Query psy3263
Match_columns 329
No_of_seqs 374 out of 2369
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 20:34:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3263.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3263hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2113|consensus 100.0 3.1E-32 6.6E-37 252.6 11.3 289 4-303 36-391 (394)
2 KOG1676|consensus 99.9 1.9E-23 4.1E-28 208.5 11.9 139 4-151 240-388 (600)
3 KOG1676|consensus 99.9 3.3E-22 7.2E-27 199.6 13.0 147 3-156 148-304 (600)
4 KOG2191|consensus 99.9 8.3E-22 1.8E-26 184.6 11.2 130 4-140 49-191 (402)
5 KOG2193|consensus 99.8 5.2E-19 1.1E-23 170.3 6.9 142 4-161 209-361 (584)
6 KOG2193|consensus 99.7 1.1E-18 2.4E-23 168.0 5.8 137 3-140 289-468 (584)
7 KOG2190|consensus 99.7 2.5E-17 5.3E-22 165.7 11.0 125 5-140 54-195 (485)
8 TIGR03665 arCOG04150 arCOG0415 99.7 1.4E-16 3.1E-21 140.6 8.9 128 4-150 8-149 (172)
9 PRK13763 putative RNA-processi 99.6 2.3E-15 5E-20 133.9 9.2 124 5-147 14-152 (180)
10 KOG2192|consensus 99.6 8.5E-15 1.9E-19 134.5 9.4 142 4-146 133-377 (390)
11 KOG2192|consensus 99.6 1.5E-14 3.3E-19 132.8 11.0 128 5-151 59-192 (390)
12 KOG2113|consensus 99.3 9E-13 2E-17 123.4 4.8 160 81-305 21-189 (394)
13 KOG2190|consensus 99.2 4.3E-11 9.2E-16 120.9 11.7 131 4-134 148-304 (485)
14 cd02396 PCBP_like_KH K homolog 99.2 2.1E-11 4.6E-16 90.6 6.1 51 4-54 10-64 (65)
15 cd02394 vigilin_like_KH K homo 99.2 1.6E-11 3.4E-16 90.2 5.0 52 4-55 10-62 (62)
16 cd02396 PCBP_like_KH K homolog 99.2 1.9E-11 4E-16 90.9 3.8 54 87-141 1-58 (65)
17 cd02393 PNPase_KH Polynucleoti 99.2 7E-11 1.5E-15 87.0 6.4 48 4-54 12-60 (61)
18 cd02394 vigilin_like_KH K homo 99.1 2.6E-11 5.6E-16 89.0 3.5 54 87-141 1-55 (62)
19 PF00013 KH_1: KH domain syndr 99.1 3.5E-11 7.7E-16 87.7 3.1 51 4-54 10-60 (60)
20 PF13920 zf-C3HC4_3: Zinc fing 99.1 3.1E-11 6.8E-16 85.1 2.2 48 253-300 2-49 (50)
21 PF00013 KH_1: KH domain syndr 99.1 1.6E-11 3.6E-16 89.4 -0.1 54 87-141 1-54 (60)
22 PF13014 KH_3: KH domain 99.1 1.7E-10 3.7E-15 78.8 4.7 39 4-42 1-43 (43)
23 KOG2191|consensus 99.1 1.7E-10 3.7E-15 109.0 6.2 121 5-125 143-283 (402)
24 cd02393 PNPase_KH Polynucleoti 99.1 1.6E-10 3.5E-15 85.1 4.4 54 86-142 2-55 (61)
25 KOG4172|consensus 99.0 2.1E-11 4.5E-16 86.3 -0.9 53 254-306 8-61 (62)
26 PF13014 KH_3: KH domain 99.0 3.9E-10 8.4E-15 77.1 4.6 39 96-134 1-43 (43)
27 cd00105 KH-I K homology RNA-bi 99.0 3.3E-10 7.2E-15 82.9 4.2 52 88-140 2-56 (64)
28 cd00105 KH-I K homology RNA-bi 99.0 9.5E-10 2.1E-14 80.5 6.6 52 3-54 9-63 (64)
29 PF15227 zf-C3HC4_4: zinc fing 98.9 5.8E-10 1.2E-14 76.1 2.9 38 256-294 1-42 (42)
30 KOG4265|consensus 98.9 6.4E-10 1.4E-14 106.6 2.1 58 251-308 288-345 (349)
31 KOG0317|consensus 98.8 2.8E-09 6E-14 99.5 2.8 51 250-301 236-286 (293)
32 cd02395 SF1_like-KH Splicing f 98.8 1.8E-08 4E-13 84.0 7.2 58 2-59 14-94 (120)
33 KOG0823|consensus 98.8 2.8E-09 6E-14 96.8 2.5 49 251-300 45-96 (230)
34 smart00322 KH K homology RNA-b 98.8 2.8E-08 6.1E-13 72.3 7.1 55 4-58 13-68 (69)
35 smart00322 KH K homology RNA-b 98.7 1.4E-08 3.1E-13 73.9 5.2 63 86-149 3-67 (69)
36 PF13923 zf-C3HC4_2: Zinc fing 98.7 4.2E-09 9.2E-14 70.4 2.1 38 256-294 1-39 (39)
37 PLN03208 E3 ubiquitin-protein 98.7 6.4E-09 1.4E-13 92.7 3.8 49 251-300 16-80 (193)
38 TIGR00599 rad18 DNA repair pro 98.7 1.2E-08 2.6E-13 100.6 3.0 52 248-300 21-72 (397)
39 PHA02929 N1R/p28-like protein; 98.6 1.5E-08 3.2E-13 93.8 3.2 50 252-302 173-230 (238)
40 PF13639 zf-RING_2: Ring finge 98.6 1.1E-08 2.4E-13 70.0 0.9 40 255-295 2-44 (44)
41 KOG0287|consensus 98.6 1.1E-08 2.4E-13 97.1 0.8 66 250-318 20-85 (442)
42 TIGR03665 arCOG04150 arCOG0415 98.5 1.4E-07 3E-12 83.5 5.9 52 4-59 99-150 (172)
43 smart00504 Ubox Modified RING 98.5 6.5E-08 1.4E-12 70.7 3.2 46 253-299 1-46 (63)
44 KOG0320|consensus 98.5 3.5E-08 7.6E-13 86.3 1.7 49 251-300 129-179 (187)
45 PRK13763 putative RNA-processi 98.5 2E-07 4.3E-12 83.1 6.0 52 4-59 105-156 (180)
46 PF00097 zf-C3HC4: Zinc finger 98.5 7.4E-08 1.6E-12 64.7 2.1 38 256-294 1-41 (41)
47 KOG2279|consensus 98.4 8.6E-08 1.9E-12 96.1 2.3 118 4-144 78-200 (608)
48 cd00162 RING RING-finger (Real 98.4 1.5E-07 3.3E-12 63.0 2.8 43 255-298 1-45 (45)
49 PHA02926 zinc finger-like prot 98.4 1.9E-07 4.1E-12 84.6 2.3 51 251-302 168-233 (242)
50 PF14634 zf-RING_5: zinc-RING 98.3 3.8E-07 8.2E-12 62.6 3.0 41 255-296 1-44 (44)
51 smart00184 RING Ring finger. E 98.3 5E-07 1.1E-11 58.4 2.8 38 256-294 1-39 (39)
52 KOG2208|consensus 98.2 1.8E-06 3.9E-11 92.0 7.1 115 4-140 357-475 (753)
53 COG5432 RAD18 RING-finger-cont 98.2 4.8E-07 1E-11 84.7 1.8 50 250-300 22-71 (391)
54 PF13445 zf-RING_UBOX: RING-ty 98.2 3.6E-07 7.7E-12 62.6 0.7 30 256-287 1-34 (43)
55 KOG1571|consensus 98.2 5.8E-07 1.3E-11 86.5 2.3 53 250-306 302-354 (355)
56 KOG2177|consensus 98.2 4.7E-07 1E-11 83.2 1.6 47 249-296 9-55 (386)
57 KOG4275|consensus 98.2 2E-07 4.4E-12 87.1 -1.1 52 251-306 298-349 (350)
58 PRK08406 transcription elongat 98.2 2E-06 4.3E-11 73.7 5.0 93 4-121 42-134 (140)
59 PF04564 U-box: U-box domain; 98.1 1.8E-06 3.8E-11 65.7 3.0 48 252-300 3-51 (73)
60 COG1094 Predicted RNA-binding 98.1 2.1E-05 4.6E-10 70.2 10.3 121 5-144 19-155 (194)
61 KOG2164|consensus 98.1 1E-06 2.2E-11 88.2 1.6 54 253-307 186-246 (513)
62 cd02395 SF1_like-KH Splicing f 98.1 3.1E-06 6.7E-11 70.6 3.6 58 94-151 14-94 (120)
63 COG5574 PEX10 RING-finger-cont 98.1 1.7E-06 3.6E-11 80.2 2.0 48 251-299 213-262 (271)
64 PF12678 zf-rbx1: RING-H2 zinc 98.0 4.7E-06 1E-10 63.5 3.2 41 254-295 20-73 (73)
65 KOG0978|consensus 98.0 1.4E-06 3E-11 90.8 -0.4 49 250-299 640-689 (698)
66 KOG0119|consensus 97.9 2.1E-05 4.6E-10 78.4 7.4 58 2-59 152-229 (554)
67 PF14835 zf-RING_6: zf-RING of 97.9 3.3E-06 7.1E-11 62.3 0.5 45 251-298 5-50 (65)
68 COG5243 HRD1 HRD ubiquitin lig 97.9 6.5E-06 1.4E-10 79.5 2.2 47 251-298 285-344 (491)
69 KOG0824|consensus 97.8 7.6E-06 1.6E-10 77.1 2.1 50 252-302 6-56 (324)
70 TIGR00570 cdk7 CDK-activating 97.8 1.3E-05 2.9E-10 76.5 3.4 47 253-300 3-55 (309)
71 KOG0311|consensus 97.7 2.6E-06 5.6E-11 81.8 -2.8 52 249-301 39-92 (381)
72 TIGR01952 nusA_arch NusA famil 97.7 3.1E-05 6.7E-10 66.4 3.9 93 4-121 43-135 (141)
73 KOG0336|consensus 97.7 8.2E-05 1.8E-09 73.4 7.1 57 3-59 56-112 (629)
74 TIGR02696 pppGpp_PNP guanosine 97.7 7.3E-05 1.6E-09 78.9 7.1 62 86-150 578-640 (719)
75 KOG1588|consensus 97.7 7.8E-05 1.7E-09 69.4 6.5 32 2-33 106-137 (259)
76 KOG4159|consensus 97.7 1.7E-05 3.7E-10 78.6 2.0 50 250-300 81-130 (398)
77 KOG1785|consensus 97.7 1.4E-05 3.1E-10 77.8 1.3 55 254-309 370-426 (563)
78 KOG0802|consensus 97.7 1.3E-05 2.8E-10 82.8 0.9 47 251-298 289-340 (543)
79 KOG1100|consensus 97.6 2.4E-05 5.3E-10 71.2 1.0 48 254-305 159-206 (207)
80 COG5540 RING-finger-containing 97.5 3.8E-05 8.3E-10 72.5 2.1 47 252-299 322-372 (374)
81 KOG4628|consensus 97.5 4E-05 8.7E-10 74.4 1.9 47 254-301 230-280 (348)
82 TIGR03591 polynuc_phos polyrib 97.4 0.00028 6.1E-09 74.9 6.2 61 86-149 551-612 (684)
83 COG1094 Predicted RNA-binding 97.4 0.00044 9.5E-09 61.9 6.4 51 5-59 113-163 (194)
84 KOG2208|consensus 97.4 0.00013 2.8E-09 78.0 3.6 136 4-140 211-401 (753)
85 KOG2879|consensus 97.3 0.00017 3.8E-09 67.3 3.8 49 250-299 236-287 (298)
86 KOG2814|consensus 97.3 0.00034 7.3E-09 67.0 5.6 56 4-59 67-124 (345)
87 COG0195 NusA Transcription elo 97.2 0.00037 7.9E-09 62.7 4.3 94 4-123 86-179 (190)
88 KOG1588|consensus 97.2 0.0012 2.7E-08 61.5 7.4 40 84-123 90-135 (259)
89 KOG4692|consensus 97.1 0.0002 4.4E-09 68.9 1.9 50 250-300 419-468 (489)
90 KOG2279|consensus 97.1 0.00049 1.1E-08 69.7 4.6 136 4-140 150-355 (608)
91 PF12861 zf-Apc11: Anaphase-pr 97.1 0.0004 8.7E-09 54.3 3.0 31 268-299 49-82 (85)
92 TIGR02696 pppGpp_PNP guanosine 97.0 0.0011 2.4E-08 70.1 6.4 51 5-58 589-640 (719)
93 COG5152 Uncharacterized conser 97.0 0.00025 5.4E-09 63.4 0.9 47 253-300 196-242 (259)
94 TIGR03591 polynuc_phos polyrib 96.9 0.001 2.2E-08 70.6 5.4 52 5-58 562-613 (684)
95 KOG0336|consensus 96.9 0.00049 1.1E-08 68.0 2.1 51 84-134 45-95 (629)
96 COG5176 MSL5 Splicing factor ( 96.9 0.0014 3.1E-08 59.1 4.9 33 2-34 162-194 (269)
97 PRK12328 nusA transcription el 96.9 0.001 2.2E-08 65.4 4.2 92 5-123 253-345 (374)
98 PLN00207 polyribonucleotide nu 96.9 0.0012 2.6E-08 71.4 5.0 52 86-140 685-737 (891)
99 TIGR01953 NusA transcription t 96.8 0.0026 5.6E-08 62.2 6.7 93 5-123 245-338 (341)
100 cd02134 NusA_KH NusA_K homolog 96.8 0.0016 3.6E-08 47.7 4.0 37 85-121 24-60 (61)
101 COG5236 Uncharacterized conser 96.8 0.00095 2.1E-08 64.3 3.0 52 246-298 54-107 (493)
102 COG5222 Uncharacterized conser 96.8 0.00071 1.5E-08 64.0 2.1 43 254-297 275-319 (427)
103 PRK12327 nusA transcription el 96.7 0.0037 8E-08 61.6 6.9 95 5-125 247-342 (362)
104 KOG0297|consensus 96.7 0.00085 1.8E-08 66.8 2.4 56 249-305 17-73 (391)
105 KOG1813|consensus 96.7 0.00083 1.8E-08 63.5 1.8 46 254-300 242-287 (313)
106 KOG1039|consensus 96.6 0.0011 2.3E-08 64.8 2.0 51 251-302 159-224 (344)
107 PRK09202 nusA transcription el 96.6 0.0034 7.3E-08 63.9 5.6 93 5-124 247-340 (470)
108 KOG2660|consensus 96.5 0.00051 1.1E-08 65.8 -0.5 51 250-301 12-63 (331)
109 KOG0119|consensus 96.5 0.005 1.1E-07 61.9 6.1 57 84-140 136-217 (554)
110 COG5176 MSL5 Splicing factor ( 96.5 0.0054 1.2E-07 55.4 5.6 31 95-125 163-193 (269)
111 PRK12329 nusA transcription el 96.5 0.0056 1.2E-07 61.4 6.2 94 5-124 279-373 (449)
112 COG1185 Pnp Polyribonucleotide 96.3 0.006 1.3E-07 63.7 5.7 52 86-140 552-603 (692)
113 KOG0828|consensus 96.2 0.0017 3.6E-08 65.2 1.1 49 250-299 568-634 (636)
114 PRK11824 polynucleotide phosph 96.2 0.0052 1.1E-07 65.5 4.6 62 86-150 554-616 (693)
115 KOG0804|consensus 96.2 0.0029 6.3E-08 62.9 2.5 47 250-299 172-222 (493)
116 PRK12704 phosphodiesterase; Pr 96.0 0.018 3.9E-07 59.5 7.3 53 85-139 209-262 (520)
117 PF14447 Prok-RING_4: Prokaryo 95.9 0.0043 9.3E-08 44.5 1.6 47 251-300 5-51 (55)
118 PRK00468 hypothetical protein; 95.7 0.012 2.7E-07 45.0 3.5 31 85-115 29-59 (75)
119 PRK02821 hypothetical protein; 95.7 0.012 2.7E-07 45.2 3.4 33 85-117 30-62 (77)
120 PRK12704 phosphodiesterase; Pr 95.6 0.022 4.8E-07 58.8 6.1 54 4-59 221-275 (520)
121 KOG4367|consensus 95.6 0.0073 1.6E-07 59.9 2.4 37 250-287 1-37 (699)
122 PF14570 zf-RING_4: RING/Ubox 95.6 0.0061 1.3E-07 42.6 1.4 42 256-298 1-47 (48)
123 PLN00207 polyribonucleotide nu 95.4 0.014 2.9E-07 63.4 4.0 51 5-58 696-748 (891)
124 cd02134 NusA_KH NusA_K homolog 95.4 0.016 3.4E-07 42.5 3.0 25 5-29 36-60 (61)
125 KOG2814|consensus 95.4 0.0078 1.7E-07 57.9 1.8 53 87-140 58-111 (345)
126 KOG1734|consensus 95.3 0.0092 2E-07 55.9 2.0 49 251-300 222-282 (328)
127 TIGR03319 YmdA_YtgF conserved 95.3 0.041 8.9E-07 56.8 6.7 58 85-144 203-261 (514)
128 KOG3002|consensus 95.3 0.013 2.7E-07 56.4 2.8 63 247-315 42-106 (299)
129 KOG0825|consensus 95.2 0.0039 8.5E-08 65.6 -1.0 51 251-302 121-174 (1134)
130 PF11789 zf-Nse: Zinc-finger o 95.2 0.015 3.2E-07 42.2 2.3 41 252-293 10-53 (57)
131 COG1185 Pnp Polyribonucleotide 95.1 0.034 7.4E-07 58.3 5.7 52 5-59 563-615 (692)
132 KOG1002|consensus 95.1 0.0063 1.4E-07 61.7 0.2 47 251-298 534-585 (791)
133 COG1837 Predicted RNA-binding 95.1 0.027 5.8E-07 43.3 3.5 31 84-114 28-58 (76)
134 PRK00106 hypothetical protein; 95.0 0.055 1.2E-06 55.9 6.9 58 85-144 224-282 (535)
135 PF14611 SLS: Mitochondrial in 94.9 0.25 5.4E-06 44.6 10.2 101 6-134 38-142 (210)
136 PRK01064 hypothetical protein; 94.8 0.038 8.2E-07 42.7 3.9 32 84-115 28-59 (78)
137 TIGR03319 YmdA_YtgF conserved 94.8 0.052 1.1E-06 56.0 5.9 54 4-59 215-269 (514)
138 PRK11824 polynucleotide phosph 94.7 0.028 6.2E-07 59.9 4.0 51 5-58 565-616 (693)
139 smart00744 RINGv The RING-vari 94.7 0.022 4.8E-07 40.0 2.1 40 255-295 1-49 (49)
140 PRK00106 hypothetical protein; 94.6 0.067 1.4E-06 55.3 6.1 54 4-59 236-290 (535)
141 PRK04163 exosome complex RNA-b 94.6 0.024 5.2E-07 52.6 2.6 50 88-140 147-196 (235)
142 KOG1001|consensus 94.5 0.015 3.3E-07 61.6 1.4 45 254-300 455-501 (674)
143 KOG0827|consensus 94.4 0.02 4.3E-07 56.2 1.6 44 254-298 5-55 (465)
144 PRK04163 exosome complex RNA-b 94.2 0.073 1.6E-06 49.4 4.9 53 4-59 155-208 (235)
145 KOG3039|consensus 94.2 0.034 7.5E-07 51.5 2.6 48 252-300 220-271 (303)
146 KOG3800|consensus 94.0 0.029 6.4E-07 53.1 1.9 43 255-298 2-50 (300)
147 PRK00468 hypothetical protein; 93.8 0.034 7.3E-07 42.6 1.6 19 5-23 41-59 (75)
148 cd02410 archeal_CPSF_KH The ar 93.8 0.1 2.2E-06 44.9 4.6 85 11-121 23-111 (145)
149 COG5219 Uncharacterized conser 93.7 0.021 4.5E-07 61.5 0.3 49 250-299 1466-1523(1525)
150 PRK02821 hypothetical protein; 93.6 0.038 8.2E-07 42.6 1.5 21 5-25 42-62 (77)
151 PF04641 Rtf2: Rtf2 RING-finge 93.5 0.049 1.1E-06 51.3 2.4 50 250-301 110-163 (260)
152 PF03854 zf-P11: P-11 zinc fin 93.5 0.043 9.4E-07 38.2 1.5 46 255-302 4-49 (50)
153 KOG1645|consensus 93.4 0.044 9.5E-07 54.1 2.1 47 252-299 3-56 (463)
154 cd02409 KH-II KH-II (K homolo 93.4 0.13 2.8E-06 37.1 4.1 34 86-119 25-58 (68)
155 PRK08406 transcription elongat 93.3 0.088 1.9E-06 45.1 3.6 38 86-123 32-69 (140)
156 PF13083 KH_4: KH domain; PDB: 93.3 0.04 8.6E-07 41.5 1.2 35 85-119 28-62 (73)
157 COG5175 MOT2 Transcriptional r 93.2 0.042 9.1E-07 53.1 1.4 48 252-300 13-65 (480)
158 KOG4739|consensus 93.0 0.045 9.7E-07 50.6 1.3 41 255-298 5-47 (233)
159 COG1837 Predicted RNA-binding 92.9 0.056 1.2E-06 41.5 1.5 18 5-22 41-58 (76)
160 PF11793 FANCL_C: FANCL C-term 92.8 0.04 8.6E-07 41.5 0.6 46 253-299 2-66 (70)
161 PRK12705 hypothetical protein; 92.1 0.15 3.2E-06 52.6 3.8 52 4-57 209-261 (508)
162 KOG4185|consensus 91.9 0.11 2.4E-06 49.4 2.6 44 254-298 4-54 (296)
163 KOG0826|consensus 91.9 0.089 1.9E-06 50.7 1.9 47 251-298 298-345 (357)
164 KOG3273|consensus 91.7 0.078 1.7E-06 47.9 1.1 50 5-58 180-229 (252)
165 PRK01064 hypothetical protein; 91.7 0.11 2.3E-06 40.2 1.8 19 5-23 41-59 (78)
166 cd02409 KH-II KH-II (K homolo 91.5 0.13 2.7E-06 37.1 2.0 23 5-27 36-58 (68)
167 KOG1814|consensus 91.2 0.078 1.7E-06 52.5 0.7 34 251-285 182-218 (445)
168 PRK12705 hypothetical protein; 91.1 0.41 8.9E-06 49.3 5.8 54 85-140 197-251 (508)
169 PF07800 DUF1644: Protein of u 91.0 0.18 3.9E-06 43.9 2.6 20 252-271 1-20 (162)
170 PF13184 KH_5: NusA-like KH do 91.0 0.077 1.7E-06 40.0 0.4 28 5-32 19-47 (69)
171 COG5194 APC11 Component of SCF 90.9 0.19 4.2E-06 38.8 2.4 31 268-299 51-81 (88)
172 cd02414 jag_KH jag_K homology 90.8 0.19 4E-06 38.4 2.4 38 86-123 24-61 (77)
173 PF07650 KH_2: KH domain syndr 90.8 0.087 1.9E-06 40.0 0.5 35 86-120 25-59 (78)
174 KOG2932|consensus 90.7 0.094 2E-06 50.2 0.8 43 255-300 92-135 (389)
175 PF05290 Baculo_IE-1: Baculovi 90.7 0.13 2.7E-06 43.6 1.4 48 253-301 80-134 (140)
176 PF13184 KH_5: NusA-like KH do 90.3 0.19 4.2E-06 37.8 2.0 34 89-122 6-45 (69)
177 COG1855 ATPase (PilT family) [ 89.9 0.21 4.6E-06 50.5 2.5 43 84-126 484-526 (604)
178 COG5220 TFB3 Cdk activating ki 89.7 0.1 2.2E-06 48.3 0.1 46 252-298 9-63 (314)
179 TIGR01952 nusA_arch NusA famil 89.3 0.42 9E-06 41.1 3.5 36 87-122 34-69 (141)
180 KOG4362|consensus 89.3 0.098 2.1E-06 55.1 -0.4 48 251-299 19-69 (684)
181 cd02413 40S_S3_KH K homology R 88.6 0.51 1.1E-05 36.6 3.3 36 86-121 30-65 (81)
182 PHA02825 LAP/PHD finger-like p 88.2 0.43 9.4E-06 41.6 2.9 48 250-298 5-58 (162)
183 COG1782 Predicted metal-depend 88.1 0.85 1.8E-05 46.7 5.3 92 8-121 43-134 (637)
184 KOG3579|consensus 88.0 0.38 8.3E-06 45.6 2.6 45 253-298 268-327 (352)
185 PRK13764 ATPase; Provisional 87.8 0.35 7.5E-06 50.9 2.5 43 84-126 479-521 (602)
186 KOG4369|consensus 87.7 0.24 5.2E-06 54.8 1.2 53 5-57 1351-1407(2131)
187 PF13083 KH_4: KH domain; PDB: 86.9 0.14 3.1E-06 38.4 -0.7 23 5-27 40-62 (73)
188 KOG4369|consensus 86.8 0.3 6.4E-06 54.1 1.3 61 86-147 1340-1404(2131)
189 KOG1493|consensus 86.4 0.24 5.2E-06 38.0 0.3 29 270-299 50-81 (84)
190 cd02414 jag_KH jag_K homology 86.3 0.34 7.4E-06 36.9 1.1 26 5-30 35-60 (77)
191 KOG1428|consensus 86.2 0.37 8E-06 54.5 1.6 50 251-301 3484-3546(3738)
192 PF07650 KH_2: KH domain syndr 85.0 0.29 6.3E-06 37.1 0.1 23 6-28 37-59 (78)
193 PF10272 Tmpp129: Putative tra 84.9 0.92 2E-05 44.7 3.6 24 276-299 315-351 (358)
194 cd02412 30S_S3_KH K homology R 84.7 0.8 1.7E-05 37.4 2.6 32 87-118 62-93 (109)
195 PF10367 Vps39_2: Vacuolar sor 84.7 0.46 1E-05 37.7 1.2 33 250-283 75-109 (109)
196 PHA03096 p28-like protein; Pro 84.6 0.47 1E-05 45.4 1.4 42 254-296 179-231 (284)
197 cd02413 40S_S3_KH K homology R 84.3 0.61 1.3E-05 36.2 1.6 26 5-30 41-66 (81)
198 PRK06418 transcription elongat 84.0 1.1 2.4E-05 39.5 3.4 36 86-122 61-96 (166)
199 PRK06418 transcription elongat 83.7 0.84 1.8E-05 40.2 2.5 26 6-31 72-97 (166)
200 KOG2930|consensus 83.7 0.54 1.2E-05 38.1 1.2 29 268-297 78-106 (114)
201 KOG2874|consensus 83.6 1.8 3.8E-05 41.2 4.7 47 7-57 162-208 (356)
202 KOG3161|consensus 82.8 0.51 1.1E-05 49.3 0.9 43 251-297 9-55 (861)
203 PHA02862 5L protein; Provision 82.7 0.92 2E-05 39.0 2.2 44 254-298 3-52 (156)
204 PF02891 zf-MIZ: MIZ/SP-RING z 81.6 0.6 1.3E-05 32.8 0.6 43 254-297 3-50 (50)
205 TIGR03675 arCOG00543 arCOG0054 81.1 2.5 5.4E-05 44.9 5.3 36 86-121 93-128 (630)
206 cd02411 archeal_30S_S3_KH K ho 80.4 1.8 3.9E-05 33.6 3.0 29 88-116 40-68 (85)
207 KOG1067|consensus 80.2 1.8 3.9E-05 44.9 3.6 51 86-140 597-647 (760)
208 KOG4445|consensus 80.0 0.34 7.5E-06 46.3 -1.4 46 252-298 114-185 (368)
209 PF05883 Baculo_RING: Baculovi 78.5 1 2.3E-05 38.2 1.2 34 253-286 26-67 (134)
210 COG1097 RRP4 RNA-binding prote 76.7 3.9 8.4E-05 38.1 4.5 53 2-57 154-207 (239)
211 KOG2114|consensus 76.5 1.6 3.5E-05 47.1 2.1 48 254-305 841-889 (933)
212 KOG1941|consensus 76.0 0.85 1.9E-05 45.1 -0.0 45 252-297 364-414 (518)
213 COG0092 RpsC Ribosomal protein 75.8 2.5 5.4E-05 39.2 2.9 64 86-155 51-115 (233)
214 cd02411 archeal_30S_S3_KH K ho 75.1 2 4.3E-05 33.4 1.9 20 5-24 49-68 (85)
215 KOG1423|consensus 74.8 8.9 0.00019 37.4 6.5 32 85-116 327-359 (379)
216 TIGR00436 era GTP-binding prot 73.7 3.6 7.9E-05 38.4 3.6 29 87-115 222-251 (270)
217 KOG2817|consensus 73.3 2.4 5.2E-05 42.1 2.3 48 250-298 331-384 (394)
218 COG1097 RRP4 RNA-binding prote 71.2 4.1 9E-05 37.9 3.3 48 88-139 148-195 (239)
219 cd02412 30S_S3_KH K homology R 71.2 2.4 5.1E-05 34.6 1.5 23 5-27 72-94 (109)
220 KOG1940|consensus 70.0 2.4 5.3E-05 40.3 1.5 50 254-305 159-212 (276)
221 KOG1812|consensus 69.4 1.8 3.8E-05 43.2 0.5 40 253-293 146-195 (384)
222 PRK15494 era GTPase Era; Provi 69.2 5.2 0.00011 39.0 3.6 28 88-115 275-303 (339)
223 COG0092 RpsC Ribosomal protein 68.8 3 6.4E-05 38.7 1.8 21 6-26 63-83 (233)
224 COG0195 NusA Transcription elo 68.2 4.6 0.0001 36.4 2.8 32 91-122 81-112 (190)
225 PRK13764 ATPase; Provisional 68.0 2.5 5.4E-05 44.6 1.3 31 5-35 492-522 (602)
226 PRK00089 era GTPase Era; Revie 66.9 6.1 0.00013 37.1 3.6 28 88-115 228-256 (292)
227 COG1855 ATPase (PilT family) [ 66.8 2.7 5.8E-05 42.9 1.1 31 4-34 496-526 (604)
228 PF14611 SLS: Mitochondrial in 65.9 12 0.00027 33.5 5.2 62 87-151 27-89 (210)
229 KOG2231|consensus 65.9 3.6 7.9E-05 43.7 1.9 46 255-300 2-53 (669)
230 COG1159 Era GTPase [General fu 65.8 5.8 0.00013 38.2 3.1 28 88-115 231-259 (298)
231 COG5166 Uncharacterized conser 65.3 6.1 0.00013 40.7 3.3 38 86-123 449-486 (657)
232 KOG0825|consensus 64.8 2.6 5.6E-05 45.3 0.6 34 270-304 120-159 (1134)
233 cd02410 archeal_CPSF_KH The ar 64.7 6.7 0.00015 33.8 3.0 25 5-29 87-111 (145)
234 KOG2068|consensus 64.2 4.9 0.00011 39.1 2.3 49 252-301 248-300 (327)
235 KOG0298|consensus 63.2 1.9 4.1E-05 48.5 -0.8 48 250-298 1150-1198(1394)
236 CHL00048 rps3 ribosomal protei 62.5 7.6 0.00016 35.6 3.2 66 86-155 66-132 (214)
237 KOG1067|consensus 62.2 4.1 8.9E-05 42.4 1.4 50 5-58 608-658 (760)
238 KOG3842|consensus 62.0 5 0.00011 38.9 1.9 47 251-299 339-414 (429)
239 KOG2874|consensus 60.4 9.2 0.0002 36.5 3.3 49 98-151 161-210 (356)
240 TIGR01008 rpsC_E_A ribosomal p 58.2 10 0.00022 34.3 3.2 64 87-156 39-103 (195)
241 PRK12329 nusA transcription el 58.2 14 0.00031 37.5 4.4 44 78-122 256-305 (449)
242 KOG3799|consensus 58.1 3.4 7.3E-05 35.2 0.0 44 250-298 62-117 (169)
243 PF07191 zinc-ribbons_6: zinc- 57.5 1.4 3E-05 33.4 -2.1 42 253-300 1-42 (70)
244 PF08746 zf-RING-like: RING-li 57.2 13 0.00027 25.2 2.8 38 256-294 1-43 (43)
245 PRK04191 rps3p 30S ribosomal p 56.9 11 0.00024 34.4 3.2 63 88-156 42-105 (207)
246 PTZ00084 40S ribosomal protein 56.4 11 0.00023 34.8 3.0 34 87-120 45-78 (220)
247 PF07975 C1_4: TFIIH C1-like d 55.9 15 0.00033 26.0 3.0 25 270-295 26-50 (51)
248 KOG3970|consensus 55.8 7.6 0.00016 35.9 1.9 45 253-298 50-104 (299)
249 PF12906 RINGv: RING-variant d 54.6 5.2 0.00011 27.6 0.5 39 256-294 1-47 (47)
250 COG1159 Era GTPase [General fu 54.2 8.9 0.00019 36.9 2.2 18 6-23 242-259 (298)
251 KOG0956|consensus 54.1 6.3 0.00014 41.9 1.2 29 269-298 44-72 (900)
252 KOG1815|consensus 52.2 7.5 0.00016 39.4 1.4 36 251-287 68-104 (444)
253 COG5183 SSM4 Protein involved 51.6 8.6 0.00019 41.6 1.8 48 251-298 10-65 (1175)
254 PF05605 zf-Di19: Drought indu 49.6 7.8 0.00017 27.3 0.8 39 253-299 2-42 (54)
255 PF04710 Pellino: Pellino; In 49.5 5.5 0.00012 39.7 0.0 46 253-300 328-402 (416)
256 PF09869 DUF2096: Uncharacteri 49.5 48 0.001 29.3 5.8 41 14-57 126-166 (169)
257 KOG1952|consensus 49.2 7.8 0.00017 42.1 1.1 46 251-297 189-245 (950)
258 KOG2034|consensus 49.0 8 0.00017 42.2 1.1 35 250-285 814-850 (911)
259 PF04216 FdhE: Protein involve 48.9 5.7 0.00012 37.8 -0.0 53 252-305 171-228 (290)
260 KOG3053|consensus 48.8 9.1 0.0002 36.1 1.3 52 248-299 15-82 (293)
261 KOG3268|consensus 48.5 8.5 0.00018 34.4 1.0 48 251-299 163-228 (234)
262 PF02749 QRPTase_N: Quinolinat 48.3 61 0.0013 25.0 5.8 48 14-61 34-87 (88)
263 PLN02189 cellulose synthase 48.1 12 0.00025 41.8 2.2 45 254-299 35-87 (1040)
264 PRK12328 nusA transcription el 47.8 13 0.00027 37.1 2.2 33 5-37 319-351 (374)
265 PRK12327 nusA transcription el 47.6 14 0.00031 36.6 2.5 28 95-122 245-273 (362)
266 KOG3039|consensus 46.3 14 0.00029 34.8 2.0 36 248-284 38-73 (303)
267 PF13240 zinc_ribbon_2: zinc-r 46.1 6.5 0.00014 23.1 -0.1 22 276-297 1-22 (23)
268 COG1847 Jag Predicted RNA-bind 45.6 11 0.00023 34.5 1.2 36 86-121 91-126 (208)
269 TIGR01953 NusA transcription t 45.1 17 0.00038 35.6 2.7 28 95-122 243-271 (341)
270 PRK04191 rps3p 30S ribosomal p 45.0 14 0.00031 33.6 2.0 22 5-26 51-72 (207)
271 TIGR01009 rpsC_bact ribosomal 43.2 22 0.00049 32.5 2.9 31 88-118 64-94 (211)
272 KOG2807|consensus 41.9 15 0.00033 35.7 1.7 44 252-296 329-375 (378)
273 KOG3899|consensus 41.4 12 0.00027 35.9 1.0 24 276-299 329-365 (381)
274 COG5109 Uncharacterized conser 40.4 17 0.00038 35.2 1.8 47 250-297 333-385 (396)
275 COG1702 PhoH Phosphate starvat 40.4 57 0.0012 32.1 5.4 45 7-55 28-72 (348)
276 PRK09202 nusA transcription el 40.1 14 0.00031 37.9 1.2 27 5-31 313-339 (470)
277 PF06937 EURL: EURL protein; 40.0 21 0.00045 33.9 2.2 39 254-298 31-78 (285)
278 CHL00048 rps3 ribosomal protei 39.8 20 0.00043 32.9 2.0 21 5-25 77-97 (214)
279 TIGR01008 rpsC_E_A ribosomal p 37.4 23 0.0005 32.0 2.1 21 5-25 49-69 (195)
280 PTZ00084 40S ribosomal protein 36.9 22 0.00048 32.8 1.9 23 5-27 55-77 (220)
281 PF14569 zf-UDP: Zinc-binding 36.8 23 0.0005 27.3 1.7 47 253-300 9-63 (80)
282 TIGR01562 FdhE formate dehydro 36.0 13 0.00029 35.9 0.3 46 251-297 182-233 (305)
283 PF10571 UPF0547: Uncharacteri 35.0 14 0.00031 22.4 0.2 21 277-297 3-23 (26)
284 PF02080 TrkA_C: TrkA-C domain 34.9 26 0.00057 25.2 1.7 42 13-54 14-70 (71)
285 TIGR03802 Asp_Ala_antiprt aspa 34.9 2.7E+02 0.0058 29.2 9.7 104 13-140 232-369 (562)
286 PF10146 zf-C4H2: Zinc finger- 34.0 23 0.0005 32.9 1.5 23 276-298 196-218 (230)
287 PRK03818 putative transporter; 33.3 1.2E+02 0.0026 31.8 6.8 105 13-140 218-352 (552)
288 PRK03564 formate dehydrogenase 33.2 19 0.00041 34.9 0.9 45 251-296 185-234 (309)
289 COG1782 Predicted metal-depend 32.9 29 0.00062 36.0 2.1 24 6-29 111-134 (637)
290 PLN02436 cellulose synthase A 32.7 26 0.00057 39.3 1.9 45 254-299 37-89 (1094)
291 COG1847 Jag Predicted RNA-bind 32.7 13 0.00028 33.9 -0.3 25 5-29 102-126 (208)
292 PRK00310 rpsC 30S ribosomal pr 32.7 38 0.00082 31.5 2.7 30 88-117 64-93 (232)
293 KOG3273|consensus 32.3 11 0.00023 34.4 -0.9 45 94-143 177-221 (252)
294 PF02318 FYVE_2: FYVE-type zin 31.6 8.4 0.00018 31.7 -1.6 44 252-296 53-102 (118)
295 KOG4185|consensus 31.4 12 0.00026 35.4 -0.9 43 254-297 208-265 (296)
296 COG3813 Uncharacterized protei 31.3 27 0.00058 26.6 1.2 21 276-298 31-51 (84)
297 KOG2169|consensus 30.7 23 0.00049 37.8 1.0 49 249-298 302-355 (636)
298 KOG3113|consensus 30.5 33 0.00072 32.4 1.9 50 252-304 110-163 (293)
299 PF09297 zf-NADH-PPase: NADH p 30.3 11 0.00023 23.7 -0.9 23 273-296 3-29 (32)
300 PF12773 DZR: Double zinc ribb 30.3 36 0.00078 23.2 1.7 24 276-299 14-40 (50)
301 KOG4621|consensus 27.2 18 0.00038 30.8 -0.4 29 251-279 79-107 (167)
302 PF10497 zf-4CXXC_R1: Zinc-fin 27.2 46 0.00099 27.0 2.0 25 272-297 37-70 (105)
303 TIGR03675 arCOG00543 arCOG0054 27.1 51 0.0011 35.1 2.9 26 5-30 104-129 (630)
304 KOG4451|consensus 27.1 33 0.00071 31.9 1.3 23 276-298 251-273 (286)
305 PF04423 Rad50_zn_hook: Rad50 26.4 24 0.00051 24.8 0.2 15 288-302 20-34 (54)
306 COG4010 Uncharacterized protei 26.1 1.8E+02 0.0039 25.3 5.4 42 14-58 126-167 (170)
307 TIGR00622 ssl1 transcription f 26.1 53 0.0012 27.1 2.2 41 254-295 56-110 (112)
308 COG5166 Uncharacterized conser 24.6 1.1E+02 0.0024 31.8 4.6 46 88-134 499-548 (657)
309 COG0331 FabD (acyl-carrier-pro 24.6 1.6E+02 0.0034 28.6 5.5 50 8-57 136-187 (310)
310 PF10235 Cript: Microtubule-as 23.5 37 0.0008 27.0 0.8 36 253-298 44-79 (90)
311 TIGR01009 rpsC_bact ribosomal 23.3 52 0.0011 30.1 1.8 20 5-24 73-92 (211)
312 PLN02638 cellulose synthase A 22.0 56 0.0012 36.8 2.1 45 254-299 18-70 (1079)
313 PF03958 Secretin_N: Bacterial 21.6 68 0.0015 23.8 1.9 26 32-57 51-76 (82)
314 PLN02400 cellulose synthase 21.2 55 0.0012 36.9 1.8 45 254-299 37-89 (1085)
315 PF13248 zf-ribbon_3: zinc-rib 21.2 32 0.00069 20.5 0.0 22 276-297 4-25 (26)
316 PF10217 DUF2039: Uncharacteri 20.8 31 0.00067 27.5 -0.1 39 250-297 52-90 (92)
No 1
>KOG2113|consensus
Probab=99.97 E-value=3.1e-32 Score=252.61 Aligned_cols=289 Identities=35% Similarity=0.374 Sum_probs=200.1
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
+|+.|+|+||++||.||+||++||+.|.++++++|.|+|.+|+|++|+++|.+.+|||...++.+...++.... ..+
T Consensus 36 ~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~~edv~~aRrei~saaeH~~l~~~s~s~Sgg~~~~---s~s 112 (394)
T KOG2113|consen 36 HVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGRHEDVRRARREIPSAAEHFGLIRASRSFSGGTNGA---SAS 112 (394)
T ss_pred cceeecccCccccchhhhhhcceeccCCCCCCCcceeccCchhHHHHhhcCccccceeeeeeecccccCCCccc---ccc
Confidence 69999999999999999999999999999999999999999999999999999999999999999888776542 357
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-------chhhhhh----hhhh-
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-------GFESHHG----QKIV- 151 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-------eie~~i~----d~~~- 151 (329)
++.+.++.+|.++||+++|.+|++||+||+.++.+|..|.++.++++.++| .|++| |||+++. |+|.
