
Q ss_conf 2588846788887732111477750588887765305
Q gi|254780788|r 365 AINVDEIIAHLLVAEGFADVEELACVKISEIASIEGF 401 (526)
Q Consensus 365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGf 401 (526)
--+|....++.|-..|+.|+.+++..+.+.|....|.
T Consensus 180 i~GIG~~t~~kL~~~GI~Ti~dLa~~~~~~l~~~fg~ 216 (344)
T cd01700 180 VWGIGRRLSKRLAAMGIHTALDLAQADPKWIRKRFSV 216 (344)
T ss_pred CCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHHH
T ss_conf 2783699999999869978999870999999999768
No 202
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=73.98 E-value=3.7 Score=20.41 Aligned_cols=41 Identities=29% Similarity=0.406 Sum_probs=36.8
Q ss_pred HHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf 43566407799989999999879847889653267752123
Q gi|254780788|r 433 VSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW 473 (526)
Q Consensus 433 ~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~ 473 (526)
+.+||..+.|+.+.+.-.|.+.||.|-.++|-++.+|+.-+
T Consensus 65 ~~DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAAwt~~di~~i 105 (133)
T COG3743 65 PKDDLTRISGIGPKLEKVLNELGIFTFAQIAAWTRADIAWI 105 (133)
T ss_pred CCCCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH
T ss_conf 86542110043788998998747763999974489999999
No 203
>PRK00024 radC DNA repair protein RadC; Reviewed
Probab=73.85 E-value=5.6 Score=19.10 Aligned_cols=41 Identities=20% Similarity=0.337 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 467888877321114777505888877653058899999999
Q gi|254780788|r 370 EIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 370 E~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
..+|+.|.+ -|.++..+..+++++|.+++|+....|..|+.
T Consensus 44 ~~lA~~ll~-~~g~l~~l~~a~~~eL~~i~GiG~~kA~~l~a 84 (224)
T PRK00024 44 LDLARELLE-RFGSLRGLLDASLEELQEIKGIGPAKAAQLKA 84 (224)
T ss_pred HHHHHHHHH-HCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH
T ss_conf 999999999-85999999870889884478988999999999
No 204
>PRK10702 endonuclease III; Provisional
Probab=73.78 E-value=6.3 Score=18.69 Aligned_cols=76 Identities=13% Similarity=0.147 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHH-H--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHH
Q ss_conf 6788887732111477750588887765-3--058899999999999999999999898775428435664077999899
Q gi|254780788|r 371 IIAHLLVAEGFADVEELACVKISEIASI-E--GFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKI 447 (526)
Q Consensus 371 ~iA~~LV~eGf~SiEeIa~a~~eeL~~I-e--Gfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~ 447 (526)
.....|... |.|++++|.++.++|.++ . ||-.-.|..|+..|+..++.-. -.+ ...-++|+.|+|+.+.+
T Consensus 49 ~~~~~L~~~-~~t~e~la~a~~~el~~~i~~~G~y~~KA~~L~~~a~~i~~~~~----G~v--P~~~~~L~~LpGIG~kT 121 (211)
T PRK10702 49 KATAKLYPV-ANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEKHN----GEV--PEDRAALEALPGVGRKT 121 (211)
T ss_pred HHHHHHHHH-CCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCC--HHHHHHHHHHHCCCHHH
T ss_conf 999999997-79999987099999999999863599999999999999999909----987--66699999876635889
Q ss_pred HHHHHH
Q ss_conf 999998
Q gi|254780788|r 448 KVALGE 453 (526)
Q Consensus 448 ~~~L~e 453 (526)
+.....
T Consensus 122 A~aIl~ 127 (211)
T PRK10702 122 ANVVLN 127 (211)
T ss_pred HHHHHH
T ss_conf 999999
No 205
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable . ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=73.52 E-value=3 Score=21.03 Aligned_cols=58 Identities=17% Similarity=0.207 Sum_probs=42.7
Q ss_pred HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 7775058888776530588999999999999999999998987754284356640779998999999987
Q gi|254780788|r 385 EELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGEN 454 (526)
Q Consensus 385 EeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~ 454 (526)
=-|-.|+.+||..++|+....|..|++ --+.+=.+ .-=|||+.+.|+.+..+.+|...
T Consensus 64 VnlN~As~~EL~~l~GiGP~kA~aIi~---------YRe~nG~F---~SvddL~kVsGIG~k~~eKLk~~ 121 (124)
T TIGR01259 64 VNLNKASLEELQALPGIGPAKAKAIIE---------YREENGAF---KSVDDLTKVSGIGEKSLEKLKDY 121 (124)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHH---------HHHHCCCC---CCHHHHHCCCCCCHHHHHHHHHC
T ss_conf 344067899986369998133799999---------99856997---77555003578854668742000
No 206
>KOG3013 consensus
Probab=73.47 E-value=1.7 Score=22.96 Aligned_cols=62 Identities=27% Similarity=0.368 Sum_probs=49.6
Q ss_pred HHHHHHHHHCCCEEEEEEEECCCCEEEEEEC-CCEEEEEH----------------HHCCCCCCCCCCCEEEEEEEEEC
Q ss_conf 7799998520838999998405763899957-93587447----------------87488751152766999997611
Q gi|254780788|r 129 RQYLEFKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRR----------------DETISRENLRPGDRVKSYIYDVR 190 (526)
Q Consensus 129 ~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~ea~Lp~----------------~e~ip~E~~~~Gdrika~i~~V~ 190 (526)
-+...|..-+|++|.|.|.-+-+.-+-||++ +..++|+- +|+--+..|+.||-|-|-+..|-
T Consensus 76 plk~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~ 154 (301)
T KOG3013 76 PLKSRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVF 154 (301)
T ss_pred EHHHHCCCCCCCEEEEEEEEEECCEEEEECCCCCCEEEEEECCCCCCHHHHCCCHHHHHHHHHHHHCCCEEHHHHHHHC
T ss_conf 4332037755777888764440233577516654337875302488614330223568999977550675317788761
No 207
>PRK01810 DNA polymerase IV; Validated
Probab=72.82 E-value=4.6 Score=19.75 Aligned_cols=34 Identities=18% Similarity=0.119 Sum_probs=14.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHC
Q ss_conf 8884678888773211147775058888776530
Q gi|254780788|r 367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEG 400 (526)
Q Consensus 367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeG 400 (526)
+|....++.|-..|+.|+.+++.++.+.|....|
T Consensus 186 GIG~~~~~~L~~~GI~Ti~dl~~~~~~~l~~~fG 219 (410)
T PRK01810 186 GIGEKTAEKLKDIHIHTIGDLAKADEHILRAKLG 219 (410)
T ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHH
T ss_conf 8677899999986996899987499999998765
No 208
>PRK03348 DNA polymerase IV; Provisional
Probab=72.77 E-value=2.8 Score=21.32 Aligned_cols=45 Identities=18% Similarity=0.297 Sum_probs=23.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 88846788887732111477750588887765305889999999999
Q gi|254780788|r 367 NVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRA 413 (526)
Q Consensus 367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA 413 (526)
+|....++.|-..|+.|+.+++.++...|....| ......|.+.|
T Consensus 186 GIG~~t~~kL~~~GI~TigDLa~~~~~~L~~~~G--~~~G~~L~~~a 230 (456)
T PRK03348 186 GIGPVAEEKLHRLGIETIGDLAALSEAEVANLLG--ATIGPALHRLA 230 (456)
T ss_pred CCCHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHH
T ss_conf 7759999999986981468776099999999981--99999999997
No 209
>PRK03858 DNA polymerase IV; Validated
Probab=72.67 E-value=4.9 Score=19.48 Aligned_cols=32 Identities=28% Similarity=0.371 Sum_probs=14.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf 88846788887732111477750588887765
Q gi|254780788|r 367 NVDEIIAHLLVAEGFADVEELACVKISEIASI 398 (526)
Q Consensus 367 dVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~I 398 (526)
+|...++..|-..|+.|+.+++.++...|...
T Consensus 180 GIG~~~~~~L~~~GI~T~~dLa~~~~~~l~~~ 211 (398)
T PRK03858 180 GVGAVTAAKLRAHGIETVADVAELSESTLSSM 211 (398)
T ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH
T ss_conf 86879999999849968999760999999999
No 210
>pfam07650 KH_2 KH domain.
Probab=71.95 E-value=3.1 Score=20.94 Aligned_cols=31 Identities=19% Similarity=0.341 Sum_probs=20.4
Q ss_pred EEEEECCCCCCCCCCCCHHHHHHHHHHHCCE
Q ss_conf 9999853422110254427899999861674
Q gi|254780788|r 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWT 338 (526)
Q Consensus 308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~ 338 (526)
..+++...+-.++|||+|+|++-..+..+-.
T Consensus 2 v~v~i~~srpGiiIGk~G~~I~~l~~~l~k~ 32 (55)
T pfam07650 2 VIVVIRTSQPGIVIGKGGSNIKKLGKELRKR 32 (55)
T ss_pred EEEEEEECCCCEEECCCCCCHHHHHHHHHHH
T ss_conf 8999991899679998960399999999998
No 211
>pfam10391 DNA_pol_lambd_f Fingers domain of DNA polymerase lambda. DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone.
Probab=71.67 E-value=4 Score=20.17 Aligned_cols=27 Identities=22% Similarity=0.329 Sum_probs=14.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 111225888467888877321114777
Q gi|254780788|r 361 FFMQAINVDEIIAHLLVAEGFADVEEL 387 (526)
Q Consensus 361 ~f~e~LdVDE~iA~~LV~eGf~SiEeI 387 (526)
.|+..-+|....|..+++.||+|++++
T Consensus 3 ~f~~I~GvGp~~A~~~~~~G~~ti~dL 29 (52)
T pfam10391 3 LFTNIWGVGPKTARKWYRQGIRTLEDL 29 (52)
T ss_pred HHHHCCCCCHHHHHHHHHHCCCCHHHH
T ss_conf 366354406999999999478889999
No 212
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=70.88 E-value=7.3 Score=18.23 Aligned_cols=82 Identities=20% Similarity=0.157 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHH
Q ss_conf 7888877321114777505888877653058---8999999999999999999998987754284356640779998999
Q gi|254780788|r 372 IAHLLVAEGFADVEELACVKISEIASIEGFD---EETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIK 448 (526)
Q Consensus 372 iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfd---ee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~ 448 (526)
+...|.....-|++.++.++.++|.++ |+. .-.|..|+.-|+........ .........+.|+.|+|+.+.++
T Consensus 21 ~~~~l~~~~~pt~~~l~~~~~~~l~~~-~~~~gy~~Ka~~i~~~a~~i~~~~~~---~~~~~~~~~~~L~~l~GIG~~TA 96 (158)
T cd00056 21 AYERLFERYGPTPEALAAADEEELREL-IRSLGYRRKAKYLKELARAIVEGFGG---LVLDDPDAREELLALPGVGRKTA 96 (158)
T ss_pred HHHHHHHHCCCCHHHHHCCCHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCC---CCCCCHHHHHHHHCCCCCCHHHH
T ss_conf 999999854998999980999999999-73356899999999988888986089---57898889999875898289999
Q ss_pred HHHHHCCCC
Q ss_conf 999987984
Q gi|254780788|r 449 VALGENGIK 457 (526)
Q Consensus 449 ~~L~e~gIk 457 (526)
....-.+-.
T Consensus 97 ~~vl~~~~~ 105 (158)
T cd00056 97 NVVLLFALG 105 (158)
T ss_pred HHHHHHHCC
T ss_conf 999999879
No 213
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659 The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are: Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO Associated components: The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP. Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2] In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , . Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too. RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.
Probab=70.34 E-value=2.5 Score=21.60 Aligned_cols=44 Identities=30% Similarity=0.456 Sum_probs=36.3
Q ss_pred HHHHCCCEEEEEEEECCCC--EEEEEECC-CEEEEEHHHCCCC-CCCC
Q ss_conf 9852083899999840576--38999579-3587447874887-5115
Q gi|254780788|r 134 FKDKVGEIISGTVKRVEYG--NVIVDLGN-SDGVIRRDETISR-ENLR 177 (526)
Q Consensus 134 f~~r~Geiv~G~V~r~e~~--~iiVdlg~-~ea~Lp~~e~ip~-E~~~ 177 (526)
-+.++|.|--|.|.|+.++ ..+||+|. -.|+||-++..++ +.|.
T Consensus 23 ~~~~~GnIY~G~V~~vlPsl~AAFvdiG~~~~GFLh~sdi~~~~~~~~ 70 (464)
T TIGR00757 23 SRQLVGNIYKGRVTRVLPSLQAAFVDIGLEKNGFLHASDIGENSEKLE 70 (464)
T ss_pred HHCCHHHHHHCEEEEECCCCCEEEEECCCCCCCCCCHHHCCCCHHHHH
T ss_conf 101100232020202203764477420688355630332033245688
No 214
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=69.35 E-value=7.1 Score=18.32 Aligned_cols=46 Identities=20% Similarity=0.517 Sum_probs=33.1
Q ss_pred HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf 9999976286654248987567879999853422110254427899
Q gi|254780788|r 284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR 329 (526)
Q Consensus 284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvr 329 (526)
..|+.+-+.-|-|++|.+.-..+.+.|.+--.---+-|||+|+++.
T Consensus 39 R~~i~~~~~~agIs~I~IeR~~~~i~V~I~tarPG~vIGk~G~~Ie 84 (109)
T cd02412 39 RKFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIE 84 (109)
T ss_pred HHHHHHHHHHCCCCEEEEEECCCEEEEEEEECCCCEEECCCCCCHH
T ss_conf 9999999976894369999857738999994699559867852489
No 215
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=68.65 E-value=7 Score=18.39 Aligned_cols=41 Identities=7% Similarity=0.284 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEE---CCCCCEEEE
Q ss_conf 99999999999999999961368745359997---499883999
Q gi|254780788|r 22 IDRDVVLSVMADSIQKAARSLYGTMSDIRVEI---NPETGDISL 62 (526)
Q Consensus 22 I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~i---D~~tG~i~i 62 (526)
+|++.+-+|+++++..+.+++|.+..++.+.+ |++.++-.+
T Consensus 3 ~d~~~l~eAv~~~~~~~k~rkF~esvel~i~Lk~iDpkk~dq~v 46 (216)
T PRK04203 3 MDREKIEEAVKEALEESKPRNFTQSVELIVNLKDLDLKKPENRI 46 (216)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCCCEE
T ss_conf 56899999999999868766887418999961688998766545
No 216
>cd03468 Pol_Y_like Pol_Y_like: a group of putative Y-family DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=68.09 E-value=8.3 Score=17.83 Aligned_cols=52 Identities=17% Similarity=0.136 Sum_probs=38.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 0111225888467888877321114777505888877653058899999999999
Q gi|254780788|r 360 QFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAR 414 (526)
Q Consensus 360 ~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~ 414 (526)
.+-+..|++....++.|-.-|+.|+.+++..+...|..-.| .+.. .+..+|+
T Consensus 167 ~lPv~~l~i~~~~~~~L~~lGi~tigdL~~lp~~~L~~RfG--~~~~-~~l~~a~ 218 (330)
T cd03468 167 PLPVAALRLPPETVERLRRLGLRTLGDLAALPRAGLARRFG--PELL-RRLDQAL 218 (330)
T ss_pred CCCHHHHCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHC--HHHH-HHHHHHC
T ss_conf 59866738898999999985996799986599999999879--7999-9999962
No 217
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=67.00 E-value=7 Score=18.39 Aligned_cols=49 Identities=24% Similarity=0.409 Sum_probs=33.1
Q ss_pred CHHHHHHHHC--CCCCCCEE-EECCCCCEEEEEECCCCCCCCCCCCHHHHHH
Q ss_conf 7899999762--86654248-9875678799998534221102544278999
Q gi|254780788|r 282 DSATFVINAL--RPAIVTKV-VLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL 330 (526)
Q Consensus 282 d~~~fi~nAl--~PA~v~~v-~~de~~~~~~v~v~~~qls~AIGk~GqNvrL 330 (526)
+...|+...| .|.+|.=- ...+......+.|.+++.-..|||+|.+++-
T Consensus 3 ~lv~~ivk~lVd~Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~A 54 (76)
T COG1837 3 ELVEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQA 54 (76)
T ss_pred HHHHHHHHHHCCCCCCEEEEEEECCCEEEEEEEECCCCCCCEECCCCHHHHH
T ss_conf 6999999986689650689998169749999998720046356678705999
No 218
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=66.77 E-value=8.8 Score=17.64 Aligned_cols=85 Identities=14% Similarity=0.073 Sum_probs=36.1
Q ss_pred CCCCCCCCEEEEECCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEC-CC--EE
Q ss_conf 88986473799850845-6207999999999999999999887799998520838999998405763899957-93--58
Q gi|254780788|r 88 DPSIDIGGVVSDPLPPM-DFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLG-NS--DG 163 (526)
Q Consensus 88 ~~~~~iGD~i~~~i~~~-~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg-~~--ea 163 (526)
-..+.-||.+...+.+. .-+| .+ ++.+.+.+. |.-..+-|+........+++-.. +. .-
T Consensus 102 ~~~a~~gD~V~v~~~~~~~~~~--~~--~~~v~~il~-------------r~~~~~vG~~~~~~~~~~~~p~d~r~~~~i 164 (706)
T COG0557 102 LNRALHGDRVLVELLPSDKRGR--FK--EAAVVRILE-------------RANSALVGELRPSQGIGRVLPDDKRLPFLI 164 (706)
T ss_pred HHHCCCCCEEEEEECCCCCCCC--CC--EEEEEHHHH-------------HHHHHHEEEEEECCCEEEEEECCCCCCCCE
T ss_conf 5320169989999676556666--62--268662555-------------532102488871477069975565565424
Q ss_pred EEEHHHCCCCCCCCCCCEEEEEEEEECCC
Q ss_conf 74478748875115276699999761135
Q gi|254780788|r 164 VIRRDETISRENLRPGDRVKSYIYDVRRE 192 (526)
Q Consensus 164 ~Lp~~e~ip~E~~~~Gdrika~i~~V~~~ 192 (526)
.+| .++.+ ....|+++.+-+..--..
