Query psy8861
Match_columns 550
No_of_seqs 495 out of 3220
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 21:15:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8861.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8861hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00013 rpoA RNA polymerase a 100.0 3.9E-65 8.4E-70 527.7 21.6 230 202-431 9-325 (327)
2 TIGR02027 rpoA DNA-directed RN 100.0 4E-62 8.7E-67 501.1 20.3 218 214-431 1-296 (297)
3 PRK05182 DNA-directed RNA poly 100.0 9.6E-62 2.1E-66 500.7 22.5 234 198-431 2-310 (310)
4 COG0202 RpoA DNA-directed RNA 100.0 5.3E-54 1.1E-58 443.4 18.4 239 199-437 1-312 (317)
5 CHL00113 rps4 ribosomal protei 100.0 8.2E-50 1.8E-54 388.5 18.2 192 1-202 1-194 (201)
6 COG0203 RplQ Ribosomal protein 100.0 1.5E-49 3.2E-54 348.4 13.1 116 430-545 1-116 (116)
7 PRK05327 rpsD 30S ribosomal pr 100.0 3.1E-47 6.8E-52 371.9 18.4 196 1-201 1-197 (203)
8 TIGR00059 L17 ribosomal protei 100.0 2.5E-47 5.4E-52 337.8 13.6 112 435-546 1-112 (112)
9 TIGR01017 rpsD_bact ribosomal 100.0 9.8E-47 2.1E-51 367.6 17.9 194 3-201 1-194 (200)
10 PRK05591 rplQ 50S ribosomal pr 100.0 5.9E-47 1.3E-51 336.2 13.6 112 434-545 2-113 (113)
11 COG0522 RpsD Ribosomal protein 100.0 2.8E-47 6E-52 371.1 10.5 198 1-201 1-199 (205)
12 PTZ00076 60S ribosomal protein 100.0 1E-43 2.3E-48 346.7 13.6 122 428-549 11-133 (253)
13 PF01196 Ribosomal_L17: Riboso 100.0 8.1E-41 1.8E-45 290.5 10.5 97 449-545 1-97 (97)
14 cd06928 RNAP_alpha_NTD N-termi 100.0 3.7E-39 8.1E-44 317.7 16.1 120 207-326 3-123 (215)
15 KOG3280|consensus 100.0 7.2E-40 1.6E-44 302.4 9.1 119 430-548 8-129 (171)
16 cd07028 RNAP_RPB3_like RPB3 su 100.0 1.7E-28 3.7E-33 241.4 14.4 139 205-347 3-211 (212)
17 PRK14979 DNA-directed RNA poly 99.9 3.4E-26 7.4E-31 221.8 12.5 123 205-347 6-184 (195)
18 smart00662 RPOLD RNA polymeras 99.9 3.6E-26 7.9E-31 226.8 12.9 103 214-326 1-119 (224)
19 cd07030 RNAP_D D subunit of Ar 99.9 3.7E-26 8.1E-31 231.0 13.2 117 204-326 2-130 (259)
20 PRK00783 DNA-directed RNA poly 99.9 2.2E-24 4.8E-29 218.6 12.9 111 204-326 2-130 (263)
21 cd07031 RNAP_II_RPB3 RPB3 subu 99.9 4.3E-22 9.4E-27 202.3 14.4 119 204-326 2-149 (265)
22 PF03118 RNA_pol_A_CTD: Bacter 99.8 1.9E-19 4.2E-24 146.5 3.4 61 364-424 6-66 (66)
23 PF00163 Ribosomal_S4: Ribosom 99.7 5.7E-19 1.2E-23 152.8 4.1 92 2-96 1-94 (94)
24 KOG3301|consensus 99.7 2.3E-18 4.9E-23 159.8 4.5 131 1-140 1-140 (183)
25 PTZ00155 40S ribosomal protein 99.7 4E-18 8.7E-23 163.5 5.1 81 48-149 79-161 (181)
26 PF01000 RNA_pol_A_bac: RNA po 99.7 1E-17 2.3E-22 149.2 5.2 73 254-326 14-90 (112)
27 PRK07758 hypothetical protein; 99.7 7E-17 1.5E-21 138.7 4.2 54 376-429 41-94 (95)
28 PLN00189 40S ribosomal protein 99.5 9E-15 2E-19 141.4 2.1 59 90-148 102-160 (194)
29 TIGR01018 rpsD_arch ribosomal 99.5 4.1E-14 8.8E-19 133.8 6.2 61 90-150 97-159 (162)
30 PRK04051 rps4p 30S ribosomal p 99.4 6.4E-13 1.4E-17 127.5 10.1 63 89-151 95-159 (177)
31 PRK14906 DNA-directed RNA poly 99.4 2.7E-13 5.9E-18 159.6 4.6 63 370-432 1314-1376(1460)
32 PF01479 S4: S4 domain; Inter 99.4 1.2E-12 2.5E-17 99.4 5.8 48 97-144 1-48 (48)
33 cd07032 RNAP_I_II_AC40 AC40 su 99.3 7.4E-12 1.6E-16 128.9 12.4 111 204-326 2-156 (291)
34 COG1188 Ribosome-associated he 99.1 6.5E-11 1.4E-15 103.2 4.9 57 95-152 7-63 (100)
35 PRK10348 ribosome-associated h 99.0 3.6E-10 7.8E-15 103.9 6.3 56 96-152 8-63 (133)
36 TIGR02988 YaaA_near_RecF S4 do 98.8 7.3E-09 1.6E-13 82.2 6.6 50 97-146 9-58 (59)
37 PF01193 RNA_pol_L: RNA polyme 98.8 2.8E-09 6.1E-14 86.6 4.0 31 219-249 1-31 (66)
38 KOG1522|consensus 98.7 6.5E-08 1.4E-12 95.9 8.6 114 201-326 5-152 (285)
39 cd00165 S4 S4/Hsp/ tRNA synthe 98.5 1.9E-07 4.1E-12 73.3 6.5 52 97-148 1-52 (70)
40 COG1189 Predicted rRNA methyla 98.5 1E-07 2.2E-12 95.4 6.0 85 96-181 2-91 (245)
41 smart00363 S4 S4 RNA-binding d 98.5 2.4E-07 5.2E-12 70.7 6.3 52 97-148 1-52 (60)
42 PLN00051 RNA-binding S4 domain 98.4 2.6E-07 5.7E-12 94.6 5.9 55 97-152 192-246 (267)
43 TIGR00478 tly hemolysin TlyA f 98.4 8.2E-07 1.8E-11 89.0 8.9 52 98-149 1-52 (228)
44 COG2302 Uncharacterized conser 98.4 2.2E-07 4.9E-12 93.1 4.7 55 97-152 181-235 (257)
45 TIGR03069 PS_II_S4 photosystem 98.4 3.4E-07 7.5E-12 93.3 5.8 55 97-152 184-238 (257)
46 cd00460 RNAP_RPB11_RPB3 RPB11 98.0 1.8E-05 3.9E-10 67.8 7.6 32 205-240 1-32 (86)
47 KOG1521|consensus 97.9 4.8E-05 1E-09 77.8 8.8 120 195-326 38-201 (338)
48 PRK11507 ribosome-associated p 97.7 8E-05 1.7E-09 61.5 6.1 53 97-149 12-64 (70)
49 COG1187 RsuA 16S rRNA uridine- 97.5 0.00016 3.4E-09 73.5 6.0 54 96-150 2-56 (248)
50 PRK10475 23S rRNA pseudouridin 97.5 0.00019 4.2E-09 74.5 6.6 50 97-148 7-56 (290)
51 PRK10839 16S rRNA pseudouridyl 97.4 0.00024 5.2E-09 71.0 6.4 51 97-148 1-51 (232)
52 PF13275 S4_2: S4 domain; PDB: 97.3 4.9E-05 1.1E-09 62.0 0.2 52 97-148 8-59 (65)
53 PRK11180 rluD 23S rRNA pseudou 97.2 0.00048 1E-08 72.4 6.1 53 96-148 17-69 (325)
54 PRK10700 23S rRNA pseudouridyl 97.1 0.0007 1.5E-08 70.3 6.3 51 96-148 2-54 (289)
55 TIGR00005 rluA_subfam pseudour 97.1 0.00082 1.8E-08 69.5 6.4 53 96-148 5-57 (299)
56 COG2501 S4-like RNA binding pr 96.8 0.0029 6.3E-08 52.7 5.7 52 99-150 14-65 (73)
57 PRK11025 23S rRNA pseudouridyl 96.8 0.0022 4.8E-08 67.2 6.2 51 97-148 20-70 (317)
58 COG0564 RluA Pseudouridylate s 96.7 0.0025 5.4E-08 66.3 6.0 52 96-149 12-63 (289)
59 PF14520 HHH_5: Helix-hairpin- 96.6 0.002 4.4E-08 51.2 3.4 49 376-424 12-60 (60)
60 cd06927 RNAP_L L subunit of Ar 96.3 0.03 6.6E-07 47.9 9.1 44 205-253 1-44 (83)
61 PRK01146 DNA-directed RNA poly 96.2 0.046 1E-06 47.0 9.7 45 204-253 2-46 (85)
62 KOG4655|consensus 96.2 0.0019 4E-08 61.4 1.1 60 92-151 102-163 (181)
63 COG1761 RPB11 DNA-directed RNA 95.9 0.076 1.6E-06 47.0 9.8 82 204-347 6-89 (99)
64 cd07027 RNAP_RPB11_like RPB11 95.5 0.11 2.3E-06 44.5 9.1 43 205-252 1-43 (83)
65 PF13656 RNA_pol_L_2: RNA poly 94.8 0.23 5.1E-06 41.8 8.8 74 213-346 1-74 (77)
66 cd07029 RNAP_I_III_AC19 AC19 s 94.1 0.39 8.4E-06 41.3 8.8 78 210-347 6-83 (85)
67 TIGR02238 recomb_DMC1 meiotic 94.1 0.05 1.1E-06 57.2 4.0 54 372-425 4-57 (313)
68 PRK04313 30S ribosomal protein 93.6 0.085 1.9E-06 53.4 4.5 46 105-150 47-92 (237)
69 PRK13354 tyrosyl-tRNA syntheta 92.9 0.16 3.6E-06 55.4 5.7 47 97-143 343-389 (410)
70 PRK05912 tyrosyl-tRNA syntheta 92.2 0.27 5.9E-06 53.7 6.4 52 97-148 343-398 (408)
71 PTZ00035 Rad51 protein; Provis 92.2 0.13 2.9E-06 54.6 3.8 54 372-425 26-79 (337)
72 PTZ00118 40S ribosomal protein 92.2 0.17 3.7E-06 51.9 4.4 45 105-149 51-95 (262)
73 PLN00036 40S ribosomal protein 92.1 0.18 3.8E-06 51.8 4.5 45 105-149 51-95 (261)
74 PTZ00223 40S ribosomal protein 92.0 0.18 4E-06 52.0 4.4 46 105-150 48-93 (273)
75 PLN03187 meiotic recombination 91.1 0.21 4.5E-06 53.4 3.9 53 372-424 34-86 (344)
76 TIGR02239 recomb_RAD51 DNA rep 91.1 0.21 4.5E-06 52.7 3.8 53 372-424 4-56 (316)
77 PRK04301 radA DNA repair and r 91.0 0.24 5.3E-06 51.8 4.3 56 369-424 5-61 (317)
78 TIGR01954 nusA_Cterm_rpt trans 91.0 0.35 7.5E-06 36.5 4.0 44 381-424 5-48 (50)
79 cd06926 RNAP_II_RPB11 RPB11 su 88.9 0.95 2.1E-05 39.6 5.5 41 208-253 12-52 (93)
80 COG1471 RPS4A Ribosomal protei 87.6 0.53 1.2E-05 47.5 3.5 45 106-150 51-95 (241)
81 PLN03186 DNA repair protein RA 87.4 0.55 1.2E-05 50.2 3.7 53 372-424 31-83 (342)
82 COG0162 TyrS Tyrosyl-tRNA synt 86.2 1.8 4E-05 47.2 7.0 78 60-138 295-377 (401)
83 PF00633 HHH: Helix-hairpin-he 80.9 1.6 3.5E-05 30.4 2.5 28 393-420 2-29 (30)
84 PRK12766 50S ribosomal protein 79.8 1.9 4.2E-05 43.6 3.8 48 376-423 10-57 (232)
85 PF14451 Ub-Mut7C: Mut7-C ubiq 79.0 1.8 3.9E-05 36.9 2.8 29 122-151 50-78 (81)
86 PF12482 DUF3701: Phage integr 76.5 1.6 3.5E-05 38.5 1.9 58 375-432 19-80 (96)
87 TIGR02236 recomb_radA DNA repa 74.6 3.4 7.4E-05 42.9 4.0 48 376-423 6-53 (310)
88 TIGR00575 dnlj DNA ligase, NAD 74.6 3.6 7.7E-05 47.8 4.5 70 376-445 439-512 (652)
89 PRK07956 ligA NAD-dependent DN 73.4 3.6 7.7E-05 47.9 4.1 70 376-445 452-525 (665)
90 PRK14351 ligA NAD-dependent DN 72.3 4.2 9.2E-05 47.5 4.4 70 376-445 469-542 (689)
91 PRK14350 ligA NAD-dependent DN 72.0 3.6 7.9E-05 47.8 3.8 73 376-448 443-519 (669)
92 PRK03858 DNA polymerase IV; Va 71.2 11 0.00025 40.4 7.2 51 368-420 171-222 (396)
93 cd03468 PolY_like DNA Polymera 70.8 12 0.00026 39.0 7.0 55 369-428 170-224 (335)
94 PRK08097 ligB NAD-dependent DN 70.6 4.5 9.7E-05 46.1 4.0 66 376-441 432-501 (562)
95 PRK01172 ski2-like helicase; P 70.2 3.2 6.9E-05 48.0 2.8 48 377-424 620-667 (674)
96 PRK03352 DNA polymerase IV; Va 70.0 3 6.6E-05 44.0 2.4 52 368-421 175-227 (346)
97 PF12826 HHH_2: Helix-hairpin- 68.4 5.3 0.00012 32.2 3.0 42 381-424 16-57 (64)
98 cd00754 MoaD Ubiquitin domain 67.9 14 0.0003 30.2 5.5 52 85-149 25-76 (80)
99 cd03586 PolY_Pol_IV_kappa DNA 67.7 14 0.0003 38.5 6.8 52 368-422 169-221 (334)
100 PRK03609 umuC DNA polymerase V 66.5 4.1 8.8E-05 44.4 2.6 43 368-412 177-220 (422)
101 cd01700 PolY_Pol_V_umuC umuC s 65.0 4.7 0.0001 42.5 2.6 51 368-421 174-225 (344)
102 PRK00254 ski2-like helicase; P 62.5 7.4 0.00016 45.4 3.9 50 376-425 652-701 (720)
103 PRK14133 DNA polymerase IV; Pr 62.2 6 0.00013 41.9 2.8 56 368-428 171-227 (347)
104 COG1948 MUS81 ERCC4-type nucle 61.9 7.1 0.00015 40.2 3.1 45 378-424 192-236 (254)
105 PRK03103 DNA polymerase IV; Re 61.7 5.5 0.00012 43.1 2.5 51 369-422 180-231 (409)
106 PRK02406 DNA polymerase IV; Va 60.9 6.3 0.00014 41.6 2.7 51 369-422 167-218 (343)
107 PRK01216 DNA polymerase IV; Va 60.7 6.3 0.00014 42.2 2.6 52 368-421 176-228 (351)
108 PRK03348 DNA polymerase IV; Pr 58.4 7.3 0.00016 43.2 2.7 51 368-420 178-229 (454)
109 cd01701 PolY_Rev1 DNA polymera 58.1 26 0.00055 38.2 6.8 57 368-428 220-279 (404)
110 PRK02794 DNA polymerase IV; Pr 57.1 7.3 0.00016 42.5 2.4 57 367-428 206-263 (419)
111 TIGR00234 tyrS tyrosyl-tRNA sy 55.2 15 0.00032 39.9 4.4 43 97-139 330-372 (377)
112 PRK01777 hypothetical protein; 54.8 12 0.00026 32.9 2.9 43 104-149 34-76 (95)
113 PRK06437 hypothetical protein; 53.9 14 0.0003 30.2 3.0 24 123-147 38-61 (67)
114 PRK02362 ski2-like helicase; P 53.2 11 0.00023 44.3 3.1 47 377-425 660-706 (737)
115 PRK01810 DNA polymerase IV; Va 52.2 9.9 0.00022 41.1 2.5 52 368-422 177-229 (407)
116 TIGR00731 ctc_TL5 ribosomal pr 50.0 16 0.00034 35.5 3.2 49 277-325 122-175 (176)
117 PRK05618 50S ribosomal protein 49.0 11 0.00025 37.1 2.1 42 288-329 142-187 (197)
118 cd00424 PolY Y-family of DNA p 47.8 13 0.00028 39.2 2.5 52 369-422 172-224 (343)
119 PF14693 Ribosomal_TL5_C: Ribo 47.1 8.7 0.00019 33.0 0.9 52 276-327 28-84 (88)
120 PRK06488 sulfur carrier protei 45.3 23 0.0005 28.3 3.0 24 124-147 33-59 (65)
121 PF14229 DUF4332: Domain of un 44.8 17 0.00036 33.2 2.4 45 377-421 3-49 (122)
122 PF05920 Homeobox_KN: Homeobox 43.6 27 0.00058 25.8 2.8 27 56-82 13-39 (40)
123 TIGR01683 thiS thiamine biosyn 43.1 27 0.00059 27.8 3.1 25 123-147 31-58 (64)
124 PF02597 ThiS: ThiS family; I 42.7 24 0.00053 28.4 2.8 50 85-148 21-72 (77)
125 smart00611 SEC63 Domain of unk 41.5 27 0.00058 36.1 3.6 95 327-425 105-207 (312)
126 PRK06944 sulfur carrier protei 41.3 30 0.00064 27.4 3.1 26 123-148 32-60 (65)
127 COG4185 Uncharacterized protei 40.2 30 0.00066 33.8 3.4 53 297-349 14-69 (187)
128 PF14716 HHH_8: Helix-hairpin- 39.1 32 0.00069 27.9 2.9 21 403-423 48-68 (68)
129 KOG3438|consensus 38.3 26 0.00057 31.3 2.5 26 211-240 14-39 (105)
130 COG0272 Lig NAD-dependent DNA 38.3 24 0.00053 41.0 2.9 68 377-444 453-524 (667)
131 PLN02799 Molybdopterin synthas 37.9 65 0.0014 26.7 4.7 26 123-149 53-78 (82)
132 cd00565 ThiS ThiaminS ubiquiti 36.6 30 0.00064 27.6 2.4 25 124-148 33-60 (65)
133 smart00278 HhH1 Helix-hairpin- 36.3 19 0.00041 23.8 1.0 19 402-420 1-19 (26)
134 PRK08364 sulfur carrier protei 35.2 43 0.00093 27.3 3.1 26 122-148 40-65 (70)
135 cd01764 Urm1 Urm1-like ubuitin 34.4 36 0.00078 29.7 2.7 59 85-148 28-89 (94)
136 cd00166 SAM Sterile alpha moti 32.5 64 0.0014 24.5 3.7 41 374-419 13-53 (63)
137 PF04994 TfoX_C: TfoX C-termin 32.3 25 0.00054 29.9 1.3 36 376-411 10-46 (81)
138 TIGR01682 moaD molybdopterin c 32.3 49 0.0011 27.3 3.1 50 86-149 27-76 (80)
139 PF00498 FHA: FHA domain; Int 32.2 35 0.00076 26.8 2.1 25 122-146 42-67 (68)
140 COG2104 ThiS Sulfur transfer p 31.7 47 0.001 27.4 2.8 24 124-147 36-62 (68)
141 PRK08053 sulfur carrier protei 30.8 60 0.0013 26.1 3.3 24 124-147 34-60 (66)
142 COG4043 Preprotein translocase 30.3 48 0.001 29.7 2.8 35 114-148 10-44 (111)
143 PRK00116 ruvA Holliday junctio 29.6 54 0.0012 32.1 3.4 77 379-462 84-161 (192)
144 PRK13482 DNA integrity scannin 29.3 54 0.0012 35.5 3.5 43 381-425 300-342 (352)
145 cd01703 PolY_Pol_iota DNA Poly 28.1 80 0.0017 34.3 4.7 51 370-422 172-238 (379)
146 TIGR03491 RecB family nuclease 27.5 45 0.00097 37.0 2.7 44 376-419 214-257 (457)
147 PRK05659 sulfur carrier protei 27.4 72 0.0016 25.3 3.2 24 124-147 34-60 (66)
148 KOG2623|consensus 26.1 69 0.0015 35.3 3.6 37 102-138 404-440 (467)
149 PRK00024 hypothetical protein; 25.8 74 0.0016 32.0 3.7 41 381-423 47-87 (224)
150 PF02824 TGS: TGS domain; Int 24.7 75 0.0016 25.2 2.8 23 123-146 36-58 (60)
151 PF14229 DUF4332: Domain of un 24.4 60 0.0013 29.5 2.5 33 373-405 57-89 (122)
152 PRK08609 hypothetical protein; 23.9 60 0.0013 37.2 2.9 51 376-426 95-147 (570)
153 COG4277 Predicted DNA-binding 23.4 75 0.0016 33.9 3.2 58 375-433 304-371 (404)
154 PRK07440 hypothetical protein; 22.9 96 0.0021 25.4 3.2 25 123-147 37-64 (70)
155 KOG1919|consensus 22.2 1.1E+02 0.0025 33.3 4.4 46 99-146 47-92 (371)
156 PF06353 DUF1062: Protein of u 22.0 88 0.0019 29.6 3.1 35 94-129 100-134 (142)
157 cd01702 PolY_Pol_eta DNA Polym 21.4 1.6E+02 0.0034 31.7 5.3 51 370-422 182-236 (359)
158 PF07647 SAM_2: SAM domain (St 20.8 1E+02 0.0022 24.2 2.8 45 374-422 15-59 (66)
No 1
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=100.00 E-value=3.9e-65 Score=527.74 Aligned_cols=230 Identities=32% Similarity=0.441 Sum_probs=207.5
Q ss_pred CeeEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhcccccee
Q psy8861 202 PRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVIL 281 (550)
Q Consensus 202 p~~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilNLK~i~~ 281 (550)
+-..++.+.+.+||+|+++||++|||+||||||||+|||++||+||++|+|+|+.|||++||||+|||+||++|||+|+|
T Consensus 9 ~ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~gv~hEfs~i~GV~Edv~eIilNLK~I~~ 88 (327)
T CHL00013 9 CVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILLNLKEIVL 88 (327)
T ss_pred ceeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECCccccccCCCCcccCHHHHHHhhhcCeE
Confidence 33456666789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeccCceEEEEEEEeceeeEEeccCccCCCeEEeCCCceEEEcCC-----------------------------------
Q psy8861 282 KLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSD----------------------------------- 326 (550)
Q Consensus 282 ~~~~~~~~~~~l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~~----------------------------------- 326 (550)
+.+..+++.++|+++||++|||+||.+|++|+|+|||||||||++
T Consensus 89 k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~ieivnpd~~Iatl~~~~~l~~el~ie~G~GY~~~~~~~~~~g~i~iDa~F 168 (327)
T CHL00013 89 KSNLYGPQKASICVQGPKYVTAQDIILPPSVEIVDPTQHIATITEPIDLEIELKIEKGRGYRLKTPKNFQDGSFPIDAVF 168 (327)
T ss_pred EccCCCcEEEEEEEeCCeEEEeeeeccCCCeEEeCCCeEEEEeCCCCEEEEEEEEECccCceeccccccCCCcEEeCCCC
Confidence 998777899999999999999999999999999999999999987
Q ss_pred ----------------------------------hHHHHHHHHHHHHHHhhhhhccCCCCC----c-cc-----------
Q psy8861 327 ----------------------------------NEEAIRQSARVLVDQLNVFAALENTPV----K-KE----------- 356 (550)
Q Consensus 327 ----------------------------------P~~Al~~Aa~iL~~~~~~f~~~~~~~~----~-~~----------- 356 (550)
|++||.+||++|++||.+|.+++.... . ..
T Consensus 169 sPV~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 248 (327)
T CHL00013 169 MPVRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFLHAEEENLKLENNENRVTLLFTFHDRL 248 (327)
T ss_pred CCeeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhcchhhhcccccccccccccccccccc
Confidence 999999999999999999998764311 0 00
Q ss_pred -cCccccccCCcccccccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh-cCccccc
Q psy8861 357 -LDSSLEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS-RGKYYMR 431 (550)
Q Consensus 357 -~~~~~~~~~~~l~~~I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~-~gl~lmr 431 (550)
..++....++.++++||+|+||||||||||+|||+||+||+++|++||+++||||+||++||+++|++ +|++|..
