Query psy4141
Match_columns 353
No_of_seqs 386 out of 2544
Neff 7.0
Searched_HMMs 46136
Date Fri Aug 16 17:58:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4141.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4141hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2113|consensus 100.0 6.7E-30 1.5E-34 237.0 12.5 317 2-352 39-393 (394)
2 KOG2191|consensus 99.8 7.8E-20 1.7E-24 171.4 15.5 148 2-154 52-211 (402)
3 KOG1676|consensus 99.8 1.2E-19 2.5E-24 181.9 14.4 140 2-149 152-302 (600)
4 KOG1676|consensus 99.8 8.2E-19 1.8E-23 175.9 11.7 136 3-147 244-389 (600)
5 KOG2190|consensus 99.7 2.4E-16 5.3E-21 159.3 13.7 137 2-148 56-209 (485)
6 KOG2193|consensus 99.7 1.3E-16 2.9E-21 153.8 9.8 148 2-149 293-483 (584)
7 TIGR03665 arCOG04150 arCOG0415 99.7 6.4E-16 1.4E-20 137.2 12.5 129 2-148 11-152 (172)
8 KOG2192|consensus 99.6 1.1E-15 2.4E-20 140.1 10.0 149 2-169 61-214 (390)
9 KOG2193|consensus 99.6 8.1E-16 1.8E-20 148.4 7.7 131 2-147 212-352 (584)
10 PRK13763 putative RNA-processi 99.6 6.7E-15 1.5E-19 131.5 12.5 128 2-147 16-157 (180)
11 KOG2192|consensus 99.6 7.9E-15 1.7E-19 134.5 12.9 145 3-147 137-384 (390)
12 cd02396 PCBP_like_KH K homolog 99.4 1.3E-12 2.8E-17 97.5 6.9 60 82-141 1-64 (65)
13 cd02394 vigilin_like_KH K homo 99.4 9.2E-13 2E-17 97.1 6.0 60 83-142 2-62 (62)
14 PF00013 KH_1: KH domain syndr 99.4 5.2E-13 1.1E-17 97.8 4.0 60 82-141 1-60 (60)
15 cd02393 PNPase_KH Polynucleoti 99.4 2.3E-12 4.9E-17 95.1 7.4 59 81-142 2-61 (61)
16 KOG2113|consensus 99.3 1.6E-12 3.4E-17 121.8 3.5 67 77-143 22-88 (394)
17 KOG2190|consensus 99.3 2.8E-11 6E-16 122.8 11.9 144 2-145 151-407 (485)
18 cd00105 KH-I K homology RNA-bi 99.3 1.4E-11 3.1E-16 90.8 7.0 60 83-142 2-64 (64)
19 KOG4172|consensus 99.2 1.6E-12 3.5E-17 91.3 -0.7 53 301-353 8-61 (62)
20 PF13920 zf-C3HC4_3: Zinc fing 99.2 1.2E-11 2.6E-16 87.4 2.4 50 299-348 1-50 (50)
21 smart00322 KH K homology RNA-b 99.1 9E-10 2E-14 81.0 8.8 65 81-145 3-68 (69)
22 KOG4265|consensus 99.0 2E-10 4.3E-15 110.2 3.6 55 298-352 288-342 (349)
23 PF13014 KH_3: KH domain 98.9 2.5E-09 5.5E-14 73.1 4.9 39 91-129 1-43 (43)
24 PF15227 zf-C3HC4_4: zinc fing 98.8 2E-09 4.4E-14 73.3 2.8 38 303-341 1-42 (42)
25 KOG2191|consensus 98.8 1.8E-08 3.9E-13 95.5 9.3 70 79-148 37-112 (402)
26 cd02394 vigilin_like_KH K homo 98.8 1.1E-08 2.5E-13 75.2 5.6 49 2-50 13-62 (62)
27 PLN03208 E3 ubiquitin-protein 98.8 6.2E-09 1.3E-13 93.0 4.6 54 298-352 16-87 (193)
28 KOG0317|consensus 98.8 4.3E-09 9.3E-14 98.3 3.6 48 299-347 238-285 (293)
29 cd02396 PCBP_like_KH K homolog 98.7 2.1E-08 4.6E-13 74.7 6.1 48 2-49 13-64 (65)
30 PF00013 KH_1: KH domain syndr 98.7 1E-08 2.2E-13 74.9 3.2 48 2-49 13-60 (60)
31 PF13923 zf-C3HC4_2: Zinc fing 98.7 7.8E-09 1.7E-13 69.1 2.2 38 303-341 1-39 (39)
32 PHA02929 N1R/p28-like protein; 98.7 1.2E-08 2.5E-13 94.7 3.8 51 299-350 173-231 (238)
33 cd02393 PNPase_KH Polynucleoti 98.7 5.4E-08 1.2E-12 71.7 6.1 45 2-49 15-60 (61)
34 KOG0823|consensus 98.7 1.1E-08 2.3E-13 93.1 2.5 54 298-352 45-103 (230)
35 KOG0320|consensus 98.6 1.4E-08 3E-13 88.8 2.7 53 299-352 130-186 (187)
36 cd02395 SF1_like-KH Splicing f 98.6 8.1E-08 1.8E-12 80.3 6.9 58 89-146 14-94 (120)
37 COG1094 Predicted RNA-binding 98.6 5.4E-07 1.2E-11 80.4 12.5 127 3-147 22-164 (194)
38 PF13639 zf-RING_2: Ring finge 98.6 1.5E-08 3.3E-13 69.5 1.4 40 302-342 2-44 (44)
39 PRK13763 putative RNA-processi 98.6 1.2E-07 2.6E-12 84.8 6.5 64 81-146 3-70 (180)
40 KOG2279|consensus 98.6 2.6E-08 5.5E-13 100.0 2.3 124 2-147 81-209 (608)
41 TIGR03665 arCOG04150 arCOG0415 98.6 7.3E-08 1.6E-12 85.6 4.9 60 85-146 2-64 (172)
42 cd00105 KH-I K homology RNA-bi 98.5 2.3E-07 5.1E-12 68.1 6.3 48 2-49 13-63 (64)
43 KOG4275|consensus 98.5 8.4E-09 1.8E-13 96.2 -2.4 51 299-353 299-349 (350)
44 TIGR00599 rad18 DNA repair pro 98.5 7.4E-08 1.6E-12 95.4 3.6 52 295-347 21-72 (397)
45 TIGR02696 pppGpp_PNP guanosine 98.5 7.9E-07 1.7E-11 93.8 10.8 67 76-147 575-642 (719)
46 KOG1571|consensus 98.4 6.7E-08 1.5E-12 93.0 1.2 54 296-353 301-354 (355)
47 KOG2208|consensus 98.4 6.6E-07 1.4E-11 95.8 8.7 125 3-147 361-488 (753)
48 PF00097 zf-C3HC4: Zinc finger 98.4 1.3E-07 2.9E-12 63.6 2.3 38 303-341 1-41 (41)
49 PF13014 KH_3: KH domain 98.4 4E-07 8.6E-12 62.1 4.6 36 2-37 4-43 (43)
50 KOG0287|consensus 98.4 9.4E-08 2E-12 90.9 1.8 51 296-347 19-69 (442)
51 smart00504 Ubox Modified RING 98.4 2.1E-07 4.6E-12 68.3 3.2 45 301-346 2-46 (63)
52 cd00162 RING RING-finger (Real 98.4 2.5E-07 5.4E-12 62.3 3.2 43 302-345 1-45 (45)
53 PHA02926 zinc finger-like prot 98.4 1.8E-07 3.9E-12 84.7 3.1 49 299-348 169-232 (242)
54 COG5432 RAD18 RING-finger-cont 98.3 1.9E-07 4.1E-12 87.2 2.3 48 298-346 23-70 (391)
55 PF14634 zf-RING_5: zinc-RING 98.3 5E-07 1.1E-11 62.0 3.5 41 302-343 1-44 (44)
56 smart00184 RING Ring finger. E 98.3 7.2E-07 1.6E-11 57.9 3.6 38 303-341 1-39 (39)
57 smart00322 KH K homology RNA-b 98.3 3.1E-06 6.7E-11 61.9 7.0 52 2-53 16-68 (69)
58 TIGR03591 polynuc_phos polyrib 98.3 3.7E-06 8E-11 89.6 9.8 96 40-147 518-615 (684)
59 KOG2164|consensus 98.2 8.3E-07 1.8E-11 89.0 2.3 47 300-347 186-237 (513)
60 PF13445 zf-RING_UBOX: RING-ty 98.1 7.7E-07 1.7E-11 60.8 1.2 30 303-334 1-34 (43)
61 KOG2177|consensus 98.1 8.9E-07 1.9E-11 82.7 1.7 48 295-343 8-55 (386)
62 PLN00207 polyribonucleotide nu 98.1 6.4E-06 1.4E-10 88.8 8.2 96 40-147 652-750 (891)
63 KOG0119|consensus 98.1 3.1E-05 6.8E-10 77.3 11.5 68 80-147 137-230 (554)
64 PF12678 zf-rbx1: RING-H2 zinc 98.0 3.6E-06 7.8E-11 64.2 3.1 41 301-342 20-73 (73)
65 COG5574 PEX10 RING-finger-cont 98.0 2.6E-06 5.7E-11 79.0 2.4 47 299-346 214-262 (271)
66 COG5243 HRD1 HRD ubiquitin lig 98.0 2.6E-06 5.7E-11 82.1 2.3 47 298-345 285-344 (491)
67 KOG0978|consensus 98.0 1.9E-06 4E-11 90.2 0.8 54 298-352 641-697 (698)
68 KOG2208|consensus 98.0 1.6E-05 3.5E-10 85.3 7.6 72 79-150 345-417 (753)
69 COG1185 Pnp Polyribonucleotide 97.9 3.2E-05 7E-10 80.4 9.1 96 40-147 519-616 (692)
70 PF04564 U-box: U-box domain; 97.9 1.1E-05 2.3E-10 61.6 3.1 48 299-347 3-51 (73)
71 cd02395 SF1_like-KH Splicing f 97.9 3.9E-05 8.4E-10 64.2 6.5 55 2-56 19-96 (120)
72 KOG1100|consensus 97.9 3.9E-06 8.5E-11 76.6 0.5 47 302-352 160-206 (207)
73 KOG0336|consensus 97.8 3E-05 6.4E-10 76.4 5.0 69 79-147 45-113 (629)
74 KOG1588|consensus 97.7 0.00038 8.2E-09 64.9 11.6 42 78-119 89-136 (259)
75 PRK11824 polynucleotide phosph 97.7 6.1E-05 1.3E-09 80.5 7.0 96 40-147 521-618 (693)
76 KOG1785|consensus 97.7 1.6E-05 3.5E-10 77.4 2.1 47 301-348 370-418 (563)
77 COG5540 RING-finger-containing 97.7 2.2E-05 4.8E-10 74.1 2.3 47 299-346 322-372 (374)
78 KOG4628|consensus 97.6 2.1E-05 4.5E-10 76.6 2.0 46 301-347 230-279 (348)
79 KOG0802|consensus 97.6 2.2E-05 4.7E-10 81.8 1.7 47 298-345 289-340 (543)
80 KOG4159|consensus 97.5 4.7E-05 1E-09 75.8 2.2 51 296-347 80-130 (398)
81 PRK08406 transcription elongat 97.5 0.00027 5.8E-09 60.7 6.4 89 3-116 46-134 (140)
82 COG5236 Uncharacterized conser 97.4 0.00015 3.4E-09 69.6 4.3 57 291-348 52-110 (493)
83 PF12861 zf-Apc11: Anaphase-pr 97.4 0.00017 3.7E-09 56.3 3.6 31 315-346 49-82 (85)
84 KOG4692|consensus 97.4 7.6E-05 1.6E-09 71.8 1.9 49 298-347 420-468 (489)
85 PF14835 zf-RING_6: zf-RING of 97.4 4.5E-05 9.8E-10 56.1 0.2 46 298-346 5-51 (65)
86 KOG2814|consensus 97.4 0.00027 5.8E-09 67.8 5.4 67 81-147 57-125 (345)
87 KOG2279|consensus 97.3 0.00036 7.9E-09 70.7 6.2 142 2-143 153-364 (608)
88 TIGR03319 YmdA_YtgF conserved 97.2 0.002 4.3E-08 66.7 9.8 66 80-147 203-270 (514)
89 PF14611 SLS: Mitochondrial in 97.2 0.0081 1.8E-07 54.8 12.9 116 3-146 40-164 (210)
90 PRK12704 phosphodiesterase; Pr 97.1 0.0023 5E-08 66.3 9.7 65 81-147 210-276 (520)
91 PRK00106 hypothetical protein; 97.1 0.0027 5.8E-08 65.8 10.0 66 80-147 224-291 (535)
92 KOG0311|consensus 97.1 8.2E-05 1.8E-09 71.7 -1.2 51 296-347 39-91 (381)
93 KOG2879|consensus 97.0 0.00059 1.3E-08 63.8 4.1 49 298-347 237-288 (298)
94 COG5152 Uncharacterized conser 97.0 0.00026 5.7E-09 63.1 1.6 49 300-349 196-244 (259)
95 TIGR00570 cdk7 CDK-activating 96.9 0.00065 1.4E-08 65.3 2.7 30 317-347 25-55 (309)
96 COG1094 Predicted RNA-binding 96.8 0.0027 5.9E-08 57.0 6.3 49 2-54 115-163 (194)
97 COG5176 MSL5 Splicing factor ( 96.8 0.0017 3.7E-08 58.5 4.9 42 78-119 145-192 (269)
98 PRK04163 exosome complex RNA-b 96.8 0.0026 5.6E-08 59.4 6.2 63 82-147 146-209 (235)
99 TIGR01952 nusA_arch NusA famil 96.8 0.0039 8.4E-08 53.6 6.5 89 3-116 47-135 (141)
100 KOG1039|consensus 96.7 0.00082 1.8E-08 65.8 2.3 50 298-348 159-223 (344)
101 cd02134 NusA_KH NusA_K homolog 96.7 0.0026 5.5E-08 46.7 4.4 36 81-116 25-60 (61)
102 KOG1067|consensus 96.6 0.0041 8.8E-08 63.6 6.4 63 81-147 597-660 (760)
103 KOG0828|consensus 96.6 0.0011 2.3E-08 66.6 2.1 50 297-347 568-635 (636)
104 COG0195 NusA Transcription elo 96.4 0.004 8.6E-08 56.2 4.5 90 3-118 90-179 (190)