T Consensus 113 ~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg-~~~nC~kra~s~eie~ta~~ra~~i~d~ 191 (394)
T KOG2113|consen 113 GQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTG-APKNCVKRARSCEIEQTAVTRAGQIHDT 191 (394)
T ss_pred CCCceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEec-CCcchhhhccccchhhhhhhhhhccccC
Confidence 889999999999999999999999999999999999999999999999999 99996 8888776 3333
Q ss_pred ------hhhcCCCCCCcccc-------cccccccC-----ccCCCC-CCCCCCCCCCC---CCCCCCCCCCCCCcceecC
Q psy3263 152 ------FILTSNLYSFFDCR-------IFQRMNHH-----VFSGSS-GCSSASSSSSS---SACAPHSSTQLDLGSIWSG 209 (329)
Q Consensus 152 ------~~~~~~~~~~~~~~-------~~~~~~~~-----~~~~~~-~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~ 209 (329)
..-+-.+.=++... .||+.||- +..... +..+.+.||.. .+..+ -....+|..
T Consensus 192 dndf~~~la~v~l~v~~~~~a~~~~~~~~~~s~f~~~~~~n~~~~~~~~~sss~~~~~s~~~~~~~-----~~~~~~~~s 266 (394)
T KOG2113|consen 192 DNDFAGQLAGVSLMVQKQQQAQQQMQEAQQQSMFYRRAFGNSNPFNQKEMSSSPFGMESSLGLDAL-----LRSFPSMRS 266 (394)
T ss_pred CccccccccccchhhhhHHHHHHHHhhcCccchHHHhcccCCCccchhhccCCCcccccccccccc-----hhhhhhhhc
Confidence 22221111122111 22222331 000000 00011111110 00001 123445554
Q ss_pred CCCCCCCCCCCCCCCcCCC------CCCCCccccCCCC---------------------------CCCCCCCCCCCCccc
Q psy3263 210 MSSLDKDEGLGDSPSFDAS------PVNPSSIWSYPPV---------------------------SSTSPSGSISGSRQC 256 (329)
Q Consensus 210 ~~~~~~~~~~~~w~~~~~~------~~~~~~~~~~~~~---------------------------sp~~~~~~l~~~~~C 256 (329)
....+.++|.+++.+.... +.++...|..-+. .--.+++-|-..+.|
T Consensus 267 s~t~~~~~g~g~s~~~~~~~~~~~~~~~~~~~~~~~~s~~~i~~~e~~s~~~~~~~a~~~~~l~~~~~~~~~~~~s~~~~ 346 (394)
T KOG2113|consen 267 SLTPESLSGTGLSRPSLGGGQSAKQDLPTYDYWGTNNSLNDIMENEILSRKYDALSAWSSMGLEKREESPTNGLMSSLKG 346 (394)
T ss_pred cCCcccccccCCCccccCCccccccCCCcCCccccCcchhhhhhhhhhhhhcchhhccccccchhccccccccchhhccc
Confidence 3333445555444333222 1223333332110 001123445567899
Q ss_pred ccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchh
Q psy3263 257 YLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR 303 (329)
Q Consensus 257 ~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~ 303 (329)
.+|-+.....++.+|+|++||.+|+.. .....||+|.......++
T Consensus 347 ~~~~~~~~st~~~~~~~n~~~~~~a~~--s~~~~~~~c~~~~~~~~~ 391 (394)
T KOG2113|consen 347 TSAGFGLLSTIWSGGNMNLSPGSLASA--SASPTSSTCDHNDHTLVP 391 (394)
T ss_pred ccccCceeeeEeecCCcccChhhhhhc--ccCCccccccccceeeee
Confidence 999999999999999999999999982 236899999876654443
No 2
>KOG1676|consensus
Probab=99.90 E-value=1.9e-23 Score=208.46 Aligned_cols=139 Identities=23% Similarity=0.211 Sum_probs=115.8
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCC----cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE----EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPP 79 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~----ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p 79 (329)
-||.||||+||+||+|+.+|||||+|-++++ ||.+.|.|+++.|++|.++|.++++ .+.....++...++|
T Consensus 240 ~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~-----~~~~~~~~~~~~G~P 314 (600)
T KOG1676|consen 240 KVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIA-----EAEAGAGGGMGGGAP 314 (600)
T ss_pred ceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHH-----HHhccCCCCcCCCCc
Confidence 5999999999999999999999999976555 9999999999999999999999963 222233333333444
Q ss_pred CCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC-C----CCCeEEEECCCCCCcchhh-hhhhhhh
Q psy3263 80 TGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-D----KEPVFEVTGNFPEGPGFES-HHGQKIV 151 (329)
Q Consensus 80 ~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~-~----~e~~i~ItG~~pe~veie~-~i~d~~~ 151 (329)
.. ...+++.||..++|+||||||+|||.|.+++||++.++.. + +|++|+|+| .+.+|+++. +|++.+.
T Consensus 315 ~~---~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG-~~~QIdhAk~LIr~kvg 388 (600)
T KOG1676|consen 315 GL---VAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRG-DKRQIDHAKQLIRDKVG 388 (600)
T ss_pred cc---eeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEec-CcccchHHHHHHHHHhc
Confidence 22 1378999999999999999999999999999999999865 2 799999999 999998888 5556555
No 3
>KOG1676|consensus
Probab=99.88 E-value=3.3e-22 Score=199.64 Aligned_cols=147 Identities=22% Similarity=0.210 Sum_probs=119.3
Q ss_pred eeeeeeecCCChHHHHHHHHhCCeEEecCCCC-----cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCC
Q psy3263 3 IFVVPSINPFGCKIKALRAKTNTYIKTPVRGE-----EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS 77 (329)
Q Consensus 3 ~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-----ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~ 77 (329)
+-+|+||||+|||||+||+++|+++.+-.++. .+.+.|+|.++.|+.|+.++++++ ++......+..+.
T Consensus 148 ~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil------~e~~~~~~g~~~~ 221 (600)
T KOG1676|consen 148 NKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADIL------REEDDEVPGSGGH 221 (600)
T ss_pred cceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHH------HhcccCCCccccc
Confidence 35899999999999999999999999876554 456799999999999999999994 4333332222233
Q ss_pred CCCCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC----CCCeEEEECCCCCCcchhh-hhhhhhhh
Q psy3263 78 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGNFPEGPGFES-HHGQKIVF 152 (329)
Q Consensus 78 ~p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~----~e~~i~ItG~~pe~veie~-~i~d~~~~ 152 (329)
.....-++.+++|.||...||+||||+|++||+|+.+||++|+|-+++ .||.+.|.| +++.|+.++ +|.+++..
T Consensus 222 ~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG-~~d~ie~Aa~lI~eii~~ 300 (600)
T KOG1676|consen 222 AGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIG-TVDQIEHAAELINEIIAE 300 (600)
T ss_pred cCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeec-CHHHHHHHHHHHHHHHHH
Confidence 322334557999999999999999999999999999999999996655 599999999 999997777 77788875
Q ss_pred hhcC
Q psy3263 153 ILTS 156 (329)
Q Consensus 153 ~~~~ 156 (329)
.-++
T Consensus 301 ~~~~ 304 (600)
T KOG1676|consen 301 AEAG 304 (600)
T ss_pred Hhcc
Confidence 5444
No 4
>KOG2191|consensus
Probab=99.86 E-value=8.3e-22 Score=184.62 Aligned_cols=130 Identities=27% Similarity=0.325 Sum_probs=107.3
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCC------cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS 77 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~ 77 (329)
-+|.||||||++|.+||.+||++||+++..| ||++.|+|+.|++......|++.+ |+......+....
T Consensus 49 AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKi------re~p~~~~k~v~~ 122 (402)
T KOG2191|consen 49 AAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKI------REKPQAVAKPVDI 122 (402)
T ss_pred cccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHH------HHhHHhhcCCccc
Confidence 3799999999999999999999999997766 999999999999999999999984 4433333332211
Q ss_pred -CCCCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC-CC-----CCCeEEEECCCCCCc
Q psy3263 78 -PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS-RD-----KEPVFEVTGNFPEGP 140 (329)
Q Consensus 78 -~p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~-~~-----~e~~i~ItG~~pe~v 140 (329)
-|-..+....+.+.||+...|.||||||+|||.|+|++|++|+|.+ .+ .||+|++.| .+|+.
T Consensus 123 ~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sg-e~e~~ 191 (402)
T KOG2191|consen 123 LQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSG-EPEQN 191 (402)
T ss_pred cCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecC-CHHHH
Confidence 1212233356899999999999999999999999999999999974 33 699999999 99998
No 5
>KOG2193|consensus
Probab=99.76 E-value=5.2e-19 Score=170.28 Aligned_cols=142 Identities=22% Similarity=0.297 Sum_probs=120.9
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCC----cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE----EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPP 79 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~----ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p 79 (329)
|||.||||.|.|||.|-..|.++|++-..+. |+.++|-|++|...+|.++|++++. -.+...
T Consensus 209 yvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimq----kEA~~~---------- 274 (584)
T KOG2193|consen 209 YVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQ----KEAVDD---------- 274 (584)
T ss_pred eeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHH----Hhhhcc----------
Confidence 8999999999999999999999999974333 8999999999999999999999853 111111
Q ss_pred CCCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC------CCCeEEEECCCCCCc-chhhhhhhhhhh
Q psy3263 80 TGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGNFPEGP-GFESHHGQKIVF 152 (329)
Q Consensus 80 ~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~------~e~~i~ItG~~pe~v-eie~~i~d~~~~ 152 (329)
.....+.++++-.+.+||.+|||-|..||+|+++||++|.|.+-. .||+|+|.| .-|.| ..|+.|...+..
T Consensus 275 -k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkG-siEac~~AE~eImkKlre 352 (584)
T KOG2193|consen 275 -KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKG-SIEACVQAEAEIMKKLRE 352 (584)
T ss_pred -chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecc-cHHHHHHHHHHHHHHHHH
Confidence 112346678888999999999999999999999999999998633 599999999 88888 888899999999
Q ss_pred hhcCCCCCC
Q psy3263 153 ILTSNLYSF 161 (329)
Q Consensus 153 ~~~~~~~~~ 161 (329)
.||+++.++
T Consensus 353 ~yEnDl~a~ 361 (584)
T KOG2193|consen 353 CYENDLAAM 361 (584)
T ss_pred HHhhhHHHh
Confidence 999976654
No 6
>KOG2193|consensus
Probab=99.74 E-value=1.1e-18 Score=168.04 Aligned_cols=137 Identities=26% Similarity=0.356 Sum_probs=106.4
Q ss_pred eeeeeeecCCChHHHHHHHHhCCeEEecCCCC------cceEEEecCHHHHHHHHHHHHHHhh-hhh-HhhhcccCC---
Q psy3263 3 IFVVPSINPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILSAAD-HFS-ALRASRKSG--- 71 (329)
Q Consensus 3 ~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------ervi~ItG~~e~v~~A~~~I~~i~e-~~~-~~~~~~~~~--- 71 (329)
.|||+||||.|.+||+|+++|||+|.+.+--| ||.|+|.|..|+|.+|..+|...+. .|. .+++-.-.+
T Consensus 289 ~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~ 368 (584)
T KOG2193|consen 289 NLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLP 368 (584)
T ss_pred chhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCC
Confidence 58999999999999999999999999975443 9999999999999999999988753 111 122211111
Q ss_pred CC--------------C-CCC-CCC------------CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263 72 AL--------------S-PLS-PPT------------GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 123 (329)
Q Consensus 72 ~~--------------~-~~~-~p~------------~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~ 123 (329)
.+ . .++ +|. ..+.+.++++.||...||.|||++|..||+|...+||.|+|.+
T Consensus 369 P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIap 448 (584)
T KOG2193|consen 369 PGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAP 448 (584)
T ss_pred cccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecC
Confidence 00 0 000 110 1235678899999999999999999999999999999999976
Q ss_pred CC----CCCeEEEECCCCCCc
Q psy3263 124 RD----KEPVFEVTGNFPEGP 140 (329)
Q Consensus 124 ~~----~e~~i~ItG~~pe~v 140 (329)
.+ .+|.|+|+| .|+..
T Consensus 449 pE~pdvseRMViItG-ppeaq 468 (584)
T KOG2193|consen 449 PEIPDVSERMVIITG-PPEAQ 468 (584)
T ss_pred CCCCCcceeEEEecC-ChHHH
Confidence 44 789999999 88766
No 7
>KOG2190|consensus
Probab=99.72 E-value=2.5e-17 Score=165.71 Aligned_cols=125 Identities=24% Similarity=0.321 Sum_probs=101.6
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEec---CCCCcceEEEec---------CHHHHHHHHHHHHHHhhhhhHhhhcccCCC
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTP---VRGEEPVFVVTG---------RKEDVARAKREILSAADHFSALRASRKSGA 72 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip---~~~~ervi~ItG---------~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~ 72 (329)
||.||||+|..||+||.+|.++|++- +...||+|+|+| ..+++.+|.++|...++ .........+
T Consensus 54 vG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~---~d~~~~~d~~ 130 (485)
T KOG2190|consen 54 VGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLE---EDDEAAEDNG 130 (485)
T ss_pred ceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccc---ccccccccCC
Confidence 79999999999999998888888875 334499999999 99999999999987643 0001111111
Q ss_pred CCCCCCCCCCCC-ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC----CCCeEEEECCCCCCc
Q psy3263 73 LSPLSPPTGVPG-HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGNFPEGP 140 (329)
Q Consensus 73 ~~~~~~p~~~~g-~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~----~e~~i~ItG~~pe~v 140 (329)
+. .+. ..+.++.||..++|.||||+|+.||+|++.|||+|++.++. .+|.|+|+| .++.|
T Consensus 131 ~~-------~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG-~~~av 195 (485)
T KOG2190|consen 131 ED-------ASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISG-EPDAV 195 (485)
T ss_pred cc-------ccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcC-chHHH
Confidence 11 111 38999999999999999999999999999999999998763 789999999 99988
No 8
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.67 E-value=1.4e-16 Score=140.64 Aligned_cols=128 Identities=16% Similarity=0.156 Sum_probs=95.9
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEE---ecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVV---TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPT 80 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~I---tG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~ 80 (329)
.+|.|||+||++||+|+++||++|++.. ++..|.| ++.++++.+|++.|.++..-|..-.|-..
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~--~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l----------- 74 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDIDS--ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKL----------- 74 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEEc--CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHh-----------
Confidence 4789999999999999999999999984 3345677 89999999999999987542211100000
Q ss_pred CCCCc-eEEEEEecC---------cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhh
Q psy3263 81 GVPGH-VTIEVRVPY---------KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQK 149 (329)
Q Consensus 81 ~~~g~-~t~~i~VP~---------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~ 149 (329)
.... ....+.|+. +..|.|||++|+|++.||+.|||+|.++. ..|.|.| .+++++++. +|.++
T Consensus 75 -~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G-~~~~~~~A~~~i~~l 148 (172)
T TIGR03665 75 -LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIG-DPEQVQIAREAIEML 148 (172)
T ss_pred -cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEEC-CHHHHHHHHHHHHHH
Confidence 0111 112233443 47999999999999999999999999985 6799999 999996655 66554
Q ss_pred h
Q psy3263 150 I 150 (329)
Q Consensus 150 ~ 150 (329)
+
T Consensus 149 i 149 (172)
T TIGR03665 149 I 149 (172)
T ss_pred H
Confidence 4
No 9
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.60 E-value=2.3e-15 Score=133.88 Aligned_cols=124 Identities=17% Similarity=0.192 Sum_probs=90.4
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEE----ecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCC
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVV----TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPT 80 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~I----tG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~ 80 (329)
+|.|||++|++||.|+++||++|++.. ++..|.| +++++++++|+++|.+++.-|..-.+-...
T Consensus 14 ig~iIG~gGk~Ik~I~e~tg~~I~i~~--~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~---------- 81 (180)
T PRK13763 14 IGVLIGKKGETKKEIEERTGVKLEIDS--ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLL---------- 81 (180)
T ss_pred hhhHhccchhHHHHHHHHHCcEEEEEC--CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHh----------
Confidence 689999999999999999999999984 3355677 589999999999999986422211110000
Q ss_pred CCCCceEE-EEEe---------cCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhh
Q psy3263 81 GVPGHVTI-EVRV---------PYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHG 147 (329)
Q Consensus 81 ~~~g~~t~-~i~V---------P~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~ 147 (329)
...... .+.+ ..+.+|+|||++|+|+|.||+.|||+|.++.+ .|.|.| .+++++++. +|.
T Consensus 82 --gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~----~v~i~G-~~~~~~~A~~~I~ 152 (180)
T PRK13763 82 --DDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK----TVAIIG-DPEQVEIAREAIE 152 (180)
T ss_pred --CCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC----EEEEEe-CHHHHHHHHHHHH
Confidence 000111 1111 12579999999999999999999999999743 488999 999995544 443
No 10
>KOG2192|consensus
Probab=99.57 E-value=8.5e-15 Score=134.47 Aligned_cols=142 Identities=23% Similarity=0.334 Sum_probs=104.3
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEec----CCCCcceEEEecCHHHHHHHHHHHHHHhhh-------------------
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTP----VRGEEPVFVVTGRKEDVARAKREILSAADH------------------- 60 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip----~~~~ervi~ItG~~e~v~~A~~~I~~i~e~------------------- 60 (329)
+.|.||||+|++||+||++..++.++- +...+||+.+.|.+.+|..+.+.|++.+..
T Consensus 133 ~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~ 212 (390)
T KOG2192|consen 133 LAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETY 212 (390)
T ss_pred hccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCccc
Confidence 458899999999999999999999985 233389999999999999999999887631
Q ss_pred ----hhHhhhccc-CCCCCC----CCCCCC--------------------------------------------------
Q psy3263 61 ----FSALRASRK-SGALSP----LSPPTG-------------------------------------------------- 81 (329)
Q Consensus 61 ----~~~~~~~~~-~~~~~~----~~~p~~-------------------------------------------------- 81 (329)
|.|+-..+. ..+.++ .+||+.
T Consensus 213 dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQg 292 (390)
T KOG2192|consen 213 DYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQG 292 (390)
T ss_pred ccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCC
Confidence 122111111 000000 000000
Q ss_pred -----------------CC-CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCc
Q psy3263 82 -----------------VP-GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGP 140 (329)
Q Consensus 82 -----------------~~-g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~v 140 (329)
+. ..+|.+|.||.+.-|.||||||++||+|++++||.|++...- .+++|+|+| +.+++
T Consensus 293 Gs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItG-TqdQI 371 (390)
T KOG2192|consen 293 GSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQI 371 (390)
T ss_pred CCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEec-cHHHH
Confidence 00 136889999999999999999999999999999999996522 689999999 88888
Q ss_pred chhhhh
Q psy3263 141 GFESHH 146 (329)
Q Consensus 141 eie~~i 146 (329)
.-+.++
T Consensus 372 qnAQYL 377 (390)
T KOG2192|consen 372 QNAQYL 377 (390)
T ss_pred hhHHHH
Confidence 555433
No 11
>KOG2192|consensus
Probab=99.57 E-value=1.5e-14 Score=132.79 Aligned_cols=128 Identities=18% Similarity=0.273 Sum_probs=103.8
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecC-CCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPV-RGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~-~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
.|.||||||++||+||.++|+.|++|. .+.+|+++|+...+-|-.-.+.|+--+|+.. ..+
T Consensus 59 agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f------------------~~~ 120 (390)
T KOG2192|consen 59 AGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGF------------------QLP 120 (390)
T ss_pred ccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCC------------------CCC
Confidence 478999999999999999999999994 4559999999999888877777765544111 223
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC----CCCCCeEEEECCCCCCc-chhhhhhhhhh
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS----RDKEPVFEVTGNFPEGP-GFESHHGQKIV 151 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~----~~~e~~i~ItG~~pe~v-eie~~i~d~~~ 151 (329)
....+++.|+..+.|.|||+.|+.||+++++..++++|-. ...+|++.|.| .|.+| ++-..|.|.+.
T Consensus 121 ~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g-~~k~v~~~i~~il~~i~ 192 (390)
T KOG2192|consen 121 SPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGG-KPKRVVECIKIILDLIS 192 (390)
T ss_pred CchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecC-CcchHHHHHHHHHHHhh
Confidence 3377899999999999999999999999999999998753 44899999999 99999 44445555444
No 12
>KOG2113|consensus
Probab=99.33 E-value=9e-13 Score=123.39 Aligned_cols=160 Identities=28% Similarity=0.365 Sum_probs=108.8
Q ss_pred CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-----chhh---hhhhhhhh
Q psy3263 81 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-----GFES---HHGQKIVF 152 (329)
Q Consensus 81 ~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-----eie~---~i~d~~~~ 152 (329)
..+++.|+.+.||+++|+.|+|++|.+||.||++|.+||..|.+.++|+|.+|| .+++| +|++ |+.-...
T Consensus 21 ~~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg-~~edv~~aRrei~saaeH~~l~~~- 98 (394)
T KOG2113|consen 21 SIGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTG-RHEDVRRARREIPSAAEHFGLIRA- 98 (394)
T ss_pred CCCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceecc-CchhHHHHhhcCccccceeeeeee-
Confidence 566889999999999999999999999999999999999999999999999999 99998 3333 3221100
Q ss_pred hhcCCCCCCcccccccccccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceecCCCCCCCCCCCCCCCCcCCCCCCC
Q psy3263 153 ILTSNLYSFFDCRIFQRMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNP 232 (329)
Q Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~ 232 (329)
+.+ ++....++. ..+....+... |+-+. +
T Consensus 99 -------------------s~s----~Sgg~~~~s-----------~s~qt~sy~sv--------------P~rvv-g-- 127 (394)
T KOG2113|consen 99 -------------------SRS----FSGGTNGAS-----------ASGQTTSYVSV--------------PLRVV-G-- 127 (394)
T ss_pred -------------------ccc----ccCCCcccc-----------ccCCCceeeec--------------cceee-e--
Confidence 000 000000000 00000000000 00000 0
Q ss_pred CccccCCCCCCCCCCCCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccccchhhh
Q psy3263 233 SSIWSYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRII 305 (329)
Q Consensus 233 ~~~~~~~~~sp~~~~~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~~~i~ 305 (329)
+-..+-.....|.+|++.....+.++|+|..||.+|+...+.+ ...|++|...+.+...+.
T Consensus 128 ------------lvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta~~ra~~i~ 189 (394)
T KOG2113|consen 128 ------------LVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTAVTRAGQIH 189 (394)
T ss_pred ------------eccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhhhhhhhhccc
Confidence 0011224567899999999999999999999999999888666 777999988776665553
No 13
>KOG2190|consensus
Probab=99.25 E-value=4.3e-11 Score=120.86 Aligned_cols=131 Identities=20% Similarity=0.254 Sum_probs=95.4
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCC----CCcceEEEecCHHHHHHHHHHHHHHhhhhhHh-----hhc---cc--
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVR----GEEPVFVVTGRKEDVARAKREILSAADHFSAL-----RAS---RK-- 69 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~----~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~-----~~~---~~-- 69 (329)
-+|.||||+|++||+||++|||+|++..+ ..+|.|+|.|.+++|.+|...|...+..+... ... +.
T Consensus 148 q~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~ 227 (485)
T KOG2190|consen 148 QVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSA 227 (485)
T ss_pred heeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcc
Confidence 48999999999999999999999999754 33899999999999999999998875321100 000 00
Q ss_pred CCCCCCC----CCC--CC------CCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEEC
Q psy3263 70 SGALSPL----SPP--TG------VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG 134 (329)
Q Consensus 70 ~~~~~~~----~~p--~~------~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG 134 (329)
..++... ... .+ .+.+....+.+|...++.|||++|..|+.|++.+|+.|.+-....+++|+++.
T Consensus 228 ~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~ 304 (485)
T KOG2190|consen 228 SQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISA 304 (485)
T ss_pred cccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCcceeeecc
Confidence 0000000 000 00 01223356789999999999999999999999999999997766558888776
No 14
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.22 E-value=2.1e-11 Score=90.62 Aligned_cols=51 Identities=25% Similarity=0.276 Sum_probs=46.9
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCC----CcceEEEecCHHHHHHHHHHH
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREI 54 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~----~ervi~ItG~~e~v~~A~~~I 54 (329)
+||.||||+|++||+|+++|||+|+++... .+|+|+|+|++++|.+|+.+|
T Consensus 10 ~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 10 QAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred HcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 589999999999999999999999998543 379999999999999999987
No 15
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.21 E-value=1.6e-11 Score=90.17 Aligned_cols=52 Identities=33% Similarity=0.446 Sum_probs=47.4
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHH
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREIL 55 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~ 55 (329)
++|.||||+|++|++|+++|||+|++|...+ ++.|+|+|++++|.+|+.+|+
T Consensus 10 ~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 10 LHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred HhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHhC
Confidence 6899999999999999999999999996543 788999999999999999873
No 16
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.17 E-value=1.9e-11 Score=90.95 Aligned_cols=54 Identities=30% Similarity=0.482 Sum_probs=49.2
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC----CCCCeEEEECCCCCCcc
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGNFPEGPG 141 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~----~~e~~i~ItG~~pe~ve 141 (329)
++++.||.+.+|.|||++|++||+|+++|||+|.+++. +++|+|+|+| .++++.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G-~~~~v~ 58 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISG-KPSAVQ 58 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEe-CHHHHH
Confidence 46899999999999999999999999999999999864 3689999999 999883
No 17
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.16 E-value=7e-11 Score=86.98 Aligned_cols=48 Identities=25% Similarity=0.281 Sum_probs=44.6
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC-HHHHHHHHHHH
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREI 54 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~-~e~v~~A~~~I 54 (329)
+||.||||+|++||+|+++|||+|+++. ++.|.|+|+ ++++++|+.+|
T Consensus 12 ~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 12 KIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred heeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHh
Confidence 6899999999999999999999999985 357899998 99999999987
No 18
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.15 E-value=2.6e-11 Score=88.97 Aligned_cols=54 Identities=31% Similarity=0.486 Sum_probs=49.0
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCcc
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGPG 141 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~ve 141 (329)
+.++.||.+++|.|||++|++|++|+++|||+|.+|... .++.|+|+| .+++|+
T Consensus 1 ~~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G-~~~~v~ 55 (62)
T cd02394 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITG-PKENVE 55 (62)
T ss_pred CeEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEc-CHHHHH
Confidence 357899999999999999999999999999999999855 678899999 888883
No 19
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.12 E-value=3.5e-11 Score=87.68 Aligned_cols=51 Identities=29% Similarity=0.439 Sum_probs=46.2
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHH
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREI 54 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I 54 (329)
++|.||||+|++||+|+++|||+|+++.++++..|+|+|++++|++|+++|
T Consensus 10 ~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 10 LVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred HcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence 578999999999999999999999999665344899999999999999987
No 20
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=99.11 E-value=3.1e-11 Score=85.14 Aligned_cols=48 Identities=40% Similarity=1.012 Sum_probs=43.2
Q ss_pred CcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
+..|.||++...+++++||||.+||..|+.++.+....||+||+++.+
T Consensus 2 ~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred cCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 578999999999999999999999999999999999999999998864
No 21
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.08 E-value=1.6e-11 Score=89.45 Aligned_cols=54 Identities=33% Similarity=0.597 Sum_probs=48.9
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcc
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPG 141 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~ve 141 (329)
|.++.||.+++|+|||++|++||+|+++|||+|.++.++++..|+|+| .+++|+
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G-~~~~v~ 54 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVE 54 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHH
Confidence 689999999999999999999999999999999998775334899999 999883
No 22
>PF13014 KH_3: KH domain
Probab=99.07 E-value=1.7e-10 Score=78.80 Aligned_cols=39 Identities=36% Similarity=0.485 Sum_probs=35.1
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecC---C-CCcceEEEec
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPV---R-GEEPVFVVTG 42 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~---~-~~ervi~ItG 42 (329)
|||.||||+|++||+|+++|||+|++|+ . ..+++|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 6899999999999999999999999997 2 2389999998
No 23
>KOG2191|consensus
Probab=99.07 E-value=1.7e-10 Score=109.01 Aligned_cols=121 Identities=21% Similarity=0.225 Sum_probs=91.8
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCC------cceEEEecCHHHHHHHHHHHHHHhhhhhH----hhhcccCCCC-
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILSAADHFSA----LRASRKSGAL- 73 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------ervi~ItG~~e~v~~A~~~I~~i~e~~~~----~~~~~~~~~~- 73 (329)
-|.||||+|.+||.++|++++.|++++..+ ||+++|.|.+|+..+|..+|++.+...++ +..+.....|
T Consensus 143 ag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGp 222 (402)
T KOG2191|consen 143 AGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGP 222 (402)
T ss_pred ccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCc
Confidence 378999999999999999999999984332 89999999999999999999998642221 2222111111
Q ss_pred ----CCCCCCC-----CCCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC
Q psy3263 74 ----SPLSPPT-----GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD 125 (329)
Q Consensus 74 ----~~~~~p~-----~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~ 125 (329)
.+.+.|+ -.+...+..+-|+....|..-|.||.++-.|-..+|+.|.+++.-
T Consensus 223 vaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l 283 (402)
T KOG2191|consen 223 VANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQAL 283 (402)
T ss_pred ccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeecccc
Confidence 1111111 133456678889999999999999999999999999999998754
No 24
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.06 E-value=1.6e-10 Score=85.06 Aligned_cols=54 Identities=22% Similarity=0.285 Sum_probs=47.5
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcch
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGF 142 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~vei 142 (329)
.+..+.||.+++|.|||+||++||+|+++|||+|.++. ++.|.|+|+.+++++.