T Consensus 165 ~i~-~~~~~--~~~~~~~v~~~i~~~~~~ 190 (706)
T COG0557 165 AIP-PEQAP--GAEEGHLVVVEITRWPDT 190 (706)
T ss_pred EEC-CCCCC--CCCCCCEEEEEEEECCCC
T ss_conf 536-10035--100486699998324665
No 219
>KOG2534 consensus
Probab=65.99 E-value=9.1 Score=17.54 Aligned_cols=40 Identities=8% Similarity=-0.046 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 88899999999998623999999999999999999961368
Q gi|254780788|r 4 ANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYG 44 (526)
Q Consensus 4 ~~~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~ 44 (526)
.||.=+..+++-++..+++.-+.. .+.-=..+++.-|.|+
T Consensus 10 ~~N~~~~~aleiLa~~~ev~g~~~-r~~~y~~Aasvlk~~p 49 (353)
T KOG2534 10 NNNQIFTEALEILAEAYEVEGEED-RARAYRRAASVLKSLP 49 (353)
T ss_pred CCCHHHHHHHHHHHHHHCCCCCHH-HHHHHHHHHHHHHHCC
T ss_conf 353878899999998632342178-9999999999998499
No 220
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=64.89 E-value=4.8 Score=19.56 Aligned_cols=23 Identities=35% Similarity=0.606 Sum_probs=13.0
Q ss_pred CCCCCCHHHHHHHHHHHCCEEEE
Q ss_conf 10254427899999861674578
Q gi|254780788|r 319 LAIGRRGQNVRLASQLTGWTIDI 341 (526)
Q Consensus 319 ~AIGk~GqNvrLas~Ltg~~idi 341 (526)
.-||++|...+.-..|||-+|-|
T Consensus 102 RIIGk~Gktr~~IE~~T~~~I~v 124 (172)
T TIGR03665 102 RIIGEGGKTRRIIEELTGVSISV 124 (172)
T ss_pred HHCCCCCHHHHHHHHHHCCEEEE
T ss_conf 31589961999999976874997
No 221
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=64.31 E-value=9.7 Score=17.32 Aligned_cols=99 Identities=17% Similarity=0.269 Sum_probs=46.6
Q ss_pred EEEEEEEECCCCC-EEEEEEECCCHHH-HHHHH-HH-----HHHHHHC------------------------------CE
Q ss_conf 9999976113587-0289871598899-99999-97-----6677755------------------------------80
Q gi|254780788|r 182 VKSYIYDVRREQR-GPQVLLSRTHPQF-MVKLF-HM-----EVPEIYN------------------------------GI 223 (526)
Q Consensus 182 ika~i~~V~~~~r-gpqi~lSRt~p~~-l~~Lf-~~-----EVPEI~~------------------------------G~ 223 (526)
+..|+...-..+. ..+|+++...++. |...+ +. .+|-..+ .+
T Consensus 291 ~~~fi~Q~Y~~~~~P~~Ill~~~~~~~~l~~~l~~~~~~~i~~p~~G~kk~l~~~A~~NA~~~l~~l~~~~~~~~~l~~l 370 (581)
T COG0322 291 LEAFILQFYKSNEIPKEILLPQELPEEELEEALSEAAGLEIRVPKRGEKKSLLELATKNAKEALEQLKERSDEKQALEAL 370 (581)
T ss_pred HHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 99999997227889645780788775899999986147731268865588999999999999999988513356899999
Q ss_pred EEEEEEECCCCCEEEEEEEECCCCCCCEEEEECC-CCHHHHHHHHHHCCCCEEEEECCCCHHHH
Q ss_conf 8785663167750349999408998812765548-86217889986277826799559878999
Q gi|254780788|r 224 VQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGM-RGSRVQAVVTELRDEKIDIVVWSPDSATF 286 (526)
Q Consensus 224 ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~-rGsRiq~I~~EL~gEkIDii~ws~d~~~f 286 (526)
=++-++. ++.|--+-=.||-..-+|||+||=- .|.-.+. +...=+|. +.-.||-+.+
T Consensus 371 ~~~l~l~--~p~rIE~~D~Sh~~g~~~V~smvvf~~g~~~k~---~YRry~i~-~~~~dDya~m 428 (581)
T COG0322 371 AALLGLP--APYRIECFDISHIQGEDTVGSMVVFEDGGPSKK---DYRRYNIK-ITGGDDYASM 428 (581)
T ss_pred HHHHCCC--CCEEEEEEECCCCCCCCCEEEEEEECCCCCCHH---HCCCCCCC-CCCCCHHHHH
T ss_conf 9985889--861689851675356664457999768987754---36522446-7897559999
No 222
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=63.89 E-value=2.7 Score=21.39 Aligned_cols=107 Identities=14% Similarity=0.147 Sum_probs=73.1
Q ss_pred ECCCCCCCCCCCCHH-----HHHHHHHHHCCEEEEEECCCHH----HHHHC--CCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 853422110254427-----8999998616745785522001----10100--122100011122588846788887732
Q gi|254780788|r 312 VPKEQLSLAIGRRGQ-----NVRLASQLTGWTIDIITEEEDS----INRQK--DFNERTQFFMQAINVDEIIAHLLVAEG 380 (526)
Q Consensus 312 v~~~qls~AIGk~Gq-----NvrLas~Ltg~~idi~~~~~~~----~~~~~--e~~~~~~~f~e~LdVDE~iA~~LV~eG 380 (526)
..-+.+.+-+--+|+ -+..|++...|+.+....-... ..... .........++.|+.+-....-|-.+|
T Consensus 185 ~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~I~~l~lsvrs~ncLk~~~ 264 (317)
T COG0202 185 TDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKAVEIEEEKPEFPILLVLEAPIDELDLSVRSYNCLKREG 264 (317)
T ss_pred CCCEEEEEEEEECCEEEHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCCCCCCCCCCCCEEEEHHHCCCC
T ss_conf 77406999976463750279999999988999999875365544010156544233233465341231333501231158
Q ss_pred HHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 11147775058888776530588999999999999999
Q gi|254780788|r 381 FADVEELACVKISEIASIEGFDEETAVEIQGRAREYLE 418 (526)
Q Consensus 381 f~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~ 418 (526)
+.++.++...+..+|.+++.|.....++++.++.++-+
T Consensus 265 i~~i~~L~~~se~~l~~v~n~G~ksleEi~~kl~~~~l 302 (317)
T COG0202 265 IETIGELVQRTEEELLKVENLGKKSLEEIKEKLAELGL 302 (317)
T ss_pred CHHHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 11468777457988850436566999999999998513
No 223
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=63.41 E-value=7.9 Score=18.00 Aligned_cols=46 Identities=22% Similarity=0.260 Sum_probs=40.7
Q ss_pred HHCCHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf 5428435664077999899999998798478896532677521231
Q gi|254780788|r 429 RELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS 474 (526)
Q Consensus 429 ~e~~~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~ 474 (526)
.-.|..+||..+.|+++.+..+|-+.||...-++|.++-|+..-+.
T Consensus 263 ~p~g~~ddl~ki~gvgp~~~~~ln~~g~~h~~qia~~t~~~~~~~d 308 (332)
T PRK12311 263 GPRGAPDDLKKLTGVSGAIEKKLNDLGIFHYWQLAELDPDTAHKIG 308 (332)
T ss_pred CCCCCCCHHHHHCCCCHHHHHHHHHCCCEEHHHHHCCCHHHHHHHH
T ss_conf 7889842577715767889998501241218988627999999888
No 224
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=62.37 E-value=11 Score=17.08 Aligned_cols=68 Identities=25% Similarity=0.284 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHCCHHHHHH---HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHH
Q ss_conf 73211147775058888776---530588999999999999999999998987754284356640779998999999
Q gi|254780788|r 378 AEGFADVEELACVKISEIAS---IEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVAL 451 (526)
Q Consensus 378 ~eGf~SiEeIa~a~~eeL~~---IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L 451 (526)
-.-|.|.++++.++.++|.+ --||-...|..|+.-|+-.++.-.- +-....++|+.|+|....++..-
T Consensus 55 f~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g------~vP~~~~eL~~LPGVGrKTAnvV 125 (211)
T COG0177 55 FKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG------EVPDTREELLSLPGVGRKTANVV 125 (211)
T ss_pred HHHCCCHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC------CCCCHHHHHHHCCCCCHHHHHHH
T ss_conf 997599999974999999999986387189999999999999997499------99815999974899665778989
No 225
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=62.09 E-value=7.9 Score=18.00 Aligned_cols=38 Identities=24% Similarity=0.146 Sum_probs=32.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCC
Q ss_conf 22588846788887732111477750588887765305
Q gi|254780788|r 364 QAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGF 401 (526)
Q Consensus 364 e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGf 401 (526)
+-.+|...++..|-..|+.|+.+++.+++..|.+..|.
T Consensus 183 ~lwGIG~~~~~kL~~~GI~Ti~dLa~~~~~~l~k~fgv 220 (422)
T PRK03609 183 EVWGVGRRISKKLNAMGIKTALDLADTDIRFIRKHFNV 220 (422)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHH
T ss_conf 98611399999999878810899872998999988889
No 226
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=61.56 E-value=7.1 Score=18.35 Aligned_cols=46 Identities=22% Similarity=0.455 Sum_probs=28.6
Q ss_pred EECCCCCEEEEEEEE-CCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf 631677503499994-089988127655488621788998627782679955987
Q gi|254780788|r 229 VSRDPGSRAKLAVFS-SDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPD 282 (526)
Q Consensus 229 iaR~pG~RsKIAV~s-~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d 282 (526)
++...+.=.+|+|.+ +++.+-|-|+| +-+.+|++++...|+..+.+
T Consensus 65 is~G~~~~~~v~v~~~~~~~~sPCG~C--------RQ~i~Ef~~~d~~ii~~~~~ 111 (134)
T COG0295 65 ISEGKRKFDAVVVVADTGKPVSPCGAC--------RQVLAEFCGDDTLIILLPKD 111 (134)
T ss_pred HHCCCCCEEEEEEECCCCCCCCCCHHH--------HHHHHHHCCCCCEEEEECCC
T ss_conf 973997179999974899975985889--------99999866877459996699
No 227
>KOG2191 consensus
Probab=61.36 E-value=11 Score=16.95 Aligned_cols=36 Identities=25% Similarity=0.133 Sum_probs=22.7
Q ss_pred CEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEE
Q ss_conf 879999853422110254427899999861674578
Q gi|254780788|r 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDI 341 (526)
Q Consensus 306 ~~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi 341 (526)
.....-|++..+-.|-|++|-|.---+..||-.+-|
T Consensus 244 tas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~i 279 (402)
T KOG2191 244 TASTISVAAGLIGGANGAGGAFGAALSGFTGALIAI 279 (402)
T ss_pred CHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCEEE
T ss_conf 012101221135654554555443430345653552
No 228
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=60.71 E-value=11 Score=16.87 Aligned_cols=159 Identities=14% Similarity=0.147 Sum_probs=76.8
Q ss_pred EECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEE
Q ss_conf 63167750349999408998812765548862178899862778267995598789999976286654248987567879
Q gi|254780788|r 229 VSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRI 308 (526)
Q Consensus 229 iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~ 308 (526)
.||.-|.|+=+.++- -.+.-|=.-+|.++-..-+.+++++.. |....+| .|..+-+||. .+
T Consensus 94 eAR~~GV~s~m~~~~-A~~lCP~li~v~~~~~~Y~~~S~~i~~---------------il~~~~~-~vE~~SIDEa--yl 154 (405)
T cd01701 94 EARKYGVKNGMFVGQ-AKKLCPELQTLPYDFDAYEEVSLAFYE---------------ILASYTD-NIEAVSCDEA--LV 154 (405)
T ss_pred HHHHHCCCCCCCHHH-HHHHCCCCEEECCCHHHHHHHHHHHHH---------------HHHHHCC-CCEECCCCCE--EE
T ss_conf 999749987895999-998788969989988999999999999---------------9998597-5145123324--67
Q ss_pred EEEE---------------------CCCC--CCCCCCCCHHHHHHHHHHHCC-EEEEEECCCHHHHHHCCCCCCCCCCCC
Q ss_conf 9998---------------------5342--211025442789999986167-457855220011010012210001112
Q gi|254780788|r 309 EVIV---------------------PKEQ--LSLAIGRRGQNVRLASQLTGW-TIDIITEEEDSINRQKDFNERTQFFMQ 364 (526)
Q Consensus 309 ~v~v---------------------~~~q--ls~AIGk~GqNvrLas~Ltg~-~idi~~~~~~~~~~~~e~~~~~~~f~e 364 (526)
++.= ..-. .|.-||-+-.=+||||.+-.= -+-+...++. .+|-.-. ..-+
T Consensus 155 Dvt~~~~~~~~~~~~~a~~Ir~~I~~~tglt~SiGIa~nK~lAKiAs~~~KP~G~~~i~~~~~-----~~~L~~l-pv~~ 228 (405)
T cd01701 155 DITSLLEETYELPEELAETIRNEIKETTGCSASVGIGPNILLARLATRKAKPNGQYYLSPEKV-----EEFLDTL-PVKD 228 (405)
T ss_pred ECCCCHHHCCCCHHHHHHHHHHHHHHHHCCCEEECCCCCHHHHHHHHHHCCCCCCCCCCHHHH-----HHHHHHC-CCCC
T ss_conf 335411112677999999999999998799756443764999999887369987323687899-----9999855-2111
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 2588846788887732111477750588-8877653058899999999999
Q gi|254780788|r 365 AINVDEIIAHLLVAEGFADVEELACVKI-SEIASIEGFDEETAVEIQGRAR 414 (526)
Q Consensus 365 ~LdVDE~iA~~LV~eGf~SiEeIa~a~~-eeL~~IeGfdee~a~eL~~rA~ 414 (526)
-.+|...+++.|-..|+.|+.+++..+. +.|....| ......|...|+
T Consensus 229 i~GIG~~t~~kL~~~gi~t~~dl~~~~~~~~L~~~fG--~k~G~~l~~~a~ 277 (405)
T cd01701 229 LPGVGSSTKEKLKSLGIDTCGDLQLISTKEKLQKVFG--KKTGEKLYNYCR 277 (405)
T ss_pred CCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHHHH--HHHHHHHHHHHC
T ss_conf 5871789999999849916899862787999999977--899999999967
No 229
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=58.01 E-value=12 Score=16.56 Aligned_cols=54 Identities=26% Similarity=0.360 Sum_probs=37.8
Q ss_pred EEEEEECCCC--EEEEEECCCEEEEEHHHCCCC-CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 9999840576--389995793587447874887-511527669999976113587028
Q gi|254780788|r 143 SGTVKRVEYG--NVIVDLGNSDGVIRRDETISR-ENLRPGDRVKSYIYDVRREQRGPQ 197 (526)
Q Consensus 143 ~G~V~r~e~~--~iiVdlg~~ea~Lp~~e~ip~-E~~~~Gdrika~i~~V~~~~rgpq 197 (526)
+|+|+-.++| ++.-+-|+-+-+++.++.-.+ ..++.||+|.+.+.+- +..++|+
T Consensus 1 tG~Vk~f~kGfGFI~~~~g~~DvFvH~s~i~~~~~~l~~Gd~V~f~v~~~-~~~~~~~ 57 (64)
T smart00357 1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSP-RGGGKPE 57 (64)
T ss_pred CCEEEEEECCEEEEEECCCCCCEEEEHHHHCCCCCCCCCCCEEEEEEEEC-CCCCCCE
T ss_conf 94796982844888618999409998699546777447587899999988-9999844
No 230
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=57.81 E-value=11 Score=16.90 Aligned_cols=65 Identities=22% Similarity=0.241 Sum_probs=34.5
Q ss_pred CCEEEEECCHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHCCCEEEEEEEE----CCC---CEEEE
Q ss_conf 737998508456207999999999999----------9999998877999985208389999984----057---63899
Q gi|254780788|r 94 GGVVSDPLPPMDFGRVAVQSAKQVIIQ----------KVREAERDRQYLEFKDKVGEIISGTVKR----VEY---GNVIV 156 (526)
Q Consensus 94 GD~i~~~i~~~~fgRiaAq~AKQvI~Q----------kireaEr~~i~~ef~~r~Geiv~G~V~r----~e~---~~iiV 156 (526)
|-..-.-.|..-+.+--.++++..+.. ..+..+|..+++..++-.-.|+.||--- +.. |-++|
T Consensus 306 g~q~a~maPTeiLa~Qh~~~~~~~~~~~~i~v~lltg~~~~~~~~~~~~~~~~g~~~i~iGTHal~~~~v~f~~Lglvvi 385 (677)
T PRK10917 306 GYQAALMAPTEILAEQHYRNLKKWLEPLGIRVALLTGSLKGKERREILEALASGEADIVIGTHALIQDDVEFHNLGLVII 385 (677)
T ss_pred CCEEEEECCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHCCCCCEEEEHHHHHHCCCCCCCCCEEEE
T ss_conf 99489987679999999999998776349889984077417789999999857997789730787735564466656995
Q ss_pred EE
Q ss_conf 95
Q gi|254780788|r 157 DL 158 (526)
Q Consensus 157 dl 158 (526)
|=
T Consensus 386 DE 387 (677)
T PRK10917 386 DE 387 (677)
T ss_pred CH
T ss_conf 30
No 231
>KOG3127 consensus
Probab=57.18 E-value=1.4 Score=23.41 Aligned_cols=48 Identities=25% Similarity=0.384 Sum_probs=31.6
Q ss_pred EECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHH--CCCCEEEEECCCCH
Q ss_conf 63167750349999408998812765548862178899862--77826799559878
Q gi|254780788|r 229 VSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTEL--RDEKIDIVVWSPDS 283 (526)
Q Consensus 229 iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL--~gEkIDii~ws~d~ 283 (526)
+|+-.-.||| ||+ --|||||+.++.||=++---. +|+--|+.+|.++.
T Consensus 73 iA~LsA~RSk------Dpn-tqVGaCiv~~~n~iVg~GYNgfP~gc~~~vfp~~~~~ 122 (230)
T KOG3127 73 IAFLSAKRSK------DPN-TQVGACIVDRENRIVGTGYNGFPRGCSDDVFPWCKAA 122 (230)
T ss_pred HHHHHHHHCC------CCC-CCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf 9999998535------965-6602699737987999603787677777777544344
No 232
>KOG1918 consensus
Probab=57.13 E-value=6.3 Score=18.69 Aligned_cols=84 Identities=23% Similarity=0.320 Sum_probs=63.6
Q ss_pred HHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH--HHHHHHHHHHCCHHHHHHCCCCCC-----HHHHHHH
Q ss_conf 321114777505888877653058899999999999999999--999898775428435664077999-----8999999
Q gi|254780788|r 379 EGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGI--DITLQKKIRELGVSEELCSIPGID-----SKIKVAL 451 (526)
Q Consensus 379 eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~--~~~~~e~~~e~~~~e~L~~l~gl~-----~~~~~~L 451 (526)
+.|-+.|.+-.++.++|.++ ||..-.+..|..-|..|.... ...-.++..+....+.|.++.|+. .-|+..|
T Consensus 108 ~~~~~pe~i~~~~~~~lrkc-G~S~rK~~yLh~lA~~~~ng~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~MflIfsL 186 (254)
T KOG1918 108 EKFPTPEFIDPLDCEELRKC-GFSKRKASYLHSLAEAYTNGYIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFLIFSL 186 (254)
T ss_pred CCCCCCHHCCCCCHHHHHHH-CCCHHHHHHHHHHHHHHHCCCCCCHHHHHHCCHHHHHHHHHHCCCCCCEEEEEEEEECC
T ss_conf 67788321276789999985-73324679999999998647777667776157999999998604755112443211014
Q ss_pred HHCCCCCHHHHH
Q ss_conf 987984788965
Q gi|254780788|r 452 GENGIKTMEDLA 463 (526)
Q Consensus 452 ~e~gIktleDlA 463 (526)
..-+|.-.+||.
T Consensus 187 ~R~DVmp~dDlg 198 (254)
T KOG1918 187 HRPDVMPADDLG 198 (254)
T ss_pred CCCCCCCCHHHH
T ss_conf 777666850366
No 233
>pfam00633 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Probab=57.06 E-value=6.1 Score=18.79 Aligned_cols=28 Identities=25% Similarity=0.294 Sum_probs=21.8
Q ss_pred HHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 4777505888877653058899999999
Q gi|254780788|r 384 VEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 384 iEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
++.+..++.++|.+++|+.+.+|..+..
T Consensus 2 ~~~~~~as~eeL~~lpGVG~~tA~~I~~ 29 (30)
T pfam00633 2 LEGLIPASREELLALPGVGPKTAEAILS 29 (30)
T ss_pred CCCCCCCCHHHHHHCCCCCHHHHHHHHC
T ss_conf 6443523599997288977688998853
No 234
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=56.85 E-value=13 Score=16.42 Aligned_cols=46 Identities=20% Similarity=0.526 Sum_probs=31.7
Q ss_pred HHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHH
Q ss_conf 9999976286654248987567879999853422110254427899
Q gi|254780788|r 284 ATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVR 329 (526)
Q Consensus 284 ~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvr 329 (526)
..|+.+-+.-|.|++|.+.-..+.+.|.+--..--+.|||+|+++.
T Consensus 40 R~yi~k~~~~agIs~I~IeR~~~~i~V~I~tarPgiiIGkkG~~Ie 85 (233)
T PRK00310 40 RKFLKKKLKKAGVSRIVIERPAKKVRVTIHTARPGIVIGKKGEDIE 85 (233)
T ss_pred HHHHHHHCHHCCEEEEEEEECCCEEEEEEEECCCCCHHCCCCCHHH
T ss_conf 9999750101572489999738879999996788631215663689
No 235
>TIGR02851 spore_V_T stage V sporulation protein T; InterPro: IPR014213 Members of this protein entry include the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB..
Probab=56.61 E-value=9.3 Score=17.47 Aligned_cols=48 Identities=33% Similarity=0.625 Sum_probs=23.9
Q ss_pred EEEEEECCCCEEEEEECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCH
Q ss_conf 999984057638999579358744787488751152766999997611358702898715988
Q gi|254780788|r 143 SGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHP 205 (526)
Q Consensus 143 ~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p 205 (526)
||+|+|+| ||||+ ++| +|.=.+=+.|-||.+-.|+- |.-.|+|-.-||
T Consensus 3 TGIVRRID------DLGRV--ViP-KEIRRTLRIrEGDPLEIF~D------r~GevILKKYSP 50 (184)
T TIGR02851 3 TGIVRRID------DLGRV--VIP-KEIRRTLRIREGDPLEIFVD------REGEVILKKYSP 50 (184)
T ss_pred CEEEEEEE------CCCCE--EEC-CCCCCCCCCCCCCCCEEEEE------CCCCEEEEECCC
T ss_conf 24677550------46867--626-43411010125997148880------789789871078
No 236
>PRK01250 inorganic pyrophosphatase; Provisional
Probab=56.57 E-value=6.2 Score=18.79 Aligned_cols=75 Identities=20% Similarity=0.216 Sum_probs=31.5
Q ss_pred HHHHHCCEEEEEEEECCCCCEE-EEEEEECCC--CCCCE---E-EEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHH
Q ss_conf 6777558087856631677503-499994089--98812---7-655488621788998627782679955987899999
Q gi|254780788|r 216 VPEIYNGIVQVKAVSRDPGSRA-KLAVFSSDS--SIDPV---G-ACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVI 288 (526)
Q Consensus 216 VPEI~~G~ieIk~iaR~pG~Rs-KIAV~s~d~--~iDpV---G-AcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~ 288 (526)
.|+..+-+|||- .|+|. |-.+--... .+|-+ + ..=+.-|-==|.. .--|--+|++..++.|. ..
T Consensus 12 ~P~~vnvvIEIP-----~gs~~~KyE~d~~~g~~~ldR~l~~~~~YP~nYGfiP~Tl--~~DgDPLDvlvl~~~p~--~p 82 (176)
T PRK01250 12 LPEDINVIIEIP-----ANSDPIKYEVDKESGALFVDRFLYTAMFYPCNYGFIPHTL--SLDGDPVDVLVVTPYPL--VP 82 (176)
T ss_pred CCCEEEEEEEEC-----CCCCCEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCCHH--CCCCCCCEEEEECCCCC--CC
T ss_conf 988899999947-----9999712898068996999986687885986543341011--16999515898527543--89
Q ss_pred HHCCCCCCCEE
Q ss_conf 76286654248
Q gi|254780788|r 289 NALRPAIVTKV 299 (526)
Q Consensus 289 nAl~PA~v~~v 299 (526)
.++-.|.+..+
T Consensus 83 G~vv~~r~IG~ 93 (176)
T PRK01250 83 GSVIRCRPVGV 93 (176)
T ss_pred CCEEEEEEEEE
T ss_conf 62899999789
No 237
>KOG2841 consensus
Probab=56.30 E-value=12 Score=16.63 Aligned_cols=45 Identities=18% Similarity=0.319 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 5888467888877321114777505888877653058899999999
Q gi|254780788|r 366 INVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQG 411 (526)
Q Consensus 366 LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~ 411 (526)
-+|...-|+.|.. -|-|++.+..||.++|..++|+..-.|.+|..