105 KOG2660|consensus 96.4 0.0012 2.5E-08 63.5 0.7 51 297-348 12-63 (331)
106 KOG1813|consensus 96.3 0.0013 2.8E-08 62.2 0.5 47 301-348 242-288 (313)
107 TIGR02696 pppGpp_PNP guanosine 96.2 0.0084 1.8E-07 63.9 6.3 52 2-55 591-642 (719)
108 PF14447 Prok-RING_4: Prokaryo 96.2 0.0016 3.5E-08 46.5 0.7 45 299-346 6-50 (55)
109 KOG0297|consensus 96.2 0.0021 4.5E-08 64.4 1.6 52 297-349 18-70 (391)
110 PRK12705 hypothetical protein; 96.2 0.013 2.8E-07 60.4 7.3 64 81-146 198-263 (508)
111 KOG2814|consensus 96.1 0.011 2.4E-07 56.9 5.7 56 2-57 70-127 (345)
112 TIGR03591 polynuc_phos polyrib 96.0 0.0091 2E-07 63.9 5.4 52 2-55 564-615 (684)
113 KOG1002|consensus 96.0 0.0031 6.7E-08 63.9 1.6 48 298-346 534-586 (791)
114 KOG0804|consensus 95.9 0.0043 9.2E-08 61.8 2.3 45 299-346 174-222 (493)
115 PRK00468 hypothetical protein; 95.8 0.011 2.3E-07 45.4 3.5 31 80-110 29-59 (75)
116 smart00744 RINGv The RING-vari 95.8 0.011 2.3E-07 41.6 3.2 40 302-342 1-49 (49)
117 KOG0336|consensus 95.7 0.017 3.7E-07 57.4 5.3 57 2-58 60-116 (629)
118 PRK02821 hypothetical protein; 95.7 0.011 2.4E-07 45.5 3.2 33 80-112 30-62 (77)
119 COG1837 Predicted RNA-binding 95.5 0.017 3.6E-07 44.3 3.6 32 79-110 28-59 (76)
120 KOG0825|consensus 95.4 0.0035 7.7E-08 66.0 -0.4 50 299-349 122-174 (1134)
121 KOG1734|consensus 95.4 0.0095 2.1E-07 55.8 2.3 47 299-346 223-281 (328)
122 PRK12328 nusA transcription el 95.4 0.042 9E-07 54.4 6.8 38 81-118 308-345 (374)
123 KOG0119|consensus 95.3 0.041 9E-07 55.6 6.5 53 3-55 158-230 (554)
124 KOG0826|consensus 95.3 0.0095 2.1E-07 57.2 1.9 55 298-353 298-355 (357)
125 TIGR01953 NusA transcription t 95.2 0.005 1.1E-07 60.5 -0.0 38 81-118 301-338 (341)
126 PRK12327 nusA transcription el 95.0 0.063 1.4E-06 53.2 7.0 39 81-119 303-341 (362)
127 PF07800 DUF1644: Protein of u 94.8 0.023 5E-07 49.3 2.8 53 299-351 1-96 (162)
128 PRK01064 hypothetical protein; 94.7 0.038 8.3E-07 42.7 3.5 32 80-111 29-60 (78)
129 KOG1001|consensus 94.5 0.016 3.5E-07 61.7 1.6 44 301-346 455-500 (674)
130 PRK12329 nusA transcription el 94.5 0.089 1.9E-06 53.1 6.6 38 81-118 335-372 (449)
131 PRK09202 nusA transcription el 94.5 0.0067 1.4E-07 62.1 -1.4 38 81-118 302-339 (470)
132 COG1185 Pnp Polyribonucleotide 94.3 0.08 1.7E-06 55.8 6.0 52 3-56 566-617 (692)
133 COG5222 Uncharacterized conser 94.1 0.028 6E-07 53.4 2.0 42 301-343 275-318 (427)
134 KOG3273|consensus 94.1 0.035 7.6E-07 50.0 2.5 125 15-146 100-230 (252)
135 PF05290 Baculo_IE-1: Baculovi 94.1 0.038 8.2E-07 46.6 2.5 47 301-348 81-134 (140)
136 KOG3002|consensus 94.1 0.027 5.9E-07 54.3 1.9 47 296-347 44-92 (299)
137 PF11793 FANCL_C: FANCL C-term 94.0 0.018 3.8E-07 43.5 0.4 46 300-346 2-66 (70)
138 KOG0824|consensus 93.8 0.032 6.8E-07 53.2 1.8 50 299-348 6-55 (324)
139 TIGR03319 YmdA_YtgF conserved 93.6 0.14 3.1E-06 53.1 6.4 52 2-55 218-270 (514)
140 PF11789 zf-Nse: Zinc-finger o 93.6 0.048 1E-06 39.5 2.0 41 299-340 10-53 (57)
141 PF14570 zf-RING_4: RING/Ubox 93.6 0.055 1.2E-06 37.8 2.2 42 303-345 1-47 (48)
142 PRK12704 phosphodiesterase; Pr 93.6 0.16 3.4E-06 52.9 6.5 53 2-56 224-277 (520)
143 KOG3039|consensus 93.5 0.047 1E-06 50.6 2.3 48 299-347 220-271 (303)
144 PRK00106 hypothetical protein; 93.5 0.17 3.8E-06 52.6 6.6 52 2-55 239-291 (535)
145 COG5175 MOT2 Transcriptional r 93.4 0.051 1.1E-06 52.5 2.4 48 299-347 13-65 (480)
146 cd02410 archeal_CPSF_KH The ar 93.3 0.14 3.1E-06 44.0 4.7 35 81-115 76-110 (145)
147 PF13083 KH_4: KH domain; PDB: 93.2 0.048 1E-06 41.2 1.6 35 80-114 28-62 (73)
148 PLN00207 polyribonucleotide nu 93.1 0.11 2.3E-06 57.0 4.5 51 2-54 698-749 (891)
149 COG5219 Uncharacterized conser 93.0 0.038 8.2E-07 59.7 1.0 49 297-346 1466-1523(1525)
150 KOG4369|consensus 93.0 0.2 4.3E-06 55.5 6.2 67 81-147 1340-1410(2131)
151 cd02409 KH-II KH-II (K homolo 92.7 0.19 4.1E-06 36.4 4.1 34 81-114 25-58 (68)
152 KOG2874|consensus 92.6 0.21 4.5E-06 47.3 5.2 51 93-147 161-211 (356)
153 COG5194 APC11 Component of SCF 92.6 0.14 3E-06 39.4 3.3 30 316-346 52-81 (88)
154 PRK04163 exosome complex RNA-b 92.5 0.26 5.6E-06 46.0 5.8 52 2-55 158-209 (235)
155 PRK11824 polynucleotide phosph 92.1 0.16 3.5E-06 54.6 4.4 52 2-55 567-618 (693)
156 KOG1814|consensus 92.0 0.081 1.8E-06 52.4 1.8 34 300-334 184-220 (445)
157 KOG1588|consensus 92.0 0.28 6E-06 46.1 5.2 26 2-27 111-136 (259)
158 PRK08406 transcription elongat 92.0 0.21 4.5E-06 43.0 4.1 36 81-116 32-67 (140)
159 KOG1493|consensus 92.0 0.074 1.6E-06 40.6 1.1 29 317-346 50-81 (84)
160 PF14611 SLS: Mitochondrial in 92.0 1.1 2.4E-05 40.7 9.2 71 82-154 27-97 (210)
161 COG1855 ATPase (PilT family) [ 92.0 0.23 5E-06 50.4 4.9 67 41-119 458-524 (604)
162 KOG2932|consensus 91.6 0.056 1.2E-06 51.7 0.1 45 301-348 91-136 (389)
163 PF04641 Rtf2: Rtf2 RING-finge 91.2 0.19 4.2E-06 47.5 3.4 48 298-347 111-162 (260)
164 PF03854 zf-P11: P-11 zinc fin 90.4 0.11 2.3E-06 36.1 0.6 47 302-350 4-50 (50)
165 cd02414 jag_KH jag_K homology 90.3 0.24 5.2E-06 37.9 2.6 35 81-115 24-58 (77)
166 PHA02825 LAP/PHD finger-like p 90.1 0.29 6.3E-06 42.7 3.2 48 298-346 6-59 (162)
167 COG5166 Uncharacterized conser 90.1 0.34 7.3E-06 49.5 4.1 119 3-147 394-524 (657)
168 COG1782 Predicted metal-depend 89.5 0.43 9.3E-06 48.9 4.3 33 81-113 99-131 (637)
169 PF07650 KH_2: KH domain syndr 89.4 0.22 4.9E-06 37.9 1.8 34 81-114 25-58 (78)
170 PF05883 Baculo_RING: Baculovi 89.4 0.19 4.1E-06 42.7 1.4 33 300-333 26-67 (134)
171 KOG2874|consensus 89.2 0.65 1.4E-05 44.0 5.0 51 2-56 162-212 (356)
172 cd02134 NusA_KH NusA_K homolog 89.1 0.34 7.3E-06 35.4 2.5 23 2-24 38-60 (61)
173 PRK13764 ATPase; Provisional 89.1 0.43 9.2E-06 50.5 4.1 67 41-119 453-519 (602)
174 COG5220 TFB3 Cdk activating ki 88.7 0.16 3.4E-06 47.1 0.5 46 299-345 9-63 (314)
175 PF13184 KH_5: NusA-like KH do 88.7 0.33 7.2E-06 36.5 2.2 35 82-116 4-44 (69)
176 KOG3273|consensus 87.7 0.37 8E-06 43.5 2.2 49 2-54 182-230 (252)
177 KOG1941|consensus 87.6 0.22 4.8E-06 49.1 0.9 46 300-346 365-416 (518)
178 KOG4362|consensus 87.4 0.17 3.6E-06 53.6 -0.2 49 297-346 18-69 (684)
179 TIGR01952 nusA_arch NusA famil 87.3 0.66 1.4E-05 39.9 3.5 35 82-116 34-68 (141)
180 KOG1428|consensus 86.5 0.46 9.9E-06 53.9 2.5 48 299-347 3485-3545(3738)
181 COG1097 RRP4 RNA-binding prote 86.2 1.6 3.5E-05 40.7 5.6 56 83-141 148-204 (239)
182 TIGR03802 Asp_Ala_antiprt aspa 86.2 5.5 0.00012 41.9 10.3 111 8-141 232-376 (562)
183 PRK12705 hypothetical protein; 86.0 0.8 1.7E-05 47.5 3.9 51 2-54 212-263 (508)
184 COG5176 MSL5 Splicing factor ( 85.7 1.2 2.5E-05 40.7 4.3 27 3-29 168-194 (269)
185 cd02413 40S_S3_KH K homology R 85.4 1 2.2E-05 35.0 3.4 36 81-116 30-65 (81)
186 PHA02862 5L protein; Provision 85.0 0.87 1.9E-05 39.1 3.0 45 301-346 3-53 (156)
187 KOG2930|consensus 84.7 0.7 1.5E-05 37.3 2.2 28 316-344 79-106 (114)
188 PRK00468 hypothetical protein; 84.2 0.65 1.4E-05 35.6 1.7 16 2-17 43-58 (75)
189 PF10367 Vps39_2: Vacuolar sor 84.1 0.35 7.6E-06 38.7 0.3 33 297-330 75-109 (109)
190 PF10272 Tmpp129: Putative tra 84.1 1.1 2.4E-05 44.3 3.8 48 299-347 270-352 (358)
191 PF04710 Pellino: Pellino; In 83.9 0.33 7.1E-06 48.1 0.0 46 300-347 328-402 (416)
192 KOG3579|consensus 83.8 0.8 1.7E-05 43.5 2.5 34 300-334 268-305 (352)
193 KOG3842|consensus 83.6 0.8 1.7E-05 44.1 2.4 46 299-346 340-414 (429)
194 PRK02821 hypothetical protein; 83.5 0.73 1.6E-05 35.5 1.8 19 2-20 44-62 (77)
195 KOG4445|consensus 83.3 0.46 1E-05 45.4 0.7 45 301-346 116-186 (368)
196 COG1837 Predicted RNA-binding 83.1 0.72 1.6E-05 35.4 1.6 16 2-17 43-58 (76)
197 PHA03096 p28-like protein; Pro 82.8 0.75 1.6E-05 44.2 1.9 43 301-344 179-235 (284)
198 TIGR03675 arCOG00543 arCOG0054 82.4 3.4 7.4E-05 44.1 6.9 36 81-116 93-128 (630)
199 KOG0827|consensus 82.2 0.78 1.7E-05 45.4 1.8 28 317-345 25-55 (465)
200 PRK03818 putative transporter; 81.7 9.8 0.00021 40.0 9.9 111 8-140 218-358 (552)
201 cd02412 30S_S3_KH K homology R 80.8 1.6 3.6E-05 35.6 3.1 31 82-112 62-92 (109)
202 KOG0825|consensus 80.2 1.7 3.8E-05 46.6 3.7 51 300-351 96-159 (1134)
203 KOG4185|consensus 79.7 1 2.2E-05 43.1 1.7 31 314-345 23-54 (296)
204 PF02891 zf-MIZ: MIZ/SP-RING z 79.2 1.5 3.2E-05 30.8 1.9 43 301-344 3-50 (50)
205 KOG4369|consensus 78.7 0.76 1.6E-05 51.2 0.5 54 2-55 1353-1410(2131)
206 PRK06418 transcription elongat 78.5 3 6.5E-05 36.9 4.1 35 81-116 61-95 (166)
207 cd02411 archeal_30S_S3_KH K ho 78.1 2.6 5.6E-05 32.8 3.3 28 83-110 40-67 (85)
208 KOG3161|consensus 77.2 1.1 2.4E-05 47.0 1.1 39 298-339 9-51 (861)
209 PRK01064 hypothetical protein; 75.1 1.9 4.2E-05 33.2 1.8 16 2-17 43-58 (78)
210 COG1847 Jag Predicted RNA-bind 75.0 12 0.00026 34.3 7.0 36 81-116 91-126 (208)
211 KOG1940|consensus 74.6 1.2 2.6E-05 42.5 0.6 45 301-347 159-207 (276)
212 cd02409 KH-II KH-II (K homolo 72.8 3 6.4E-05 29.9 2.2 21 2-22 38-58 (68)