T Consensus 249 ~~~~~~~~~~~~~~~~Ie~L~LSvRs~NcLk~a~I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~L~~~~gl~l~~ 325 (327)
T CHL00013 249 TDLKKNKKEIALKQIFIEQLELSVRAYNCLKRANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEALQKRFGIDLPK 325 (327)
T ss_pred cccccchhhhhhhceeHHhccCchhhhhhhhhcCccCHHHHHhcCHHHHhhhhccCHhHHHHHHHHHHHHhCCCCCC
Confidence 10111123467889999999999999999999999999999999999999999999999999999988 9999864
No 2
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. 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.
Probab=100.00 E-value=4e-62 Score=501.07 Aligned_cols=218 Identities=44% Similarity=0.686 Sum_probs=199.5
Q ss_pred EEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhccccceeeeccCceEEEEE
Q psy8861 214 HAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILNL 293 (550)
Q Consensus 214 y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilNLK~i~~~~~~~~~~~~~l 293 (550)
||+|+++||++|||+||||||||+|||++||+||++|+|+|+.|||++||||+|||++|++|||+|+|+.++.++..++|
T Consensus 1 y~~f~i~Ple~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~gv~HEf~~I~GV~Edv~eIllNlK~i~~~~~~~~~~~~~l 80 (297)
T TIGR02027 1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDGVLHEFSTIEGVKEDVTEIILNLKQLVVKSEGDGERTMTL 80 (297)
T ss_pred CcEEEEecCCCCchhHHHHHHHHHHHhcCCceEEEEEEEcceecccccCCCccccHHHHHhhhhceEEeccCCCcEEEEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999998777789999
Q ss_pred EEeceeeEEeccCc-cCCCeEEeCCCceEEEcCC----------------------------------------------
Q psy8861 294 KKFGKCVVLASDIE-LLSDIELVNPNHIIAHLSD---------------------------------------------- 326 (550)
Q Consensus 294 ~~~Gp~~V~A~DI~-~~~~veivnpd~~IatL~~---------------------------------------------- 326 (550)
+++||++|||+||+ .|++|+|+|||+|||||++
T Consensus 81 ~~~gp~~VtA~Di~~~p~~ieivnpd~~IatL~~~~~L~iel~i~~G~Gy~~~~~~~~~~~~~~~i~iDa~FsPV~~Vny 160 (297)
T TIGR02027 81 SKKGPGVVTAGDIKAPPGDVEIVNPDLVIATLTEPADLEIELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPVLKVNY 160 (297)
T ss_pred EEeCCEEEEhhhcccCCCCcEEeCCCeEEEEECCCCEEEEEEEEEcccccCcccccccccCccccccccccccCeEEEEE
Confidence 99999999999999 7999999999999999987
Q ss_pred ---------------------------hHHHHHHHHHHHHHHhhhhhccCCCCCc--c--ccCccccccCCccccccccc
Q psy8861 327 ---------------------------NEEAIRQSARVLVDQLNVFAALENTPVK--K--ELDSSLEKVDPILLRPVDDL 375 (550)
Q Consensus 327 ---------------------------P~~Al~~Aa~iL~~~~~~f~~~~~~~~~--~--~~~~~~~~~~~~l~~~I~~L 375 (550)
|.+|+.+|+++|.+||++|.+++..... . ...++..+.+++++++||+|
T Consensus 161 ~ve~~rv~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~L 240 (297)
T TIGR02027 161 EVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVNLDEEIEAFEEEQEEEEEELEDAKLLSIKIEEL 240 (297)
T ss_pred EEeeeeccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhcchhccccccccccccccccccchhccccHHHh
Confidence 9999999999999999999887542111 1 11101123346789999999
Q ss_pred CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhcCccccc
Q psy8861 376 ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMR 431 (550)
Q Consensus 376 ~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~lmr 431 (550)
+|||||+||||+|||+||+||+++|++||++++|||+||++||+++|+++|+.|++
T Consensus 241 ~LSvR~~n~Lk~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l~~~gl~~~~ 296 (297)
T TIGR02027 241 DLSVRSYNCLKRAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLAELGLELGM 296 (297)
T ss_pred CccHHHHhHHHHcCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHHHHcCCCcCC
Confidence 99999999999999999999999999999999999999999999999999999865
No 3
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=100.00 E-value=9.6e-62 Score=500.68 Aligned_cols=234 Identities=52% Similarity=0.788 Sum_probs=213.6
Q ss_pred ccCCCeeEEEEeeC--CcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhc
Q psy8861 198 DLLKPRIIDVKTLG--SNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILN 275 (550)
Q Consensus 198 Ell~p~~i~v~~~~--~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilN 275 (550)
.+.+|..+++.+.+ ++||+|.++||++|||+|+||||||+|||++||+||++|+|+|+.|||++||||+|||++|++|
T Consensus 2 ~~~~~~~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~gv~hEf~~Ipgv~Edv~eIllN 81 (310)
T PRK05182 2 EFLKPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDGVLHEFSTIPGVREDVTEIILN 81 (310)
T ss_pred CcccCcEEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEcceeeeccccCCcccchhHhhhh
Confidence 46789888888864 8999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccceeeeccCceEEEEEEEeceeeEEeccCccCCCeEEeCCCceEEEcCC-----------------------------
Q psy8861 276 LKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSD----------------------------- 326 (550)
Q Consensus 276 LK~i~~~~~~~~~~~~~l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~~----------------------------- 326 (550)
||+++|+.++.+++.++|+++||++|||+||.+|++|+|+|||+|||||++
T Consensus 82 lk~i~~~~~~~~~~~~~l~~~gp~~VtA~Di~~~~~v~ivn~d~~IatL~~~~~l~ie~~~~kG~Gy~~~~~~~~~~~~g 161 (310)
T PRK05182 82 LKGLRLKLHGDEPVTLTLSKKGPGEVTAGDIETDGDVEIVNPDLVIATLNEGAKLEMELTVERGRGYVPAEENKEDAPIG 161 (310)
T ss_pred hccceeecCCCceEEEEEEecCCeEEEHHHcCCCCCcEEeCCCeEEEEECCCCEEEEEEEEECcCCCcccccccccCCcc
Confidence 999999998889999999999999999999999999999999999999986
Q ss_pred -------------------------------------------hHHHHHHHHHHHHHHhhhhhccCCCCC-ccccCcccc
Q psy8861 327 -------------------------------------------NEEAIRQSARVLVDQLNVFAALENTPV-KKELDSSLE 362 (550)
Q Consensus 327 -------------------------------------------P~~Al~~Aa~iL~~~~~~f~~~~~~~~-~~~~~~~~~ 362 (550)
|++||.+|+++|++||++|.++..... ....+.+.+
T Consensus 162 ~i~iDa~f~PV~~vny~ve~~~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~~~~~~~~~~~~~~~~~ 241 (310)
T PRK05182 162 RIPVDAIFSPVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVDLEEAEEAEEEVEEEEP 241 (310)
T ss_pred cEEecCCcCCccceEEEecccccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhCcccccccccccccccc
Confidence 999999999999999999998763211 111111112
Q ss_pred ccCCcccccccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhcCccccc
Q psy8861 363 KVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMR 431 (550)
Q Consensus 363 ~~~~~l~~~I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~lmr 431 (550)
..++.++++|++|+|||||+||||++||+|++||+++|++||++++|||+||++||+++|+++|+.|++
T Consensus 242 ~~~~~l~~~I~~L~LS~R~~n~Lk~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~L~~~gl~l~~ 310 (310)
T PRK05182 242 EFDPILLRPIEELELSVRSYNCLKRAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAELGLSLGM 310 (310)
T ss_pred cccccccccHHHhccchHHHHHHHHcCCcCHHHHHhCCHHHHhcCCCCChhhHHHHHHHHHHcCCCcCC
Confidence 344678999999999999999999999999999999999999999999999999999999999999864
No 4
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=100.00 E-value=5.3e-54 Score=443.44 Aligned_cols=239 Identities=47% Similarity=0.696 Sum_probs=214.8
Q ss_pred cCCCeeEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhcccc
Q psy8861 199 LLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKG 278 (550)
Q Consensus 199 ll~p~~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilNLK~ 278 (550)
+.+|..+++.+.+..|++|.++|+++|||+||||||||+||||+||+||++|+|+|+.|||++++||.|||++|+||||.
T Consensus 1 ~~~p~~i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~~v~hef~s~~gv~Edvl~~~LnLk~ 80 (317)
T COG0202 1 FLKPKKVKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEGVQEDVLAHRLNLKP 80 (317)
T ss_pred CCcccceEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEEeccccccccCcCcHHHHHHHHhcCce
Confidence 35777789988888899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeeccCceEEEEEEEeceeeEEeccCccCCCeEEeCCCceEEEcCC--------------------------------
Q psy8861 279 VILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSD-------------------------------- 326 (550)
Q Consensus 279 i~~~~~~~~~~~~~l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~~-------------------------------- 326 (550)
|.++.+.....++.+.+.|||.+||+|+..|.++||+|||++|||+++
T Consensus 81 L~~~~~~~~~~~~~~~~~g~g~v~a~d~~~~~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~~~~~~~~~v~~i 160 (317)
T COG0202 81 LAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNREDDPPVGPI 160 (317)
T ss_pred eeeecccccceEEEEeccCCccccHhhcccceeEEEECCCceeeeccCCcceEEEEEEEcCccEeccccccccCCCceee
Confidence 999988665588999999999999999999999999999999999987
Q ss_pred -----------------------------------------hHHHHHHHHHHHHHHhhhhhccCCCCCccccCccccccC
Q psy8861 327 -----------------------------------------NEEAIRQSARVLVDQLNVFAALENTPVKKELDSSLEKVD 365 (550)
Q Consensus 327 -----------------------------------------P~~Al~~Aa~iL~~~~~~f~~~~~~~~~~~~~~~~~~~~ 365 (550)
|++|+..|++||.+|++.|.++.+.....+.+....+..
T Consensus 161 ~~D~~~spv~kvqy~ve~~r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~~~~~~~e~~~~~~~ 240 (317)
T COG0202 161 AVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKAVEIEEEKPEFPIL 240 (317)
T ss_pred eCCCceeeeeeceEEEEeEEEeccCCceeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHHhhccccceeeccccccccc
Confidence 999999999999999999999876542211111101233
Q ss_pred CcccccccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhcCccccccccccc
Q psy8861 366 PILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGFR 437 (550)
Q Consensus 366 ~~l~~~I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~lmrhrk~~r 437 (550)
..+..+|++|+|||||+||||++||+|++||+++|+.+|++++|||+||++||+++|+++|+.|.+..-.+.
T Consensus 241 ~~~~~~I~~l~lsvrs~ncLk~~~i~~i~~L~~~~e~~l~~v~n~G~ksleEi~~kl~~~~l~l~~~~e~~~ 312 (317)
T COG0202 241 LVLEAPIDELDLSVRSYNCLKREGIETIGELVQRTEEELLKVENLGKKSLEEIKEKLAELGLELGMELENWP 312 (317)
T ss_pred ccccccccccccceeeehhhcccCchhhHHHHhcCHHHHhcccccccCCHHHHHHHHHHhhhhhcccchhcc
Confidence 456679999999999999999999999999999999999999999999999999999999999988765443
No 5
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=100.00 E-value=8.2e-50 Score=388.49 Aligned_cols=192 Identities=39% Similarity=0.609 Sum_probs=178.2
Q ss_pred CCCCCCCchhhhhhcCCCCccccccccccccccCCCCCCCCCC--CCcccccchhhhhHhhhhhHhhhCCcHHHHHHHHH
Q psy8861 1 MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGR--ISGSRTSDYGYQFREKQKVKRMYGILEKQFRRYFI 78 (550)
Q Consensus 1 M~r~~gp~~Ki~Rrlg~~l~~~~~~~~~~~k~~~~~~pg~~~~--~~~~k~s~y~~~L~~Kqkl~~~YG~~ekq~~~~~~ 78 (550)
||||+||++|+|||+|+ +++. +.+ .++|||||. .+++|.|+|++||+||||++++||++|+||++||.
T Consensus 1 M~r~~gp~~k~~Rrlg~-l~g~------~~~---~~~pg~~g~~~~~~~k~S~y~~~L~eKqk~~~~Yg~~ekq~~~~~~ 70 (201)
T CHL00113 1 MSRYRGPRLKIIRRLGA-LPGL------TSK---TPRPGSDLRNQSRSGKKSQYRIRLEEKQKLRFNYGLTERQLLKYVR 70 (201)
T ss_pred CCCccccHhHhhccCCC-Cccc------ccC---CCCCCCCcccccccccccHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 99999999999999999 6532 233 478999984 23358999999999999999999999999999999
Q ss_pred HhhccCCCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchhhHHHHh
Q psy8861 79 EGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIAN 158 (550)
Q Consensus 79 ~a~~~~g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~~~~i~~ 158 (550)
+|.+.+|+||++|+++||+|||++|++.||+.||.+|+|+|.||||+|||++|++||+.|++||+|+|++.+++...|++
T Consensus 71 ~a~~~~g~tg~~ll~~LE~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~~~~~~~~~~ 150 (201)
T CHL00113 71 IARKAKGSTGQVLLQLLEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQN 150 (201)
T ss_pred HHHhcCCcHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEccccchHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCCCCCCcEEEecCccEEEEecccCcccccccccccCCC
Q psy8861 159 SLELSEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLKP 202 (550)
Q Consensus 159 ~~~~~~~~~~p~~l~vd~~~~~g~~~~~P~~~~Ipl~inEll~p 202 (550)
+++......+|+||++|.++++|+++++|+++|||.++||+++.
T Consensus 151 ~~~~~~~~~~p~~l~~~~~~~~~~~~~~p~r~~i~~~~~e~lvv 194 (201)
T CHL00113 151 NLESSPREELPNHLTLDKLQYKGLVNQIIDRKWVGLKINELLVV 194 (201)
T ss_pred HHHhhccCCCCCeEEeechhCEEEEEeccCHHHCCCCCccceee
Confidence 99866556789999999999999999999999999999999774
No 6
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-49 Score=348.37 Aligned_cols=116 Identities=66% Similarity=0.975 Sum_probs=115.3
Q ss_pred cccccccccCCCChHHHHHHHHHHHHHHHhcCcEEechhhHHHHhhhhHHHHhhhccCChhHHHHHHhhcCChHHHHHHH
Q psy8861 430 MRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLF 509 (550)
Q Consensus 430 mrhrk~~rklgr~~~hR~~llrnl~t~Li~~erI~TT~~kAke~r~~aeklIt~ak~~~~~~~r~~~~~l~~~~~~~kLf 509 (550)
|+|+.++++|||+++||+||+|||++|||+||+|+||++||||+|+++|+|||+||+||+++||+|.++|.|+++++|||
T Consensus 1 Mrh~~~~rkl~rtsshR~amlrnla~sLi~he~I~TT~~KAKelr~~vEkLITlaK~~~l~~RR~a~~~l~d~~~v~kLF 80 (116)
T COG0203 1 MRHRKKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANRRLAFARLRDKDAVKKLF 80 (116)
T ss_pred CCCCccCCCCCCCHHHHHHHHHHHHHHHHHcCceeecHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHcccHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCCCCCCeEEEEeccCCCCCCCCeEEEEec
Q psy8861 510 SELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELL 545 (550)
Q Consensus 510 ~~l~pry~~r~gGyTRi~k~~~R~gD~A~ma~iElv 545 (550)
++|+|||++|+||||||+|+++|+||+|||||||||
T Consensus 81 ~~iapry~~R~GGYtRIlK~g~R~GD~A~maiiElV 116 (116)
T COG0203 81 DEIAPRYAERNGGYTRILKLGFRRGDNAPMAIIELV 116 (116)
T ss_pred HHhChhhcCCCCCeeEEEecCCCCCCCCceEEEEeC
Confidence 999999999999999999999999999999999998
No 7
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=100.00 E-value=3.1e-47 Score=371.86 Aligned_cols=196 Identities=59% Similarity=0.948 Sum_probs=179.8
Q ss_pred CCCCCCCchhhhhhcCCCCccccccccccccccCCCCCCCCCCCC-cccccchhhhhHhhhhhHhhhCCcHHHHHHHHHH
Q psy8861 1 MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRIS-GSRTSDYGYQFREKQKVKRMYGILEKQFRRYFIE 79 (550)
Q Consensus 1 M~r~~gp~~Ki~Rrlg~~l~~~~~~~~~~~k~~~~~~pg~~~~~~-~~k~s~y~~~L~~Kqkl~~~YG~~ekq~~~~~~~ 79 (550)
||||+||++|+|||+|+++|++ +.++.. + .|+|||||+.+ ++|.|+|++||+||||++++||+.|+||.+||..
T Consensus 1 m~r~~gp~~k~~Rr~g~~l~~~-~~~~~~-~---~~~pg~hg~~~~~~k~s~y~~~L~eKQk~~~~Y~~~e~q~~~~~~~ 75 (203)
T PRK05327 1 MARYTGPKCKLSRRLGVDLFKS-GKRCLK-R---KYPPGQHGQRRRKPKLSDYGLQLREKQKLRRIYGVLEKQFRRYFKE 75 (203)
T ss_pred CCCccCchhhhhccCCCCCCCC-CcCccc-C---CCCCCCCCcccCCccccHHHHHHHHHHHhHHHhcCcHHHHHHHHHH
Confidence 9999999999999999999986 333221 1 28999999653 4489999999999999999999999999999999
Q ss_pred hhccCCCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchhhHHHHhh
Q psy8861 80 GARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANS 159 (550)
Q Consensus 80 a~~~~g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~~~~i~~~ 159 (550)
|.+..|.|+.+|+++||+|||++|++.||+.||.+|+|+|.||+|+|||+.+++||+.|++||+|+|.+.++....++.+
T Consensus 76 a~~~~g~t~~~ll~~lE~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~~sr~~~~l~~~ 155 (203)
T PRK05327 76 AARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEA 155 (203)
T ss_pred HHhccCCcHhHHHHHHHHHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECCcCcccHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998888888999
Q ss_pred hhccCCCCCCCcEEEecCccEEEEecccCcccccccccccCC
Q psy8861 160 LELSEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLK 201 (550)
Q Consensus 160 ~~~~~~~~~p~~l~vd~~~~~g~~~~~P~~~~Ipl~inEll~ 201 (550)
++......+|+|+++|...++|.|++.|+++|||+++|++++
T Consensus 156 l~~~~~~~~p~~l~~D~~~~tg~f~~~p~~~~~~~~~~~~lv 197 (203)
T PRK05327 156 LELAERRGVPDWLEVDAEKLEGTFKRLPEREEIPVPINEQLI 197 (203)
T ss_pred HHhhcccCCCCeEEEecCcCEEEEEeccCHHHCCCCCCccEE
Confidence 887654568999999999999999999999999999998865
No 8
>TIGR00059 L17 ribosomal protein L17. Eubacterial and mitochondrial. The mitochondrial form, from yeast, contains an additional 110 amino acids C-terminal to the region found by this model.
Probab=100.00 E-value=2.5e-47 Score=337.80 Aligned_cols=112 Identities=56% Similarity=0.867 Sum_probs=110.3
Q ss_pred ccccCCCChHHHHHHHHHHHHHHHhcCcEEechhhHHHHhhhhHHHHhhhccCChhHHHHHHhhcCChHHHHHHHhhhhh
Q psy8861 435 GFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGP 514 (550)
Q Consensus 435 ~~rklgr~~~hR~~llrnl~t~Li~~erI~TT~~kAke~r~~aeklIt~ak~~~~~~~r~~~~~l~~~~~~~kLf~~l~p 514 (550)
+++||||+++||++|||||+||||+||+|+||++||||+|++||+|||+||+|++|++|+|.+||.|+++++|||++|+|
T Consensus 1 ~~~klgr~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rR~~~~~l~~~~~v~KLf~~lap 80 (112)
T TIGR00059 1 SYRKLGRTSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRREAKAYIRNKEIVHKLFSEIAP 80 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHCCeEEECHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCeEEEEeccCCCCCCCCeEEEEecc
Q psy8861 515 RYIKINGGYVRILKMGFRVGDNAPMAFIELLN 546 (550)
Q Consensus 515 ry~~r~gGyTRi~k~~~R~gD~A~ma~iElv~ 546 (550)
||++|+||||||+|+++|.||+||||||||||
T Consensus 81 ry~~R~GGYTRI~kl~~R~gD~A~maiiElVd 112 (112)
T TIGR00059 81 RYAQRPGGYTRILKLGPRRGDAAEMAIIELVD 112 (112)
T ss_pred HhCCCCCCeEEEEECCCCCCCCCCeEEEEecC
Confidence 99999999999999999999999999999997
No 9
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=100.00 E-value=9.8e-47 Score=367.62 Aligned_cols=194 Identities=54% Similarity=0.836 Sum_probs=178.3
Q ss_pred CCCCCchhhhhhcCCCCccccccccccccccCCCCCCCCCCCCcccccchhhhhHhhhhhHhhhCCcHHHHHHHHHHhhc
Q psy8861 3 RYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKVKRMYGILEKQFRRYFIEGAR 82 (550)
Q Consensus 3 r~~gp~~Ki~Rrlg~~l~~~~~~~~~~~k~~~~~~pg~~~~~~~~k~s~y~~~L~~Kqkl~~~YG~~ekq~~~~~~~a~~ 82 (550)
||+||++|+|||+|+++|+.+ +++..++ +++|||||+++ +|.|+|++||+||||++++||+.|+||.+||..|.+
T Consensus 1 r~~gp~~k~~Rr~g~~l~~~~--~~~~~~~--~~~pg~hg~~~-~k~S~y~~~l~eKQk~~~~Yg~~e~q~~~~~~~a~~ 75 (200)
T TIGR01017 1 RYTGPKFKLSRRLGVNLFGKS--RKLLLKR--KYPPGQHGQRR-KKLSDYGLQLQEKQKLKFMYGITEKQFRKYFKEAKK 75 (200)
T ss_pred CCCCCchhhhccCCCCCCCCC--ccccccc--CCCCCCCCcCC-CcccHHHHHHHHHHHHHHHHhchHHHHHHHHHHHhc
Confidence 799999999999999999762 3343332 58999999744 589999999999999999999999999999999999
Q ss_pred cCCCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchhhHHHHhhhhc
Q psy8861 83 LKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSLEL 162 (550)
Q Consensus 83 ~~g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~~~~i~~~~~~ 162 (550)
..|.++.+|+++||+|||++|+++||+.||.+|+|+|.||+|.|||+++++||+.|++||+|+|++.......++++++.