T Consensus 201 ~~VnKtda~~LL~-~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~ 245 (254)
T KOG2841 201 PGVNKTDAQLLLQ-KFGSLQQISNASEGELEQCPGLGPAKAKRLHK 245 (254)
T ss_pred CCCCCCCHHHHHH-HCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHH
T ss_conf 8977001899988-55359998741776798675737899999999
No 238
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=56.10 E-value=13 Score=16.34 Aligned_cols=138 Identities=14% Similarity=0.176 Sum_probs=71.1
Q ss_pred CCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHH
Q ss_conf 88127655488621788998627782679955987899999762866542489875678799998534221102544278
Q gi|254780788|r 248 IDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQN 327 (526)
Q Consensus 248 iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqN 327 (526)
||+-=--.|-.|--|+-=.+||-+-. ++.-.-||..-.+--++ |. -..-++|.--.-+.=-|
T Consensus 205 I~~yv~ELG~eGrli~mQl~EL~~d~------d~e~~l~i~DY~~~~e~-----d~-------~~~l~~l~~ls~~~lL~ 266 (349)
T COG1623 205 IDRYVVELGTEGRLIRMQLSELIGDN------DEERELIIRDYHKEDEV-----DI-------EAVLEELQSLSDEELLD 266 (349)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHCCC------HHHHHHHHHHHHCCCCC-----CH-------HHHHHHHHHCCCHHHCC
T ss_conf 78999971644211363299885632------78899999987507556-----88-------99999998455040178
Q ss_pred HHHHHHHHCCEEEEEECCCHHHHHHCCC-CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHH
Q ss_conf 9999986167457855220011010012-210001112258884678888773211147775058888776530588999
Q gi|254780788|r 328 VRLASQLTGWTIDIITEEEDSINRQKDF-NERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETA 406 (526)
Q Consensus 328 vrLas~Ltg~~idi~~~~~~~~~~~~e~-~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a 406 (526)
.--.+++.||.= ..+-...-. ...+-.+....-+.-.+.+.||. -|.++.++..|+.++|.+++|+.+-.|
T Consensus 267 ~~~i~kvlGY~~-------~~~~~d~~vspRGYR~l~kIpRlp~~iv~nlV~-~F~~l~~il~As~edL~~VeGIGe~rA 338 (349)
T COG1623 267 PENIAKVLGYPK-------TTEADDSLVSPRGYRLLNKIPRLPFAIVENLVR-AFGTLDGILEASAEDLDAVEGIGEARA 338 (349)
T ss_pred HHHHHHHHCCCC-------CCHHCCCCCCCHHHHHHHCCCCCCHHHHHHHHH-HHHHHHHHHHHCHHHHHHHCCHHHHHH
T ss_conf 899999967997-------210013425722668871176763789999999-975289998714767766213669999
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780788|r 407 VEIQG 411 (526)
Q Consensus 407 ~eL~~ 411 (526)
..+++
T Consensus 339 r~i~~ 343 (349)
T COG1623 339 RAIKE 343 (349)
T ss_pred HHHHH
T ss_conf 99997
No 239
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=55.15 E-value=14 Score=16.23 Aligned_cols=60 Identities=15% Similarity=0.242 Sum_probs=42.1
Q ss_pred HHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 147775058888776530588999999999999999999998987754284356640779998999999987
Q gi|254780788|r 383 DVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGEN 454 (526)
Q Consensus 383 SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~ 454 (526)
..=.|-.++.++|..++|+....|..|+.- .++-.....-+||....|+.+.++.+|...
T Consensus 87 ~~vNiNtAs~eeL~~lpgIG~~kA~aIi~y------------Re~~G~f~sv~dL~~v~GiG~~~~ekl~~~ 146 (149)
T COG1555 87 KKVNINTASAEELQALPGIGPKKAQAIIDY------------REENGPFKSVDDLAKVKGIGPKTLEKLKDY 146 (149)
T ss_pred CCCCCCCCCHHHHHHCCCCCHHHHHHHHHH------------HHHCCCCCCHHHHCCCCCCCHHHHHHHHHH
T ss_conf 413666108999988679899999999999------------997399765788710777789999987756
No 240
>KOG1433 consensus
Probab=52.74 E-value=7.2 Score=18.26 Aligned_cols=58 Identities=21% Similarity=0.148 Sum_probs=40.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 0111225888467888877321114777505888877653058899999999999999
Q gi|254780788|r 360 QFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL 417 (526)
Q Consensus 360 ~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L 417 (526)
-.|.....++......|-..+|.+++.+++++..++..|.|+.......+...+...-
T Consensus 24 ~~~~~~~~ita~~v~~l~~~~l~~v~~l~~~~~~el~~i~~~s~~~~~k~~~~l~~~~ 81 (326)
T KOG1433 24 VRFLLAGGITAEDVLLLSEGELSTVEGLAYAGKEELLLIIGLSEAKSGKTVLGLHKLV 81 (326)
T ss_pred HHHHHCCCCCHHHHHHHCCCCEEEEECCCCCCCHHHHHEEEECHHHCCCHHHHHHHHH
T ss_conf 3456215666777654143524788501457604443200001220010899999851
No 241
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=51.42 E-value=16 Score=15.82 Aligned_cols=56 Identities=16% Similarity=0.236 Sum_probs=40.5
Q ss_pred CCEEE-EEEEECCCC-EEEEEEC-CCEEEEEHHHC------CCCCCCCCCCEEEEEEEEECCCCC
Q ss_conf 83899-999840576-3899957-93587447874------887511527669999976113587
Q gi|254780788|r 139 GEIIS-GTVKRVEYG-NVIVDLG-NSDGVIRRDET------ISRENLRPGDRVKSYIYDVRREQR 194 (526)
Q Consensus 139 Geiv~-G~V~r~e~~-~iiVdlg-~~ea~Lp~~e~------ip~E~~~~Gdrika~i~~V~~~~r 194 (526)
|.|+- .+|.|++.+ +++++|+ +..|+.-.+.. -+...|++|...+|=|..-..--.
T Consensus 1 G~i~~~~~V~~v~~~~G~~~~l~~g~~gfvhiS~lsD~kv~~~~~~fk~Gs~H~~RVig~s~~D~ 65 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDG 65 (71)
T ss_pred CCCCCEEEEEEECCCCCEEEEECCCCEEEEEEHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCCC
T ss_conf 96233405999858853799969996899996012666423665786479988899983474341
No 242
>TIGR01008 rpsC_E_A ribosomal protein S3; InterPro: IPR005703 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 of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein S3 is one of the proteins from the small ribosomal subunit. This family describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=50.80 E-value=16 Score=15.76 Aligned_cols=56 Identities=18% Similarity=0.361 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCC
Q ss_conf 99999997667775580878566316775034999940899881276554886217889986277
Q gi|254780788|r 207 FMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRD 271 (526)
Q Consensus 207 ~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~g 271 (526)
++.+-|+.|+-+=.=|=++|+.- -.-|+|-+|+..| |-.+|-+|.||+++..-|+.
T Consensus 14 ~idE~l~~El~~AGYsgvdv~~T----PlGT~vii~AerP-----g~VIGr~G~rIr~LT~~l~~ 69 (204)
T TIGR01008 14 LIDEFLKKELREAGYSGVDVRKT----PLGTKVIIYAERP-----GLVIGRGGRRIRELTEKLQK 69 (204)
T ss_pred HHHHHHHHHHHHCCCCCCEEEEC----CCCCEEEEEEECC-----CCEECCCCCHHHHHHHHHHH
T ss_conf 78889999886517775516877----7896799998368-----63772797218899999987
No 243
>PRK09890 cold shock protein CspG; Provisional
Probab=50.50 E-value=16 Score=15.72 Aligned_cols=55 Identities=25% Similarity=0.369 Sum_probs=37.2
Q ss_pred CEEEEEEEECC--CC--EEEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 38999998405--76--389995793587447874887--511527669999976113587028
Q gi|254780788|r 140 EIISGTVKRVE--YG--NVIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQ 197 (526)
Q Consensus 140 eiv~G~V~r~e--~~--~iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpq 197 (526)
+-++|+|+.++ +| +|.-|-|+-+-++..+..-.. ..++.|++|.+- |....||||
T Consensus 3 ~~~tG~VKwFn~~KGyGFI~~ddg~~DvFvH~s~i~~~~~~~L~~Gq~V~f~---v~~g~kG~~ 63 (70)
T PRK09890 3 NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFS---IEQGQRGPA 63 (70)
T ss_pred CCEEEEEEEECCCCCEEEECCCCCCCCEEEEHHHHCCCCCCCCCCCCEEEEE---EEECCCCCC
T ss_conf 7506999988399986997038999429998689272688332999999999---997999861
No 244
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=49.34 E-value=9.2 Score=17.52 Aligned_cols=73 Identities=12% Similarity=0.190 Sum_probs=43.8
Q ss_pred HHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHH--------HHCCEEEEE-ECCCHHHHHHCCCC
Q ss_conf 999762866542489875678799998534221102544278999998--------616745785-52200110100122
Q gi|254780788|r 286 FVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQ--------LTGWTIDII-TEEEDSINRQKDFN 356 (526)
Q Consensus 286 fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls~AIGk~GqNvrLas~--------Ltg~~idi~-~~~~~~~~~~~e~~ 356 (526)
.+.-.|.|. ..|.++++.+.+.+-..-++..+-||+.|++..=--- .+|-...|. ....|.++|++++.
T Consensus 73 ell~~m~~~--~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~yRerR~e~L~ 150 (208)
T COG1847 73 ELLELMDFE--VTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGDYRERRKETLI 150 (208)
T ss_pred HHHHHHCCC--EEEEEEECCCEEEEEECCCCHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEHHHHHHHHHHHHH
T ss_conf 999983986--599996247579999448861023036774017999999998535059615899982068999999999
Q ss_pred CCCC
Q ss_conf 1000
Q gi|254780788|r 357 ERTQ 360 (526)
Q Consensus 357 ~~~~ 360 (526)
..++
T Consensus 151 ~LA~ 154 (208)
T COG1847 151 KLAE 154 (208)
T ss_pred HHHH
T ss_conf 9999
No 245
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=48.97 E-value=17 Score=15.56 Aligned_cols=48 Identities=29% Similarity=0.376 Sum_probs=37.9
Q ss_pred HHHCCCEEEEEEEECCCCEEEEEECCCE-EEEEHHHCCCCCCCCCCCEEEEEEEEE
Q ss_conf 8520838999998405763899957935-874478748875115276699999761
Q gi|254780788|r 135 KDKVGEIISGTVKRVEYGNVIVDLGNSD-GVIRRDETISRENLRPGDRVKSYIYDV 189 (526)
Q Consensus 135 ~~r~Geiv~G~V~r~e~~~iiVdlg~~e-a~Lp~~e~ip~E~~~~Gdrika~i~~V 189 (526)
+.++|++--|.|.++.....+||+|... +.|+. + +.+|.|+-+-+...
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~~~~~l~~--~-----~~~~~RvTvri~~~ 150 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGKDKLAKLSS--P-----APPGARVTVRIISR 150 (272)
T ss_pred CCCCEEECCEEEEEECCCCEEEECCCCCCEECCC--C-----CCCCCEEEEEEEEC
T ss_conf 8662561050798736882389805875133058--7-----89985699999731
No 246
>PRK10880 adenine DNA glycosylase; Provisional
Probab=48.16 E-value=17 Score=15.47 Aligned_cols=68 Identities=21% Similarity=0.277 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCHHHHHHCCCCCCHHHHHHHH
Q ss_conf 32111477750588887765-30588999999999999999999998987-7542843566407799989999999
Q gi|254780788|r 379 EGFADVEELACVKISEIASI-EGFDEETAVEIQGRAREYLEGIDITLQKK-IRELGVSEELCSIPGIDSKIKVALG 452 (526)
Q Consensus 379 eGf~SiEeIa~a~~eeL~~I-eGfdee~a~eL~~rA~~~L~~~~~~~~e~-~~e~~~~e~L~~l~gl~~~~~~~L~ 452 (526)
+-|-|++++|.++.++++.. +|+.= ..||++.......-..+- -.-...-++|+.|+|+.+-++.+..
T Consensus 57 ~~fP~~~~LA~A~~~~vl~~W~GLGY------Y~RArnLh~aA~~i~~~~~G~~P~~~~~L~~LPGIG~yTA~AI~ 126 (350)
T PRK10880 57 ARFPTVTDLANAPLDEVLHLWTGLGY------YARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAIL 126 (350)
T ss_pred HHCCCHHHHHCCCHHHHHHHHHHCCC------HHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCHHHHHHHH
T ss_conf 98839999977999999998640693------89999999999999997589898259998626688727999999
No 247
>TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=46.65 E-value=18 Score=15.31 Aligned_cols=67 Identities=22% Similarity=0.308 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHCCHHHHHHH---HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHH
Q ss_conf 32111477750588887765---30588999999999999999999998987754284356640779998999999
Q gi|254780788|r 379 EGFADVEELACVKISEIASI---EGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVAL 451 (526)
Q Consensus 379 eGf~SiEeIa~a~~eeL~~I---eGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L 451 (526)
+-|.|.+++|+++.|+|.+. -||=-..|..|+.-++.-++.-. . +=....++|+.|+|....+|..-
T Consensus 54 ~~Y~tp~~~a~a~~eel~~~Ik~iGlYr~KAk~I~~~~~~LvE~y~---G---eVP~~~~eL~~LPGVGRKTANVV 123 (192)
T TIGR01083 54 EVYPTPQALAAAGLEELEEYIKSIGLYRNKAKNIIALCRKLVERYG---G---EVPEDREELVKLPGVGRKTANVV 123 (192)
T ss_pred HCCCCHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHC---C---CCCCCHHHHHCCCCCCCHHHHHH
T ss_conf 1277868996089313477642258645689999999999999818---9---87755376617899871145624
No 248
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
Probab=45.66 E-value=19 Score=15.21 Aligned_cols=93 Identities=14% Similarity=0.070 Sum_probs=53.4
Q ss_pred CCCCCCCHHHHHHHHHHHCC-EEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC-HHHH
Q ss_conf 11025442789999986167-457855220011010012210001112258884678888773211147775058-8887
Q gi|254780788|r 318 SLAIGRRGQNVRLASQLTGW-TIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVK-ISEI 395 (526)
Q Consensus 318 s~AIGk~GqNvrLas~Ltg~-~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~-~eeL 395 (526)
|.-||.+-.=++|||.+-.= ..-++.-... .++-...-.+-+.-+|...+++.|-..|..++.+++..+ .+.|
T Consensus 172 S~GIa~NKlLAKlas~~~KPngqt~l~p~~~-----~~~l~~~~~i~ki~GIG~kt~~~L~~~gi~ti~dl~~~~~~~~l 246 (394)
T cd01703 172 CAGIASNKLLAKLVGSVHKPNQQTTLLPESA-----DHLIMDLGSLRKIPGIGYKTAKKLEDHGISSVRDLQECSELLLL 246 (394)
T ss_pred EEEECCCHHHHHHHHHCCCCCCEEEECCCCH-----HHHHCCCCCHHHHCCCCHHHHHHHHHCCCEEHHHHHCCCHHHHH
T ss_conf 7766340328987753258898059777118-----77843668805527817999999998389267987658879999
Q ss_pred HHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 7653058899999999999999
Q gi|254780788|r 396 ASIEGFDEETAVEIQGRAREYL 417 (526)
Q Consensus 396 ~~IeGfdee~a~eL~~rA~~~L 417 (526)
... |....+..|.+.|+-..
T Consensus 247 ~~~--fG~~~g~~l~~~a~GiD 266 (394)
T cd01703 247 EKG--FGKGIAQRIWGLAHGRD 266 (394)
T ss_pred HHH--HHHHHHHHHHHHHCCCC
T ss_conf 998--78899999999956978
No 249
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=45.51 E-value=19 Score=15.19 Aligned_cols=15 Identities=40% Similarity=0.651 Sum_probs=8.0
Q ss_pred CCCCCEEEEEEEEEC
Q ss_conf 152766999997611
Q gi|254780788|r 176 LRPGDRVKSYIYDVR 190 (526)
Q Consensus 176 ~~~Gdrika~i~~V~ 190 (526)
|++||++++.+.=++
T Consensus 21 f~~GDtvrv~vki~E 35 (115)
T COG0335 21 FRPGDTVRVHVKIVE 35 (115)
T ss_pred CCCCCEEEEEEEEEE
T ss_conf 999988999999986
No 250
>KOG1004 consensus
Probab=45.32 E-value=19 Score=15.17 Aligned_cols=84 Identities=21% Similarity=0.266 Sum_probs=56.4
Q ss_pred HHHHHHHHCCCEEEEEEEECCCCEEEEEECCC-EEEEEHH-----HCCCCCCCCCCCEEEEEEEEECCC-----------
Q ss_conf 79999852083899999840576389995793-5874478-----748875115276699999761135-----------
Q gi|254780788|r 130 QYLEFKDKVGEIISGTVKRVEYGNVIVDLGNS-DGVIRRD-----ETISRENLRPGDRVKSYIYDVRRE----------- 192 (526)
Q Consensus 130 i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~-ea~Lp~~-----e~ip~E~~~~Gdrika~i~~V~~~----------- 192 (526)
.-..|...+|+.|.|+|.--..+++-||+|+. -|.||.- -.=.+-++++||-|-|-+.+-.++
T Consensus 57 ~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~~~Epel~Cids~ 136 (230)
T KOG1004 57 QQKRYIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANKDMEPELTCIDST 136 (230)
T ss_pred CCCEECCCCCCEEEEEEEECCCCEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEECCC
T ss_conf 45043378899899999850465179963898665331002368543578864316578999870677766406887355
Q ss_pred CC--E--E--EEEEECCCHHHHHHHHH
Q ss_conf 87--0--2--89871598899999999
Q gi|254780788|r 193 QR--G--P--QVLLSRTHPQFMVKLFH 213 (526)
Q Consensus 193 ~r--g--p--qi~lSRt~p~~l~~Lf~ 213 (526)
.| | + -=++--+++.+.++|+-
T Consensus 137 graaGfG~LkdG~if~vs~~~~R~Ll~ 163 (230)
T KOG1004 137 GRAAGFGVLKDGMIFKVSLGLCRKLLL 163 (230)
T ss_pred CCCCCCCCCCCCEEEEECHHHHHHHHC
T ss_conf 754575342686698605888678875
No 251
>KOG0187 consensus
Probab=44.66 E-value=16 Score=15.69 Aligned_cols=55 Identities=22% Similarity=0.253 Sum_probs=42.0
Q ss_pred CEEEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 7457855220011010012210001112258884678888773211147775058
Q gi|254780788|r 337 WTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVK 391 (526)
Q Consensus 337 ~~idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~ 391 (526)
-.|-|+..+|+.|++..-.-+.+.+-.+...||.++-++|-..||.++-.+..++
T Consensus 67 RGISiKLQEEERErrdnyVPevSaLd~d~ieVD~dT~eMlk~lg~~~~~~~~~~~ 121 (134)
T KOG0187 67 RGISIKLQEEERERRDNYVPEVSALDQDIIEVDPDTKEMLKLLGFGSLSGVQVTE 121 (134)
T ss_pred CCEEEEECHHHHHHHCCCCCCHHHCCHHHEEECHHHHHHHHHCCCCCCCCEEEEC
T ss_conf 6446860277887552557622220334404276599999984877767536646
No 252
>PRK00296 minE cell division topological specificity factor MinE; Reviewed
Probab=44.02 E-value=20 Score=15.03 Aligned_cols=55 Identities=20% Similarity=0.198 Sum_probs=40.8
Q ss_pred HHHHCC-CCHHHHHHHHHHHHHHHHHHCCCC-CCCEEEEECCCCCEEEEEEEEEEEC
Q ss_conf 986239-999999999999999999613687-4535999749988399999988517
Q gi|254780788|r 16 VAYEKS-IDRDVVLSVMADSIQKAARSLYGT-MSDIRVEINPETGDISLFRLLEVVE 70 (526)
Q Consensus 16 va~EK~-I~~e~i~~aie~Al~~a~kK~~~~-~~~i~V~iD~~tG~i~i~~~~~VVe 70 (526)
++.|++ ...-..+..++.-|.....|+..- ..++.|.++...|++.+........
T Consensus 26 laheR~~~~~pd~l~~lk~eil~VI~KYv~Id~d~i~v~le~~~~~~~vLE~nI~lP 82 (85)
T PRK00296 26 VAHERRSDGEPDYLPQLRKEILEVICKYVQIDPDMVHVQLEQKDGDISTLELNITLP 82 (85)
T ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHEEECHHHEEEEEEECCCCEEEEEEEEECC
T ss_conf 342005799868999999999999987603662674999986489778999986778
No 253
>cd00501 Peptidase_C15 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from proteolysis by other proteases until the pGlu is removed by a PGP. PGPs are cysteine proteases with a Cys-His-Glu/Asp catalytic triad. Type I PGPs are found in a wide variety of prokaryotes and eukaryotes. It is not clear whether the functional form is a monomer, a homodimer, or a homotetramer.