213 TIGR00436 era GTP-binding prot 72.3 4.5 9.6E-05 38.1 3.9 30 81-110 221-251 (270)
214 KOG2114|consensus 71.9 1.9 4.2E-05 46.6 1.4 46 300-349 840-886 (933)
215 COG0092 RpsC Ribosomal protein 71.8 4.1 8.9E-05 37.9 3.3 30 81-110 51-80 (233)
216 KOG1812|consensus 70.7 1.8 3.9E-05 43.4 0.8 34 300-334 146-183 (384)
217 PF13184 KH_5: NusA-like KH do 70.5 3 6.5E-05 31.3 1.8 23 3-25 22-45 (69)
218 COG5183 SSM4 Protein involved 70.0 2.9 6.2E-05 45.2 2.1 49 298-346 10-66 (1175)
219 COG1159 Era GTPase [General fu 69.9 5.6 0.00012 38.3 3.9 30 81-110 229-259 (298)
220 PRK15494 era GTPase Era; Provi 68.8 5.6 0.00012 39.0 3.9 30 81-110 273-303 (339)
221 PF12906 RINGv: RING-variant d 68.1 2.5 5.4E-05 29.2 0.8 39 303-341 1-47 (47)
222 PRK00089 era GTPase Era; Revie 68.1 6.1 0.00013 37.5 3.8 30 81-110 226-256 (292)
223 COG0490 Putative regulatory, l 67.8 6.9 0.00015 34.4 3.7 61 77-142 82-158 (162)
224 KOG1067|consensus 66.8 4.5 9.7E-05 42.2 2.7 51 2-55 610-660 (760)
225 COG0195 NusA Transcription elo 66.3 6.3 0.00014 35.6 3.3 33 84-116 79-111 (190)
226 PF08746 zf-RING-like: RING-li 65.7 6.3 0.00014 26.7 2.5 38 303-341 1-43 (43)
227 COG1702 PhoH Phosphate starvat 65.4 15 0.00032 36.3 5.8 58 89-150 23-83 (348)
228 KOG1423|consensus 64.9 6 0.00013 38.5 3.1 35 80-114 327-362 (379)
229 KOG2068|consensus 64.5 4.9 0.00011 39.1 2.4 46 301-347 250-299 (327)
230 KOG3799|consensus 61.9 2.1 4.5E-05 36.4 -0.6 42 298-344 63-116 (169)
231 KOG2817|consensus 61.8 5.6 0.00012 39.6 2.3 44 301-345 335-384 (394)
232 KOG3268|consensus 60.9 5.9 0.00013 35.3 2.0 49 298-347 163-229 (234)
233 KOG3970|consensus 59.7 7.7 0.00017 35.8 2.6 44 301-345 51-104 (299)
234 KOG1952|consensus 58.9 5.9 0.00013 43.1 2.0 48 298-346 189-247 (950)
235 KOG1960|consensus 58.9 16 0.00035 36.6 4.8 142 6-147 111-295 (531)
236 PRK04972 putative transporter; 58.6 69 0.0015 33.8 9.9 113 8-141 230-371 (558)
237 KOG1815|consensus 58.4 6.8 0.00015 40.0 2.3 36 298-334 68-104 (444)
238 KOG1645|consensus 58.3 5.1 0.00011 40.1 1.3 32 314-346 23-56 (463)
239 COG1097 RRP4 RNA-binding prote 58.1 22 0.00048 33.2 5.4 48 2-52 159-207 (239)
240 KOG0298|consensus 57.0 3.6 7.7E-05 46.6 0.0 46 299-345 1152-1198(1394)
241 CHL00048 rps3 ribosomal protei 54.2 14 0.00029 34.1 3.3 31 81-111 66-96 (214)
242 KOG3053|consensus 53.6 8.3 0.00018 36.3 1.8 52 295-346 15-82 (293)
243 PF07650 KH_2: KH domain syndr 53.4 4.2 9.2E-05 30.7 -0.1 21 3-23 39-59 (78)
244 COG1855 ATPase (PilT family) [ 53.3 8 0.00017 39.6 1.8 28 2-29 499-526 (604)
245 cd02414 jag_KH jag_K homology 53.1 9.1 0.0002 29.0 1.7 22 2-23 37-58 (77)
246 cd00652 TBP_TLF TATA box bindi 53.0 1.6E+02 0.0036 26.0 11.2 95 32-146 57-173 (174)
247 PRK04191 rps3p 30S ribosomal p 52.1 15 0.00033 33.6 3.3 30 83-112 42-71 (207)
248 TIGR01008 rpsC_E_A ribosomal p 50.9 17 0.00037 33.0 3.4 30 82-111 39-68 (195)
249 PRK06418 transcription elongat 50.8 11 0.00024 33.3 2.1 23 3-25 74-96 (166)
250 KOG2034|consensus 49.7 9.2 0.0002 41.9 1.7 29 301-330 818-848 (911)
251 KOG3039|consensus 49.7 11 0.00025 35.2 2.1 36 296-332 39-74 (303)
252 PTZ00084 40S ribosomal protein 49.2 18 0.00039 33.5 3.3 30 82-111 45-74 (220)
253 PRK13764 ATPase; Provisional 48.6 10 0.00022 40.3 1.8 28 2-29 494-521 (602)
254 KOG3899|consensus 48.5 12 0.00026 36.0 2.0 28 318-346 325-365 (381)
255 cd02413 40S_S3_KH K homology R 48.4 10 0.00022 29.4 1.3 23 3-25 44-66 (81)
256 PF02080 TrkA_C: TrkA-C domain 48.2 25 0.00055 25.4 3.5 41 8-48 14-69 (71)
257 COG0331 FabD (acyl-carrier-pro 48.2 44 0.00095 32.5 6.0 80 92-171 133-214 (310)
258 COG1702 PhoH Phosphate starvat 48.1 45 0.00097 33.0 6.0 45 2-50 28-72 (348)
259 PF04216 FdhE: Protein involve 44.9 5.4 0.00012 38.2 -0.8 50 300-350 172-226 (290)
260 PF10146 zf-C4H2: Zinc finger- 44.6 14 0.0003 34.4 1.9 23 323-345 196-218 (230)
261 PF02080 TrkA_C: TrkA-C domain 43.2 17 0.00038 26.3 1.9 42 100-141 14-70 (71)
262 PF09869 DUF2096: Uncharacteri 41.7 77 0.0017 28.0 5.8 57 78-144 110-166 (169)
263 PF07191 zinc-ribbons_6: zinc- 41.3 1.8 3.9E-05 32.6 -3.7 41 301-347 2-42 (70)
264 TIGR01009 rpsC_bact ribosomal 38.4 33 0.00071 31.5 3.2 28 83-110 64-91 (211)
265 KOG4185|consensus 37.3 6.5 0.00014 37.5 -1.6 44 300-344 207-265 (296)
266 PF02749 QRPTase_N: Quinolinat 37.1 1.2E+02 0.0026 23.4 5.9 47 10-56 35-87 (88)
267 PRK11895 ilvH acetolactate syn 36.7 2.8E+02 0.006 24.3 8.7 115 11-144 19-141 (161)
268 PRK12327 nusA transcription el 36.2 29 0.00062 34.6 2.7 27 90-116 245-272 (362)
269 PF07837 FTCD_N: Formiminotran 36.2 73 0.0016 28.5 5.0 50 97-146 12-69 (178)
270 PF13240 zinc_ribbon_2: zinc-r 35.8 6.8 0.00015 22.9 -1.1 22 323-344 1-22 (23)
271 KOG2807|consensus 35.7 21 0.00045 34.9 1.5 44 299-343 329-375 (378)
272 PF10217 DUF2039: Uncharacteri 34.0 16 0.00034 29.1 0.4 37 299-344 54-90 (92)
273 PF14569 zf-UDP: Zinc-binding 33.7 35 0.00075 26.3 2.1 47 300-347 9-63 (80)
274 COG2985 Predicted permease [Ge 33.6 1.4E+02 0.003 31.1 7.0 89 30-141 253-355 (544)
275 TIGR01953 NusA transcription t 33.4 35 0.00075 33.7 2.7 27 90-116 243-270 (341)
276 KOG0824|consensus 33.1 12 0.00026 36.1 -0.5 51 296-347 101-152 (324)
277 COG3813 Uncharacterized protei 32.9 26 0.00057 26.6 1.4 23 320-345 29-51 (84)
278 KOG4451|consensus 32.8 27 0.00059 32.4 1.7 28 318-346 247-274 (286)
279 PF07975 C1_4: TFIIH C1-like d 32.8 31 0.00068 24.4 1.7 25 317-342 26-50 (51)
280 TIGR01562 FdhE formate dehydro 32.8 8.9 0.00019 37.2 -1.5 44 300-344 184-233 (305)
281 CHL00100 ilvH acetohydroxyacid 31.9 3.7E+02 0.008 23.9 8.8 104 32-154 47-154 (174)
282 PF10497 zf-4CXXC_R1: Zinc-fin 31.8 42 0.00092 27.3 2.6 42 301-343 8-69 (105)
283 PRK12329 nusA transcription el 31.5 34 0.00073 35.0 2.3 27 90-116 277-304 (449)
284 PRK03564 formate dehydrogenase 30.9 16 0.00034 35.6 -0.1 44 299-343 186-234 (309)
285 TIGR00119 acolac_sm acetolacta 29.9 3.8E+02 0.0081 23.4 8.4 115 11-143 18-139 (157)
286 PF05605 zf-Di19: Drought indu 29.8 26 0.00056 24.6 0.9 39 300-346 2-42 (54)
287 COG0092 RpsC Ribosomal protein 29.7 34 0.00074 31.9 1.9 20 3-22 65-84 (233)
288 PF03958 Secretin_N: Bacterial 29.6 1.5E+02 0.0032 22.0 5.2 32 111-144 45-76 (82)
289 COG5166 Uncharacterized conser 29.3 98 0.0021 32.3 5.1 53 82-135 498-554 (657)
290 COG5109 Uncharacterized conser 28.9 35 0.00075 33.2 1.8 43 301-344 337-385 (396)
291 KOG3113|consensus 28.8 41 0.00089 31.7 2.2 36 309-347 124-159 (293)
292 PRK12328 nusA transcription el 28.5 37 0.0008 33.9 2.0 27 90-116 251-278 (374)
293 TIGR02024 FtcD glutamate formi 28.4 1.7E+02 0.0036 28.4 6.3 50 97-146 14-71 (298)
294 cd02412 30S_S3_KH K homology R 28.4 32 0.0007 28.0 1.3 21 2-22 74-94 (109)
295 PRK00310 rpsC 30S ribosomal pr 27.9 58 0.0013 30.3 3.1 29 82-110 63-91 (232)
296 PF04710 Pellino: Pellino; In 27.8 20 0.00043 35.9 0.0 33 311-344 302-337 (416)
297 PF04423 Rad50_zn_hook: Rad50 26.6 26 0.00057 24.6 0.4 11 336-346 21-31 (54)
298 COG0331 FabD (acyl-carrier-pro 26.5 1.1E+02 0.0025 29.7 5.0 51 3-53 136-188 (310)
299 PF10369 ALS_ss_C: Small subun 26.4 98 0.0021 23.3 3.6 43 100-143 16-58 (75)
300 PRK09202 nusA transcription el 26.0 46 0.001 34.3 2.3 27 90-116 245-272 (470)
301 COG4010 Uncharacterized protei 25.6 2E+02 0.0043 25.0 5.6 42 101-145 126-167 (170)
302 PF09297 zf-NADH-PPase: NADH p 24.6 8.6 0.00019 24.1 -2.1 23 320-343 3-29 (32)
303 PF10083 DUF2321: Uncharacteri 24.2 39 0.00084 29.5 1.1 27 320-350 28-54 (158)
304 cd04517 TLF TBP-like factors ( 24.1 5E+02 0.011 22.9 11.2 94 33-146 58-173 (174)
305 cd02410 archeal_CPSF_KH The ar 23.7 84 0.0018 27.2 3.0 24 2-25 89-112 (145)
306 PF06844 DUF1244: Protein of u 23.2 45 0.00098 24.9 1.1 12 323-334 12-23 (68)
307 PF09383 NIL: NIL domain; Int 22.6 88 0.0019 23.2 2.7 45 100-144 16-69 (76)
308 PLN00062 TATA-box-binding prot 22.6 5.5E+02 0.012 22.8 10.9 25 123-147 147-173 (179)
309 PF02318 FYVE_2: FYVE-type zin 21.7 6.4 0.00014 32.5 -4.1 44 299-343 53-102 (118)
310 TIGR00622 ssl1 transcription f 21.6 64 0.0014 26.7 1.9 41 301-342 56-110 (112)
311 KOG1960|consensus 21.3 35 0.00076 34.3 0.3 117 5-147 231-375 (531)
312 PF10235 Cript: Microtubule-as 21.3 47 0.001 26.3 1.0 35 301-345 45-79 (90)
313 KOG0006|consensus 20.2 62 0.0013 31.6 1.7 34 300-334 221-256 (446)
314 PF02749 QRPTase_N: Quinolinat 20.2 3.2E+02 0.007 20.9 5.6 48 99-146 32-85 (88)
315 KOG4621|consensus 20.1 27 0.00058 29.6 -0.7 29 298-326 79-107 (167)
No 1
>KOG2113|consensus
Probab=99.96 E-value=6.7e-30 Score=236.98 Aligned_cols=317 Identities=35% Similarity=0.404 Sum_probs=232.3
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcce
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHV 81 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 81 (353)
-|+|++|++||.|+.||+++|+.|.++++++|.++|.+++|++|+++|....+|+..+++.+.+....+. ...+++.