T Consensus 76 ~~g~t~~~ll~~le~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~~~~~~~~i~~~~~~ 155 (200)
T TIGR01017 76 LKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLET 155 (200)
T ss_pred cCCCchhHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEeeCcccHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999988877788888887
Q ss_pred cCCCCCCCcEEEecCccEEEEecccCcccccccccccCC
Q psy8861 163 SEHSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLK 201 (550)
Q Consensus 163 ~~~~~~p~~l~vd~~~~~g~~~~~P~~~~Ipl~inEll~ 201 (550)
.....+|+||++|.+.++|+|++.|+++|||+++|++++
T Consensus 156 ~~~~~~p~~l~~d~~~~~g~~~~~p~~~~~~~~~~~~li 194 (200)
T TIGR01017 156 NGQRNIPSWLEVDKKTLEGKVLRVPERSQLPLPINESLV 194 (200)
T ss_pred hcccCCCCeEEEecccCEEEEEeccCHHHCCCCCCccEE
Confidence 655678999999999999999999999999999998765
No 10
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=100.00 E-value=5.9e-47 Score=336.16 Aligned_cols=112 Identities=63% Similarity=0.918 Sum_probs=110.5
Q ss_pred cccccCCCChHHHHHHHHHHHHHHHhcCcEEechhhHHHHhhhhHHHHhhhccCChhHHHHHHhhcCChHHHHHHHhhhh
Q psy8861 434 HGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELG 513 (550)
Q Consensus 434 k~~rklgr~~~hR~~llrnl~t~Li~~erI~TT~~kAke~r~~aeklIt~ak~~~~~~~r~~~~~l~~~~~~~kLf~~l~ 513 (550)
++++||||+++||++|||||+||||+||+|+||++||||+|++||+|||+||+|++|++|+|.+||+|+++++|||++|+
T Consensus 2 ~~~rkl~r~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~aK~~~~~~rR~~~~~L~~~~~v~KLf~~la 81 (113)
T PRK05591 2 KKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQAFARLRDKEAVHKLFDEIA 81 (113)
T ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHcCeEEecHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccCCCCCCeEEEEeccCCCCCCCCeEEEEec
Q psy8861 514 PRYIKINGGYVRILKMGFRVGDNAPMAFIELL 545 (550)
Q Consensus 514 pry~~r~gGyTRi~k~~~R~gD~A~ma~iElv 545 (550)
|||++|+||||||+|+++|.||+|||||||||
T Consensus 82 pry~~R~GGYTRI~k~~~R~gD~A~ma~iElV 113 (113)
T PRK05591 82 PRYADRNGGYTRILKLGFRRGDNAPMAIIELV 113 (113)
T ss_pred HHhCcCCCCeEEEEECCCCCCCCCCeEEEEeC
Confidence 99999999999999999999999999999998
No 11
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-47 Score=371.11 Aligned_cols=198 Identities=55% Similarity=0.866 Sum_probs=181.3
Q ss_pred CCCCCCCchhhhhhcCCCCccccccccccccccCCCCCCCCCCCCcccccchhhhhHhhhhhHhhhCCcHHHHHHHHHHh
Q psy8861 1 MARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQFREKQKVKRMYGILEKQFRRYFIEG 80 (550)
Q Consensus 1 M~r~~gp~~Ki~Rrlg~~l~~~~~~~~~~~k~~~~~~pg~~~~~~~~k~s~y~~~L~~Kqkl~~~YG~~ekq~~~~~~~a 80 (550)
|+||+||+.|++||+|.++|++ ...+ ......++|||||+.+++|.|+|+.||+||||++++||++|+||.++|..|
T Consensus 1 M~r~~~~~~K~~rr~g~~~~~~-~~~~--~~~~~~~~pGqhk~~~~~k~s~yg~qL~ekqkl~~~yg~~ekqf~~~l~~a 77 (205)
T COG0522 1 MARYPGPKKKLSRRLGFNPWLK-ERLC--KERKLPYKPGQHGQERWKKLSDYGLQLREKQKLRAFYGVLEKQFRRYLKEA 77 (205)
T ss_pred CCCCcCcccceeeecCCChHHH-HHHH--HHhhcCCCccccchhHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHH
Confidence 9999999999999999999987 2221 112235899999997666899999999999999999999999999999999
Q ss_pred hccCCCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchhhHHHHhhh
Q psy8861 81 ARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKKQTRIANSL 160 (550)
Q Consensus 81 ~~~~g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~~~~i~~~~ 160 (550)
...+|+++.+++++||+|||++|||+|||+|+.+|||||+||||.|||++||+|||+|++||+|+|++++.+...++.+.
T Consensus 78 ~~l~g~~~~~~~~~LErRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~~~~~~~ 157 (205)
T COG0522 78 GRLKGVTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEAL 157 (205)
T ss_pred hccCChHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeecccchhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999988888888
Q ss_pred hccC-CCCCCCcEEEecCccEEEEecccCcccccccccccCC
Q psy8861 161 ELSE-HSTPFSWITVDAKKMEGVFKSEPNRSEFANDINDLLK 201 (550)
Q Consensus 161 ~~~~-~~~~p~~l~vd~~~~~g~~~~~P~~~~Ipl~inEll~ 201 (550)
+... ...+|+|+++|.+++.|++.+.|+++|+|.++|+.++
T Consensus 158 ~~~~~~~~~~~~~e~d~~~~~~~~~~~p~~~~~~~~~~e~~i 199 (205)
T COG0522 158 ELAAQRGIPPAWLEVDEEKLEGTFKRLPERSDLPAPINEQLI 199 (205)
T ss_pred hhhhhccCcchhhhcchhhheeeeeeCCcccccCCCCChheE
Confidence 7653 2456899999999999999999999999999999876
No 12
>PTZ00076 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=1e-43 Score=346.72 Aligned_cols=122 Identities=31% Similarity=0.428 Sum_probs=117.5
Q ss_pred cccccccccccCCCChHHHHHHHHHHHHHHHhcCcEEechhhHHHHhhhhHHHHhhhccCChhHHHHHHhhcCChHHHHH
Q psy8861 428 YYMRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIK 507 (550)
Q Consensus 428 ~lmrhrk~~rklgr~~~hR~~llrnl~t~Li~~erI~TT~~kAke~r~~aeklIt~ak~~~~~~~r~~~~~l~~~~~~~k 507 (550)
.++-.++.++||||+++||++|||||+||||+||||+||++||||+|+|||||||+||+|++|++|+|.++|.|+++++|
T Consensus 11 ~~g~~~r~~rKLgR~ssHR~AlLRNLvtsLI~hERIeTTlaKAKELR~~AEKLITlAKk~tl~sRR~a~s~L~d~~av~K 90 (253)
T PTZ00076 11 NLGVRRRLFRRAHGQPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVESMLRTPQGRRK 90 (253)
T ss_pred HhhhcccccCCCCCCHHHHHHHHHHHHHHHHHcCcEEecHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCHHHHHH
Confidence 45667888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhhccCCCCCCeEEEEec-cCCCCCCCCeEEEEeccCCC
Q psy8861 508 LFSELGPRYIKINGGYVRILKM-GFRVGDNAPMAFIELLNQTK 549 (550)
Q Consensus 508 Lf~~l~pry~~r~gGyTRi~k~-~~R~gD~A~ma~iElv~~~~ 549 (550)
||++|||||++|+||||||+|+ ++|.||+||||||||||+|+
T Consensus 91 LF~eLAPRY~dR~GGYTRIlK~~g~R~GD~ApMAiIELVd~p~ 133 (253)
T PTZ00076 91 LYEKYVPLYRDRPFFFTRVVNQWRLRLRDAAPMAYIEFVDRPG 133 (253)
T ss_pred HHHHhhhHhcCCCCCeeEEEeCCCCCCCCCCCEEEEEeccCcC
Confidence 9999999999999999999996 69999999999999999874
No 13
>PF01196 Ribosomal_L17: Ribosomal protein L17; InterPro: IPR000456 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3F1F_R 1VSP_L 3PYV_N 3PYR_N 3PYO_N 1VSA_L 3MS1_N 3F1H_R 3D5B_R 3MRZ_N ....
Probab=100.00 E-value=8.1e-41 Score=290.45 Aligned_cols=97 Identities=57% Similarity=0.873 Sum_probs=95.3
Q ss_pred HHHHHHHHHHhcCcEEechhhHHHHhhhhHHHHhhhccCChhHHHHHHhhcCChHHHHHHHhhhhhccCCCCCCeEEEEe
Q psy8861 449 MLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLSKKNTLSNKRLAFSYLRDRKITIKLFSELGPRYIKINGGYVRILK 528 (550)
Q Consensus 449 llrnl~t~Li~~erI~TT~~kAke~r~~aeklIt~ak~~~~~~~r~~~~~l~~~~~~~kLf~~l~pry~~r~gGyTRi~k 528 (550)
|||||+|+||+||||+||++||||+|+|||||||+||+|++|++|++.+||.|+++++|||++|+|||++|+||||||+|
T Consensus 1 llrnlvt~Li~herI~TT~~KAke~r~~aErlIt~ak~~~~~~~r~~~~~l~~~~~v~KLf~~l~pRy~~r~GgYTRi~k 80 (97)
T PF01196_consen 1 LLRNLVTSLIRHERIETTLAKAKELRPYAERLITLAKKGDLHARRQALSWLRDKELVKKLFKELAPRYADRNGGYTRIIK 80 (97)
T ss_dssp HHHHHHHHHHHHSEEEEEHHHHHHHHHHHHHHHHHHTSSTHHHHHHHHHCSSSHHHHHHHHTTHHHHTTTSSS-SEEEEE
T ss_pred ChHHHHHHHHhCCeEEecHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHhcchHHHHHHHHHHHHHHccCCCCeEEEEe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCeEEEEec
Q psy8861 529 MGFRVGDNAPMAFIELL 545 (550)
Q Consensus 529 ~~~R~gD~A~ma~iElv 545 (550)
+++|.||+|||||||||
T Consensus 81 l~~R~gD~A~maiiElV 97 (97)
T PF01196_consen 81 LGPRRGDAAPMAIIELV 97 (97)
T ss_dssp EEECSSSTCEEEEEEET
T ss_pred CCCCCCCCCCEEEEEeC
Confidence 99999999999999998
No 14
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=100.00 E-value=3.7e-39 Score=317.67 Aligned_cols=120 Identities=50% Similarity=0.764 Sum_probs=116.0
Q ss_pred EEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhccccceeeecc-
Q psy8861 207 VKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYN- 285 (550)
Q Consensus 207 v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilNLK~i~~~~~~- 285 (550)
+++.+++|++|.++||++|+|+|+||||||+|||++||+||++|+|+|+.|||++||||+|||++|++|||+++|+.++
T Consensus 3 ~~~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~~~~He~~~Ipgv~Edv~~IllNlk~~~~~~~~~ 82 (215)
T cd06928 3 VENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFKSDSE 82 (215)
T ss_pred eccCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEcccccccccCCCccccHHHHhhccccEEEEecCC
Confidence 4556789999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred CceEEEEEEEeceeeEEeccCccCCCeEEeCCCceEEEcCC
Q psy8861 286 RDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSD 326 (550)
Q Consensus 286 ~~~~~~~l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~~ 326 (550)
.+++.++|+++||++|||+||.+|++++|+|||+|||||++
T Consensus 83 ~~~~~~~l~~~gp~~V~a~Di~~~~~i~ivnp~~~IatL~~ 123 (215)
T cd06928 83 DEPQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIATLTE 123 (215)
T ss_pred CceEEEEEEEecCeEEEhHhcCcCCCcEEeCCCcEEEEECC
Confidence 78999999999999999999999999999999999999987
No 15
>KOG3280|consensus
Probab=100.00 E-value=7.2e-40 Score=302.39 Aligned_cols=119 Identities=44% Similarity=0.705 Sum_probs=115.5
Q ss_pred cccccccccCCCChHHHHHHHHHHHHHHHhcCcEEechhhHHHHhhhhHHHHhhh-ccCChhHH--HHHHhhcCChHHHH
Q psy8861 430 MRHRHGFRKLNRTSSHRLIMLRNMTISLLRYEIIKTTLPKAKELRRVVEPILTLS-KKNTLSNK--RLAFSYLRDRKITI 506 (550)
Q Consensus 430 mrhrk~~rklgr~~~hR~~llrnl~t~Li~~erI~TT~~kAke~r~~aeklIt~a-k~~~~~~~--r~~~~~l~~~~~~~ 506 (550)
|.|...++|+||+++||.+|||||||+||+||||+|||+||||+|+|||+|||+| |.|+++++ +++..||..+++++
T Consensus 8 mt~~~~~~Klgr~~~~R~~lLR~lvt~LvkHErIe~t~ara~Ear~~aEklIt~~~k~g~~~~~~~~~a~~~l~ekdli~ 87 (171)
T KOG3280|consen 8 MTHGRRKLKLGRPPAHRLALLRNLVTQLVKHERIETTWARAKEARRYAEKLITLGKKAGSLHERTARMADGWLREKDLLH 87 (171)
T ss_pred ecccchhhhcCCCcHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhcCcHhHHHHHHHhcccccchHHH
Confidence 7788888999999999999999999999999999999999999999999999999 67999998 99999999999999
Q ss_pred HHHhhhhhccCCCCCCeEEEEeccCCCCCCCCeEEEEeccCC
Q psy8861 507 KLFSELGPRYIKINGGYVRILKMGFRVGDNAPMAFIELLNQT 548 (550)
Q Consensus 507 kLf~~l~pry~~r~gGyTRi~k~~~R~gD~A~ma~iElv~~~ 548 (550)
|||++|+|||+||+|||||++|+++|.||+|||||||+++|+
T Consensus 88 KlF~vl~pRY~dr~ggYTRllrlppr~~d~apmavlE~~Gn~ 129 (171)
T KOG3280|consen 88 KLFTVLAPRYKDRNGGYTRLLRLPPRRGDRAPMAVLELVGNP 129 (171)
T ss_pred HHHHHhchhhccCCCCceehhccCcccccccCceeeeecCCc
Confidence 999999999999999999999999999999999999999876
No 16
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=99.96 E-value=1.7e-28 Score=241.38 Aligned_cols=139 Identities=16% Similarity=0.245 Sum_probs=129.8
Q ss_pred EEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECC---------cccccccccCccccHHHHHhc
Q psy8861 205 IDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG---------ALHEYSSLEGVQEDIIDIILN 275 (550)
Q Consensus 205 i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~g---------v~hEfs~i~Gv~Edv~~IilN 275 (550)
+++.+.++.+.+|.++ |+|+|+||||||+|||++||+||+.|+|+| +.|||+.|||+.||++++++|
T Consensus 3 i~i~~~~~~~~~f~l~----g~~~t~aNaLRRiLLsevP~~AI~~V~I~~NtS~~~DE~iaHrlglIP~~~e~~~~~~~n 78 (212)
T cd07028 3 VKIREADKDNVDFILS----GVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQLYRS 78 (212)
T ss_pred EEEEEcCCCEEEEEEE----ccChhHHHHHHHHHHHcCcceEEEEEEEEcCCCcccceeeeeeeeecccccCcHHHhhhc
Confidence 7888899999999999 999999999999999999999999999999 999999999999999999999
Q ss_pred cccce-eeeccC-ceEEEEEEEecee----eEEeccCccCC------CeEEeCCCceEEEcCC-----------------
Q psy8861 276 LKGVI-LKLYNR-DYAILNLKKFGKC----VVLASDIELLS------DIELVNPNHIIAHLSD----------------- 326 (550)
Q Consensus 276 LK~i~-~~~~~~-~~~~~~l~~~Gp~----~V~A~DI~~~~------~veivnpd~~IatL~~----------------- 326 (550)
+|++. ++..+. +.+.++|+++||+ +|||+||++++ +++++|||++||+|.+
T Consensus 79 ~k~~~~~~~~~~~~~v~~~l~~~g~~~~~~~V~s~DL~~~~~~~~~~~v~pv~~di~I~kL~~gq~i~le~~~~~G~G~~ 158 (212)
T cd07028 79 PEEDCECEDHCDKCSVVLTLQAFAESESTTNVYSKDLVIVSNLMGRNIGHPIIQDILICKLRKGQEIKLTCVAKKGIGKE 158 (212)
T ss_pred ccccccccccccceeEEEEEEccCCCCCcceEEHHHcccCCccccCCCeEEeCCCcEEEEECCCCEEEEEEEEECCCcCC
Confidence 99988 444444 7889999999997 89999999775 9999999999999987
Q ss_pred --------------------------------hHHHHHHHHHHHHHHhhhhhc
Q psy8861 327 --------------------------------NEEAIRQSARVLVDQLNVFAA 347 (550)
Q Consensus 327 --------------------------------P~~Al~~Aa~iL~~~~~~f~~ 347 (550)
|++|+.+|+++|++||..|.+
T Consensus 159 hAk~sPV~~v~y~~~~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~ 211 (212)
T cd07028 159 HAKFGPVAAIEFRYDPVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILL 211 (212)
T ss_pred CCEeCCceEEEEEEEccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999998864
No 17
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=99.93 E-value=3.4e-26 Score=221.82 Aligned_cols=123 Identities=23% Similarity=0.299 Sum_probs=112.4
Q ss_pred EEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECC---------cccccccccCccccHHHHHhc
Q psy8861 205 IDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG---------ALHEYSSLEGVQEDIIDIILN 275 (550)
Q Consensus 205 i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~g---------v~hEfs~i~Gv~Edv~~IilN 275 (550)
+++...++...+|.++ ... |+||||||+|||++||+||++|+|+| +.|||++||
T Consensus 6 ~~~~~~~~~~~~f~l~-~~~----tlgNaLRRvLLssipg~AI~~V~I~~Nts~~~DEivaHe~~lIp------------ 68 (195)
T PRK14979 6 EKEKTRIGEEFKFSLK-API----SFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIP------------ 68 (195)
T ss_pred eeeeccCCcEEEEEEE-cCc----cHHHHHHHHHHhcCcceeEEEEEEecCcccccchheeeeeeeee------------
Confidence 5566668899999999 766 99999999999999999999999999 999999999
Q ss_pred cccceeeeccCceEEEEEEEeceeeEEeccCccCCCeEEeCCCceEEEcCC-----------------------------
Q psy8861 276 LKGVILKLYNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSD----------------------------- 326 (550)
Q Consensus 276 LK~i~~~~~~~~~~~~~l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~~----------------------------- 326 (550)
||++.++. ++.+.++|+++||++|||+||+++++ +|+|||+|||||++
T Consensus 69 LK~~~~~~--~~~~~l~L~~~gp~~Vta~Di~~~~~-~ivnpdi~I~tL~~g~~l~~e~~~~~G~Gy~hAk~~pvda~y~ 145 (195)
T PRK14979 69 IKGKPVSG--DEVITFTLSKEGPCTVYSSDLKSENG-EVAFKNIPIVKLAEGQKLEIECEALVGTGKIHAKWQPCNAVYK 145 (195)
T ss_pred eeeeeccC--CCcEEEEEEEeCCceEEHHHcCCCCC-cccCCCcEEEEECCCCEEEEEEEEECCCccccccccceeeEEe
Confidence 77777644 56789999999999999999998888 99999999999987
Q ss_pred ------------------hHHHHHHHHHHHHHHhhhhhc
Q psy8861 327 ------------------NEEAIRQSARVLVDQLNVFAA 347 (550)
Q Consensus 327 ------------------P~~Al~~Aa~iL~~~~~~f~~ 347 (550)
|++|+.+||+||++||+.|.+
T Consensus 146 ~~~~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~ 184 (195)
T PRK14979 146 QISNDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQ 184 (195)
T ss_pred cCCCcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999965
No 18
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=99.93 E-value=3.6e-26 Score=226.83 Aligned_cols=103 Identities=45% Similarity=0.572 Sum_probs=96.1
Q ss_pred EEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhccccceeeeccC-------
Q psy8861 214 HAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNR------- 286 (550)
Q Consensus 214 y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilNLK~i~~~~~~~------- 286 (550)
|++|.++| +|+|+||||||+|||++||+||++|+|+| +++||.|||++++|||+.|.++.+..
T Consensus 1 ~~~f~l~~----~~~t~~NaLRRilLs~vp~~aI~~V~I~~------n~~~v~eev~~~rLnL~pl~~~~~~~~~~~~~~ 70 (224)
T smart00662 1 RAKFVLEP----YGLTLANALRRVLLSSVPGMAVTEVEIEG------NTSGVQDEVLAHRLGLKPLASDPDGDEYQRDCE 70 (224)
T ss_pred CeEEEEEc----CCchHHHHHHHHHHHcCccceEEEEEEec------CCcchhHHHHHHHhCCeeEEEechhcccccccc
Confidence 68999997 89999999999999999999999999988 99999999999999999999986422
Q ss_pred -------ceEEEEEEEeceeeEEeccCccCC--CeEEeCCCceEEEcCC
Q psy8861 287 -------DYAILNLKKFGKCVVLASDIELLS--DIELVNPNHIIAHLSD 326 (550)
Q Consensus 287 -------~~~~~~l~~~Gp~~V~A~DI~~~~--~veivnpd~~IatL~~ 326 (550)
+.+.++|+++||++|||+||++|+ +|+++|||+|||||++
T Consensus 71 ~~~~~~~~~~~~~L~~~gp~~V~a~Dl~~~~~~~v~~vnp~~~I~~L~~ 119 (224)
T smart00662 71 CEEGCEKCSVTLTLDVKGPGEVTAGDLKSDSDPDVEIVNPDIPIAKLRE 119 (224)
T ss_pred ccccCCCceEEEEEEEEcCCcEEHHHcccCCCCCcEEeCCCcEEEEECC
Confidence 377999999999999999999887 9999999999999987
No 19
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=99.93 E-value=3.7e-26 Score=231.02 Aligned_cols=117 Identities=21% Similarity=0.167 Sum_probs=108.0
Q ss_pred eEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECC---------cccccccccCccccHHHHHh
Q psy8861 204 IIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG---------ALHEYSSLEGVQEDIIDIIL 274 (550)
Q Consensus 204 ~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~g---------v~hEfs~i~Gv~Edv~~Iil 274 (550)
.+++.+.+++|++|.++ |+|.|+||||||+|||++||+||++|+|++ +.|||+.|||+.||+.++++
T Consensus 2 ~~~~~~~~~~~~~f~~~----g~~~s~~NalRRills~vp~~Ai~~V~i~~n~s~~~de~i~hrl~~ip~~~e~~~~~~~ 77 (259)
T cd07030 2 EIEVLELDDDRARFVLE----GVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYKYR 77 (259)
T ss_pred ceEEEecCCCEEEEEEe----CCCHHHHHHHHHHHHhcCCeeeEEEEEEEeCCchhhHHHHHHhhcCcccccCHHHhccc
Confidence 37888888999999999 999999999999999999999999999987 79999999999999999999
Q ss_pred ccccce--eeeccCceEEEEEEEeceeeEEeccCcc-CCCeEEeCCCceEEEcCC
Q psy8861 275 NLKGVI--LKLYNRDYAILNLKKFGKCVVLASDIEL-LSDIELVNPNHIIAHLSD 326 (550)
Q Consensus 275 NLK~i~--~~~~~~~~~~~~l~~~Gp~~V~A~DI~~-~~~veivnpd~~IatL~~ 326 (550)
| ++. ++..+.+.+.++|+++||++|||+||.+ |++|+++|||++||||++
T Consensus 78 ~--~~~~~~~~~~~~~~~~~l~~~~~~~v~s~dl~~~~~~v~~~~~~~~I~~l~~ 130 (259)
T cd07030 78 S--ECSCGGAGCPLCTVTLTLSVEGPGTVYSGDLKSSDPDVKPVYDNIPIVKLGK 130 (259)
T ss_pred c--cccccCCCCCCcEEEEEEEccCCceEEccccccCCCCccccCCCcEEEEeCC
Confidence 9 555 3455567899999999999999999997 899999999999999986
No 20
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=99.91 E-value=2.2e-24 Score=218.55 Aligned_cols=111 Identities=22% Similarity=0.256 Sum_probs=102.2
Q ss_pred eEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECC---------cccccccccCccccHHHHHh
Q psy8861 204 IIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG---------ALHEYSSLEGVQEDIIDIIL 274 (550)
Q Consensus 204 ~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~g---------v~hEfs~i~Gv~Edv~~Iil 274 (550)
++++.+.+++|++|.+. |||+||||||||+|||++||+||++|+|++ +.|||+.|||+.