Probab=42.43 E-value=8.8 Score=17.64 Aligned_cols=56 Identities=25% Similarity=0.274 Sum_probs=35.6
Q ss_pred HHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE-ECCCCCEEEEEEC--CCCCC
Q ss_conf 788998627782679955987899999762866542489-8756787999985--34221
Q gi|254780788|r 262 VQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV-LDEDVGRIEVIVP--KEQLS 318 (526)
Q Consensus 262 iq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~-~de~~~~~~v~v~--~~qls 318 (526)
+.++++.|+...|+ +.||.|+-.|+||.+.=--..... -....+...|-|| ++|.+
T Consensus 117 ~~~~~~~l~~~g~~-~~~S~dAG~YlCN~~~Y~sL~~~~~~~~~~~~~FvHvP~~~e~~~ 175 (194)
T cd00501 117 VKAIVKALREAGIP-ARVSNDAGTYLCNHVYYGSLHESATRGPFIRAGFIHVPYSPEQVA 175 (194)
T ss_pred HHHHHHHHHHCCCC-CEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHC
T ss_conf 99999999974999-468078753434699999999999729998166987289978816
No 254
>pfam00719 Pyrophosphatase Inorganic pyrophosphatase.
Probab=41.73 E-value=16 Score=15.71 Aligned_cols=64 Identities=20% Similarity=0.212 Sum_probs=32.2
Q ss_pred CCCEEEEEEEECCC--CCCCE----EEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE
Q ss_conf 77503499994089--98812----7655488621788998627782679955987899999762866542489
Q gi|254780788|r 233 PGSRAKLAVFSSDS--SIDPV----GACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV 300 (526)
Q Consensus 233 pG~RsKIAV~s~d~--~iDpV----GAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~ 300 (526)
.|+|.|..+-...+ .+|.+ -.|-+.-|.==|.. +--|.=+|++..++.|. ...++-+|++..+.
T Consensus 8 ~gs~~KyE~d~~~~~~~ldr~l~~~~~yP~nYGfiP~T~--~~DgDPLDvlvl~~~~~--~~G~vv~~r~iG~l 77 (156)
T pfam00719 8 KGSRVKYEIDKESGLLPVDRVLYTSMGYPFNYGFIPQTL--EGDGDPLDVLVLGPEPL--FPGSVVRVRPIGVL 77 (156)
T ss_pred CCCCEEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCC--CCCCCCEEEEEECCCCC--CCCCEEEEEEEEEE
T ss_conf 999867998368897038766467888983540346611--36999468998448743--89418999888999
No 255
>pfam02738 Ald_Xan_dh_C2 Molybdopterin-binding domain of aldehyde dehydrogenase.
Probab=41.68 E-value=22 Score=14.78 Aligned_cols=15 Identities=7% Similarity=0.295 Sum_probs=8.3
Q ss_pred EEEEECCCCCEEEEEE
Q ss_conf 5999749988399999
Q gi|254780788|r 49 IRVEINPETGDISLFR 64 (526)
Q Consensus 49 i~V~iD~~tG~i~i~~ 64 (526)
+.+..| .+|.+.+|.
T Consensus 52 ~vA~~d-~~g~l~i~~ 66 (543)
T pfam02738 52 ALAVPD-EDDELTIYS 66 (543)
T ss_pred EEEEEC-CCCCEEEEE
T ss_conf 999987-899399998
No 256
>KOG4384 consensus
Probab=41.66 E-value=22 Score=14.78 Aligned_cols=95 Identities=15% Similarity=0.186 Sum_probs=53.6
Q ss_pred CCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHCCC--------CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf 25442789999986167457855220011010012--------2100011122588846788887732111477750588
Q gi|254780788|r 321 IGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDF--------NERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKI 392 (526)
Q Consensus 321 IGk~GqNvrLas~Ltg~~idi~~~~~~~~~~~~e~--------~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~ 392 (526)
++-++-|-+-++ .+=-.+++.++++...++-.-. ......+...+++.+ -.+.|..+||.++|.+..+..
T Consensus 173 ~~~g~~~~kv~~-f~~~~v~~~s~e~~~~~~p~~~~~~~~~~~~~~~~ewL~~i~le~-y~~~~L~nGYd~le~~k~i~e 250 (361)
T KOG4384 173 TWLGLLNNKVGS-FKFIYVDVISEEEPAPKRPLRRLRRSPHPHPKSLEEWLRRIGLEE-YIETLLENGYDTLEDLKDITE 250 (361)
T ss_pred CCCCCCCCCCCC-CCCCEECCCCCCCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHH-HHHHHHHCCHHHHHHHHHCCH
T ss_conf 233544676533-356400232322346301456532378987048999999863888-878998706488899875268
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 8877653058899999999999999
Q gi|254780788|r 393 SEIASIEGFDEETAVEIQGRAREYL 417 (526)
Q Consensus 393 eeL~~IeGfdee~a~eL~~rA~~~L 417 (526)
++|.++-=-+.+.-..|...++-..
T Consensus 251 ~dL~~lgI~nP~Hr~kLL~av~~~~ 275 (361)
T KOG4384 251 EDLEELGIDNPDHRKKLLSAVELLK 275 (361)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 7799847898789999999999987
No 257
>pfam05557 MAD Mitotic checkpoint protein. This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated.
Probab=41.65 E-value=13 Score=16.29 Aligned_cols=17 Identities=29% Similarity=0.440 Sum_probs=14.1
Q ss_pred HHHHHCCEEEEEECCCH
Q ss_conf 99861674578552200
Q gi|254780788|r 331 ASQLTGWTIDIITEEED 347 (526)
Q Consensus 331 as~Ltg~~idi~~~~~~ 347 (526)
+-.|+||+||+.++..|
T Consensus 640 cY~L~GYkID~~~~~~y 656 (722)
T pfam05557 640 CYMLFGYKIDITPNSQY 656 (722)
T ss_pred HHHHHCEEEEECCCCEE
T ss_conf 99985703674478727
No 258
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family; InterPro: IPR003282 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia. The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. One of the outer membrane protein subunit families, termed "K" here for nomenclature purposes, aids in the structural assembly of the invasion complex . It is also described as a lipoprotein. Members of this family include the Salmonella PrgK and SsaJ genes, MxiJ from Shigella, YscJ from Yersinia, and from the plant enteropathogens NolT (Rhizobium) and HrcJ Erwinia). The flagellar M-ring protein FliF also shares a low level of similarity, presumably due to evolution of the type III secretion system from the flagellar biosynthetic pathway.; GO: 0009306 protein secretion.
Probab=41.51 E-value=14 Score=16.15 Aligned_cols=20 Identities=20% Similarity=0.263 Sum_probs=9.8
Q ss_pred HHHHHHHHCCCEEEEEEEEC
Q ss_conf 79999852083899999840
Q gi|254780788|r 130 QYLEFKDKVGEIISGTVKRV 149 (526)
Q Consensus 130 i~~ef~~r~Geiv~G~V~r~ 149 (526)
..+.=-..+.-++++.|+=+
T Consensus 119 ~Le~tLs~IdGV~~ArVhVv 138 (203)
T TIGR02544 119 ELEQTLSQIDGVISARVHVV 138 (203)
T ss_pred HHHHHHHHCCCEEEEEEEEE
T ss_conf 99998601792686679997
No 259
>CHL00162 thiG thiamin biosynthesis protein G; Validated
Probab=41.30 E-value=20 Score=14.97 Aligned_cols=11 Identities=27% Similarity=0.549 Sum_probs=5.6
Q ss_pred CCEEEEEEEEC
Q ss_conf 83899999840
Q gi|254780788|r 139 GEIISGTVKRV 149 (526)
Q Consensus 139 Geiv~G~V~r~ 149 (526)
-||||--++|+
T Consensus 41 aeiVTVAlRR~ 51 (267)
T CHL00162 41 CEIVTVAIRRA 51 (267)
T ss_pred CCEEEEEEECC
T ss_conf 98799997325
No 260
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509 This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This domain represents a region of two tandem copies of a helix-hairpin-helix domain, each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to this domain..
Probab=40.91 E-value=22 Score=14.70 Aligned_cols=54 Identities=17% Similarity=0.289 Sum_probs=39.5
Q ss_pred HHHHCCHHHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHH
Q ss_conf 775058888776-530588999999999999999999998987754284356640779998999999
Q gi|254780788|r 386 ELACVKISEIAS-IEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVAL 451 (526)
Q Consensus 386 eIa~a~~eeL~~-IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L 451 (526)
.|-.|+.+||.. |.|+....|+.|.. ..|+.-...--|||+.++||....+.+-
T Consensus 10 nINtAtaeElq~~~~GvG~kKAeAIv~------------YREe~G~F~t~Edl~~V~GiG~~~~Ek~ 64 (70)
T TIGR00426 10 NINTATAEELQKALSGVGAKKAEAIVA------------YREEYGRFKTVEDLKKVSGIGEKLLEKN 64 (70)
T ss_pred ECCHHCHHHHHHHHCCCCHHHHHHHHH------------HHHCCCCCCCHHHHHHCCCCCHHHHHHH
T ss_conf 101104788887642887237899988------------7532779576222321478762455556
No 261
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=40.74 E-value=22 Score=14.68 Aligned_cols=33 Identities=24% Similarity=0.320 Sum_probs=26.9
Q ss_pred CCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHH
Q ss_conf 211025442789999986167457855220011
Q gi|254780788|r 317 LSLAIGRRGQNVRLASQLTGWTIDIITEEEDSI 349 (526)
Q Consensus 317 ls~AIGk~GqNvrLas~Ltg~~idi~~~~~~~~ 349 (526)
..+-||-+|.+.|---+-||.+|-|....-...
T Consensus 17 vg~ilGprG~t~k~l~~~t~~~i~irG~GS~Kd 49 (120)
T cd02395 17 VGLILGPRGNTLKQLEKETGAKISIRGKGSMKD 49 (120)
T ss_pred EEEEECCCCCHHHHHHHHHCCEEEEEECCCCCC
T ss_conf 678877985069999998798799971787667
No 262
>TIGR00118 acolac_lg acetolactate synthase, large subunit, biosynthetic type; InterPro: IPR012846 Two groups of proteins form acetolactate from two molecules of pyruvate. The type of acetolactate synthase described in this entry also catalyzes the formation of acetohydroxybutyrate from pyruvate and 2-oxobutyrate, an early step in the branched chain amino acid biosynthesis; it is therefore also termed acetohydroxyacid synthase. In bacteria, this catalytic chain is associated with a smaller regulatory chain in an alpha2/beta2 heterotetramer. Acetolactate synthase is a thiamine pyrophosphate enzyme. In this type, FAD and Mg++ are also found. Several isozymes of this enzyme are found in E. coli K12, one of which contains a frameshift in the large subunit gene and is not expressed.; GO: 0000287 magnesium ion binding, 0003984 acetolactate synthase activity, 0030976 thiamin pyrophosphate binding, 0050660 FAD binding, 0009082 branched chain family amino acid biosynthetic process.
Probab=40.36 E-value=14 Score=16.24 Aligned_cols=63 Identities=17% Similarity=0.460 Sum_probs=41.3
Q ss_pred CCCCCEEEEEEEEEEECCCCCCCCEECHHHHHHHCCCCC------CCCEEEEECCHHHHHHHHH------HHHHHHHHHH
Q ss_conf 499883999999885176778753234899986288986------4737998508456207999------9999999999
Q gi|254780788|r 54 NPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSID------IGGVVSDPLPPMDFGRVAV------QSAKQVIIQK 121 (526)
Q Consensus 54 D~~tG~i~i~~~~~VVedved~~~eI~l~~A~~~~~~~~------iGD~i~~~i~~~~fgRiaA------q~AKQvI~Qk 121 (526)
||-||++.-|. |+++ -|..|-.+|+|.+.|.+-. --||+|+.|-
T Consensus 293 DRvTGnl~~FA------------------------p~AkraaaeGrGGiiHiDIDPaeIgK~v~~diPiVGDAr~VL~~l 348 (593)
T TIGR00118 293 DRVTGNLAKFA------------------------PNAKRAAAEGRGGIIHIDIDPAEIGKNVRVDIPIVGDARNVLEEL 348 (593)
T ss_pred CCCCCCHHHHC------------------------HHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf 66348776723------------------------165675414787369998537655771146401036758999999
Q ss_pred HHHHHHH----HHHH--HHHHHCCC
Q ss_conf 9999988----7799--99852083
Q gi|254780788|r 122 VREAERD----RQYL--EFKDKVGE 140 (526)
Q Consensus 122 ireaEr~----~i~~--ef~~r~Ge 140 (526)
+...... ..-+ .|.+++.+
T Consensus 349 l~~~~~~~~~~~~~~~~~W~~~i~~ 373 (593)
T TIGR00118 349 LKKLEKEKALKERSEEQAWLEQINK 373 (593)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf 9998763035672248899999999
No 263
>KOG2279 consensus
Probab=39.24 E-value=15 Score=15.86 Aligned_cols=36 Identities=22% Similarity=0.210 Sum_probs=18.2
Q ss_pred EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEE
Q ss_conf 999985342211025442789999986167457855
Q gi|254780788|r 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIIT 343 (526)
Q Consensus 308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~ 343 (526)
.++-+|.-+..+-||..|--+.--|.-+|-++-|.+
T Consensus 298 ~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t 333 (608)
T KOG2279 298 PEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWT 333 (608)
T ss_pred CEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf 024447665410221013444465641575424775
No 264
>KOG3297 consensus
Probab=39.04 E-value=24 Score=14.50 Aligned_cols=123 Identities=22% Similarity=0.271 Sum_probs=70.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHHHHHCCCCCCCCEEEE
Q ss_conf 39999999999999999999613687453599974998839999998851767787532348999862889864737998
Q gi|254780788|r 20 KSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSD 99 (526)
Q Consensus 20 K~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A~~~~~~~~iGD~i~~ 99 (526)
=.|+...+-.-++.|+..-.+++|-...-..+.+ .+.+|....|-+-. +..||--..
T Consensus 11 VrI~P~qf~~~~~~ai~~eL~~k~anKvl~nvGL-----CI~vyDi~~v~e~~------------------v~pGDGas~ 67 (202)
T KOG3297 11 VRIPPSQFEKPLEDAIKEELNRKLANKVLPNVGL-----CICVYDILEVEEGI------------------VLPGDGASY 67 (202)
T ss_pred EECCHHHHCCHHHHHHHHHHHHHHHHHHCCCCCE-----EEEEEEEEEECCEE------------------EECCCCCEE
T ss_conf 6449689074578999999999987543246647-----99986750313407------------------803888657
Q ss_pred ECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECC-CEEEEEHHHCCCCCCCCC
Q ss_conf 5084562079999999999999999998877999985208389999984057638999579-358744787488751152
Q gi|254780788|r 100 PLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGN-SDGVIRRDETISRENLRP 178 (526)
Q Consensus 100 ~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~-~ea~Lp~~e~ip~E~~~~ 178 (526)
- ..-|-- --|+.-+||+|+|.++.-.+..+-|.||= -+-++|+.-+-+.-.|.+
T Consensus 68 ~--~V~FR~-----------------------vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~ 122 (202)
T KOG3297 68 A--RVWFRV-----------------------VVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEP 122 (202)
T ss_pred E--EEEEEE-----------------------EEEECCCCEEEEEEEECCCCCCEEEEEEEEECEEECHHHCCCCCCCCC
T ss_conf 9--999999-----------------------998514650899883037725418998831011306645899731560
Q ss_pred CCEEEEEEEEEC
Q ss_conf 766999997611
Q gi|254780788|r 179 GDRVKSYIYDVR 190 (526)
Q Consensus 179 Gdrika~i~~V~ 190 (526)
-.++=+..++-+
T Consensus 123 ~e~vWVWey~~E 134 (202)
T KOG3297 123 DEQVWVWEYEQE 134 (202)
T ss_pred CCEEEEEEECCC
T ss_conf 347999985166
No 265
>KOG3853 consensus
Probab=38.89 E-value=24 Score=14.49 Aligned_cols=71 Identities=15% Similarity=0.367 Sum_probs=41.4
Q ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEE------EECCCCCCCEEEEECCCCHHHHHHHH
Q ss_conf 702898715988999999997667775580878566316775034999------94089988127655488621788998
Q gi|254780788|r 194 RGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAV------FSSDSSIDPVGACVGMRGSRVQAVVT 267 (526)
Q Consensus 194 rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV------~s~d~~iDpVGAcVG~rGsRiq~I~~ 267 (526)
+.|-|++||+|...++.+-+. ++-.-+.|-- |--+|++.---| +-+-..|----.|-| .||.+
T Consensus 228 q~PiivVSRSH~g~vK~ia~~----vfG~~~~i~p-AgGaGYKvL~lv~~~A~lYlHtt~IKKWDiCAG------dAIL~ 296 (350)
T KOG3853 228 QNPIIVVSRSHAGKVKEIAEK----VFGDKMNIEP-AGGAGYKVLRLVNGTAELYLHTTAIKKWDICAG------DAILR 296 (350)
T ss_pred CCCEEEEECCCCCHHHHHHHH----HHCCCCEEEE-CCCCCEEEEEEECCCCEEEEEEHHHHHCCCCCH------HHHHH
T ss_conf 798799963444038999998----7367624665-587761566763375348987013201110330------89999
Q ss_pred HHCCCCEE
Q ss_conf 62778267
Q gi|254780788|r 268 ELRDEKID 275 (526)
Q Consensus 268 EL~gEkID 275 (526)
-|+|---+
T Consensus 297 alGG~Mtt 304 (350)
T KOG3853 297 ALGGAMTT 304 (350)
T ss_pred HCCCCEEC
T ss_conf 70463012
No 266
>KOG2767 consensus
Probab=37.66 E-value=25 Score=14.35 Aligned_cols=71 Identities=14% Similarity=0.208 Sum_probs=48.9
Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 99989999999879847889653267752123123444321124533435889999999999841225788800024564
Q gi|254780788|r 442 GIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVADEE 521 (526)
Q Consensus 442 gl~~~~~~~L~e~gIktleDlAels~dEL~~~~~~~~~~~~~~~gil~~~~l~~~~A~~lIM~AR~~~gWf~~e~~~~~~ 521 (526)
++....+......=++.+-|.-=|+-++++.|.++...+ -.+++.+..+.-.|..-+-|+.+.+.++++
T Consensus 327 ~~~~~el~~kva~ilk~lYd~DI~~e~vi~~w~~K~skk-----------~vsk~~sk~i~e~a~Pfi~WL~~AESe~ee 395 (400)
T KOG2767 327 EKHEAELISKVAGILKELYDEDILEEEVIIKWGEKPSKK-----------YVSKEKSKKIRENAKPFIEWLKNAESEDEE 395 (400)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-----------CCCHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 860787888889999998761022089999987514444-----------442544234676332799998741355532
Q ss_pred HH
Q ss_conf 11
Q gi|254780788|r 522 VQ 523 (526)
Q Consensus 522 ~~ 523 (526)
++
T Consensus 396 Ee 397 (400)
T KOG2767 396 EE 397 (400)
T ss_pred CC
T ss_conf 23
No 267
>pfam01470 Peptidase_C15 Pyroglutamyl peptidase.
Probab=37.06 E-value=20 Score=15.10 Aligned_cols=67 Identities=25% Similarity=0.293 Sum_probs=41.2
Q ss_pred CCEEEEECCCCH-------HHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE-ECCCCCEEEEEEC--CCC
Q ss_conf 812765548862-------1788998627782679955987899999762866542489-8756787999985--342
Q gi|254780788|r 249 DPVGACVGMRGS-------RVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV-LDEDVGRIEVIVP--KEQ 316 (526)
Q Consensus 249 DpVGAcVG~rGs-------Riq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~-~de~~~~~~v~v~--~~q 316 (526)
-|.+.|+-..|. -++++++.|+..-|+. .||.|.-.|+||.+.=--....- -....+...|-|| .+|
T Consensus 97 ~p~~~~i~~~gp~ay~stLp~~~i~~~l~~~gip~-~iS~dAG~ylCN~v~Y~sL~~~~~~~~~~~agFiHvP~~~~q 173 (203)
T pfam01470 97 QPIDEPIVPDGPAAYFATLPVKAMVKAMREAGIPA-AVSNTAGTFVCNHVMYLLLHHSAKKGPPVRAGFIHVPYLPEQ 173 (203)
T ss_pred CCCCCCEECCCCCHHHCCCCHHHHHHHHHHCCCCC-EECCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHH
T ss_conf 65897451599733205899999999999639984-773775523028999999999996299973899986899688
No 268
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=35.86 E-value=26 Score=14.16 Aligned_cols=68 Identities=18% Similarity=0.278 Sum_probs=45.5
Q ss_pred HHHHHHHHCCHHHHHHH---HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHH
Q ss_conf 11477750588887765---30588999999999999999999998987754284356640779998999999
Q gi|254780788|r 382 ADVEELACVKISEIASI---EGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVAL 451 (526)
Q Consensus 382 ~SiEeIa~a~~eeL~~I---eGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L 451 (526)
.+++.|+..+.++|.++ -||=--.|..|++-++.++..-. .-+........+.|+++.|+.++++...