T Consensus 39 ~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~~edv~~aRrei~saaeH~~l~~~s~s~Sgg~~~---~s~s~qt 115 (394)
T KOG2113|consen 39 EIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGRHEDVRRARREIPSAAEHFGLIRASRSFSGGTNG---ASASGQT 115 (394)
T ss_pred eecccCccccchhhhhhcceeccCCCCCCCcceeccCchhHHHHhhcCccccceeeeeeecccccCCCcc---ccccCCC
Confidence 3789999999999999999999999999999999999999999999999999999887777765433222 1245678
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHH-HHHHH-HHHHHHHHhhhCCCCc-cCcc
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDS-VEIAR-QEIESHIIRRTGSCVT-PAEA 158 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~-V~~A~-~~I~~~i~~r~g~~~~-~~d~ 158 (353)
+.++.+|.+++|.|+|.+|++|++||+.++.+|..+.+..++++.++|.+++ +++|. .+|++.+..|.+...+ .+||
T Consensus 116 ~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta~~ra~~i~d~dndf 195 (394)
T KOG2113|consen 116 TSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTAVTRAGQIHDTDNDF 195 (394)
T ss_pred ceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhhhhhhhhccccCCccc
Confidence 9999999999999999999999999999999999999999999999999998 88898 8999999999999888 4799
Q ss_pred ccCCCCccchHHHhhhhCCCCCccccccccCCCCCCCCCCCCCCCCCcccCCCCCccccCccccc--CCCCCCCCCCCCC
Q psy4141 159 VLNGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFS--GSSGCSSASSSSS 236 (353)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~ 236 (353)
+.+..+++.+++.+.-.. ..++...+ .+..|. .+|. ....|+.++|+++
T Consensus 196 ~~~la~v~l~v~~~~~a~------~~~~~~~~----~s~f~~-------------------~~~~n~~~~~~~~~sss~~ 246 (394)
T KOG2113|consen 196 AGQLAGVSLMVQKQQQAQ------QQMQEAQQ----QSMFYR-------------------RAFGNSNPFNQKEMSSSPF 246 (394)
T ss_pred cccccccchhhhhHHHHH------HHHhhcCc----cchHHH-------------------hcccCCCccchhhccCCCc
Confidence 999999988765421000 00111111 122221 1222 1123455555555
Q ss_pred CCCCCCCCCCcccccccccCCCCCCCCCCCCCCCCCCCCCCCCC------CCCCCCCC----------------------
Q psy4141 237 SSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPS------SIWSYPPV---------------------- 288 (353)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~------~~~~~p~~---------------------- 288 (353)
+..+.....+.......|...+..+.+++.|.+++....+...- --|+..+.
T Consensus 247 ~~~s~~~~~~~~~~~~~~~ss~t~~~~~g~g~s~~~~~~~~~~~~~~~~~~~~~~~~s~~~i~~~e~~s~~~~~~~a~~~ 326 (394)
T KOG2113|consen 247 GMESSLGLDALLRSFPSMRSSLTPESLSGTGLSRPSLGGGQSAKQDLPTYDYWGTNNSLNDIMENEILSRKYDALSAWSS 326 (394)
T ss_pred ccccccccccchhhhhhhhccCCcccccccCCCccccCCccccccCCCcCCccccCcchhhhhhhhhhhhhcchhhcccc
Confidence 44443333344555667776555556677777766555433211 11111100
Q ss_pred -----CCCCCCCCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141 289 -----SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 352 (353)
Q Consensus 289 -----~~~~~~~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~ 352 (353)
--.++...+...++|.+|-+.....++.+|+|++||++|+.. .-...||+|......+++|.
T Consensus 327 ~~l~~~~~~~~~~~~s~~~~~~~~~~~~st~~~~~~~n~~~~~~a~~--s~~~~~~~c~~~~~~~~~i~ 393 (394)
T KOG2113|consen 327 MGLEKREESPTNGLMSSLKGTSAGFGLLSTIWSGGNMNLSPGSLASA--SASPTSSTCDHNDHTLVPIN 393 (394)
T ss_pred ccchhccccccccchhhcccccccCceeeeEeecCCcccChhhhhhc--ccCCccccccccceeeeecC
Confidence 011233344557999999999999999999999999999983 23789999999888888774
No 2
>KOG2191|consensus
Probab=99.83 E-value=7.8e-20 Score=171.41 Aligned_cols=148 Identities=26% Similarity=0.316 Sum_probs=119.7
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC------CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG------EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPT 75 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~------e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~ 75 (353)
+||||+|++|.+|+++||++|++.... .|||+.|+|+.+++......|++.+++..+.... +.....+.
T Consensus 52 sIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~k----~v~~~~pq- 126 (402)
T KOG2191|consen 52 SIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVAK----PVDILQPQ- 126 (402)
T ss_pred ceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhcC----CccccCCC-
Confidence 599999999999999999999998664 3799999999999999999999999987653222 11111111
Q ss_pred CCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcC-CCC-----CCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141 76 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP-SRD-----KEPVFEVTGAPDSVEIARQEIESHIIRRT 149 (353)
Q Consensus 76 ~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip-~~~-----~e~~v~I~G~~e~V~~A~~~I~~~i~~r~ 149 (353)
.......+++.||+...|.||||+|++||.|++++|+.|++. ... ++|+|++.|++|+..+|..+|+++|.+..
T Consensus 127 t~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDp 206 (402)
T KOG2191|consen 127 TPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDP 206 (402)
T ss_pred CccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCC
Confidence 011125589999999999999999999999999999999886 432 47899999999999999999999999844
Q ss_pred CCCCc
Q psy4141 150 GSCVT 154 (353)
Q Consensus 150 g~~~~ 154 (353)
.....
T Consensus 207 qs~sc 211 (402)
T KOG2191|consen 207 QSGSC 211 (402)
T ss_pred cccce
Confidence 43333
No 3
>KOG1676|consensus
Probab=99.82 E-value=1.2e-19 Score=181.94 Aligned_cols=140 Identities=25% Similarity=0.356 Sum_probs=114.9
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC-----CcCeEEEecCHHHHHHHHHHHHHHHhhhhh-h-hhccCCCCCCCCCCC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG-----EEPVFVVTGRKEDVARAKREILSAADHFSA-L-RASRKSGALSPLSPP 74 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~-~-~~~~~~g~~~~~~~~ 74 (353)
-||||+|++||.|++++|+++.+-.++ ..+.+.|+|+++.|+.|+.+|.++|++... . +.....|.
T Consensus 152 lIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~~~~g~------- 224 (600)
T KOG1676|consen 152 LIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSGGHAGV------- 224 (600)
T ss_pred eEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCCccccccCc-------
Confidence 489999999999999999999976554 246799999999999999999999996322 1 11111110
Q ss_pred CCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC----CCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141 75 TGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD----KEPVFEVTGAPDSVEIARQEIESHIIRRT 149 (353)
Q Consensus 75 ~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~----~e~~v~I~G~~e~V~~A~~~I~~~i~~r~ 149 (353)
..-+..+.+|.||...||.||||+|++||+|+-+|||+|+|-.++ .||.+.|.|+++.|+.|.++|.++|+..+
T Consensus 225 -~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~ 302 (600)
T KOG1676|consen 225 -RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAE 302 (600)
T ss_pred -CccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHh
Confidence 112235899999999999999999999999999999999886553 47999999999999999999999999843
No 4
>KOG1676|consensus
Probab=99.78 E-value=8.2e-19 Score=175.85 Aligned_cols=136 Identities=25% Similarity=0.311 Sum_probs=112.4
Q ss_pred eecCCCchHHHHHHHcCceEEecCC-C---CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCC
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVR-G---EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 78 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~-~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~ 78 (353)
||||+|++||+|+.+||++|+|-.. + .+|.+.|.|+++.|+.|.++|.+|+++.... .+.....+ .|
T Consensus 244 IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~-----~~~~~~~G----~P 314 (600)
T KOG1676|consen 244 IIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG-----AGGGMGGG----AP 314 (600)
T ss_pred EEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc-----CCCCcCCC----Cc
Confidence 8999999999999999999997533 3 4799999999999999999999999876331 11111111 12
Q ss_pred c-ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC-----CCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141 79 G-HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-----DKEPVFEVTGAPDSVEIARQEIESHIIR 147 (353)
Q Consensus 79 ~-~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-----~~e~~v~I~G~~e~V~~A~~~I~~~i~~ 147 (353)
. ...+.|.||.+.+|+||||+|+|||.|.+++|+++.++.. ..+++|+|.|.+.+|+.|+.||.+++..
T Consensus 315 ~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~ 389 (600)
T KOG1676|consen 315 GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGD 389 (600)
T ss_pred cceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhcc
Confidence 1 1378899999999999999999999999999999976554 2478999999999999999999998875
No 5
>KOG2190|consensus
Probab=99.69 E-value=2.4e-16 Score=159.30 Aligned_cols=137 Identities=27% Similarity=0.426 Sum_probs=112.5
Q ss_pred eeecCCCchHHHHHHHcCceEEecCC--C-CcCeEEEec---------CHHHHHHHHHHHHHHHhhhhhhhhccCCCCCC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVR--G-EEPVFVVTG---------RKEDVARAKREILSAADHFSALRASRKSGALS 69 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~--~-e~~vv~I~G---------~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~ 69 (353)
+||||+|..||+||++|.++|++-.. + .+|+++|+| ..+++.+|.++|...+++... +....+
T Consensus 56 ~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~--~~~d~~--- 130 (485)
T KOG2190|consen 56 SIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDE--AAEDNG--- 130 (485)
T ss_pred eEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccc--ccccCC---
Confidence 69999999999999988888887543 2 579999999 999999999999888663311 111111
Q ss_pred CCCCCCCCCc-ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEcCHHHHHHHHHHHHHH
Q psy4141 70 PLSPPTGVPG-HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGAPDSVEIARQEIESH 144 (353)
Q Consensus 70 ~~~~~~~~~~-~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G~~e~V~~A~~~I~~~ 144 (353)
..... .++++|.||..++|.||||+|+.||+|+++|||+|++.++ ..++.|+|.|.+++|.+|...|...
T Consensus 131 -----~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~ 205 (485)
T KOG2190|consen 131 -----EDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSR 205 (485)
T ss_pred -----ccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHH
Confidence 01111 3899999999999999999999999999999999987665 3578899999999999999999999
Q ss_pred HHhh
Q psy4141 145 IIRR 148 (353)
Q Consensus 145 i~~r 148 (353)
|.+.
T Consensus 206 L~~~ 209 (485)
T KOG2190|consen 206 LLEN 209 (485)
T ss_pred HHhc
Confidence 8884
No 6
>KOG2193|consensus
Probab=99.68 E-value=1.3e-16 Score=153.77 Aligned_cols=148 Identities=24% Similarity=0.317 Sum_probs=117.2
Q ss_pred eeecCCCchHHHHHHHcCceEEecCC------CCcCeEEEecCHHHHHHHHHHHHHHHhhh-hh-hhhccCC--------
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVR------GEEPVFVVTGRKEDVARAKREILSAADHF-SA-LRASRKS-------- 65 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~------~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~-~~-~~~~~~~-------- 65 (353)
++|||.|.+||+|+.+||++|.+... +.||.+++.|+.|+|.+|..+|++.+++. .+ +.+-...