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~ 55 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEK 55 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHH
Confidence 46789999999999999999999999999999999987 4679999933788743
No 25
>KOG4172|consensus
Probab=99.04 E-value=2.1e-11 Score=86.29 Aligned_cols=53 Identities=28% Similarity=0.778 Sum_probs=48.7
Q ss_pred cccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccccchhhhh
Q psy3263 254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRIIF 306 (329)
Q Consensus 254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~~~i~~ 306 (329)
.+|.||+|...+.++.-|||.|+|.+|..++++. ...||+||+++...++.+.
T Consensus 8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkTY~ 61 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKTYR 61 (62)
T ss_pred cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHhhc
Confidence 6999999999999999999999999999999886 8899999999988877653
No 26
>PF13014 KH_3: KH domain
Probab=99.02 E-value=3.9e-10 Score=77.06 Aligned_cols=39 Identities=38% Similarity=0.635 Sum_probs=35.6
Q ss_pred ccceeecCCCchHHHHHHhcCceEEcCC----CCCCCeEEEEC
Q psy3263 96 VVGLVVGPKGATIKRIQHQTNTYIVTPS----RDKEPVFEVTG 134 (329)
Q Consensus 96 ~vG~IIGkgG~tIk~Iq~~tga~I~ip~----~~~e~~i~ItG 134 (329)
+||+|||++|++||+|+++|||+|+||+ .+++++|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999998 22788899998
No 27
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.01 E-value=3.3e-10 Score=82.92 Aligned_cols=52 Identities=37% Similarity=0.592 Sum_probs=47.7
Q ss_pred EEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCc
Q psy3263 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGP 140 (329)
Q Consensus 88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~v 140 (329)
.++.||.+++|+|||++|++|++|+++|||+|.++... .++.|+|+| .++++
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G-~~~~v 56 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITG-TPEAV 56 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEc-CHHHH
Confidence 57999999999999999999999999999999998763 688899999 87777
No 28
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.00 E-value=9.5e-10 Score=80.49 Aligned_cols=52 Identities=38% Similarity=0.485 Sum_probs=47.4
Q ss_pred eeeeeeecCCChHHHHHHHHhCCeEEecCCC---CcceEEEecCHHHHHHHHHHH
Q psy3263 3 IFVVPSINPFGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREI 54 (329)
Q Consensus 3 ~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~---~ervi~ItG~~e~v~~A~~~I 54 (329)
-+||.|||++|++|++|+++||++|.++... .++.|.|.|+.+++++|+.+|
T Consensus 9 ~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 9 SLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred hhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 3789999999999999999999999999653 378899999999999999887
No 29
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.93 E-value=5.8e-10 Score=76.06 Aligned_cols=38 Identities=39% Similarity=0.940 Sum_probs=31.0
Q ss_pred cccccccCcccEEeCCCChhccHhhHHhhcCC--C--CCCccc
Q psy3263 256 CYLCNDREVTHALIPCGHNFFCSECAERTCDF--D--RTCPMC 294 (329)
Q Consensus 256 C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~--~--~~CP~C 294 (329)
|+||++.+.+|+.++|||+ ||..|+.++++. . ..||.|
T Consensus 1 CpiC~~~~~~Pv~l~CGH~-FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHS-FCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSE-EEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccccCCcCH-HHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999999999999999 999999999988 2 479987
No 30
>KOG4265|consensus
Probab=98.88 E-value=6.4e-10 Score=106.56 Aligned_cols=58 Identities=28% Similarity=0.764 Sum_probs=52.0
Q ss_pred CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhhhh
Q psy3263 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQ 308 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~~~ 308 (329)
+...+|+||+...++.+++||.|.|+|..|++.+.-+...||+||+++...+.+...+
T Consensus 288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~i~~~~ 345 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEELLEIYVNK 345 (349)
T ss_pred cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHhhheecccc
Confidence 4468999999999999999999999999999999877889999999998887776554
No 31
>KOG0317|consensus
Probab=98.78 E-value=2.8e-09 Score=99.50 Aligned_cols=51 Identities=31% Similarity=0.806 Sum_probs=46.4
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 301 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~ 301 (329)
.+....|.+|++...+|...||||. ||+.|+..|+.....||+||..+...
T Consensus 236 ~~a~~kC~LCLe~~~~pSaTpCGHi-FCWsCI~~w~~ek~eCPlCR~~~~ps 286 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSNPSATPCGHI-FCWSCILEWCSEKAECPLCREKFQPS 286 (293)
T ss_pred CCCCCceEEEecCCCCCCcCcCcch-HHHHHHHHHHccccCCCcccccCCCc
Confidence 3566899999999999999999999 99999999999999999999988543
No 32
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.77 E-value=1.8e-08 Score=84.00 Aligned_cols=58 Identities=24% Similarity=0.315 Sum_probs=50.0
Q ss_pred ceeeeeeecCCChHHHHHHHHhCCeEEecCCCC--------------------cceEEEecC---HHHHHHHHHHHHHHh
Q psy3263 2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGE--------------------EPVFVVTGR---KEDVARAKREILSAA 58 (329)
Q Consensus 2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~--------------------ervi~ItG~---~e~v~~A~~~I~~i~ 58 (329)
|+|+|.|||.+|.+||+|+++|||+|.|-.++. .-.|.|++. .+++++|+.+|..++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 899999999999999999999999999986531 245788885 499999999999885
Q ss_pred h
Q psy3263 59 D 59 (329)
Q Consensus 59 e 59 (329)
.
T Consensus 94 ~ 94 (120)
T cd02395 94 K 94 (120)
T ss_pred c
Confidence 3
No 33
>KOG0823|consensus
Probab=98.77 E-value=2.8e-09 Score=96.82 Aligned_cols=49 Identities=29% Similarity=0.684 Sum_probs=44.5
Q ss_pred CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC---CCCCccccccccc
Q psy3263 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVNQ 300 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~~ 300 (329)
...++|-||+|..++|++..|||. ||+.|+.+|++. ...||+|+..+..
T Consensus 45 ~~~FdCNICLd~akdPVvTlCGHL-FCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVTLCGHL-FCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccccCCCEEeecccc-eehHHHHHHHhhcCCCeeCCcccccccc
Confidence 456899999999999999999999 999999999987 7789999998843
No 34
>smart00322 KH K homology RNA-binding domain.
Probab=98.76 E-value=2.8e-08 Score=72.28 Aligned_cols=55 Identities=35% Similarity=0.379 Sum_probs=49.5
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCC-CcceEEEecCHHHHHHHHHHHHHHh
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAA 58 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~-~ervi~ItG~~e~v~~A~~~I~~i~ 58 (329)
++|.+||++|.+|++|+++||++|.++... ...++.|.|..+++..|+.+|.+.+
T Consensus 13 ~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 13 KVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred hcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 579999999999999999999999998554 3688999999999999999998764
No 35
>smart00322 KH K homology RNA-binding domain.
Probab=98.75 E-value=1.4e-08 Score=73.87 Aligned_cols=63 Identities=40% Similarity=0.536 Sum_probs=53.9
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCcchhh-hhhhh
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGPGFES-HHGQK 149 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~veie~-~i~d~ 149 (329)
.+.++.||...+|.+||++|++|++|++.+|++|.++... ....++|.| .+++++.+. +|.+.
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g-~~~~v~~a~~~i~~~ 67 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITG-PPENVEKAAELILEI 67 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEc-CHHHHHHHHHHHHHH
Confidence 5788999999999999999999999999999999998755 677899999 888884443 65543
No 36
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.75 E-value=4.2e-09 Score=70.41 Aligned_cols=38 Identities=39% Similarity=1.065 Sum_probs=33.7
Q ss_pred cccccccCccc-EEeCCCChhccHhhHHhhcCCCCCCccc
Q psy3263 256 CYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMC 294 (329)
Q Consensus 256 C~IC~e~~~~~-~~lpCgH~~fC~~Cl~~~~~~~~~CP~C 294 (329)
|+||++.+.++ +.++|||. ||.+|+.++.+....||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~-fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHS-FCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEE-EEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCc-hhHHHHHHHHHCcCCCcCC
Confidence 89999999999 58999999 9999999999888899998
No 37
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.74 E-value=6.4e-09 Score=92.75 Aligned_cols=49 Identities=29% Similarity=0.714 Sum_probs=42.9
Q ss_pred CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC----------------CCCCccccccccc
Q psy3263 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF----------------DRTCPMCRVPVNQ 300 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~----------------~~~CP~Cr~~i~~ 300 (329)
.++.+|+||++...++++++|||. ||..|+..|+.. ...||+||..+..
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~-FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHL-FCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCch-hHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 457899999999999999999999 999999998631 4689999999854
No 38
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.65 E-value=1.2e-08 Score=100.60 Aligned_cols=52 Identities=31% Similarity=0.685 Sum_probs=47.2
Q ss_pred CCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
+.++..+.|.||.+.+.++++++|||. ||..|+..++.....||+|+..+..
T Consensus 21 ~~Le~~l~C~IC~d~~~~PvitpCgH~-FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 21 YPLDTSLRCHICKDFFDVPVLTSCSHT-FCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred cccccccCCCcCchhhhCccCCCCCCc-hhHHHHHHHHhCCCCCCCCCCcccc
Confidence 457888999999999999999999999 9999999998887789999998743
No 39
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.65 E-value=1.5e-08 Score=93.76 Aligned_cols=50 Identities=30% Similarity=0.746 Sum_probs=42.1
Q ss_pred CCcccccccccCcc--------cEEeCCCChhccHhhHHhhcCCCCCCcccccccccch
Q psy3263 252 GSRQCYLCNDREVT--------HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM 302 (329)
Q Consensus 252 ~~~~C~IC~e~~~~--------~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~ 302 (329)
.+.+|+||++.+.+ +++.+|+|. ||..|+.+|++....||+||..+....
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~-FC~~CI~~Wl~~~~tCPlCR~~~~~v~ 230 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHV-FCIECIDIWKKEKNTCPVCRTPFISVI 230 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCc-ccHHHHHHHHhcCCCCCCCCCEeeEEe
Confidence 45799999997654 256689999 999999999988899999999887544
No 40
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.60 E-value=1.1e-08 Score=70.02 Aligned_cols=40 Identities=30% Similarity=0.819 Sum_probs=34.8
Q ss_pred ccccccccCc---ccEEeCCCChhccHhhHHhhcCCCCCCcccc
Q psy3263 255 QCYLCNDREV---THALIPCGHNFFCSECAERTCDFDRTCPMCR 295 (329)
Q Consensus 255 ~C~IC~e~~~---~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr 295 (329)
.|+||++.+. ..+.++|+|. ||.+|+..|++....||+||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHV-FHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEE-EEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCe-eCHHHHHHHHHhCCcCCccC
Confidence 6999999873 4567899999 99999999999888999997
No 41
>KOG0287|consensus
Probab=98.59 E-value=1.1e-08 Score=97.12 Aligned_cols=66 Identities=23% Similarity=0.596 Sum_probs=53.9
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhhhhhhhhcchhhh
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLWEPV 318 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~~~~~~~~v~~~~ 318 (329)
+..-+.|-||+|.+..|++.||+|+ ||.-|++..+...+.||.|+..++.. .++++++++++++..
T Consensus 20 lD~lLRC~IC~eyf~ip~itpCsHt-fCSlCIR~~L~~~p~CP~C~~~~~Es--~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 20 LDDLLRCGICFEYFNIPMITPCSHT-FCSLCIRKFLSYKPQCPTCCVTVTES--DLRNNRILDEIVKSL 85 (442)
T ss_pred hHHHHHHhHHHHHhcCceeccccch-HHHHHHHHHhccCCCCCceecccchh--hhhhhhHHHHHHHHH
Confidence 4566899999999999999999999 99999999999999999999988553 344555555554433
No 42
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.53 E-value=1.4e-07 Score=83.47 Aligned_cols=52 Identities=17% Similarity=0.088 Sum_probs=48.1
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD 59 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e 59 (329)
.+|+||||+|++++.||+.|||+|.++ +..|.|.|.+++++.|+++|.++++
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~----~~~v~i~G~~~~~~~A~~~i~~li~ 150 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVY----GKTVGIIGDPEQVQIAREAIEMLIE 150 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEc----CCEEEEECCHHHHHHHHHHHHHHHc
Confidence 368999999999999999999999998 3778999999999999999999864
No 43
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.52 E-value=6.5e-08 Score=70.74 Aligned_cols=46 Identities=15% Similarity=0.238 Sum_probs=42.4
Q ss_pred CcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 299 (329)
Q Consensus 253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~ 299 (329)
++.|+||.+.+.+|+.++|||. ||..|+..+++....||+|+.++.
T Consensus 1 ~~~Cpi~~~~~~~Pv~~~~G~v-~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 1 EFLCPISLEVMKDPVILPSGQT-YERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred CcCCcCCCCcCCCCEECCCCCE-EeHHHHHHHHHHCCCCCCCcCCCC
Confidence 3689999999999999999999 999999999988889999999874
No 44
>KOG0320|consensus
Probab=98.51 E-value=3.5e-08 Score=86.32 Aligned_cols=49 Identities=31% Similarity=0.793 Sum_probs=41.4
Q ss_pred CCCcccccccccCccc--EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 251 SGSRQCYLCNDREVTH--ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~--~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
+....|+||++....- +...|||. ||..|++..++....||+||+.++.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHv-FC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHV-FCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchh-HHHHHHHHHHHhCCCCCCcccccch
Confidence 3447999999977654 45799999 9999999999999999999987743
No 45
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.49 E-value=2e-07 Score=83.06 Aligned_cols=52 Identities=17% Similarity=0.105 Sum_probs=47.3
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD 59 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e 59 (329)
.+|+||||+|+++|.||+.|||+|.++ +..+.|.|.+++++.|++.|.++++
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~----~~~v~i~G~~~~~~~A~~~I~~li~ 156 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVY----GKTVAIIGDPEQVEIAREAIEMLIE 156 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEc----CCEEEEEeCHHHHHHHHHHHHHHHc
Confidence 479999999999999999999999998 3448899999999999999998864
No 46
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.47 E-value=7.4e-08 Score=64.74 Aligned_cols=38 Identities=34% Similarity=1.011 Sum_probs=35.3
Q ss_pred cccccccCcccE-EeCCCChhccHhhHHhhcC-C-CCCCccc
Q psy3263 256 CYLCNDREVTHA-LIPCGHNFFCSECAERTCD-F-DRTCPMC 294 (329)
Q Consensus 256 C~IC~e~~~~~~-~lpCgH~~fC~~Cl~~~~~-~-~~~CP~C 294 (329)
|.||++.+.++. +++|||. ||..|+.++++ . ...||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~-fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHS-FCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEE-EEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCc-chHHHHHHHHHhcCCccCCcC
Confidence 899999999999 8999999 99999999998 3 7889998
No 47
>KOG2279|consensus
Probab=98.43 E-value=8.6e-08 Score=96.11 Aligned_cols=118 Identities=25% Similarity=0.349 Sum_probs=95.1
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCC--CCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVR--GEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTG 81 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~--~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~ 81 (329)
+|.+|+||+|++||.|+.+|+++|.+-.+ +++++-++.|-+..|.+|+.++..+.. +
T Consensus 78 ~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~-----~---------------- 136 (608)
T KOG2279|consen 78 AVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILT-----E---------------- 136 (608)
T ss_pred ceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHh-----c----------------
Confidence 68899999999999999999999999643 347888888899999999999988753 1
Q ss_pred CCCceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC---CCCeEEEECCCCCCcchhh
Q psy3263 82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD---KEPVFEVTGNFPEGPGFES 144 (329)
Q Consensus 82 ~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~---~e~~i~ItG~~pe~veie~ 144 (329)
...+..+.-+|.+.++.|+|++|++|..|..-++++|.+-.+- ..+.+.|.| ....++++.
T Consensus 137 -~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~-qqk~~~~a~ 200 (608)
T KOG2279|consen 137 -NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISG-QQKEVAAAK 200 (608)
T ss_pred -CCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceeccc-ccchHHHHH
Confidence 1114556778999999999999999999999999999987544 455677777 555554444
No 48
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.43 E-value=1.5e-07 Score=63.03 Aligned_cols=43 Identities=35% Similarity=1.015 Sum_probs=36.6
Q ss_pred ccccccccCcccEEe-CCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263 255 QCYLCNDREVTHALI-PCGHNFFCSECAERTCDF-DRTCPMCRVPV 298 (329)
Q Consensus 255 ~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i 298 (329)
.|.||++.+.+++.+ +|||. ||..|+..+... ...||+|+..+
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~-~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHV-FCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhCceEecCCCCh-hcHHHHHHHHHhCcCCCCCCCCcC
Confidence 599999998666655 59999 999999999887 78899998753
No 49
>PHA02926 zinc finger-like protein; Provisional
Probab=98.35 E-value=1.9e-07 Score=84.62 Aligned_cols=51 Identities=25% Similarity=0.616 Sum_probs=40.3
Q ss_pred CCCcccccccccCcc---------cEEeCCCChhccHhhHHhhcCC------CCCCcccccccccch
Q psy3263 251 SGSRQCYLCNDREVT---------HALIPCGHNFFCSECAERTCDF------DRTCPMCRVPVNQAM 302 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~---------~~~lpCgH~~fC~~Cl~~~~~~------~~~CP~Cr~~i~~~~ 302 (329)
..+.+|.||+|...+ .++.+|+|. ||..|+..|... ...||+||..+....
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHs-FCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~ 233 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHI-FCITCINIWHRTRRETGASDNCPICRTRFRNIT 233 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCch-HHHHHHHHHHHhccccCcCCcCCCCcceeeeec
Confidence 456899999997532 356799999 999999999874 356999999886543
No 50
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.33 E-value=3.8e-07 Score=62.58 Aligned_cols=41 Identities=32% Similarity=0.877 Sum_probs=35.0
Q ss_pred ccccccccC---cccEEeCCCChhccHhhHHhhcCCCCCCccccc
Q psy3263 255 QCYLCNDRE---VTHALIPCGHNFFCSECAERTCDFDRTCPMCRV 296 (329)
Q Consensus 255 ~C~IC~e~~---~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~ 296 (329)
.|.+|++.+ ..+.+++|||. ||..|+..+......||+||+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~-~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHI-FCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCH-HHHHHHHhhcCCCCCCcCCCC
Confidence 488999888 35668999999 999999999855789999985
No 51
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.29 E-value=5e-07 Score=58.37 Aligned_cols=38 Identities=34% Similarity=1.027 Sum_probs=34.4
Q ss_pred cccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccc
Q psy3263 256 CYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMC 294 (329)
Q Consensus 256 C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~C 294 (329)
|.||++....++.++|+|. ||..|+..+.+. ...||+|
T Consensus 1 C~iC~~~~~~~~~~~C~H~-~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLPCGHT-FCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEecCCCh-HHHHHHHHHHHhCcCCCCCC
Confidence 7899999989999999999 999999999874 6789987
No 52
>KOG2208|consensus
Probab=98.24 E-value=1.8e-06 Score=91.98 Aligned_cols=115 Identities=21% Similarity=0.293 Sum_probs=93.4
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV 82 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~ 82 (329)
++.-++||+|.+|.+|++++.+.|.++..++ +..++++|...++++|.+.+..+.. ..
T Consensus 357 ~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~~~~ka~~~v~~~~~---------------------ei 415 (753)
T KOG2208|consen 357 ELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSANDEKAVEDVEKIIA---------------------EI 415 (753)
T ss_pred hhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccccchhHHHHHHHHHHH---------------------hh
Confidence 4567899999999999999999999997544 6788999999999999999988743 11
Q ss_pred CC-ceEEEEEecCcccceeecCCCchHHHHHHhcC-ceEEcCCCCCCCe-EEEECCCCCCc
Q psy3263 83 PG-HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTN-TYIVTPSRDKEPV-FEVTGNFPEGP 140 (329)
Q Consensus 83 ~g-~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tg-a~I~ip~~~~e~~-i~ItG~~pe~v 140 (329)
++ .....+.+|...+..|||.+|+.|..|...++ .+|+++.....+. .++.| .-..+
T Consensus 416 ~n~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~~~~~~~~~-~~~dv 475 (753)
T KOG2208|consen 416 LNSIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNSSDMVTIRG-ISKDV 475 (753)
T ss_pred hcccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcccccceEec-ccccc
Confidence 11 24456889999999999999999999999999 8999887664333 66666 55555
No 53
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.22 E-value=4.8e-07 Score=84.66 Aligned_cols=50 Identities=30% Similarity=0.705 Sum_probs=45.5
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
|...+.|-||-+.+..++..+|||. ||.-|+++.+...+.||+||.+...
T Consensus 22 LDs~lrC~IC~~~i~ip~~TtCgHt-FCslCIR~hL~~qp~CP~Cr~~~~e 71 (391)
T COG5432 22 LDSMLRCRICDCRISIPCETTCGHT-FCSLCIRRHLGTQPFCPVCREDPCE 71 (391)
T ss_pred chhHHHhhhhhheeecceecccccc-hhHHHHHHHhcCCCCCccccccHHh
Confidence 4556899999999999999999999 9999999999999999999998643
No 54
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.22 E-value=3.6e-07 Score=62.61 Aligned_cols=30 Identities=33% Similarity=0.978 Sum_probs=21.0
Q ss_pred cccccccCcc----cEEeCCCChhccHhhHHhhcCC
Q psy3263 256 CYLCNDREVT----HALIPCGHNFFCSECAERTCDF 287 (329)
Q Consensus 256 C~IC~e~~~~----~~~lpCgH~~fC~~Cl~~~~~~ 287 (329)
|+||.+ +.+ |+.|+|||. ||.+|++++...
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~-~c~~cl~~l~~~ 34 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHV-FCKDCLQKLSKK 34 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-E-EEHHHHHHHHHH
T ss_pred CCcccc-ccCCCCCCEEEeCccH-HHHHHHHHHHhc
Confidence 899999 877 899999999 999999999774
No 55
>KOG1571|consensus
Probab=98.21 E-value=5.8e-07 Score=86.51 Aligned_cols=53 Identities=25% Similarity=0.702 Sum_probs=45.8
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF 306 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~ 306 (329)
+.....|.||.+.+.+++++||||.|.|..|...+ ..||+||+.+....+.|.
T Consensus 302 ~~~p~lcVVcl~e~~~~~fvpcGh~ccct~cs~~l----~~CPvCR~rI~~~~k~y~ 354 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKSAVFVPCGHVCCCTLCSKHL----PQCPVCRQRIRLVRKRYR 354 (355)
T ss_pred cCCCCceEEecCCccceeeecCCcEEEchHHHhhC----CCCchhHHHHHHHHHHhc
Confidence 34456999999999999999999999999998886 679999999988777664
No 56
>KOG2177|consensus
Probab=98.21 E-value=4.7e-07 Score=83.18 Aligned_cols=47 Identities=34% Similarity=0.851 Sum_probs=42.6
Q ss_pred CCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccc
Q psy3263 249 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRV 296 (329)
Q Consensus 249 ~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~ 296 (329)
.+.+...|+||++.+.+++++||+|+ ||..|+..++.....||.||.
T Consensus 9 ~~~~~~~C~iC~~~~~~p~~l~C~H~-~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 9 VLQEELTCPICLEYFREPVLLPCGHN-FCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred hccccccChhhHHHhhcCccccccch-HhHHHHHHhcCCCcCCcccCC
Confidence 45678999999999999999999999 999999999876679999995
No 57
>KOG4275|consensus
Probab=98.19 E-value=2e-07 Score=87.13 Aligned_cols=52 Identities=31% Similarity=0.797 Sum_probs=47.1
Q ss_pred CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhhh
Q psy3263 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF 306 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~ 306 (329)
.....|.||++...+.++|+|||..-|.+|-+++ ..||+||+.+....++|.
T Consensus 298 ~~~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 298 ATRRLCAICMDAPRDCVFLECGHMVTCTKCGKRM----NECPICRQYIVRVVRIFR 349 (350)
T ss_pred hHHHHHHHHhcCCcceEEeecCcEEeehhhcccc----ccCchHHHHHHHHHhhhc
Confidence 3478999999999999999999999999999887 699999999988888875
No 58
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.19 E-value=2e-06 Score=73.70 Aligned_cols=93 Identities=16% Similarity=0.105 Sum_probs=64.9
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
.||..||++|++|++|++..|-+|++-...+ .++..|..++.......-. .. ...
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------d~~~fI~n~l~Pa~V~~v~----------I~-~~~ 96 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------DPEEFIKNIFAPAAVRSVT----------IK-KKN 96 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEEcCC--------------CHHHHHHHHcCCCEEEEEE----------EE-ecC
Confidence 3699999999999999999998888753333 1344444442100000000 00 112
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 121 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i 121 (329)
+.....+.|+.+..|..|||+|.+|+.+++-++-++.+
T Consensus 97 ~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 97 GDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred CcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 23667888999999999999999999999999998876
No 59
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=98.13 E-value=1.8e-06 Score=65.73 Aligned_cols=48 Identities=21% Similarity=0.390 Sum_probs=40.3
Q ss_pred CCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263 252 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 300 (329)
Q Consensus 252 ~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~ 300 (329)
+.+.|+||.+.+.+|+++||||. |+..|+.+|+.. ...||+|+.++..
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~t-yer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHT-YERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEE-EEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cccCCcCcCcHhhCceeCCcCCE-EcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 56899999999999999999999 999999999999 9999999998864
No 60
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.13 E-value=2.1e-05 Score=70.24 Aligned_cols=121 Identities=17% Similarity=0.236 Sum_probs=85.5
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-----CHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCC
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-----RKEDVARAKREILSAADHFSALRASRKSGALSPLSPP 79 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-----~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p 79 (329)
+|.+||+.|+.-|.|.+.+++++.+. .++..|.|.. +|-.+.+|++.|.++..-|+--.|-.-..
T Consensus 19 ~~~lig~~g~v~k~ie~~~~~~~~iD--~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~-------- 88 (194)
T COG1094 19 IGVLIGKWGEVKKAIEEKTGVKLRID--SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLLE-------- 88 (194)
T ss_pred heeeecccccchHHHHhhcCeEEEEE--CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHhc--------
Confidence 57899999999999999999999997 4445555543 57899999999988743222211111100
Q ss_pred CCCCCceEEE-EEe------c----CcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh
Q psy3263 80 TGVPGHVTIE-VRV------P----YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES 144 (329)
Q Consensus 80 ~~~~g~~t~~-i~V------P----~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~ 144 (329)
....+. |.+ + .+..|.|||++|.|-+.|++.|+|+|.+-.. .|.|-| .+++|+++.
T Consensus 89 ----d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~----tVaiiG-~~~~v~iAr 155 (194)
T COG1094 89 ----DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK----TVAIIG-GFEQVEIAR 155 (194)
T ss_pred ----CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc----EEEEec-ChhhhHHHH
Confidence 011111 111 1 2456999999999999999999999999543 689999 999995444
No 61
>KOG2164|consensus
Probab=98.10 E-value=1e-06 Score=88.21 Aligned_cols=54 Identities=24% Similarity=0.707 Sum_probs=45.3
Q ss_pred CcccccccccCcccEEeCCCChhccHhhHHhhcCC-----CCCCccccccccc--chhhhhh
Q psy3263 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPVNQ--AMRIIFN 307 (329)
Q Consensus 253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-----~~~CP~Cr~~i~~--~~~i~~~ 307 (329)
+..|+||++.+.-|+...|||. ||..|+-+.|.. ...||+|+..|.. ...++..
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHi-FC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~e 246 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHI-FCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFIE 246 (513)
T ss_pred CCcCCcccCCCCcccccccCce-eeHHHHHHHHhhhcccCCccCCchhhhccccceeeeeec
Confidence 6799999999999998899999 999999988766 5799999998855 4444443
No 62
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.07 E-value=3.1e-06 Score=70.65 Aligned_cols=58 Identities=24% Similarity=0.398 Sum_probs=42.8
Q ss_pred CcccceeecCCCchHHHHHHhcCceEEcCCCC-------------------CC-CeEEEECCC--CCCc-chhhhhhhhh
Q psy3263 94 YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-------------------KE-PVFEVTGNF--PEGP-GFESHHGQKI 150 (329)
Q Consensus 94 ~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-------------------~e-~~i~ItG~~--pe~v-eie~~i~d~~ 150 (329)
++++|.|||+||+|||+|+++|||+|.|-.+. ++ -.|.|+++. .+.+ ++..+|..++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 47899999999999999999999999998651 22 348999955 3566 2333555444
Q ss_pred h
Q psy3263 151 V 151 (329)
Q Consensus 151 ~ 151 (329)
.
T Consensus 94 ~ 94 (120)
T cd02395 94 K 94 (120)
T ss_pred c
Confidence 4
No 63
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.06 E-value=1.7e-06 Score=80.24 Aligned_cols=48 Identities=31% Similarity=0.728 Sum_probs=41.9
Q ss_pred CCCcccccccccCcccEEeCCCChhccHhhHHh-hcCC-CCCCcccccccc
Q psy3263 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAER-TCDF-DRTCPMCRVPVN 299 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~-~~~~-~~~CP~Cr~~i~ 299 (329)
..+..|.+|++....++-.+|||. ||..|+.. |..+ ...||+||+...
T Consensus 213 ~~d~kC~lC~e~~~~ps~t~CgHl-FC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 213 LADYKCFLCLEEPEVPSCTPCGHL-FCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccccceeeeecccCCcccccccch-hhHHHHHHHHHhhccccCchhhhhcc
Confidence 567899999999999999999999 99999998 6666 455999999763
No 64
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=98.00 E-value=4.7e-06 Score=63.47 Aligned_cols=41 Identities=32% Similarity=0.771 Sum_probs=33.2
Q ss_pred cccccccccCc-------------ccEEeCCCChhccHhhHHhhcCCCCCCcccc
Q psy3263 254 RQCYLCNDREV-------------THALIPCGHNFFCSECAERTCDFDRTCPMCR 295 (329)
Q Consensus 254 ~~C~IC~e~~~-------------~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr 295 (329)
..|.||++.+. ..++.+|||. |...|+.+|++....||+||
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~-FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHI-FHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEE-EEHHHHHHHHTTSSB-TTSS
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCC-EEHHHHHHHHhcCCcCCCCC
Confidence 35999998772 1245699999 99999999999988999997
No 65
>KOG0978|consensus
Probab=97.97 E-value=1.4e-06 Score=90.82 Aligned_cols=49 Identities=31% Similarity=0.784 Sum_probs=44.4
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVN 299 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~ 299 (329)
+.+-+.|++|.++.++.++..|||. ||..|++..... ...||.|...|-
T Consensus 640 yK~~LkCs~Cn~R~Kd~vI~kC~H~-FC~~Cvq~r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 640 YKELLKCSVCNTRWKDAVITKCGHV-FCEECVQTRYETRQRKCPKCNAAFG 689 (698)
T ss_pred HHhceeCCCccCchhhHHHHhcchH-HHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 3566899999999999999999998 999999998777 899999999983
No 66
>KOG0119|consensus
Probab=97.94 E-value=2.1e-05 Score=78.44 Aligned_cols=58 Identities=26% Similarity=0.318 Sum_probs=47.1
Q ss_pred ceeeeeeecCCChHHHHHHHHhCCeEEecCCCC------------------cc-eEEEecC-HHHHHHHHHHHHHHhh
Q psy3263 2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGE------------------EP-VFVVTGR-KEDVARAKREILSAAD 59 (329)
Q Consensus 2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~------------------er-vi~ItG~-~e~v~~A~~~I~~i~e 59 (329)
|+|||+|||..|.|.|+|++||||+|.|=.++. |+ -+.|++. .|.|++|...|..+++
T Consensus 152 ~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~ 229 (554)
T KOG0119|consen 152 INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQ 229 (554)
T ss_pred cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHH
Confidence 789999999999999999999999999853111 32 4678875 6788899999888764
No 67
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.89 E-value=3.3e-06 Score=62.31 Aligned_cols=45 Identities=31% Similarity=0.713 Sum_probs=26.1
Q ss_pred CCCcccccccccCcccE-EeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263 251 SGSRQCYLCNDREVTHA-LIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~-~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
++.+.|.+|.+.+..|+ +-.|.|. ||..|+..... ..||+|+.+.
T Consensus 5 e~lLrCs~C~~~l~~pv~l~~CeH~-fCs~Ci~~~~~--~~CPvC~~Pa 50 (65)
T PF14835_consen 5 EELLRCSICFDILKEPVCLGGCEHI-FCSSCIRDCIG--SECPVCHTPA 50 (65)
T ss_dssp HHTTS-SSS-S--SS-B---SSS---B-TTTGGGGTT--TB-SSS--B-
T ss_pred HHhcCCcHHHHHhcCCceeccCccH-HHHHHhHHhcC--CCCCCcCChH
Confidence 45678999999999997 5799999 99999987544 4699999987
No 68
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=97.86 E-value=6.5e-06 Score=79.48 Aligned_cols=47 Identities=36% Similarity=0.843 Sum_probs=41.0
Q ss_pred CCCcccccccccCc-------------ccEEeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263 251 SGSRQCYLCNDREV-------------THALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 251 ~~~~~C~IC~e~~~-------------~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
.++..|.||+|.+. .|.-+||||- |-.+|++.|++....||+||.++
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHi-lHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHI-LHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccce-eeHHHHHHHHHhccCCCcccCcc
Confidence 56789999999742 2467899998 99999999999999999999995
No 69
>KOG0824|consensus
Probab=97.83 E-value=7.6e-06 Score=77.14 Aligned_cols=50 Identities=24% Similarity=0.733 Sum_probs=44.8
Q ss_pred CCcccccccccCcccEEeCCCChhccHhhHHhhcCC-CCCCcccccccccch
Q psy3263 252 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAM 302 (329)
Q Consensus 252 ~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~~ 302 (329)
-..+|.||+.....|+.++|+|. ||..|++...+. +..|++||.+|+..+
T Consensus 6 ~~~eC~IC~nt~n~Pv~l~C~Hk-FCyiCiKGsy~ndk~~CavCR~pids~i 56 (324)
T KOG0824|consen 6 KKKECLICYNTGNCPVNLYCFHK-FCYICIKGSYKNDKKTCAVCRFPIDSTI 56 (324)
T ss_pred cCCcceeeeccCCcCccccccch-hhhhhhcchhhcCCCCCceecCCCCcch
Confidence 45699999999999999999999 999999998777 677999999997754
No 70
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.81 E-value=1.3e-05 Score=76.49 Aligned_cols=47 Identities=23% Similarity=0.752 Sum_probs=36.2
Q ss_pred CcccccccccC-cccE---Ee-CCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263 253 SRQCYLCNDRE-VTHA---LI-PCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 300 (329)
Q Consensus 253 ~~~C~IC~e~~-~~~~---~l-pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~ 300 (329)
+..|++|.... .++- ++ +|||+ ||..|+.+++.. ...||.|+..+..
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~-~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHT-LCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCc-ccHHHHHHHhcCCCCCCCCCCCccch
Confidence 45899999842 2221 22 79999 999999998866 6789999998754
No 71
>KOG0311|consensus
Probab=97.73 E-value=2.6e-06 Score=81.78 Aligned_cols=52 Identities=21% Similarity=0.461 Sum_probs=44.7
Q ss_pred CCCCCcccccccccCcccEE-eCCCChhccHhhHHhhcCC-CCCCcccccccccc
Q psy3263 249 SISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQA 301 (329)
Q Consensus 249 ~l~~~~~C~IC~e~~~~~~~-lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~ 301 (329)
.+..+..|+||++..+.++. ..|+|. ||.+|+..-+.. ...||.||+.+...