T Consensus 67 ~~l~~i~~l~~e~La~lIrPaGFy~~KA~rLk~l~~~~~~d~~--~~~~~~~~~~Re~LL~lkGIG~ETADsI 137 (218)
T PRK13913 67 INLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSKNILKDFQ--SFENFKQEVTREWLLDQKGIGKESADAI 137 (218)
T ss_pred CCHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--HHHHCCCHHHHHHHHCCCCCCHHHHHHH
T ss_conf 5999997189999999950401589999999999999998752--5751453658999974898663339999
No 269
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=35.84 E-value=26 Score=14.16 Aligned_cols=33 Identities=9% Similarity=0.216 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf 999999999999999999961368745359997
Q gi|254780788|r 21 SIDRDVVLSVMADSIQKAARSLYGTMSDIRVEI 53 (526)
Q Consensus 21 ~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~i 53 (526)
-++++.+.+|+++++..+-+++|.+..++.+.+
T Consensus 3 ~v~~~~l~eai~~~l~~~k~rkF~ESvdl~i~L 35 (214)
T PTZ00225 3 KIPPQTLSEAIQAVLKVDKERKFKESIDLQVNL 35 (214)
T ss_pred CCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEEC
T ss_conf 788899999999999747677887308999973
No 270
>pfam00833 Ribosomal_S17e Ribosomal S17.
Probab=35.74 E-value=20 Score=15.10 Aligned_cols=46 Identities=24% Similarity=0.357 Sum_probs=19.4
Q ss_pred EEEEECCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 5785522001101001221000111225888467888877321114
Q gi|254780788|r 339 IDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADV 384 (526)
Q Consensus 339 idi~~~~~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~Si 384 (526)
|-++.-++..+++..-.-+.+.+-.+...||.+..++|...||.++
T Consensus 69 is~klqEeErerr~~yvPe~S~ld~~~ievd~~T~~ml~~~~~~~~ 114 (122)
T pfam00833 69 ISLKLQEEERERRDNYVPEVSELDVPLIEVDPDTKEMLKSLGFGNI 114 (122)
T ss_pred CCEEHHHHHHHHHCCCCCCCCCCCCCCEEECHHHHHHHHHCCCCCC
T ss_conf 0103447888755034776320246415788789999997598888
No 271
>TIGR00643 recG ATP-dependent DNA helicase RecG; InterPro: IPR004609 The ATP-dependent DNA helicase RecG 3.6.1 from EC plays a critical role in recombination and DNA repair. It helps to process Holliday junction intermediates to mature products by catalysing branch migration. RecG has DNA unwinding activity characteristic of a DNA helicase with 3' to 5' polarity.; GO: 0004003 ATP-dependent DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=35.15 E-value=23 Score=14.56 Aligned_cols=33 Identities=21% Similarity=0.389 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEE-EEEEC
Q ss_conf 9999999999887799998520838999-99840
Q gi|254780788|r 117 VIIQKVREAERDRQYLEFKDKVGEIISG-TVKRV 149 (526)
Q Consensus 117 vI~QkireaEr~~i~~ef~~r~Geiv~G-~V~r~ 149 (526)
.+--|+.+.||+.++.+|+.+.++|+.. +|.-|
T Consensus 569 LlHGrm~~~eK~~vm~~F~~~~~~ILVsTTVIEV 602 (721)
T TIGR00643 569 LLHGRMKSDEKEAVMEEFREGEVDILVSTTVIEV 602 (721)
T ss_pred EECCCCCHHHHHHHHHHHHHCCCEEEEEEEEEEE
T ss_conf 3306898478999999852158369999768999
No 272
>PRK13910 DNA glycosylase MutY; Provisional
Probab=34.24 E-value=28 Score=13.98 Aligned_cols=16 Identities=13% Similarity=0.372 Sum_probs=6.9
Q ss_pred EEEEECCCHHHHHHHH
Q ss_conf 8987159889999999
Q gi|254780788|r 197 QVLLSRTHPQFMVKLF 212 (526)
Q Consensus 197 qi~lSRt~p~~l~~Lf 212 (526)
++.|-|....++..|+
T Consensus 199 ~ilL~k~~~~~~~Glw 214 (290)
T PRK13910 199 QIALEKIEQKLYLGMH 214 (290)
T ss_pred EEEEEECCCCCCCCCC
T ss_conf 9999817886667766
No 273
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=33.53 E-value=28 Score=13.90 Aligned_cols=156 Identities=14% Similarity=0.218 Sum_probs=88.7
Q ss_pred CHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCE---EEE----CCCCCEEEEEECCCCCCCCCCC--------
Q ss_conf 6217889986277826799559878999997628665424---898----7567879999853422110254--------
Q gi|254780788|r 259 GSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTK---VVL----DEDVGRIEVIVPKEQLSLAIGR-------- 323 (526)
Q Consensus 259 GsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~---v~~----de~~~~~~v~v~~~qls~AIGk-------- 323 (526)
.+......++...+..|.+.+|......+...|....-.. ++. ........|.+-...-+.+|.-
T Consensus 60 ~~~f~~~L~~y~~~~~dF~~fS~~a~~~L~~~l~~~~~a~gG~llf~~Y~~~~~dyL~IalL~~~~g~~v~~~L~l~~~~ 139 (334)
T PRK00378 60 ESEFAQALREYREGELDFLAFSRQAAKRLQDELAKYPFAEGGFLLFCHYQYLATDYLFIALLSSKESMRVNEELDISPTH 139 (334)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCEEEEEEECCCCCEEECCCCCCCCCE
T ss_conf 86439999999707987799999999999999724886556189999997288538999998376725788875724140
Q ss_pred --CHHHHHHHHH--HHCCEEEEEECC--CHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf --4278999998--616745785522--0011010012210001112258884678888773211147775058888776
Q gi|254780788|r 324 --RGQNVRLASQ--LTGWTIDIITEE--EDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIAS 397 (526)
Q Consensus 324 --~GqNvrLas~--Ltg~~idi~~~~--~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~eeL~~ 397 (526)
.=.+..||++ ||.|..+--+.. -+...|. -...++-|++-|+..+-+.-.--+..+-. .+++..+
T Consensus 140 ~LDl~kl~~AaRInLt~w~~~~~s~rYlsFikgr~--grkvsdyF~~flGc~e~~~~~~~t~~Ll~-------av~df~~ 210 (334)
T PRK00378 140 YLDINQLDLAARIDLTEWETNPESNRYLSFIKGRV--GRKVADFFLDFLGAEEGLNTKAQNRTLLQ-------AVSDFVA 210 (334)
T ss_pred EEEHHHCCEEEEEEHHHHHCCCCCCCEEEEECCCC--CCHHHHHHHHHHCCCCCCCHHHHHHHHHH-------HHHHHHH
T ss_conf 86066621667998278526887771799985778--76199999997287445764999999999-------9999997
Q ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 53058899999999999999999999
Q gi|254780788|r 398 IEGFDEETAVEIQGRAREYLEGIDIT 423 (526)
Q Consensus 398 IeGfdee~a~eL~~rA~~~L~~~~~~ 423 (526)
-.+++.+.+.+.+.++-+|+..+...
T Consensus 211 ~~~l~~~~~~~~r~~v~~Yc~eq~~~ 236 (334)
T PRK00378 211 SADLDKEERQEVRKQVYDYCNEQLKA 236 (334)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 55899899999999999999999866
No 274
>TIGR01077 L13_A_E ribosomal protein L13; InterPro: IPR005755 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 of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein L13 is one of the proteins from the large ribosomal subunit . In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=33.14 E-value=26 Score=14.16 Aligned_cols=15 Identities=33% Similarity=0.426 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 620799999999999
Q gi|254780788|r 105 DFGRVAVQSAKQVII 119 (526)
Q Consensus 105 ~fgRiaAq~AKQvI~ 119 (526)
-+||.|+..|||++.
T Consensus 9 ilGRLAS~VAK~lL~ 23 (144)
T TIGR01077 9 ILGRLASVVAKRLLN 23 (144)
T ss_pred HHHHHHHHHHHHHHC
T ss_conf 137689999998757
No 275
>cd01702 Pol_eta Pol eta is member of the DNA polimerase Y-family. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced cis-syn cyclobutane thymine-thumine (T-T) lesions. It synthesizes AA opposite a TT dimer. Pol eta is able to replicate through a variety of other distorting DNA lesion as well.
Probab=33.01 E-value=29 Score=13.84 Aligned_cols=48 Identities=15% Similarity=0.189 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHH-HHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 8884678888773-21114777505888877653058899999999999
Q gi|254780788|r 367 NVDEIIAHLLVAE-GFADVEELACVKISEIASIEGFDEETAVEIQGRAR 414 (526)
Q Consensus 367 dVDE~iA~~LV~e-Gf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~ 414 (526)
+|...+++.|... |..++.+++.....+..-+..+.......|.+.|+
T Consensus 189 GvG~k~~~~L~~~lgi~ti~dl~~~~~~~~~l~~~~~~~~g~~l~~~a~ 237 (358)
T cd01702 189 GLGGKLGESIIEVLGVPTEGDLLWFRSSEAQLQEKLGDKTGTWLYNLVR 237 (358)
T ss_pred CCCHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 8678999999998399658989875148599999982799999999975
No 276
>KOG0438 consensus
Probab=32.93 E-value=29 Score=13.83 Aligned_cols=34 Identities=26% Similarity=0.460 Sum_probs=27.8
Q ss_pred EEEEECCCCCEEEEEEEEC-CCCCCCEEEEECCCC
Q ss_conf 8566316775034999940-899881276554886
Q gi|254780788|r 226 VKAVSRDPGSRAKLAVFSS-DSSIDPVGACVGMRG 259 (526)
Q Consensus 226 Ik~iaR~pG~RsKIAV~s~-d~~iDpVGAcVG~rG 259 (526)
|-.|-+|||--+|||+... ++..--+=||.||+-
T Consensus 105 v~~i~yDP~Rs~~iaLv~~~~~~~~~Ila~egm~a 139 (312)
T KOG0438 105 VIEIEYDPGRSAKIALVAGGTGELRYILATEGLKA 139 (312)
T ss_pred EEEEEECCCCCCCEEEEECCCCCEEEEEEECCCCC
T ss_conf 79999789864317888326777059998468878
No 277
>pfam11694 DUF3290 Protein of unknown function (DUF3290). This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=32.83 E-value=22 Score=14.65 Aligned_cols=64 Identities=14% Similarity=0.221 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCC
Q ss_conf 999999999986239999999999999999999613687453599974998839999998851767
Q gi|254780788|r 7 LELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEV 72 (526)
Q Consensus 7 ~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedv 72 (526)
..++..+++||++++++++.|.-.-...---+. =+.+ +...+|.+|.+...+.+-+...+..++
T Consensus 79 sq~~~Fi~~va~d~~V~~~~v~VNst~l~dG~i-Vki~-~~~Yrv~~n~d~~sY~Lek~~li~~~i 142 (149)
T pfam11694 79 QQIVHFIESVAKDLGVDKSEVYVNTSALTDGMI-VKIG-KNYYRVNLNTDNNSYTLEKATLIQPKI 142 (149)
T ss_pred HHHHHHHHHHHHHCCCCHHHEEEECCCCCCCEE-EEEC-CEEEEEEECCCCCEEEEEEEEEECCCC
T ss_conf 999999999988729987888994355657769-9987-827999987998706899999807874
No 278
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=32.77 E-value=29 Score=13.81 Aligned_cols=16 Identities=13% Similarity=0.067 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999999999999
Q gi|254780788|r 406 AVEIQGRAREYLEGID 421 (526)
Q Consensus 406 a~eL~~rA~~~L~~~~ 421 (526)
++.+++.|+..+....
T Consensus 112 a~~i~~~A~~~Ie~ek 127 (173)
T PRK13453 112 ANGMIETAQSEINSQK 127 (173)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9999999999999999
No 279
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=32.54 E-value=29 Score=13.79 Aligned_cols=39 Identities=26% Similarity=0.250 Sum_probs=18.6
Q ss_pred HHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCC
Q ss_conf 664077999899999998798478896532677521231
Q gi|254780788|r 436 ELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS 474 (526)
Q Consensus 436 ~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~~~ 474 (526)
.+.++.|+...++.+|...||.|.-||+.+..|.|....
T Consensus 177 pv~~~~GvG~~~~~~l~~~Gi~ti~dl~~~~~~~L~~~~ 215 (354)
T COG0389 177 PVLEFWGVGKVTAEKLRRLGISTIGDLAETDLDALKKRF 215 (354)
T ss_pred CHHHHCCCCHHHHHHHHHCCCHHHHHHHHCCHHHHHHHH
T ss_conf 567726845899999997284889998735899999999
No 280
>TIGR02660 nifV_homocitr homocitrate synthase; InterPro: IPR013477 Most NifV-type homocitrate synthases are encoded within operons for nitrogen fixation. They are homologous to enzymes that include 2-isopropylmalate synthase, (R)-citramalate synthase, and homocitrate synthases associated with other processes. The homocitrate made by these enzymes becomes a part of the iron-molybdenum cofactor of nitrogenase.; GO: 0004410 homocitrate synthase activity, 0051188 cofactor biosynthetic process.
Probab=31.43 E-value=30 Score=13.76 Aligned_cols=63 Identities=24% Similarity=0.290 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHH
Q ss_conf 67888877321114777505888877653058899999999999999999999898775428435664077999899999
Q gi|254780788|r 371 IIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVA 450 (526)
Q Consensus 371 ~iA~~LV~eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~ 450 (526)
.||+.|...|...+| ..||.|.++-...|+. +-.+++.-.|+.=.=|....+..
T Consensus 27 aIA~aLd~aGV~ElE----------vGiPAMG~~E~~~ira----------------I~~~~l~a~l~~WcR~~~~Di~a 80 (369)
T TIGR02660 27 AIARALDEAGVDELE----------VGIPAMGEEERAVIRA----------------IVALGLKARLMAWCRARDADIEA 80 (369)
T ss_pred HHHHHHHHHCCCEEE----------ECCCCCCHHHHHHHHH----------------HHHCCCCCEEEHHHHCCHHHHHH
T ss_conf 999999980962476----------1577687889999999----------------99628993031100104799999
Q ss_pred HHHCCCCCH
Q ss_conf 998798478
Q gi|254780788|r 451 LGENGIKTM 459 (526)
Q Consensus 451 L~e~gIktl 459 (526)
-.+.|+..+
T Consensus 81 a~~~G~~~V 89 (369)
T TIGR02660 81 AARCGVDAV 89 (369)
T ss_pred HHHHHHHEE
T ss_conf 987205203
No 281
>PRK13763 putative RNA-processing protein; Provisional
Probab=31.18 E-value=31 Score=13.63 Aligned_cols=38 Identities=26% Similarity=0.502 Sum_probs=24.5
Q ss_pred EEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECC
Q ss_conf 99998534221102544278999998616745785522
Q gi|254780788|r 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEE 345 (526)
Q Consensus 308 ~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~ 345 (526)
..+-||.+-+...||+.|...+-.-+.+|-+|+|-+++
T Consensus 6 ~~v~IP~~Ri~~Lig~~g~~~~~Iee~~~~~i~idsk~ 43 (185)
T PRK13763 6 EYVKIPKDRIGVLIGKKGETKKEIEEKTGVKLEIDSET 43 (185)
T ss_pred EEEECCCHHEEEEECCCCCCHHHHHHHHCCEEEEECCC
T ss_conf 56417805456455788563789999979779995899
No 282
>PRK00642 inorganic pyrophosphatase; Provisional
Probab=30.88 E-value=29 Score=13.84 Aligned_cols=22 Identities=23% Similarity=0.205 Sum_probs=13.3
Q ss_pred HHHCC-CHHHHHHHHHHHHHHHH
Q ss_conf 65305-88999999999999999
Q gi|254780788|r 397 SIEGF-DEETAVEIQGRAREYLE 418 (526)
Q Consensus 397 ~IeGf-dee~a~eL~~rA~~~L~ 418 (526)
.+.|+ +.+.|.+++.+|.+...
T Consensus 184 ~v~g~~~~e~A~~iI~~s~e~Y~ 206 (212)
T PRK00642 184 EIVGIYGKKEAQKVIQLAHEDYL 206 (212)
T ss_pred EECCCCCHHHHHHHHHHHHHHHH
T ss_conf 98868699999999999999999
No 283
>KOG2093 consensus
Probab=30.81 E-value=31 Score=13.59 Aligned_cols=137 Identities=21% Similarity=0.207 Sum_probs=77.1
Q ss_pred CCCC-CCHHHHHHHHHHHCCEEEEEE--CCCHHHHHHC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf 1025-442789999986167457855--2200110100--1221000111225888467888877321114777505888
Q gi|254780788|r 319 LAIG-RRGQNVRLASQLTGWTIDIIT--EEEDSINRQK--DFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKIS 393 (526)
Q Consensus 319 ~AIG-k~GqNvrLas~Ltg~~idi~~--~~~~~~~~~~--e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a~~e 393 (526)
.+-| |+|.=||-|-+|+- ++-++- -+.+.+.-+. |....+.+++++...||..- ...
T Consensus 421 R~~GIKNGMfV~~A~klCP-qL~~lPY~FE~Ykevs~tlYetlasytl~I~aVSCDEa~v-----------------d~s 482 (1016)
T KOG2093 421 RAYGIKNGMFVRHAKKLCP-QLVILPYDFEAYKEVSETLYETLASYTLNIEAVSCDEAFV-----------------DVS 482 (1016)
T ss_pred HHHCCCCCEEHHHHHHHCC-CCEEECCCHHHHHHHHHHHHHHHHHHCCCEEEECCHHHHH-----------------HHH
T ss_conf 8738413401788987493-2076166389999999999999986400102312016552-----------------110
Q ss_pred HHHHHHCCCH-HHHHHHHHHHH-------------HHHHH-HHHH----------HHHHHHHCCHHHHHHCCCCCCHHHH
Q ss_conf 8776530588-99999999999-------------99999-9999----------8987754284356640779998999
Q gi|254780788|r 394 EIASIEGFDE-ETAVEIQGRAR-------------EYLEG-IDIT----------LQKKIRELGVSEELCSIPGIDSKIK 448 (526)
Q Consensus 394 eL~~IeGfde-e~a~eL~~rA~-------------~~L~~-~~~~----------~~e~~~e~~~~e~L~~l~gl~~~~~ 448 (526)
+|..+...+. ..|..||.--. .-|++ .+.. .-++.++.-....|-+|+|....|.
T Consensus 483 ~~~~~~~~tp~~la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~~veeFis~~~v~~LPGVG~sm~ 562 (1016)
T KOG2093 483 DLSDEENETPAVLAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSAEKVEEFISQLKVDDLPGVGSSMK 562 (1016)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCCCCCHHHH
T ss_conf 13544316899999999999986249862313144799999987305888616635889999861055566877428999
Q ss_pred HHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf 9999879847889653267752123
Q gi|254780788|r 449 VALGENGIKTMEDLAGCSVDDLLGW 473 (526)
Q Consensus 449 ~~L~e~gIktleDlAels~dEL~~~ 473 (526)
.+|...+|+|.-||--.+-+.|.--
T Consensus 563 ~kL~s~~i~tCgdLq~~T~~kl~k~ 587 (1016)
T KOG2093 563 SKLVSQFIQTCGDLQLITLIKLRKV 587 (1016)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 9999852424688999999987765
No 284
>PRK05578 cytidine deaminase; Validated
Probab=30.36 E-value=32 Score=13.54 Aligned_cols=30 Identities=17% Similarity=0.479 Sum_probs=19.4
Q ss_pred CCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf 89988127655488621788998627782679955987
Q gi|254780788|r 245 DSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPD 282 (526)
Q Consensus 245 d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d 282 (526)
+.-+-|-|+| +-+..|+.+..+.|+..+.+
T Consensus 80 ~~~~~PCG~C--------RQvl~Ef~~~~~~i~l~~~~ 109 (132)
T PRK05578 80 GEPLSPCGRC--------RQVLAEFGGPDLLVTLVAKK 109 (132)
T ss_pred CCCCCCCHHH--------HHHHHHHCCCCCEEEEECCC
T ss_conf 9826975248--------99999856899489998799
No 285
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=30.35 E-value=32 Score=13.54 Aligned_cols=90 Identities=24% Similarity=0.409 Sum_probs=63.0
Q ss_pred EEECCCHHHHHHHHHHHHHHHHCCEEE-EEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEE
Q ss_conf 871598899999999766777558087-8566316775034999940899881276554886217889986277826799
Q gi|254780788|r 199 LLSRTHPQFMVKLFHMEVPEIYNGIVQ-VKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIV 277 (526)
Q Consensus 199 ~lSRt~p~~l~~Lf~~EVPEI~~G~ie-Ik~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii 277 (526)
+=|-+..+|=-.||-+..| +|-.. |.+|| +|- |-...++.+| +-.|.++-.|=|-|=+|-..
T Consensus 201 ID~~sT~DmDDALy~~~~~---~~~~~L~vAIA-DPT-----AyI~~~s~ld--------~~A~~R~FTnYLPGfNIPML 263 (645)
T COG4776 201 IDSESTEDMDDALYAEPLP---DGDWQLIVAIA-DPT-----AYIAEGSKLD--------KEAKIRAFTNYLPGFNIPML 263 (645)
T ss_pred ECCCCCCCCCHHHHCCCCC---CCCEEEEEEEC-CCC-----CCCCCCCHHH--------HHHHHHHHHHCCCCCCCCCC
T ss_conf 5586545522234221278---99769999961-874-----2027842676--------99998777504887887778
Q ss_pred EC--CCCHHHHHHHHCCCCCCCEEEECCCC
Q ss_conf 55--98789999976286654248987567
Q gi|254780788|r 278 VW--SPDSATFVINALRPAIVTKVVLDEDV 305 (526)
Q Consensus 278 ~w--s~d~~~fi~nAl~PA~v~~v~~de~~ 305 (526)
+- |||.-.+..|-.-||-+..|.++.+.