T Consensus 293 RLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~ 372 (584)
T KOG2193|consen 293 RLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLN 372 (584)
T ss_pred hhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccC
Confidence 68999999999999999999997643 45899999999999999999999998863 22 3221110
Q ss_pred --------------CCCCCCCC------CC---CCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---
Q psy4141 66 --------------GALSPLSP------PT---GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR--- 119 (353)
Q Consensus 66 --------------g~~~~~~~------~~---~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~--- 119 (353)
.+++++.+ +. ..+....++|.||...||.|||++|++||.|...+|+.|+|...
T Consensus 373 ~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~p 452 (584)
T KOG2193|consen 373 LPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIP 452 (584)
T ss_pred ccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCC
Confidence 01111100 00 11356778999999999999999999999999999999987554
Q ss_pred -CCCCeEEEEcCHHHHHHHHHHHHHHHHhhh
Q psy4141 120 -DKEPVFEVTGAPDSVEIARQEIESHIIRRT 149 (353)
Q Consensus 120 -~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~ 149 (353)
-.+|.|+|+|+|++.-+|+-.|..+|++..
T Consensus 453 dvseRMViItGppeaqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 453 DVSERMVIITGPPEAQFKAQGRIFGKIKEEN 483 (584)
T ss_pred CcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence 247899999999999999999999998843
No 7
>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=6.4e-16 Score=137.16 Aligned_cols=129 Identities=19% Similarity=0.260 Sum_probs=100.1
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEE---ecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVV---TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP 78 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I---~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~ 78 (353)
.|||++|++||.|+++||++|++... +..+.| +++++++.+|+..|..+...+.--.|-+..+
T Consensus 11 ~vIG~gG~~Ik~I~~~tgv~I~Id~~--~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~g------------ 76 (172)
T TIGR03665 11 VLIGKGGETKKEIEERTGVKLDIDSE--TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLD------------ 76 (172)
T ss_pred hHhCCchhHHHHHHHHhCcEEEEEcC--CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcC------------
Confidence 37999999999999999999999854 244666 8999999999999999877432100000001
Q ss_pred cceEE-EEEecC---------CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141 79 GHVTI-EVRVPY---------KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRR 148 (353)
Q Consensus 79 ~~~t~-~v~VP~---------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~r 148 (353)
..+.. -+.|+. +.+|+|||++|++++.||..|||+|.++. ..|.|.|.+++++.|+++|+++++.+
T Consensus 77 d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 77 DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 11122 233433 47999999999999999999999999874 57999999999999999999999654
No 8
>KOG2192|consensus
Probab=99.63 E-value=1.1e-15 Score=140.07 Aligned_cols=149 Identities=18% Similarity=0.255 Sum_probs=120.7
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcc
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGH 80 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~ 80 (353)
.||||+|++||+|+.++++.|.+|+.+ .+++++|+.+.+-|-...+.|+-.+++-. .++.-
T Consensus 61 avigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f------------------~~~~p 122 (390)
T KOG2192|consen 61 AVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGF------------------QLPSP 122 (390)
T ss_pred ceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCC------------------CCCCc
Confidence 389999999999999999999999875 78999999999988887777777777531 12333
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEcCHHHHHHHHHHHHHHHHhhhCCCCccC
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPA 156 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~~~~~~ 156 (353)
..++|+|+..+.|.|||++|.+||+|+++..++++|-.. ..+|+|.|.|.+.+|-.+.+.|+++|.+.-=+... -
T Consensus 123 ce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa-~ 201 (390)
T KOG2192|consen 123 CELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSA-Q 201 (390)
T ss_pred hhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcC-C
Confidence 788999999999999999999999999999999976543 57889999999999999999999999984322221 1
Q ss_pred ccccCCCCccchH
Q psy4141 157 EAVLNGDDNSADL 169 (353)
Q Consensus 157 d~~~~~~~~~~~~ 169 (353)
.+..|++|+.+|+
T Consensus 202 py~p~fyd~t~dy 214 (390)
T KOG2192|consen 202 PYDPNFYDETYDY 214 (390)
T ss_pred cCCccccCccccc
Confidence 2334556776665
No 9
>KOG2193|consensus
Probab=99.61 E-value=8.1e-16 Score=148.44 Aligned_cols=131 Identities=21% Similarity=0.340 Sum_probs=113.4
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV 77 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~ 77 (353)
-||||.|.+||.|-+.|.++|++-... .+++++|-+++|...+|.++|++++..... ...+
T Consensus 212 aIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~---------------~~k~ 276 (584)
T KOG2193|consen 212 AIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAV---------------DDKV 276 (584)
T ss_pred EEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhh---------------ccch
Confidence 389999999999999999999986432 578999999999999999999999886422 1122
Q ss_pred CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC------CCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141 78 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGAPDSVEIARQEIESHIIR 147 (353)
Q Consensus 78 ~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~------~~e~~v~I~G~~e~V~~A~~~I~~~i~~ 147 (353)
...+.+++...+.+||++|||.|.+||+|+++||++|.|.+- ..||+|+|.|+-|+|.+|..+|..+|++
T Consensus 277 ~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre 352 (584)
T KOG2193|consen 277 AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRE 352 (584)
T ss_pred hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHH
Confidence 345778889999999999999999999999999999977542 4589999999999999999999999987
No 10
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.61 E-value=6.7e-15 Score=131.50 Aligned_cols=128 Identities=22% Similarity=0.300 Sum_probs=97.4
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEE----ecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVV----TGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV 77 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I----~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~ 77 (353)
.|||++|.+||.|+++||++|++... +..|.| +++++++.+|+..|..++..+..-.+-+..+
T Consensus 16 ~iIG~gGk~Ik~I~e~tg~~I~i~~~--~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~g----------- 82 (180)
T PRK13763 16 VLIGKKGETKKEIEERTGVKLEIDSE--TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD----------- 82 (180)
T ss_pred hHhccchhHHHHHHHHHCcEEEEECC--CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHhC-----------
Confidence 37999999999999999999999854 244555 5899999999999999987432111100011
Q ss_pred CcceEEE-EEec---------CCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141 78 PGHVTIE-VRVP---------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR 147 (353)
Q Consensus 78 ~~~~t~~-v~VP---------~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~ 147 (353)
..+..+ +.|. .+.+|+|||++|++++.||+.|||+|.++. ..|.|.|.+++++.|++.|+++++.
T Consensus 83 -d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----~~v~i~G~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 83 -DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----KTVAIIGDPEQVEIAREAIEMLIEG 157 (180)
T ss_pred -CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----CEEEEEeCHHHHHHHHHHHHHHHcC
Confidence 011111 1111 247999999999999999999999999874 3599999999999999999998854
No 11
>KOG2192|consensus
Probab=99.61 E-value=7.9e-15 Score=134.54 Aligned_cols=145 Identities=22% Similarity=0.372 Sum_probs=112.1
Q ss_pred eecCCCchHHHHHHHcCceEEecC----CCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccC--------------
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPV----RGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRK-------------- 64 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~----~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~-------------- 64 (353)
||||+|++||+||++..+++++-. ...+||+++.|.+.+|....+.|++++.+..--.....
T Consensus 137 iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dygg 216 (390)
T KOG2192|consen 137 IIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGG 216 (390)
T ss_pred eecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCC
Confidence 899999999999999999999632 12479999999999999999999999887542100000
Q ss_pred -----------CCC------CCCC--------------------------------------------------------
Q psy4141 65 -----------SGA------LSPL-------------------------------------------------------- 71 (353)
Q Consensus 65 -----------~g~------~~~~-------------------------------------------------------- 71 (353)
.++ ..|+
T Consensus 217 f~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~y 296 (390)
T KOG2192|consen 217 FTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGY 296 (390)
T ss_pred ceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCC
Confidence 000 0000
Q ss_pred --------CCCCCC-CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---CCCCeEEEEcCHHHHHHHHH
Q psy4141 72 --------SPPTGV-PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTGAPDSVEIARQ 139 (353)
Q Consensus 72 --------~~~~~~-~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---~~e~~v~I~G~~e~V~~A~~ 139 (353)
+.+..+ -...+.+|.||.++-|.||||+|+.|++|++++|+.|.+... ..++.++|+|+.++++.|+.
T Consensus 297 dysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQY 376 (390)
T KOG2192|consen 297 DYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQY 376 (390)
T ss_pred CccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHH
Confidence 000000 025778999999999999999999999999999999988653 35789999999999999999
Q ss_pred HHHHHHHh
Q psy4141 140 EIESHIIR 147 (353)
Q Consensus 140 ~I~~~i~~ 147 (353)
++++.|+.
T Consensus 377 LlQn~Vkq 384 (390)
T KOG2192|consen 377 LLQNSVKQ 384 (390)
T ss_pred HHHHHHHh
Confidence 99998885
No 12
>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=99.37 E-value=1.3e-12 Score=97.53 Aligned_cols=60 Identities=32% Similarity=0.486 Sum_probs=55.0
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEcCHHHHHHHHHHH
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTGAPDSVEIARQEI 141 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G~~e~V~~A~~~I 141 (353)
+++|.||...+|.|||++|++|++|+++|||+|.+.+. +.++.|+|+|++++|++|+.||
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 36899999999999999999999999999999988764 3468999999999999999998
No 13
>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=99.37 E-value=9.2e-13 Score=97.12 Aligned_cols=60 Identities=33% Similarity=0.550 Sum_probs=55.3
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHH
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIE 142 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~ 142 (353)
.+|.||.+++|+|||++|++|++|+++|||+|.+|..+ .++.|+|+|++++|..|+++|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999999763 4679999999999999999873
No 14
>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=99.36 E-value=5.2e-13 Score=97.81 Aligned_cols=60 Identities=35% Similarity=0.650 Sum_probs=55.0
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHH
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEI 141 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I 141 (353)
|.+|.||.+++|+|||++|.+|++|+++|||+|.++.++.+..|+|+|++++|++|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence 678999999999999999999999999999999998765234899999999999999987
No 15
>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=99.36 E-value=2.3e-12 Score=95.08 Aligned_cols=59 Identities=25% Similarity=0.385 Sum_probs=54.4
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHH
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIE 142 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~ 142 (353)
....+.||.+++|+|||++|++||+|+++|||+|.++. ++.|.|+|+ +++|++|+++|+
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHhC
Confidence 56789999999999999999999999999999999886 468999998 999999999884
No 16
>KOG2113|consensus
Probab=99.29 E-value=1.6e-12 Score=121.79 Aligned_cols=67 Identities=46% Similarity=0.692 Sum_probs=63.6
Q ss_pred CCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHH
Q psy4141 77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIES 143 (353)
Q Consensus 77 ~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~ 143 (353)
.++++++.+.||+++|+.|+|++|.+||.|+.+|.+||+.|.++++++|.++|.+++|++|++.|..
T Consensus 22 ~p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 22 IGQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CCCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccCchhHHHHhhcCcc
Confidence 4567999999999999999999999999999999999999999999999999999999999999864
No 17
>KOG2190|consensus
Probab=99.27 E-value=2.8e-11 Score=122.78 Aligned_cols=144 Identities=24% Similarity=0.340 Sum_probs=108.3
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhh---h--------hh--ccC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREILSAADHFSA---L--------RA--SRK 64 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~---~--------~~--~~~ 64 (353)
.||||+|++||+|+++|||+|++.... .++.|+|.|.+++|.+|...|...|.+... . +. .+.
T Consensus 151 slIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~ 230 (485)
T KOG2190|consen 151 SLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQG 230 (485)
T ss_pred eeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCccccc
Confidence 589999999999999999999976442 467899999999999999999999887421 1 00 000
Q ss_pred C------CCCC---------------------C-------------------------------C-C-----CCCCC---
Q psy4141 65 S------GALS---------------------P-------------------------------L-S-----PPTGV--- 77 (353)
Q Consensus 65 ~------g~~~---------------------~-------------------------------~-~-----~~~~~--- 77 (353)
. +... + . . .....