T Consensus 39 ~~~~~v~c~icl~llk~tmttkeClhr-fc~~ci~~a~r~gn~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 39 MFDIQVICPICLSLLKKTMTTKECLHR-FCFDCIWKALRSGNNECPTCRKKLVSK 92 (381)
T ss_pred HhhhhhccHHHHHHHHhhcccHHHHHH-HHHHHHHHHHHhcCCCCchHHhhcccc
Confidence 45678999999999988774 479999 999999998887 89999999987544
No 72
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.72 E-value=3.1e-05 Score=66.36 Aligned_cols=93 Identities=15% Similarity=0.079 Sum_probs=63.0
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
-||..||++|++|++|++..|-+|++-...+ .+ ...|..++. +....... .. ..+
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdVVeys~--------D~------~~fI~N~l~--------PA~V~~V~--i~-~~~ 97 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIELIEYSE--------NL------EEFVANKLA--------PAEVKNVT--VS-EFN 97 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEEEEcCC--------CH------HHHHHHcCC--------CceEEEEE--EE-cCC
Confidence 3789999999999999999998888753322 21 122222210 00000000 00 113
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 121 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i 121 (329)
+.....+.||.+..++.|||+|.+|+...+-++-++.+
T Consensus 98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 45677899999999999999999999999999988865
No 73
>KOG0336|consensus
Probab=97.71 E-value=8.2e-05 Score=73.36 Aligned_cols=57 Identities=28% Similarity=0.196 Sum_probs=51.2
Q ss_pred eeeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263 3 IFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD 59 (329)
Q Consensus 3 ~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e 59 (329)
.|||.+|||||++||+||..||++|++-..+.+-.|+|-|..+--.+|+..|...++
T Consensus 56 ~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 56 EMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred hhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhhh
Confidence 489999999999999999999999999877778889999999988889888877654
No 74
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.70 E-value=7.3e-05 Score=78.89 Aligned_cols=62 Identities=23% Similarity=0.302 Sum_probs=50.2
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhhh
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQKI 150 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~~ 150 (329)
...++.||.+++|.|||+||.+||+|+++||++|.+.. +..|.|.+...+.++.+. +|.++.
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~ 640 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIA 640 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhh
Confidence 67789999999999999999999999999999999864 567999996666663222 444433
No 75
>KOG1588|consensus
Probab=97.70 E-value=7.8e-05 Score=69.36 Aligned_cols=32 Identities=34% Similarity=0.433 Sum_probs=29.8
Q ss_pred ceeeeeeecCCChHHHHHHHHhCCeEEecCCC
Q psy3263 2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRG 33 (329)
Q Consensus 2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~ 33 (329)
|+|||+|+|..|.++|+|+++|+|+|-|-.++
T Consensus 106 fNFVGRILGPrGnSlkrLe~eTgCki~IrGrg 137 (259)
T KOG1588|consen 106 FNFVGRILGPRGNSLKRLEEETGCKIMIRGRG 137 (259)
T ss_pred CccccccccCCcchHHHHHHHHCCeEEEecCC
Confidence 89999999999999999999999999996544
No 76
>KOG4159|consensus
Probab=97.69 E-value=1.7e-05 Score=78.57 Aligned_cols=50 Identities=34% Similarity=0.895 Sum_probs=45.9
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
+..+++|.||+..+..++.+||||. ||..|+.+.+.+...||.||..+..
T Consensus 81 ~~sef~c~vc~~~l~~pv~tpcghs-~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 81 IRSEFECCVCSRALYPPVVTPCGHS-FCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred ccchhhhhhhHhhcCCCcccccccc-ccHHHHHHHhccCCCCccccccccc
Confidence 3678999999999999999999999 9999999988889999999998854
No 77
>KOG1785|consensus
Probab=97.68 E-value=1.4e-05 Score=77.79 Aligned_cols=55 Identities=29% Similarity=0.798 Sum_probs=47.4
Q ss_pred cccccccccCcccEEeCCCChhccHhhHHhhcCC--CCCCcccccccccchhhhhhhh
Q psy3263 254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQAMRIIFNQF 309 (329)
Q Consensus 254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~~~~~i~~~~~ 309 (329)
..|.||-|..++..+-||||. +|..|+..|... ...||.||..|...-++....|
T Consensus 370 eLCKICaendKdvkIEPCGHL-lCt~CLa~WQ~sd~gq~CPFCRcEIKGte~viid~F 426 (563)
T KOG1785|consen 370 ELCKICAENDKDVKIEPCGHL-LCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVIIDPF 426 (563)
T ss_pred HHHHHhhccCCCcccccccch-HHHHHHHhhcccCCCCCCCceeeEeccccceeeecc
Confidence 589999999999999999999 999999999866 6899999999977666554433
No 78
>KOG0802|consensus
Probab=97.66 E-value=1.3e-05 Score=82.85 Aligned_cols=47 Identities=28% Similarity=0.704 Sum_probs=42.9
Q ss_pred CCCcccccccccCcc-----cEEeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263 251 SGSRQCYLCNDREVT-----HALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~-----~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
..+..|.||.|.+.. +..++|+|. ||..|++.|+++...||.||..+
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hi-fh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHI-FHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccc-hHHHHHHHHHHHhCcCCcchhhh
Confidence 346899999999988 789999999 99999999999999999999954
No 79
>KOG1100|consensus
Probab=97.56 E-value=2.4e-05 Score=71.20 Aligned_cols=48 Identities=40% Similarity=0.953 Sum_probs=40.4
Q ss_pred cccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhh
Q psy3263 254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 305 (329)
Q Consensus 254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~ 305 (329)
..|..|.+.....+++||.|.++|..|.... ..||+|+.+......++
T Consensus 159 ~~Cr~C~~~~~~VlllPCrHl~lC~~C~~~~----~~CPiC~~~~~s~~~v~ 206 (207)
T KOG1100|consen 159 RSCRKCGEREATVLLLPCRHLCLCGICDESL----RICPICRSPKTSSVEVN 206 (207)
T ss_pred ccceecCcCCceEEeecccceEecccccccC----ccCCCCcChhhceeecc
Confidence 3499999999999999999999999998753 57999999877665543
No 80
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.54 E-value=3.8e-05 Score=72.51 Aligned_cols=47 Identities=23% Similarity=0.675 Sum_probs=40.1
Q ss_pred CCcccccccccCcc---cEEeCCCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263 252 GSRQCYLCNDREVT---HALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVN 299 (329)
Q Consensus 252 ~~~~C~IC~e~~~~---~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~ 299 (329)
...+|.||++.+.. .+.+||.|. |-..|+.+|+.. ...||+||.++.
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~-FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHR-FHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCce-echhHHHHHHhhhcccCCccCCCCC
Confidence 34799999998742 347899999 999999999985 889999999874
No 81
>KOG4628|consensus
Probab=97.51 E-value=4e-05 Score=74.36 Aligned_cols=47 Identities=21% Similarity=0.647 Sum_probs=39.6
Q ss_pred cccccccccCccc---EEeCCCChhccHhhHHhhcCC-CCCCcccccccccc
Q psy3263 254 RQCYLCNDREVTH---ALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQA 301 (329)
Q Consensus 254 ~~C~IC~e~~~~~---~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~~ 301 (329)
..|.||+|.+..- ..|||.|. |-..|+..|+.+ ...||+|++.+...
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~-FH~~CIDpWL~~~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHK-FHVNCIDPWLTQTRTFCPVCKRDIRTD 280 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCc-hhhccchhhHhhcCccCCCCCCcCCCC
Confidence 4999999988643 36899999 999999999999 46699999987443
No 82
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.36 E-value=0.00028 Score=74.86 Aligned_cols=61 Identities=15% Similarity=0.173 Sum_probs=47.9
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-chhhhhhhh
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-GFESHHGQK 149 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-eie~~i~d~ 149 (329)
...++.||.+.+|.|||+||++||+|+++||++|.|-. +..|.|.+...+.+ +...+|..+
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---dG~V~i~~~~~~~~~~a~~~I~~~ 612 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---DGTVKIAASDGEAAEAAIKMIEGI 612 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---CeEEEEEECcHHHHHHHHHHHHhh
Confidence 67789999999999999999999999999999999954 46678887344444 333355443
No 83
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.36 E-value=0.00044 Score=61.92 Aligned_cols=51 Identities=20% Similarity=0.165 Sum_probs=47.2
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhh
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD 59 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e 59 (329)
.|+|||++|-|-+.|++-||++|.+- ...|-|-|..++|+.|+++|..+++
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~I~V~----g~tVaiiG~~~~v~iAr~AVemli~ 163 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVYISVY----GKTVAIIGGFEQVEIAREAVEMLIN 163 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCeEEEe----CcEEEEecChhhhHHHHHHHHHHHc
Confidence 48999999999999999999999998 6678999999999999999988864
No 84
>KOG2208|consensus
Probab=97.36 E-value=0.00013 Score=77.97 Aligned_cols=136 Identities=18% Similarity=0.219 Sum_probs=91.1
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCC-cceEEEecCHHHHHHHHHHHHHHhhhhh--------------Hhhhcc
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILSAADHFS--------------ALRASR 68 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~-ervi~ItG~~e~v~~A~~~I~~i~e~~~--------------~~~~~~ 68 (329)
++++||||||.+|+.++.++.+.|.+|...+ .+...+.|..+.+..+.-.|.+.+.+.. ......
T Consensus 211 ~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~~~~~~~~~~~~ 290 (753)
T KOG2208|consen 211 LHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEIIYRRLPRFIRGI 290 (753)
T ss_pred chhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhhhcccccccccc
Confidence 5789999999999999999999999995444 4555666666655555555444321000 000000
Q ss_pred c------------CCCCCCCCCCCC---------------------------CCCceEEEEEecCcccceeecCCCchHH
Q psy3263 69 K------------SGALSPLSPPTG---------------------------VPGHVTIEVRVPYKVVGLVVGPKGATIK 109 (329)
Q Consensus 69 ~------------~~~~~~~~~p~~---------------------------~~g~~t~~i~VP~~~vG~IIGkgG~tIk 109 (329)
. .......-++.. ......+.+.+-.+.+..|+||+|+.|.
T Consensus 291 ~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~~v~GK~~~ni~ 370 (753)
T KOG2208|consen 291 PGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELKFVIGKKGANIE 370 (753)
T ss_pred ccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhhhhcCCCCccHH
Confidence 0 000000000000 0123557788888999999999999999
Q ss_pred HHHHhcCceEEcCC-CCCCCeEEEECCCCCCc
Q psy3263 110 RIQHQTNTYIVTPS-RDKEPVFEVTGNFPEGP 140 (329)
Q Consensus 110 ~Iq~~tga~I~ip~-~~~e~~i~ItG~~pe~v 140 (329)
+|++++.+.|.++. .+++..+.++| .-.++
T Consensus 371 ki~e~~~~~i~~~~~~~~~~~v~~~~-~~~~~ 401 (753)
T KOG2208|consen 371 KIREESQVKIDLPKQGSNNKKVVITG-VSAND 401 (753)
T ss_pred HHHHhhhhceecccccCCCCCeEEec-cccch
Confidence 99999999999998 44778899999 88887
No 85
>KOG2879|consensus
Probab=97.35 E-value=0.00017 Score=67.31 Aligned_cols=49 Identities=27% Similarity=0.693 Sum_probs=42.0
Q ss_pred CCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCC--CCCCcccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDF--DRTCPMCRVPVN 299 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~ 299 (329)
.+.+.+|++|.+....|... +|||. ||..|+..-+.. ...||.|.....
T Consensus 236 ~t~~~~C~~Cg~~PtiP~~~~~C~Hi-yCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIPHVIGKCGHI-YCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred ccCCceeeccCCCCCCCeeeccccce-eehhhhhhhhcchhhcccCccCCCCc
Confidence 35678999999999999865 59999 999999887665 689999988764
No 86
>KOG2814|consensus
Probab=97.32 E-value=0.00034 Score=67.03 Aligned_cols=56 Identities=25% Similarity=0.204 Sum_probs=47.2
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCC--cceEEEecCHHHHHHHHHHHHHHhh
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE--EPVFVVTGRKEDVARAKREILSAAD 59 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~--ervi~ItG~~e~v~~A~~~I~~i~e 59 (329)
|.|.|||++|.|-|+|++||+++|.+|.+.+ +.++.+.+..+.|.+|.++|..+++
T Consensus 67 ~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~id 124 (345)
T KOG2814|consen 67 FIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLID 124 (345)
T ss_pred HhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999999997664 4444445578999999999988765
No 87
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.21 E-value=0.00037 Score=62.65 Aligned_cols=94 Identities=19% Similarity=0.145 Sum_probs=63.0
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
-||..||++|.+|+.|+++.|-+|++-...++ - ...|..++. +........- ..+
T Consensus 86 ~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d----------~----~~fI~nal~--------Pa~v~~V~~~---~~d 140 (190)
T COG0195 86 PVGACIGKRGSRVKAVSEELGEKIDVVEWSED----------P----AEFIKNALA--------PAEVLSVNIK---EDD 140 (190)
T ss_pred chhhhccCCChHHHHHHHHhCCceEEEEeCCC----------H----HHHHHHhcC--------cceEeEEEEE---eCC
Confidence 37899999999999999999977776422221 1 122222210 0000000000 001
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 123 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~ 123 (329)
+ ....+.||.+..++.|||+|.+++.+.+-||-+|.+-.
T Consensus 141 ~-~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 141 G-HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred C-cEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 2 26788899999999999999999999999999999854
No 88
>KOG1588|consensus
Probab=97.17 E-value=0.0012 Score=61.49 Aligned_cols=40 Identities=33% Similarity=0.597 Sum_probs=35.0
Q ss_pred CceEEEEEecC------cccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263 84 GHVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPS 123 (329)
Q Consensus 84 g~~t~~i~VP~------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~ 123 (329)
-..+..|.||. ++||.|+|++|.|+|+|+++|||+|-|=.
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 34677888876 58999999999999999999999999953
No 89
>KOG4692|consensus
Probab=97.13 E-value=0.0002 Score=68.94 Aligned_cols=50 Identities=22% Similarity=0.539 Sum_probs=45.4
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
..++..|+||+..+.++++.||+|. -|..|+.+.+.+.+.|-.|+..+..
T Consensus 419 ~sEd~lCpICyA~pi~Avf~PC~H~-SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 419 DSEDNLCPICYAGPINAVFAPCSHR-SCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred CcccccCcceecccchhhccCCCCc-hHHHHHHHHHhcCCeeeEecceeee
Confidence 3577899999999999999999999 9999999999999999999887643
No 90
>KOG2279|consensus
Probab=97.12 E-value=0.00049 Score=69.68 Aligned_cols=136 Identities=18% Similarity=0.161 Sum_probs=92.1
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCC---cceEEEecCHHHHHHHHHHHHHHhhhhh----------HhhhcccC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE---EPVFVVTGRKEDVARAKREILSAADHFS----------ALRASRKS 70 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~---ervi~ItG~~e~v~~A~~~I~~i~e~~~----------~~~~~~~~ 70 (329)
.|+.|+||+|++|+.++.-++++|.+-..+- .+...|.|....++.|+.++.+.++... +.|.-+..
T Consensus 150 ~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~ 229 (608)
T KOG2279|consen 150 SVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQ 229 (608)
T ss_pred hcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCC
Confidence 3789999999999999999999999986554 7888899999999999999877553211 11111100
Q ss_pred C-----CCC------C-------------CCCC--------------------CCCCC-------ceEEEEEecCcccce
Q psy3263 71 G-----ALS------P-------------LSPP--------------------TGVPG-------HVTIEVRVPYKVVGL 99 (329)
Q Consensus 71 ~-----~~~------~-------------~~~p--------------------~~~~g-------~~t~~i~VP~~~vG~ 99 (329)
. .++ . .+.+ .+.+| ...-.+.+|...+|.
T Consensus 230 p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~ 309 (608)
T KOG2279|consen 230 PINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGD 309 (608)
T ss_pred CccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccc
Confidence 0 000 0 0000 00001 122478899999999
Q ss_pred eecCCCchHHHHHHhcCceEEcCCCC-CCC-----eEEEECCCCCCc
Q psy3263 100 VVGPKGATIKRIQHQTNTYIVTPSRD-KEP-----VFEVTGNFPEGP 140 (329)
Q Consensus 100 IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~-----~i~ItG~~pe~v 140 (329)
+||..|++++.+...+++++.|-... ..+ ++.+.| ...-+
T Consensus 310 lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~eg-kqh~~ 355 (608)
T KOG2279|consen 310 LIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEG-KQHYE 355 (608)
T ss_pred hhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecc-hhHHH
Confidence 99999999999999999999886544 333 355666 44433
No 91
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.11 E-value=0.0004 Score=54.28 Aligned_cols=31 Identities=35% Similarity=0.730 Sum_probs=27.1
Q ss_pred EeCCCChhccHhhHHhhcCC---CCCCcccccccc
Q psy3263 268 LIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN 299 (329)
Q Consensus 268 ~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~ 299 (329)
.-.|+|. |-..|+.+|+.. ...||+||++..
T Consensus 49 ~g~C~H~-FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 49 WGKCSHN-FHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred eccCccH-HHHHHHHHHHccccCCCCCCCcCCeee
Confidence 4479999 999999999986 689999999764
No 92
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.03 E-value=0.0011 Score=70.13 Aligned_cols=51 Identities=18% Similarity=0.178 Sum_probs=44.3
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHh
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAA 58 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~ 58 (329)
+|.|||.||.+||+|+++||++|++.. +-.|.|.+ ..+.+++|+.+|..++
T Consensus 589 i~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~ 640 (719)
T TIGR02696 589 IGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIA 640 (719)
T ss_pred hhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhh
Confidence 688999999999999999999999973 34566766 6899999999999885
No 93
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.98 E-value=0.00025 Score=63.43 Aligned_cols=47 Identities=28% Similarity=0.631 Sum_probs=42.5
Q ss_pred CcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
.+.|.||...+..|+...|||. ||..|+.+-.+....|-+|.+....
T Consensus 196 PF~C~iCKkdy~spvvt~CGH~-FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 196 PFLCGICKKDYESPVVTECGHS-FCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred ceeehhchhhccchhhhhcchh-HHHHHHHHHhccCCcceecchhhcc
Confidence 3799999999999999999999 9999999988888999999886544
No 94
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.95 E-value=0.001 Score=70.62 Aligned_cols=52 Identities=19% Similarity=0.199 Sum_probs=43.5
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHh
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA 58 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~ 58 (329)
+|.|||+||.+||+|+++||++|++-. +..+.......+.+++|++.|..+.
T Consensus 562 I~~vIG~gGk~Ik~I~~~tg~~I~i~d--dG~V~i~~~~~~~~~~a~~~I~~~~ 613 (684)
T TIGR03591 562 IRDVIGPGGKVIREITEETGAKIDIED--DGTVKIAASDGEAAEAAIKMIEGIT 613 (684)
T ss_pred HHhhcCCCcHHHHHHHHHHCCEEEEec--CeEEEEEECcHHHHHHHHHHHHhhh
Confidence 688999999999999999999999963 3444444557899999999998774
No 95
>KOG0336|consensus
Probab=96.88 E-value=0.00049 Score=67.99 Aligned_cols=51 Identities=35% Similarity=0.473 Sum_probs=46.9
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEEC
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG 134 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG 134 (329)
+....-+.+-.++||.|||+||+.||+||..|.++|++-+.+.+-.|+|-|
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg 95 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFG 95 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEec
Confidence 455667888999999999999999999999999999999999888899999
No 96
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.88 E-value=0.0014 Score=59.08 Aligned_cols=33 Identities=27% Similarity=0.263 Sum_probs=29.6
Q ss_pred ceeeeeeecCCChHHHHHHHHhCCeEEecCCCC
Q psy3263 2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGE 34 (329)
Q Consensus 2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ 34 (329)
.+|||+|||..|.|.|+|++.|+|+|-|-..+.
T Consensus 162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gs 194 (269)
T COG5176 162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS 194 (269)
T ss_pred cceeEEEecCCcchHHHHHHHhCCeEEEecccc
Confidence 379999999999999999999999999975554
No 97
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.86 E-value=0.001 Score=65.42 Aligned_cols=92 Identities=14% Similarity=0.038 Sum_probs=65.1
Q ss_pred eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
||..||++|.+|++|.++. |=+|++-...+++. ..|..++. +...... .. . +
T Consensus 253 vGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~--------------~fI~Nal~--------Pa~V~~V--~i--~-~ 305 (374)
T PRK12328 253 IGATVGVKGVRINAVSKELNGENIDCIEYSNVPE--------------IFIARALA--------PAIISSV--KI--E-E 305 (374)
T ss_pred HHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhCC--------CceeeEE--EE--c-C
Confidence 7899999999999999998 87888764444322 22322210 0000000 00 1 2
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 123 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~ 123 (329)
......+.||.+..++.|||+|.+++-..+-||.+|.|-+
T Consensus 306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 3367889999999999999999999999999999999853
No 98
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.86 E-value=0.0012 Score=71.41 Aligned_cols=52 Identities=19% Similarity=0.258 Sum_probs=44.4
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCce-EEcCCCCCCCeEEEECCCCCCc
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY-IVTPSRDKEPVFEVTGNFPEGP 140 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~-I~ip~~~~e~~i~ItG~~pe~v 140 (329)
....+.||.+++|.|||+||.|||+|+++||+. |.+-. +-.|.|.+...+.+
T Consensus 685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---dg~V~I~a~d~~~i 737 (891)
T PLN00207 685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---DGTVKITAKDLSSL 737 (891)
T ss_pred eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---CeeEEEEeCCHHHH
Confidence 677899999999999999999999999999999 77744 45688888566666
No 99
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.83 E-value=0.0026 Score=62.18 Aligned_cols=93 Identities=19% Similarity=0.220 Sum_probs=65.0
Q ss_pred eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
||..||++|.+|+.|.++. |-+|++-...+++. ..|..++. +...... .-. . +
T Consensus 245 vga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~--------------~fi~nal~--------Pa~v~~v--~i~-~-~ 298 (341)
T TIGR01953 245 VGACVGPKGSRIQAISKELNGEKIDIIEYSDDPA--------------EFIANALS--------PAKVISV--EVL-D-E 298 (341)
T ss_pred ceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhcC--------CceEEEE--EEE-c-C
Confidence 7999999999999999998 88888764444332 12222210 0000000 000 1 1
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 123 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~ 123 (329)
......+.||.+..++.|||+|.+++-...-||.+|.|-+
T Consensus 299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 2357889999999999999999999999999999999854
No 100
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.82 E-value=0.0016 Score=47.69 Aligned_cols=37 Identities=22% Similarity=0.303 Sum_probs=34.2
Q ss_pred ceEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263 85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 121 (329)
Q Consensus 85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i 121 (329)
.....+.||.+.+|..|||+|.+|+.+++.+|-+|.+
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3788999999999999999999999999999988875
No 101
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.76 E-value=0.00095 Score=64.28 Aligned_cols=52 Identities=29% Similarity=0.760 Sum_probs=43.7
Q ss_pred CCCCCCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC--CCCCccccccc
Q psy3263 246 PSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPV 298 (329)
Q Consensus 246 ~~~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i 298 (329)
..+..+++..|.||-+...-..++||+|. .|.-|+-++..- .+.||+||..-
T Consensus 54 addtDEen~~C~ICA~~~TYs~~~PC~H~-~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 54 ADDTDEENMNCQICAGSTTYSARYPCGHQ-ICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccccccceeEEecCCceEEEeccCCch-HHHHHHHHHHHHHhccCCCcccccc
Confidence 34456788999999999888889999999 999999876444 78999999864
No 102
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.76 E-value=0.00071 Score=63.97 Aligned_cols=43 Identities=35% Similarity=0.717 Sum_probs=37.5
Q ss_pred cccccccccCcccEEeC-CCChhccHhhHHhhcCC-CCCCcccccc
Q psy3263 254 RQCYLCNDREVTHALIP-CGHNFFCSECAERTCDF-DRTCPMCRVP 297 (329)
Q Consensus 254 ~~C~IC~e~~~~~~~lp-CgH~~fC~~Cl~~~~~~-~~~CP~Cr~~ 297 (329)
+.|+.|..++.+++..| |+|. ||.+|+...+.. ...||.|...
T Consensus 275 LkCplc~~Llrnp~kT~cC~~~-fc~eci~~al~dsDf~CpnC~rk 319 (427)
T COG5222 275 LKCPLCHCLLRNPMKTPCCGHT-FCDECIGTALLDSDFKCPNCSRK 319 (427)
T ss_pred ccCcchhhhhhCcccCccccch-HHHHHHhhhhhhccccCCCcccc
Confidence 79999999999999775 6888 999999876665 8999999873
No 103
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.73 E-value=0.0037 Score=61.59 Aligned_cols=95 Identities=16% Similarity=0.149 Sum_probs=66.5
Q ss_pred eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
||..||++|.+|++|.++. |-+|++-...+++. ..|..++. +...... ... . +
T Consensus 247 vGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~--------------~fi~nal~--------Pa~v~~v--~i~-~-~ 300 (362)
T PRK12327 247 KGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPA--------------EFVANALS--------PAKVVSV--EVD-D-E 300 (362)
T ss_pred hheeECCCChhHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhCC--------CceEEEE--EEE-c-C
Confidence 7999999999999999998 88888764444321 22322210 0000000 000 1 2
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD 125 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~ 125 (329)
......+.||.+..++.|||+|.+++-...-||.+|.|-+.+
T Consensus 301 ~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 301 EEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred CCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 336788999999999999999999999999999999986544
No 104
>KOG0297|consensus
Probab=96.72 E-value=0.00085 Score=66.76 Aligned_cols=56 Identities=25% Similarity=0.611 Sum_probs=49.1
Q ss_pred CCCCCcccccccccCcccEE-eCCCChhccHhhHHhhcCCCCCCcccccccccchhhh
Q psy3263 249 SISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 305 (329)
Q Consensus 249 ~l~~~~~C~IC~e~~~~~~~-lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~ 305 (329)
++++++.|++|.....+|+. ..|||. ||..|+..+......||.|+..+.....+.
T Consensus 17 ~~~~~l~C~~C~~vl~~p~~~~~cgh~-fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~ 73 (391)
T KOG0297|consen 17 PLDENLLCPICMSVLRDPVQTTTCGHR-FCAGCLLESLSNHQKCPVCRQELTQAEELP 73 (391)
T ss_pred CCcccccCccccccccCCCCCCCCCCc-ccccccchhhccCcCCcccccccchhhccC
Confidence 37888999999999999998 599999 999999999888899999999886654443
No 105
>KOG1813|consensus
Probab=96.67 E-value=0.00083 Score=63.47 Aligned_cols=46 Identities=24% Similarity=0.678 Sum_probs=42.3
Q ss_pred cccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
+.|.||...+.+++...|+|. ||..|+..-.+....|++|.+.+..
T Consensus 242 f~c~icr~~f~~pVvt~c~h~-fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVVTKCGHY-FCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred ccccccccccccchhhcCCce-eehhhhccccccCCcceeccccccc
Confidence 679999999999999999999 9999999988888999999987754
No 106
>KOG1039|consensus
Probab=96.58 E-value=0.0011 Score=64.76 Aligned_cols=51 Identities=29% Similarity=0.759 Sum_probs=41.9
Q ss_pred CCCcccccccccCcccE-----E---eCCCChhccHhhHHhhcC--C-----CCCCcccccccccch
Q psy3263 251 SGSRQCYLCNDREVTHA-----L---IPCGHNFFCSECAERTCD--F-----DRTCPMCRVPVNQAM 302 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~-----~---lpCgH~~fC~~Cl~~~~~--~-----~~~CP~Cr~~i~~~~ 302 (329)
..+..|-||++...+.. + .+|.|. ||..|+..|.. + .+.||.||.......
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~-~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~ 224 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHS-FCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVN 224 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchh-hhhcHhHhhhhhhccccccccCCCcccCcccccc
Confidence 45789999999887766 4 679999 99999999983 3 589999999875544
No 107
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.58 E-value=0.0034 Score=63.89 Aligned_cols=93 Identities=18% Similarity=0.229 Sum_probs=65.2
Q ss_pred eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
||..||++|.+|+.|..+. |=+|++-...+++. ..|...+. .+ ..... .. . .
T Consensus 247 vga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~--------------~fi~nal~-----pa---~v~~v---~~-~-~ 299 (470)
T PRK09202 247 VGACVGMRGSRIQAISNELGGEKIDIILWSDDPA--------------QFIINALS-----PA---EVSSV---VV-D-E 299 (470)
T ss_pred hHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhCC-----CC---EEEEE---EE-e-C
Confidence 7999999999999999998 88888764444332 22222210 00 00000 00 0 1
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 124 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~ 124 (329)
......+.||....++-|||+|.+|+...+.||.+|.|-..
T Consensus 300 ~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 300 DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 12578899999999999999999999999999999998653
No 108
>KOG2660|consensus
Probab=96.54 E-value=0.00051 Score=65.76 Aligned_cols=51 Identities=24% Similarity=0.678 Sum_probs=44.6
Q ss_pred CCCCcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 301 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~ 301 (329)
+.....|.+|...+.++.++ -|-|. ||..|+.+.+.....||.|...+.+.
T Consensus 12 ~n~~itC~LC~GYliDATTI~eCLHT-FCkSCivk~l~~~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 12 LNPHITCRLCGGYLIDATTITECLHT-FCKSCIVKYLEESKYCPTCDIVIHKT 63 (331)
T ss_pred cccceehhhccceeecchhHHHHHHH-HHHHHHHHHHHHhccCCccceeccCc
Confidence 34567999999999999855 79999 99999999999899999999888554
No 109
>KOG0119|consensus
Probab=96.50 E-value=0.005 Score=61.87 Aligned_cols=57 Identities=30% Similarity=0.554 Sum_probs=43.5
Q ss_pred CceEEEEEecC------cccceeecCCCchHHHHHHhcCceEEcCC-----------CC-------CCCe-EEEECCCCC
Q psy3263 84 GHVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPS-----------RD-------KEPV-FEVTGNFPE 138 (329)
Q Consensus 84 g~~t~~i~VP~------~~vG~IIGkgG~tIk~Iq~~tga~I~ip~-----------~~-------~e~~-i~ItG~~pe 138 (329)
+..+.+|.||. ++||+|||..|.|.|+|+.+|||+|.|=. ++ +|++ +.|++.+-|
T Consensus 136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~e 215 (554)
T KOG0119|consen 136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQE 215 (554)
T ss_pred cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHH
Confidence 34556677764 78999999999999999999999999943 11 3444 788885556
Q ss_pred Cc
Q psy3263 139 GP 140 (329)
Q Consensus 139 ~v 140 (329)
+|
T Consensus 216 ki 217 (554)
T KOG0119|consen 216 KI 217 (554)
T ss_pred HH
Confidence 66
No 110
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.47 E-value=0.0054 Score=55.44 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=28.6
Q ss_pred cccceeecCCCchHHHHHHhcCceEEcCCCC
Q psy3263 95 KVVGLVVGPKGATIKRIQHQTNTYIVTPSRD 125 (329)
Q Consensus 95 ~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~ 125 (329)
++||+|||+.|.|.|++++.|+|+|-|-..-
T Consensus 163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred ceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 7999999999999999999999999996544
No 111
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.45 E-value=0.0056 Score=61.38 Aligned_cols=94 Identities=19% Similarity=0.173 Sum_probs=65.2
Q ss_pred eeeeecCCChHHHHHHHHh-CCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCC
Q psy3263 5 VVPSINPFGCKIKALRAKT-NTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 83 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~ 83 (329)
||..||++|.+|+.|..+. |=+|++-...+++. ..|..++. +...... ... . +
T Consensus 279 vGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~--------------~fI~NaLs--------PA~V~~V--~i~-~-~ 332 (449)
T PRK12329 279 VGACIGARGSRIQAVVNELRGEKIDVIRWSPDPA--------------TYIANALS--------PARVDEV--RLV-D-P 332 (449)
T ss_pred hhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHH--------------HHHHHhcC--------CceeeEE--EEE-c-C
Confidence 7999999999999999998 87888754444322 22222210 0000000 000 1 2
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCC
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 124 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~ 124 (329)
......+.||.+..++-|||+|.+++-...-||-+|.|-..
T Consensus 333 ~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 333 EGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373 (449)
T ss_pred CCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence 23567899999999999999999999999999999998653
No 112
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.32 E-value=0.006 Score=63.74 Aligned_cols=52 Identities=21% Similarity=0.287 Sum_probs=44.0
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP 140 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v 140 (329)
...++.|+.+.++-+||+||.+||+|.++||++|.+- ++..|.|.+...+.+
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie---ddGtv~i~~s~~~~~ 603 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE---DDGTVKIAASDGESA 603 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec---CCCcEEEEecchHHH
Confidence 6678899999999999999999999999999999996 455688888333444
No 113
>KOG0828|consensus
Probab=96.24 E-value=0.0017 Score=65.21 Aligned_cols=49 Identities=29% Similarity=0.686 Sum_probs=39.5
Q ss_pred CCCCcccccccccC-----------------cccEEeCCCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263 250 ISGSRQCYLCNDRE-----------------VTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVN 299 (329)
Q Consensus 250 l~~~~~C~IC~e~~-----------------~~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~ 299 (329)
.+....|+||+... .+.++.||.|. |-..|+.+|.+. +-.||+||.++.
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~Hi-fH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHI-FHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHH-HHHHHHHHHHhhhcccCCccCCCCC
Confidence 45678999999632 22456799998 999999999996 669999999875
No 114
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.19 E-value=0.0052 Score=65.47 Aligned_cols=62 Identities=18% Similarity=0.273 Sum_probs=45.8
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-chhhhhhhhh
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-GFESHHGQKI 150 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-eie~~i~d~~ 150 (329)
....+.||.+.++.+||+||.|||+|+++||+.|.+ +++-.|.|.+...+.+ +...+|..+.
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi---~d~G~v~i~~~~~~~~~~a~~~I~~~~ 616 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDI---EDDGTVKIAATDGEAAEAAKERIEGIT 616 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCcccc---CCCceEEEEcccHHHHHHHHHHHHHhc
Confidence 556777899999999999999999999999998877 3345677888445555 2223444433
No 115
>KOG0804|consensus
Probab=96.18 E-value=0.0029 Score=62.87 Aligned_cols=47 Identities=28% Similarity=0.663 Sum_probs=37.7
Q ss_pred CCCCcccccccccCcccE----EeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHA----LIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 299 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~----~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~ 299 (329)
+.+-..|+||+|++-.-+ ...|.|. |-..|+..|+. .+||+||.-..
T Consensus 172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hs-fh~~cl~~w~~--~scpvcR~~q~ 222 (493)
T KOG0804|consen 172 LTELPTCPVCLERMDSSTTGILTILCNHS-FHCSCLMKWWD--SSCPVCRYCQS 222 (493)
T ss_pred cccCCCcchhHhhcCccccceeeeecccc-cchHHHhhccc--CcChhhhhhcC
Confidence 455679999999886443 5799999 99999999976 58999987443
No 116
>PRK12704 phosphodiesterase; Provisional
Probab=95.99 E-value=0.018 Score=59.46 Aligned_cols=53 Identities=19% Similarity=0.339 Sum_probs=44.5
Q ss_pred ceEEEEEecC-cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCC
Q psy3263 85 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEG 139 (329)
Q Consensus 85 ~~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~ 139 (329)
.++-.|.+|+ ++-|.|||+-|.+||.+..-||+-|.|. |+..+|.|||..|-.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~~~~~r 262 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPIR 262 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc--CCCCeEEEecCChhh
Confidence 3556788998 7779999999999999999999999994 455678899966666
No 117
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=95.90 E-value=0.0043 Score=44.50 Aligned_cols=47 Identities=26% Similarity=0.721 Sum_probs=37.5
Q ss_pred CCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
.....|..|...-...+++||||. .|..|..-. ....||.|.+++..