T Consensus 2 ~~~~~~~~~~~~~f~~~----g~~~t~~NalRRvlls~vp~~Ai~~v~i~~n~s~~~de~i~hrl~lip~~~-------- 69 (263)
T PRK00783 2 EIEILELDDRSARFVVE----GVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAHRLGLIPLTT-------- 69 (263)
T ss_pred ceEEEEcCCcEEEEEEe----CCCHHHHHHHHHHHHHcCCeeeEEEEEEEECCcchhHHHHHHhhcCccccc--------
Confidence 37888888999999994 999999999999999999999999999999 999999999988
Q ss_pred ccccceeeeccC--------ceEEEEEEEeceeeEEeccCcc-CCCeEEeCCCceEEEcCC
Q psy8861 275 NLKGVILKLYNR--------DYAILNLKKFGKCVVLASDIEL-LSDIELVNPNHIIAHLSD 326 (550)
Q Consensus 275 NLK~i~~~~~~~--------~~~~~~l~~~Gp~~V~A~DI~~-~~~veivnpd~~IatL~~ 326 (550)
|+|++.++.+.+ +.+.++|+++||++|||+||.. |++|+++|||+|||||++
T Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~V~a~dl~~~~~~v~~v~~~~~I~~L~~ 130 (263)
T PRK00783 70 DLDKYKPPEECTCEGEGCPDCTVTLSLEVEGPKTVYSGDLKSSDPDVKPVDPNIPIVKLKE 130 (263)
T ss_pred CHHHCCCcccccccCCCCCCcEEEEEEEecCCCcEEccccccCCCCceecCCCcEEEEeCC
Confidence 789888876532 3789999999999999999997 999999999999999987
No 21
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=99.88 E-value=4.3e-22 Score=202.26 Aligned_cols=119 Identities=18% Similarity=0.232 Sum_probs=105.3
Q ss_pred eEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECC---------cccccccccCccccHHHHHh
Q psy8861 204 IIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG---------ALHEYSSLEGVQEDIIDIIL 274 (550)
Q Consensus 204 ~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~g---------v~hEfs~i~Gv~Edv~~Iil 274 (550)
.|++.+.++++++|.++|++ .|+||||||+|||++||+||+.|+|++ ++|+|+.|||+.||+.++++
T Consensus 2 ~i~i~~~~~~~~~F~l~~~~----~s~aNALRRillsevPt~AI~~V~I~~NtSvl~DE~iaHRlglIPl~~e~~~~~~~ 77 (265)
T cd07031 2 RVEITELTDDKVKFILENTD----LSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAHRLGLIPLTSDDVDEFLY 77 (265)
T ss_pred cEEEEEcCCCEEEEEEEcCc----HHHHHHHHHHHHHcCccceEEEEEEecCCcccccceeeeecccCCCccCcHHHHhh
Confidence 38888989999999999888 599999999999999999999999999 89999999999999999999
Q ss_pred ccccceeeec-cCceEEEEEEEe----ceeeEEeccCccC-------CCeEEeC--------CCceEEEcCC
Q psy8861 275 NLKGVILKLY-NRDYAILNLKKF----GKCVVLASDIELL-------SDIELVN--------PNHIIAHLSD 326 (550)
Q Consensus 275 NLK~i~~~~~-~~~~~~~~l~~~----Gp~~V~A~DI~~~-------~~veivn--------pd~~IatL~~ 326 (550)
|+|....... ..+.+.++|+++ ||++|||+||+++ ..+.|.| ||++||+|.+
T Consensus 78 ~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~~~~~~pi~~~~~~~~~~~~i~I~kL~~ 149 (265)
T cd07031 78 YSRDCDCDEFCDKCSVELTLDVKCTGDQTREVTSRDLVSSGPKVNDVVPVPIRNDSEDNGEEDGILIVKLRK 149 (265)
T ss_pred hhhhccccCCCCCCeEEEEEEEEeccCCCceEEHHHcccccccccccCCcccccccccccCCCCeEEEEECC
Confidence 9986544322 237889999998 8999999999976 3567776 9999999987
No 22
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=99.76 E-value=1.9e-19 Score=146.51 Aligned_cols=61 Identities=49% Similarity=0.820 Sum_probs=54.3
Q ss_pred cCCcccccccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 364 VDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 364 ~~~~l~~~I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
....++.||++|+||+||+|||+++||+||+||+.+|++||++++|||++|++||+++|++
T Consensus 6 ~~~~~~~~I~~L~LS~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~e 66 (66)
T PF03118_consen 6 EEELLDTPIEDLGLSVRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLKE 66 (66)
T ss_dssp -HHHHCSBGGGSTSBHHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHHH
T ss_pred hHHHhcCcHHHhCCCHHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHcC
Confidence 3456789999999999999999999999999999999999999999999999999999975
No 23
>PF00163 Ribosomal_S4: Ribosomal protein S4/S9 N-terminal domain; InterPro: IPR001912 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S4 is one of the proteins from the small ribosomal subunit. S4 is known to bind directly to 16S ribosomal RNA. The crystal structure of a bacterial S4 protein revealed a two domain molecule. The first domain is composed of four helices in the known structure. The second domain is an insertion within domain 1 and displays some structural homology with the ETS DNA binding domain []. This entry represents the domain found at the N terminus of small ribosomal subunits S4 and S9. ; GO: 0019843 rRNA binding, 0005622 intracellular; PDB: 3BBN_D 2WWL_D 3OR9_D 3OFA_D 2QBB_D 3OFP_D 4A2I_D 2QB9_D 3OFO_D 2QBF_D ....
Probab=99.75 E-value=5.7e-19 Score=152.84 Aligned_cols=92 Identities=55% Similarity=0.802 Sum_probs=79.1
Q ss_pred CCCCCCchhhhhhcCCCCccccccccccccccCCCCCCCCCCCCc--ccccchhhhhHhhhhhHhhhCCcHHHHHHHHHH
Q psy8861 2 ARYIGPKAKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISG--SRTSDYGYQFREKQKVKRMYGILEKQFRRYFIE 79 (550)
Q Consensus 2 ~r~~gp~~Ki~Rrlg~~l~~~~~~~~~~~k~~~~~~pg~~~~~~~--~k~s~y~~~L~~Kqkl~~~YG~~ekq~~~~~~~ 79 (550)
|||+||++|+|||+|+.+|+++. .+...+ ..++||+|+.+.. +|.|+|++||.|||+++++||++|+||.+||..
T Consensus 1 ~R~~~~~~k~~Rr~g~~~~~~~~-~~~~~~--~~~~~~~~~~~~~~~rk~s~y~~qL~eKqk~r~~yg~lekql~~~~~~ 77 (94)
T PF00163_consen 1 ARYRGPKCKLPRRLGEKLWLTEK-AKLIRR--YGLRPGQHGWRRKSRRKLSRYGLQLREKQKLRFYYGILEKQLRRYGKI 77 (94)
T ss_dssp -CSHSCCCHHHHHCTSHCTCSCC-CSHCCS--SSSSSSSSTTSHHHHHCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred CCcCCCccccCCCCCCCccCCCc-cccccc--cccccccccccccccccchhhhcccccCCchhhhhhhHHHHHHHHHHH
Confidence 68999999999999999998732 111111 1378999997654 489999999999999999999999999999999
Q ss_pred hhccCCCchHHHHHHHh
Q psy8861 80 GARLKGKTGEIILKLLE 96 (550)
Q Consensus 80 a~~~~g~~~~~ll~~LE 96 (550)
|.+.+|+|+++|+++||
T Consensus 78 a~k~~g~tg~~l~~lLE 94 (94)
T PF00163_consen 78 AAKLKGVTGENLLQLLE 94 (94)
T ss_dssp HHHSSSHHHHHHHHHHH
T ss_pred HHhcCCCHHHHHHHHhC
Confidence 99999999999999998
No 24
>KOG3301|consensus
Probab=99.72 E-value=2.3e-18 Score=159.76 Aligned_cols=131 Identities=21% Similarity=0.304 Sum_probs=104.0
Q ss_pred CCCCCCCc--hhhhhhcCCCCccccccccccccccCCCCCCCCCCCCcccccchhhh----hHhhhhhHhhhCCcHHHHH
Q psy8861 1 MARYIGPK--AKLCRREGIDLFLKSARRSLDSKCKLDLRPGQHGRISGSRTSDYGYQ----FREKQKVKRMYGILEKQFR 74 (550)
Q Consensus 1 M~r~~gp~--~Ki~Rrlg~~l~~~~~~~~~~~k~~~~~~pg~~~~~~~~k~s~y~~~----L~~Kqkl~~~YG~~ekq~~ 74 (550)
|.+|.+|+ |+..|..+...... ...+..|. +. ...++.-+++.|+.+ ..++|++ |.||.+++|+.
T Consensus 1 ~k~y~~PRrpfek~Rld~elkl~g--~yglknk~--el----wr~~~~l~K~r~aaR~ll~~k~p~rl-f~g~allrrLv 71 (183)
T KOG3301|consen 1 SKTYKTPRRPFEKERLDAELKLVG--EYGLKNKR--EL----WRVSRSLSKIRYAARELLDEKDPKRL-FEGNALLRRLV 71 (183)
T ss_pred CCccCCCCChHHHHHHHhhhcccc--ccccccch--HH----HHHHHHHHHHHHHHHHHhccccHHHH-hcchHHHHHHH
Confidence 78999999 99999998754322 10010110 00 000111135667777 8888999 88899999999
Q ss_pred HHHHHh---hccCCCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCC
Q psy8861 75 RYFIEG---ARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKP 140 (550)
Q Consensus 75 ~~~~~a---~~~~g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~ 140 (550)
+|-..+ .+.+++++..+.++||+|||+.||++|+|+|+++||+||.|+||.||+++||+|||+|+.
T Consensus 72 r~g~l~e~~~Kldyvl~l~ie~fLErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrl 140 (183)
T KOG3301|consen 72 RYGVLDERKNKLDYVLALTVEDFLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRL 140 (183)
T ss_pred HHhhhhccccchhHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence 998877 567889999999999999999999999999999999999999999999999999999983
No 25
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=99.72 E-value=4e-18 Score=163.50 Aligned_cols=81 Identities=28% Similarity=0.496 Sum_probs=74.4
Q ss_pred cccchhhhhHhhhhhHhhhCCcHHHHHHHHHHhhccCCCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEEC
Q psy8861 48 RTSDYGYQFREKQKVKRMYGILEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVN 127 (550)
Q Consensus 48 k~s~y~~~L~~Kqkl~~~YG~~ekq~~~~~~~a~~~~g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VN 127 (550)
|.++||+++.+||+|.+.||+++. ++||+|||++||++|||.|+.+|||+|.||||.||
T Consensus 79 kL~~~Gi~~~~k~~l~~~~~l~~~---------------------~~leRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~ 137 (181)
T PTZ00155 79 RMHRLGLLDEDERKLDYVLGLTVE---------------------KLLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVG 137 (181)
T ss_pred HHHHhCCcchhhccHHHHHCccHH---------------------HHHHHhhhhHHHhccCcCCHHHhhhheeCCCEEEC
Confidence 579999999999999999999888 46899999999999999999999999999999999
Q ss_pred cEEeccCCcccCCCCE--EEEccC
Q psy8861 128 KKIVNIASYKIKPGDI--ISVREK 149 (550)
Q Consensus 128 g~~v~~ps~~vk~gDi--I~v~~~ 149 (550)
|++|++|||.|++||. |+..+.
T Consensus 138 ~~~V~~Ps~~V~~~~Ed~I~~~~~ 161 (181)
T PTZ00155 138 KQIVDIPSFLVRVDSEKHIDFADT 161 (181)
T ss_pred CEEeccCceEeccCccCceeeecC
Confidence 9999999999999854 665543
No 26
>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (IPR009025 from INTERPRO), dividing it into two halves []. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_O 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3GTK_C 1TWH_C 3HOV_C 3S17_C ....
Probab=99.70 E-value=1e-17 Score=149.16 Aligned_cols=73 Identities=42% Similarity=0.625 Sum_probs=66.0
Q ss_pred CcccccccccCccccHHHHHhcccccee---eeccCceEEEEEEEeceeeEEeccCcc-CCCeEEeCCCceEEEcCC
Q psy8861 254 GALHEYSSLEGVQEDIIDIILNLKGVIL---KLYNRDYAILNLKKFGKCVVLASDIEL-LSDIELVNPNHIIAHLSD 326 (550)
Q Consensus 254 gv~hEfs~i~Gv~Edv~~IilNLK~i~~---~~~~~~~~~~~l~~~Gp~~V~A~DI~~-~~~veivnpd~~IatL~~ 326 (550)
++.|||++||||+||+++|++|||++++ ...+.+.+.++|+++||+.|||+||++ |++++++|||+|||||++
T Consensus 14 ~v~He~~~Ipgv~Edv~~iilnlk~i~~~~~~~~~~~~~~~~L~~~g~~~V~a~di~~~~~~i~ivn~d~~I~tl~~ 90 (112)
T PF01000_consen 14 GVAHEFGLIPGVSEDVLEIILNLKKIVIDCEEGCDDCSVTFSLKVKGPGEVTAGDIKLEPSGIEIVNPDIYIATLSE 90 (112)
T ss_dssp HHHCHHHBSTCBSSCHHHHHHHHHTT-ESSSSSTTTSEEEEEEEEESSSCEEGGGSEESBTTEEESSTTSEEEEEES
T ss_pred eeEeccccCCccccchhhhhhcchhhccccccCCCCceEEEEEEecCCCccccceeEecCCceEEecCCeEEEEECC
Confidence 4999999999999999999999999984 123457899999999999999999998 999999999999999975
No 27
>PRK07758 hypothetical protein; Provisional
Probab=99.65 E-value=7e-17 Score=138.71 Aligned_cols=54 Identities=26% Similarity=0.462 Sum_probs=53.0
Q ss_pred CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhcCccc
Q psy8861 376 ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYY 429 (550)
Q Consensus 376 ~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~l 429 (550)
.||+||+|||++|||+||+||+++|++||++++|||+||++||+++|+++|++|
T Consensus 41 ~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIkekL~E~GLsf 94 (95)
T PRK07758 41 LLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94 (95)
T ss_pred cccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHHcCCCC
Confidence 799999999999999999999999999999999999999999999999999986
No 28
>PLN00189 40S ribosomal protein S9; Provisional
Probab=99.48 E-value=9e-15 Score=141.45 Aligned_cols=59 Identities=27% Similarity=0.475 Sum_probs=53.8
Q ss_pred HHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 90 IILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 90 ~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
+.-.+||+|||+++|++|||.|+.+|||||.||||.|||++|++|||.|+.||.+.|..
T Consensus 102 tvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw 160 (194)
T PLN00189 102 TVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDF 160 (194)
T ss_pred cHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEE
Confidence 33457999999999999999999999999999999999999999999999998876643
No 29
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=99.48 E-value=4.1e-14 Score=133.82 Aligned_cols=61 Identities=28% Similarity=0.439 Sum_probs=55.5
Q ss_pred HHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCC--CEEEEccCc
Q psy8861 90 IILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPG--DIISVREKA 150 (550)
Q Consensus 90 ~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~g--DiI~v~~~~ 150 (550)
+.-.+||+|||+++|++|||.|+.+|||+|.||||.|||++|++|||.|++| |.|+..+.+
T Consensus 97 tv~~~leRRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~~~S 159 (162)
T TIGR01018 97 TVEDFLERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFAPSS 159 (162)
T ss_pred cHHHHHHHhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeeecCC
Confidence 3455899999999999999999999999999999999999999999999999 778876654
No 30
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=99.42 E-value=6.4e-13 Score=127.53 Aligned_cols=63 Identities=32% Similarity=0.485 Sum_probs=56.8
Q ss_pred HHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCC--CEEEEccCch
Q psy8861 89 EIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPG--DIISVREKAK 151 (550)
Q Consensus 89 ~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~g--DiI~v~~~~~ 151 (550)
.+.-++||+|||.+|++.|||.|+++|+|||.||||.|||++|++|||.|+++ |.|++.+.+.
T Consensus 95 L~v~~~lerRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~S~ 159 (177)
T PRK04051 95 LTVEDILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPTSP 159 (177)
T ss_pred ccHHHHHHhHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCCCC
Confidence 33455899999999999999999999999999999999999999999999998 6788877663
No 31
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=99.37 E-value=2.7e-13 Score=159.62 Aligned_cols=63 Identities=33% Similarity=0.542 Sum_probs=60.1
Q ss_pred ccccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhcCcccccc
Q psy8861 370 RPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRH 432 (550)
Q Consensus 370 ~~I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~lmrh 432 (550)
-.||+|+|||||+|||+++||+|++||+.+|++||++++|||+||++||+++|+++||++.-.
T Consensus 1314 ~~ieeL~LSvRs~NcLk~agI~tvgdLv~~se~eLlkikN~GkKSl~EIkekL~e~gL~~~~~ 1376 (1460)
T PRK14906 1314 YLYDDLGVSQRWANKFSEAGIETVGDLIGKTEEDLLRIEGIGAKAIEELKDGLEAHNLLYILE 1376 (1460)
T ss_pred hhhcccchhhhHHHHHHHcCCCcHHHHhhCCHHHHhhccCCCcchHHHHHHHHHHCCCCcccc
Confidence 469999999999999999999999999999999999999999999999999999999987654
No 32
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=99.35 E-value=1.2e-12 Score=99.40 Aligned_cols=48 Identities=48% Similarity=0.762 Sum_probs=47.0
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEE
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDII 144 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI 144 (550)
||||.+|+++|++.|+++|+++|.+|+|+|||+.++.|+|.|++||+|
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence 699999999999999999999999999999999999999999999987
No 33
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=99.34 E-value=7.4e-12 Score=128.87 Aligned_cols=111 Identities=21% Similarity=0.246 Sum_probs=92.1
Q ss_pred eEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECC---------cccccccccCccccHHHHHh
Q psy8861 204 IIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG---------ALHEYSSLEGVQEDIIDIIL 274 (550)
Q Consensus 204 ~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~g---------v~hEfs~i~Gv~Edv~~Iil 274 (550)
+|++.+.++...+|.+. |.-.+++|||||+|++++|.+||..|.|.. .+|....||-..
T Consensus 2 ~i~i~~~~~~~~~f~l~----~~d~s~ANAlRRimiaEVPt~AId~V~i~~NTSvl~DE~lAHRLGLIPL~~-------- 69 (291)
T cd07032 2 KIEIISLSDEELEFDLI----GVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKA-------- 69 (291)
T ss_pred eEEEEECCCCEEEEEEe----cCCHHHHHHHHHHHHhcCcceeEEEEEEEECCccchhHHHHHhhcCceeec--------
Confidence 47888889999999999 778899999999999999999999999963 578888888765
Q ss_pred ccccceeeec------cCceEEEEEEEece------------------eeEEeccCc-----------cCCCeEEeCCCc
Q psy8861 275 NLKGVILKLY------NRDYAILNLKKFGK------------------CVVLASDIE-----------LLSDIELVNPNH 319 (550)
Q Consensus 275 NLK~i~~~~~------~~~~~~~~l~~~Gp------------------~~V~A~DI~-----------~~~~veivnpd~ 319 (550)
+.+.+.++.+ ..+.+.++|+++++ ..|||+||+ .++.|+++|||+
T Consensus 70 d~~~~~~~~~~~~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~~~~~VyS~dl~~~p~g~q~~~~~~~~v~~v~~dI 149 (291)
T cd07032 70 DPRLFEYREDSDDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLKWVPIGSQEKRFADNPIRPVHPDI 149 (291)
T ss_pred CHHHcccccccccCCCCCcEEEEEEEEEccCCcccccccccccccccccEEECCCCEecCCCccccccCCCCcEEeCCCc
Confidence 3344444332 24689999999976 579999998 346799999999
Q ss_pred eEEEcCC
Q psy8861 320 IIAHLSD 326 (550)
Q Consensus 320 ~IatL~~ 326 (550)
+||+|.+
T Consensus 150 ~I~kL~~ 156 (291)
T cd07032 150 LIAKLRP 156 (291)
T ss_pred EEEEECC
Confidence 9999987
No 34
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=99.11 E-value=6.5e-11 Score=103.20 Aligned_cols=57 Identities=28% Similarity=0.364 Sum_probs=53.5
Q ss_pred HhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchh
Q psy8861 95 LESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKK 152 (550)
Q Consensus 95 LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~ 152 (550)
.+||||+|||.++|++||+.|+.+|..|+|.|||+.+ +||+.|++||+|+|....+.
T Consensus 7 ~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 7 DRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNKE 63 (100)
T ss_pred cceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeCCcE
Confidence 5799999999999999999999999999999999999 99999999999999866544
No 35
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=99.03 E-value=3.6e-10 Score=103.94 Aligned_cols=56 Identities=21% Similarity=0.298 Sum_probs=51.9
Q ss_pred hhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchh
Q psy8861 96 ESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKK 152 (550)
Q Consensus 96 E~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~ 152 (550)
.+|||.|||..||++||+.|+++|.+|+|.|||+. .+||..|++||+|+|......
T Consensus 8 ~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~ 63 (133)
T PRK10348 8 EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDE 63 (133)
T ss_pred cccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEE
Confidence 37999999999999999999999999999999999 899999999999999765533
No 36
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=98.84 E-value=7.3e-09 Score=82.23 Aligned_cols=50 Identities=22% Similarity=0.448 Sum_probs=48.1
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEE
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISV 146 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v 146 (550)
+|||.+|.+.+++.||..|+++|..|+|+|||+.++.|++.|++||.|+|
T Consensus 9 ~rLd~~L~~~~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 9 ITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred HHHHHHHHHcCCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 79999999998888999999999999999999999999999999999987
No 37
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=98.83 E-value=2.8e-09 Score=86.59 Aligned_cols=31 Identities=48% Similarity=0.611 Sum_probs=28.7
Q ss_pred EeeCccchhhhHHHHHHHHHhhcCccceeEE
Q psy8861 219 MEPFERGYGYTLGNALRRVLLSSMIGCAPTE 249 (550)
Q Consensus 219 i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~ 249 (550)
|+|+..|+++|+||+|||+||+++||+||++
T Consensus 1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~ 31 (66)
T PF01193_consen 1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG 31 (66)
T ss_dssp EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE
T ss_pred CEeEEcCCchHHHHHHHHHHHhcCCCceEEe
Confidence 4566779999999999999999999999999
No 38
>KOG1522|consensus
Probab=98.67 E-value=6.5e-08 Score=95.92 Aligned_cols=114 Identities=18% Similarity=0.249 Sum_probs=89.8
Q ss_pred CCeeEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECC---------cccccccccCccccHHH
Q psy8861 201 KPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG---------ALHEYSSLEGVQEDIID 271 (550)
Q Consensus 201 ~p~~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~g---------v~hEfs~i~Gv~Edv~~ 271 (550)
.|. |+|.+.++.+.+|+++ .--++++||||||+++++|..||+.|.|+- ..|..+.||-..+++.+
T Consensus 5 ~p~-v~I~Elt~d~vkF~L~----nTdlsvANsLRRV~iaEvPTiAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~~ 79 (285)
T KOG1522|consen 5 QPT-VKIRELTDDNVKFVLS----NTDLSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIVE 79 (285)
T ss_pred CCc-eEEEecCCCceEEEEe----cChHHHHHHHHHHHHhcCceeEEEEEEEecccccccHHHHHhhhcceeccchhhhh
Confidence 454 8999999999999999 445589999999999999999999999972 57899999999999887
Q ss_pred HHhccccceeeec-------cCceEEEEEEEece----eeEEeccCc-cCCCeEEeCC-------------CceEEEcCC
Q psy8861 272 IILNLKGVILKLY-------NRDYAILNLKKFGK----CVVLASDIE-LLSDIELVNP-------------NHIIAHLSD 326 (550)
Q Consensus 272 IilNLK~i~~~~~-------~~~~~~~~l~~~Gp----~~V~A~DI~-~~~~veivnp-------------d~~IatL~~ 326 (550)
+.+.-+ ..|.+.+.|++++- ..||+.||. .+|.|.+|+- ...||.|-.
T Consensus 80 -------l~ytrdC~C~~~C~eCSVef~L~~kc~~d~T~~VtsrDL~s~~~~v~pv~~~~~~~~~~~~e~~gilI~KLRk 152 (285)
T KOG1522|consen 80 -------LQYTRDCECDEFCPECSVEFTLDVKCTDDQTRDVTSRDLVSLDPTVTPVDSNRGSEIDDDSESKGILIVKLRK 152 (285)
T ss_pred -------hhhcccCchhccCCcceEEEEEeeeecccceeeeehHhhhccCCcccccccCCCCccccccccCCcEEEEeec
Confidence 222222 34788999988765 479999997 5665655543 456777754
No 39
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=98.54 E-value=1.9e-07 Score=73.34 Aligned_cols=52 Identities=52% Similarity=0.845 Sum_probs=49.1
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
+|||.++...+++.|+.+|+++|.+|+|+|||+.++.|++.+.+||.|++..
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~ 52 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDG 52 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcC
Confidence 5899999988889999999999999999999999999999999999999874
No 40
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=98.54 E-value=1e-07 Score=95.36 Aligned_cols=85 Identities=24% Similarity=0.305 Sum_probs=63.7
Q ss_pred hhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCch---hh--HHHHhhhhccCCCCCCC
Q psy8861 96 ESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAK---KQ--TRIANSLELSEHSTPFS 170 (550)
Q Consensus 96 E~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~---~~--~~i~~~~~~~~~~~~p~ 170 (550)
.+|||.+|++.|++.||..|+.+|..|.|.|||.++++||+.|+.++.|+|..... +. .-+..+++.+. ..++.
T Consensus 2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~~~yVSRG~~KL~~ale~F~-l~~k~ 80 (245)
T COG1189 2 KMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPYVSRGGLKLEKALEEFE-LDVKG 80 (245)
T ss_pred cchHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcccCcCccccHHHHHHHHHHhcC-cCCCC
Confidence 48999999999999999999999999999999999999999999999999984322 11 12345555443 22344
Q ss_pred cEEEecCccEE
Q psy8861 171 WITVDAKKMEG 181 (550)
Q Consensus 171 ~l~vd~~~~~g 181 (550)
-..+|-..-+|
T Consensus 81 kv~LDiGsSTG 91 (245)
T COG1189 81 KVVLDIGSSTG 91 (245)
T ss_pred CEEEEecCCCc
Confidence 44555443333
No 41
>smart00363 S4 S4 RNA-binding domain.
Probab=98.52 E-value=2.4e-07 Score=70.68 Aligned_cols=52 Identities=46% Similarity=0.723 Sum_probs=48.9
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
+|||.++...+++.|+.+|++++.+|.|.|||+.++.|++.+++||.|++..