T Consensus 231 ~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~ 310 (485)
T KOG2190|consen 231 GPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISARENPED 310 (485)
T ss_pred CccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCcceeeeccccCccc
Confidence 0 0000 0 0 0 00000
Q ss_pred ------------------------CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-----CCCeEEEE
Q psy4141 78 ------------------------PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-----KEPVFEVT 128 (353)
Q Consensus 78 ------------------------~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-----~e~~v~I~ 128 (353)
...++.++.||.+++|.||||+|++|.+|++.||+.|.+...+ .++.++|+
T Consensus 311 ~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~ 390 (485)
T KOG2190|consen 311 RYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQIT 390 (485)
T ss_pred ccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcceeEEEec
Confidence 1126788999999999999999999999999999999886654 36799999
Q ss_pred cCHHHHHHHHHHHHHHH
Q psy4141 129 GAPDSVEIARQEIESHI 145 (353)
Q Consensus 129 G~~e~V~~A~~~I~~~i 145 (353)
|...+...|+.+|...+
T Consensus 391 ~~~~~~~~~~~~~~~~~ 407 (485)
T KOG2190|consen 391 GMLREDLLAQYLIRARL 407 (485)
T ss_pred chhHHHHhhhhhccccc
Confidence 99999999998885433
No 18
>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=99.26 E-value=1.4e-11 Score=90.78 Aligned_cols=60 Identities=37% Similarity=0.595 Sum_probs=54.9
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC---CCCCeEEEEcCHHHHHHHHHHHH
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR---DKEPVFEVTGAPDSVEIARQEIE 142 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---~~e~~v~I~G~~e~V~~A~~~I~ 142 (353)
.+|.||.+++|+|||++|++|++|+++|||+|.++.. ..++.|.|.|+.++|+.|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence 5799999999999999999999999999999999875 34679999999999999999873
No 19
>KOG4172|consensus
Probab=99.20 E-value=1.6e-12 Score=91.28 Aligned_cols=53 Identities=28% Similarity=0.797 Sum_probs=49.8
Q ss_pred cccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCcccccccceeccC
Q psy4141 301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRIIS 353 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~~~ri~~ 353 (353)
.+|.||++..++.++.-|||.|+|.+|..++|.. ...||+||+++..+||.|.
T Consensus 8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkTY~ 61 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKTYR 61 (62)
T ss_pred cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHhhc
Confidence 7899999999999999999999999999999986 8899999999999998773
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=99.17 E-value=1.2e-11 Score=87.40 Aligned_cols=50 Identities=38% Similarity=0.967 Sum_probs=43.9
Q ss_pred CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141 299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 348 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~ 348 (353)
++..|.||++...+++++||||.+||..|+.+++.....||+||+++.++
T Consensus 1 ~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~V 50 (50)
T PF13920_consen 1 EDEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIESV 50 (50)
T ss_dssp -HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SEE
T ss_pred CcCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcCC
Confidence 35789999999999999999999999999999999899999999998753
No 21
>smart00322 KH K homology RNA-binding domain.
Probab=99.07 E-value=9e-10 Score=80.97 Aligned_cols=65 Identities=43% Similarity=0.648 Sum_probs=59.3
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEcCHHHHHHHHHHHHHHH
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHI 145 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G~~e~V~~A~~~I~~~i 145 (353)
.+.+|.||.+.+|++||++|++|++|++.||++|.++... ....++|.|.+++++.|+.+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 6789999999999999999999999999999999887653 4568999999999999999998876
No 22
>KOG4265|consensus
Probab=99.00 E-value=2e-10 Score=110.20 Aligned_cols=55 Identities=27% Similarity=0.773 Sum_probs=51.1
Q ss_pred CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 352 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~ 352 (353)
+...+|+||+...++.+++||+|.|+|..|++.+.-+...||+||+++.+.+.|+
T Consensus 288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~i~ 342 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEELLEIY 342 (349)
T ss_pred cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHhhheec
Confidence 4458999999999999999999999999999999877899999999999998875
No 23
>PF13014 KH_3: KH domain
Probab=98.89 E-value=2.5e-09 Score=73.08 Aligned_cols=39 Identities=38% Similarity=0.647 Sum_probs=35.0
Q ss_pred CccceeccCChHHHHHHHHhCceEEcCCC----CCCCeEEEEc
Q psy4141 91 VVGLVVGPKGATIKRIQHQTNTYIVTPSR----DKEPVFEVTG 129 (353)
Q Consensus 91 ~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~----~~e~~v~I~G 129 (353)
+||+|||++|++|++|+++|||+|.|+++ +.++.|+|+|
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 58999999999999999999999999982 3567999987
No 24
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.83 E-value=2e-09 Score=73.32 Aligned_cols=38 Identities=39% Similarity=0.944 Sum_probs=31.1
Q ss_pred cccccccccccEEeCCCCHhhhHHhHHHHhcc-C---CCCCCc
Q psy4141 303 CYLCNDREVTHALIPCGHNFFCSECAERTCDF-D---RTCPMC 341 (353)
Q Consensus 303 C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~---~~CP~C 341 (353)
|+||++.+.+++.++|||+ ||..|+.++|.. . ..||.|
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 999999999998 2 469987
No 25
>KOG2191|consensus
Probab=98.81 E-value=1.8e-08 Score=95.49 Aligned_cols=70 Identities=23% Similarity=0.386 Sum_probs=64.5
Q ss_pred cceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC------CCCCeEEEEcCHHHHHHHHHHHHHHHHhh
Q psy4141 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGAPDSVEIARQEIESHIIRR 148 (353)
Q Consensus 79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~------~~e~~v~I~G~~e~V~~A~~~I~~~i~~r 148 (353)
+...++|+||...+|.||||||++|.++|++|||+|+..+. ..||++.|+|+-+++-...+.|.++|++.
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~ 112 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREK 112 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHh
Confidence 34889999999999999999999999999999999987654 46899999999999999999999999993
No 26
>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=98.78 E-value=1.1e-08 Score=75.15 Aligned_cols=49 Identities=35% Similarity=0.540 Sum_probs=44.4
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREIL 50 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~ 50 (353)
.|||++|++|++|+++|||+|.+|..+ .++.|+|+|++++|..|+.+|+
T Consensus 13 ~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 13 FIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred hccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHhC
Confidence 589999999999999999999999754 4588999999999999999874
No 27
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.77 E-value=6.2e-09 Score=92.96 Aligned_cols=54 Identities=28% Similarity=0.666 Sum_probs=45.2
Q ss_pred CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc----------------CCCCCCccccccc--ceecc
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF----------------DRTCPMCRVPVNQ--AMRII 352 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~----------------~~~CP~Cr~~i~~--~~ri~ 352 (353)
.++.+|.||++...++++++|||. ||..|+.+|+.. ...||+||.++.. ++.+|
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~-FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiy 87 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHL-FCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIY 87 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCch-hHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEee
Confidence 456899999999999999999999 999999998642 3589999999965 44444
No 28
>KOG0317|consensus
Probab=98.77 E-value=4.3e-09 Score=98.34 Aligned_cols=48 Identities=33% Similarity=0.865 Sum_probs=44.5
Q ss_pred CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
....|.+|++...++...||||. ||..|+..|+.....||+||..+..
T Consensus 238 a~~kC~LCLe~~~~pSaTpCGHi-FCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 238 ATRKCSLCLENRSNPSATPCGHI-FCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CCCceEEEecCCCCCCcCcCcch-HHHHHHHHHHccccCCCcccccCCC
Confidence 35789999999999999999999 9999999999999999999998853
No 29
>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=98.75 E-value=2.1e-08 Score=74.67 Aligned_cols=48 Identities=27% Similarity=0.390 Sum_probs=43.7
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC----CcCeEEEecCHHHHHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG----EEPVFVVTGRKEDVARAKREI 49 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~----e~~vv~I~G~~e~v~~Ak~~I 49 (353)
+||||+|.+|++|+++|||+|+++... .+++++|.|+++++.+|+.+|
T Consensus 13 ~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 13 SIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred eeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 589999999999999999999998653 458999999999999999987
No 30
>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=98.70 E-value=1e-08 Score=74.86 Aligned_cols=48 Identities=29% Similarity=0.521 Sum_probs=43.1
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREI 49 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I 49 (353)
.|||++|.+|++|+++|||.|+++..+++..+.|.|++++|++|+++|
T Consensus 13 ~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 13 RIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp HHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred EEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence 479999999999999999999999765335899999999999999986
No 31
>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=98.70 E-value=7.8e-09 Score=69.15 Aligned_cols=38 Identities=39% Similarity=1.065 Sum_probs=33.8
Q ss_pred ccccccccccc-EEeCCCCHhhhHHhHHHHhccCCCCCCc
Q psy4141 303 CYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMC 341 (353)
Q Consensus 303 C~IC~~~~~~~-~llpCgH~~fC~~C~~~~~~~~~~CP~C 341 (353)
|.||++...++ ++++|||. ||.+|+.++.+....||+|
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 68999999 9999999999988899998
No 32
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.69 E-value=1.2e-08 Score=94.67 Aligned_cols=51 Identities=29% Similarity=0.749 Sum_probs=43.2
Q ss_pred CCcccccccccccc--------cEEeCCCCHhhhHHhHHHHhccCCCCCCccccccccee
Q psy4141 299 GSRQCYLCNDREVT--------HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR 350 (353)
Q Consensus 299 ~~~~C~IC~~~~~~--------~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~r 350 (353)
.+.+|.||++.... +++.+|+|. ||..|+.+|......||+||.++..+++
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~-FC~~CI~~Wl~~~~tCPlCR~~~~~v~~ 231 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHV-FCIECIDIWKKEKNTCPVCRTPFISVIK 231 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCc-ccHHHHHHHHhcCCCCCCCCCEeeEEee
Confidence 35789999997543 356789999 9999999998888999999999987754
No 33
>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=98.66 E-value=5.4e-08 Score=71.70 Aligned_cols=45 Identities=24% Similarity=0.298 Sum_probs=41.4
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecC-HHHHHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGR-KEDVARAKREI 49 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~-~e~v~~Ak~~I 49 (353)
+||||+|++||+|+++|||+|+++. +..|.|.|. ++++++|+.+|
T Consensus 15 ~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 15 DVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHh
Confidence 5899999999999999999999996 467999998 99999999987
No 34
>KOG0823|consensus
Probab=98.65 E-value=1.1e-08 Score=93.08 Aligned_cols=54 Identities=26% Similarity=0.639 Sum_probs=46.5
Q ss_pred CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc---CCCCCCccccccc--ceecc
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVNQ--AMRII 352 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~~--~~ri~ 352 (353)
....+|.||+|...++++..|||. ||..|+-+|+.. ...||+|+..++. ++-||
T Consensus 45 ~~~FdCNICLd~akdPVvTlCGHL-FCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVTLCGHL-FCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLY 103 (230)
T ss_pred CCceeeeeeccccCCCEEeecccc-eehHHHHHHHhhcCCCeeCCccccccccceEEeee
Confidence 346899999999999999999999 999999999987 5679999998863 44444
No 35
>KOG0320|consensus
Probab=98.64 E-value=1.4e-08 Score=88.81 Aligned_cols=53 Identities=34% Similarity=0.769 Sum_probs=45.4
Q ss_pred CCcccccccccccccE--EeCCCCHhhhHHhHHHHhccCCCCCCcccccc--cceecc
Q psy4141 299 GSRQCYLCNDREVTHA--LIPCGHNFFCSECAERTCDFDRTCPMCRVPVN--QAMRII 352 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~--llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~--~~~ri~ 352 (353)
....|+|||+.+...+ ...|||. ||..|++........||+||..|+ ++++||
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHv-FC~~Cik~alk~~~~CP~C~kkIt~k~~~rI~ 186 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHV-FCSQCIKDALKNTNKCPTCRKKITHKQFHRIY 186 (187)
T ss_pred cccCCCceecchhhccccccccchh-HHHHHHHHHHHhCCCCCCcccccchhhheecc
Confidence 3478999999876554 4799999 999999999988999999998775 678887
No 36
>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=98.63 E-value=8.1e-08 Score=80.29 Aligned_cols=58 Identities=26% Similarity=0.491 Sum_probs=50.3
Q ss_pred CCCccceeccCChHHHHHHHHhCceEEcCCCC--------------------CCCeEEEEcC---HHHHHHHHHHHHHHH
Q psy4141 89 YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD--------------------KEPVFEVTGA---PDSVEIARQEIESHI 145 (353)
Q Consensus 89 ~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~--------------------~e~~v~I~G~---~e~V~~A~~~I~~~i 145 (353)
.+++|.|||++|.|||+|+++|||+|.|-.+. +.-.|.|++. .+++++|+++|+.++
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 48899999999999999999999999887651 1247999995 489999999999988
Q ss_pred H
Q psy4141 146 I 146 (353)
Q Consensus 146 ~ 146 (353)
.
T Consensus 94 ~ 94 (120)
T cd02395 94 K 94 (120)
T ss_pred c
Confidence 8
No 37
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.63 E-value=5.4e-07 Score=80.41 Aligned_cols=127 Identities=20% Similarity=0.285 Sum_probs=94.0
Q ss_pred eecCCCchHHHHHHHcCceEEecCCCCcCeEEEe-----cCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCC
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVT-----GRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGV 77 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~-----G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~ 77 (353)
+||+.|+..+.|++.++++|.+... +..|.|. .++-.+.+|+..|..+-.-|+--.|-+-..
T Consensus 22 lig~~g~v~k~ie~~~~~~~~iD~~--~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~----------- 88 (194)
T COG1094 22 LIGKWGEVKKAIEEKTGVKLRIDSK--TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLLE----------- 88 (194)
T ss_pred eecccccchHHHHhhcCeEEEEECC--CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHhc-----------
Confidence 7999999999999999999998854 3444443 268889999999988855443211111100
Q ss_pred CcceEEE-EEe----------cCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHH
Q psy4141 78 PGHVTIE-VRV----------PYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHII 146 (353)
Q Consensus 78 ~~~~t~~-v~V----------P~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~ 146 (353)
....+. +.+ -.+..|+|||++|.|.+.|++.|||+|.+. ...|.|.|.+++|+.|++.|++++.