T Consensus 5 ~~~~~~~~~~~~~~~~~~~pCgH~-I~~~~f~~~--rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 5 QPEQPCVFCGFVGTKGTVLPCGHL-ICDNCFPGE--RYNGCPFCGTPFEF 51 (55)
T ss_pred ccceeEEEccccccccccccccce-eeccccChh--hccCCCCCCCcccC
Confidence 345678899988888889999999 999997543 24789999998853
No 118
>PRK00468 hypothetical protein; Provisional
Probab=95.69 E-value=0.012 Score=45.03 Aligned_cols=31 Identities=29% Similarity=0.468 Sum_probs=27.6
Q ss_pred ceEEEEEecCcccceeecCCCchHHHHHHhc
Q psy3263 85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 115 (329)
Q Consensus 85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~t 115 (329)
...+++.|..+-+|.||||+|.+|+.|+.--
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3678899999999999999999999998753
No 119
>PRK02821 hypothetical protein; Provisional
Probab=95.65 E-value=0.012 Score=45.25 Aligned_cols=33 Identities=30% Similarity=0.383 Sum_probs=29.0
Q ss_pred ceEEEEEecCcccceeecCCCchHHHHHHhcCc
Q psy3263 85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNT 117 (329)
Q Consensus 85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga 117 (329)
...+.+.|..+-+|.||||+|.+|+.|+.--.+
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 377899999999999999999999999987543
No 120
>PRK12704 phosphodiesterase; Provisional
Probab=95.61 E-value=0.022 Score=58.79 Aligned_cols=54 Identities=15% Similarity=0.107 Sum_probs=44.0
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHhh
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAAD 59 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~e 59 (329)
|-|+||||.|-|||.|+.-||+-|-|. +...+|+|+| .+-.-+.|+..+..++.
T Consensus 221 mkgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 221 MKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPIRREIARLALEKLVQ 275 (520)
T ss_pred hhcceeCCCcchHHHHHHHhCCeEEEc--CCCCeEEEecCChhhHHHHHHHHHHHHh
Confidence 569999999999999999999998886 4456778999 56666678887777653
No 121
>KOG4367|consensus
Probab=95.59 E-value=0.0073 Score=59.90 Aligned_cols=37 Identities=24% Similarity=0.628 Sum_probs=34.1
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF 287 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~ 287 (329)
+++++.|+||..-+.+|.++||+|+ +|..|+..+..+
T Consensus 1 meeelkc~vc~~f~~epiil~c~h~-lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 1 MEEELKCPVCGSFYREPIILPCSHN-LCQACARNILVQ 37 (699)
T ss_pred CcccccCceehhhccCceEeecccH-HHHHHHHhhccc
Confidence 3678999999999999999999999 999999988766
No 122
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.59 E-value=0.0061 Score=42.63 Aligned_cols=42 Identities=29% Similarity=0.745 Sum_probs=21.6
Q ss_pred cccccccCc--ccEEe--CCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263 256 CYLCNDREV--THALI--PCGHNFFCSECAERTCDF-DRTCPMCRVPV 298 (329)
Q Consensus 256 C~IC~e~~~--~~~~l--pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i 298 (329)
|++|.+.+. +..+. +||+. .|..|..++.+. ...||-||+++
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~-IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQ-ICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS-----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCc-HHHHHHHHHHhccCCCCCCCCCCC
Confidence 677887662 22345 57998 999999999975 89999999875
No 123
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.42 E-value=0.014 Score=63.44 Aligned_cols=51 Identities=24% Similarity=0.201 Sum_probs=42.5
Q ss_pred eeeeecCCChHHHHHHHHhCCe-EEecCCCCcceEEEec-CHHHHHHHHHHHHHHh
Q psy3263 5 VVPSINPFGCKIKALRAKTNTY-IKTPVRGEEPVFVVTG-RKEDVARAKREILSAA 58 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~-I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~ 58 (329)
+|.|||.||.+||+|+++||+. |++-. +.. |.|.+ ..+.+++|+..|..+.
T Consensus 696 i~~vIG~GGktIk~I~eetg~~~Idi~d--dg~-V~I~a~d~~~i~~A~~~I~~l~ 748 (891)
T PLN00207 696 VNMIIGSGGKKVKSIIEETGVEAIDTQD--DGT-VKITAKDLSSLEKSKAIISSLT 748 (891)
T ss_pred HHHHhcCCchhHHHHHHHHCCCccCcCC--Cee-EEEEeCCHHHHHHHHHHHHHHh
Confidence 5789999999999999999999 88863 333 45555 7899999999998884
No 124
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.39 E-value=0.016 Score=42.48 Aligned_cols=25 Identities=12% Similarity=0.034 Sum_probs=23.2
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEe
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKT 29 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~i 29 (329)
+|..|||+|.+|+.++..+|-+|++
T Consensus 36 ~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 36 LGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred ceeeECCCCHHHHHHHHHHCCCeEE
Confidence 5899999999999999999988875
No 125
>KOG2814|consensus
Probab=95.38 E-value=0.0078 Score=57.87 Aligned_cols=53 Identities=21% Similarity=0.426 Sum_probs=45.9
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCC-CCCeEEEECCCCCCc
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGNFPEGP 140 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~-~e~~i~ItG~~pe~v 140 (329)
...+.|+..+.|.|||+.|.|-|+|+++|+++|.+|.+. +...|+|+| .-.++
T Consensus 58 ~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~-~~~~~ 111 (345)
T KOG2814|consen 58 SSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIG-ISRNC 111 (345)
T ss_pred hhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEee-hhHHH
Confidence 346789999999999999999999999999999999766 777788888 55555
No 126
>KOG1734|consensus
Probab=95.32 E-value=0.0092 Score=55.89 Aligned_cols=49 Identities=24% Similarity=0.594 Sum_probs=39.9
Q ss_pred CCCcccccccccCc----------ccEEeCCCChhccHhhHHhhcCC--CCCCccccccccc
Q psy3263 251 SGSRQCYLCNDREV----------THALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQ 300 (329)
Q Consensus 251 ~~~~~C~IC~e~~~----------~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~~ 300 (329)
.++..|.||-.... +...+.|+|. |-..|++-|+-. ...||.|+..++.
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHv-FHEfCIrGWcivGKkqtCPYCKekVdl 282 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHV-FHEFCIRGWCIVGKKQTCPYCKEKVDL 282 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheeeecccc-hHHHhhhhheeecCCCCCchHHHHhhH
Confidence 34679999987553 3346899999 999999999877 7899999988743
No 127
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.27 E-value=0.041 Score=56.75 Aligned_cols=58 Identities=17% Similarity=0.310 Sum_probs=45.7
Q ss_pred ceEEEEEecC-cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh
Q psy3263 85 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES 144 (329)
Q Consensus 85 ~~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~ 144 (329)
.++..|.+|+ ++-|.|||+-|.+||.+...||+-|.|. |+...|.|+|-.|-.-||+.
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~fdp~rreia~ 261 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPVRREIAR 261 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc--CCCCeEEecCCchHHHHHHH
Confidence 3556788999 6779999999999999999999999994 44557889995555444443
No 128
>KOG3002|consensus
Probab=95.26 E-value=0.013 Score=56.38 Aligned_cols=63 Identities=22% Similarity=0.494 Sum_probs=47.3
Q ss_pred CCCCCCCcccccccccCcccEEeCC--CChhccHhhHHhhcCCCCCCcccccccccchhhhhhhhhhhcch
Q psy3263 247 SGSISGSRQCYLCNDREVTHALIPC--GHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKLW 315 (329)
Q Consensus 247 ~~~l~~~~~C~IC~e~~~~~~~lpC--gH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~~~~~~~~~v~ 315 (329)
.....+-++|+||++....|.. .| ||. .|..|-.++ ...||.||.++. .+|.+..+.....+.
T Consensus 42 ~~~~~~lleCPvC~~~l~~Pi~-QC~nGHl-aCssC~~~~---~~~CP~Cr~~~g-~~R~~amEkV~e~~~ 106 (299)
T KOG3002|consen 42 TLLDLDLLDCPVCFNPLSPPIF-QCDNGHL-ACSSCRTKV---SNKCPTCRLPIG-NIRCRAMEKVAEAVL 106 (299)
T ss_pred cccchhhccCchhhccCcccce-ecCCCcE-ehhhhhhhh---cccCCccccccc-cHHHHHHHHHHHhce
Confidence 3344566899999999988864 66 898 999998655 578999999998 556666555555443
No 129
>KOG0825|consensus
Probab=95.17 E-value=0.0039 Score=65.58 Aligned_cols=51 Identities=24% Similarity=0.385 Sum_probs=42.0
Q ss_pred CCCcccccccccCcccE---EeCCCChhccHhhHHhhcCCCCCCcccccccccch
Q psy3263 251 SGSRQCYLCNDREVTHA---LIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM 302 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~---~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~ 302 (329)
.....|++|+....+-. -.+|+|- ||..|+..|......||+||..|.+.+
T Consensus 121 ~~~~~CP~Ci~s~~DqL~~~~k~c~H~-FC~~Ci~sWsR~aqTCPiDR~EF~~v~ 174 (1134)
T KOG0825|consen 121 HVENQCPNCLKSCNDQLEESEKHTAHY-FCEECVGSWSRCAQTCPVDRGEFGEVK 174 (1134)
T ss_pred hhhhhhhHHHHHHHHHhhccccccccc-cHHHHhhhhhhhcccCchhhhhhheee
Confidence 34578999997665543 3599999 999999999999999999999886654
No 130
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.16 E-value=0.015 Score=42.20 Aligned_cols=41 Identities=22% Similarity=0.344 Sum_probs=29.6
Q ss_pred CCcccccccccCcccEE-eCCCChhccHhhHHhhcCC--CCCCcc
Q psy3263 252 GSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDF--DRTCPM 293 (329)
Q Consensus 252 ~~~~C~IC~e~~~~~~~-lpCgH~~fC~~Cl~~~~~~--~~~CP~ 293 (329)
-.+.|+|.+..+.+|+. ..|+|. |..+.+..++.. ...||+
T Consensus 10 ~~~~CPiT~~~~~~PV~s~~C~H~-fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 10 ISLKCPITLQPFEDPVKSKKCGHT-FEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp --SB-TTTSSB-SSEEEESSS--E-EEHHHHHHHCTTTS-EE-SC
T ss_pred eccCCCCcCChhhCCcCcCCCCCe-ecHHHHHHHHHhcCCCCCCC
Confidence 35799999999999986 599999 999999999944 789998
No 131
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.14 E-value=0.034 Score=58.27 Aligned_cols=52 Identities=23% Similarity=0.306 Sum_probs=43.2
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC-HHHHHHHHHHHHHHhh
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREILSAAD 59 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~-~e~v~~A~~~I~~i~e 59 (329)
.+.+||+||.+||+|.++||++|++- ++..+.|.+. .+.+.+|+..|..+++
T Consensus 563 I~dvIG~gGk~I~~I~eetg~~Idie---ddGtv~i~~s~~~~~~~ak~~I~~i~~ 615 (692)
T COG1185 563 IRDVIGPGGKTIKAITEETGVKIDIE---DDGTVKIAASDGESAKKAKERIEAITR 615 (692)
T ss_pred HhhccCCcccchhhhhhhhCcEEEec---CCCcEEEEecchHHHHHHHHHHHHHHh
Confidence 35689999999999999999999997 3445567665 5899999999998853
No 132
>KOG1002|consensus
Probab=95.10 E-value=0.0063 Score=61.68 Aligned_cols=47 Identities=30% Similarity=0.759 Sum_probs=40.7
Q ss_pred CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC-----CCCCccccccc
Q psy3263 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPV 298 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~-----~~~CP~Cr~~i 298 (329)
.++.+|.+|.+...++....|.|. ||.-|+...... ...||+|...+
T Consensus 534 k~~~~C~lc~d~aed~i~s~ChH~-FCrlCi~eyv~~f~~~~nvtCP~C~i~L 585 (791)
T KOG1002|consen 534 KGEVECGLCHDPAEDYIESSCHHK-FCRLCIKEYVESFMENNNVTCPVCHIGL 585 (791)
T ss_pred cCceeecccCChhhhhHhhhhhHH-HHHHHHHHHHHhhhcccCCCCccccccc
Confidence 456899999999999999999999 999999776544 68999998876
No 133
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.07 E-value=0.027 Score=43.26 Aligned_cols=31 Identities=42% Similarity=0.588 Sum_probs=27.7
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHh
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQ 114 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~ 114 (329)
...++++.|...-+|.||||+|.||+.|+.-
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 3467899999999999999999999999865
No 134
>PRK00106 hypothetical protein; Provisional
Probab=95.05 E-value=0.055 Score=55.93 Aligned_cols=58 Identities=19% Similarity=0.343 Sum_probs=45.6
Q ss_pred ceEEEEEecC-cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh
Q psy3263 85 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES 144 (329)
Q Consensus 85 ~~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~ 144 (329)
.++..|.+|+ ++-|.|||+-|.+|+.+..-||+-|.|. |+...|.|+|-.|-.-||+.
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid--dtp~~v~lS~fdpvRReiAr 282 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID--DTPEVVVLSGFDPIRREIAR 282 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc--CCCCeEEEeCCChHHHHHHH
Confidence 3556788999 6779999999999999999999999994 45557889995554444433
No 135
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.92 E-value=0.25 Score=44.62 Aligned_cols=101 Identities=17% Similarity=0.151 Sum_probs=72.4
Q ss_pred eeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCCCc
Q psy3263 6 VPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGH 85 (329)
Q Consensus 6 G~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~g~ 85 (329)
-+|...+|..++.|-+..|++|.+. -++..+.|+|++..++.+...|.+++. ..
T Consensus 38 ~LLl~~~~~~L~~l~~~~~~~I~~~--~~~~~i~I~g~k~~~~~i~~~i~~~l~------------------------~i 91 (210)
T PF14611_consen 38 FLLLTGNGRILENLAARNGAKIEVS--RSENRIRITGTKSTAEYIEASINEILS------------------------NI 91 (210)
T ss_pred eeeecCCchHHHHHHHhcCceEEEe--cCCcEEEEEccHHHHHHHHHHHHHHHh------------------------hc
Confidence 4677889999999988889999997 445678999999999999999988853 11
Q ss_pred eEEEEEecCcccceee-c---CCCchHHHHHHhcCceEEcCCCCCCCeEEEEC
Q psy3263 86 VTIEVRVPYKVVGLVV-G---PKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG 134 (329)
Q Consensus 86 ~t~~i~VP~~~vG~II-G---kgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG 134 (329)
.+..+.++.-.--+.. + .....++.|++.|+++|....+++. +.|++
T Consensus 92 ~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~~~--~~i~~ 142 (210)
T PF14611_consen 92 RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDGNK--LKISW 142 (210)
T ss_pred EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCCCe--EEEEE
Confidence 4444555432111111 1 1356789999999999998776643 44444
No 136
>PRK01064 hypothetical protein; Provisional
Probab=94.85 E-value=0.038 Score=42.69 Aligned_cols=32 Identities=28% Similarity=0.436 Sum_probs=28.1
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhc
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 115 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~t 115 (329)
....+++.|..+-.|.+|||+|.+|+.||.-.
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 34678899999999999999999999998853
No 137
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.78 E-value=0.052 Score=55.98 Aligned_cols=54 Identities=15% Similarity=0.109 Sum_probs=43.1
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHhh
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAAD 59 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~e 59 (329)
|=|+||||.|-|||.|+.-||+-|-|. +...+|+|+| .|-.-+-|+..|..++.
T Consensus 215 ~kgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 215 MKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred hhccccCCCcchHHHHHHHhCceEEEc--CCCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 459999999999999999999998886 3345677888 67777778777766653
No 138
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.75 E-value=0.028 Score=59.94 Aligned_cols=51 Identities=20% Similarity=0.253 Sum_probs=42.1
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHh
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAA 58 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~ 58 (329)
++.+||.||.+||+|+++||++|++- ++ -.|.|.+ ..+.+++|++.|..+.
T Consensus 565 I~~vIG~gg~~ik~I~~~~~~~idi~--d~-G~v~i~~~~~~~~~~a~~~I~~~~ 616 (693)
T PRK11824 565 IRDVIGPGGKTIREITEETGAKIDIE--DD-GTVKIAATDGEAAEAAKERIEGIT 616 (693)
T ss_pred HHHHhcCCchhHHHHHHHHCCccccC--CC-ceEEEEcccHHHHHHHHHHHHHhc
Confidence 57899999999999999999988873 33 3356666 7899999999998874
No 139
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=94.73 E-value=0.022 Score=39.96 Aligned_cols=40 Identities=33% Similarity=0.775 Sum_probs=31.5
Q ss_pred ccccccc--cCcccEEeCCC-----ChhccHhhHHhhcCC--CCCCcccc
Q psy3263 255 QCYLCND--REVTHALIPCG-----HNFFCSECAERTCDF--DRTCPMCR 295 (329)
Q Consensus 255 ~C~IC~e--~~~~~~~lpCg-----H~~fC~~Cl~~~~~~--~~~CP~Cr 295 (329)
.|.||++ ...++...||. |. +-.+|+.+|... ...||+|+
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~-vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKY-VHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhH-HHHHHHHHHHHHcCCCcCCCCC
Confidence 4889997 44566778995 55 788999999966 56999995
No 140
>PRK00106 hypothetical protein; Provisional
Probab=94.60 E-value=0.067 Score=55.35 Aligned_cols=54 Identities=19% Similarity=0.126 Sum_probs=43.7
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHHhh
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAAD 59 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i~e 59 (329)
|=|+||||.|-|||.|+.-||+-|-|. +....|+|+| .|-.-+-|+..+..++.
T Consensus 236 mkGriIGreGrNir~~E~~tGvdliid--dtp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 236 MKGRIIGREGRNIRTLESLTGIDVIID--DTPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred hhcceeCCCcchHHHHHHHhCceEEEc--CCCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 459999999999999999999988886 4445677888 67777778877766653
No 141
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.56 E-value=0.024 Score=52.61 Aligned_cols=50 Identities=22% Similarity=0.234 Sum_probs=42.9
Q ss_pred EEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP 140 (329)
Q Consensus 88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v 140 (329)
..+.||..+++.+||++|.+|+.|.+.+++.|.+-. +-.|.|+|+.++++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---NG~VwI~~~~~~~~ 196 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---NGRIWIKGPDEEDE 196 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---CcEEEEeeCCHHHH
Confidence 568899999999999999999999999999999843 35688999555566
No 142
>KOG1001|consensus
Probab=94.53 E-value=0.015 Score=61.59 Aligned_cols=45 Identities=31% Similarity=0.885 Sum_probs=39.6
Q ss_pred cccccccccCcccEEeCCCChhccHhhHHhhcCC--CCCCccccccccc
Q psy3263 254 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQ 300 (329)
Q Consensus 254 ~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~~ 300 (329)
..|.+|.+ ...++..+|+|. ||.+|+....+. ...||.||..+..
T Consensus 455 ~~c~ic~~-~~~~~it~c~h~-~c~~c~~~~i~~~~~~~~~~cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRCGHD-FCVECLKKSIQQSENAPCPLCRNVLKE 501 (674)
T ss_pred cccccccc-cccceeecccch-HHHHHHHhccccccCCCCcHHHHHHHH
Confidence 79999999 777888999999 999999998887 5679999987743
No 143
>KOG0827|consensus
Probab=94.35 E-value=0.02 Score=56.16 Aligned_cols=44 Identities=27% Similarity=0.773 Sum_probs=33.4
Q ss_pred cccccccccCccc---E-EeCCCChhccHhhHHhhcCC---CCCCccccccc
Q psy3263 254 RQCYLCNDREVTH---A-LIPCGHNFFCSECAERTCDF---DRTCPMCRVPV 298 (329)
Q Consensus 254 ~~C~IC~e~~~~~---~-~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i 298 (329)
-.|.||.+.+-.. . +-.|||. |-..|+..|.+. .+.||.|+-.+
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~cGhi-fh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGTCGHI-FHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred ceeeEeccCCccccccccccchhhH-HHHHHHHHHHccCCccCCCCceeecc
Confidence 4899996654322 1 3359999 999999999998 46899999433
No 144
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.16 E-value=0.073 Score=49.40 Aligned_cols=53 Identities=23% Similarity=0.153 Sum_probs=42.8
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecC-HHHHHHHHHHHHHHhh
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREILSAAD 59 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~-~e~v~~A~~~I~~i~e 59 (329)
+++.+||++|.+|+.|.++|++.|.+-. +-.|-|.|. .+++++|++.|..+.+
T Consensus 155 ~i~~lig~~g~~i~~l~~~~~~~I~ig~---NG~VwI~~~~~~~~~~a~~~I~~~e~ 208 (235)
T PRK04163 155 KVPRVIGKKGSMINMLKEETGCDIIVGQ---NGRIWIKGPDEEDEEIAIEAIKKIER 208 (235)
T ss_pred HHHhhcCCCChhHhhhhhhhCcEEEEcC---CcEEEEeeCCHHHHHHHHHHHHHHHh
Confidence 4678999999999999999999999953 234567775 6699999999987643
No 145
>KOG3039|consensus
Probab=94.15 E-value=0.034 Score=51.53 Aligned_cols=48 Identities=25% Similarity=0.414 Sum_probs=41.8
Q ss_pred CCcccccccccCccc----EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 252 GSRQCYLCNDREVTH----ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 252 ~~~~C~IC~e~~~~~----~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
....|++|.+.+.++ ++-||||. ||.+|..++......||+|-.++..
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~V-v~~ecvEklir~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHV-VTKECVEKLIRKDMVDPVTDKPLKD 271 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcE-eeHHHHHHhccccccccCCCCcCcc
Confidence 457899999988765 36799999 9999999999999999999998744
No 146
>KOG3800|consensus
Probab=94.01 E-value=0.029 Score=53.07 Aligned_cols=43 Identities=28% Similarity=0.818 Sum_probs=33.5
Q ss_pred ccccccccC-cccE----EeCCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263 255 QCYLCNDRE-VTHA----LIPCGHNFFCSECAERTCDF-DRTCPMCRVPV 298 (329)
Q Consensus 255 ~C~IC~e~~-~~~~----~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i 298 (329)
.|++|.... .+|. .-+|+|+ .|.+|..++... ...||.|...+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~-lCEsCvd~iF~~g~~~CpeC~~iL 50 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHR-LCESCVDRIFSLGPAQCPECMVIL 50 (300)
T ss_pred CCcccccceecCccceeeeccccch-HHHHHHHHHHhcCCCCCCcccchh
Confidence 588887533 2332 2399999 999999999888 88999998765
No 147
>PRK00468 hypothetical protein; Provisional
Probab=93.80 E-value=0.034 Score=42.63 Aligned_cols=19 Identities=26% Similarity=0.202 Sum_probs=16.8
Q ss_pred eeeeecCCChHHHHHHHHh
Q psy3263 5 VVPSINPFGCKIKALRAKT 23 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~T 23 (329)
+|+||||+|.+|++||.--
T Consensus 41 ~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CcceecCCChhHHHHHHHH
Confidence 5999999999999999653
No 148
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=93.78 E-value=0.1 Score=44.88 Aligned_cols=85 Identities=21% Similarity=0.110 Sum_probs=56.2
Q ss_pred CCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHH---HHHHHHHHHHhhhhhHhhhcccCCCCCCC-CCCCCCCCce
Q psy3263 11 PFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDV---ARAKREILSAADHFSALRASRKSGALSPL-SPPTGVPGHV 86 (329)
Q Consensus 11 kgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v---~~A~~~I~~i~e~~~~~~~~~~~~~~~~~-~~p~~~~g~~ 86 (329)
..|.-||+|-.+-.-+|.+= ..+... +.|++.|.+++- +.. +... .+ ...
T Consensus 23 ~~~dli~~lAk~lrKRIvvR-----------~dps~l~~~e~A~~~I~~ivP------~ea----~i~di~F-----d~~ 76 (145)
T cd02410 23 EDGDLVKDLAKDLRKRIVIR-----------PDPSVLKPPEEAIKIILEIVP------EEA----GITDIYF-----DDD 76 (145)
T ss_pred cccHHHHHHHHHHhceEEEc-----------CChhhcCCHHHHHHHHHHhCC------Ccc----CceeeEe-----cCC
Confidence 45677777777777666653 333322 458888888741 110 0100 00 124
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 121 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i 121 (329)
|-+|.|-.+.-|++||++|.++++|..+||=.-.+
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEE
Confidence 56788888999999999999999999999987666
No 149
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.69 E-value=0.021 Score=61.51 Aligned_cols=49 Identities=22% Similarity=0.607 Sum_probs=39.0
Q ss_pred CCCCcccccccccCc-------ccEEeCCCChhccHhhHHhhcCC--CCCCcccccccc
Q psy3263 250 ISGSRQCYLCNDREV-------THALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN 299 (329)
Q Consensus 250 l~~~~~C~IC~e~~~-------~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~ 299 (329)
+.+..+|.||+.... ....-.|.|. |-..|+.+|... ...||+||..++
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknK-FH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNK-FHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhh-hhHHHHHHHHHhcCCCCCCccccccc
Confidence 567789999997542 1123469999 999999999988 789999998765
No 150
>PRK02821 hypothetical protein; Provisional
Probab=93.57 E-value=0.038 Score=42.59 Aligned_cols=21 Identities=24% Similarity=0.150 Sum_probs=18.2
Q ss_pred eeeeecCCChHHHHHHHHhCC
Q psy3263 5 VVPSINPFGCKIKALRAKTNT 25 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga 25 (329)
+|+||||+|.+|++||.--.+
T Consensus 42 ~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 42 LGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CcceeCCCCchHHHHHHHHHH
Confidence 699999999999999976544
No 151
>PF04641 Rtf2: Rtf2 RING-finger
Probab=93.48 E-value=0.049 Score=51.25 Aligned_cols=50 Identities=22% Similarity=0.453 Sum_probs=39.8
Q ss_pred CCCCcccccccccCcc----cEEeCCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263 250 ISGSRQCYLCNDREVT----HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 301 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~----~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~ 301 (329)
....+.|+|....+.. .++.||||. |+..++..+. ....||+|-.++...
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V-~s~~alke~k-~~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCV-FSEKALKELK-KSKKCPVCGKPFTEE 163 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCE-eeHHHHHhhc-ccccccccCCccccC
Confidence 3567899999987742 346699999 9999999995 356799999998644
No 152
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=93.46 E-value=0.043 Score=38.16 Aligned_cols=46 Identities=24% Similarity=0.691 Sum_probs=27.6
Q ss_pred ccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccccccch
Q psy3263 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM 302 (329)
Q Consensus 255 ~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~ 302 (329)
-|.-|+-.. .-++.|.....|..|+..++.....||+|..++...+
T Consensus 4 nCKsCWf~~--k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtki 49 (50)
T PF03854_consen 4 NCKSCWFAN--KGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTKI 49 (50)
T ss_dssp ---SS-S----SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----S
T ss_pred cChhhhhcC--CCeeeecchhHHHHHHHHHhccccCCCcccCcCcccc
Confidence 467777443 3478896555999999999999999999999886544
No 153
>KOG1645|consensus
Probab=93.45 E-value=0.044 Score=54.15 Aligned_cols=47 Identities=30% Similarity=0.635 Sum_probs=38.6
Q ss_pred CCcccccccccCccc-----EEeCCCChhccHhhHHhhcCC--CCCCcccccccc
Q psy3263 252 GSRQCYLCNDREVTH-----ALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN 299 (329)
Q Consensus 252 ~~~~C~IC~e~~~~~-----~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~ 299 (329)
....|+||++...-+ +.+.|||. |-.+|+++|+.+ ...||.|.....
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghl-Fgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHL-FGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred ccccCceeeeeeeecCceEEeeeccccc-ccHHHHHHHHhhhhhhhCcccCChhH
Confidence 357899999976543 36799999 999999999976 789999987653
No 154
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=93.41 E-value=0.13 Score=37.10 Aligned_cols=34 Identities=29% Similarity=0.481 Sum_probs=28.1
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceE
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I 119 (329)
..+.+.+.....|.+||++|.+|+.+++.++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 5556666666789999999999999999998665
No 155
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=93.34 E-value=0.088 Score=45.10 Aligned_cols=38 Identities=24% Similarity=0.289 Sum_probs=34.1
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 123 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~ 123 (329)
..+-+.|+...+|..||++|++||.|++..|-+|.+-.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 56778889999999999999999999999999998743
No 156
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.31 E-value=0.04 Score=41.52 Aligned_cols=35 Identities=26% Similarity=0.302 Sum_probs=30.2
Q ss_pred ceEEEEEecCcccceeecCCCchHHHHHHhcCceE
Q psy3263 85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119 (329)
Q Consensus 85 ~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I 119 (329)
...+.+.+..+..|.+|||+|.|++.||.-.+..+
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 46788999999999999999999999998765544
No 157
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=93.16 E-value=0.042 Score=53.11 Aligned_cols=48 Identities=25% Similarity=0.636 Sum_probs=37.3
Q ss_pred CCcccccccccCcc--cEEe--CCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263 252 GSRQCYLCNDREVT--HALI--PCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 300 (329)
Q Consensus 252 ~~~~C~IC~e~~~~--~~~l--pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~ 300 (329)
++..|+.|+|.+-. .-+. |||.. .|..|...+.+. ...||.||+.++.
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~-ic~fc~~~irq~lngrcpacrr~y~d 65 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQ-ICQFCYNNIRQNLNGRCPACRRKYDD 65 (480)
T ss_pred ccccCcccccccccccCCcccCCcccH-HHHHHHHHHHhhccCCChHhhhhccc
Confidence 34459999987642 2233 67888 999999999888 8999999998744
No 158
>KOG4739|consensus
Probab=92.96 E-value=0.045 Score=50.59 Aligned_cols=41 Identities=27% Similarity=0.771 Sum_probs=30.0
Q ss_pred ccccccccCc-ccE-EeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263 255 QCYLCNDREV-THA-LIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 255 ~C~IC~e~~~-~~~-~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
-|-.|+-... ++. ++.|+|. ||..|...... ..||+|++.+
T Consensus 5 hCn~C~~~~~~~~f~LTaC~Hv-fC~~C~k~~~~--~~C~lCkk~i 47 (233)
T KOG4739|consen 5 HCNKCFRFPSQDPFFLTACRHV-FCEPCLKASSP--DVCPLCKKSI 47 (233)
T ss_pred EeccccccCCCCceeeeechhh-hhhhhcccCCc--ccccccccee
Confidence 4667765443 333 6799999 99999876532 3899999985
No 159
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=92.89 E-value=0.056 Score=41.53 Aligned_cols=18 Identities=28% Similarity=0.303 Sum_probs=16.4
Q ss_pred eeeeecCCChHHHHHHHH
Q psy3263 5 VVPSINPFGCKIKALRAK 22 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~ 22 (329)
+|.+|||+|-+|++||.-
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 589999999999999964
No 160
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=92.79 E-value=0.04 Score=41.54 Aligned_cols=46 Identities=22% Similarity=0.541 Sum_probs=22.7
Q ss_pred CcccccccccCc-c---cEE----eCCCChhccHhhHHhhcCC-----------CCCCcccccccc
Q psy3263 253 SRQCYLCNDREV-T---HAL----IPCGHNFFCSECAERTCDF-----------DRTCPMCRVPVN 299 (329)
Q Consensus 253 ~~~C~IC~e~~~-~---~~~----lpCgH~~fC~~Cl~~~~~~-----------~~~CP~Cr~~i~ 299 (329)
+.+|.||+.... + +.+ -.|++. |-..|+..|+.. ...||.|++++.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~-fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKK-FHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT-----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCH-HHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 468999998754 2 211 267777 888999999764 236999999874
No 161
>PRK12705 hypothetical protein; Provisional
Probab=92.11 E-value=0.15 Score=52.57 Aligned_cols=52 Identities=13% Similarity=0.065 Sum_probs=37.3
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEec-CHHHHHHHHHHHHHH
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSA 57 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG-~~e~v~~A~~~I~~i 57 (329)
|=|+||||.|.|||.++..||+-|-|. +...+|+|++ .+..-+.|+..+..+
T Consensus 209 mkGriIGreGrNir~~E~~tGvdliid--dtp~~V~ls~fdp~rreia~~~l~~L 261 (508)
T PRK12705 209 MKGRIIGREGRNIRAFEGLTGVDLIID--DTPEAVVISSFNPIRREIARLTLEKL 261 (508)
T ss_pred hhccccCccchhHHHHHHhhCCceEec--CCccchhhcccCccchHHHHHHHHHH
Confidence 459999999999999999999998886 3333445555 355555555555544
No 162
>KOG4185|consensus
Probab=91.88 E-value=0.11 Score=49.36 Aligned_cols=44 Identities=30% Similarity=0.821 Sum_probs=37.0
Q ss_pred cccccccccCc------ccEEeCCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263 254 RQCYLCNDREV------THALIPCGHNFFCSECAERTCDF-DRTCPMCRVPV 298 (329)
Q Consensus 254 ~~C~IC~e~~~------~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i 298 (329)
..|-||-+.+. .|..+.|||. +|..|+..+... ...||.||.+.
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~-~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHT-ICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCccccccCcccCCcccccCce-ehHhHHHHHhcCceeeccCCCCcc
Confidence 47888987664 3567789999 999999999888 77899999984
No 163
>KOG0826|consensus
Probab=91.88 E-value=0.089 Score=50.68 Aligned_cols=47 Identities=19% Similarity=0.438 Sum_probs=39.0
Q ss_pred CCCcccccccccCcccEEe-CCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263 251 SGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~l-pCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
.+...|++|....+++..+ -.|-. ||..|+.........||+-..+.
T Consensus 298 ~~~~~CpvClk~r~Nptvl~vSGyV-fCY~Ci~~Yv~~~~~CPVT~~p~ 345 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTVLEVSGYV-FCYPCIFSYVVNYGHCPVTGYPA 345 (357)
T ss_pred CccccChhHHhccCCCceEEecceE-EeHHHHHHHHHhcCCCCccCCcc
Confidence 4557999999988877654 56888 99999999988889999976665
No 164
>KOG3273|consensus
Probab=91.69 E-value=0.078 Score=47.86 Aligned_cols=50 Identities=16% Similarity=0.091 Sum_probs=46.1
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHh
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA 58 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~ 58 (329)
+|+|+||+|.|=-.|+.-|.++|-+. +..|.|-|..+++..|++.|-+++
T Consensus 180 IGRiaGk~GkTkfaIEn~trtrIVla----d~kIHiLG~~~niriAR~avcsLI 229 (252)
T KOG3273|consen 180 IGRIAGKGGKTKFAIENVTRTRIVLA----DSKIHILGAFQNIRIARDAVCSLI 229 (252)
T ss_pred HHHhhcCCCcceeeeeccceeEEEec----CceEEEeecchhhHHHHHhhHhhh
Confidence 69999999999999999999999997 567899999999999999998874
No 165
>PRK01064 hypothetical protein; Provisional
Probab=91.68 E-value=0.11 Score=40.20 Aligned_cols=19 Identities=32% Similarity=0.284 Sum_probs=16.9
Q ss_pred eeeeecCCChHHHHHHHHh
Q psy3263 5 VVPSINPFGCKIKALRAKT 23 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~T 23 (329)
+|.+|||+|.+|++||.-.
T Consensus 41 ~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred ceEEECCCCccHHHHHHHH
Confidence 4999999999999999754
No 166
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=91.55 E-value=0.13 Score=37.12 Aligned_cols=23 Identities=22% Similarity=0.169 Sum_probs=20.7
Q ss_pred eeeeecCCChHHHHHHHHhCCeE
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYI 27 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I 27 (329)
.|.+|||+|.+|++|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 57899999999999999998665
No 167
>KOG1814|consensus
Probab=91.23 E-value=0.078 Score=52.51 Aligned_cols=34 Identities=24% Similarity=0.777 Sum_probs=27.8
Q ss_pred CCCcccccccccCcc---cEEeCCCChhccHhhHHhhc
Q psy3263 251 SGSRQCYLCNDREVT---HALIPCGHNFFCSECAERTC 285 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~---~~~lpCgH~~fC~~Cl~~~~ 285 (329)
.....|.||++...- -.++||+|. ||..|+....