T Consensus 264 PreLsd~lCSL~~ne~RPaL~C~it~~~~G 293 (645)
T COG4776 264 PRELSDDLCSLRANEVRPALACRITIDKDG 293 (645)
T ss_pred CHHHHHHHHHCCCCCCCCEEEEEEEECCCC
T ss_conf 823405664235466673389999981477
No 286
>PRK10929 hypothetical protein; Provisional
Probab=30.26 E-value=32 Score=13.53 Aligned_cols=36 Identities=8% Similarity=0.142 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 888999999999986239999999999999999999
Q gi|254780788|r 4 ANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAA 39 (526)
Q Consensus 4 ~~~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~ 39 (526)
.+..++-+=++.+...|+-+...+++.++.|+..-.
T Consensus 23 P~~~~iq~~L~~~~~~k~p~q~~~i~~lq~aL~~L~ 58 (1109)
T PRK10929 23 PDEKQITQELEQAKAAKTPAQPEVVEALQSALNALE 58 (1109)
T ss_pred CCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 898999999999764799437999999999999999
No 287
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: 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 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.95 E-value=32 Score=13.49 Aligned_cols=56 Identities=18% Similarity=0.234 Sum_probs=40.6
Q ss_pred EEEEEECCCCEEEEEECC--CEEEEEHH-H-----CCCCCCCCCCCEEEEEEEEECCCCCEEEE
Q ss_conf 999984057638999579--35874478-7-----48875115276699999761135870289
Q gi|254780788|r 143 SGTVKRVEYGNVIVDLGN--SDGVIRRD-E-----TISRENLRPGDRVKSYIYDVRREQRGPQV 198 (526)
Q Consensus 143 ~G~V~r~e~~~iiVdlg~--~ea~Lp~~-e-----~ip~E~~~~Gdrika~i~~V~~~~rgpqi 198 (526)
+++|+..+..+.++.|-. --+..|-. . +--.|++++|..+.+-++.++....||-+
T Consensus 5 ~a~VQH~~k~FAi~SL~~Tg~L~afp~~sHlNdtFrfdSeKL~vGq~~~v~lk~~~~~~~g~ll 68 (69)
T cd05701 5 TAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLL 68 (69)
T ss_pred HHHHHHHHHCEEEEEEECCCCEEEEECHHHCCCCCCCCCCEEECCCEEEEEEECCCCCCCCEEC
T ss_conf 2533212110689996044647999714643664345731153365499998137767654111
No 288
>PRK13193 pyrrolidone-carboxylate peptidase; Provisional
Probab=29.78 E-value=21 Score=14.90 Aligned_cols=116 Identities=18% Similarity=0.109 Sum_probs=62.2
Q ss_pred CCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEE-----EECCCC------
Q ss_conf 766999997611358702898715988999999997667775580878566316775034999-----940899------
Q gi|254780788|r 179 GDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAV-----FSSDSS------ 247 (526)
Q Consensus 179 Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV-----~s~d~~------ 247 (526)
|.++...+.-|... .+.+.+..+.+..=| ..|- .-=.+|.|++|.+ --.|.+
T Consensus 33 ~~~v~~~~LPv~~~----------~~~~~l~~~i~~~~P----d~vi---~lG~a~gr~~i~lErvAiN~~d~~ipDn~G 95 (201)
T PRK13193 33 KEEVKGVILPVEYD----------KIEDMIVTKIREYKP----ILTL---GIGLAPGRAKITPEKIAINYKYSREGDNAG 95 (201)
T ss_pred CCEEEEEEECCCHH----------HHHHHHHHHHHHCCC----CEEE---ECCCCCCCCCCCHHHHHHHHCCCCCCCCCC
T ss_conf 84589999687088----------899999999985199----6899---805678977110768510010067897788
Q ss_pred CCCEEEEECCCC-------HHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEEC
Q ss_conf 881276554886-------217889986277826799559878999997628665424898756787999985
Q gi|254780788|r 248 IDPVGACVGMRG-------SRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVP 313 (526)
Q Consensus 248 iDpVGAcVG~rG-------sRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~ 313 (526)
--|.+.||=..| --++++++.|+..-|+. .+|.+.-.|+||.+.=--... .-....+...|-||
T Consensus 96 ~~p~~~~i~~~Gp~ay~stLPi~~i~~~l~~~Gipa-~vS~~AGtyvCN~~~Y~~L~~-~~~~~~~~gFIHvP 166 (201)
T PRK13193 96 KKYKGEKIDPLGQDGIFTNIPVEDLVDLLNENGIPA-ELSLSAGSYLCNNAMYIIIRE-ARKYNSLGGFIHVP 166 (201)
T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEECCCCCCHHHHHHHHHHHH-HCCCCCEEEEEECC
T ss_conf 987998637899751445789999999998679987-995886531416999999997-35699815899848
No 289
>PRK13194 pyrrolidone-carboxylate peptidase; Provisional
Probab=29.56 E-value=20 Score=15.00 Aligned_cols=52 Identities=17% Similarity=0.149 Sum_probs=33.6
Q ss_pred HHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE-ECCCCCEEEEEEC
Q ss_conf 1788998627782679955987899999762866542489-8756787999985
Q gi|254780788|r 261 RVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV-LDEDVGRIEVIVP 313 (526)
Q Consensus 261 Riq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~-~de~~~~~~v~v~ 313 (526)
-++++++.|+...|+. .||.|.-.|+||.+.=--..... -....+...|-||
T Consensus 116 P~~~i~~~l~~~gipa-~vS~~AGtyvCN~~~Y~~L~~~~~~~~~~~~gFiHvP 168 (204)
T PRK13194 116 PTREIVEEMKENGIPA-VLSYTAGTYLCNFVMYLTLHHSATKGYPKMAGFIHVP 168 (204)
T ss_pred CHHHHHHHHHHCCCCE-EEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECC
T ss_conf 9999999999769981-7847875216379999999999974999747899889
No 290
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=29.02 E-value=33 Score=13.38 Aligned_cols=40 Identities=23% Similarity=0.446 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHH---HHHHHHHH
Q ss_conf 32111477750588887765305889999999---99999999
Q gi|254780788|r 379 EGFADVEELACVKISEIASIEGFDEETAVEIQ---GRAREYLE 418 (526)
Q Consensus 379 eGf~SiEeIa~a~~eeL~~IeGfdee~a~eL~---~rA~~~L~ 418 (526)
.-|.|+..+..++.++|..+.|+....+..++ +.++.++.
T Consensus 52 ~~fg~L~~l~~a~~~el~~v~GiG~aka~~l~a~~El~~R~~~ 94 (224)
T COG2003 52 QEFGSLAELLKASVEELSSVKGIGLAKAIQIKAAIELGKRILA 94 (224)
T ss_pred HHCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 9732588887379999951788338899999999999999999
No 291
>PRK11281 potassium efflux protein KefA; Provisional
Probab=28.77 E-value=34 Score=13.35 Aligned_cols=33 Identities=9% Similarity=0.212 Sum_probs=18.4
Q ss_pred CHHHHHHHHHHHHHHCCCCHH--HHHHHHHHHHHH
Q ss_conf 889999999999862399999--999999999999
Q gi|254780788|r 5 NRLELLQIADAVAYEKSIDRD--VVLSVMADSIQK 37 (526)
Q Consensus 5 ~~~ell~vie~va~EK~I~~e--~i~~aie~Al~~ 37 (526)
+..++-+=++.+.+.|..+.+ .++..++++|..
T Consensus 35 t~~~iq~~L~~l~~~~~~~~~~k~~~q~Lq~aL~~ 69 (1107)
T PRK11281 35 TEADVQAQLDKLNKQKDLEAQDKLVQQDLEQTLAL 69 (1107)
T ss_pred CHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 99999999998626779997789999999999999
No 292
>cd00412 pyrophosphatase Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.
Probab=28.46 E-value=34 Score=13.31 Aligned_cols=67 Identities=19% Similarity=0.172 Sum_probs=32.9
Q ss_pred CCCEEEEEEEECCC--CCCCE----EEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE--ECC
Q ss_conf 77503499994089--98812----7655488621788998627782679955987899999762866542489--875
Q gi|254780788|r 233 PGSRAKLAVFSSDS--SIDPV----GACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV--LDE 303 (526)
Q Consensus 233 pG~RsKIAV~s~d~--~iDpV----GAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~--~de 303 (526)
.|+|.|.-+-.... .+|-+ ...=+.-|-==|.. +--|--+|++..++.|.. ..++-.|++..+. +|+
T Consensus 11 ~gs~~KyE~d~~~g~~~~DR~l~~~~~yP~nYGfIP~T~--~~DgDPLDvlvl~~~p~~--~G~vv~~r~iG~l~m~D~ 85 (155)
T cd00412 11 KGSNAKYEIDKETGPIKVDRFLYSSMGYPWNYGFIPQTL--EDDGDPLDVLVIGEEPLF--PGSVIRVRPLGVLKMIDE 85 (155)
T ss_pred CCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHH--CCCCCCEEEEEECCCCCC--CCCEEEEEEEEEEEECCC
T ss_conf 999857999168898889565167898986623012344--269997579985487538--930899999899996228
No 293
>TIGR02701 shell_carb_anhy carboxysome shell carbonic anhydrase; InterPro: IPR014074 This entry describes a carboxysome shell protein that proves to be a novel class, designated epsilon, of carbonic anhydrase. It tends to be encoded near genes for RuBisCo and other carboxysome shell proteins..
Probab=28.29 E-value=34 Score=13.35 Aligned_cols=112 Identities=16% Similarity=0.301 Sum_probs=58.0
Q ss_pred EEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 59997499883999999885176778753234899986288986473799850845620799999999999999999988
Q gi|254780788|r 49 IRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERD 128 (526)
Q Consensus 49 i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A~~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~ 128 (526)
|||+|=-..|++..||.. +. .++ ..+-=-.+|+.|||.|.|.|-++.+.
T Consensus 263 irvH~PdadG~~~lyR~V---~~-------------~~L---------------Y~eT~~L~a~~Ar~~I~~~i~~a~~~ 311 (463)
T TIGR02701 263 IRVHVPDADGKVNLYRYV---DT-------------EEL---------------YKETVGLTADEARQHIAERIDAANAK 311 (463)
T ss_pred CEEECCCCCCCCCCCCCC---CH-------------HHH---------------HHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_conf 166122267855700035---76-------------899---------------98510688889999999999997626
Q ss_pred H--------HHHHHHHHCCCEEEEEEEECCC-----CEEEE--EECCCEEEEEHHHCCCCCCCCCCCEEEEEEEEECCC
Q ss_conf 7--------7999985208389999984057-----63899--957935874478748875115276699999761135
Q gi|254780788|r 129 R--------QYLEFKDKVGEIISGTVKRVEY-----GNVIV--DLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRRE 192 (526)
Q Consensus 129 ~--------i~~ef~~r~Geiv~G~V~r~e~-----~~iiV--dlg~~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~ 192 (526)
. --+=-...++.++..-..++++ ++=|= |+|..|=++---+-- .|.--.+-.+-||+--|+..
T Consensus 312 dgwa~G~Gvp~eGmr~lI~~L~~NNlSQI~YV~~~h~GrYpPnDiGHaERFI~VG~GF-~EVQ~RNL~YfahLDTVEEG 389 (463)
T TIGR02701 312 DGWAKGNGVPQEGMRRLIAKLLANNLSQIEYVVRSHGGRYPPNDIGHAERFISVGDGF-DEVQLRNLAYFAHLDTVEEG 389 (463)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEECCCCC-CEEEEEECEEEEEEEEEEEC
T ss_conf 8851256667645899999999863005888536787988823367464412016761-23464311024554457537
No 294
>PRK09970 xanthine dehydrogenase subunit XdhA; Provisional
Probab=28.24 E-value=34 Score=13.29 Aligned_cols=27 Identities=11% Similarity=0.128 Sum_probs=11.3
Q ss_pred CCCCCEEEE-EEEECCCCCCCEEEEECCCCH
Q ss_conf 167750349-999408998812765548862
Q gi|254780788|r 231 RDPGSRAKL-AVFSSDSSIDPVGACVGMRGS 260 (526)
Q Consensus 231 R~pG~RsKI-AV~s~d~~iDpVGAcVG~rGs 260 (526)
+.|..|... +|+||.+ |.||+=|..+.
T Consensus 338 ~i~~~~~~~~~v~TN~~---~~ga~RG~G~p 365 (762)
T PRK09970 338 PRCAYKYSSKTCYTNLP---SAGAMRGYGAP 365 (762)
T ss_pred CCCEEEEEEEEEECCCC---CCCCCCCCCHH
T ss_conf 67607999899978999---87762169658
No 295
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=27.81 E-value=35 Score=13.23 Aligned_cols=70 Identities=17% Similarity=0.277 Sum_probs=35.5
Q ss_pred CCCCCCCEEEEECCHHH-HHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECC
Q ss_conf 89864737998508456-207999999999---9999999998877999985208389999984057638999579
Q gi|254780788|r 89 PSIDIGGVVSDPLPPMD-FGRVAVQSAKQV---IIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGN 160 (526)
Q Consensus 89 ~~~~iGD~i~~~i~~~~-fgRiaAq~AKQv---I~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~ 160 (526)
...++||...+.|+|.+ ||-.--....++ .++...+.+--+++ ....--|. +.++|..++.+.|.||.+.
T Consensus 50 ~G~~~Gd~~~vtl~peeAYG~~de~lv~~vp~~~f~~~~~le~Gm~~-~~~~~~G~-~~~~V~eV~~~~VtvD~NH 123 (196)
T PRK10737 50 EGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMRF-LAETDQGP-VPVEITAVEDDHVVVDGNH 123 (196)
T ss_pred CCCCCCCEEEEEECHHHHCCCCCHHHEEEECHHHCCCCCCCCCCCEE-EECCCCCE-EEEEEEEECCCEEEEECCC
T ss_conf 79999977899978799168889799488258896876434567099-88079984-8899999779989995898
No 296
>cd01296 Imidazolone-5PH Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria, the enzyme is part of histidine utilization (hut) operon.
Probab=27.50 E-value=35 Score=13.20 Aligned_cols=13 Identities=8% Similarity=0.335 Sum_probs=4.3
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999999976677
Q gi|254780788|r 206 QFMVKLFHMEVPE 218 (526)
Q Consensus 206 ~~l~~Lf~~EVPE 218 (526)
.++..++..-.|.
T Consensus 159 ~~~~~~~~~~~~~ 171 (371)
T cd01296 159 EYIDLVIEEVLPA 171 (371)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999999
No 297
>COG1529 CoxL Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]
Probab=27.41 E-value=36 Score=13.18 Aligned_cols=17 Identities=18% Similarity=0.180 Sum_probs=6.5
Q ss_pred EEEEEECCCHHHHHHHH
Q ss_conf 28987159889999999
Q gi|254780788|r 196 PQVLLSRTHPQFMVKLF 212 (526)
Q Consensus 196 pqi~lSRt~p~~l~~Lf 212 (526)
.-+..|-.+|-.++..+
T Consensus 197 lt~~~~tQ~~~~~~~~l 213 (731)
T COG1529 197 LTVWASTQIPHRLRGML 213 (731)
T ss_pred EEEEECCCCCHHHHHHH
T ss_conf 89997655523558899
No 298
>TIGR03194 4hydrxCoA_A 4-hydroxybenzoyl-CoA reductase, alpha subunit. This model represents the largest chain, alpha, of the enzyme 4-hydroxybenzoyl-CoA reductase. In species capable of degrading various aromatic compounds by way of benzoyl-CoA, this enzyme can convert 4-hydroxybenzoyl-CoA to benzoyl-CoA.
Probab=27.20 E-value=36 Score=13.16 Aligned_cols=28 Identities=21% Similarity=0.366 Sum_probs=13.2
Q ss_pred CCCCEEE-EEEEECCCCCCCEEEEECCCCHHH
Q ss_conf 6775034-999940899881276554886217
Q gi|254780788|r 232 DPGSRAK-LAVFSSDSSIDPVGACVGMRGSRV 262 (526)
Q Consensus 232 ~pG~RsK-IAV~s~d~~iDpVGAcVG~rGsRi 262 (526)
.|-.|.. .+|+||.+ |.||+=|.-+.-.
T Consensus 323 ipn~~~~~~~V~TN~~---p~ga~RG~G~pq~ 351 (746)
T TIGR03194 323 IPAVKYDGYRVYTNTP---PCGAMRGHGTVDT 351 (746)
T ss_pred CCEEEEEEEEEECCCC---CCCCEECCCCCCH
T ss_conf 6607999999956899---9751567886202
No 299
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=27.16 E-value=36 Score=13.15 Aligned_cols=54 Identities=15% Similarity=0.295 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHC
Q ss_conf 999999766777558087856631677503499994089988127655488621788998627
Q gi|254780788|r 208 MVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELR 270 (526)
Q Consensus 208 l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~ 270 (526)
|.++|..|..+=.-+-+||+ ---.||+|.+++..| |.++|-+|.||+....-|+
T Consensus 7 LnEfl~reL~~~GYsGvevr----~Tp~~teIiI~atrp-----~~ViG~kg~rIreLt~~lq 60 (81)
T cd02413 7 LNEFLTRELAEDGYSGVEVR----VTPTRTEIIIRATRT-----QNVLGEKGRRIRELTSLVQ 60 (81)
T ss_pred HHHHHHHHHHHCCCCCEEEE----ECCCCEEEEEEECCC-----CEEECCCCEEHHHHHHHHH
T ss_conf 89999999986787735999----658861999995365-----1556358804999999999
No 300
>pfam09953 DUF2187 Uncharacterized protein conserved in bacteria (DUF2187). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=27.08 E-value=36 Score=13.14 Aligned_cols=18 Identities=44% Similarity=0.696 Sum_probs=15.8
Q ss_pred EEEEEEECCCCEEEEEEC
Q ss_conf 999998405763899957
Q gi|254780788|r 142 ISGTVKRVEYGNVIVDLG 159 (526)
Q Consensus 142 v~G~V~r~e~~~iiVdlg 159 (526)
+.|+|.++..+.+||||-
T Consensus 16 l~GiVeKvNeNSVIVdlT 33 (57)
T pfam09953 16 LQGIVEKVNENSVIVDLT 33 (57)
T ss_pred CEEEEEEECCCCEEEEEE
T ss_conf 201001304783899988
No 301
>TIGR02704 carboxysome_B carboxysome peptide B; InterPro: IPR014077 This entry describes the carboxysome operon protein orfB (protein B of Thiobacillus denitrificans). It distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins are components of other types of shell such as the shell of the ethanolamine degradation organelle..
Probab=26.80 E-value=36 Score=13.11 Aligned_cols=32 Identities=34% Similarity=0.559 Sum_probs=20.3
Q ss_pred EEEEECCCCCEE-EEEEEECCCC-----CCCEEEEECC
Q ss_conf 856631677503-4999940899-----8812765548
Q gi|254780788|r 226 VKAVSRDPGSRA-KLAVFSSDSS-----IDPVGACVGM 257 (526)
Q Consensus 226 Ik~iaR~pG~Rs-KIAV~s~d~~-----iDpVGAcVG~ 257 (526)
..+--|.||... ..=|..+... .|||||-.|.
T Consensus 10 Lv~TrR~pGL~~~sLRvL~~~~G~~~VA~DPvG~p~G~ 47 (80)
T TIGR02704 10 LVCTRRIPGLKNASLRVLEDAKGKISVAVDPVGAPEGK 47 (80)
T ss_pred EEEEECCCCCCCCEEEEECCCCCCEEEEECCCCCCCCC
T ss_conf 13420255655502565229996467854576789897
No 302
>KOG0196 consensus
Probab=25.81 E-value=38 Score=12.98 Aligned_cols=25 Identities=32% Similarity=0.470 Sum_probs=15.9
Q ss_pred HHHHHCCCCCHHHHHHCCHHHHCCC
Q ss_conf 9999879847889653267752123
Q gi|254780788|r 449 VALGENGIKTMEDLAGCSVDDLLGW 473 (526)
Q Consensus 449 ~~L~e~gIktleDlAels~dEL~~~ 473 (526)
..+.++|+.|++++|.++.++|.-+
T Consensus 940 ~~F~~ag~~s~~~V~q~s~eDl~~~ 964 (996)
T KOG0196 940 EHFAAAGYTSFEDVAQMSAEDLLRL 964 (996)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf 7777638541999976248889863
No 303
>KOG1921 consensus
Probab=25.78 E-value=38 Score=12.98 Aligned_cols=75 Identities=23% Similarity=0.247 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHH---HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHCCCCCCH
Q ss_conf 678888773211147775058888776---5305889999999999999999999989877542--84356640779998
Q gi|254780788|r 371 IIAHLLVAEGFADVEELACVKISEIAS---IEGFDEETAVEIQGRAREYLEGIDITLQKKIREL--GVSEELCSIPGIDS 445 (526)
Q Consensus 371 ~iA~~LV~eGf~SiEeIa~a~~eeL~~---IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~--~~~e~L~~l~gl~~ 445 (526)
.-...|-..|--|+|.|..++...|.+ --||-.-.| .||..-+.-...+...- ..-++|+.|+|+.+
T Consensus 98 ~Am~rL~~~~gLT~e~v~~~de~~l~~LI~~VgFy~rKA--------~ylkkta~IL~d~f~gDIP~~v~dLlsLPGVGP 169 (286)
T KOG1921 98 AAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYTRKA--------KYLKKTAKILQDKFDGDIPDTVEDLLSLPGVGP 169 (286)
T ss_pred HHHHHHHHHCCCCHHHHHCCCHHHHHHHHHHCCCHHHHH--------HHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCH
T ss_conf 999999985597899986167576876500012157888--------999999999998707997555998855899765
Q ss_pred HHHHHHHH
Q ss_conf 99999998
Q gi|254780788|r 446 KIKVALGE 453 (526)
Q Consensus 446 ~~~~~L~e 453 (526)
.|+...-.