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 5899999988889999999999999999999999988999999999999875
No 42
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=98.43 E-value=2.6e-07 Score=94.58 Aligned_cols=55 Identities=33% Similarity=0.428 Sum_probs=51.9
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchh
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKK 152 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~ 152 (550)
.|||.++. .+|-.||+.|.++|.+|+|+|||+.+++||+.|++||+|+|++.++-
T Consensus 192 ~RLD~vla-~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~GR~ 246 (267)
T PLN00051 192 LRLDALAS-AGFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGKGRL 246 (267)
T ss_pred ccHHHHHH-HHhccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeCCEE
Confidence 79999885 67899999999999999999999999999999999999999998865
No 43
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=98.41 E-value=8.2e-07 Score=89.05 Aligned_cols=52 Identities=29% Similarity=0.349 Sum_probs=50.3
Q ss_pred hhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccC
Q psy8861 98 RFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREK 149 (550)
Q Consensus 98 RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~ 149 (550)
|||.+|...|++.||.+|+++|.+|+|+|||+++++|++.|.+||.|+|...
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~~ 52 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQN 52 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccCc
Confidence 8999999999999999999999999999999999999999999999999865
No 44
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=98.41 E-value=2.2e-07 Score=93.06 Aligned_cols=55 Identities=40% Similarity=0.597 Sum_probs=52.3
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchh
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKK 152 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~ 152 (550)
+|||.++. .+|-.||+.|.|+|..|.|.||++.|++|||.|+.||.|++++.++-
T Consensus 181 lRLD~vis-~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~GR~ 235 (257)
T COG2302 181 LRLDVVIS-EGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGFGRL 235 (257)
T ss_pred hhHHHHHH-HHHhhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEeccccE
Confidence 69999994 88999999999999999999999999999999999999999998865
No 45
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=98.40 E-value=3.4e-07 Score=93.27 Aligned_cols=55 Identities=29% Similarity=0.392 Sum_probs=51.0
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCchh
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKAKK 152 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~~~ 152 (550)
+|||.++ ..+|..||++|+++|.+|+|.|||+.++.|++.|++||+|+|++.++-
T Consensus 184 ~RLD~ll-s~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~IsvrG~Gr~ 238 (257)
T TIGR03069 184 LRIDAIA-SAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGKGRL 238 (257)
T ss_pred ccHHHHH-HhhhhhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEcCCceE
Confidence 6999654 789988999999999999999999999999999999999999998865
No 46
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=98.03 E-value=1.8e-05 Score=67.79 Aligned_cols=32 Identities=34% Similarity=0.539 Sum_probs=29.2
Q ss_pred EEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhh
Q psy8861 205 IDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLS 240 (550)
Q Consensus 205 i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLs 240 (550)
+++.+.++++..|.++ |..+|+||+||+.|+.
T Consensus 1 ~ki~~~~~~~~~~~~~----~edhTl~n~L~~~l~~ 32 (86)
T cd00460 1 VKILEKEKNYVDFVLE----NEDHTLGNSLRRILLK 32 (86)
T ss_pred CceecCCCCEEEEEEe----CCCchHHHHHHHHHhC
Confidence 3566778999999999 9999999999999999
No 47
>KOG1521|consensus
Probab=97.88 E-value=4.8e-05 Score=77.76 Aligned_cols=120 Identities=18% Similarity=0.225 Sum_probs=86.4
Q ss_pred cccccCCCeeEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECC---------cccccccccCc
Q psy8861 195 DINDLLKPRIIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISG---------ALHEYSSLEGV 265 (550)
Q Consensus 195 ~inEll~p~~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~g---------v~hEfs~i~Gv 265 (550)
.++.|..--+|.|.+.+..-..|.+- |.--+|+||+||+|+|++|++||..|-|++ ..|....+|--
T Consensus 38 ~~~~f~~~~~V~iv~~~~~~leFDli----gIda~IANAfRRILiaEVPtmAiEkVyi~nNTSViqDEvLaHRlGLvPl~ 113 (338)
T KOG1521|consen 38 DLENFKDNFKVDIVSLDEETLEFDLI----GIDASIANAFRRILIAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLVPLR 113 (338)
T ss_pred cHHHhhhceEEEEEeccCcceeEEEe----eccHHHHHHHHHHHHhhcchhheeeeEEecCccccHHHHHHHhhcCcccc
Confidence 44555555567888888888999999 666699999999999999999999999975 46777666643
Q ss_pred cccHHHHHhccccceeeecc-----C-ceEEEEEEEecee------------------eEEeccCccCC-----------
Q psy8861 266 QEDIIDIILNLKGVILKLYN-----R-DYAILNLKKFGKC------------------VVLASDIELLS----------- 310 (550)
Q Consensus 266 ~Edv~~IilNLK~i~~~~~~-----~-~~~~~~l~~~Gp~------------------~V~A~DI~~~~----------- 310 (550)
.+ =..+.+..+. . .+..++|.++-+. .|+++|+.+-|
T Consensus 114 aD--------PrlFe~~~e~d~~~e~~ntlvF~L~VkC~~n~~a~~~~sdpk~Ly~ns~vyS~~~~w~P~g~Q~~~f~e~ 185 (338)
T KOG1521|consen 114 AD--------PRLFEYRSENDEDDEKENTLVFKLNVKCTKNPNAKKDSSDPKELYNNSEVYSRDLTWKPKGYQAEIFAEN 185 (338)
T ss_pred cC--------cchhhccccCCCccCccceEEEEEEeeccCCCCcccCCCChhHhccCcEEecCcceeccccchhhhcccC
Confidence 32 1112222221 1 3556666665433 39999998544
Q ss_pred CeEEeCCCceEEEcCC
Q psy8861 311 DIELVNPNHIIAHLSD 326 (550)
Q Consensus 311 ~veivnpd~~IatL~~ 326 (550)
-|.+++||..||.|..
T Consensus 186 ~i~~~~~DILiAkLrP 201 (338)
T KOG1521|consen 186 PIRPVHDDILIAKLRP 201 (338)
T ss_pred CccccCcceEEEecCC
Confidence 3889999999999976
No 48
>PRK11507 ribosome-associated protein; Provisional
Probab=97.72 E-value=8e-05 Score=61.55 Aligned_cols=53 Identities=17% Similarity=0.238 Sum_probs=50.3
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccC
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREK 149 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~ 149 (550)
.+||.+|--+|++.|=-+|+.+|..|.|.|||.+.+.-+..+.+||+|++...
T Consensus 12 I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~g~ 64 (70)
T PRK11507 12 VELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH 64 (70)
T ss_pred EEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEECCE
Confidence 47899999999999999999999999999999999999999999999999763
No 49
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=97.50 E-value=0.00016 Score=73.50 Aligned_cols=54 Identities=26% Similarity=0.470 Sum_probs=49.5
Q ss_pred hhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCC-CEEEEccCc
Q psy8861 96 ESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPG-DIISVREKA 150 (550)
Q Consensus 96 E~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~g-DiI~v~~~~ 150 (550)
.+|||++|.++|++ ||.+|.+||..|.|.|||+++..++..+.++ |+|.+.+..
T Consensus 2 ~~RL~K~La~~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~ 56 (248)
T COG1187 2 SMRLNKFLAEAGVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKR 56 (248)
T ss_pred ccchHHHHHHcCCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEE
Confidence 58999999999976 9999999999999999999999999999999 578887654
No 50
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=97.48 E-value=0.00019 Score=74.52 Aligned_cols=50 Identities=24% Similarity=0.460 Sum_probs=46.1
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
+|||.+|...|+ .||.+|+++|.+|.|+|||+++ .+++.|.+||.|+|..
T Consensus 7 ~RL~k~La~~g~-~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g 56 (290)
T PRK10475 7 TRLNKYISESGI-CSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNG 56 (290)
T ss_pred HHHHHHHHhCCC-CCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECC
Confidence 599999998885 4899999999999999999998 6999999999999975
No 51
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=97.44 E-value=0.00024 Score=70.95 Aligned_cols=51 Identities=18% Similarity=0.261 Sum_probs=46.8
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
+|||.++.+.+ ..|+..++++|..|.|+|||+.+..|++.|++||.|++..
T Consensus 1 ~rld~~L~~~~-~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~ 51 (232)
T PRK10839 1 MRLDKFISQQL-GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDG 51 (232)
T ss_pred CcHHHHHHHcC-CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECC
Confidence 48999998775 6799999999999999999999988999999999999874
No 52
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.34 E-value=4.9e-05 Score=62.01 Aligned_cols=52 Identities=23% Similarity=0.415 Sum_probs=39.1
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
..||.+|-.+|++.|=-+|+.+|..|.|+|||...+..+..+.+||+|++..
T Consensus 8 I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~~ 59 (65)
T PF13275_consen 8 ITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEIDG 59 (65)
T ss_dssp --HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEETT
T ss_pred EEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEECC
Confidence 3688899999999999999999999999999999999999999999999954
No 53
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=97.23 E-value=0.00048 Score=72.42 Aligned_cols=53 Identities=23% Similarity=0.347 Sum_probs=48.1
Q ss_pred hhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 96 ESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 96 E~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
.+|||.++.......|+..++++|.+|.|.|||+.+..|++.|++||.|++..
T Consensus 17 g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~ 69 (325)
T PRK11180 17 GQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDA 69 (325)
T ss_pred CccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEee
Confidence 47999999766556799999999999999999999999999999999999974
No 54
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=97.15 E-value=0.0007 Score=70.30 Aligned_cols=51 Identities=20% Similarity=0.290 Sum_probs=45.0
Q ss_pred hhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCC--CEEEEcc
Q psy8861 96 ESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPG--DIISVRE 148 (550)
Q Consensus 96 E~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~g--DiI~v~~ 148 (550)
.+|||.+|.++|+ -||.+|+++|.+|.|.|||+++ .|++.|.++ |.|++..
T Consensus 2 ~~RL~k~La~~g~-~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g 54 (289)
T PRK10700 2 SEKLQKVLARAGH-GSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDG 54 (289)
T ss_pred chhHHHHHHHCCC-CCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECC
Confidence 3799999999885 5999999999999999999988 699999887 5688764
No 55
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=97.11 E-value=0.00082 Score=69.46 Aligned_cols=53 Identities=30% Similarity=0.390 Sum_probs=46.6
Q ss_pred hhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 96 ESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 96 E~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
.+|||.+|......-|+..++++|.+|.|+|||+.+..+++.|++||.|+|..
T Consensus 5 g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~ 57 (299)
T TIGR00005 5 GQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRV 57 (299)
T ss_pred chhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEec
Confidence 47999999766434799999999999999999987788999999999999853
No 56
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=96.79 E-value=0.0029 Score=52.73 Aligned_cols=52 Identities=15% Similarity=0.339 Sum_probs=48.0
Q ss_pred hhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCc
Q psy8861 99 FDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKA 150 (550)
Q Consensus 99 LD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~ 150 (550)
|+.+|--.|++.|=-+|+++|..|.|+|||..-+.-+..+..||+|++.+..
T Consensus 14 L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~~ 65 (73)
T COG2501 14 LGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQR 65 (73)
T ss_pred HHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECCEE
Confidence 5667788999999999999999999999999999999999999999997643
No 57
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=96.78 E-value=0.0022 Score=67.24 Aligned_cols=51 Identities=24% Similarity=0.335 Sum_probs=46.0
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
+|||.+|.......|+..++.+|.+|.|.|||+++ .|++.|+.||.|++..
T Consensus 20 ~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~~ 70 (317)
T PRK11025 20 QRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIPP 70 (317)
T ss_pred chHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeCC
Confidence 79999998665567999999999999999999999 6999999999999853
No 58
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=96.72 E-value=0.0025 Score=66.26 Aligned_cols=52 Identities=33% Similarity=0.495 Sum_probs=46.6
Q ss_pred hhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccC
Q psy8861 96 ESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREK 149 (550)
Q Consensus 96 E~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~ 149 (550)
.+|||.+|....- -|+++...++..|.|+|||++++ +++.|++||+|++...
T Consensus 12 g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~ 63 (289)
T COG0564 12 GQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLP 63 (289)
T ss_pred CCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecc
Confidence 4799999987333 79999999999999999999998 9999999999999653
No 59
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=96.60 E-value=0.002 Score=51.20 Aligned_cols=49 Identities=24% Similarity=0.356 Sum_probs=43.6
Q ss_pred CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 376 ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 376 ~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
++.......|.++||.|+.||...+.++|.+++++|+++.+.|.+.+++
T Consensus 12 Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 12 GIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAARE 60 (60)
T ss_dssp TCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHhC
Confidence 3455667789999999999999999999999999999999999988764
No 60
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=96.31 E-value=0.03 Score=47.88 Aligned_cols=44 Identities=27% Similarity=0.255 Sum_probs=34.6
Q ss_pred EEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEEC
Q psy8861 205 IDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIIS 253 (550)
Q Consensus 205 i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~ 253 (550)
++|.+.+++++.|.+. |..+||||+||-.|+.. |+.-.-+-+++
T Consensus 1 ikvi~~~~n~~~~~i~----~EDHTlgNlLr~~L~~~-~~V~fAgY~vp 44 (83)
T cd06927 1 LKVIEKEDNELELEIE----GEDHTLLNLLKEELLRD-PGVKVASYDIE 44 (83)
T ss_pred CeEEEcCCCEEEEEEe----CCCchHHHHHHHHHhcC-CCeEEEEeecC
Confidence 3677889999999999 99999999999888876 55544444433
No 61
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=96.22 E-value=0.046 Score=46.97 Aligned_cols=45 Identities=29% Similarity=0.242 Sum_probs=36.3
Q ss_pred eEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEEC
Q psy8861 204 IIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIIS 253 (550)
Q Consensus 204 ~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~ 253 (550)
+++|.+.+++++.|.+. |-.+||||+||-.|+. -|+..+-+-+++
T Consensus 2 ~ikvi~~~~n~~~~~i~----~EDHTlgNlLr~~L~~-~~~V~fAgY~vp 46 (85)
T PRK01146 2 EIKVLEKEDNELELEIE----GEDHTLMNLLKEELLE-DPGVEAASYDID 46 (85)
T ss_pred eEEEEecCCCEEEEEEe----CCCchHHHHHHHHHhc-CCCeeEEEeecC
Confidence 47888889999999999 9999999999999985 455555444444
No 62
>KOG4655|consensus
Probab=96.19 E-value=0.0019 Score=61.42 Aligned_cols=60 Identities=17% Similarity=0.265 Sum_probs=52.5
Q ss_pred HHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccC--CCCEEEEccCch
Q psy8861 92 LKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIK--PGDIISVREKAK 151 (550)
Q Consensus 92 l~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk--~gDiI~v~~~~~ 151 (550)
-.+-++||-.++.+.+||.|...|-.+|.||||+|.-+.|+.|+|.|. ..|.|+--..++
T Consensus 102 ssfCrRRLP~Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SK 163 (181)
T KOG4655|consen 102 SSFCRRRLPVVMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSK 163 (181)
T ss_pred HHHhhhccceeeeechhhhhHHHHHHHHHcCceeeCCeeccCchHHhhhhhhhhhhhhhhHH
Confidence 346789999999999999999999999999999999999999999996 447777655554
No 63
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=95.91 E-value=0.076 Score=46.99 Aligned_cols=82 Identities=24% Similarity=0.282 Sum_probs=59.3
Q ss_pred eEEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhccccceeee
Q psy8861 204 IIDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKL 283 (550)
Q Consensus 204 ~i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilNLK~i~~~~ 283 (550)
.+++...+.++..|.++ |..+||||.||-+|+. -++.-..+-. +.|....
T Consensus 6 ~l~ii~~~~n~~~i~i~----gEdHTL~NlL~~~L~~-d~~V~~a~Y~---i~HP~~~---------------------- 55 (99)
T COG1761 6 ELRIIKKDDNSLELEIE----GEDHTLGNLLREELLK-DEDVEFAAYS---IPHPLID---------------------- 55 (99)
T ss_pred EEEEeccCCCEEEEEEe----cCCchHHHHHHHHHhC-CCCeeEEEEe---CCCCCCC----------------------
Confidence 46777788999999999 9999999999999987 2322222222 2222211
Q ss_pred ccCceEEEEEEEeceeeEEeccCccCCCeEEeCCCceEEEcCC--hHHHHHHHHHHHHHHhhhhhc
Q psy8861 284 YNRDYAILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSD--NEEAIRQSARVLVDQLNVFAA 347 (550)
Q Consensus 284 ~~~~~~~~~l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~~--P~~Al~~Aa~iL~~~~~~f~~ 347 (550)
||..+|-|-.+ |.+||..|++.+.+.+.-|.+
T Consensus 56 --------------------------------~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~~l~~ 89 (99)
T COG1761 56 --------------------------------NPKIRIKTKGGVDPKEALKRAARKILKDLEELLD 89 (99)
T ss_pred --------------------------------CceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 56666655543 999999999999999888765
No 64
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=95.55 E-value=0.11 Score=44.52 Aligned_cols=43 Identities=30% Similarity=0.281 Sum_probs=32.8
Q ss_pred EEEEeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEE
Q psy8861 205 IDVKTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVII 252 (550)
Q Consensus 205 i~v~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI 252 (550)
++|.+.+++++.|.++ |-.+||||+||-.|+.. |+.-+-+-+|
T Consensus 1 ~kii~~~~n~~~~~i~----~EdHTLgNlLr~~L~~~-~~V~fAgY~v 43 (83)
T cd07027 1 LRIISKEKNSVTVEME----NEDHTLGNLLREELLKD-DQVDFARYYI 43 (83)
T ss_pred CeeEecCCCEEEEEEe----CCCchHHHHHHHHHhcC-CCeeEEEEec
Confidence 3567778999999999 99999999999887765 4444333333
No 65
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=94.79 E-value=0.23 Score=41.80 Aligned_cols=74 Identities=22% Similarity=0.221 Sum_probs=51.2
Q ss_pred cEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhccccceeeeccCceEEEE
Q psy8861 213 NHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYAILN 292 (550)
Q Consensus 213 ~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilNLK~i~~~~~~~~~~~~~ 292 (550)
+++.|.+. |-.+||||+||-.|+.. |+....+-+++.-. .....++
T Consensus 1 n~~~f~i~----~EDHTlgNlLr~~L~~~-p~V~fagY~vpHPl-----------------------------~~~i~l~ 46 (77)
T PF13656_consen 1 NEITFTIY----GEDHTLGNLLRYELLKD-PDVEFAGYRVPHPL-----------------------------ENKINLR 46 (77)
T ss_dssp TEEEEEEE----S--HHHHHHHHHCCTTS-TTEEEEEEEESETT-----------------------------SSEEEEE
T ss_pred CeEEEEEe----CCCccHHHHHHHHHhhC-CCeEEEEeccCCCC-----------------------------CCceEEE
Confidence 46789999 99999999999999886 77777666665332 1122344
Q ss_pred EEEeceeeEEeccCccCCCeEEeCCCceEEEcCChHHHHHHHHHHHHHHhhhhh
Q psy8861 293 LKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFA 346 (550)
Q Consensus 293 l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~~P~~Al~~Aa~iL~~~~~~f~ 346 (550)
+..+|-. .|.+||.+|++-|.+-+..|.
T Consensus 47 Iqt~~~~--------------------------~p~~~l~~a~~~l~~~~~~l~ 74 (77)
T PF13656_consen 47 IQTKGGI--------------------------TPIEALKKALEDLIKICEELK 74 (77)
T ss_dssp EEESTTS---------------------------HHHHHHHHHHHHHHHHHHHH
T ss_pred EEECCCC--------------------------CHHHHHHHHHHHHHHHHHHHH
Confidence 4444332 599999999999988877664
No 66
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=94.11 E-value=0.39 Score=41.32 Aligned_cols=78 Identities=18% Similarity=0.198 Sum_probs=54.3
Q ss_pred eCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEECCcccccccccCccccHHHHHhccccceeeeccCceE
Q psy8861 210 LGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIISGALHEYSSLEGVQEDIIDIILNLKGVILKLYNRDYA 289 (550)
Q Consensus 210 ~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~gv~hEfs~i~Gv~Edv~~IilNLK~i~~~~~~~~~~ 289 (550)
..++++.|.+. |-.+||||+||-.|+. -|+.-+-+=+|+ |-... ++
T Consensus 6 ~~~n~~~~~i~----~EdHTLgNlLr~~L~~-~p~V~fagY~vp---HPl~~----------------~~---------- 51 (85)
T cd07029 6 TDESCATFVFY----GEDHTLGNSLRYVIMK-NPEVEFCGYSIP---HPSEN----------------KI---------- 51 (85)
T ss_pred CCCCeEEEEEe----CCCcchHHHHHHHHhh-CCCceEEeeccc---CCCCC----------------cc----------
Confidence 46889999999 9999999999999887 455544444433 32111 11
Q ss_pred EEEEEEeceeeEEeccCccCCCeEEeCCCceEEEcCChHHHHHHHHHHHHHHhhhhhc
Q psy8861 290 ILNLKKFGKCVVLASDIELLSDIELVNPNHIIAHLSDNEEAIRQSARVLVDQLNVFAA 347 (550)
Q Consensus 290 ~~~l~~~Gp~~V~A~DI~~~~~veivnpd~~IatL~~P~~Al~~Aa~iL~~~~~~f~~ 347 (550)
.+++...| =.+|.+||.+|++-|.+.+..|.+
T Consensus 52 ~lriqT~~--------------------------~~~p~~al~~a~~~l~~~~~~~~~ 83 (85)
T cd07029 52 NLRIQTKG--------------------------GEPAVDVLKKGLEDLEQICDHILS 83 (85)
T ss_pred EEEEEeCC--------------------------CCCHHHHHHHHHHHHHHHHHHHHh
Confidence 33334444 035999999999999998877653
No 67
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model 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 (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=94.06 E-value=0.05 Score=57.25 Aligned_cols=54 Identities=17% Similarity=0.268 Sum_probs=49.7
Q ss_pred ccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhc
Q psy8861 372 VDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASR 425 (550)
Q Consensus 372 I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~ 425 (550)
+.+++++....|-|+++||+|+.|++..+..||.++.+++...+++|++.+.+.
T Consensus 4 ~~~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~ 57 (313)
T TIGR02238 4 LQAHGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKI 57 (313)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhh
Confidence 456789999999999999999999999999999999999999999999877653
No 68
>PRK04313 30S ribosomal protein S4e; Validated
Probab=93.61 E-value=0.085 Score=53.45 Aligned_cols=46 Identities=24% Similarity=0.444 Sum_probs=42.2
Q ss_pred HcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCc
Q psy8861 105 RMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKA 150 (550)
Q Consensus 105 r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~ 150 (550)
++++|.|..+|+..+..|.|+|||++.+.+.|.|-.-|+|+|....
T Consensus 47 ~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~~ 92 (237)
T PRK04313 47 VLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPETG 92 (237)
T ss_pred HhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccCC
Confidence 4689999999999999999999999999999999999999996543
No 69
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=92.90 E-value=0.16 Score=55.39 Aligned_cols=47 Identities=26% Similarity=0.417 Sum_probs=42.5
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCE
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDI 143 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDi 143 (550)
..|-.+++..|+++|..+||.+|..|-|.|||.+|+.+.+.+.++|.
T Consensus 343 ~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~ 389 (410)
T PRK13354 343 KNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDA 389 (410)
T ss_pred CCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhh
Confidence 45667888999999999999999999999999999999998888774
No 70
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=92.24 E-value=0.27 Score=53.65 Aligned_cols=52 Identities=21% Similarity=0.356 Sum_probs=42.9
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCC----CCEEEEcc
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKP----GDIISVRE 148 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~----gDiI~v~~ 148 (550)
..+-.+++..|+++|..+||.+|..|-|.|||.+|..+.+.+.+ |..+-++.
T Consensus 343 ~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~~~~~~~~~~lr~ 398 (408)
T PRK05912 343 IDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTADDRFGKYTVLQR 398 (408)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccccccccccCCCEEEEEe
Confidence 35666788999999999999999999999999999988888876 44444443
No 71
>PTZ00035 Rad51 protein; Provisional
Probab=92.22 E-value=0.13 Score=54.63 Aligned_cols=54 Identities=13% Similarity=0.225 Sum_probs=48.0
Q ss_pred ccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhc
Q psy8861 372 VDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASR 425 (550)
Q Consensus 372 I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~ 425 (550)
+...+|+....+-|+++||+|+.||+..+..||.++.+++....++|.+...+.
T Consensus 26 l~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 26 LQSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL 79 (337)
T ss_pred HhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence 334678999999999999999999999999999999999999888888766543
No 72
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=92.16 E-value=0.17 Score=51.95 Aligned_cols=45 Identities=18% Similarity=0.350 Sum_probs=41.6
Q ss_pred HcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccC
Q psy8861 105 RMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREK 149 (550)
Q Consensus 105 r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~ 149 (550)
++++|.|..+|+..+..|.|+|||++.+.+.|.|-.-|+|+|...