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv-~Ck~C~kdY~ 218 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHV-FCKSCLKDYF 218 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchH-HHHHHHHHHH
Confidence 456899999998764 347899999 9999998764
No 168
>PRK12705 hypothetical protein; Provisional
Probab=91.09 E-value=0.41 Score=49.31 Aligned_cols=54 Identities=15% Similarity=0.236 Sum_probs=41.0
Q ss_pred ceEEEEEecC-cccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263 85 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP 140 (329)
Q Consensus 85 ~~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v 140 (329)
.++-.|.+|+ ++-|.|||+-|.+|+.+...||+-|.|...+ +.|.|++-.|..-
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp--~~V~ls~fdp~rr 251 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP--EAVVISSFNPIRR 251 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc--cchhhcccCccch
Confidence 3555778898 6669999999999999999999999995433 3466666344443
No 169
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=91.01 E-value=0.18 Score=43.94 Aligned_cols=20 Identities=20% Similarity=0.580 Sum_probs=17.6
Q ss_pred CCcccccccccCcccEEeCC
Q psy3263 252 GSRQCYLCNDREVTHALIPC 271 (329)
Q Consensus 252 ~~~~C~IC~e~~~~~~~lpC 271 (329)
++..|+||+|.+-++|+|-|
T Consensus 1 ed~~CpICme~PHNAVLLlC 20 (162)
T PF07800_consen 1 EDVTCPICMEHPHNAVLLLC 20 (162)
T ss_pred CCccCceeccCCCceEEEEe
Confidence 35689999999999999877
No 170
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=91.00 E-value=0.077 Score=39.97 Aligned_cols=28 Identities=25% Similarity=0.236 Sum_probs=22.5
Q ss_pred eeeeecCCChHHHHHHHHh-CCeEEecCC
Q psy3263 5 VVPSINPFGCKIKALRAKT-NTYIKTPVR 32 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~T-ga~I~ip~~ 32 (329)
||..||++|.+||.|.++. |-+|++=..
T Consensus 19 vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 19 VGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp HHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred ceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 6889999999999999999 888887533
No 171
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=90.90 E-value=0.19 Score=38.80 Aligned_cols=31 Identities=29% Similarity=0.475 Sum_probs=27.6
Q ss_pred EeCCCChhccHhhHHhhcCCCCCCcccccccc
Q psy3263 268 LIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 299 (329)
Q Consensus 268 ~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~ 299 (329)
.--|.|. |-..|+.+|+.....||++|+...
T Consensus 51 wG~CnHa-FH~HCI~rWL~Tk~~CPld~q~w~ 81 (88)
T COG5194 51 WGVCNHA-FHDHCIYRWLDTKGVCPLDRQTWV 81 (88)
T ss_pred EEecchH-HHHHHHHHHHhhCCCCCCCCceeE
Confidence 3479999 999999999999999999998763
No 172
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=90.84 E-value=0.19 Score=38.37 Aligned_cols=38 Identities=26% Similarity=0.444 Sum_probs=30.7
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 123 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~ 123 (329)
..+.+.+..+..|.+|||+|+|++.||.-+...++-..
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~~~ 61 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNRNT 61 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhhcc
Confidence 34667777788999999999999999998776665443
No 173
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=90.78 E-value=0.087 Score=40.02 Aligned_cols=35 Identities=26% Similarity=0.427 Sum_probs=29.6
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEE
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV 120 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ 120 (329)
..+.+.+....-|.|||++|++|++|.+..+-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 44677788899999999999999999988776664
No 174
>KOG2932|consensus
Probab=90.75 E-value=0.094 Score=50.18 Aligned_cols=43 Identities=37% Similarity=0.835 Sum_probs=29.9
Q ss_pred ccccccccCccc-EEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 255 QCYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 255 ~C~IC~e~~~~~-~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
-|.-|---.... ..+||.|. ||.+|+..- ..+.||.|--++..
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHv-FCl~CAr~~--~dK~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHV-FCLECARSD--SDKICPLCDDRVQR 135 (389)
T ss_pred eecccCCcceeeecccccchh-hhhhhhhcC--ccccCcCcccHHHH
Confidence 466665333322 26799999 999998654 36799999877643
No 175
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=90.74 E-value=0.13 Score=43.59 Aligned_cols=48 Identities=21% Similarity=0.736 Sum_probs=40.3
Q ss_pred CcccccccccCcccEEe----CCCChhccHhhHHhhcCC---CCCCcccccccccc
Q psy3263 253 SRQCYLCNDREVTHALI----PCGHNFFCSECAERTCDF---DRTCPMCRVPVNQA 301 (329)
Q Consensus 253 ~~~C~IC~e~~~~~~~l----pCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~~~ 301 (329)
--+|-||.|...+..++ =||-+ .|..|.-.+|+. .+.||+|+..+...
T Consensus 80 lYeCnIC~etS~ee~FLKPneCCgY~-iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 80 LYECNICKETSAEERFLKPNECCGYS-ICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred ceeccCcccccchhhcCCcccccchH-HHHHHHHHHHHHcccCCCCCccccccccc
Confidence 35899999988887765 38998 999999988887 78999999988543
No 176
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=90.30 E-value=0.19 Score=37.80 Aligned_cols=34 Identities=32% Similarity=0.380 Sum_probs=26.3
Q ss_pred EEEecCcc-----cceeecCCCchHHHHHHhc-CceEEcC
Q psy3263 89 EVRVPYKV-----VGLVVGPKGATIKRIQHQT-NTYIVTP 122 (329)
Q Consensus 89 ~i~VP~~~-----vG~IIGkgG~tIk~Iq~~t-ga~I~ip 122 (329)
.+.|-... +|..||++|++||.|.++. |-+|.+-
T Consensus 6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEE
Confidence 34455555 8999999999999999999 8888874
No 177
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=89.90 E-value=0.21 Score=50.54 Aligned_cols=43 Identities=28% Similarity=0.377 Sum_probs=38.2
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCC
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 126 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~ 126 (329)
+.....+.||.+.++.+|||+|.+|++|.+..|.+|.+-..+.
T Consensus 484 gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 484 GDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred cCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 4466789999999999999999999999999999999966553
No 178
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=89.70 E-value=0.1 Score=48.32 Aligned_cols=46 Identities=26% Similarity=0.756 Sum_probs=34.5
Q ss_pred CCccccccccc-Cccc--EEe--C-CCChhccHhhHHhhcCC-CCCCc--cccccc
Q psy3263 252 GSRQCYLCNDR-EVTH--ALI--P-CGHNFFCSECAERTCDF-DRTCP--MCRVPV 298 (329)
Q Consensus 252 ~~~~C~IC~e~-~~~~--~~l--p-CgH~~fC~~Cl~~~~~~-~~~CP--~Cr~~i 298 (329)
.+..|++|... .-+| .++ | |-|. +|.+|..++... ...|| -|.+-+
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHr-mCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHR-MCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHH-HHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 35689999853 3333 222 5 9999 999999999888 78899 786644
No 179
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=89.31 E-value=0.42 Score=41.07 Aligned_cols=36 Identities=19% Similarity=0.269 Sum_probs=32.5
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCceEEcC
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP 122 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip 122 (329)
.+-+.|....+|..||++|++||.|++..|-+|.+-
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 667788889999999999999999999999998874
No 180
>KOG4362|consensus
Probab=89.28 E-value=0.098 Score=55.11 Aligned_cols=48 Identities=19% Similarity=0.581 Sum_probs=41.8
Q ss_pred CCCcccccccccCcccEEeCCCChhccHhhHHhhcCC---CCCCcccccccc
Q psy3263 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN 299 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~ 299 (329)
....+|+||......++++.|.|. ||..|+...+.. ...||+|+..+.
T Consensus 19 ~k~lEc~ic~~~~~~p~~~kc~~~-~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 19 QKILECPICLEHVKEPSLLKCDHI-FLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred hhhccCCceeEEeeccchhhhhHH-HHhhhhhceeeccCccccchhhhhhhh
Confidence 456899999999999999999999 999999887766 578999997653
No 181
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=88.62 E-value=0.51 Score=36.62 Aligned_cols=36 Identities=17% Similarity=0.202 Sum_probs=29.8
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 121 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i 121 (329)
..++|.|-...-|+|||++|++|++|++.-.....+
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 346778888888999999999999999987666655
No 182
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=88.23 E-value=0.43 Score=41.60 Aligned_cols=48 Identities=21% Similarity=0.486 Sum_probs=36.1
Q ss_pred CCCCcccccccccCcccEEeCCCChh----ccHhhHHhhcCC--CCCCccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNF----FCSECAERTCDF--DRTCPMCRVPV 298 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~----fC~~Cl~~~~~~--~~~CP~Cr~~i 298 (329)
...+..|-||++... ....||.... .-.+|+++|... ...|++|+.++
T Consensus 5 s~~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 5 SLMDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCCCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 456789999998764 3345775321 246899999887 78999999987
No 183
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=88.13 E-value=0.85 Score=46.74 Aligned_cols=92 Identities=22% Similarity=0.122 Sum_probs=60.3
Q ss_pred eecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCCCCCCCCCceE
Q psy3263 8 SINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT 87 (329)
Q Consensus 8 IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~~p~~~~g~~t 87 (329)
++-+.|.-||+|-.+...||.+-++- .+ .-. -+.|++.|.+++- +..... .-.+ ...+
T Consensus 43 ~~~~~~dlik~lAk~lrKRI~iR~dP---sv--l~~---~e~A~~~I~eivP------~ea~i~---~i~F-----d~~t 100 (637)
T COG1782 43 LFAKDGDLIKDLAKDLRKRIIIRPDP---SV--LKP---PEEARKIILEIVP------EEAGIT---DIYF-----DDDT 100 (637)
T ss_pred HhccchhHHHHHHHHHhhceEeccCc---hh--cCC---HHHHHHHHHHhCc------cccCce---eEEe-----cCCC
Confidence 45567888899988888888874222 11 112 2457777877741 111100 0000 1245
Q ss_pred EEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 121 (329)
Q Consensus 88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i 121 (329)
-+|.|-.+.=|++|||+|++.++|.++||-.-++
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~i 134 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKI 134 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCccee
Confidence 6788889999999999999999999999875544
No 184
>KOG3579|consensus
Probab=87.95 E-value=0.38 Score=45.59 Aligned_cols=45 Identities=27% Similarity=0.715 Sum_probs=35.4
Q ss_pred CcccccccccCcccEEeCC----CChhccHhhHHhhcCC-----------CCCCccccccc
Q psy3263 253 SRQCYLCNDREVTHALIPC----GHNFFCSECAERTCDF-----------DRTCPMCRVPV 298 (329)
Q Consensus 253 ~~~C~IC~e~~~~~~~lpC----gH~~fC~~Cl~~~~~~-----------~~~CP~Cr~~i 298 (329)
.+.|.+|.|++.|+-++.| .|. ||+.|-+...++ ..+||+-...+
T Consensus 268 pLcCTLC~ERLEDTHFVQCPSVp~HK-FCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~v 327 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTHFVQCPSVPSHK-FCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNV 327 (352)
T ss_pred ceeehhhhhhhccCceeecCCCcccc-eecccCHHHHHhhcCCCceeCCCCCcCcccCCcc
Confidence 4899999999999999998 688 999998776554 24677665544
No 185
>PRK13764 ATPase; Provisional
Probab=87.85 E-value=0.35 Score=50.88 Aligned_cols=43 Identities=28% Similarity=0.317 Sum_probs=38.4
Q ss_pred CceEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCC
Q psy3263 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 126 (329)
Q Consensus 84 g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~ 126 (329)
......|.||.+.++.+|||||.+|++|.++.|.+|.+-..+.
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 4467889999999999999999999999999999999965553
No 186
>KOG4369|consensus
Probab=87.70 E-value=0.24 Score=54.81 Aligned_cols=53 Identities=21% Similarity=0.110 Sum_probs=46.0
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecC----CCCcceEEEecCHHHHHHHHHHHHHH
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPV----RGEEPVFVVTGRKEDVARAKREILSA 57 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~----~~~ervi~ItG~~e~v~~A~~~I~~i 57 (329)
..++|||||.+|+.+|+-||+.|.+-+ +..||.+.+.|+++.+.-|...|.-.
T Consensus 1351 ~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~ 1407 (2131)
T KOG4369|consen 1351 SSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLP 1407 (2131)
T ss_pred hhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccce
Confidence 468999999999999999999998853 22389999999999999999888654
No 187
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=86.91 E-value=0.14 Score=38.42 Aligned_cols=23 Identities=22% Similarity=0.147 Sum_probs=19.3
Q ss_pred eeeeecCCChHHHHHHHHhCCeE
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYI 27 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I 27 (329)
.|.||||.|.++++||.-.+..+
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHHHHH
Confidence 47899999999999998766544
No 188
>KOG4369|consensus
Probab=86.79 E-value=0.3 Score=54.13 Aligned_cols=61 Identities=15% Similarity=0.100 Sum_probs=50.7
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC----CCCCCeEEEECCCCCCcchhhhhh
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS----RDKEPVFEVTGNFPEGPGFESHHG 147 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~----~~~e~~i~ItG~~pe~veie~~i~ 147 (329)
..-.+.+|....-.|||+||.+|..++.-||+.|.+-+ +..||.+.+.| .|+.+..+.++.
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg-~p~~~r~a~~~I 1404 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKG-RPPSQRVATSPI 1404 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCC-CChhhhhhhccc
Confidence 34566788888899999999999999999999999965 22589999999 999996665443
No 189
>KOG1493|consensus
Probab=86.45 E-value=0.24 Score=37.96 Aligned_cols=29 Identities=31% Similarity=0.675 Sum_probs=25.3
Q ss_pred CCCChhccHhhHHhhcCC---CCCCcccccccc
Q psy3263 270 PCGHNFFCSECAERTCDF---DRTCPMCRVPVN 299 (329)
Q Consensus 270 pCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i~ 299 (329)
-|.|. |-..|+.+|... ...||+||+...
T Consensus 50 ~C~h~-fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 50 YCLHA-FHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred HHHHH-HHHHHHHHHhcCccccccCCcchheeE
Confidence 69998 999999999876 679999998653
No 190
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=86.33 E-value=0.34 Score=36.92 Aligned_cols=26 Identities=19% Similarity=0.147 Sum_probs=22.3
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEec
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTP 30 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip 30 (329)
.|.+|||.|+++++||--++..++-.
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHHhhc
Confidence 48899999999999999988776654
No 191
>KOG1428|consensus
Probab=86.17 E-value=0.37 Score=54.49 Aligned_cols=50 Identities=22% Similarity=0.637 Sum_probs=38.6
Q ss_pred CCCcccccccccCcc--c-EEeCCCChhccHhhHHhhcCC----------CCCCcccccccccc
Q psy3263 251 SGSRQCYLCNDREVT--H-ALIPCGHNFFCSECAERTCDF----------DRTCPMCRVPVNQA 301 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~--~-~~lpCgH~~fC~~Cl~~~~~~----------~~~CP~Cr~~i~~~ 301 (329)
..+..|.||+...-. | ..+.|+|. |-..|.+++++. .-.||+|..++...
T Consensus 3484 D~DDmCmICFTE~L~AAP~IqL~C~Hi-FHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~ 3546 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHI-FHLQCCRRVLENRWLGPRITFGFISCPICKNKINHI 3546 (3738)
T ss_pred ccCceEEEEehhhhCCCcceecCCccc-hhHHHHHHHHHhcccCCeeEEeeeecccccchhhhH
Confidence 456789999975532 2 36899999 999999888765 34899999887543
No 192
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=85.04 E-value=0.29 Score=37.12 Aligned_cols=23 Identities=22% Similarity=0.248 Sum_probs=19.7
Q ss_pred eeeecCCChHHHHHHHHhCCeEE
Q psy3263 6 VPSINPFGCKIKALRAKTNTYIK 28 (329)
Q Consensus 6 G~IIGkgG~~Ik~Lr~~Tga~I~ 28 (329)
|.+|||+|++|++|+++.+-.+.
T Consensus 37 ~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 37 GIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp HHHHTGGGHHHHHHHHHHHHHHH
T ss_pred cHhHHhhhHHHHHHHHHHHHHHh
Confidence 67999999999999998876654
No 193
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=84.90 E-value=0.92 Score=44.73 Aligned_cols=24 Identities=29% Similarity=0.733 Sum_probs=18.8
Q ss_pred ccHhhHHhhcCC-------------CCCCcccccccc
Q psy3263 276 FCSECAERTCDF-------------DRTCPMCRVPVN 299 (329)
Q Consensus 276 fC~~Cl~~~~~~-------------~~~CP~Cr~~i~ 299 (329)
-|.+|+.+|... ...||.||+.+.
T Consensus 315 WC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 315 WCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred HHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 488999887532 468999999875
No 194
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=84.72 E-value=0.8 Score=37.37 Aligned_cols=32 Identities=25% Similarity=0.546 Sum_probs=26.4
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCce
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY 118 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~ 118 (329)
.++|.|-...-|+|||++|++|++|++.....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 36677777778999999999999998876554
No 195
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=84.68 E-value=0.46 Score=37.72 Aligned_cols=33 Identities=30% Similarity=0.721 Sum_probs=26.8
Q ss_pred CCCCcccccccccCcccE--EeCCCChhccHhhHHh
Q psy3263 250 ISGSRQCYLCNDREVTHA--LIPCGHNFFCSECAER 283 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~--~lpCgH~~fC~~Cl~~ 283 (329)
+.++..|.+|...+...+ ..||||. |...|+.|
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~p~~~v-~H~~C~~r 109 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVFPCGHV-VHYSCIKR 109 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEeCCCeE-EecccccC
Confidence 456778999999887655 5699998 99999764
No 196
>PHA03096 p28-like protein; Provisional
Probab=84.60 E-value=0.47 Score=45.38 Aligned_cols=42 Identities=21% Similarity=0.245 Sum_probs=30.4
Q ss_pred cccccccccCcc--------cEEeCCCChhccHhhHHhhcCC---CCCCccccc
Q psy3263 254 RQCYLCNDREVT--------HALIPCGHNFFCSECAERTCDF---DRTCPMCRV 296 (329)
Q Consensus 254 ~~C~IC~e~~~~--------~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~ 296 (329)
..|.||++.... ..+-.|-|. ||..|+..|... ...||.||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~-fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHE-FNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcH-HHHHHHHHHHHhhhhcccCccccc
Confidence 789999986542 234589999 999999988665 444555544
No 197
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=84.29 E-value=0.61 Score=36.17 Aligned_cols=26 Identities=15% Similarity=0.243 Sum_probs=22.0
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEec
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTP 30 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip 30 (329)
-|.+|||+|++|++|+++-.....++
T Consensus 41 Pg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 41 TQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred CceEECCCchhHHHHHHHHHHHhCCC
Confidence 37899999999999999987766664
No 198
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=84.00 E-value=1.1 Score=39.46 Aligned_cols=36 Identities=11% Similarity=0.108 Sum_probs=30.0
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcC
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP 122 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip 122 (329)
..+-+.|-... |+-|||+|.+||++++..|-+|.+-
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 34555665555 9999999999999999999999974
No 199
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=83.73 E-value=0.84 Score=40.25 Aligned_cols=26 Identities=23% Similarity=0.086 Sum_probs=23.7
Q ss_pred eeeecCCChHHHHHHHHhCCeEEecC
Q psy3263 6 VPSINPFGCKIKALRAKTNTYIKTPV 31 (329)
Q Consensus 6 G~IIGkgG~~Ik~Lr~~Tga~I~ip~ 31 (329)
|.-|||+|.+||+|+++.|-+|.+-.
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEE
Confidence 67899999999999999999998863
No 200
>KOG2930|consensus
Probab=83.72 E-value=0.54 Score=38.08 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=26.1
Q ss_pred EeCCCChhccHhhHHhhcCCCCCCcccccc
Q psy3263 268 LIPCGHNFFCSECAERTCDFDRTCPMCRVP 297 (329)
Q Consensus 268 ~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~ 297 (329)
---|.|. |-.-|+.+|++....||+|.+.
T Consensus 78 WG~CNHa-FH~hCisrWlktr~vCPLdn~e 106 (114)
T KOG2930|consen 78 WGVCNHA-FHFHCISRWLKTRNVCPLDNKE 106 (114)
T ss_pred eeecchH-HHHHHHHHHHhhcCcCCCcCcc
Confidence 3479999 9999999999999999999775
No 201
>KOG2874|consensus
Probab=83.64 E-value=1.8 Score=41.18 Aligned_cols=47 Identities=23% Similarity=0.314 Sum_probs=41.2
Q ss_pred eeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHH
Q psy3263 7 PSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSA 57 (329)
Q Consensus 7 ~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i 57 (329)
++||..|.|+|+|+=-|+|+|-+. ...|.+.|+...+..+++-+.+-
T Consensus 162 RLiGpng~TLKAlelLT~CYilVq----G~TVsaiGpfkGlkevr~IV~Dc 208 (356)
T KOG2874|consen 162 RLIGPNGSTLKALELLTNCYILVQ----GNTVSAIGPFKGLKEVRKIVEDC 208 (356)
T ss_pred HhcCCCchhHHHHHHHhhcEEEee----CcEEEeecCcchHHHHHHHHHHH
Confidence 589999999999999999999997 45678889999999988887663
No 202
>KOG3161|consensus
Probab=82.83 E-value=0.51 Score=49.34 Aligned_cols=43 Identities=21% Similarity=0.581 Sum_probs=32.9
Q ss_pred CCCcccccccccC----cccEEeCCCChhccHhhHHhhcCCCCCCcccccc
Q psy3263 251 SGSRQCYLCNDRE----VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 297 (329)
Q Consensus 251 ~~~~~C~IC~e~~----~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~ 297 (329)
.+-+.|.||+..+ ..|+.+-|||. .|..|++.+.. ..|| |...
T Consensus 9 ~~~l~c~ic~n~f~~~~~~Pvsl~cght-ic~~c~~~lyn--~scp-~~~D 55 (861)
T KOG3161|consen 9 VLLLLCDICLNLFVVQRLEPVSLQCGHT-ICGHCVQLLYN--ASCP-TKRD 55 (861)
T ss_pred HHHhhchHHHHHHHHHhcCcccccccch-HHHHHHHhHhh--ccCC-CCcc
Confidence 3457899997665 35778899999 99999988755 5777 5543
No 203
>PHA02862 5L protein; Provisional
Probab=82.67 E-value=0.92 Score=39.03 Aligned_cols=44 Identities=23% Similarity=0.577 Sum_probs=33.9
Q ss_pred cccccccccCcccEEeCCCChh----ccHhhHHhhcCC--CCCCccccccc
Q psy3263 254 RQCYLCNDREVTHALIPCGHNF----FCSECAERTCDF--DRTCPMCRVPV 298 (329)
Q Consensus 254 ~~C~IC~e~~~~~~~lpCgH~~----fC~~Cl~~~~~~--~~~CP~Cr~~i 298 (329)
..|-||++...+. ..||..+. .-.+|+.+|... ...|++|+.++
T Consensus 3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY 52 (156)
T PHA02862 3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKY 52 (156)
T ss_pred CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeE
Confidence 5799999987554 46875321 346999999987 78999999987
No 204
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=81.63 E-value=0.6 Score=32.82 Aligned_cols=43 Identities=26% Similarity=0.455 Sum_probs=21.1
Q ss_pred cccccccccCcccE-EeCCCChhccHhhH---HhhcCC-CCCCcccccc
Q psy3263 254 RQCYLCNDREVTHA-LIPCGHNFFCSECA---ERTCDF-DRTCPMCRVP 297 (329)
Q Consensus 254 ~~C~IC~e~~~~~~-~lpCgH~~fC~~Cl---~~~~~~-~~~CP~Cr~~ 297 (329)
+.|++.+.....|+ ...|.|. -|++=. ....+. ...||+|.++
T Consensus 3 L~CPls~~~i~~P~Rg~~C~H~-~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVRGKNCKHL-QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SSEEEETT--SS---EEHHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEeCccCCcCccc-ceECHHHHHHHhhccCCeECcCCcCc
Confidence 67999999999998 5699998 554331 111112 6789999864
No 205
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=81.14 E-value=2.5 Score=44.88 Aligned_cols=36 Identities=33% Similarity=0.374 Sum_probs=31.9
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 121 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i 121 (329)
.|-+|.|-.+.-|+||||+|+|+++|.++||=.-++
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~ 128 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKV 128 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeE
Confidence 456788889999999999999999999999987666
No 206
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=80.45 E-value=1.8 Score=33.59 Aligned_cols=29 Identities=17% Similarity=0.397 Sum_probs=22.9
Q ss_pred EEEEecCcccceeecCCCchHHHHHHhcC
Q psy3263 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTN 116 (329)
Q Consensus 88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tg 116 (329)
+++.|-...-|.+||++|++|+++++.-.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l~ 68 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEILE 68 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHHH
Confidence 45555557789999999999999987753
No 207
>KOG1067|consensus
Probab=80.22 E-value=1.8 Score=44.93 Aligned_cols=51 Identities=20% Similarity=0.232 Sum_probs=40.6
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP 140 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v 140 (329)
...++.|+......+||++|-..|+|+.+||+.-. -++..|+|-.+++..+
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~----vDe~t~~i~A~~~~am 647 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQ----VDEGTFSIFAPTQAAM 647 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceee----ecCceEEEEecCHHHH
Confidence 67789999999999999999999999999994322 2566788888444444
No 208
>KOG4445|consensus
Probab=79.95 E-value=0.34 Score=46.27 Aligned_cols=46 Identities=24% Similarity=0.584 Sum_probs=34.3
Q ss_pred CCcccccccccCccc---EEeCCCChhccHhhHHhhcC----------------------C-CCCCccccccc
Q psy3263 252 GSRQCYLCNDREVTH---ALIPCGHNFFCSECAERTCD----------------------F-DRTCPMCRVPV 298 (329)
Q Consensus 252 ~~~~C~IC~e~~~~~---~~lpCgH~~fC~~Cl~~~~~----------------------~-~~~CP~Cr~~i 298 (329)
....|+||+--+.+. ...+|-|. |-..|+.+.+. + ...||+||..+
T Consensus 114 p~gqCvICLygfa~~~~ft~T~C~Hy-~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i 185 (368)
T KOG4445|consen 114 PNGQCVICLYGFASSPAFTVTACDHY-MHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERI 185 (368)
T ss_pred CCCceEEEEEeecCCCceeeehhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhc
Confidence 357899999777543 35699998 88889876542 1 45799999987
No 209
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=78.52 E-value=1 Score=38.20 Aligned_cols=34 Identities=26% Similarity=0.644 Sum_probs=26.2
Q ss_pred CcccccccccCcc---cEEeCCCChh-----ccHhhHHhhcC
Q psy3263 253 SRQCYLCNDREVT---HALIPCGHNF-----FCSECAERTCD 286 (329)
Q Consensus 253 ~~~C~IC~e~~~~---~~~lpCgH~~-----fC~~Cl~~~~~ 286 (329)
..+|.||++...+ .+.++||-.+ ||.+|+.+|..
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 5799999998766 3456887432 99999999943
No 210
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=76.74 E-value=3.9 Score=38.11 Aligned_cols=53 Identities=25% Similarity=0.169 Sum_probs=39.5
Q ss_pred ceeeeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHH-HHHHHHHHHHH
Q psy3263 2 FIFVVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKED-VARAKREILSA 57 (329)
Q Consensus 2 ~~~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~-v~~A~~~I~~i 57 (329)
+..|-++|||+|+.++.|.++|++.|-+-.++- |=|.|..+. .+.|...|..+
T Consensus 154 p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG~---IWV~~~~~~~e~~~~~aI~~i 207 (239)
T COG1097 154 PSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNGR---IWVDGENESLEELAIEAIRKI 207 (239)
T ss_pred hhhcceEecCCCcHHHHhhhhcCeEEEEecCCE---EEecCCCcchHHHHHHHHHHH
Confidence 346778999999999999999999999975543 567777663 44455555443
No 211
>KOG2114|consensus
Probab=76.46 E-value=1.6 Score=47.11 Aligned_cols=48 Identities=25% Similarity=0.599 Sum_probs=37.6
Q ss_pred cccccccccCcccE-EeCCCChhccHhhHHhhcCCCCCCcccccccccchhhh
Q psy3263 254 RQCYLCNDREVTHA-LIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 305 (329)
Q Consensus 254 ~~C~IC~e~~~~~~-~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~ 305 (329)
..|..|--.+.-|+ ...|||. |-..|+. +....||.|+.........+
T Consensus 841 skCs~C~~~LdlP~VhF~CgHs-yHqhC~e---~~~~~CP~C~~e~~~~m~l~ 889 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVHFLCGHS-YHQHCLE---DKEDKCPKCLPELRGVMDLK 889 (933)
T ss_pred eeecccCCccccceeeeecccH-HHHHhhc---cCcccCCccchhhhhhHHHH
Confidence 48999998877665 6799999 9999998 34789999998665544433
No 212
>KOG1941|consensus
Probab=76.01 E-value=0.85 Score=45.13 Aligned_cols=45 Identities=29% Similarity=0.640 Sum_probs=36.1
Q ss_pred CCcccccccccCc----ccEEeCCCChhccHhhHHhhcCC--CCCCcccccc
Q psy3263 252 GSRQCYLCNDREV----THALIPCGHNFFCSECAERTCDF--DRTCPMCRVP 297 (329)
Q Consensus 252 ~~~~C~IC~e~~~----~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~ 297 (329)
-.+-|-.|-+..- .--.+||.|- |-..|+..++++ ...||.||+-
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHI-fH~rCl~e~L~~n~~rsCP~Crkl 414 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHI-FHLRCLQEILENNGTRSCPNCRKL 414 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHH-HHHHHHHHHHHhCCCCCCccHHHH
Confidence 4578999987552 2225799999 999999999887 8899999953
No 213
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=75.77 E-value=2.5 Score=39.21 Aligned_cols=64 Identities=17% Similarity=0.279 Sum_probs=40.2
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhhhhhhhc
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQKIVFILT 155 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~~~~~~~ 155 (329)
..++|.|....=|+|||++|+.|++|++.-...+... +..|.|. .-++-++.| ++++.+..-+|
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~----~v~I~i~--EV~~peL~A~lvA~~IA~qLE 115 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE----NVQINIE--EVKKPELDAQLVAESIAQQLE 115 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCC----CceEEEE--EcCCCCcCHHHHHHHHHHHHH
Confidence 4567888888889999999999999877654433332 1222222 112224555 66666665555
No 214
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=75.08 E-value=2 Score=33.36 Aligned_cols=20 Identities=20% Similarity=0.042 Sum_probs=17.2
Q ss_pred eeeeecCCChHHHHHHHHhC
Q psy3263 5 VVPSINPFGCKIKALRAKTN 24 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tg 24 (329)
-|.+|||+|++|++|++.-.
T Consensus 49 pg~iIGk~G~~I~~l~~~l~ 68 (85)
T cd02411 49 PGMVIGRGGKNIRELTEILE 68 (85)
T ss_pred CCceECCCchhHHHHHHHHH
Confidence 47899999999999998753
No 215
>KOG1423|consensus
Probab=74.81 E-value=8.9 Score=37.40 Aligned_cols=32 Identities=28% Similarity=0.487 Sum_probs=25.5
Q ss_pred ceEEEEEecC-cccceeecCCCchHHHHHHhcC
Q psy3263 85 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTN 116 (329)
Q Consensus 85 ~~t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~tg 116 (329)
....++.||. +...+||||||..|++|-++.+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 3566788888 5667999999999999977643
No 216
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=73.75 E-value=3.6 Score=38.44 Aligned_cols=29 Identities=21% Similarity=0.307 Sum_probs=22.1
Q ss_pred EEEEEecC-cccceeecCCCchHHHHHHhc
Q psy3263 87 TIEVRVPY-KVVGLVVGPKGATIKRIQHQT 115 (329)
Q Consensus 87 t~~i~VP~-~~vG~IIGkgG~tIk~Iq~~t 115 (329)
...|.|.. .+-|.|||++|++||+|....
T Consensus 222 ~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 222 HALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 34566766 445999999999999996654
No 217
>KOG2817|consensus
Probab=73.33 E-value=2.4 Score=42.06 Aligned_cols=48 Identities=19% Similarity=0.438 Sum_probs=38.0
Q ss_pred CCCCcccccccccC---cccEEeCCCChhccHhhHHhhcCC---CCCCccccccc
Q psy3263 250 ISGSRQCYLCNDRE---VTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPV 298 (329)
Q Consensus 250 l~~~~~C~IC~e~~---~~~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~i 298 (329)
+..-+.|+|=.+.- .-|+.+.|||. .|.+-+.++.+. ..+||.|-...
T Consensus 331 fHSvF~CPVlKeqtsdeNPPm~L~CGHV-ISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 331 FHSVFICPVLKEQTSDENPPMMLICGHV-ISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred ccceeecccchhhccCCCCCeeeeccce-ecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 45568899876543 45788999999 999999999888 48999997643
No 218
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=71.23 E-value=4.1 Score=37.90 Aligned_cols=48 Identities=25% Similarity=0.333 Sum_probs=40.0
Q ss_pred EEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCC
Q psy3263 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEG 139 (329)
Q Consensus 88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~ 139 (329)
.-+.||...|..+||++|+.++-+.+.|+|.|.+-.+- .|=|.| ..+.
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG---~IWV~~-~~~~ 195 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG---RIWVDG-ENES 195 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC---EEEecC-CCcc
Confidence 45788999999999999999999999999999995543 366777 6664
No 219
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=71.17 E-value=2.4 Score=34.59 Aligned_cols=23 Identities=22% Similarity=0.199 Sum_probs=19.5
Q ss_pred eeeeecCCChHHHHHHHHhCCeE
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYI 27 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I 27 (329)
-|.||||.|++|++|+++.....
T Consensus 72 Pg~vIG~~G~~i~~L~~~l~~~~ 94 (109)
T cd02412 72 PGIIIGKKGAGIEKLRKELQKLL 94 (109)
T ss_pred CCcccCCchHHHHHHHHHHHHHh
Confidence 48899999999999998876553
No 220
>KOG1940|consensus
Probab=69.98 E-value=2.4 Score=40.31 Aligned_cols=50 Identities=24% Similarity=0.542 Sum_probs=36.6
Q ss_pred cccccccccC----cccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhhh
Q psy3263 254 RQCYLCNDRE----VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 305 (329)
Q Consensus 254 ~~C~IC~e~~----~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~ 305 (329)
.-|++|.+.. ..+..++|||. .=..|........-.||+|.+ +......+
T Consensus 159 ~ncPic~e~l~~s~~~~~~~~CgH~-~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~ 212 (276)
T KOG1940|consen 159 FNCPICKEYLFLSFEDAGVLKCGHY-MHSRCFEEMICEGYTCPICSK-PGDMSHYF 212 (276)
T ss_pred CCCchhHHHhccccccCCccCcccc-hHHHHHHHHhccCCCCCcccc-hHHHHHHH
Confidence 3499999755 44557899998 668888887666789999999 54433333
No 221
>KOG1812|consensus
Probab=69.41 E-value=1.8 Score=43.20 Aligned_cols=40 Identities=25% Similarity=0.810 Sum_probs=27.7
Q ss_pred CcccccccccCccc----EEeCCCChhccHhhHHhhcCC------CCCCcc
Q psy3263 253 SRQCYLCNDREVTH----ALIPCGHNFFCSECAERTCDF------DRTCPM 293 (329)
Q Consensus 253 ~~~C~IC~e~~~~~----~~lpCgH~~fC~~Cl~~~~~~------~~~CP~ 293 (329)
..+|.||+...... ....|+|. ||.+|..+..+. ...||-
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~-fC~~C~k~~iev~~~~~~~~~C~~ 195 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHR-FCKDCVKQHIEVKLLSGTVIRCPH 195 (384)
T ss_pred cccCccCccccccHhhhHHHhcccch-hhhHHhHHHhhhhhccCCCccCCC
Confidence 46899999333222 14579999 999999987663 456653
No 222
>PRK15494 era GTPase Era; Provisional
Probab=69.16 E-value=5.2 Score=39.00 Aligned_cols=28 Identities=21% Similarity=0.366 Sum_probs=21.4
Q ss_pred EEEEecC-cccceeecCCCchHHHHHHhc
Q psy3263 88 IEVRVPY-KVVGLVVGPKGATIKRIQHQT 115 (329)
Q Consensus 88 ~~i~VP~-~~vG~IIGkgG~tIk~Iq~~t 115 (329)
..|.|.. .+-+.|||++|++||+|....