T Consensus 170 KMa~L~m~ 177 (286)
T KOG1921 170 KMAHLTMQ 177 (286)
T ss_pred HHHHHHHH
T ss_conf 99999999
No 304
>KOG3873 consensus
Probab=24.54 E-value=35 Score=13.23 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=17.3
Q ss_pred EEEECCCCHHHHHHHHHHC--CCCEEEEECCCCH
Q ss_conf 7655488621788998627--7826799559878
Q gi|254780788|r 252 GACVGMRGSRVQAVVTELR--DEKIDIVVWSPDS 283 (526)
Q Consensus 252 GAcVG~rGsRiq~I~~EL~--gEkIDii~ws~d~ 283 (526)
++|--+..+-..+--++=. |-|||-+.++.+-
T Consensus 225 ~tcd~~~N~y~~aqk~~ddp~~~RiDYvl~k~~~ 258 (422)
T KOG3873 225 NTCDSPLNCYTSAQKREDDPLGKRIDYVLVKPGD 258 (422)
T ss_pred CCCCCCCHHHHHHHHCCCCCCCEEEEEEEECCCC
T ss_conf 7656751036678747887543156689973761
No 305
>PRK13680 hypothetical protein; Provisional
Probab=24.35 E-value=28 Score=13.90 Aligned_cols=45 Identities=20% Similarity=0.395 Sum_probs=35.0
Q ss_pred EEEEECCCCCCCEEEEECCCCHHHHHHHHH--HCCCCEEEEECCCCHHHH
Q ss_conf 999940899881276554886217889986--277826799559878999
Q gi|254780788|r 239 LAVFSSDSSIDPVGACVGMRGSRVQAVVTE--LRDEKIDIVVWSPDSATF 286 (526)
Q Consensus 239 IAV~s~d~~iDpVGAcVG~rGsRiq~I~~E--L~gEkIDii~ws~d~~~f 286 (526)
+++.+.+++..++.+|.|+.-+-|-+=++. |+| -|..|.+|...+
T Consensus 23 ~~a~~ee~r~akf~~C~gL~~~qIAaqVKrDflQN---Ri~rW~~DkK~l 69 (121)
T PRK13680 23 FSANAEESKSVKFPKCEGLDAAGIAASVKRDYQQN---RIVRWADDQKQV 69 (121)
T ss_pred HHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC---CCCCHHHHHHHH
T ss_conf 76650576533445457989899999999999871---142205558760
No 306
>pfam03459 TOBE TOBE domain. The TOBE domain (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum and sulfate. Found in ABC transporters immediately after the ATPase domain.
Probab=24.28 E-value=40 Score=12.79 Aligned_cols=48 Identities=38% Similarity=0.389 Sum_probs=34.7
Q ss_pred CCEEEEEEEECCCCE----EEEEECC--CEEEEEHHHCCCCCCCCCCCEEEEEEEEE
Q ss_conf 838999998405763----8999579--35874478748875115276699999761
Q gi|254780788|r 139 GEIISGTVKRVEYGN----VIVDLGN--SDGVIRRDETISRENLRPGDRVKSYIYDV 189 (526)
Q Consensus 139 Geiv~G~V~r~e~~~----iiVdlg~--~ea~Lp~~e~ip~E~~~~Gdrika~i~~V 189 (526)
-..+.|+|..++.+. +.+++|+ ..+.++++.... +++|+.+.+.++-.
T Consensus 4 rN~l~g~V~~ie~~g~~~~V~v~~~~~~l~a~it~~s~~~---L~~G~~V~~~ik~~ 57 (61)
T pfam03459 4 RNQLPGTVDVVEPLGSETEVRVDLGGGELTARITRRSAEE---LAPGDEVYAGIKAE 57 (61)
T ss_pred CCEEEEEEEEEEECCCEEEEEEEECCCEEEEEECHHHHHH---CCCCCEEEEEEEHH
T ss_conf 4388799999998997699999979938999984889965---59998899999822
No 307
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=24.24 E-value=40 Score=12.78 Aligned_cols=31 Identities=35% Similarity=0.574 Sum_probs=21.2
Q ss_pred HHCCCEEEEEEEECC---CCEEEEEECCCEEEEE
Q ss_conf 520838999998405---7638999579358744
Q gi|254780788|r 136 DKVGEIISGTVKRVE---YGNVIVDLGNSDGVIR 166 (526)
Q Consensus 136 ~r~Geiv~G~V~r~e---~~~iiVdlg~~ea~Lp 166 (526)
+-.|+.++|+|.++. .|.+.+.|+....|.|
T Consensus 102 ~~dg~~~sG~V~sv~~~~~g~v~~~ldnG~~i~~ 135 (146)
T PRK09618 102 HGDGEIVKGTVTSVKTGINGQVMVELDDGKWYVA 135 (146)
T ss_pred CCCCCEEEEEEEEEEECCCCEEEEEECCCCEECH
T ss_conf 3899888778999998659849999769949857
No 308
>TIGR02592 cas_Cas5h CRISPR-associated protein Cas5, Hmari subtype; InterPro: IPR013421 This entry represents a CRISPR-associated protein unique to the hmari subtype of cas genes and CRISPR repeats, which is the only subtype present in Haloarcula marismortui ATCC 43049. The hmari type, though uncommon, is also found in the Aquificae, Thermotogae, Firmicutes, and Dictyoglomi..
Probab=24.20 E-value=24 Score=14.40 Aligned_cols=64 Identities=19% Similarity=0.233 Sum_probs=45.4
Q ss_pred HHHHHHHHH---CCEEEEEECC-CHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 899999861---6745785522-001101001221000111225888467888877321114777505
Q gi|254780788|r 327 NVRLASQLT---GWTIDIITEE-EDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACV 390 (526)
Q Consensus 327 NvrLas~Lt---g~~idi~~~~-~~~~~~~~e~~~~~~~f~e~LdVDE~iA~~LV~eGf~SiEeIa~a 390 (526)
|.+.-.++. .|+|+|.-++ +.-+.-..-+......|+-.||+.|-+|.+=...-|+..+.++..
T Consensus 114 r~~~~~~~L~dP~Yrifv~~~~s~~~~~L~~~L~~~~~~y~PyLG~~~~~A~l~y~~~~~~~~~~~~~ 181 (268)
T TIGR02592 114 RLRVNLELLKDPAYRIFVSWEDSEKYKELKDRLENSKSIYTPYLGVSEHIANLDYVGKLEAEEKLDDT 181 (268)
T ss_pred CCEEEHHHHCCCCEEEEEEECCCCCHHHHHHHHHCCCEEEECCCCHHHHHHCCCCCCEEEEEECCCCC
T ss_conf 61220454249653798853668887899999871871242146634553225500024342045677
No 309
>pfam08414 NADPH_Ox Respiratory burst NADPH oxidase. This domain is found in plant proteins such as respiratory burst NADPH oxidase proteins which produce reactive oxygen species as a defence mechanism. It tends to occur to the N-terminus of an EF-hand (pfam00036), which suggests a direct regulatory effect of Ca2+ on the activity of the NADPH oxidase in plants.
Probab=24.12 E-value=19 Score=15.11 Aligned_cols=16 Identities=19% Similarity=0.428 Sum_probs=7.5
Q ss_pred HHHHCCCCCHHHHHHC
Q ss_conf 9998798478896532
Q gi|254780788|r 450 ALGENGIKTMEDLAGC 465 (526)
Q Consensus 450 ~L~e~gIktleDlAel 465 (526)
.|+.+|....++|++|
T Consensus 34 ~la~dG~L~rs~Fg~C 49 (96)
T pfam08414 34 KLAVDGYLPRSKFGEC 49 (96)
T ss_pred HHHHCCCCCHHHHHHH
T ss_conf 9874376128888674
No 310
>TIGR01522 ATPase-IIA2_Ca calcium-transporting P-type ATPase, PMR1-type; InterPro: IPR006413 This family describes the P-type ATPase responsible for translocating calcium ions across the golgi membrane of fungi and animals , , and is of particular importance in the sarcoplasmic reticulum of skeletal and cardiac muscle in vertebrates . The calcium P-type ATPases have been characterised as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump represented by IPR006408 from INTERPRO. ; GO: 0005388 calcium-transporting ATPase activity, 0006816 calcium ion transport, 0016021 integral to membrane.
Probab=23.90 E-value=37 Score=13.03 Aligned_cols=34 Identities=24% Similarity=0.392 Sum_probs=24.7
Q ss_pred EEEECCCEEEEEHHHCCCCCC--CCCCCEEEEEEEEE
Q ss_conf 999579358744787488751--15276699999761
Q gi|254780788|r 155 IVDLGNSDGVIRRDETISREN--LRPGDRVKSYIYDV 189 (526)
Q Consensus 155 iVdlg~~ea~Lp~~e~ip~E~--~~~Gdrika~i~~V 189 (526)
.|--|+.+.+|- +..+||+- |++||||=|=+.=|
T Consensus 121 ~~R~G~~~hvlA-s~LVPGDlV~l~vGDRvPADlRiv 156 (856)
T TIGR01522 121 LIRAGKEEHVLA-STLVPGDLVILSVGDRVPADLRIV 156 (856)
T ss_pred EEECCCCCEEEE-ECCCCCCEEEEEECCCCCCCCEEE
T ss_conf 473588430575-107898679986278563140256
No 311
>TIGR00350 lytR_cpsA_psr cell envelope-related function transcriptional attenuator common domain; InterPro: IPR004474 This entry describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is protein psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. These proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor..
Probab=23.58 E-value=41 Score=12.70 Aligned_cols=21 Identities=29% Similarity=0.452 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 45620799999999999999999
Q gi|254780788|r 103 PMDFGRVAVQSAKQVIIQKVREA 125 (526)
Q Consensus 103 ~~~fgRiaAq~AKQvI~Qkirea 125 (526)
..|||||--| ||++.+-++.+
T Consensus 160 ~gD~GRi~rQ--~~~l~aL~~~~ 180 (182)
T TIGR00350 160 RGDYGRIDRQ--QQVLSALLERM 180 (182)
T ss_pred CCCHHHHHHH--HHHHHHHHHHH
T ss_conf 8833267899--99999999986
No 312
>PRK13197 pyrrolidone-carboxylate peptidase; Provisional
Probab=23.57 E-value=27 Score=14.11 Aligned_cols=103 Identities=17% Similarity=0.221 Sum_probs=58.5
Q ss_pred CHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEE-----ECCCC------CCCEEEEECCCCH-------HHHHH
Q ss_conf 889999999976677755808785663167750349999-----40899------8812765548862-------17889
Q gi|254780788|r 204 HPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVF-----SSDSS------IDPVGACVGMRGS-------RVQAV 265 (526)
Q Consensus 204 ~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~-----s~d~~------iDpVGAcVG~rGs-------Riq~I 265 (526)
+...+.++++..-|.+ |--.+ .+|.|++|.+- -.|.+ --|++.||=..|. =++++
T Consensus 49 ~~~~l~~~l~~~~Pd~----Vl~lG---~a~gr~~i~lErvAiN~~d~~ipDn~G~~p~~~~i~~~Gp~ay~stLPv~~i 121 (215)
T PRK13197 49 SLDVLKEAIEEVQPDA----VIAIG---QAGGRADITPERVAINIDDARIPDNEGNQPIDEPIVEDGPAAYFSTLPIKAM 121 (215)
T ss_pred HHHHHHHHHHHHCCCE----EEEEC---CCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCHHHH
T ss_conf 8999999999879988----99924---5689871002667872454756787899869974138997312068999999
Q ss_pred HHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEE-CCCCCEEEEEECC
Q ss_conf 986277826799559878999997628665424898-7567879999853
Q gi|254780788|r 266 VTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVL-DEDVGRIEVIVPK 314 (526)
Q Consensus 266 ~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~-de~~~~~~v~v~~ 314 (526)
++.|+.+-|+. .||.|--.|+||.+.=--...+.- ....+...|-||-
T Consensus 122 ~~~l~~~gipa-~iS~~AGtYvCN~v~Y~~l~~~~~~~~~~~agFIHvP~ 170 (215)
T PRK13197 122 VKAIREAGIPA-SVSNTAGTFVCNHVMYGLLHLLDKHYPNIRGGFIHIPY 170 (215)
T ss_pred HHHHHHCCCCC-EEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf 99999779982-68578752121699999999999639997068997899
No 313
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=23.52 E-value=42 Score=12.69 Aligned_cols=97 Identities=18% Similarity=0.144 Sum_probs=35.8
Q ss_pred EEEEEEEECCCCE----EEEEECC----CEEEEEHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHH--HHHH
Q ss_conf 8999998405763----8999579----3587447874887511527669999976113587028987159889--9999
Q gi|254780788|r 141 IISGTVKRVEYGN----VIVDLGN----SDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQ--FMVK 210 (526)
Q Consensus 141 iv~G~V~r~e~~~----iiVdlg~----~ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~--~l~~ 210 (526)
-..|+|..+..+. +.+.+.. .-+.+. .+-..+=.+.+|..+-|+|+ -|-|+|+...+. =-+-
T Consensus 130 qf~G~V~~I~~g~Vn~eV~l~l~~G~~~I~A~IT-~~S~~~LgL~~G~~v~AlIK-------As~V~L~~~~~~~~SArN 201 (262)
T PRK10676 130 QWFGTITARDHDQVQQHVDVLLADGKTRLKVAIT-AQSGERLGLDEGKEVLILLK-------APWVGITQDPAVAQAADN 201 (262)
T ss_pred CCCCEEEEEEECCCCEEEEEEECCCCCEEEEEEE-HHHHHHCCCCCCCEEEEEEE-------CCEEEEECCCCCCCCCCC
T ss_conf 0164479988758612999998799848999973-79998649889999999997-------476799738766655543
Q ss_pred HHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECC
Q ss_conf 99976677755808785663167750349999408
Q gi|254780788|r 211 LFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSD 245 (526)
Q Consensus 211 Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d 245 (526)
.|.=.|-.|.+|-+.--=....||..+=.|+.+++
T Consensus 202 ~l~GtV~~I~~G~vnaEV~l~l~~G~tl~A~it~~ 236 (262)
T PRK10676 202 QLPGTISHIERGAEQCEVLMALPDGQTLCATVPNN 236 (262)
T ss_pred EEEEEEEEEEECCCCEEEEEEECCCCEEEEEECCH
T ss_conf 67689999987784159999958999999997677
No 314
>TIGR03196 pucD xanthine dehydrogenase D subunit. This gene has been characterized in B. subtilis as the molybdopterin binding-subunit of xanthine dehydrogenase (pucD), acting in conjunction with pucC, the FAD-binding subunit and pucE, the FeS-binding subunit. The more common XDH complex (GenProp0640) includes the xdhB gene which is related to pucD. It appears that most of the relatives of pucD outside of this narrow clade are involved in other processes as they are found in unrelated genomic contexts, contain the more common XDH complex and/or do not appear to process purines to allantoin.
Probab=23.32 E-value=42 Score=12.66 Aligned_cols=22 Identities=14% Similarity=0.049 Sum_probs=8.7
Q ss_pred CEEEEEHHHCCCCCCCCCCCEE
Q ss_conf 3587447874887511527669
Q gi|254780788|r 161 SDGVIRRDETISRENLRPGDRV 182 (526)
Q Consensus 161 ~ea~Lp~~e~ip~E~~~~Gdri 182 (526)
+.-++.|.|..-.-.+|+.-++
T Consensus 258 Vk~~~~R~e~~~~~~~r~~~~~ 279 (768)
T TIGR03196 258 VKIAQDRKESFLGGIHRHPAKI 279 (768)
T ss_pred EEEEEEHHHCCCCCCCCCCEEE
T ss_conf 7999511110044578675599
No 315
>pfam03293 Pox_RNA_pol Poxvirus DNA-directed RNA polymerase, 18 kD subunit.
Probab=23.07 E-value=42 Score=12.63 Aligned_cols=64 Identities=23% Similarity=0.342 Sum_probs=33.0
Q ss_pred HCCCEEEEEEEECCCCEEEEEECCCEEEEEHHH------------CCCCCCCCCCCEEEEEEEEECCCCCEEEEEE
Q ss_conf 208389999984057638999579358744787------------4887511527669999976113587028987
Q gi|254780788|r 137 KVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDE------------TISRENLRPGDRVKSYIYDVRREQRGPQVLL 200 (526)
Q Consensus 137 r~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e------------~ip~E~~~~Gdrika~i~~V~~~~rgpqi~l 200 (526)
|+|++|+|+..-.+-.++.|.-|..-.-|.|+. .-.|-.|..|+++.+.+++-+......-+||
T Consensus 80 k~GDvV~GTLnIedESnitV~cgDLiCkl~rdsGtVSf~dsKYCfirng~vY~ngs~Vsv~LkEaq~g~~S~FvFl 155 (160)
T pfam03293 80 KVGDVVSGTLNIEDESNITVQCGDLICKLSRDSGTVSFNDSKYCFIRNGKVYDNGSTVSVVLKEAQSGMESNFVFL 155 (160)
T ss_pred EECCEEEEEEEECCCCCEEEECCCEEEEEECCCCEEEECCCEEEEEECCEEECCCCEEEEEEHHHHCCCCCEEEEE
T ss_conf 6087889899841567528972768999724686178658607999788996289889999547347864148999
No 316
>pfam07431 DUF1512 Protein of unknown function (DUF1512). This family consists of several archaeal proteins of around 370 residues in length. The function of this family is unknown.
Probab=23.03 E-value=42 Score=12.62 Aligned_cols=63 Identities=27% Similarity=0.338 Sum_probs=37.0
Q ss_pred EEEEECCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCC
Q ss_conf 99994089988127655488621788998627782679955987899999762866542489875678799998534221
Q gi|254780788|r 239 LAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLS 318 (526)
Q Consensus 239 IAV~s~d~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~~de~~~~~~v~v~~~qls 318 (526)
+-|++.-| |+.||.-|.-++.|+++|+| |.|.|.--|-- | --|-+++..|. +-.-
T Consensus 220 ~v~KAeGP-----gstvGrpg~ave~iv~~~~~-k~~~IItiDAA-------l---------KLEGE~tg~iA---eG~G 274 (356)
T pfam07431 220 YIVKAEGP-----GSTVGRPGEAVENVVERLDG-KVSRIITVDAA-------L---------KLEGEKTGAVA---EGVG 274 (356)
T ss_pred EEEECCCC-----CCCCCCHHHHHHHHHHHHCC-CCCEEEEEEHH-------H---------HCCCCCCCCHH---CCCC
T ss_conf 99964589-----88789857999999997068-97689996055-------5---------51787562132---0556
Q ss_pred CCCCCCHH
Q ss_conf 10254427
Q gi|254780788|r 319 LAIGRRGQ 326 (526)
Q Consensus 319 ~AIGk~Gq 326 (526)
.|||--|.
T Consensus 275 ~AiG~~G~ 282 (356)
T pfam07431 275 VAMGDPGP 282 (356)
T ss_pred CCCCCCCC
T ss_conf 01378871
No 317
>PRK07352 F0F1 ATP synthase subunit B; Validated
Probab=22.99 E-value=43 Score=12.62 Aligned_cols=12 Identities=17% Similarity=0.191 Sum_probs=4.3
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999999
Q gi|254780788|r 407 VEIQGRAREYLE 418 (526)
Q Consensus 407 ~eL~~rA~~~L~ 418 (526)
+.+...|+.-+.