T Consensus 51 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt 95 (262)
T PTZ00118 51 RLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKT 95 (262)
T ss_pred hhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCC
Confidence 468899999999999999999999999999999988899999643
No 73
>PLN00036 40S ribosomal protein S4; Provisional
Probab=92.14 E-value=0.18 Score=51.84 Aligned_cols=45 Identities=22% Similarity=0.338 Sum_probs=41.6
Q ss_pred HcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccC
Q psy8861 105 RMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREK 149 (550)
Q Consensus 105 r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~ 149 (550)
++++|.|..+|+..+..|.|+|||++.+.+.|.|-.-|+|+|...
T Consensus 51 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt 95 (261)
T PLN00036 51 RLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKT 95 (261)
T ss_pred HhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCC
Confidence 468999999999999999999999999999999988899999643
No 74
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=92.03 E-value=0.18 Score=52.02 Aligned_cols=46 Identities=15% Similarity=0.244 Sum_probs=42.1
Q ss_pred HcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCc
Q psy8861 105 RMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKA 150 (550)
Q Consensus 105 r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~ 150 (550)
++++|.|..+|+..+..|.|+|||++.+.+.|.|-.-|+|+|....
T Consensus 48 ~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt~ 93 (273)
T PTZ00223 48 RLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKTG 93 (273)
T ss_pred HhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCCC
Confidence 4689999999999999999999999999999999888999996533
No 75
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=91.13 E-value=0.21 Score=53.41 Aligned_cols=53 Identities=13% Similarity=0.174 Sum_probs=47.0
Q ss_pred ccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 372 VDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 372 I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
+.+++++....+-|+.+||+|+.||+..+..||.+++|+...-.++|.+...+
T Consensus 34 l~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~ 86 (344)
T PLN03187 34 LISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEK 86 (344)
T ss_pred HhhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 44467899999999999999999999999999999999999988887765544
No 76
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=91.12 E-value=0.21 Score=52.68 Aligned_cols=53 Identities=13% Similarity=0.233 Sum_probs=48.2
Q ss_pred ccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 372 VDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 372 I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
+..++||....|-|+++||.|+.||+..+..||.++.++.....+++.+.+.+
T Consensus 4 ~~~~~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~~ 56 (316)
T TIGR02239 4 LEGNGITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEAAK 56 (316)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999888876654
No 77
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=91.05 E-value=0.24 Score=51.78 Aligned_cols=56 Identities=18% Similarity=0.264 Sum_probs=50.4
Q ss_pred ccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 369 LRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 369 ~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
..+|.++ +++-.+..-|+++||+|++||...+++||.++.+++.+..+++.+....
T Consensus 5 ~~~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 5 EKDLEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAARE 61 (317)
T ss_pred cccHhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 4677777 6889999999999999999999999999999999999999988887764
No 78
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model 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.
Probab=91.00 E-value=0.35 Score=36.45 Aligned_cols=44 Identities=20% Similarity=0.230 Sum_probs=38.0
Q ss_pred hhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 381 SANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 381 s~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
...-|..+||.|+.||...+.++|..+++++....++|.....+
T Consensus 5 ~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a~~ 48 (50)
T TIGR01954 5 IAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARN 48 (50)
T ss_pred HHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 45678999999999999999999999999998877777766553
No 79
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=88.87 E-value=0.95 Score=39.55 Aligned_cols=41 Identities=27% Similarity=0.162 Sum_probs=32.6
Q ss_pred EeeCCcEEEEEEeeCccchhhhHHHHHHHHHhhcCccceeEEEEEC
Q psy8861 208 KTLGSNHAKVIMEPFERGYGYTLGNALRRVLLSSMIGCAPTEVIIS 253 (550)
Q Consensus 208 ~~~~~~y~~F~i~Ple~G~g~TlgNaLRRvLLssi~G~AI~~vkI~ 253 (550)
+...++++.|.+. |-.+||||+||-.|+. -|+..+-+-+|+
T Consensus 12 d~k~~n~~~~~i~----~EdHTLgNlLr~~L~~-~~~V~fagY~vp 52 (93)
T cd06926 12 DTKVPNAATFTIN----KEDHTLGNLLRMQLLK-DPNVLFAGYKVP 52 (93)
T ss_pred cCCCCcEEEEEEe----CCCchHHHHHHHHHhc-CCCeeEEeeccC
Confidence 3457899999999 9999999999999988 566555554443
No 80
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=87.63 E-value=0.53 Score=47.49 Aligned_cols=45 Identities=22% Similarity=0.398 Sum_probs=40.4
Q ss_pred cCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccCc
Q psy8861 106 MGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREKA 150 (550)
Q Consensus 106 ~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~~ 150 (550)
+++|.+..+|+..|+.|+|+|||++....-|.|-.=|+|+|...+
T Consensus 51 LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~tg 95 (241)
T COG1471 51 LKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKTG 95 (241)
T ss_pred HHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECCCC
Confidence 467899999999999999999999999999999888999997544
No 81
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=87.37 E-value=0.55 Score=50.17 Aligned_cols=53 Identities=17% Similarity=0.283 Sum_probs=47.0
Q ss_pred ccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 372 VDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 372 I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
+...+||.-..+-|+++||+|+.|++..+..||.++.++.....+++.+.+.+
T Consensus 31 l~~~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~~~ 83 (342)
T PLN03186 31 LQASGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAASK 83 (342)
T ss_pred HHhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 33457899999999999999999999999999999999999999888876644
No 82
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=86.23 E-value=1.8 Score=47.23 Aligned_cols=78 Identities=26% Similarity=0.376 Sum_probs=50.4
Q ss_pred hhhHhhhCC-----cHHHHHHHHHHhhccCCCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccC
Q psy8861 60 QKVKRMYGI-----LEKQFRRYFIEGARLKGKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIA 134 (550)
Q Consensus 60 qkl~~~YG~-----~ekq~~~~~~~a~~~~g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~p 134 (550)
-..+.+||- .+..+.+.|... .........|-+.++..+=..+...|+++|+.+||.+|..|-|.+||.+|..+
T Consensus 295 e~~~~~hG~~~a~~a~~~~~~~F~~g-~~~~l~~~dlk~~~~~~~~~~lv~~~L~psr~earr~i~~g~v~in~~~v~d~ 373 (401)
T COG0162 295 EVTKLVHGEEAAEAAEEEFEKLFSEG-LPENLPPADLKQKLEDGLVDLLVDAGLAPSRSEARRLIQQGGVKINGEKVEDE 373 (401)
T ss_pred HhhHhhcCHHHHHHHHHHHHHHHhcC-CcccCCHHHHhhhhHHHHHHHHHHhCCcccHHHHHhhcccCCEEECCEecccc
Confidence 345667772 223455555543 11111122222233334555667899999999999999999999999999988
Q ss_pred Cccc
Q psy8861 135 SYKI 138 (550)
Q Consensus 135 s~~v 138 (550)
.+.+
T Consensus 374 ~~~~ 377 (401)
T COG0162 374 NYVL 377 (401)
T ss_pred ccch
Confidence 8665
No 83
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=80.89 E-value=1.6 Score=30.37 Aligned_cols=28 Identities=36% Similarity=0.576 Sum_probs=23.5
Q ss_pred hHHHhhcCHHHhhccCccccccHHHHHH
Q psy8861 393 IGDLIQRSENELLRTPNLGRKSLNEIKE 420 (550)
Q Consensus 393 v~dL~~~s~~dL~~~~n~G~kSl~Ei~~ 420 (550)
.+.++.-|.+||+++|+.|++..+.|.+
T Consensus 2 ~~g~~pas~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 2 LDGLIPASIEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHHHTSSHHHHHTSTT-SHHHHHHHHH
T ss_pred CCCcCCCCHHHHHhCCCcCHHHHHHHHh
Confidence 4677888999999999999999988864
No 84
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=79.84 E-value=1.9 Score=43.64 Aligned_cols=48 Identities=17% Similarity=0.261 Sum_probs=44.0
Q ss_pred CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHH
Q psy8861 376 ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILA 423 (550)
Q Consensus 376 ~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~ 423 (550)
+++-.....|.++|+.|+.+|..-|.+||.+++++|.+..+.|.+.|.
T Consensus 10 GIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 10 GVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred CcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence 456677788999999999999999999999999999999999999886
No 85
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=79.00 E-value=1.8 Score=36.91 Aligned_cols=29 Identities=31% Similarity=0.409 Sum_probs=25.3
Q ss_pred CcEEECcEEeccCCcccCCCCEEEEccCch
Q psy8861 122 RAFLVNKKIVNIASYKIKPGDIISVREKAK 151 (550)
Q Consensus 122 G~V~VNg~~v~~ps~~vk~gDiI~v~~~~~ 151 (550)
|-|+|||+.+ .++|.+++||.|.|-+-.+
T Consensus 50 ~~i~vNG~~v-~~~~~~~~Gd~v~V~P~~~ 78 (81)
T PF14451_consen 50 GLILVNGRPV-DFDYRLKDGDRVAVYPVFR 78 (81)
T ss_pred EEEEECCEEC-CCcccCCCCCEEEEEeccc
Confidence 7799999999 6799999999999977543
No 86
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=76.51 E-value=1.6 Score=38.46 Aligned_cols=58 Identities=28% Similarity=0.314 Sum_probs=46.9
Q ss_pred cCCchhhhhhhhccCccchHHHhhcCHH----HhhccCccccccHHHHHHHHHhcCcccccc
Q psy8861 375 LELTVRSANCLKAENIHCIGDLIQRSEN----ELLRTPNLGRKSLNEIKEILASRGKYYMRH 432 (550)
Q Consensus 375 L~LsvRs~NcLk~a~I~tv~dL~~~s~~----dL~~~~n~G~kSl~Ei~~~L~~~gl~lmrh 432 (550)
+=|..+..-.|..+||.|++||+.+=.. =-..++++|.++-..|..-|..++-.+++.
T Consensus 19 ~Wf~p~va~~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~awLa~h~~~~~~~ 80 (96)
T PF12482_consen 19 LWFPPRVARRLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAGARRIEAWLAAHPALLGRA 80 (96)
T ss_pred HhcCHHHHHHHHHcCCchHHHHHHHHHHccchHHHhCcccchHHHHHHHHHHHHhHHHHhhh
Confidence 3467888899999999999999976442 236799999999999999999877665544
No 87
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=74.62 E-value=3.4 Score=42.91 Aligned_cols=48 Identities=13% Similarity=0.133 Sum_probs=42.5
Q ss_pred CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHH
Q psy8861 376 ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILA 423 (550)
Q Consensus 376 ~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~ 423 (550)
+++-....-|.++||+|++||...+.+||.++.+++.+..++|.+...
T Consensus 6 gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 6 GVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAAR 53 (310)
T ss_pred CCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence 456777888999999999999999999999999998888888877775
No 88
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=74.58 E-value=3.6 Score=47.76 Aligned_cols=70 Identities=19% Similarity=0.288 Sum_probs=50.3
Q ss_pred CCchhhhhhhhcc-CccchHHHhhcCHHHhhccCccccccHHHHHHHHHhc-Cccccc--cccccccCCCChHH
Q psy8861 376 ELTVRSANCLKAE-NIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASR-GKYYMR--HRHGFRKLNRTSSH 445 (550)
Q Consensus 376 ~LsvRs~NcLk~a-~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~-gl~lmr--hrk~~rklgr~~~h 445 (550)
+|+-.+..-|-.+ +|+++.||..+++++|..+++||+||.+-|.+.++.. ...|.+ ..-+.+..|...+.
T Consensus 439 GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~aLgIpgVG~~~ak 512 (652)
T TIGR00575 439 GLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLFALGIRHVGEVTAK 512 (652)
T ss_pred CcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCcHHHHHhhccCCCcCHHHHH
Confidence 3444455555554 5899999999999999999999999999999999853 334433 22344566665544
No 89
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=73.38 E-value=3.6 Score=47.87 Aligned_cols=70 Identities=20% Similarity=0.284 Sum_probs=51.3
Q ss_pred CCchhhhhhhhcc-CccchHHHhhcCHHHhhccCccccccHHHHHHHHHhc-Ccccccc--ccccccCCCChHH
Q psy8861 376 ELTVRSANCLKAE-NIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASR-GKYYMRH--RHGFRKLNRTSSH 445 (550)
Q Consensus 376 ~LsvRs~NcLk~a-~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~-gl~lmrh--rk~~rklgr~~~h 445 (550)
+|.-.+..-|-.+ +|.++.||..+++++|..+++||+||.+-|.+.++.. ...|.+- ..+.+..|...+.
T Consensus 452 GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~algi~~IG~~~ak 525 (665)
T PRK07956 452 GLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAK 525 (665)
T ss_pred CcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHHhhcCCHHHhhHhhhccCcCHHHHH
Confidence 4455555556655 5899999999999999999999999999999998853 4444432 2344666765554
No 90
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=72.31 E-value=4.2 Score=47.46 Aligned_cols=70 Identities=16% Similarity=0.195 Sum_probs=51.8
Q ss_pred CCchhhhhhhhccC-ccchHHHhhcCHHHhhccCccccccHHHHHHHHHh-cCccccc--cccccccCCCChHH
Q psy8861 376 ELTVRSANCLKAEN-IHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS-RGKYYMR--HRHGFRKLNRTSSH 445 (550)
Q Consensus 376 ~LsvRs~NcLk~a~-I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~-~gl~lmr--hrk~~rklgr~~~h 445 (550)
+|+-.+..-|-.+| |+++.||..+++++|.++++||+||.+-|.+.+++ .+..|.+ ..-+.+..|...+.
T Consensus 469 GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALgIpgIG~~~ak 542 (689)
T PRK14351 469 GLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEASREPPLADFLVALGIPEVGPTTAR 542 (689)
T ss_pred CcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHHcCCCCcCHHHHH
Confidence 45556666677776 79999999999999999999999999999998874 4555554 22344556654433
No 91
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=71.97 E-value=3.6 Score=47.81 Aligned_cols=73 Identities=18% Similarity=0.267 Sum_probs=55.8
Q ss_pred CCchhhhhhhhccC-ccchHHHhhcCHHHhhccCccccccHHHHHHHHHh-cCccccc--cccccccCCCChHHHHH
Q psy8861 376 ELTVRSANCLKAEN-IHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS-RGKYYMR--HRHGFRKLNRTSSHRLI 448 (550)
Q Consensus 376 ~LsvRs~NcLk~a~-I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~-~gl~lmr--hrk~~rklgr~~~hR~~ 448 (550)
+|+-.+..-|-.+| |.++.||..++.+||.++++||+||.+-+.+.+++ .+..|.+ ..-+.+..|.+.+.+.+
T Consensus 443 GlG~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~Ie~sk~~~l~r~l~ALGI~~vG~~~ak~La 519 (669)
T PRK14350 443 GLSDKTIEFLFEKKFISSEIDLYTFNFDRLINLKGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLI 519 (669)
T ss_pred CcCHHHHHHHHHcCCcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHHHHHhCCCHHHHHHHcCCCchhHHHHHHHH
Confidence 44555566566555 78899999999999999999999999999999974 5666665 34456777876666544
No 92
>PRK03858 DNA polymerase IV; Validated
Probab=71.20 E-value=11 Score=40.40 Aligned_cols=51 Identities=25% Similarity=0.331 Sum_probs=42.3
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHH
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKE 420 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~ 420 (550)
-.+||++| ++.-++..-|++.||+|++||..++.++|.+ -||....+.+.+
T Consensus 171 ~~lpl~~l~Gig~~~~~~L~~~Gi~t~~dl~~l~~~~L~~--~fG~~~~~~l~~ 222 (396)
T PRK03858 171 HPLPVRRLWGVGPVTAAKLRAHGITTVGDVAELPESALVS--LLGPAAGRHLHA 222 (396)
T ss_pred hcCChhhcCCCCHHHHHHHHHhCCCcHHHHhcCCHHHHHH--HhCcHHHHHHHH
Confidence 34799999 9999999999999999999999999988876 577654444443
No 93
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=70.77 E-value=12 Score=39.01 Aligned_cols=55 Identities=25% Similarity=0.294 Sum_probs=43.3
Q ss_pred cccccccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhcCcc
Q psy8861 369 LRPVDDLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKY 428 (550)
Q Consensus 369 ~~~I~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~ 428 (550)
..||+-++++-++..-|++.||+|++||..++.++|.+ -||.. ...+.+.+ .|..
T Consensus 170 ~lp~~~~gig~~~~~~L~~~Gi~t~~dl~~~~~~~l~~--rfG~~-~~~l~~~~--~G~d 224 (335)
T cd03468 170 PLPVAALRLPPETVELLARLGLRTLGDLAALPRAELAR--RFGLA-LLLRLDQA--YGRD 224 (335)
T ss_pred CCChhHhCCCHHHHHHHHHhCcccHHHHHhCChHHHHh--hcCHH-HHHHHHHH--CCCC
Confidence 36888889999999999999999999999999999876 68854 34444433 3544
No 94
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=70.65 E-value=4.5 Score=46.14 Aligned_cols=66 Identities=12% Similarity=0.193 Sum_probs=51.1
Q ss_pred CCchhhhhhhhccC-ccchHHHhhcCHHHhhccCccccccHHHHHHHHHh-cCccccc--cccccccCCC
Q psy8861 376 ELTVRSANCLKAEN-IHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS-RGKYYMR--HRHGFRKLNR 441 (550)
Q Consensus 376 ~LsvRs~NcLk~a~-I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~-~gl~lmr--hrk~~rklgr 441 (550)
+|+-.+..-|-.+| |+++.||-.++.+||+++++||+||.+-+.+.+++ ....|.+ ..-+.+..|+
T Consensus 432 GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aLGI~~vG~ 501 (562)
T PRK08097 432 GIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKALGIPLPQA 501 (562)
T ss_pred CcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHcCCccHHH
Confidence 55666777788888 69999999999999999999999999999999874 4555554 2223344554
No 95
>PRK01172 ski2-like helicase; Provisional
Probab=70.20 E-value=3.2 Score=47.96 Aligned_cols=48 Identities=13% Similarity=0.114 Sum_probs=41.5
Q ss_pred CchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 377 LTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 377 LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
+.--...-|.++||+|+.||+.++++|+.++.++|++-+++|.+.+++
T Consensus 620 ~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 620 VGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRAMK 667 (674)
T ss_pred CCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHHHH
Confidence 333444668899999999999999999999999999999999988764
No 96
>PRK03352 DNA polymerase IV; Validated
Probab=70.02 E-value=3 Score=44.03 Aligned_cols=52 Identities=25% Similarity=0.255 Sum_probs=42.8
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHH
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEI 421 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~ 421 (550)
-.+||++| ++.-++.--|.+.||+|++||..++.++|.+ -||.+....+.+.
T Consensus 175 ~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~--~fG~~~~~~l~~~ 227 (346)
T PRK03352 175 GDRPTDALWGVGPKTAKRLAALGITTVADLAAADPAELAA--TFGPTTGPWLLLL 227 (346)
T ss_pred hcCCHHHcCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHH--HhChHHHHHHHHH
Confidence 35899999 9999999999999999999999999998764 5776544444444
No 97
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=68.42 E-value=5.3 Score=32.20 Aligned_cols=42 Identities=24% Similarity=0.298 Sum_probs=30.4
Q ss_pred hhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 381 SANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 381 s~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
+..-++. ..|+..|..-|.+||.+++++|++..+.|.+-+++
T Consensus 16 ak~L~~~--f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~ 57 (64)
T PF12826_consen 16 AKLLAKH--FGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQD 57 (64)
T ss_dssp HHHHHHC--CSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-
T ss_pred HHHHHHH--cCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCC
Confidence 3444444 44999999999999999999999999999988864
No 98
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=67.86 E-value=14 Score=30.20 Aligned_cols=52 Identities=25% Similarity=0.382 Sum_probs=34.8
Q ss_pred CCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccC
Q psy8861 85 GKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREK 149 (550)
Q Consensus 85 g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~ 149 (550)
+.|-..++..|..+.... ....-..-.|.|||+.+. .++.++.||.|.|-+.
T Consensus 25 ~~tv~~ll~~l~~~~~~~------------~~~~~~~~~v~vNg~~v~-~~~~l~~gD~v~i~pp 76 (80)
T cd00754 25 GATVGELLDALEARYPGL------------LEELLARVRIAVNGEYVR-LDTPLKDGDEVAIIPP 76 (80)
T ss_pred CCcHHHHHHHHHHHCchH------------HHhhhhcEEEEECCeEcC-CCcccCCCCEEEEeCC
Confidence 445555666665555433 222223346899999997 8999999999998543
No 99
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=67.73 E-value=14 Score=38.50 Aligned_cols=52 Identities=29% Similarity=0.307 Sum_probs=41.9
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHH
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEIL 422 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L 422 (550)
-.+||.+| ++.-++..-|++.||+|++||..++.++|.+ -|| +....+.+.+
T Consensus 169 ~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~--~~g-~~~~~l~~~~ 221 (334)
T cd03586 169 APLPVRKIPGVGKVTAEKLKELGIKTIGDLAKLDVELLKK--LFG-KSGRRLYELA 221 (334)
T ss_pred hcCCchhhCCcCHHHHHHHHHcCCcCHHHHHcCCHHHHHH--HHh-HHHHHHHHHh
Confidence 34799999 7999999999999999999999999999877 455 3444555444
No 100
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=66.54 E-value=4.1 Score=44.44 Aligned_cols=43 Identities=21% Similarity=0.254 Sum_probs=37.6
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCcccc
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGR 412 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~ 412 (550)
..+||++| ++.-++..-|++.||+|++||.+++.+.|.+. ||.
T Consensus 177 ~~lPv~~l~GiG~~~~~~L~~lGi~TigdL~~~~~~~L~~~--fG~ 220 (422)
T PRK03609 177 SLQPVEEVWGVGRRISKKLNAMGIKTALDLADTNIRFIRKH--FNV 220 (422)
T ss_pred hcCChhhcCCccHHHHHHHHHcCCCcHHHHhcCCHHHHHHH--HCH
Confidence 34799999 99999999999999999999999999887654 563
No 101
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=64.95 E-value=4.7 Score=42.53 Aligned_cols=51 Identities=29% Similarity=0.362 Sum_probs=41.6
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHH
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEI 421 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~ 421 (550)
-.+||+.| ++.-++.--|++.||+|++||..++.++|. +-||. ....+.+.
T Consensus 174 ~~lpl~~l~gig~~~~~~L~~~Gi~ti~dL~~~~~~~L~--~rfG~-~~~~l~~~ 225 (344)
T cd01700 174 KILPVGDVWGIGRRTAKKLNAMGIHTAGDLAQADPDLLR--KKFGV-VGERLVRE 225 (344)
T ss_pred ccCChhhcCccCHHHHHHHHHcCCCcHHHHhcCCHHHHH--HHHHH-HHHHHHHH
Confidence 35899998 999999999999999999999999998876 46884 34444443
No 102
>PRK00254 ski2-like helicase; Provisional
Probab=62.53 E-value=7.4 Score=45.43 Aligned_cols=50 Identities=22% Similarity=0.344 Sum_probs=42.8
Q ss_pred CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhc
Q psy8861 376 ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASR 425 (550)
Q Consensus 376 ~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~ 425 (550)
++.-.....|.++|+.|+.|+...+.+||.+++++|+|-.+.|++.|+..
T Consensus 652 gig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~~ 701 (720)
T PRK00254 652 MIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGVE 701 (720)
T ss_pred CCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhccc
Confidence 44444555577899999999999999999999999999999999998743
No 103
>PRK14133 DNA polymerase IV; Provisional
Probab=62.17 E-value=6 Score=41.87 Aligned_cols=56 Identities=27% Similarity=0.296 Sum_probs=45.0
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhcCcc
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKY 428 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~ 428 (550)
..+||+.| ++.-++.--|.+.||+|++||..++.++|.+. ||. ....+.+.+ .|..
T Consensus 171 ~~lpv~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~r--fG~-~g~~l~~~a--~G~d 227 (347)
T PRK14133 171 KPLPISKVHGIGKKSVEKLNNIGIYTIEDLLKLSREFLIEY--FGK-FGVEIYERI--RGID 227 (347)
T ss_pred HhCCccccCCCCHHHHHHHHHcCCccHHHHhhCCHHHHHHH--HhH-HHHHHHHHh--CCCC
Confidence 35799998 99999999999999999999999999987654 784 555665555 3544
No 104
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=61.89 E-value=7.1 Score=40.20 Aligned_cols=45 Identities=27% Similarity=0.402 Sum_probs=40.9
Q ss_pred chhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh
Q psy8861 378 TVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS 424 (550)
Q Consensus 378 svRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~ 424 (550)
+..++|||+.-| ++++++.-|++||++++|.|.+.-.+|.+.|..