T Consensus 275 ~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 275 QVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 4566766 455899999999999986543
No 223
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=68.82 E-value=3 Score=38.72 Aligned_cols=21 Identities=24% Similarity=0.246 Sum_probs=17.7
Q ss_pred eeeecCCChHHHHHHHHhCCe
Q psy3263 6 VPSINPFGCKIKALRAKTNTY 26 (329)
Q Consensus 6 G~IIGkgG~~Ik~Lr~~Tga~ 26 (329)
|.+|||+|++|++|+++....
T Consensus 63 g~VIGk~G~~I~~L~~~l~k~ 83 (233)
T COG0092 63 GLVIGKKGSNIEKLRKELEKL 83 (233)
T ss_pred cceEcCCCccHHHHHHHHHHH
Confidence 789999999999998875433
No 224
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=68.22 E-value=4.6 Score=36.40 Aligned_cols=32 Identities=22% Similarity=0.358 Sum_probs=27.5
Q ss_pred EecCcccceeecCCCchHHHHHHhcCceEEcC
Q psy3263 91 RVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP 122 (329)
Q Consensus 91 ~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip 122 (329)
.+-...+|..||++|++||.|++..|-+|.+-
T Consensus 81 ~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVV 112 (190)
T COG0195 81 VVKIDPVGACIGKRGSRVKAVSEELGEKIDVV 112 (190)
T ss_pred ecCcCchhhhccCCChHHHHHHHHhCCceEEE
Confidence 33447889999999999999999999888874
No 225
>PRK13764 ATPase; Provisional
Probab=68.05 E-value=2.5 Score=44.56 Aligned_cols=31 Identities=26% Similarity=0.219 Sum_probs=26.9
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCc
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEE 35 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~e 35 (329)
++.+|||+|.+|++|+.+.|..|++-..+++
T Consensus 492 ~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~ 522 (602)
T PRK13764 492 IPKVIGKGGKRIKKIEKKLGIDIDVRPLDEE 522 (602)
T ss_pred hhHHhccCcchHHHHHHHhCCceEEEEcccc
Confidence 5789999999999999999999999655543
No 226
>PRK00089 era GTPase Era; Reviewed
Probab=66.85 E-value=6.1 Score=37.13 Aligned_cols=28 Identities=25% Similarity=0.489 Sum_probs=20.7
Q ss_pred EEEEecC-cccceeecCCCchHHHHHHhc
Q psy3263 88 IEVRVPY-KVVGLVVGPKGATIKRIQHQT 115 (329)
Q Consensus 88 ~~i~VP~-~~vG~IIGkgG~tIk~Iq~~t 115 (329)
..|.|.. .+-+.|||++|++||+|....
T Consensus 228 ~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 228 ATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 3455655 445899999999999986553
No 227
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=66.79 E-value=2.7 Score=42.92 Aligned_cols=31 Identities=23% Similarity=0.240 Sum_probs=26.7
Q ss_pred eeeeeecCCChHHHHHHHHhCCeEEecCCCC
Q psy3263 4 FVVPSINPFGCKIKALRAKTNTYIKTPVRGE 34 (329)
Q Consensus 4 ~VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ 34 (329)
+++.+|||+|.+|++|+.+.|-+|++-..++
T Consensus 496 ~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 496 YIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred HhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 3578999999999999999999999964444
No 228
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=65.93 E-value=12 Score=33.51 Aligned_cols=62 Identities=11% Similarity=0.176 Sum_probs=51.1
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-chhhhhhhhhh
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-GFESHHGQKIV 151 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-eie~~i~d~~~ 151 (329)
.+.+.++....=++...+|..++.|....|++|.+....+ .|.|+| +...+ .|+.+|.+++.
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~~--~i~I~g-~k~~~~~i~~~i~~~l~ 89 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRSEN--RIRITG-TKSTAEYIEASINEILS 89 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecCCc--EEEEEc-cHHHHHHHHHHHHHHHh
Confidence 3445556778889999999999999888999999976665 699999 88888 77778887776
No 229
>KOG2231|consensus
Probab=65.88 E-value=3.6 Score=43.65 Aligned_cols=46 Identities=30% Similarity=0.608 Sum_probs=37.8
Q ss_pred ccccccccCcccEEeCCCChhccHhhHHhhcCC------CCCCccccccccc
Q psy3263 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDF------DRTCPMCRVPVNQ 300 (329)
Q Consensus 255 ~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~------~~~CP~Cr~~i~~ 300 (329)
.|.||-........-.|||+-.|..|..++... ...||+||..+..
T Consensus 2 ~c~ic~~s~~~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~ 53 (669)
T KOG2231|consen 2 SCAICAFSPDFVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVET 53 (669)
T ss_pred CcceeecCccccccccccccccchhhhhhhhhhcccccccccCcccccceee
Confidence 699999999888889999977999999887544 4567999986633
No 230
>COG1159 Era GTPase [General function prediction only]
Probab=65.81 E-value=5.8 Score=38.16 Aligned_cols=28 Identities=29% Similarity=0.503 Sum_probs=21.3
Q ss_pred EEEEecC-cccceeecCCCchHHHHHHhc
Q psy3263 88 IEVRVPY-KVVGLVVGPKGATIKRIQHQT 115 (329)
Q Consensus 88 ~~i~VP~-~~vG~IIGkgG~tIk~Iq~~t 115 (329)
..|.|+. .+=|.||||+|++||+|-..+
T Consensus 231 a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 231 ATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 3566776 445999999999999985543
No 231
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=65.33 E-value=6.1 Score=40.70 Aligned_cols=38 Identities=13% Similarity=0.128 Sum_probs=34.3
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCC
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 123 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~ 123 (329)
..+.+.||...|..|||-||..|.+++..-++.|++..
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n 486 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKN 486 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhh
Confidence 45678899999999999999999999999999999864
No 232
>KOG0825|consensus
Probab=64.81 E-value=2.6 Score=45.29 Aligned_cols=34 Identities=21% Similarity=0.281 Sum_probs=27.2
Q ss_pred CCCChhccHhhHHhhcCC------CCCCcccccccccchhh
Q psy3263 270 PCGHNFFCSECAERTCDF------DRTCPMCRVPVNQAMRI 304 (329)
Q Consensus 270 pCgH~~fC~~Cl~~~~~~------~~~CP~Cr~~i~~~~~i 304 (329)
.|+|+ ||..|+..|..+ ...|++|..-|..+-++
T Consensus 120 ~~~~~-~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~ 159 (1134)
T KOG0825|consen 120 THVEN-QCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC 159 (1134)
T ss_pred hhhhh-hhhHHHHHHHHHhhccccccccccHHHHhhhhhhh
Confidence 49999 999999998776 56789998877555544
No 233
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=64.70 E-value=6.7 Score=33.82 Aligned_cols=25 Identities=16% Similarity=0.049 Sum_probs=22.8
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEe
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKT 29 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~i 29 (329)
-|.+|||+|.++++|..+||=+-.+
T Consensus 87 PG~ViGk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 87 PGLVIGKGGSTLREITRETGWAPKV 111 (145)
T ss_pred CeEEEecCchhHHHHHHHhCCeeEE
Confidence 4899999999999999999988766
No 234
>KOG2068|consensus
Probab=64.22 E-value=4.9 Score=39.06 Aligned_cols=49 Identities=29% Similarity=0.708 Sum_probs=37.4
Q ss_pred CCcccccccccC--cccEE--eCCCChhccHhhHHhhcCCCCCCcccccccccc
Q psy3263 252 GSRQCYLCNDRE--VTHAL--IPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 301 (329)
Q Consensus 252 ~~~~C~IC~e~~--~~~~~--lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~ 301 (329)
....|++|.+.. .+... .||+|. .|..|+..+......||.||++....
T Consensus 248 v~~s~p~~~~~~~~~d~~~lP~~~~~~-~~l~~~~t~~~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 248 VPPSCPICYEDLDLTDSNFLPCPCGFR-LCLFCHKTISDGDGRCPGCRKPYERN 300 (327)
T ss_pred cCCCCCCCCCccccccccccccccccc-chhhhhhcccccCCCCCccCCccccC
Confidence 345788888855 22223 378999 99999999999999999999876543
No 235
>KOG0298|consensus
Probab=63.19 E-value=1.9 Score=48.55 Aligned_cols=48 Identities=29% Similarity=0.626 Sum_probs=40.6
Q ss_pred CCCCcccccccccCc-ccEEeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263 250 ISGSRQCYLCNDREV-THALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 250 l~~~~~C~IC~e~~~-~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
+-....|.+|.+... .....-|||. +|..|...|......||.|....
T Consensus 1150 ~~~~~~c~ic~dil~~~~~I~~cgh~-~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1150 LSGHFVCEICLDILRNQGGIAGCGHE-PCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred hhcccchHHHHHHHHhcCCeeeechh-HhhhHHHHHHHHhccCcchhhhh
Confidence 345569999999887 5557799998 99999999999999999998543
No 236
>CHL00048 rps3 ribosomal protein S3
Probab=62.53 E-value=7.6 Score=35.62 Aligned_cols=66 Identities=18% Similarity=0.138 Sum_probs=40.4
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhhhhhhhc
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQKIVFILT 155 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~~~~~~~ 155 (329)
..++|.|-...-|+|||++|++|++|++.-.-..... ++...|.|.- ... .++.| .+++++..-+|
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~k~~~~~--~~~i~I~v~e-v~~-p~~~A~~iA~~ia~~Le 132 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINLQKELNSV--NRKLNINITE-VKK-PYGEPNILAEYIAGQLE 132 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHHHHHhCCC--CceEEEEEEE-ecC-CCcCHHHHHHHHHHHHh
Confidence 3466777777889999999999999988764333221 1222243433 111 24444 66666665555
No 237
>KOG1067|consensus
Probab=62.17 E-value=4.1 Score=42.38 Aligned_cols=50 Identities=20% Similarity=0.191 Sum_probs=39.0
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcceEEE-ecCHHHHHHHHHHHHHHh
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVV-TGRKEDVARAKREILSAA 58 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~I-tG~~e~v~~A~~~I~~i~ 58 (329)
+-.+||.+|-+.|+|+.|||+.-++. +..+.| .-++.+.++|++.|..+.
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~vD----e~t~~i~A~~~~am~~Ak~~I~~i~ 658 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQVD----EGTFSIFAPTQAAMEEAKEFIDGII 658 (760)
T ss_pred hheeecCccceeeeEeeeccceeeec----CceEEEEecCHHHHHHHHHHHHHHh
Confidence 34689999999999999999655554 444455 456788899999998873
No 238
>KOG3842|consensus
Probab=61.97 E-value=5 Score=38.85 Aligned_cols=47 Identities=34% Similarity=0.745 Sum_probs=31.6
Q ss_pred CCCcccccccccC-------------------cccEEeCCCChhccHhhHHhhcCC----------CCCCcccccccc
Q psy3263 251 SGSRQCYLCNDRE-------------------VTHALIPCGHNFFCSECAERTCDF----------DRTCPMCRVPVN 299 (329)
Q Consensus 251 ~~~~~C~IC~e~~-------------------~~~~~lpCgH~~fC~~Cl~~~~~~----------~~~CP~Cr~~i~ 299 (329)
..+.+|++|+..- -.-++-||||. |.+=....|.+ ...||.|-..+.
T Consensus 339 ~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv--~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ 414 (429)
T KOG3842|consen 339 QRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHV--CSEKTVKYWSQIPLPHGTHAFHAACPFCATQLA 414 (429)
T ss_pred cccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccc--cchhhhhHhhcCcCCCccccccccCcchhhhhc
Confidence 3468999998632 12245799995 76665555544 468999988763
No 239
>KOG2874|consensus
Probab=60.38 E-value=9.2 Score=36.48 Aligned_cols=49 Identities=22% Similarity=0.350 Sum_probs=38.7
Q ss_pred ceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCc-chhhhhhhhhh
Q psy3263 98 GLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGP-GFESHHGQKIV 151 (329)
Q Consensus 98 G~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~v-eie~~i~d~~~ 151 (329)
-.+||+.|+|+|.|+=.|.|||-+-.. +|.+.| .=..+ ++...+.|-++
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~----TVsaiG-pfkGlkevr~IV~DcM~ 210 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN----TVSAIG-PFKGLKEVRKIVEDCMK 210 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc----EEEeec-CcchHHHHHHHHHHHHh
Confidence 368999999999999999999998543 577888 66666 66667776554
No 240
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=58.22 E-value=10 Score=34.30 Aligned_cols=64 Identities=19% Similarity=0.315 Sum_probs=39.0
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhhhhhhhcC
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQKIVFILTS 156 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~~~~~~~~ 156 (329)
.++|.|....-|.|||++|++|++|++.-.-.... +...|.|.- .. +-++.| .+++++..-++.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~----~~~~I~v~e-v~-~p~l~A~lvA~~Ia~qLe~ 103 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGL----ENPQIDVEE-VE-NPELNAQVQAERIARSLER 103 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHHHhCC----CceEEEEEE-Ee-CCCcCHHHHHHHHHHHHHc
Confidence 36677777778999999999999998876443321 112233322 11 114444 666777766663
No 241
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=58.17 E-value=14 Score=37.52 Aligned_cols=44 Identities=25% Similarity=0.391 Sum_probs=31.9
Q ss_pred CCCCCCCceEEEEEe----cC-cccceeecCCCchHHHHHHhc-CceEEcC
Q psy3263 78 PPTGVPGHVTIEVRV----PY-KVVGLVVGPKGATIKRIQHQT-NTYIVTP 122 (329)
Q Consensus 78 ~p~~~~g~~t~~i~V----P~-~~vG~IIGkgG~tIk~Iq~~t-ga~I~ip 122 (329)
||...||..|. |.| |. +-||..||++|++|+.|.+.. |=+|.+-
T Consensus 256 ~~~ripG~RtK-VAV~S~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI 305 (449)
T PRK12329 256 PPSRYVGPRTK-IAVDTLERDVDPVGACIGARGSRIQAVVNELRGEKIDVI 305 (449)
T ss_pred CCCCCCcceeE-EEEEcCCCCCChhhccCCCCcchHHHHHHHhCCCeEEEE
Confidence 34455665543 222 22 668999999999999998887 8899874
No 242
>KOG3799|consensus
Probab=58.06 E-value=3.4 Score=35.21 Aligned_cols=44 Identities=32% Similarity=0.785 Sum_probs=28.2
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCC------------CCCCccccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF------------DRTCPMCRVPV 298 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~------------~~~CP~Cr~~i 298 (329)
..++-.|-||..... .--|||+ |.+|-.+.+.. ...|-+|+...
T Consensus 62 v~ddatC~IC~KTKF---ADG~GH~--C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~q 117 (169)
T KOG3799|consen 62 VGDDATCGICHKTKF---ADGCGHN--CSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQQ 117 (169)
T ss_pred cCcCcchhhhhhccc---ccccCcc--cchhhhhHHHhcCCeeeeccCceEEeccCCcHHH
Confidence 356789999996432 2379997 55555544321 45788887753
No 243
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=57.46 E-value=1.4 Score=33.35 Aligned_cols=42 Identities=24% Similarity=0.623 Sum_probs=23.3
Q ss_pred CcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccccc
Q psy3263 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300 (329)
Q Consensus 253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~ 300 (329)
+..|+.|...+...- +|. .|..|...... ...||-|.+++..
T Consensus 1 e~~CP~C~~~L~~~~----~~~-~C~~C~~~~~~-~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 1 ENTCPKCQQELEWQG----GHY-HCEACQKDYKK-EAFCPDCGQPLEV 42 (70)
T ss_dssp --B-SSS-SBEEEET----TEE-EETTT--EEEE-EEE-TTT-SB-EE
T ss_pred CCcCCCCCCccEEeC----CEE-ECcccccccee-cccCCCcccHHHH
Confidence 357999998754322 676 89999877543 4789999988743
No 244
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=57.24 E-value=13 Score=25.23 Aligned_cols=38 Identities=18% Similarity=0.594 Sum_probs=21.1
Q ss_pred cccccccCcccEEeC---CCChhccHhhHHhhcCC--CCCCccc
Q psy3263 256 CYLCNDREVTHALIP---CGHNFFCSECAERTCDF--DRTCPMC 294 (329)
Q Consensus 256 C~IC~e~~~~~~~lp---CgH~~fC~~Cl~~~~~~--~~~CP~C 294 (329)
|.+|.+.......=+ |+=. +-..|+...+.. ...||.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r-~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVR-LHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--E-E-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHeeeccCCCCccCch-HHHHHHHHHHhcCCCCCCcCC
Confidence 667777766555423 6656 677999998887 3479987
No 245
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=56.88 E-value=11 Score=34.36 Aligned_cols=63 Identities=16% Similarity=0.280 Sum_probs=36.9
Q ss_pred EEEEecCcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchhh-hhhhhhhhhhcC
Q psy3263 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFES-HHGQKIVFILTS 156 (329)
Q Consensus 88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie~-~i~d~~~~~~~~ 156 (329)
+++.|-...-|++||++|++|+++++.-.-+..+. +..|.|.- -++-+..| .+++++..-++.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~~~~----~v~I~v~e--v~~p~~~a~~vA~~ia~qLe~ 105 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKKFGLE----NPQIDVKE--VENPELNARVVAFRLANALER 105 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHHhCCC----ceeEEEEE--EeCCCcCHHHHHHHHHHHHHc
Confidence 44445547789999999999999988865543221 12222221 11113444 566666655553
No 246
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=56.39 E-value=11 Score=34.83 Aligned_cols=34 Identities=18% Similarity=0.212 Sum_probs=27.1
Q ss_pred EEEEEecCcccceeecCCCchHHHHHHhcCceEE
Q psy3263 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV 120 (329)
Q Consensus 87 t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~ 120 (329)
.++|.|-...-|.|||++|..|++|++.-.-.+.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~ 78 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKRFG 78 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHHhC
Confidence 3567777777899999999999999888655543
No 247
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=55.88 E-value=15 Score=26.03 Aligned_cols=25 Identities=28% Similarity=0.812 Sum_probs=16.6
Q ss_pred CCCChhccHhhHHhhcCCCCCCcccc
Q psy3263 270 PCGHNFFCSECAERTCDFDRTCPMCR 295 (329)
Q Consensus 270 pCgH~~fC~~Cl~~~~~~~~~CP~Cr 295 (329)
.|.+. ||.+|-.=+-+....||-|.
T Consensus 26 ~C~~~-FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 26 KCKNH-FCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp TTT---B-HHHHHTTTTTS-SSSTT-
T ss_pred CCCCc-cccCcChhhhccccCCcCCC
Confidence 68888 99999877666678999884
No 248
>KOG3970|consensus
Probab=55.81 E-value=7.6 Score=35.93 Aligned_cols=45 Identities=24% Similarity=0.569 Sum_probs=35.8
Q ss_pred CcccccccccCc--ccEEeCCCChhccHhhHHhhcCC--------CCCCccccccc
Q psy3263 253 SRQCYLCNDREV--THALIPCGHNFFCSECAERTCDF--------DRTCPMCRVPV 298 (329)
Q Consensus 253 ~~~C~IC~e~~~--~~~~lpCgH~~fC~~Cl~~~~~~--------~~~CP~Cr~~i 298 (329)
.--|..|-..+. +.+-+-|-|. |-..|+..+..+ ...||.|..+|
T Consensus 50 ~pNC~LC~t~La~gdt~RLvCyhl-fHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRLVCYHL-FHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CCCCceeCCccccCcceeehhhhh-HHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 346888877553 6677899999 999999988655 35899999887
No 249
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=54.58 E-value=5.2 Score=27.61 Aligned_cols=39 Identities=28% Similarity=0.650 Sum_probs=23.5
Q ss_pred cccccccCcc--cEEeCCCChh----ccHhhHHhhcCC--CCCCccc
Q psy3263 256 CYLCNDREVT--HALIPCGHNF----FCSECAERTCDF--DRTCPMC 294 (329)
Q Consensus 256 C~IC~e~~~~--~~~lpCgH~~----fC~~Cl~~~~~~--~~~CP~C 294 (329)
|.||++...+ +...||.-.. .-..|+.+|... ...|++|
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 7889976543 4567885331 345899999875 6778887
No 250
>COG1159 Era GTPase [General function prediction only]
Probab=54.23 E-value=8.9 Score=36.92 Aligned_cols=18 Identities=22% Similarity=0.152 Sum_probs=15.3
Q ss_pred eeeecCCChHHHHHHHHh
Q psy3263 6 VPSINPFGCKIKALRAKT 23 (329)
Q Consensus 6 G~IIGkgG~~Ik~Lr~~T 23 (329)
|-||||+|++||+|-.+.
T Consensus 242 ~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 242 GIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred ceEECCCcHHHHHHHHHH
Confidence 579999999999997543
No 251
>KOG0956|consensus
Probab=54.13 E-value=6.3 Score=41.87 Aligned_cols=29 Identities=24% Similarity=0.647 Sum_probs=19.8
Q ss_pred eCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263 269 IPCGHNFFCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 269 lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
+|-|-. ||+.|-..-......|-+|-...
T Consensus 44 VPtGpW-fCrKCesqeraarvrCeLCP~kd 72 (900)
T KOG0956|consen 44 VPTGPW-FCRKCESQERAARVRCELCPHKD 72 (900)
T ss_pred cCCCch-hhhhhhhhhhhccceeecccCcc
Confidence 344444 99999876544467888887654
No 252
>KOG1815|consensus
Probab=52.15 E-value=7.5 Score=39.39 Aligned_cols=36 Identities=28% Similarity=0.556 Sum_probs=30.1
Q ss_pred CCCcccccccccCcc-cEEeCCCChhccHhhHHhhcCC
Q psy3263 251 SGSRQCYLCNDREVT-HALIPCGHNFFCSECAERTCDF 287 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~-~~~lpCgH~~fC~~Cl~~~~~~ 287 (329)
.....|-||.+.... ...+.|||. ||..|.......
T Consensus 68 ~~~~~c~ic~~~~~~~~~~~~c~H~-~c~~cw~~yl~~ 104 (444)
T KOG1815|consen 68 KGDVQCGICVESYDGEIIGLGCGHP-FCPPCWTGYLGT 104 (444)
T ss_pred CccccCCcccCCCcchhhhcCCCcH-HHHHHHHHHhhh
Confidence 456799999998885 678899999 999999886654
No 253
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=51.57 E-value=8.6 Score=41.63 Aligned_cols=48 Identities=19% Similarity=0.502 Sum_probs=37.6
Q ss_pred CCCccccccccc--CcccEEeCCCChh----ccHhhHHhhcCC--CCCCccccccc
Q psy3263 251 SGSRQCYLCNDR--EVTHALIPCGHNF----FCSECAERTCDF--DRTCPMCRVPV 298 (329)
Q Consensus 251 ~~~~~C~IC~e~--~~~~~~lpCgH~~----fC~~Cl~~~~~~--~~~CP~Cr~~i 298 (329)
+++..|.||... .-+|...||..+. .-.+|+-.|... ..+|-+|+.++
T Consensus 10 ~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~ 65 (1175)
T COG5183 10 EDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEY 65 (1175)
T ss_pred ccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeeccee
Confidence 556899999854 4577788996432 356999999887 78999999887
No 254
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=49.63 E-value=7.8 Score=27.26 Aligned_cols=39 Identities=21% Similarity=0.532 Sum_probs=24.9
Q ss_pred CcccccccccCcccEEeCCCChhccHhhHHhhcCC--CCCCcccccccc
Q psy3263 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN 299 (329)
Q Consensus 253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~--~~~CP~Cr~~i~ 299 (329)
.+.|+.|.+.+ +... ++.-|....... ...||+|...+.
T Consensus 2 ~f~CP~C~~~~-~~~~-------L~~H~~~~H~~~~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESS-------LVEHCEDEHRSESKNVVCPICSSRVT 42 (54)
T ss_pred CcCCCCCCCcc-CHHH-------HHHHHHhHCcCCCCCccCCCchhhhh
Confidence 57899999843 3221 555566555443 578999987543
No 255
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=49.51 E-value=5.5 Score=39.66 Aligned_cols=46 Identities=43% Similarity=0.917 Sum_probs=0.0
Q ss_pred CcccccccccC-------------------cccEEeCCCChhccHh-hHHhhcCC---------CCCCccccccccc
Q psy3263 253 SRQCYLCNDRE-------------------VTHALIPCGHNFFCSE-CAERTCDF---------DRTCPMCRVPVNQ 300 (329)
Q Consensus 253 ~~~C~IC~e~~-------------------~~~~~lpCgH~~fC~~-Cl~~~~~~---------~~~CP~Cr~~i~~ 300 (329)
..+|++|...- -.-++.||||. |.+ .+.-|.+- ...||.|-.++..
T Consensus 328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv--~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g 402 (416)
T PF04710_consen 328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHV--CSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDG 402 (416)
T ss_dssp -----------------------------------------------------------------------------
T ss_pred cccCCCccccCCceeEeeccccceeecCCCCceeecccccc--cchhhhhhhhcCCCCCCcccccccCCcccCcccC
Confidence 68999998521 12346799996 544 33333322 3689999988853
No 256
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=49.51 E-value=48 Score=29.27 Aligned_cols=41 Identities=20% Similarity=0.292 Sum_probs=34.2
Q ss_pred hHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHH
Q psy3263 14 CKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSA 57 (329)
Q Consensus 14 ~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i 57 (329)
+.+..|-+-+|+-|.+ +++.+|.|.|.++.|.+|.+++..+
T Consensus 126 erl~ei~E~~gvI~Ef---ee~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 126 ERLQEISEWHGVIFEF---EEDDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred HHHHHHHHHhceeEEe---cCCcEEEEeccHHHHHHHHHHHHHH
Confidence 4677888888988888 4556789999999999999998765
No 257
>KOG1952|consensus
Probab=49.21 E-value=7.8 Score=42.07 Aligned_cols=46 Identities=24% Similarity=0.578 Sum_probs=36.3
Q ss_pred CCCcccccccccCcccE--E--eCCCChhccHhhHHhhcCC-------CCCCcccccc
Q psy3263 251 SGSRQCYLCNDREVTHA--L--IPCGHNFFCSECAERTCDF-------DRTCPMCRVP 297 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~--~--lpCgH~~fC~~Cl~~~~~~-------~~~CP~Cr~~ 297 (329)
.+..+|.||++...... . -.|-|. |-..|+++|..+ .+.||.|+..
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhV-FHl~CI~~WArs~ek~~~~~WrCP~Cqsv 245 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHV-FHLNCIKKWARSSEKTGQDGWRCPACQSV 245 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhh-hhHHHHHHHHHHhhhccCccccCCcccch
Confidence 45689999999876433 2 368998 999999999764 5799999853
No 258
>KOG2034|consensus
Probab=49.04 E-value=8 Score=42.18 Aligned_cols=35 Identities=26% Similarity=0.638 Sum_probs=25.2
Q ss_pred CCCCcccccccccCcc-c-EEeCCCChhccHhhHHhhc
Q psy3263 250 ISGSRQCYLCNDREVT-H-ALIPCGHNFFCSECAERTC 285 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~-~-~~lpCgH~~fC~~Cl~~~~ 285 (329)
++....|-+|...+.. | .+.||||. |-.+|+.+..
T Consensus 814 ~ep~d~C~~C~~~ll~~pF~vf~CgH~-FH~~Cl~~~v 850 (911)
T KOG2034|consen 814 LEPQDSCDHCGRPLLIKPFYVFPCGHC-FHRDCLIRHV 850 (911)
T ss_pred ecCccchHHhcchhhcCcceeeeccch-HHHHHHHHHH
Confidence 4566789999875532 2 35699998 9999987653
No 259
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=48.91 E-value=5.7 Score=37.84 Aligned_cols=53 Identities=19% Similarity=0.328 Sum_probs=26.6
Q ss_pred CCcccccccccCcccEEeCC-----CChhccHhhHHhhcCCCCCCcccccccccchhhh
Q psy3263 252 GSRQCYLCNDREVTHALIPC-----GHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 305 (329)
Q Consensus 252 ~~~~C~IC~e~~~~~~~lpC-----gH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i~ 305 (329)
....|+||-....-.++..= .|. +|.-|-..|......||.|-..-...+..+
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L-~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~ 228 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYL-HCSLCGTEWRFVRIKCPYCGNTDHEKLEYF 228 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEE-EETTT--EEE--TTS-TTT---SS-EEE--
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEE-EcCCCCCeeeecCCCCcCCCCCCCcceeeE
Confidence 34799999998876666543 455 899999999777889999988655444443
No 260
>KOG3053|consensus
Probab=48.81 E-value=9.1 Score=36.07 Aligned_cols=52 Identities=23% Similarity=0.486 Sum_probs=36.9
Q ss_pred CCCCCCcccccccccCcccEE----eCCCChh----ccHhhHHhhcCC--------CCCCcccccccc
Q psy3263 248 GSISGSRQCYLCNDREVTHAL----IPCGHNF----FCSECAERTCDF--------DRTCPMCRVPVN 299 (329)
Q Consensus 248 ~~l~~~~~C~IC~e~~~~~~~----lpCgH~~----fC~~Cl~~~~~~--------~~~CP~Cr~~i~ 299 (329)
+..+.++.|.||+....|..+ .||..+. .-..|+.+|... .-.||-|+..+.
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 345678999999987766543 4775321 346899999765 347999998763
No 261
>KOG3268|consensus
Probab=48.47 E-value=8.5 Score=34.37 Aligned_cols=48 Identities=23% Similarity=0.492 Sum_probs=36.1
Q ss_pred CCCcccccccccCcccE-------EeCCCChhccHhhHHhhcCC-----------CCCCcccccccc
Q psy3263 251 SGSRQCYLCNDREVTHA-------LIPCGHNFFCSECAERTCDF-----------DRTCPMCRVPVN 299 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~-------~lpCgH~~fC~~Cl~~~~~~-----------~~~CP~Cr~~i~ 299 (329)
++...|-||+...-+.. -..||.. |-.-|+..|++. ...||.|..++.
T Consensus 163 d~~~~cgicyayqldGTipDqtCdN~qCgkp-FHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 163 DELGACGICYAYQLDGTIPDQTCDNIQCGKP-FHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred hhhhcccceeeeecCCccccccccccccCCc-HHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 34468999987654432 3689998 999999999764 358999998874
No 262
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=48.33 E-value=61 Score=25.01 Aligned_cols=48 Identities=15% Similarity=0.228 Sum_probs=37.9
Q ss_pred hHHHHHHHHhCCeEEecC-CCC-----cceEEEecCHHHHHHHHHHHHHHhhhh
Q psy3263 14 CKIKALRAKTNTYIKTPV-RGE-----EPVFVVTGRKEDVARAKREILSAADHF 61 (329)
Q Consensus 14 ~~Ik~Lr~~Tga~I~ip~-~~~-----ervi~ItG~~e~v~~A~~~I~~i~e~~ 61 (329)
+-++++=++.|..++... +++ +.++.|+|+..++..|.+-++.+++|.
T Consensus 34 ~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~~ 87 (88)
T PF02749_consen 34 EEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQRL 87 (88)
T ss_dssp HHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHHh
Confidence 345677777798888773 443 789999999999999999999987654
No 263
>PLN02189 cellulose synthase
Probab=48.11 E-value=12 Score=41.83 Aligned_cols=45 Identities=24% Similarity=0.680 Sum_probs=32.7
Q ss_pred cccccccccCc----ccEEeC---CCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263 254 RQCYLCNDREV----THALIP---CGHNFFCSECAERTCDF-DRTCPMCRVPVN 299 (329)
Q Consensus 254 ~~C~IC~e~~~----~~~~lp---CgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~ 299 (329)
..|.||-|..- .-.++. |+-- .|..|..--.+. ...||-|+..+.
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fp-vCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFP-VCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCc-cccchhhhhhhcCCccCcccCCchh
Confidence 48999998743 123444 4444 899999665555 899999999875
No 264
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=47.84 E-value=13 Score=37.07 Aligned_cols=33 Identities=18% Similarity=0.087 Sum_probs=27.4
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecCCCCcce
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPVRGEEPV 37 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~erv 37 (329)
.++-|||+|.|+|--..-||-+|++-.-++..-
T Consensus 319 lslAIGk~GqNvrLA~~LtGwkIDI~s~~~~~~ 351 (374)
T PRK12328 319 KSKAIGKNGINIRLASMLTGYEIELNEIGSKEN 351 (374)
T ss_pred hhhhhcCCChhHHHHHHHhCCEEEEEECCCCcc
Confidence 367899999999999999999999975555443
No 265
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=47.59 E-value=14 Score=36.58 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=25.0
Q ss_pred cccceeecCCCchHHHHHHhc-CceEEcC
Q psy3263 95 KVVGLVVGPKGATIKRIQHQT-NTYIVTP 122 (329)
Q Consensus 95 ~~vG~IIGkgG~tIk~Iq~~t-ga~I~ip 122 (329)
+-+|..||++|++|+.|.+.. |-+|.+-
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv 273 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDII 273 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEE
Confidence 668999999999999998887 8899874
No 266
>KOG3039|consensus
Probab=46.32 E-value=14 Score=34.79 Aligned_cols=36 Identities=22% Similarity=0.132 Sum_probs=30.8
Q ss_pred CCCCCCcccccccccCcccEEeCCCChhccHhhHHhh
Q psy3263 248 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERT 284 (329)
Q Consensus 248 ~~l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~ 284 (329)
+++..-..|..|+....+|+..|=||. ||++|+-..
T Consensus 38 DsiK~FdcCsLtLqPc~dPvit~~Gyl-fdrEaILe~ 73 (303)
T KOG3039|consen 38 DSIKPFDCCSLTLQPCRDPVITPDGYL-FDREAILEY 73 (303)
T ss_pred cccCCcceeeeecccccCCccCCCCee-eeHHHHHHH
Confidence 445556789999999999999999999 999998664
No 267
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=46.08 E-value=6.5 Score=23.08 Aligned_cols=22 Identities=32% Similarity=0.940 Sum_probs=12.6
Q ss_pred ccHhhHHhhcCCCCCCcccccc
Q psy3263 276 FCSECAERTCDFDRTCPMCRVP 297 (329)
Q Consensus 276 fC~~Cl~~~~~~~~~CP~Cr~~ 297 (329)
||..|-..+......||.|.++
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 3555555555456667777654
No 268
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=45.62 E-value=11 Score=34.46 Aligned_cols=36 Identities=22% Similarity=0.370 Sum_probs=30.4
Q ss_pred eEEEEEecCcccceeecCCCchHHHHHHhcCceEEc
Q psy3263 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 121 (329)
Q Consensus 86 ~t~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~I~i 121 (329)
.++.+.+-.+..|.+||+.|.+++.||--+...++-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 456667777779999999999999999998887765
No 269
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=45.09 E-value=17 Score=35.64 Aligned_cols=28 Identities=36% Similarity=0.501 Sum_probs=25.1
Q ss_pred cccceeecCCCchHHHHHHhc-CceEEcC
Q psy3263 95 KVVGLVVGPKGATIKRIQHQT-NTYIVTP 122 (329)
Q Consensus 95 ~~vG~IIGkgG~tIk~Iq~~t-ga~I~ip 122 (329)
+-+|..||++|++|+.|.+.- |-+|.+-
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv 271 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDII 271 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEE
Confidence 668999999999999999887 8899874
No 270
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=44.96 E-value=14 Score=33.58 Aligned_cols=22 Identities=18% Similarity=0.009 Sum_probs=18.4
Q ss_pred eeeeecCCChHHHHHHHHhCCe
Q psy3263 5 VVPSINPFGCKIKALRAKTNTY 26 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~ 26 (329)
-|.+|||+|++|++|++.-.-+
T Consensus 51 PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 51 PGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred CCeEECCCchhHHHHHHHHHHH
Confidence 4789999999999999886543
No 271
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=43.20 E-value=22 Score=32.46 Aligned_cols=31 Identities=26% Similarity=0.532 Sum_probs=24.7
Q ss_pred EEEEecCcccceeecCCCchHHHHHHhcCce
Q psy3263 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTY 118 (329)
Q Consensus 88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga~ 118 (329)
++|.|-...-|+|||++|+.|++|++.-.-.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~~~ 94 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQKL 94 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHHHH
Confidence 5666767777999999999999998775433
No 272
>KOG2807|consensus
Probab=41.93 E-value=15 Score=35.72 Aligned_cols=44 Identities=27% Similarity=0.691 Sum_probs=32.0
Q ss_pred CCcccccccccCcccE---EeCCCChhccHhhHHhhcCCCCCCccccc
Q psy3263 252 GSRQCYLCNDREVTHA---LIPCGHNFFCSECAERTCDFDRTCPMCRV 296 (329)
Q Consensus 252 ~~~~C~IC~e~~~~~~---~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~ 296 (329)
....|..|.+.....- .-.|.|. ||.+|-.-+-+....||-|..