T Consensus 89 -d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~----g~tVaiiG~~~~v~iAr~AVemli~ 163 (194)
T COG1094 89 -DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY----GKTVAIIGGFEQVEIAREAVEMLIN 163 (194)
T ss_pred -CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe----CcEEEEecChhhhHHHHHHHHHHHc
Confidence 001111 111 135679999999999999999999999866 3479999999999999999999987
Q ss_pred h
Q psy4141 147 R 147 (353)
Q Consensus 147 ~ 147 (353)
.
T Consensus 164 G 164 (194)
T COG1094 164 G 164 (194)
T ss_pred C
Confidence 5
No 38
>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=1.5e-08 Score=69.48 Aligned_cols=40 Identities=30% Similarity=0.819 Sum_probs=35.1
Q ss_pred ccccccccc---cccEEeCCCCHhhhHHhHHHHhccCCCCCCcc
Q psy4141 302 QCYLCNDRE---VTHALIPCGHNFFCSECAERTCDFDRTCPMCR 342 (353)
Q Consensus 302 ~C~IC~~~~---~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr 342 (353)
.|.||++.+ ...+.++|+|. ||..|+..|......||+||
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 699999987 35667899999 99999999999889999997
No 39
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.56 E-value=1.2e-07 Score=84.82 Aligned_cols=64 Identities=23% Similarity=0.294 Sum_probs=57.6
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEE----cCHHHHHHHHHHHHHHHH
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT----GAPDSVEIARQEIESHII 146 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~----G~~e~V~~A~~~I~~~i~ 146 (353)
....+.||.+.+|.|||++|++||.|+++||++|.+..+ +..|.|. ++++++++|+++|.+++.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--TGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 567899999999999999999999999999999988753 3578885 789999999999999877
No 40
>KOG2279|consensus
Probab=98.56 E-value=2.6e-08 Score=99.97 Aligned_cols=124 Identities=27% Similarity=0.432 Sum_probs=105.0
Q ss_pred eeecCCCchHHHHHHHcCceEEecCC--CCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCc
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVR--GEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPG 79 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~--~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~ 79 (353)
.|+||+|.+||.|+++|+++|.+-.. +++++.++.|-+.++..|+.+++.++.+- .+
T Consensus 81 li~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~--------------------~p- 139 (608)
T KOG2279|consen 81 LIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTEN--------------------TP- 139 (608)
T ss_pred eeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhcC--------------------Cc-
Confidence 47999999999999999999998755 36788888889999999999999887643 12
Q ss_pred ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCC---CCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141 80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK---EPVFEVTGAPDSVEIARQEIESHIIR 147 (353)
Q Consensus 80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~---e~~v~I~G~~e~V~~A~~~I~~~i~~ 147 (353)
+..++.+|.+.++.|+|++|.+++.|...++++|.+....+ .+...|.|...-++.|+.++.+.+.+
T Consensus 140 -vk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 140 -VSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSE 209 (608)
T ss_pred -ccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccc
Confidence 67788899999999999999999999999999997665432 45677777788888999999888776
No 41
>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=98.55 E-value=7.3e-08 Score=85.64 Aligned_cols=60 Identities=23% Similarity=0.344 Sum_probs=53.7
Q ss_pred EEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEE---EcCHHHHHHHHHHHHHHHH
Q psy4141 85 VRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEV---TGAPDSVEIARQEIESHII 146 (353)
Q Consensus 85 v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I---~G~~e~V~~A~~~I~~~i~ 146 (353)
|.||.+.+|.|||+||++||+|+++||++|.+..+ +..|.| +++++++.+|+++|.++..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~--~g~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--TGEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--CceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 67899999999999999999999999999988753 356888 7889999999999998766
No 42
>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=98.53 E-value=2.3e-07 Score=68.06 Aligned_cols=48 Identities=40% Similarity=0.607 Sum_probs=43.7
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREI 49 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I 49 (353)
+|||++|.+|++|+++||+.|.++... .++.+.|.|+.+++..|+.+|
T Consensus 13 ~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 13 RIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred eeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 589999999999999999999999764 368899999999999999887
No 43
>KOG4275|consensus
Probab=98.51 E-value=8.4e-09 Score=96.21 Aligned_cols=51 Identities=31% Similarity=0.825 Sum_probs=48.1
Q ss_pred CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceeccC
Q psy4141 299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS 353 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~~ 353 (353)
....|.|||+...+.++|+|||.+-|..|-+++ ..||+||+.+..+.|||.
T Consensus 299 ~~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~rvvrif~ 349 (350)
T KOG4275|consen 299 TRRLCAICMDAPRDCVFLECGHMVTCTKCGKRM----NECPICRQYIVRVVRIFR 349 (350)
T ss_pred HHHHHHHHhcCCcceEEeecCcEEeehhhcccc----ccCchHHHHHHHHHhhhc
Confidence 378999999999999999999999999999997 699999999999999984
No 44
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.49 E-value=7.4e-08 Score=95.44 Aligned_cols=52 Identities=31% Similarity=0.685 Sum_probs=46.9
Q ss_pred CCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 295 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 295 ~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
..++....|.||++.+..+++++|||. ||..|+..++.....||+||..+..
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 456778999999999999999999999 9999999998887789999998753
No 45
>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=98.47 E-value=7.9e-07 Score=93.81 Aligned_cols=67 Identities=31% Similarity=0.422 Sum_probs=59.7
Q ss_pred CCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141 76 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR 147 (353)
Q Consensus 76 ~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~ 147 (353)
..| ....+.||.+.+|.|||+||++||+|+++||++|.+.. +..|.|.+. .+.+++|+++|+.++..
T Consensus 575 ~aP--~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 575 YAP--RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CCC--eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 445 77889999999999999999999999999999998763 468999985 88999999999999884
No 46
>KOG1571|consensus
Probab=98.42 E-value=6.7e-08 Score=93.02 Aligned_cols=54 Identities=24% Similarity=0.709 Sum_probs=47.9
Q ss_pred CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceeccC
Q psy4141 296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS 353 (353)
Q Consensus 296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~~ 353 (353)
.+.....|.||.+.+.+.+++||||.|.|-.|.+.+ ..||+||..|...+++|.
T Consensus 301 ~~~~p~lcVVcl~e~~~~~fvpcGh~ccct~cs~~l----~~CPvCR~rI~~~~k~y~ 354 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDEPKSAVFVPCGHVCCCTLCSKHL----PQCPVCRQRIRLVRKRYR 354 (355)
T ss_pred ccCCCCceEEecCCccceeeecCCcEEEchHHHhhC----CCCchhHHHHHHHHHHhc
Confidence 344567899999999999999999999999999886 779999999999998873
No 47
>KOG2208|consensus
Probab=98.42 E-value=6.6e-07 Score=95.83 Aligned_cols=125 Identities=21% Similarity=0.317 Sum_probs=105.6
Q ss_pred eecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcce
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHV 81 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 81 (353)
|+||+|.+|.+|++++++.|.++..+ ++..++++|...++.+|+..|..+..++.+ . ..
T Consensus 361 v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n-----------------~---~~ 420 (753)
T KOG2208|consen 361 VIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSANDEKAVEDVEKIIAEILN-----------------S---IV 420 (753)
T ss_pred hcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccccchhHHHHHHHHHHHhhhc-----------------c---cc
Confidence 79999999999999999999999865 457899999999999999999999988743 0 25
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhC-ceEEcCCCCC-CCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTN-TYIVTPSRDK-EPVFEVTGAPDSVEIARQEIESHIIR 147 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tg-a~I~ip~~~~-e~~v~I~G~~e~V~~A~~~I~~~i~~ 147 (353)
...+.||...+.+|||.+|..|..|..+++ ++|.++.... ...+++.|.-..|.+++.++..+...
T Consensus 421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~~~~ 488 (753)
T KOG2208|consen 421 KEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKALKAD 488 (753)
T ss_pred cceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcccccceEeccccccchhHHHHHhhhhh
Confidence 677999999999999999999999999999 8888887643 34688888877777776666655554
No 48
>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=98.42 E-value=1.3e-07 Score=63.60 Aligned_cols=38 Identities=34% Similarity=1.009 Sum_probs=35.2
Q ss_pred cccccccccccE-EeCCCCHhhhHHhHHHHhcc--CCCCCCc
Q psy4141 303 CYLCNDREVTHA-LIPCGHNFFCSECAERTCDF--DRTCPMC 341 (353)
Q Consensus 303 C~IC~~~~~~~~-llpCgH~~fC~~C~~~~~~~--~~~CP~C 341 (353)
|.||++....+. +++|||. ||..|+.+++.. ...||+|
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 889999999999 8999999 999999999993 7789988
No 49
>PF13014 KH_3: KH domain
Probab=98.41 E-value=4e-07 Score=62.13 Aligned_cols=36 Identities=36% Similarity=0.629 Sum_probs=31.7
Q ss_pred eeecCCCchHHHHHHHcCceEEecC---CC-CcCeEEEec
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPV---RG-EEPVFVVTG 37 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~---~~-e~~vv~I~G 37 (353)
.||||+|++|++|+++|+|+|++|. .+ .+++|+|+|
T Consensus 4 ~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 4 RIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred eEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999998 22 468899887
No 50
>KOG0287|consensus
Probab=98.41 E-value=9.4e-08 Score=90.92 Aligned_cols=51 Identities=27% Similarity=0.729 Sum_probs=46.6
Q ss_pred CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
.+..-+.|.||++.+..+++.||+|+ ||..|+..++...+.||.|+.+++.
T Consensus 19 ~lD~lLRC~IC~eyf~ip~itpCsHt-fCSlCIR~~L~~~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 19 TLDDLLRCGICFEYFNIPMITPCSHT-FCSLCIRKFLSYKPQCPTCCVTVTE 69 (442)
T ss_pred hhHHHHHHhHHHHHhcCceeccccch-HHHHHHHHHhccCCCCCceecccch
Confidence 34556899999999999999999999 9999999999999999999998864
No 51
>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=98.40 E-value=2.1e-07 Score=68.34 Aligned_cols=45 Identities=16% Similarity=0.242 Sum_probs=42.1
Q ss_pred cccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141 301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~ 346 (353)
..|+||.+...+++.++|||. ||..|+.+|+.....||+|+.+++
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v-~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQT-YERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCE-EeHHHHHHHHHHCCCCCCCcCCCC
Confidence 579999999999999999999 999999999988889999999874
No 52
>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=98.40 E-value=2.5e-07 Score=62.34 Aligned_cols=43 Identities=35% Similarity=1.015 Sum_probs=36.3
Q ss_pred ccccccccccccEEe-CCCCHhhhHHhHHHHhcc-CCCCCCccccc
Q psy4141 302 QCYLCNDREVTHALI-PCGHNFFCSECAERTCDF-DRTCPMCRVPV 345 (353)
Q Consensus 302 ~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i 345 (353)
.|.||++.....+.+ +|+|. ||..|+..|... ...||+||..+
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 489999998655555 49999 999999999887 77899998753
No 53
>PHA02926 zinc finger-like protein; Provisional
Probab=98.39 E-value=1.8e-07 Score=84.75 Aligned_cols=49 Identities=24% Similarity=0.605 Sum_probs=39.6
Q ss_pred CCccccccccccc---------ccEEeCCCCHhhhHHhHHHHhcc------CCCCCCcccccccc
Q psy4141 299 GSRQCYLCNDREV---------THALIPCGHNFFCSECAERTCDF------DRTCPMCRVPVNQA 348 (353)
Q Consensus 299 ~~~~C~IC~~~~~---------~~~llpCgH~~fC~~C~~~~~~~------~~~CP~Cr~~i~~~ 348 (353)
++.+|.||++... -.++.+|+|. ||..|+..|... ...||+||..+..+
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHs-FCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I 232 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHI-FCITCINIWHRTRRETGASDNCPICRTRFRNI 232 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCch-HHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence 4589999999742 2467799999 999999999874 24599999988754
No 54
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.35 E-value=1.9e-07 Score=87.21 Aligned_cols=48 Identities=31% Similarity=0.703 Sum_probs=44.3
Q ss_pred CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~ 346 (353)
..-..|.||.+++..+++.+|||. ||..|+.+++...+.||+||.+..
T Consensus 23 Ds~lrC~IC~~~i~ip~~TtCgHt-FCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 23 DSMLRCRICDCRISIPCETTCGHT-FCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred hhHHHhhhhhheeecceecccccc-hhHHHHHHHhcCCCCCccccccHH
Confidence 345899999999999999999999 999999999999999999999864
No 55
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.33 E-value=5e-07 Score=62.04 Aligned_cols=41 Identities=32% Similarity=0.877 Sum_probs=35.1
Q ss_pred ccccccccc---cccEEeCCCCHhhhHHhHHHHhccCCCCCCccc
Q psy4141 302 QCYLCNDRE---VTHALIPCGHNFFCSECAERTCDFDRTCPMCRV 343 (353)
Q Consensus 302 ~C~IC~~~~---~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~ 343 (353)
.|.+|++.+ ..+.+++|||. ||..|+..+......||+||+
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 488999988 45778999999 999999999744789999984
No 56
>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=98.30 E-value=7.2e-07 Score=57.94 Aligned_cols=38 Identities=34% Similarity=1.027 Sum_probs=34.5
Q ss_pred cccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCc
Q psy4141 303 CYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMC 341 (353)
Q Consensus 303 C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~C 341 (353)
|.||++....+++++|+|. ||..|+..|... ...||+|
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 7899999999999999999 999999999874 6779987
No 57
>smart00322 KH K homology RNA-binding domain.