T Consensus 192 ~~~a~~ll~~fg--S~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t 236 (254)
T COG1948 192 PKLAERLLKKFG--SVEDVLTASEEELMKVKGIGEKKAREIYRFLRT 236 (254)
T ss_pred HHHHHHHHHHhc--CHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhc
Confidence 467889998755 999999999999999999999999999999974
No 105
>PRK03103 DNA polymerase IV; Reviewed
Probab=61.67 E-value=5.5 Score=43.10 Aligned_cols=51 Identities=22% Similarity=0.240 Sum_probs=41.5
Q ss_pred ccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHH
Q psy8861 369 LRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEIL 422 (550)
Q Consensus 369 ~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L 422 (550)
.+||++| ++.-++..-|++.||+|++||..++.++|.+. ||. ....+.+.+
T Consensus 180 ~lpi~~l~gig~~~~~~L~~~Gi~tigdl~~~~~~~L~~~--fG~-~~~~l~~~a 231 (409)
T PRK03103 180 PLPVRKLFGVGSRMEKHLRRMGIRTIGQLANTPLERLKKR--WGI-NGEVLWRTA 231 (409)
T ss_pred cCCHhhcCCccHHHHHHHHHcCCCCHHHHhcCCHHHHHHH--HCH-HHHHHHHHh
Confidence 4799997 89999999999999999999999999888644 785 344444444
No 106
>PRK02406 DNA polymerase IV; Validated
Probab=60.91 E-value=6.3 Score=41.57 Aligned_cols=51 Identities=25% Similarity=0.271 Sum_probs=41.4
Q ss_pred ccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHH
Q psy8861 369 LRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEIL 422 (550)
Q Consensus 369 ~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L 422 (550)
.+||.+| ++.-++.--|++.||+|++||..++.++|.+. ||. ....+.+.+
T Consensus 167 ~lpi~~l~giG~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~--fG~-~~~~l~~~a 218 (343)
T PRK02406 167 TLPVEKIPGVGKVTAEKLHALGIYTCADLQKYDLAELIRH--FGK-FGRRLYERA 218 (343)
T ss_pred cCCcchhcCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHH--HhH-HHHHHHHHh
Confidence 4789999 79999999999999999999999999998764 885 344444443
No 107
>PRK01216 DNA polymerase IV; Validated
Probab=60.71 E-value=6.3 Score=42.22 Aligned_cols=52 Identities=15% Similarity=0.124 Sum_probs=42.8
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHH
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEI 421 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~ 421 (550)
-.+||..| ++.-++.--|.+.||+|++||..++.++|.+ -||......+.+.
T Consensus 176 ~~LPi~~l~giG~~~~~~L~~~Gi~TigdL~~~~~~~L~~--rfG~~~~~~L~~~ 228 (351)
T PRK01216 176 NELDIADIPGIGDITAEKLKKLGVNKLVDTLRIEFDELKG--IIGEAKAKYLFSL 228 (351)
T ss_pred hcCCcccccCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHH--HHCHHHHHHHHHH
Confidence 44799999 8888999999999999999999999988876 5886555555543
No 108
>PRK03348 DNA polymerase IV; Provisional
Probab=58.40 E-value=7.3 Score=43.16 Aligned_cols=51 Identities=27% Similarity=0.274 Sum_probs=42.1
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHH
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKE 420 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~ 420 (550)
-.+||..| ++.-++..-|++.||+|++||..+++++|.+ -||......+.+
T Consensus 178 ~~LPv~~L~GIG~~t~~~L~~lGI~TigDLa~l~~~~L~~--~fG~~~g~~L~~ 229 (454)
T PRK03348 178 APLPVRRLWGIGPVTEEKLHRLGIETIGDLAALSEAEVAN--LLGATVGPALHR 229 (454)
T ss_pred HhCCccccCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHH--HHCHHHHHHHHH
Confidence 35899999 6999999999999999999999999999865 577554544443
No 109
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=58.10 E-value=26 Score=38.17 Aligned_cols=57 Identities=26% Similarity=0.191 Sum_probs=46.3
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcC--HHHhhccCccccccHHHHHHHHHhcCcc
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRS--ENELLRTPNLGRKSLNEIKEILASRGKY 428 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s--~~dL~~~~n~G~kSl~Ei~~~L~~~gl~ 428 (550)
-.+||.+| ++.-++.--|.+.||+|++||..++ .++|.+ -||.+....+.+.+ .|..
T Consensus 220 ~~lPv~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~~~~~~L~~--~fG~~~g~~L~~~a--~G~d 279 (404)
T cd01701 220 SQLKVGDLPGVGSSLAEKLVKLFGDTCGGLELRSKTKEKLQK--VLGPKTGEKLYDYC--RGID 279 (404)
T ss_pred hcCCHhHhCCCCHHHHHHHHHcCCcchHHHHhCcccHHHHHH--HHCHHHHHHHHHHh--CCcC
Confidence 34799999 8899999999999999999999998 888775 68876677766654 4444
No 110
>PRK02794 DNA polymerase IV; Provisional
Probab=57.11 E-value=7.3 Score=42.47 Aligned_cols=57 Identities=25% Similarity=0.352 Sum_probs=45.0
Q ss_pred ccccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhcCcc
Q psy8861 367 ILLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASRGKY 428 (550)
Q Consensus 367 ~l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~ 428 (550)
+-.+||.+| ++.-++..-|.+.||+|++||..++.++|. +-||. ....+.+.+ .|..
T Consensus 206 L~~lPl~~L~GiG~~~~~~L~~~GI~tigdL~~l~~~~L~--~rfG~-~g~~l~~~a--~G~d 263 (419)
T PRK02794 206 LAPKPVGIIWGVGPATAARLARDGIRTIGDLQRADEADLM--RRFGS-MGLRLWRLA--RGID 263 (419)
T ss_pred HhcCChhhhCCCCHHHHHHHHHhccchHHHHhhCCHHHHH--HHHhH-HHHHHHHHh--CCCC
Confidence 344799999 899999999999999999999999999886 57885 344444443 4554
No 111
>TIGR00234 tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.
Probab=55.19 E-value=15 Score=39.87 Aligned_cols=43 Identities=21% Similarity=0.204 Sum_probs=37.7
Q ss_pred hhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccC
Q psy8861 97 SRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIK 139 (550)
Q Consensus 97 ~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk 139 (550)
..+..++...|+++|...||++|..|-|.|||.+++.+.+.+.
T Consensus 330 ~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~v~~ 372 (377)
T TIGR00234 330 ITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLEPIRK 372 (377)
T ss_pred cCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCchhhhc
Confidence 4666788889999999999999999999999999988776553
No 112
>PRK01777 hypothetical protein; Validated
Probab=54.76 E-value=12 Score=32.91 Aligned_cols=43 Identities=9% Similarity=0.154 Sum_probs=30.1
Q ss_pred HHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccC
Q psy8861 104 YRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREK 149 (550)
Q Consensus 104 ~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~ 149 (550)
-.+|+.....+- -..++.|.|||+.+ .+.+.++.||.|+|-..
T Consensus 34 ~~sgi~~~~pei--~~~~~~vgI~Gk~v-~~d~~L~dGDRVeIyrP 76 (95)
T PRK01777 34 RASGLLELRTDI--DLAKNKVGIYSRPA-KLTDVLRDGDRVEIYRP 76 (95)
T ss_pred HHcCCCccCccc--ccccceEEEeCeEC-CCCCcCCCCCEEEEecC
Confidence 345654432222 12357899999999 58999999999998543
No 113
>PRK06437 hypothetical protein; Provisional
Probab=53.94 E-value=14 Score=30.17 Aligned_cols=24 Identities=21% Similarity=0.194 Sum_probs=21.2
Q ss_pred cEEECcEEeccCCcccCCCCEEEEc
Q psy8861 123 AFLVNKKIVNIASYKIKPGDIISVR 147 (550)
Q Consensus 123 ~V~VNg~~v~~ps~~vk~gDiI~v~ 147 (550)
.|.+||..+. +.+.+++||.|+|-
T Consensus 38 aV~vNg~iv~-~~~~L~dgD~Veiv 61 (67)
T PRK06437 38 VVIVNGSPVL-EDHNVKKEDDVLIL 61 (67)
T ss_pred EEEECCEECC-CceEcCCCCEEEEE
Confidence 4679999996 99999999999874
No 114
>PRK02362 ski2-like helicase; Provisional
Probab=53.21 E-value=11 Score=44.32 Aligned_cols=47 Identities=26% Similarity=0.234 Sum_probs=39.7
Q ss_pred CchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhc
Q psy8861 377 LTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASR 425 (550)
Q Consensus 377 LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~ 425 (550)
+.-.....|.++||.|+.||...++++|.++ ||+|..+.|.+.+..+
T Consensus 660 i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~~~ 706 (737)
T PRK02362 660 VGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENILEQAGRR 706 (737)
T ss_pred CCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhCcc
Confidence 3334445566799999999999999999999 9999999999988754
No 115
>PRK01810 DNA polymerase IV; Validated
Probab=52.21 E-value=9.9 Score=41.13 Aligned_cols=52 Identities=27% Similarity=0.343 Sum_probs=42.2
Q ss_pred cccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHH
Q psy8861 368 LLRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEIL 422 (550)
Q Consensus 368 l~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L 422 (550)
-.+||++| ++.-++.--|.+.||+|++||..++.++|. +-||. ....+.+.+
T Consensus 177 ~~lpv~~l~giG~~~~~~L~~~Gi~tigdL~~~~~~~L~--~rfG~-~g~~l~~~a 229 (407)
T PRK01810 177 WPLPVGEMHGIGEKTAEKLKDIGIQTIGDLAKADEHILR--AKLGI-NGVRLQRRA 229 (407)
T ss_pred HhCCHhhcCCcCHHHHHHHHHcCCCcHHHHHhCCHHHHH--HHHhH-HHHHHHHHh
Confidence 34799997 898899999999999999999999998876 55785 455555544
No 116
>TIGR00731 ctc_TL5 ribosomal protein L25, Ctc-form. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology.
Probab=50.02 E-value=16 Score=35.55 Aligned_cols=49 Identities=12% Similarity=0.205 Sum_probs=32.5
Q ss_pred ccceeeeccC-ceEEEEEEEec--e-eeEEeccCccCCCeEEe-CCCceEEEcC
Q psy8861 277 KGVILKLYNR-DYAILNLKKFG--K-CVVLASDIELLSDIELV-NPNHIIAHLS 325 (550)
Q Consensus 277 K~i~~~~~~~-~~~~~~l~~~G--p-~~V~A~DI~~~~~veiv-npd~~IatL~ 325 (550)
..|.++.... =|-.+.+++++ - ..++.+||..|++++++ +||..||++.
T Consensus 122 ~~v~v~~~p~~IPe~I~VDvs~L~iGd~i~v~Dl~lp~gv~~~~d~~~~v~~V~ 175 (176)
T TIGR00731 122 RRIEVECKPKDIPDFLELDVSSLGVGESLKLSDLELPAGVSFITDDDEVVVTVI 175 (176)
T ss_pred EEEEEEECHHHCCccEEEECccCCCCCEEEEeeccCCCCcEEccCCCcEEEEEe
Confidence 3344444322 24444444443 2 36999999999999988 7789999875
No 117
>PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed
Probab=49.02 E-value=11 Score=37.10 Aligned_cols=42 Identities=17% Similarity=0.350 Sum_probs=30.7
Q ss_pred eEEEEEEEec--e-eeEEeccCccCCCeEEe-CCCceEEEcCChHH
Q psy8861 288 YAILNLKKFG--K-CVVLASDIELLSDIELV-NPNHIIAHLSDNEE 329 (550)
Q Consensus 288 ~~~~~l~~~G--p-~~V~A~DI~~~~~veiv-npd~~IatL~~P~~ 329 (550)
|-.+.++++| . ..++.+||..|++++++ +||..||++..|+.
T Consensus 142 P~~I~VDVs~L~~Gd~i~v~Dl~lp~~v~i~~~~~~~v~~V~~~~~ 187 (197)
T PRK05618 142 PEFIEVDVSGLEIGDSIHVSDLKLPEGVKLLDDPDEVVATVVAPRG 187 (197)
T ss_pred CccEEEEcccCCCCCEEEeeeecCCCCcEEcCCCCcEEEEEEcCCc
Confidence 3344444443 3 36999999999999997 67799999976543
No 118
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=47.77 E-value=13 Score=39.24 Aligned_cols=52 Identities=33% Similarity=0.326 Sum_probs=38.6
Q ss_pred ccccccc-CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHH
Q psy8861 369 LRPVDDL-ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEIL 422 (550)
Q Consensus 369 ~~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L 422 (550)
.+||.+| ++.-++..-|++.||+|++||..++..+++.- =|| +....+.+.+
T Consensus 172 ~lpi~~l~giG~~~~~~L~~~Gi~ti~dl~~~~~~~~l~~-~fg-~~~~~l~~~a 224 (343)
T cd00424 172 KLPLTDLPGIGAVTAKRLEAVGINPIGDLLAASPDALLAL-WGG-VSGERLWYAL 224 (343)
T ss_pred cCChhhcCCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHH-Hhh-HHHHHHHHHh
Confidence 3689888 69999999999999999999999994444332 245 4455555554
No 119
>PF14693 Ribosomal_TL5_C: Ribosomal protein TL5, C-terminal domain; PDB: 1FEU_D 2HGQ_Y 2HGJ_Y 2Y19_Z 2WRL_Z 3KIT_Z 2WH2_Z 2WDN_Z 3V25_Z 3HUZ_Z ....
Probab=47.14 E-value=8.7 Score=33.03 Aligned_cols=52 Identities=17% Similarity=0.281 Sum_probs=32.7
Q ss_pred cccceeeeccC-ceEEEEEEEece---eeEEeccCccCCCeEEe-CCCceEEEcCCh
Q psy8861 276 LKGVILKLYNR-DYAILNLKKFGK---CVVLASDIELLSDIELV-NPNHIIAHLSDN 327 (550)
Q Consensus 276 LK~i~~~~~~~-~~~~~~l~~~Gp---~~V~A~DI~~~~~veiv-npd~~IatL~~P 327 (550)
+..|.++.... =|-.+.++++|= ..++.+||..|++++++ +||..||++..|
T Consensus 28 ~~~v~V~~~p~~iPe~I~vDvs~l~~g~~i~v~Dl~lp~gv~~~~d~~~vV~~v~~~ 84 (88)
T PF14693_consen 28 LREVEVECLPADIPESIEVDVSGLEIGDSIHVSDLKLPEGVEILDDPETVVASVVAP 84 (88)
T ss_dssp TSEEEEEE-TTS--SSEEEETTTSSTTCEEEGCCSB-STTEEESS-TTSEEEEEE-S
T ss_pred EeEEEEEEcHHHCCccEEEECccCcCCCEEEEeeccCCCCcEEcCCCCcEEEEEecc
Confidence 44455555433 245556665542 48999999999999886 578888988654
No 120
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=45.29 E-value=23 Score=28.29 Aligned_cols=24 Identities=29% Similarity=0.447 Sum_probs=21.3
Q ss_pred EEECcEEecc---CCcccCCCCEEEEc
Q psy8861 124 FLVNKKIVNI---ASYKIKPGDIISVR 147 (550)
Q Consensus 124 V~VNg~~v~~---ps~~vk~gDiI~v~ 147 (550)
|-||+..+.+ +++.++.||.|+|=
T Consensus 33 vavN~~iv~~~~~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 33 TAVNGELVHKEARAQFVLHEGDRIEIL 59 (65)
T ss_pred EEECCEEcCHHHcCccccCCCCEEEEE
Confidence 8899999987 58899999999874
No 121
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=44.83 E-value=17 Score=33.18 Aligned_cols=45 Identities=24% Similarity=0.247 Sum_probs=32.1
Q ss_pred CchhhhhhhhccCccchHHHhhcCHHHhhc--cCccccccHHHHHHH
Q psy8861 377 LTVRSANCLKAENIHCIGDLIQRSENELLR--TPNLGRKSLNEIKEI 421 (550)
Q Consensus 377 LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~--~~n~G~kSl~Ei~~~ 421 (550)
++-....-|+++||+|++||+..+...+-+ +-+-+.-|.+.|.+-
T Consensus 3 i~~~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w 49 (122)
T PF14229_consen 3 IGPKEAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKLGISERNLLKW 49 (122)
T ss_pred CCHHHHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHH
Confidence 445566789999999999999998877665 444444455555544
No 122
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=43.63 E-value=27 Score=25.84 Aligned_cols=27 Identities=30% Similarity=0.535 Sum_probs=22.7
Q ss_pred hHhhhhhHhhhCCcHHHHHHHHHHhhc
Q psy8861 56 FREKQKVKRMYGILEKQFRRYFIEGAR 82 (550)
Q Consensus 56 L~~Kqkl~~~YG~~ekq~~~~~~~a~~ 82 (550)
-.||+.|....|++.+|+.++|.-+++
T Consensus 13 ~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 13 KEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 468899999999999999999988764
No 123
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=43.12 E-value=27 Score=27.82 Aligned_cols=25 Identities=36% Similarity=0.391 Sum_probs=20.7
Q ss_pred cEEECcEEec---cCCcccCCCCEEEEc
Q psy8861 123 AFLVNKKIVN---IASYKIKPGDIISVR 147 (550)
Q Consensus 123 ~V~VNg~~v~---~ps~~vk~gDiI~v~ 147 (550)
-|.|||+.+. -+.+.++.||.|+|-
T Consensus 31 ~v~vN~~iv~~~~~~~~~L~~gD~veii 58 (64)
T TIGR01683 31 AVAVNGEIVPRSEWDDTILKEGDRIEIV 58 (64)
T ss_pred EEEECCEEcCHHHcCceecCCCCEEEEE
Confidence 4789999997 445789999999874
No 124
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=42.67 E-value=24 Score=28.41 Aligned_cols=50 Identities=28% Similarity=0.353 Sum_probs=35.6
Q ss_pred CCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEecc--CCcccCCCCEEEEcc
Q psy8861 85 GKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNI--ASYKIKPGDIISVRE 148 (550)
Q Consensus 85 g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~--ps~~vk~gDiI~v~~ 148 (550)
+.|-..++..|..|.+... ....=.|.|||+.++. ..+.|+.||.|.|-+
T Consensus 21 ~~tv~~ll~~l~~~~p~~~--------------~~~~~~v~vN~~~v~~~~~~~~l~~gD~V~i~p 72 (77)
T PF02597_consen 21 GSTVRDLLEALAERYPELA--------------LRDRVAVAVNGEIVPDDGLDTPLKDGDEVAILP 72 (77)
T ss_dssp TSBHHHHHHHHCHHTGGGH--------------TTTTEEEEETTEEEGGGTTTSBEETTEEEEEEE
T ss_pred CCcHHHHHHHHHhhccccc--------------cCccEEEEECCEEcCCccCCcCcCCCCEEEEEC
Confidence 5566667777766665544 1122348899999977 688999999998854
No 125
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=41.49 E-value=27 Score=36.09 Aligned_cols=95 Identities=13% Similarity=0.148 Sum_probs=61.8
Q ss_pred hHHHHHHHHHHHHHHhhhhhccCCCCCc----c---ccCcc-ccccCCcccccccccCCchhhhhhhhccCccchHHHhh
Q psy8861 327 NEEAIRQSARVLVDQLNVFAALENTPVK----K---ELDSS-LEKVDPILLRPVDDLELTVRSANCLKAENIHCIGDLIQ 398 (550)
Q Consensus 327 P~~Al~~Aa~iL~~~~~~f~~~~~~~~~----~---~~~~~-~~~~~~~l~~~I~~L~LsvRs~NcLk~a~I~tv~dL~~ 398 (550)
-...+..|.+|+...+............ . ..... -+...+++..| .++......|.++||.+++||..
T Consensus 105 ~~~vl~~a~rll~al~di~~~~~~~~~~~~~l~L~q~i~q~~w~~~~~L~Qlp----~i~~~~~~~l~~~~i~s~~~l~~ 180 (312)
T smart00611 105 TVYVLQNAGRLLQAMVDIALERGWLSTALNALNLSQMIIQALWPTDSPLLQLP----HLPEEILKRLEKKKVLSLEDLLE 180 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhhCCCCCccccCC----CCCHHHHHHHHhCCCCCHHHHHh
Confidence 4557777888887777765544321110 0 00000 00011222222 34556778899999999999999
Q ss_pred cCHHHhhccCccccccHHHHHHHHHhc
Q psy8861 399 RSENELLRTPNLGRKSLNEIKEILASR 425 (550)
Q Consensus 399 ~s~~dL~~~~n~G~kSl~Ei~~~L~~~ 425 (550)
++.+|+..+-|++.+-.++|.+.++.+
T Consensus 181 ~~~~~~~~ll~~~~~~~~~i~~~~~~~ 207 (312)
T smart00611 181 LEDEERGELLGLLDAEGERVYKVLSRL 207 (312)
T ss_pred cCHHHHHHHHcCCHHHHHHHHHHHHhC
Confidence 999999999998888888898888876
No 126
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=41.32 E-value=30 Score=27.39 Aligned_cols=26 Identities=23% Similarity=0.328 Sum_probs=21.6
Q ss_pred cEEECcEEeccC---CcccCCCCEEEEcc
Q psy8861 123 AFLVNKKIVNIA---SYKIKPGDIISVRE 148 (550)
Q Consensus 123 ~V~VNg~~v~~p---s~~vk~gDiI~v~~ 148 (550)
.|.|||..+.+. +..++.||.|+|-+
T Consensus 32 ~v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 32 AVAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred EEEECCEEcCchhcccccCCCCCEEEEEe
Confidence 478999999665 78899999998843
No 127
>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.25 E-value=30 Score=33.78 Aligned_cols=53 Identities=38% Similarity=0.503 Sum_probs=43.9
Q ss_pred ceeeEEeccCc-cCCCeEEeCCCceEEEcCC--hHHHHHHHHHHHHHHhhhhhccC
Q psy8861 297 GKCVVLASDIE-LLSDIELVNPNHIIAHLSD--NEEAIRQSARVLVDQLNVFAALE 349 (550)
Q Consensus 297 Gp~~V~A~DI~-~~~~veivnpd~~IatL~~--P~~Al~~Aa~iL~~~~~~f~~~~ 349 (550)
|...|+|.-+- +-+++++||+|+.-+.+++ |+.|=.+|++..++.+....+..
T Consensus 14 GKstv~~~~~~~~~~~~~~VN~D~iA~~i~p~~p~~~~i~A~r~ai~~i~~~I~~~ 69 (187)
T COG4185 14 GKSTVYASTLAPLLPGIVFVNADEIAAQISPDNPTSAAIQAARVAIDRIARLIDLG 69 (187)
T ss_pred CceeeeeccchhhcCCeEEECHHHHhhhcCCCCchHHHHHHHHHHHHHHHHHHHcC
Confidence 44577776653 5679999999999999976 99999999999999999887653
No 128
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=39.08 E-value=32 Score=27.91 Aligned_cols=21 Identities=33% Similarity=0.656 Sum_probs=18.6
Q ss_pred HhhccCccccccHHHHHHHHH
Q psy8861 403 ELLRTPNLGRKSLNEIKEILA 423 (550)
Q Consensus 403 dL~~~~n~G~kSl~Ei~~~L~ 423 (550)
++.++||+|++..+.|.+.|+
T Consensus 48 ~~~~l~gIG~~ia~kI~E~le 68 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDEILE 68 (68)
T ss_dssp HHCTSTTTTHHHHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHHHHC
Confidence 699999999999999988774
No 129
>KOG3438|consensus
Probab=38.33 E-value=26 Score=31.31 Aligned_cols=26 Identities=35% Similarity=0.415 Sum_probs=21.6
Q ss_pred CCcEEEEEEeeCccchhhhHHHHHHHHHhh
Q psy8861 211 GSNHAKVIMEPFERGYGYTLGNALRRVLLS 240 (550)
Q Consensus 211 ~~~y~~F~i~Ple~G~g~TlgNaLRRvLLs 240 (550)
+.+...|.+. --++|||||||-++..