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~~-FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKNV-FCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccce-eeccchHHHHhhhhcCCCcCC
Confidence 4456999966554332 3478998 999998776666789999963
No 273
>KOG3899|consensus
Probab=41.37 E-value=12 Score=35.87 Aligned_cols=24 Identities=25% Similarity=0.650 Sum_probs=18.4
Q ss_pred ccHhhHHhhcC-------------CCCCCcccccccc
Q psy3263 276 FCSECAERTCD-------------FDRTCPMCRVPVN 299 (329)
Q Consensus 276 fC~~Cl~~~~~-------------~~~~CP~Cr~~i~ 299 (329)
-|.+|+-+|.. +...||+||+.+.
T Consensus 329 wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc 365 (381)
T KOG3899|consen 329 WCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC 365 (381)
T ss_pred HHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence 57889887642 2679999999874
No 274
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=40.44 E-value=17 Score=35.23 Aligned_cols=47 Identities=19% Similarity=0.377 Sum_probs=36.9
Q ss_pred CCCCccccccccc---CcccEEeCCCChhccHhhHHhhcCC---CCCCcccccc
Q psy3263 250 ISGSRQCYLCNDR---EVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVP 297 (329)
Q Consensus 250 l~~~~~C~IC~e~---~~~~~~lpCgH~~fC~~Cl~~~~~~---~~~CP~Cr~~ 297 (329)
+..-+.|+|=.+. +..|+.+.|||. .-.+-+.++.+. ...||.|...
T Consensus 333 fHs~FiCPVlKe~~t~ENpP~ml~CgHV-Iskeal~~LS~nG~~~FKCPYCP~~ 385 (396)
T COG5109 333 FHSLFICPVLKELCTDENPPVMLECGHV-ISKEALSVLSQNGVLSFKCPYCPEM 385 (396)
T ss_pred ccceeeccccHhhhcccCCCeeeeccce-eeHHHHHHHhhcCcEEeeCCCCCcc
Confidence 4556788886653 345788999999 999999998877 7899999653
No 275
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=40.40 E-value=57 Score=32.14 Aligned_cols=45 Identities=18% Similarity=0.197 Sum_probs=39.3
Q ss_pred eeecCCChHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHH
Q psy3263 7 PSINPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREIL 55 (329)
Q Consensus 7 ~IIGkgG~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~ 55 (329)
.+-|..|.+++.|.+.+|+.|... .+.+.|+|..+.|+.|.+.+.
T Consensus 28 ~l~G~~~~~l~l~e~~~gv~i~~r----G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 28 ALFGPTDTNLSLLEIALGVSIVAR----GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred hhcCCCCccHHHHHHHhCcEEEeC----CceEEEEechHHHHHHHHHHh
Confidence 477999999999999999888876 456789999889999998887
No 276
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=40.09 E-value=14 Score=37.88 Aligned_cols=27 Identities=15% Similarity=0.062 Sum_probs=24.1
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEecC
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTPV 31 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip~ 31 (329)
.++-|||+|.|||....-||-+|.+-.
T Consensus 313 ~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 313 LSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred HHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 367899999999999999999999863
No 277
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=39.95 E-value=21 Score=33.86 Aligned_cols=39 Identities=26% Similarity=0.641 Sum_probs=21.8
Q ss_pred cccccccccCcccE----Ee----CCCChhccHhhHHhhcCC-CCCCccccccc
Q psy3263 254 RQCYLCNDREVTHA----LI----PCGHNFFCSECAERTCDF-DRTCPMCRVPV 298 (329)
Q Consensus 254 ~~C~IC~e~~~~~~----~l----pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i 298 (329)
--|.||++.....+ ++ -=||. +|..++-.- ...|| |..+
T Consensus 31 sfChiCfEl~iegvpks~llHtkSlRGHr----dCFEK~HlIanQ~~p--rsk~ 78 (285)
T PF06937_consen 31 SFCHICFELSIEGVPKSNLLHTKSLRGHR----DCFEKYHLIANQDCP--RSKL 78 (285)
T ss_pred eecceeeccccccCccccccccccccchH----HHHHHHHHHHcCCCC--cccc
Confidence 35777777654332 11 25776 676665333 56788 4444
No 278
>CHL00048 rps3 ribosomal protein S3
Probab=39.84 E-value=20 Score=32.92 Aligned_cols=21 Identities=19% Similarity=0.102 Sum_probs=18.0
Q ss_pred eeeeecCCChHHHHHHHHhCC
Q psy3263 5 VVPSINPFGCKIKALRAKTNT 25 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga 25 (329)
.|.||||+|.+|++|+++-.-
T Consensus 77 Pg~vIG~~g~~i~~l~~~L~k 97 (214)
T CHL00048 77 PKLLIERKGRGIEELQINLQK 97 (214)
T ss_pred CceEECCCcHhHHHHHHHHHH
Confidence 478999999999999988643
No 279
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=37.36 E-value=23 Score=32.04 Aligned_cols=21 Identities=24% Similarity=0.164 Sum_probs=17.6
Q ss_pred eeeeecCCChHHHHHHHHhCC
Q psy3263 5 VVPSINPFGCKIKALRAKTNT 25 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga 25 (329)
-|.+|||+|.+|++|+++-.-
T Consensus 49 Pg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 49 PGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred CceEECCCchHHHHHHHHHHH
Confidence 378999999999999887543
No 280
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=36.90 E-value=22 Score=32.78 Aligned_cols=23 Identities=13% Similarity=0.161 Sum_probs=18.7
Q ss_pred eeeeecCCChHHHHHHHHhCCeE
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYI 27 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I 27 (329)
-|.||||+|..|++|+++-....
T Consensus 55 Pg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 55 TREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred CccEEcCCchHHHHHHHHHHHHh
Confidence 37899999999999998765443
No 281
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=36.84 E-value=23 Score=27.34 Aligned_cols=47 Identities=21% Similarity=0.641 Sum_probs=18.9
Q ss_pred CcccccccccCccc----EEe---CCCChhccHhhHHhhcCC-CCCCccccccccc
Q psy3263 253 SRQCYLCNDREVTH----ALI---PCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 300 (329)
Q Consensus 253 ~~~C~IC~e~~~~~----~~l---pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~~ 300 (329)
...|.||-+..-.. +++ .|+-- .|+.|..--.+. ...||-|+.++..
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fP-vCr~CyEYErkeg~q~CpqCkt~ykr 63 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFP-VCRPCYEYERKEGNQVCPQCKTRYKR 63 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS------HHHHHHHHHTS-SB-TTT--B---
T ss_pred CcccccccCccccCCCCCEEEEEcccCCc-cchhHHHHHhhcCcccccccCCCccc
Confidence 46899999855221 233 45554 799998665555 8999999987653
No 282
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=36.04 E-value=13 Score=35.89 Aligned_cols=46 Identities=22% Similarity=0.390 Sum_probs=33.8
Q ss_pred CCCcccccccccCcccEEeC----CC--ChhccHhhHHhhcCCCCCCcccccc
Q psy3263 251 SGSRQCYLCNDREVTHALIP----CG--HNFFCSECAERTCDFDRTCPMCRVP 297 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lp----Cg--H~~fC~~Cl~~~~~~~~~CP~Cr~~ 297 (329)
.....|+||-....-.++.. =| |. +|.-|-..|-.....||.|...
T Consensus 182 ~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL-~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 182 ESRTLCPACGSPPVASMVRQGGKETGLRYL-SCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCCCcCCCCCChhhhhhhcccCCCCCceEE-EcCCCCCcccccCccCCCCCCC
Confidence 34569999999886544332 22 44 7999999987778899999874
No 283
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=35.04 E-value=14 Score=22.36 Aligned_cols=21 Identities=29% Similarity=0.815 Sum_probs=10.1
Q ss_pred cHhhHHhhcCCCCCCcccccc
Q psy3263 277 CSECAERTCDFDRTCPMCRVP 297 (329)
Q Consensus 277 C~~Cl~~~~~~~~~CP~Cr~~ 297 (329)
|-+|-..+......||.|...
T Consensus 3 CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 3 CPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred CCCCcCCchhhcCcCCCCCCC
Confidence 334444444445556666543
No 284
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=34.93 E-value=26 Score=25.16 Aligned_cols=42 Identities=24% Similarity=0.404 Sum_probs=29.5
Q ss_pred ChHHHH--HHHHhCCeEEec--------CCCC-----cceEEEecCHHHHHHHHHHH
Q psy3263 13 GCKIKA--LRAKTNTYIKTP--------VRGE-----EPVFVVTGRKEDVARAKREI 54 (329)
Q Consensus 13 G~~Ik~--Lr~~Tga~I~ip--------~~~~-----ervi~ItG~~e~v~~A~~~I 54 (329)
|.+|++ +++.+++.|--- +.++ ...+.|.|.+++++++.+.+
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~~ 70 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFRELF 70 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHHT
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHhh
Confidence 667888 888888876431 2222 45678999999999987653
No 285
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=34.87 E-value=2.7e+02 Score=29.25 Aligned_cols=104 Identities=22% Similarity=0.267 Sum_probs=60.6
Q ss_pred ChHHHHHHHHhCCeEEe-----------cCCCC----cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCC
Q psy3263 13 GCKIKALRAKTNTYIKT-----------PVRGE----EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS 77 (329)
Q Consensus 13 G~~Ik~Lr~~Tga~I~i-----------p~~~~----ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~ 77 (329)
|.+|+++.......+.+ |..+. ..++.|.|++|+++++.+.+-..+++ . ...
T Consensus 232 GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~~~~------~-~~~------ 298 (562)
T TIGR03802 232 GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEEVQE------V-EGL------ 298 (562)
T ss_pred CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCccCC------c-ccc------
Confidence 77899988777544433 21111 35678999999998887765322110 0 000
Q ss_pred CCCCCCCceEEEEEecCcccceeecCCCchHHHHH------HhcCceEEcCCCC-------------CCCeEEEECCCCC
Q psy3263 78 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQ------HQTNTYIVTPSRD-------------KEPVFEVTGNFPE 138 (329)
Q Consensus 78 ~p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~Iq------~~tga~I~ip~~~-------------~e~~i~ItG~~pe 138 (329)
+.+ ....++.+|++ .++|| ||++++ ++.|+.|.--.+. ...++.+.| .++
T Consensus 299 ---~~~-~~~e~VV~~~S---~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G-~~~ 367 (562)
T TIGR03802 299 ---DVP-METKDVVLTNK---EYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVG-TPQ 367 (562)
T ss_pred ---CCc-eEEEEEEECCc---ccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEe-CHH
Confidence 111 12455666653 45665 888886 3677777643332 133478888 777
Q ss_pred Cc
Q psy3263 139 GP 140 (329)
Q Consensus 139 ~v 140 (329)
++
T Consensus 368 ~l 369 (562)
T TIGR03802 368 DV 369 (562)
T ss_pred HH
Confidence 77
No 286
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=34.02 E-value=23 Score=32.86 Aligned_cols=23 Identities=22% Similarity=0.741 Sum_probs=20.1
Q ss_pred ccHhhHHhhcCCCCCCccccccc
Q psy3263 276 FCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 276 fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
-|..|-+.+-.+.+-||+|.+.-
T Consensus 196 ~C~sC~qqIHRNAPiCPlCK~Ks 218 (230)
T PF10146_consen 196 TCQSCHQQIHRNAPICPLCKAKS 218 (230)
T ss_pred hhHhHHHHHhcCCCCCccccccc
Confidence 79999999988899999998754
No 287
>PRK03818 putative transporter; Validated
Probab=33.32 E-value=1.2e+02 Score=31.80 Aligned_cols=105 Identities=19% Similarity=0.223 Sum_probs=61.5
Q ss_pred ChHHHHHHHHhCCeEEec-----------CCCC----cceEEEecCHHHHHHHHHHHHHHhhhhhHhhhcccCCCCCCCC
Q psy3263 13 GCKIKALRAKTNTYIKTP-----------VRGE----EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS 77 (329)
Q Consensus 13 G~~Ik~Lr~~Tga~I~ip-----------~~~~----ervi~ItG~~e~v~~A~~~I~~i~e~~~~~~~~~~~~~~~~~~ 77 (329)
|.++++++...+..+.+. ..+. ..++.|.|++|+++++.+.+-...+ ..
T Consensus 218 GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~~------~~---------- 281 (552)
T PRK03818 218 GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEVD------TS---------- 281 (552)
T ss_pred CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCccC------cc----------
Confidence 779999998877655542 1111 4567899999998888766532110 00
Q ss_pred CCCCCCCceEEEEEecCcccceeecCCCchHHHH--HHhcCceEEcCCCC-------------CCCeEEEECCCCCCc
Q psy3263 78 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRI--QHQTNTYIVTPSRD-------------KEPVFEVTGNFPEGP 140 (329)
Q Consensus 78 ~p~~~~g~~t~~i~VP~~~vG~IIGkgG~tIk~I--q~~tga~I~ip~~~-------------~e~~i~ItG~~pe~v 140 (329)
............+.+|++ .++|| ||+++ +++.|+.|.--.+. ...++.+.| .++++
T Consensus 282 ~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG-~~~~i 352 (552)
T PRK03818 282 LSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVG-RPEAI 352 (552)
T ss_pred ccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEE-CHHHH
Confidence 000001124445555653 56666 88887 56677765532221 133478888 77777
No 288
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=33.20 E-value=19 Score=34.93 Aligned_cols=45 Identities=16% Similarity=0.345 Sum_probs=33.4
Q ss_pred CCCcccccccccCcccEEe---CC--CChhccHhhHHhhcCCCCCCccccc
Q psy3263 251 SGSRQCYLCNDREVTHALI---PC--GHNFFCSECAERTCDFDRTCPMCRV 296 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~l---pC--gH~~fC~~Cl~~~~~~~~~CP~Cr~ 296 (329)
+....|+||-....-.++. .= .|. .|.-|-..|-.....||.|..
T Consensus 185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL-~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYL-HCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred cCCCCCCCCCCcchhheeeccCCCCceEE-EcCCCCCcccccCccCCCCCC
Confidence 4568999999987655432 22 233 799999988777889999986
No 289
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=32.85 E-value=29 Score=36.05 Aligned_cols=24 Identities=21% Similarity=0.109 Sum_probs=21.7
Q ss_pred eeeecCCChHHHHHHHHhCCeEEe
Q psy3263 6 VPSINPFGCKIKALRAKTNTYIKT 29 (329)
Q Consensus 6 G~IIGkgG~~Ik~Lr~~Tga~I~i 29 (329)
|++|||+|++.+.|-++||-.-++
T Consensus 111 Glvigk~g~~~reI~~~tgW~p~i 134 (637)
T COG1782 111 GLVIGKGGSTLREITAETGWAPKI 134 (637)
T ss_pred ceEEecCchHHHHHHHHhCCccee
Confidence 789999999999999999977655
No 290
>PLN02436 cellulose synthase A
Probab=32.73 E-value=26 Score=39.29 Aligned_cols=45 Identities=22% Similarity=0.685 Sum_probs=32.7
Q ss_pred cccccccccCccc----EEeC---CCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263 254 RQCYLCNDREVTH----ALIP---CGHNFFCSECAERTCDF-DRTCPMCRVPVN 299 (329)
Q Consensus 254 ~~C~IC~e~~~~~----~~lp---CgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~ 299 (329)
..|.||-|..-.. .++. |+-- .|..|..--.+. ...||-|+..+.
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fp-vCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFP-VCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCc-cccchhhhhhhcCCccCcccCCchh
Confidence 4899999875221 2444 4444 899999665555 899999999875
No 291
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=32.73 E-value=13 Score=33.93 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=22.3
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEe
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKT 29 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~i 29 (329)
.|+||||.|.++..||--++..++-
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhhh
Confidence 3789999999999999999988765
No 292
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=32.69 E-value=38 Score=31.47 Aligned_cols=30 Identities=27% Similarity=0.565 Sum_probs=23.6
Q ss_pred EEEEecCcccceeecCCCchHHHHHHhcCc
Q psy3263 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNT 117 (329)
Q Consensus 88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~tga 117 (329)
++|.|-...-|+|||++|..|++|++.-.-
T Consensus 64 i~I~I~~~rP~~iiG~~g~~i~~l~~~L~~ 93 (232)
T PRK00310 64 VRVTIHTARPGIVIGKKGAEIEKLRKELEK 93 (232)
T ss_pred EEEEEEECCCccccCCCcHHHHHHHHHHHH
Confidence 555565666799999999999999877543
No 293
>KOG3273|consensus
Probab=32.30 E-value=11 Score=34.43 Aligned_cols=45 Identities=22% Similarity=0.270 Sum_probs=36.0
Q ss_pred CcccceeecCCCchHHHHHHhcCceEEcCCCCCCCeEEEECCCCCCcchh
Q psy3263 94 YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFE 143 (329)
Q Consensus 94 ~~~vG~IIGkgG~tIk~Iq~~tga~I~ip~~~~e~~i~ItG~~pe~veie 143 (329)
.+.+|.|+||+|.|=-.|.+.|.++|.+... .|-|-| .=+|+.++
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~----kIHiLG-~~~niriA 221 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS----KIHILG-AFQNIRIA 221 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecCc----eEEEee-cchhhHHH
Confidence 4778999999999988999999999998543 366778 66666444
No 294
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=31.60 E-value=8.4 Score=31.72 Aligned_cols=44 Identities=23% Similarity=0.568 Sum_probs=28.7
Q ss_pred CCcccccccccCc-----ccEEeCCCChhccHhhHHhhcCC-CCCCccccc
Q psy3263 252 GSRQCYLCNDREV-----THALIPCGHNFFCSECAERTCDF-DRTCPMCRV 296 (329)
Q Consensus 252 ~~~~C~IC~e~~~-----~~~~lpCgH~~fC~~Cl~~~~~~-~~~CP~Cr~ 296 (329)
+...|..|...+. ...-..|.|. +|..|-...... ...|-+|++
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~-VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHR-VCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEE-EETTSEEETSSSCCEEEHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCcc-ccCccCCcCCCCCCEEChhhHH
Confidence 4568999987542 2235688888 898887663222 668999976
No 295
>KOG4185|consensus
Probab=31.37 E-value=12 Score=35.45 Aligned_cols=43 Identities=23% Similarity=0.631 Sum_probs=33.9
Q ss_pred cccccccccCc------ccEEeC--------CCChhccHhhHHhhcCC-CCCCcccccc
Q psy3263 254 RQCYLCNDREV------THALIP--------CGHNFFCSECAERTCDF-DRTCPMCRVP 297 (329)
Q Consensus 254 ~~C~IC~e~~~------~~~~lp--------CgH~~fC~~Cl~~~~~~-~~~CP~Cr~~ 297 (329)
..|.+|...+. .+.++. |||. .|..|......+ ...||.|+..
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~ht-lc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHT-LCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHH-HHhcchHHHHHHhhhcCCcccce
Confidence 57888886654 233455 9999 999999999877 6799999874
No 296
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.32 E-value=27 Score=26.63 Aligned_cols=21 Identities=38% Similarity=0.982 Sum_probs=17.1
Q ss_pred ccHhhHHhhcCCCCCCccccccc
Q psy3263 276 FCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 276 fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
||.+|+...+. ..||-|.-.+
T Consensus 31 FCadCae~~l~--g~CPnCGGel 51 (84)
T COG3813 31 FCADCAENRLH--GLCPNCGGEL 51 (84)
T ss_pred hhHhHHHHhhc--CcCCCCCchh
Confidence 99999987655 6899997665
No 297
>KOG2169|consensus
Probab=30.68 E-value=23 Score=37.76 Aligned_cols=49 Identities=24% Similarity=0.331 Sum_probs=32.3
Q ss_pred CCCCCcccccccccCcccE-EeCCCChhccHhhHHhhcCC----CCCCccccccc
Q psy3263 249 SISGSRQCYLCNDREVTHA-LIPCGHNFFCSECAERTCDF----DRTCPMCRVPV 298 (329)
Q Consensus 249 ~l~~~~~C~IC~e~~~~~~-~lpCgH~~fC~~Cl~~~~~~----~~~CP~Cr~~i 298 (329)
.+.-.+.|+++.-+..-++ -+.|.|. =|++=+.-+..+ .+.||+|.+.+
T Consensus 302 ~~~vSL~CPl~~~Rm~~P~r~~~CkHl-QcFD~~~~lq~n~~~pTW~CPVC~~~~ 355 (636)
T KOG2169|consen 302 SLRVSLNCPLSKMRMSLPARGHTCKHL-QCFDALSYLQMNEQKPTWRCPVCQKAA 355 (636)
T ss_pred cceeEecCCcccceeecCCcccccccc-eecchhhhHHhccCCCeeeCccCCccc
Confidence 3556689999998776554 4566666 454444333222 78999998865
No 298
>KOG3113|consensus
Probab=30.50 E-value=33 Score=32.36 Aligned_cols=50 Identities=18% Similarity=0.250 Sum_probs=34.7
Q ss_pred CCcccccccccC----cccEEeCCCChhccHhhHHhhcCCCCCCcccccccccchhh
Q psy3263 252 GSRQCYLCNDRE----VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 304 (329)
Q Consensus 252 ~~~~C~IC~e~~----~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i~~~~~i 304 (329)
..+.|+|---.+ .-.++.+|||. |-..-+..+. ...|++|.+.+.....+
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV-~SerAlKeik--as~C~~C~a~y~~~dvI 163 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCV-FSERALKEIK--ASVCHVCGAAYQEDDVI 163 (293)
T ss_pred ceeecccccceecceEEEEEEecccee-ccHHHHHHhh--hccccccCCcccccCeE
Confidence 456787755333 33457799999 8887776664 57899999988554433
No 299
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=30.27 E-value=11 Score=23.70 Aligned_cols=23 Identities=39% Similarity=0.924 Sum_probs=11.5
Q ss_pred ChhccHhhHHhhcCC----CCCCccccc
Q psy3263 273 HNFFCSECAERTCDF----DRTCPMCRV 296 (329)
Q Consensus 273 H~~fC~~Cl~~~~~~----~~~CP~Cr~ 296 (329)
|. ||..|-...... ...||.|..
T Consensus 3 ~r-fC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HR-FCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TS-B-TTT--BEEE-SSSS-EEESSSS-
T ss_pred Cc-ccCcCCccccCCCCcCEeECCCCcC
Confidence 56 777776655433 567888865
No 300
>PF12773 DZR: Double zinc ribbon
Probab=30.26 E-value=36 Score=23.17 Aligned_cols=24 Identities=29% Similarity=0.757 Sum_probs=16.3
Q ss_pred ccHhhHHhhc--CC-CCCCcccccccc
Q psy3263 276 FCSECAERTC--DF-DRTCPMCRVPVN 299 (329)
Q Consensus 276 fC~~Cl~~~~--~~-~~~CP~Cr~~i~ 299 (329)
||..|-..+. .. ...||.|.+.+.
T Consensus 14 fC~~CG~~l~~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 14 FCPHCGTPLPPPDQSKKICPNCGAENP 40 (50)
T ss_pred CChhhcCChhhccCCCCCCcCCcCCCc
Confidence 7777776665 22 567888877653
No 301
>KOG4621|consensus
Probab=27.18 E-value=18 Score=30.78 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=25.4
Q ss_pred CCCcccccccccCcccEEeCCCChhccHh
Q psy3263 251 SGSRQCYLCNDREVTHALIPCGHNFFCSE 279 (329)
Q Consensus 251 ~~~~~C~IC~e~~~~~~~lpCgH~~fC~~ 279 (329)
.+.+.|..|-+..+.....|-||.|||+.
T Consensus 79 q~~Lhcdlceeplk~ccfspnghhcfcrt 107 (167)
T KOG4621|consen 79 QDKLHCDLCEEPLKSCCFSPNGHHCFCRT 107 (167)
T ss_pred CCceehHHHHhHHHHhccCCCCccccccC
Confidence 46689999999999888899999999975
No 302
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=27.18 E-value=46 Score=27.01 Aligned_cols=25 Identities=28% Similarity=0.690 Sum_probs=17.7
Q ss_pred CChhccHhhHHhhcCC---------CCCCcccccc
Q psy3263 272 GHNFFCSECAERTCDF---------DRTCPMCRVP 297 (329)
Q Consensus 272 gH~~fC~~Cl~~~~~~---------~~~CP~Cr~~ 297 (329)
.-. ||..|+...... ...||.||..
T Consensus 37 ~~~-fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi 70 (105)
T PF10497_consen 37 RGK-FCGGCLRNRYGENVEEVLEDPNWKCPKCRGI 70 (105)
T ss_pred cce-ehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence 444 999998665432 5789999873
No 303
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=27.12 E-value=51 Score=35.08 Aligned_cols=26 Identities=19% Similarity=0.067 Sum_probs=23.2
Q ss_pred eeeeecCCChHHHHHHHHhCCeEEec
Q psy3263 5 VVPSINPFGCKIKALRAKTNTYIKTP 30 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tga~I~ip 30 (329)
-|++|||+|.++++|-++||=+-++-
T Consensus 104 p~~~~~~~~~~~~~i~~~~~w~~~~~ 129 (630)
T TIGR03675 104 PGLVIGKGGSTLREITAETGWTPKVV 129 (630)
T ss_pred CeEEEecCcchHHHHHHHhCCeeeEE
Confidence 48999999999999999999887763
No 304
>KOG4451|consensus
Probab=27.11 E-value=33 Score=31.88 Aligned_cols=23 Identities=22% Similarity=0.741 Sum_probs=20.2
Q ss_pred ccHhhHHhhcCCCCCCccccccc
Q psy3263 276 FCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 276 fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
.|..|-.++-.+.+.||+|+..-
T Consensus 251 ~ClsChqqIHRNAPiCPlCKaKs 273 (286)
T KOG4451|consen 251 VCLSCHQQIHRNAPICPLCKAKS 273 (286)
T ss_pred HHHHHHHHHhcCCCCCcchhhcc
Confidence 79999999988899999998754
No 305
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=26.42 E-value=24 Score=24.79 Aligned_cols=15 Identities=27% Similarity=0.919 Sum_probs=7.9
Q ss_pred CCCCcccccccccch
Q psy3263 288 DRTCPMCRVPVNQAM 302 (329)
Q Consensus 288 ~~~CP~Cr~~i~~~~ 302 (329)
...||+|.++++.--
T Consensus 20 ~~~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 20 KGCCPLCGRPLDEEH 34 (54)
T ss_dssp SEE-TTT--EE-HHH
T ss_pred CCcCCCCCCCCCHHH
Confidence 338999999996543
No 306
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.09 E-value=1.8e+02 Score=25.30 Aligned_cols=42 Identities=19% Similarity=0.226 Sum_probs=33.1
Q ss_pred hHHHHHHHHhCCeEEecCCCCcceEEEecCHHHHHHHHHHHHHHh
Q psy3263 14 CKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAA 58 (329)
Q Consensus 14 ~~Ik~Lr~~Tga~I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i~ 58 (329)
+.+..|-+-.|+-|.+. +-.+|.|.|..+.|.+|.++|.++.
T Consensus 126 eRlqDi~E~hgvIiE~~---E~D~V~i~Gd~drVk~aLke~~~~w 167 (170)
T COG4010 126 ERLQDIAETHGVIIEFE---EYDLVAIYGDSDRVKKALKEIGSFW 167 (170)
T ss_pred HHHHHHHHhhheeEEee---eccEEEEeccHHHHHHHHHHHHHHH
Confidence 45566667778777775 4467899999999999999998764
No 307
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.09 E-value=53 Score=27.12 Aligned_cols=41 Identities=24% Similarity=0.570 Sum_probs=29.8
Q ss_pred cccccccccCccc--------------EEeCCCChhccHhhHHhhcCCCCCCcccc
Q psy3263 254 RQCYLCNDREVTH--------------ALIPCGHNFFCSECAERTCDFDRTCPMCR 295 (329)
Q Consensus 254 ~~C~IC~e~~~~~--------------~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr 295 (329)
..|.-|+..+... .--.|.+. ||.+|-.=+-+....||-|.
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~-FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNV-FCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCc-cccccchhhhhhccCCcCCC
Confidence 4588887765432 13478888 99999877766677899995
No 308
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=24.57 E-value=1.1e+02 Score=31.84 Aligned_cols=46 Identities=17% Similarity=0.271 Sum_probs=33.0
Q ss_pred EEEEecCcccceeecCCCchHHHHHHhc----CceEEcCCCCCCCeEEEEC
Q psy3263 88 IEVRVPYKVVGLVVGPKGATIKRIQHQT----NTYIVTPSRDKEPVFEVTG 134 (329)
Q Consensus 88 ~~i~VP~~~vG~IIGkgG~tIk~Iq~~t----ga~I~ip~~~~e~~i~ItG 134 (329)
+-++.|.+-++.|+|++......++|+. ..-|.+.+... +.+.+.|
T Consensus 499 V~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~~~~-sI~~v~~ 548 (657)
T COG5166 499 VLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCPQST-SIFTVDI 548 (657)
T ss_pred eEEECCccCccchhcccccHHHHHhhhcccccccceEEcCCce-EEEEEcc
Confidence 5678899999999999999888888765 34455544332 2666666
No 309
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=24.56 E-value=1.6e+02 Score=28.60 Aligned_cols=50 Identities=12% Similarity=0.125 Sum_probs=39.6
Q ss_pred eecCCChHHHHHHHHhCCe--EEecCCCCcceEEEecCHHHHHHHHHHHHHH
Q psy3263 8 SINPFGCKIKALRAKTNTY--IKTPVRGEEPVFVVTGRKEDVARAKREILSA 57 (329)
Q Consensus 8 IIGkgG~~Ik~Lr~~Tga~--I~ip~~~~ervi~ItG~~e~v~~A~~~I~~i 57 (329)
++|=-=+.|+++-++.+-. |.+-..+.+.-++|+|.++++++|...+.++
T Consensus 136 v~gl~~e~v~~~~~~~~~~~~v~iaN~N~~~QiVIsG~~~ale~a~~~~~~~ 187 (310)
T COG0331 136 VLGLDDEQVEKACEEAAQGTVVEIANYNSPGQIVISGTKEALEKAAEILKEA 187 (310)
T ss_pred HcCCCHHHHHHHHHHhccCCeEEEeeeCCCCcEEEECCHHHHHHHHHHHHHh
Confidence 4555668899999998764 6665555568889999999999999888775
No 310
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=23.51 E-value=37 Score=26.96 Aligned_cols=36 Identities=28% Similarity=0.802 Sum_probs=27.6
Q ss_pred CcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCccccccc
Q psy3263 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298 (329)
Q Consensus 253 ~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~i 298 (329)
...|.+|-.... .=||. ||..|+..- ..|.+|-..+
T Consensus 44 ~~~C~~CK~~v~-----q~g~~-YCq~CAYkk----GiCamCGKki 79 (90)
T PF10235_consen 44 SSKCKICKTKVH-----QPGAK-YCQTCAYKK----GICAMCGKKI 79 (90)
T ss_pred Cccccccccccc-----cCCCc-cChhhhccc----CcccccCCee
Confidence 357999986443 23677 999998774 7899999877
No 311
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=23.30 E-value=52 Score=30.09 Aligned_cols=20 Identities=25% Similarity=0.214 Sum_probs=16.9
Q ss_pred eeeeecCCChHHHHHHHHhC
Q psy3263 5 VVPSINPFGCKIKALRAKTN 24 (329)
Q Consensus 5 VG~IIGkgG~~Ik~Lr~~Tg 24 (329)
-|.|||++|.+|++|++.-.
T Consensus 73 pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 73 PGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred CcceeCCCchHHHHHHHHHH
Confidence 37899999999999997653
No 312
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=21.98 E-value=56 Score=36.84 Aligned_cols=45 Identities=22% Similarity=0.674 Sum_probs=31.6
Q ss_pred cccccccccCccc----EEe---CCCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263 254 RQCYLCNDREVTH----ALI---PCGHNFFCSECAERTCDF-DRTCPMCRVPVN 299 (329)
Q Consensus 254 ~~C~IC~e~~~~~----~~l---pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~ 299 (329)
..|.||-|..-.. .++ .|+-- .|+.|..--.+. ...||-|+..+.
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~FP-VCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCAFP-VCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCCCc-cccchhhhhhhcCCccCCccCCchh
Confidence 4899999864221 234 45544 799998544444 899999999875
No 313
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=21.62 E-value=68 Score=23.76 Aligned_cols=26 Identities=19% Similarity=0.302 Sum_probs=21.7
Q ss_pred CCCcceEEEecCHHHHHHHHHHHHHH
Q psy3263 32 RGEEPVFVVTGRKEDVARAKREILSA 57 (329)
Q Consensus 32 ~~~ervi~ItG~~e~v~~A~~~I~~i 57 (329)
+.....++|+|+++.+++.++.|..+
T Consensus 51 d~~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 51 DERTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp ECTTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred ECCCCEEEEEeCHHHHHHHHHHHHHH
Confidence 34467789999999999999999775
No 314
>PLN02400 cellulose synthase
Probab=21.17 E-value=55 Score=36.92 Aligned_cols=45 Identities=22% Similarity=0.637 Sum_probs=31.4
Q ss_pred cccccccccCccc----EEe---CCCChhccHhhHHhhcCC-CCCCcccccccc
Q psy3263 254 RQCYLCNDREVTH----ALI---PCGHNFFCSECAERTCDF-DRTCPMCRVPVN 299 (329)
Q Consensus 254 ~~C~IC~e~~~~~----~~l---pCgH~~fC~~Cl~~~~~~-~~~CP~Cr~~i~ 299 (329)
-.|.||-|..-.. .++ .|+-- .|+.|..--.+. ...||-|+..+.
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCaFP-VCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECAFP-VCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCCCc-cccchhheecccCCccCcccCCccc
Confidence 4899999864222 233 45544 799998544444 899999999875
No 315
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.15 E-value=32 Score=20.53 Aligned_cols=22 Identities=27% Similarity=0.762 Sum_probs=10.5
Q ss_pred ccHhhHHhhcCCCCCCcccccc
Q psy3263 276 FCSECAERTCDFDRTCPMCRVP 297 (329)
Q Consensus 276 fC~~Cl~~~~~~~~~CP~Cr~~ 297 (329)
+|..|-..+......||.|-++
T Consensus 4 ~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcCCcccccChhhCCC
Confidence 4444444333335556666543
No 316
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=20.82 E-value=31 Score=27.49 Aligned_cols=39 Identities=26% Similarity=0.773 Sum_probs=28.1
Q ss_pred CCCCcccccccccCcccEEeCCCChhccHhhHHhhcCCCCCCcccccc
Q psy3263 250 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 297 (329)
Q Consensus 250 l~~~~~C~IC~e~~~~~~~lpCgH~~fC~~Cl~~~~~~~~~CP~Cr~~ 297 (329)
|.....|..|.+.-+. -=-|. .|..|+... ..|+-|..+
T Consensus 52 Lt~p~kC~~C~qktVk----~AYh~-iC~~Ca~~~----~vCaKC~k~ 90 (92)
T PF10217_consen 52 LTQPKKCNKCQQKTVK----HAYHV-ICDPCAKEL----KVCAKCGKP 90 (92)
T ss_pred CCCCccccccccchHH----HHHHH-HHHHHHHhh----ccCcccCCC
Confidence 4455678888865543 23477 999999887 789999764
Done!