T Consensus 114 e~i~~~A~~~Ie 125 (174)
T PRK07352 114 ARLKQTAAADLS 125 (174)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999999
No 318
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=22.82 E-value=43 Score=12.59 Aligned_cols=40 Identities=23% Similarity=0.401 Sum_probs=23.8
Q ss_pred EEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCC
Q ss_conf 7999985342211025442789999986167457855220
Q gi|254780788|r 307 RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346 (526)
Q Consensus 307 ~~~v~v~~~qls~AIGk~GqNvrLas~Ltg~~idi~~~~~ 346 (526)
+..|.+|++-++.-||+.|.-.|+--+.||-++.+-+.+-
T Consensus 9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~ 48 (194)
T COG1094 9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTG 48 (194)
T ss_pred EEEEECCCHHHEEEECCCCCCHHHHHHHCCEEEEEECCCC
T ss_conf 0455457045101225663105898861575899977877
No 319
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 The bacterial core RNA polymerase complex, which consists of five subunits, 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 . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=22.68 E-value=43 Score=12.57 Aligned_cols=23 Identities=9% Similarity=0.156 Sum_probs=13.6
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 23999999999999999999961
Q gi|254780788|r 19 EKSIDRDVVLSVMADSIQKAARS 41 (526)
Q Consensus 19 EK~I~~e~i~~aie~Al~~a~kK 41 (526)
.+|-+.|++|++=.-.|.+|.-|
T Consensus 33 nRGYe~eDlFQIGciGLvKAidk 55 (231)
T TIGR02885 33 NRGYEYEDLFQIGCIGLVKAIDK 55 (231)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 06887000022211556665542
No 320
>CHL00127 rpl11 ribosomal protein L11; Validated
Probab=21.52 E-value=42 Score=12.63 Aligned_cols=35 Identities=26% Similarity=0.458 Sum_probs=25.6
Q ss_pred EEEEEECCCCC-CCEEEEECCCCHHHHHHHHHHCCC
Q ss_conf 49999408998-812765548862178899862778
Q gi|254780788|r 238 KLAVFSSDSSI-DPVGACVGMRGSRVQAVVTELRDE 272 (526)
Q Consensus 238 KIAV~s~d~~i-DpVGAcVG~rGsRiq~I~~EL~gE 272 (526)
|+-|.+-..+- -|+|.-.|++|.-+...+++.|..
T Consensus 10 kl~v~aG~A~p~PPvGpaLG~~GvNi~~Fck~fN~~ 45 (140)
T CHL00127 10 KLALPAGKATPAPPVGPALGQHGVNINLFCKEYNAR 45 (140)
T ss_pred EEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf 998516777899998631134697999999999998
No 321
>pfam01330 RuvA_N RuvA N terminal domain. The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts.
Probab=21.28 E-value=46 Score=12.38 Aligned_cols=50 Identities=20% Similarity=0.301 Sum_probs=36.4
Q ss_pred EEEEEEEECCCCEEEEEECCC--EEEEEHHHCCCCCCCCCCCEEEEEEEEECCCC
Q ss_conf 899999840576389995793--58744787488751152766999997611358
Q gi|254780788|r 141 IISGTVKRVEYGNVIVDLGNS--DGVIRRDETISRENLRPGDRVKSYIYDVRREQ 193 (526)
Q Consensus 141 iv~G~V~r~e~~~iiVdlg~~--ea~Lp~~e~ip~E~~~~Gdrika~i~~V~~~~ 193 (526)
-+.|+|...+.+.+++|.|++ +-.+|.+.. ..+..|..++.|..-+-++.
T Consensus 4 ~l~G~i~~~~~~~ivi~~~GvGY~v~is~~~~---~~l~~~~~v~l~t~~~vRED 55 (61)
T pfam01330 4 YLRGKVTEVGPDYIVVEVNGVGYEINVSARTL---AELPEGGEVKLFTHLIVRED 55 (61)
T ss_pred EEEEEEEEECCCEEEEEECCEEEEEEECHHHH---HHCCCCCEEEEEEEEEEEEC
T ss_conf 99999999729999999678799999888999---76799988999999999016
No 322
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=21.15 E-value=46 Score=12.36 Aligned_cols=53 Identities=30% Similarity=0.449 Sum_probs=36.5
Q ss_pred EEEEEEECC--CCE--EEEEECCCEEEEEHHHCCCC--CCCCCCCEEEEEEEEECCCCCEEE
Q ss_conf 999998405--763--89995793587447874887--511527669999976113587028
Q gi|254780788|r 142 ISGTVKRVE--YGN--VIVDLGNSDGVIRRDETISR--ENLRPGDRVKSYIYDVRREQRGPQ 197 (526)
Q Consensus 142 v~G~V~r~e--~~~--iiVdlg~~ea~Lp~~e~ip~--E~~~~Gdrika~i~~V~~~~rgpq 197 (526)
++|+|+..+ +|+ |..+-++-+-++..+..... ..+++|++|..-+..- .+||+
T Consensus 1 ~~G~Vk~f~~~kGfGFI~~~~~~~diF~H~s~~~~~~~~~l~~G~~V~f~~~~~---~~g~~ 59 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG---DKGPQ 59 (65)
T ss_pred CEEEEEEEECCCCEEEEEECCCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEEC---CCCCE
T ss_conf 938999997999969999579982299995892434697479898999999989---89976
No 323
>pfam09883 DUF2110 Uncharacterized protein conserved in archaea (DUF2110). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=21.13 E-value=46 Score=12.36 Aligned_cols=36 Identities=22% Similarity=0.222 Sum_probs=28.5
Q ss_pred CCCEEEEEEEECCCCEEEEEECCCEEEEEHHHCCCC
Q ss_conf 083899999840576389995793587447874887
Q gi|254780788|r 138 VGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISR 173 (526)
Q Consensus 138 ~Geiv~G~V~r~e~~~iiVdlg~~ea~Lp~~e~ip~ 173 (526)
.|++..|+....+...+.++.++.-.-.|.++.+|-
T Consensus 75 ~Ge~y~G~l~~~~e~G~~~~v~G~~~~ip~deL~~L 110 (226)
T pfam09883 75 EGEVYVGTLISWDEDGYGLDVDGVTVPIPADELLPL 110 (226)
T ss_pred CCCEEEEEEEECCCCCEEEEECCEECCCCHHHHCCC
T ss_conf 887789998760664169986573646717885345
No 324
>pfam00029 Connexin Connexin.
Probab=21.11 E-value=25 Score=14.37 Aligned_cols=17 Identities=41% Similarity=0.952 Sum_probs=14.1
Q ss_pred ECCCCHHHHHHHHCCCC
Q ss_conf 55987899999762866
Q gi|254780788|r 278 VWSPDSATFVINALRPA 294 (526)
Q Consensus 278 ~ws~d~~~fi~nAl~PA 294 (526)
.|+|+...|++|.++|.
T Consensus 42 V~~DEQs~F~CNT~QPG 58 (107)
T pfam00029 42 VWGDEQSDFVCNTLQPG 58 (107)
T ss_pred CCCCHHHHCCCCCCCCC
T ss_conf 32421442644799998
No 325
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=20.93 E-value=47 Score=12.33 Aligned_cols=85 Identities=20% Similarity=0.325 Sum_probs=53.0
Q ss_pred HHCCCEE-----EEEEEECCCC-EEEEEECCCEEEEEHHHCCCCC--CCCCCCEEEEEEEEECCCCCEEEEEEECCCHHH
Q ss_conf 5208389-----9999840576-3899957935874478748875--115276699999761135870289871598899
Q gi|254780788|r 136 DKVGEII-----SGTVKRVEYG-NVIVDLGNSDGVIRRDETISRE--NLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQF 207 (526)
Q Consensus 136 ~r~Geiv-----~G~V~r~e~~-~iiVdlg~~ea~Lp~~e~ip~E--~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~ 207 (526)
=|+|+-| +|+|+|+.-+ ..|-+-.+.+-++|.+..|.+- |+..++.+.-+...|--.- -|+|+.
T Consensus 661 vkvGD~It~g~~~G~V~~I~vRAT~I~~fd~~~vIVPNs~fI~~qV~NWs~~~~~~R~~i~v~vay--------~sD~~~ 732 (835)
T COG3264 661 VKVGDTVTIGTVSGTVRKISVRATTIRTFDRKEVIVPNSAFITEQVINWSLRDTTTRLVIPVGVAY--------GSDPEL 732 (835)
T ss_pred CCCCCEEEECCCEEEEEEEEEEEEEEEECCCCEEEECCHHHHHHHEEEEECCCCEEEEEEEECCCC--------CCCHHH
T ss_conf 356777998782489999875579998278875970557887644023102572389999830567--------898899
Q ss_pred HHHHHHHHHHHHHCCEEEEEEEECCCCC
Q ss_conf 9999997667775580878566316775
Q gi|254780788|r 208 MVKLFHMEVPEIYNGIVQVKAVSRDPGS 235 (526)
Q Consensus 208 l~~Lf~~EVPEI~~G~ieIk~iaR~pG~ 235 (526)
|++++-+ ++.+. ..|-++|--
T Consensus 733 V~~~Ll~----~A~~~---p~Vl~~P~P 753 (835)
T COG3264 733 VRELLLE----AAREH---PRVLKDPAP 753 (835)
T ss_pred HHHHHHH----HHHHC---CCCCCCCCC
T ss_conf 9999999----99739---876599997
No 326
>COG1255 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.93 E-value=47 Score=12.33 Aligned_cols=66 Identities=20% Similarity=0.216 Sum_probs=33.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEEC
Q ss_conf 999999986239999999999-99999999961368745359997499883999999885176778753234
Q gi|254780788|r 10 LQIADAVAYEKSIDRDVVLSV-MADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQIS 80 (526)
Q Consensus 10 l~vie~va~EK~I~~e~i~~a-ie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~ 80 (526)
+++++.+++|.+=.|=+=+.+ .--.+ +.+-+++|-+- +-+.|+++++. .-.+-||+|+.+|...|.
T Consensus 2 ~e~a~~iAre~~~gkVvEVGiG~~~~V-A~~L~e~g~dv-~atDI~~~~a~---~g~~~v~DDitnP~~~iY 68 (129)
T COG1255 2 IEVAEYIARENARGKVVEVGIGFFLDV-AKRLAERGFDV-LATDINEKTAP---EGLRFVVDDITNPNISIY 68 (129)
T ss_pred CCHHHHHHHHHCCCCEEEECCCHHHHH-HHHHHHCCCCE-EEEECCCCCCC---CCCEEEECCCCCCCHHHH
T ss_conf 418999998705883799814117999-99999748868-99852301376---553388724779647776
No 327
>PRK13460 F0F1 ATP synthase subunit B; Provisional
Probab=20.91 E-value=47 Score=12.33 Aligned_cols=15 Identities=13% Similarity=-0.004 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999999
Q gi|254780788|r 406 AVEIQGRAREYLEGI 420 (526)
Q Consensus 406 a~eL~~rA~~~L~~~ 420 (526)
+..+.++|+.-+...
T Consensus 110 a~~i~~~A~~~Ie~e 124 (173)
T PRK13460 110 VKAQKDQAVKEIELA 124 (173)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999999999999
No 328
>TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family; InterPro: IPR014238 Proteins in this entry belong to the broader family of PRC-barrel domain proteins, but are found only in endospore-forming bacteria within the Firmicutes (low-GC, Gram-positive bacteria). Most species encode two of these proteins, though their function is unknown. In Bacillus subtilis, which encodes YlmC and YmxH, YmxH is strongly induced by the mother cell-specific sigma-E factor ..
Probab=20.65 E-value=47 Score=12.29 Aligned_cols=46 Identities=20% Similarity=0.358 Sum_probs=29.4
Q ss_pred HCCCCCCCEEEEECCCCCEEEEEEEEEEECC--------CCCCCCEECHHHHHHHCCC
Q ss_conf 1368745359997499883999999885176--------7787532348999862889
Q gi|254780788|r 41 SLYGTMSDIRVEINPETGDISLFRLLEVVEE--------VENYTCQISLKVARDRDPS 90 (526)
Q Consensus 41 K~~~~~~~i~V~iD~~tG~i~i~~~~~VVed--------ved~~~eI~l~~A~~~~~~ 90 (526)
++||.=.+..++||.++|.+..+ |++. -..+..+|+=+.-+++-++
T Consensus 17 ~rLG~~~~~D~~ID~~~G~I~~l----Iip~~g~~~glf~~~~~~~IpW~~IkKIG~d 70 (76)
T TIGR02888 17 KRLGLIGNIDLEIDEEDGKIESL----IIPGKGKKFGLFSKGEEIEIPWKAIKKIGSD 70 (76)
T ss_pred EEEEEECCCCEEEECCCCEEEEE----EECCCCEEEECEECCCCEEECCHHCEEECCE
T ss_conf 38873348457980899959898----8718970522100687548663002780790
No 329
>TIGR01578 MiaB-like-B MiaB-like tRNA modifying enzyme, archaeal-type; InterPro: IPR006466 This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see IPR006463 from INTERPRO). Sequence alignments suggest that this family of sequences perform the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade represents a subfamily that spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this group of sequences , , ..
Probab=20.52 E-value=47 Score=12.27 Aligned_cols=161 Identities=17% Similarity=0.222 Sum_probs=101.8
Q ss_pred CCCCCCCCEECHHHHHHHCCCC-CCCCEEEEECC-HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCCCEEEEEE
Q ss_conf 7677875323489998628898-64737998508-456207999999999999999999-88779999852083899999
Q gi|254780788|r 70 EEVENYTCQISLKVARDRDPSI-DIGGVVSDPLP-PMDFGRVAVQSAKQVIIQKVREAE-RDRQYLEFKDKVGEIISGTV 146 (526)
Q Consensus 70 edved~~~eI~l~~A~~~~~~~-~iGD~i~~~i~-~~~fgRiaAq~AKQvI~QkireaE-r~~i~~ef~~r~Geiv~G~V 146 (526)
....|...|=+++--+++.|+. -+--|-.=|.+ ..+|-++-++.-|+- =+... -=.-|+-|.+|+|+|-+-.|
T Consensus 309 p~EtdddFE~T~~l~~k~RPe~In~~~fS~RpgT~Aa~~~~~~~~i~K~R----s~~l~dlfysyePyadrvGeiytvlv 384 (487)
T TIGR01578 309 PTETDDDFEETMELLRKYRPEKINVTKFSPRPGTEAAKMKRLDTNIKKKR----SKALTDLFYSYEPYADRVGEIYTVLV 384 (487)
T ss_pred CCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHCCCCCCEEHHH----HHHHHHHHHHCCCCCCCCCCEEEEEE
T ss_conf 89883558999999998289834530246888871133058996201166----67777654202630012241577877
Q ss_pred EECCCCEE-EEEECCCEEEEEHHHCCCCCC--CCCCCEEEEEEEE-ECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCC
Q ss_conf 84057638-999579358744787488751--1527669999976-1135870289871598899999999766777558
Q gi|254780788|r 147 KRVEYGNV-IVDLGNSDGVIRRDETISREN--LRPGDRVKSYIYD-VRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNG 222 (526)
Q Consensus 147 ~r~e~~~i-iVdlg~~ea~Lp~~e~ip~E~--~~~Gdrika~i~~-V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G 222 (526)
..+..+-+ ||-.++. .+||..+. =-.|.|.+++|.+ -+.+..|--+.-.+..-. ---.+|.|. -
T Consensus 385 tevshdklhyvGhnk~------~~~~~~~~~~~~iG~~~~Vlv~~asKy~g~G~~~~~~d~~~r---CaknqelPn---~ 452 (487)
T TIGR01578 385 TEVSHDKLHYVGHNKL------KEEVLLEKKENLIGKREKVLVTEASKYEGKGDSLKDEDDAYR---CAKNQELPN---R 452 (487)
T ss_pred EEEECCCEEECCHHHH------HHHHHCCHHHCCCCCCEEEEEEECCCCCCCCCEECCCHHHHH---HHHCCCCCC---C
T ss_conf 5310131011140567------887510001105640104899731210242431446414565---331056898---5
Q ss_pred EEEEEEEE---CCCCCEEEEEEEECCC
Q ss_conf 08785663---1677503499994089
Q gi|254780788|r 223 IVQVKAVS---RDPGSRAKLAVFSSDS 246 (526)
Q Consensus 223 ~ieIk~ia---R~pG~RsKIAV~s~d~ 246 (526)
-|.|.+-- |.||.=++|++.+..+
T Consensus 453 ~Vv~~~~~dhGl~~gef~~V~iT~~~~ 479 (487)
T TIGR01578 453 QVVISEKTDHGLEPGEFAKVEITGAKT 479 (487)
T ss_pred CEEEECCCCCCCCCCCEEEEEEECCCE
T ss_conf 458724866566443301278962310
No 330
>TIGR01204 bioW 6-carboxyhexanoate--CoA ligase; InterPro: IPR005499 This family contains the enzyme 6-carboxyhexanoate--CoA ligase 6.2.1.14 from EC. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA . The enzyme requires magnesium as a cofactor and forms a homodimer .; GO: 0009102 biotin biosynthetic process.
Probab=20.46 E-value=33 Score=13.40 Aligned_cols=38 Identities=13% Similarity=0.384 Sum_probs=18.9
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHCCCCCCC-EEEEECCCC
Q ss_conf 239999999999999999999613687453-599974998
Q gi|254780788|r 19 EKSIDRDVVLSVMADSIQKAARSLYGTMSD-IRVEINPET 57 (526)
Q Consensus 19 EK~I~~e~i~~aie~Al~~a~kK~~~~~~~-i~V~iD~~t 57 (526)
|+=+++..+-.++++-|.++-...-|. .| +.|.+-.-+
T Consensus 11 ERi~~~~e~e~~Vk~LLnk~~~HSRG~-~DF~qi~vEkv~ 49 (238)
T TIGR01204 11 ERIVKKEELETIVKELLNKAKSHSRGE-ADFMQIKVEKVK 49 (238)
T ss_pred EECCCHHHHHHHHHHHHHCCCCCCCCC-CCEEEEEEEEEE
T ss_conf 003655568899999873223467898-653567899870
No 331
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=20.27 E-value=45 Score=12.47 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=14.8
Q ss_pred EEECCCCCEEEEEECCCCCCCCCCCCHHHHHH
Q ss_conf 89875678799998534221102544278999
Q gi|254780788|r 299 VVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRL 330 (526)
Q Consensus 299 v~~de~~~~~~v~v~~~qls~AIGk~GqNvrL 330 (526)
|.+++..-++++. .|=|.+||||.=
T Consensus 217 i~i~~~dl~idt~-------RssGaGGQhVNk 241 (360)
T PRK00591 217 VEINPKDLRIDTF-------RSSGAGGQHVNT 241 (360)
T ss_pred CCCCCCCEEEEEE-------ECCCCCCCCCCC
T ss_conf 2568540258875-------357999887676
No 332
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.15 E-value=48 Score=12.22 Aligned_cols=87 Identities=26% Similarity=0.260 Sum_probs=50.8
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCC
Q ss_conf 88776530588999999999999999999998987754284356640779998999999987984788965326775212
Q gi|254780788|r 393 SEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLG 472 (526)
Q Consensus 393 eeL~~IeGfdee~a~eL~~rA~~~L~~~~~~~~e~~~e~~~~e~L~~l~gl~~~~~~~L~e~gIktleDlAels~dEL~~ 472 (526)
.+++.=-+-+.++. -.+.+|-+|+..-..-.-++.++ .-++|+++.+|++..+++++.=-=.|. +||.-
T Consensus 19 k~il~~~~~~~eL~-y~~~~al~y~~kFakldpe~a~e--~veEL~~i~~~~e~~avkIadI~P~t~--------~ElRs 87 (114)
T COG1460 19 KKILSKVEREEELT-YEQREALEYAEKFAKLDPEKARE--LVEELLSIVKMSEKIAVKIADIMPRTP--------DELRS 87 (114)
T ss_pred HHHHHHHCCCCCCH-HHHHHHHHHHHHHHCCCHHHHHH--HHHHHHHHCCCCHHHHHHHHHHCCCCH--------HHHHH
T ss_conf 99999861242103-89999999999871589999999--999998632456999999998089988--------99999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 312344432112453343588999999999
Q gi|254780788|r 473 WSENKGGNIEKFDGFLSSLGTPKDQVESMI 502 (526)
Q Consensus 473 ~~~~~~~~~~~~~gil~~~~l~~~~A~~lI 502 (526)
|+.+ ...-++.+++++|.
T Consensus 88 Ila~------------e~~~~s~E~l~~Il 105 (114)
T COG1460 88 ILAK------------ERVMLSDEELDKIL 105 (114)
T ss_pred HHHH------------CCCCCCHHHHHHHH
T ss_conf 9998------------06889899999999
No 333
>PRK00140 rplK 50S ribosomal protein L11; Validated
Probab=20.09 E-value=47 Score=12.32 Aligned_cols=63 Identities=17% Similarity=0.310 Sum_probs=37.1
Q ss_pred EEEEEECCCCC-CCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCC--CEEEECCCCCEEEEEECC
Q ss_conf 49999408998-812765548862178899862778267995598789999976286654--248987567879999853
Q gi|254780788|r 238 KLAVFSSDSSI-DPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIV--TKVVLDEDVGRIEVIVPK 314 (526)
Q Consensus 238 KIAV~s~d~~i-DpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v--~~v~~de~~~~~~v~v~~ 314 (526)
|+-|..-..+- -|||--.|++|.-+..++++.|..-=| +.+-.+ +.|.+++| +++++.+..
T Consensus 10 kl~i~aG~A~p~PPvGpaLG~~GiNi~~F~k~fN~~T~~---------------~~~g~~vpV~Itv~~D-ksf~f~ikt 73 (142)
T PRK00140 10 KLQIPAGKANPSPPVGPALGQRGVNIMEFCKAFNARTQD---------------QEKGLPIPVVITVYAD-RSFTFITKT 73 (142)
T ss_pred EEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH---------------CCCCCEEEEEEEECCC-CEEEEEECC
T ss_conf 999745777899998731134698999999999998861---------------5799807589999389-719999818
Q ss_pred CC
Q ss_conf 42
Q gi|254780788|r 315 EQ 316 (526)
Q Consensus 315 ~q 316 (526)
--
T Consensus 74 Pp 75 (142)
T PRK00140 74 PP 75 (142)
T ss_pred CC
T ss_conf 86
Done!