T Consensus 14 d~~~~Tf~~~----eEDHTlgNalR~vI~k 39 (105)
T KOG3438|consen 14 DLSSATFQLR----EEDHTLGNALRYVIMK 39 (105)
T ss_pred CCCceEEEEE----ecCcchhHHHHHHHhc
Confidence 4567889988 7789999999988765
No 130
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=38.29 E-value=24 Score=40.96 Aligned_cols=68 Identities=24% Similarity=0.325 Sum_probs=46.7
Q ss_pred Cchhhhhhh-hccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHh-cCccccc--cccccccCCCChH
Q psy8861 377 LTVRSANCL-KAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILAS-RGKYYMR--HRHGFRKLNRTSS 444 (550)
Q Consensus 377 LsvRs~NcL-k~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~-~gl~lmr--hrk~~rklgr~~~ 444 (550)
|+-..-.-| ...-|+++.||-.++++||+.++.||+||.+-+.+.+++ ..-.|-| -..+.+..|-+.+
T Consensus 453 LG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~A 524 (667)
T COG0272 453 LGEKIIEQLFEKGLIKDIADLYTLTEEDLLSLEGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTA 524 (667)
T ss_pred cCHHHHHHHHHcCccCCHHHHHhCCHHHHhhccchhhhHHHHHHHHHHHhccCCHHHHHHHcCCchhhHHHH
Confidence 333444434 344599999999999999999999999999999999875 3333333 2223444554333
No 131
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=37.86 E-value=65 Score=26.71 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=22.1
Q ss_pred cEEECcEEeccCCcccCCCCEEEEccC
Q psy8861 123 AFLVNKKIVNIASYKIKPGDIISVREK 149 (550)
Q Consensus 123 ~V~VNg~~v~~ps~~vk~gDiI~v~~~ 149 (550)
.|.|||+.++ .++.|+.||.|.|-+.
T Consensus 53 ~vavN~~~v~-~~~~l~dgDeVai~Pp 78 (82)
T PLN02799 53 VLALNEEYTT-ESAALKDGDELAIIPP 78 (82)
T ss_pred EEEECCEEcC-CCcCcCCCCEEEEeCC
Confidence 4789999985 8999999999998653
No 132
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=36.60 E-value=30 Score=27.63 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=20.2
Q ss_pred EEECcEEeccC---CcccCCCCEEEEcc
Q psy8861 124 FLVNKKIVNIA---SYKIKPGDIISVRE 148 (550)
Q Consensus 124 V~VNg~~v~~p---s~~vk~gDiI~v~~ 148 (550)
|.|||+.+... ++.++.||.|++-+
T Consensus 33 V~vNg~~v~~~~~~~~~L~~gD~V~ii~ 60 (65)
T cd00565 33 VALNGEIVPRSEWASTPLQDGDRIEIVT 60 (65)
T ss_pred EEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 67999999654 28899999998743
No 133
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=36.29 E-value=19 Score=23.77 Aligned_cols=19 Identities=42% Similarity=0.751 Sum_probs=16.5
Q ss_pred HHhhccCccccccHHHHHH
Q psy8861 402 NELLRTPNLGRKSLNEIKE 420 (550)
Q Consensus 402 ~dL~~~~n~G~kSl~Ei~~ 420 (550)
++|++++++|+++.+.|.+
T Consensus 1 ~~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 1 EELLKVPGIGPKTAEKILE 19 (26)
T ss_pred ChhhhCCCCCHHHHHHHHH
Confidence 4789999999999988875
No 134
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=35.19 E-value=43 Score=27.35 Aligned_cols=26 Identities=27% Similarity=0.342 Sum_probs=21.8
Q ss_pred CcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 122 RAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 122 G~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
--|.+||..+ .+++.++.||.|++=+
T Consensus 40 v~v~vNg~iv-~~~~~l~~gD~Veii~ 65 (70)
T PRK08364 40 AIAKVNGKVA-LEDDPVKDGDYVEVIP 65 (70)
T ss_pred EEEEECCEEC-CCCcCcCCCCEEEEEc
Confidence 3578999999 5899999999998743
No 135
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=34.43 E-value=36 Score=29.66 Aligned_cols=59 Identities=15% Similarity=0.087 Sum_probs=36.8
Q ss_pred CCchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEec---cCCcccCCCCEEEEcc
Q psy8861 85 GKTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVN---IASYKIKPGDIISVRE 148 (550)
Q Consensus 85 g~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~---~ps~~vk~gDiI~v~~ 148 (550)
+.|-..++..|+.+.... +..++..- -++..+=.|+|||..+. -..+.|+.||.|+|-+
T Consensus 28 ~~tV~dll~~L~~~~~~~--~~~lf~~~---g~lr~~i~VlvN~~di~~l~g~~t~L~dgD~v~i~P 89 (94)
T cd01764 28 PVTVGDLLDYVASNLLEE--RPDLFIEG---GSVRPGIIVLINDTDWELLGEEDYILEDGDHVVFIS 89 (94)
T ss_pred CCcHHHHHHHHHHhCchh--hhhhEecC---CcccCCEEEEECCccccccCCcccCCCCcCEEEEEC
Confidence 456677788887776432 12222110 11222236899999874 5679999999999855
No 136
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=32.49 E-value=64 Score=24.49 Aligned_cols=41 Identities=24% Similarity=0.207 Sum_probs=29.2
Q ss_pred ccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHH
Q psy8861 374 DLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIK 419 (550)
Q Consensus 374 ~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~ 419 (550)
.+++ -.-..++++.|| |..+|+.+|++||. .+|-++.....
T Consensus 13 ~~~~-~~y~~~f~~~~i-~g~~L~~l~~~dL~---~lgi~~~g~r~ 53 (63)
T cd00166 13 SLGL-GQYADNFRENGI-DGDLLLLLTEEDLK---ELGITLPGHRK 53 (63)
T ss_pred HcCh-HHHHHHHHHcCC-CHHHHhHCCHHHHH---HcCCCCHHHHH
Confidence 3445 345578899999 99999999999976 55655544333
No 137
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. 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 in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=32.34 E-value=25 Score=29.91 Aligned_cols=36 Identities=28% Similarity=0.346 Sum_probs=24.0
Q ss_pred CCchhhhhhhhccCccchHHHhhcCHHH-hhccCccc
Q psy8861 376 ELTVRSANCLKAENIHCIGDLIQRSENE-LLRTPNLG 411 (550)
Q Consensus 376 ~LsvRs~NcLk~a~I~tv~dL~~~s~~d-L~~~~n~G 411 (550)
+|+..+-..|.++||+|+.||.+....+ .++++..|
T Consensus 10 Nig~~~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~~ 46 (81)
T PF04994_consen 10 NIGPKSERMLAKVGIHTVEDLRELGAVEAYLRLKASG 46 (81)
T ss_dssp T--HHHHHHHHHTT--SHHHHHHHHHHHHHHHHHHH-
T ss_pred CCCHHHHHHHHHcCCCCHHHHHHhCHHHHHHHHHHHC
Confidence 7888899999999999999999887643 34444443
No 138
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=32.26 E-value=49 Score=27.34 Aligned_cols=50 Identities=14% Similarity=0.088 Sum_probs=33.3
Q ss_pred CchHHHHHHHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEEccC
Q psy8861 86 KTGEIILKLLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISVREK 149 (550)
Q Consensus 86 ~~~~~ll~~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~~ 149 (550)
.|-..|+..|..|-..+. . ...+=.|.||++.++ .+..|+.||.|.+=+.
T Consensus 27 ~tv~~L~~~L~~~~p~l~------~-------~~~~~~v~vn~~~v~-~~~~l~dgDevai~Pp 76 (80)
T TIGR01682 27 TTVGELKEHLAKEGPELA------A-------SRGQVMVAVNEEYVT-DDALLNEGDEVAFIPP 76 (80)
T ss_pred cCHHHHHHHHHHhCchhh------h-------hccceEEEECCEEcC-CCcCcCCCCEEEEeCC
Confidence 455667777776654211 0 011114889999997 5899999999998553
No 139
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=32.22 E-value=35 Score=26.82 Aligned_cols=25 Identities=28% Similarity=0.383 Sum_probs=18.7
Q ss_pred CcEEECcEEecc-CCcccCCCCEEEE
Q psy8861 122 RAFLVNKKIVNI-ASYKIKPGDIISV 146 (550)
Q Consensus 122 G~V~VNg~~v~~-ps~~vk~gDiI~v 146 (550)
.-++|||+.+.. ..+.++.||+|.+
T Consensus 42 ngt~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 42 NGTFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp S-EEETTEEESSTSEEEE-TTEEEEE
T ss_pred CcEEECCEEcCCCCEEECCCCCEEEc
Confidence 458899999865 4688899999976
No 140
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=31.68 E-value=47 Score=27.43 Aligned_cols=24 Identities=42% Similarity=0.407 Sum_probs=21.0
Q ss_pred EEECcEEecc---CCcccCCCCEEEEc
Q psy8861 124 FLVNKKIVNI---ASYKIKPGDIISVR 147 (550)
Q Consensus 124 V~VNg~~v~~---ps~~vk~gDiI~v~ 147 (550)
|-|||..|.+ +.+.|+.||.|+|-
T Consensus 36 v~vNg~iVpr~~~~~~~l~~gD~ievv 62 (68)
T COG2104 36 VAVNGEIVPRSQWADTILKEGDRIEVV 62 (68)
T ss_pred EEECCEEccchhhhhccccCCCEEEEE
Confidence 6799999987 88899999999874
No 141
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=30.80 E-value=60 Score=26.09 Aligned_cols=24 Identities=25% Similarity=0.379 Sum_probs=20.0
Q ss_pred EEECcEEec---cCCcccCCCCEEEEc
Q psy8861 124 FLVNKKIVN---IASYKIKPGDIISVR 147 (550)
Q Consensus 124 V~VNg~~v~---~ps~~vk~gDiI~v~ 147 (550)
|-||+..|. -.++.++.||.|+|-
T Consensus 34 VavN~~iv~r~~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 34 LAINQQIIPREQWAQHIVQDGDQILLF 60 (66)
T ss_pred EEECCEEeChHHcCccccCCCCEEEEE
Confidence 779999998 456689999999874
No 142
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.33 E-value=48 Score=29.75 Aligned_cols=35 Identities=26% Similarity=0.323 Sum_probs=30.7
Q ss_pred HHHHHHHcCcEEECcEEeccCCcccCCCCEEEEcc
Q psy8861 114 EARQLISHRAFLVNKKIVNIASYKIKPGDIISVRE 148 (550)
Q Consensus 114 ~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v~~ 148 (550)
.-=.+|.+|+=.|.++..+----.+++||.|.+..
T Consensus 10 eylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~ 44 (111)
T COG4043 10 EYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNG 44 (111)
T ss_pred HHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcC
Confidence 34578999999999999988888999999999984
No 143
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=29.64 E-value=54 Score=32.12 Aligned_cols=77 Identities=12% Similarity=0.096 Sum_probs=48.6
Q ss_pred hhhhhhhhccCccchHH-HhhcCHHHhhccCccccccHHHHHHHHHhcCccccccccccccCCCChHHHHHHHHHHHHHH
Q psy8861 379 VRSANCLKAENIHCIGD-LIQRSENELLRTPNLGRKSLNEIKEILASRGKYYMRHRHGFRKLNRTSSHRLIMLRNMTISL 457 (550)
Q Consensus 379 vRs~NcLk~a~I~tv~d-L~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~gl~lmrhrk~~rklgr~~~hR~~llrnl~t~L 457 (550)
-++...|...|..++-+ +.+-+.++|.++|++|+|..+.|...|+..--.+.... .....+.. .++.++..|
T Consensus 84 k~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~~~~~~~------~~~~~~~~-~~~ev~~aL 156 (192)
T PRK00116 84 KLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLAAAASAA------AAAAAASS-ALEEAVSAL 156 (192)
T ss_pred HHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhhcccccc------cccccccc-hHHHHHHHH
Confidence 34556677777766654 44557889999999999999999999986422221000 00111111 146777888
Q ss_pred HhcCc
Q psy8861 458 LRYEI 462 (550)
Q Consensus 458 i~~er 462 (550)
..+|-
T Consensus 157 ~~LG~ 161 (192)
T PRK00116 157 VALGY 161 (192)
T ss_pred HHcCC
Confidence 88775
No 144
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=29.25 E-value=54 Score=35.48 Aligned_cols=43 Identities=19% Similarity=0.204 Sum_probs=36.8
Q ss_pred hhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHHhc
Q psy8861 381 SANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILASR 425 (550)
Q Consensus 381 s~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~~~ 425 (550)
+-|-|++-| ++..++.-|.+||.+++++|++....|++.+..+
T Consensus 300 Ak~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~Rl 342 (352)
T PRK13482 300 IENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARAIREGLSRL 342 (352)
T ss_pred HHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHHH
Confidence 445566665 9999999999999999999999999999988754
No 145
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=28.06 E-value=80 Score=34.26 Aligned_cols=51 Identities=20% Similarity=0.268 Sum_probs=39.1
Q ss_pred cccccc-CCchhhhhhhhccCccchHHHhhcC---------------HHHhhccCccccccHHHHHHHH
Q psy8861 370 RPVDDL-ELTVRSANCLKAENIHCIGDLIQRS---------------ENELLRTPNLGRKSLNEIKEIL 422 (550)
Q Consensus 370 ~~I~~L-~LsvRs~NcLk~a~I~tv~dL~~~s---------------~~dL~~~~n~G~kSl~Ei~~~L 422 (550)
+||.+| ++.-++..-|.+.||+|++||...+ .+.|.+ -||.+....+.+.+
T Consensus 172 lpv~~l~GiG~~~~~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~--~fG~~~g~~l~~~a 238 (379)
T cd01703 172 HDLRKIPGIGYKTAAKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVK--EFGEGIGQRIWKLL 238 (379)
T ss_pred CCccccCCcCHHHHHHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHH--HHCHHHHHHHHHHH
Confidence 567776 4888999999999999999999998 655544 57766566665554
No 146
>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=27.47 E-value=45 Score=36.99 Aligned_cols=44 Identities=18% Similarity=0.189 Sum_probs=36.4
Q ss_pred CCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHH
Q psy8861 376 ELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIK 419 (550)
Q Consensus 376 ~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~ 419 (550)
+++...++-|+++||+||.||...+..+|..++++|......+.
T Consensus 214 gi~~~~~~~L~~~GI~ti~~La~~~~~~l~~~~~~~~~~~~~l~ 257 (457)
T TIGR03491 214 GIGPSRYRLLQELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLV 257 (457)
T ss_pred CCCHHHHHHHHHcCCCcHHHHhcCCccccccccccCHHHHHHHH
Confidence 46788899999999999999999987778888888876666533
No 147
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=27.41 E-value=72 Score=25.29 Aligned_cols=24 Identities=33% Similarity=0.487 Sum_probs=20.0
Q ss_pred EEECcEEec---cCCcccCCCCEEEEc
Q psy8861 124 FLVNKKIVN---IASYKIKPGDIISVR 147 (550)
Q Consensus 124 V~VNg~~v~---~ps~~vk~gDiI~v~ 147 (550)
|-+||..+. -+++.|+.||.|+|-
T Consensus 34 v~vNg~iv~r~~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 34 VEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred EEECCeEeCHHHcCcccCCCCCEEEEE
Confidence 789998876 378889999999874
No 148
>KOG2623|consensus
Probab=26.05 E-value=69 Score=35.26 Aligned_cols=37 Identities=22% Similarity=0.249 Sum_probs=31.8
Q ss_pred HHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCccc
Q psy8861 102 VVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKI 138 (550)
Q Consensus 102 ~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~v 138 (550)
.+..++.++|...|+.+|..|-|.||+++++.+|-.+
T Consensus 404 l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~es~~~ 440 (467)
T KOG2623|consen 404 LLRKASRFPSGKEARRMIQQGGVSLNHEKVRDESVSI 440 (467)
T ss_pred HHHHhhcCCCcHHHHHHHHccceeecCccccCchhhc
Confidence 3456888999999999999999999999998866544
No 149
>PRK00024 hypothetical protein; Reviewed
Probab=25.85 E-value=74 Score=32.05 Aligned_cols=41 Identities=20% Similarity=0.272 Sum_probs=33.0
Q ss_pred hhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHHH
Q psy8861 381 SANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEILA 423 (550)
Q Consensus 381 s~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L~ 423 (550)
|.+-|++.| ++.+|...+.+||.+++++|......|...++
T Consensus 47 A~~LL~~fg--sL~~l~~as~~eL~~i~GIG~akA~~L~a~~E 87 (224)
T PRK00024 47 ARELLQRFG--SLRGLLDASLEELQSIKGIGPAKAAQLKAALE 87 (224)
T ss_pred HHHHHHHcC--CHHHHHhCCHHHHhhccCccHHHHHHHHHHHH
Confidence 334444444 89999999999999999999998888877664
No 150
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=24.71 E-value=75 Score=25.17 Aligned_cols=23 Identities=26% Similarity=0.416 Sum_probs=18.9
Q ss_pred cEEECcEEeccCCcccCCCCEEEE
Q psy8861 123 AFLVNKKIVNIASYKIKPGDIISV 146 (550)
Q Consensus 123 ~V~VNg~~v~~ps~~vk~gDiI~v 146 (550)
...|||+.+ -.++.++.||+|+|
T Consensus 36 ~A~Vng~~v-dl~~~L~~~d~v~i 58 (60)
T PF02824_consen 36 AAKVNGQLV-DLDHPLEDGDVVEI 58 (60)
T ss_dssp EEEETTEEE-ETTSBB-SSEEEEE
T ss_pred EEEEcCEEC-CCCCCcCCCCEEEE
Confidence 357999998 68899999999987
No 151
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=24.43 E-value=60 Score=29.55 Aligned_cols=33 Identities=18% Similarity=0.220 Sum_probs=28.8
Q ss_pred cccCCchhhhhhhhccCccchHHHhhcCHHHhh
Q psy8861 373 DDLELTVRSANCLKAENIHCIGDLIQRSENELL 405 (550)
Q Consensus 373 ~~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~ 405 (550)
...+++..-..-|..+||.||.||...+.++|.
T Consensus 57 ri~gi~~~~a~LL~~AGv~Tv~~LA~~~p~~L~ 89 (122)
T PF14229_consen 57 RIPGIGPQYAELLEHAGVDTVEELAQRNPQNLH 89 (122)
T ss_pred hcCCCCHHHHHHHHHhCcCcHHHHHhCCHHHHH
Confidence 446778888889999999999999999998875
No 152
>PRK08609 hypothetical protein; Provisional
Probab=23.89 E-value=60 Score=37.20 Aligned_cols=51 Identities=22% Similarity=0.229 Sum_probs=39.7
Q ss_pred CCchhhhhhh-hccCccchHHHhhcCHH-HhhccCccccccHHHHHHHHHhcC
Q psy8861 376 ELTVRSANCL-KAENIHCIGDLIQRSEN-ELLRTPNLGRKSLNEIKEILASRG 426 (550)
Q Consensus 376 ~LsvRs~NcL-k~a~I~tv~dL~~~s~~-dL~~~~n~G~kSl~Ei~~~L~~~g 426 (550)
++..++..-| +..||.|+.||..-.++ .+..+++||.|+-+.|.+.++.+.
T Consensus 95 GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~~~~ 147 (570)
T PRK08609 95 GLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELG 147 (570)
T ss_pred CCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHHHHh
Confidence 4455555555 47899999999976654 478999999999999988887553
No 153
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=23.36 E-value=75 Score=33.92 Aligned_cols=58 Identities=31% Similarity=0.361 Sum_probs=46.6
Q ss_pred cCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHH----------HHHHhcCccccccc
Q psy8861 375 LELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIK----------EILASRGKYYMRHR 433 (550)
Q Consensus 375 L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~----------~~L~~~gl~lmrhr 433 (550)
++|...+.=+|+...+.-| |+-.-+.++|+++|++|.||..-|. +-|+++|..+.+-+
T Consensus 304 ~~lDPK~~wAl~~~d~FPV-dvn~A~~~~llRVPGiG~ksa~rIv~~Rr~~rl~~e~Lkk~GvvlkRak 371 (404)
T COG4277 304 PDLDPKTAWALKHMDRFPV-DVNKAPYKELLRVPGIGVKSARRIVMTRRRTRLTLEDLKKLGVVLKRAK 371 (404)
T ss_pred CCCChhhHHHHhccccccc-cccccCHHHhcccCCCChHHHHHHHHHhhhcccCHHHHhhhceeeeccc
Confidence 5566677788888888776 6777788999999999999999986 45777888776644
No 154
>PRK07440 hypothetical protein; Provisional
Probab=22.88 E-value=96 Score=25.45 Aligned_cols=25 Identities=24% Similarity=0.429 Sum_probs=20.5
Q ss_pred cEEECcEEecc---CCcccCCCCEEEEc
Q psy8861 123 AFLVNKKIVNI---ASYKIKPGDIISVR 147 (550)
Q Consensus 123 ~V~VNg~~v~~---ps~~vk~gDiI~v~ 147 (550)
-|-+||..|.+ +++.|+.||.|+|-
T Consensus 37 av~~N~~iv~r~~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 37 AVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70)
T ss_pred EEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 36799999964 77889999999873
No 155
>KOG1919|consensus
Probab=22.17 E-value=1.1e+02 Score=33.29 Aligned_cols=46 Identities=24% Similarity=0.237 Sum_probs=35.9
Q ss_pred hhHHHHHcCCCCCHHHHHHHHHcCcEEECcEEeccCCcccCCCCEEEE
Q psy8861 99 FDNVVYRMGFSSTRSEARQLISHRAFLVNKKIVNIASYKIKPGDIISV 146 (550)
Q Consensus 99 LD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~~v~~ps~~vk~gDiI~v 146 (550)
+|.++.+.. ...+.-.+..|++|.|.|||..+. .++.++.||.+..
T Consensus 47 ~~~~~~ef~-~~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~ 92 (371)
T KOG1919|consen 47 VDVFVSEFR-LRERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCH 92 (371)
T ss_pred HHHHHHHHh-cCchHhhhhhhhcCceEECcEeee-eEEEeccCCEEEE
Confidence 444444332 445555789999999999999997 9999999999885
No 156
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.95 E-value=88 Score=29.60 Aligned_cols=35 Identities=17% Similarity=0.271 Sum_probs=30.4
Q ss_pred HHhhhhhHHHHHcCCCCCHHHHHHHHHcCcEEECcE
Q psy8861 94 LLESRFDNVVYRMGFSSTRSEARQLISHRAFLVNKK 129 (550)
Q Consensus 94 ~LE~RLD~~l~r~gfa~Sr~~ArqlI~hG~V~VNg~ 129 (550)
-+..|||.+| +.++.-||++-++|+..|.|..+..
T Consensus 100 ~~~~Rld~lL-a~~L~lSrs~l~~l~~~G~I~~~~~ 134 (142)
T PF06353_consen 100 PFPLRLDRLL-ARQLGLSRSRLKRLIEQGLIRSDPD 134 (142)
T ss_pred CCCccHHHHH-HHHhCcCHHHHHHHHHCCCEEecCc
Confidence 4668999998 6889999999999999999987643
No 157
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=21.37 E-value=1.6e+02 Score=31.72 Aligned_cols=51 Identities=18% Similarity=0.229 Sum_probs=37.4
Q ss_pred ccccccCC-chhhh-hhhhccCccchHHHhhc--CHHHhhccCccccccHHHHHHHH
Q psy8861 370 RPVDDLEL-TVRSA-NCLKAENIHCIGDLIQR--SENELLRTPNLGRKSLNEIKEIL 422 (550)
Q Consensus 370 ~~I~~L~L-svRs~-NcLk~a~I~tv~dL~~~--s~~dL~~~~n~G~kSl~Ei~~~L 422 (550)
+||++|-. .-++. -.|.+.||+|++||..+ +.++|.+ -||.+..+.+.+.+
T Consensus 182 lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~--~fG~~~g~~l~~~a 236 (359)
T cd01702 182 LPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQE--HFGEKLGEWLYNLL 236 (359)
T ss_pred CcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHH--HHHHHHHHHHHHHh
Confidence 57777754 43553 44689999999999999 8988876 47876667776554
No 158
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=20.80 E-value=1e+02 Score=24.16 Aligned_cols=45 Identities=29% Similarity=0.478 Sum_probs=32.9
Q ss_pred ccCCchhhhhhhhccCccchHHHhhcCHHHhhccCccccccHHHHHHHH
Q psy8861 374 DLELTVRSANCLKAENIHCIGDLIQRSENELLRTPNLGRKSLNEIKEIL 422 (550)
Q Consensus 374 ~L~LsvRs~NcLk~a~I~tv~dL~~~s~~dL~~~~n~G~kSl~Ei~~~L 422 (550)
.++| -.-...++..||+.+..|+.+|++||. .+|-.+...-...|
T Consensus 15 ~~gl-~~y~~~f~~~~i~g~~~L~~l~~~~L~---~lGI~~~~~r~kll 59 (66)
T PF07647_consen 15 SLGL-EQYADNFRENGIDGLEDLLQLTEEDLK---ELGITNLGHRRKLL 59 (66)
T ss_dssp HTTC-GGGHHHHHHTTCSHHHHHTTSCHHHHH---HTTTTHHHHHHHHH
T ss_pred HCCc-HHHHHHHHHcCCcHHHHHhhCCHHHHH---HcCCCCHHHHHHHH
Confidence 4555 334467899999999999999999984 67766666544433
Done!