Probab=98.28 E-value=3.1e-06 Score=61.85 Aligned_cols=52 Identities=35% Similarity=0.477 Sum_probs=46.6
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC-CcCeEEEecCHHHHHHHHHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG-EEPVFVVTGRKEDVARAKREILSAA 53 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~-e~~vv~I~G~~e~v~~Ak~~I~~i~ 53 (353)
.+||++|.+|++|++++|++|.++... ...++.|.|..+++..|+..|.+.+
T Consensus 16 ~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 16 LIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 589999999999999999999998654 3578999999999999999998875
No 58
>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=98.25 E-value=3.7e-06 Score=89.56 Aligned_cols=96 Identities=18% Similarity=0.265 Sum_probs=70.2
Q ss_pred HHHHHHHHHHHHHHhhhhh-hhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141 40 EDVARAKREILSAADHFSA-LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118 (353)
Q Consensus 40 e~v~~Ak~~I~~i~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~ 118 (353)
+.++.|+.....+++.+.. +...+.. .....| ...++.||.+.+|.|||+||++||+|+++|||+|.+..
T Consensus 518 ~al~~a~~~~~~I~~~m~~~l~~~~~~-------~~~~~p--~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d 588 (684)
T TIGR03591 518 QALEQAKEGRLHILGEMNKVISEPRAE-------LSPYAP--RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED 588 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcc-------ccccCC--eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec
Confidence 4455565555555554433 2222211 122345 77889999999999999999999999999999998763
Q ss_pred CCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141 119 RDKEPVFEVTGA-PDSVEIARQEIESHIIR 147 (353)
Q Consensus 119 ~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~ 147 (353)
+..|.|.+. .+.+++|+++|..+...
T Consensus 589 ---dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 589 ---DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred ---CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 467888874 78999999999988664
No 59
>KOG2164|consensus
Probab=98.16 E-value=8.3e-07 Score=88.98 Aligned_cols=47 Identities=28% Similarity=0.764 Sum_probs=43.1
Q ss_pred CcccccccccccccEEeCCCCHhhhHHhHHHHhcc-----CCCCCCccccccc
Q psy4141 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPVNQ 347 (353)
Q Consensus 300 ~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-----~~~CP~Cr~~i~~ 347 (353)
+..|+||++....++.+.|||. ||..|+-++|.. -..||+||..|..
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHi-FC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHI-FCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCcccccccCce-eeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 6899999999999999999999 999999999987 3589999998875
No 60
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.15 E-value=7.7e-07 Score=60.83 Aligned_cols=30 Identities=33% Similarity=0.978 Sum_probs=21.3
Q ss_pred cccccccccc----cEEeCCCCHhhhHHhHHHHhcc
Q psy4141 303 CYLCNDREVT----HALIPCGHNFFCSECAERTCDF 334 (353)
Q Consensus 303 C~IC~~~~~~----~~llpCgH~~fC~~C~~~~~~~ 334 (353)
|+||++ +.+ ++.|+|||. ||.+|++++...
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 777 899999999 999999999885
No 61
>KOG2177|consensus
Probab=98.13 E-value=8.9e-07 Score=82.71 Aligned_cols=48 Identities=33% Similarity=0.827 Sum_probs=42.7
Q ss_pred CCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccc
Q psy4141 295 GSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRV 343 (353)
Q Consensus 295 ~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~ 343 (353)
....+...|.||++.+..+.++||+|+ ||..|+..++.....||.||.
T Consensus 8 ~~~~~~~~C~iC~~~~~~p~~l~C~H~-~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 8 EVLQEELTCPICLEYFREPVLLPCGHN-FCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred hhccccccChhhHHHhhcCccccccch-HhHHHHHHhcCCCcCCcccCC
Confidence 345678999999999999999999999 999999999875678999993
No 62
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.12 E-value=6.4e-06 Score=88.81 Aligned_cols=96 Identities=20% Similarity=0.220 Sum_probs=73.0
Q ss_pred HHHHHHHHHHHHHHhhhhhh-hhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCce-EEcC
Q psy4141 40 EDVARAKREILSAADHFSAL-RASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY-IVTP 117 (353)
Q Consensus 40 e~v~~Ak~~I~~i~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~-I~ip 117 (353)
++++.|++.+..+++.+... .+.+.. .+...| ....+.||.+.+|.|||+||.+||+|+++||+. |.+.
T Consensus 652 eAL~~A~~g~~~Il~~M~~~i~~pr~~-------~s~~aP--~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~ 722 (891)
T PLN00207 652 RALLQAKDGRKHILAEMSKCSPPPSKR-------LSKYAP--LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ 722 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhh-------hcccCC--eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC
Confidence 55667777777777666552 222221 123445 778899999999999999999999999999999 7654
Q ss_pred CCCCCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141 118 SRDKEPVFEVTG-APDSVEIARQEIESHIIR 147 (353)
Q Consensus 118 ~~~~e~~v~I~G-~~e~V~~A~~~I~~~i~~ 147 (353)
. +..|.|.+ ..+.+++|+++|++++.+
T Consensus 723 d---dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 723 D---DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred C---CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 2 45788888 588999999999998764
No 63
>KOG0119|consensus
Probab=98.08 E-value=3.1e-05 Score=77.32 Aligned_cols=68 Identities=25% Similarity=0.434 Sum_probs=54.8
Q ss_pred ceEEEEEecC------CCccceeccCChHHHHHHHHhCceEEcCCC-------------------CCCCeEEEEcC-HHH
Q psy4141 80 HVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSR-------------------DKEPVFEVTGA-PDS 133 (353)
Q Consensus 80 ~~t~~v~VP~------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-------------------~~e~~v~I~G~-~e~ 133 (353)
..+.+|.||. ++||+|||..|.|.|+|+++|||+|.|-.. +++--+.|++. .|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 4566677654 789999999999999999999999987541 01125778884 789
Q ss_pred HHHHHHHHHHHHHh
Q psy4141 134 VEIARQEIESHIIR 147 (353)
Q Consensus 134 V~~A~~~I~~~i~~ 147 (353)
|++|.++|+.+|..
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999986
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=98.03 E-value=3.6e-06 Score=64.25 Aligned_cols=41 Identities=32% Similarity=0.786 Sum_probs=33.3
Q ss_pred cccccccccc-------------cccEEeCCCCHhhhHHhHHHHhccCCCCCCcc
Q psy4141 301 RQCYLCNDRE-------------VTHALIPCGHNFFCSECAERTCDFDRTCPMCR 342 (353)
Q Consensus 301 ~~C~IC~~~~-------------~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr 342 (353)
..|.||++.+ ...++.+|||. |...|+.+|......||+||
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 3499999877 23355799999 99999999999888999997
No 65
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.02 E-value=2.6e-06 Score=78.98 Aligned_cols=47 Identities=32% Similarity=0.766 Sum_probs=40.7
Q ss_pred CCcccccccccccccEEeCCCCHhhhHHhHHH-HhccCC-CCCCcccccc
Q psy4141 299 GSRQCYLCNDREVTHALIPCGHNFFCSECAER-TCDFDR-TCPMCRVPVN 346 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~-~~~~~~-~CP~Cr~~i~ 346 (353)
.+..|.||++....++..+|||. ||..|+-. |..+.. .||+||+.+.
T Consensus 214 ~d~kC~lC~e~~~~ps~t~CgHl-FC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTPCGHL-FCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred cccceeeeecccCCcccccccch-hhHHHHHHHHHhhccccCchhhhhcc
Confidence 46899999999999999999999 99999999 555544 4999999763
No 66
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.01 E-value=2.6e-06 Score=82.13 Aligned_cols=47 Identities=36% Similarity=0.854 Sum_probs=40.8
Q ss_pred CCCcccccccccc-------------cccEEeCCCCHhhhHHhHHHHhccCCCCCCccccc
Q psy4141 298 SGSRQCYLCNDRE-------------VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345 (353)
Q Consensus 298 ~~~~~C~IC~~~~-------------~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i 345 (353)
.+++.|.||+|.. ..+-.+||||- +...|++.|++....||+||.++
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 4679999999972 23456899998 99999999999999999999984
No 67
>KOG0978|consensus
Probab=97.98 E-value=1.9e-06 Score=90.18 Aligned_cols=54 Identities=31% Similarity=0.748 Sum_probs=48.2
Q ss_pred CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc--ceecc
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ--AMRII 352 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~--~~ri~ 352 (353)
..-..|++|.++..++++..|+|. ||..|++..+.. .+.||.|.+.|.. +.+||
T Consensus 641 K~~LkCs~Cn~R~Kd~vI~kC~H~-FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 641 KELLKCSVCNTRWKDAVITKCGHV-FCEECVQTRYETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred HhceeCCCccCchhhHHHHhcchH-HHHHHHHHHHHHhcCCCCCCCCCCCcccccccC
Confidence 455899999999999999999998 999999999888 8999999999854 66665
No 68
>KOG2208|consensus
Probab=97.97 E-value=1.6e-05 Score=85.35 Aligned_cols=72 Identities=22% Similarity=0.332 Sum_probs=64.3
Q ss_pred cceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC-CCCCeEEEEcCHHHHHHHHHHHHHHHHhhhC
Q psy4141 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQEIESHIIRRTG 150 (353)
Q Consensus 79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~-~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g 150 (353)
....+.+.|-...+..|+||+|.+|.+|++++.+.|.++.. +....+.++|...++++|.+.++..+.+-..
T Consensus 345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n 417 (753)
T KOG2208|consen 345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSANDEKAVEDVEKIIAEILN 417 (753)
T ss_pred cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence 34778899999999999999999999999999999999984 4567899999999999999999988887555
No 69
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.94 E-value=3.2e-05 Score=80.42 Aligned_cols=96 Identities=21% Similarity=0.266 Sum_probs=72.6
Q ss_pred HHHHHHHHHHHHHHhhhhh-hhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141 40 EDVARAKREILSAADHFSA-LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118 (353)
Q Consensus 40 e~v~~Ak~~I~~i~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~ 118 (353)
+++.+|+..-+.++..+.+ +...+..- ....| ...++.|+.+.++-|||+||++|++|.++||++|.+.
T Consensus 519 ~AL~QAk~aRlhIL~~M~~ai~~pr~el-------s~~aP--ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie- 588 (692)
T COG1185 519 KALEQAKGARLHILIVMNEAISEPRKEL-------SPYAP--RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE- 588 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhh-------hccCC--ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-
Confidence 4556677666666666554 33332111 11223 6678999999999999999999999999999999887
Q ss_pred CCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141 119 RDKEPVFEVTGA-PDSVEIARQEIESHIIR 147 (353)
Q Consensus 119 ~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~ 147 (353)
++..|.|.+. .+.+++|++.|.+++++
T Consensus 589 --ddGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 589 --DDGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred --CCCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 3457999997 48999999999999876
No 70
>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=97.87 E-value=1.1e-05 Score=61.55 Aligned_cols=48 Identities=21% Similarity=0.390 Sum_probs=40.2
Q ss_pred CCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141 299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 347 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~ 347 (353)
+...|+||.+...+++++||||. |++.|+.+|... ...||+|+.++..
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 46899999999999999999999 999999999999 8999999998865
No 71
>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=97.85 E-value=3.9e-05 Score=64.21 Aligned_cols=55 Identities=22% Similarity=0.238 Sum_probs=45.3
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC--------------------CcCeEEEec-C--HHHHHHHHHHHHHHHhhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG--------------------EEPVFVVTG-R--KEDVARAKREILSAADHF 56 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~--------------------e~~vv~I~G-~--~e~v~~Ak~~I~~i~~~~ 56 (353)
+|||.+|.+||+|+++|||+|.|..++ +.-.|.|++ + .+.+++|+.+|..++...
T Consensus 19 ~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~~~ 96 (120)
T cd02395 19 LILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLKPA 96 (120)
T ss_pred EEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhccC
Confidence 589999999999999999999998663 113466666 4 699999999999998743
No 72
>KOG1100|consensus
Probab=97.85 E-value=3.9e-06 Score=76.61 Aligned_cols=47 Identities=38% Similarity=0.940 Sum_probs=42.2
Q ss_pred ccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccceecc
Q psy4141 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRII 352 (353)
Q Consensus 302 ~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ri~ 352 (353)
.|..|.+....++++||.|.++|..|.... ..||+|+.+....+.+|
T Consensus 160 ~Cr~C~~~~~~VlllPCrHl~lC~~C~~~~----~~CPiC~~~~~s~~~v~ 206 (207)
T KOG1100|consen 160 SCRKCGEREATVLLLPCRHLCLCGICDESL----RICPICRSPKTSSVEVN 206 (207)
T ss_pred cceecCcCCceEEeecccceEecccccccC----ccCCCCcChhhceeecc
Confidence 399999999999999999999999998752 67999999998887775
No 73
>KOG0336|consensus
Probab=97.76 E-value=3e-05 Score=76.40 Aligned_cols=69 Identities=29% Similarity=0.358 Sum_probs=61.7
Q ss_pred cceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR 147 (353)
Q Consensus 79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~ 147 (353)
+....-+.|-.++||.|||++|.+||+||..|+++|++.+.+.+-.|+|.|..+.-.+|+..|...+..
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 456778889999999999999999999999999999999888888999999999888888888776655
No 74
>KOG1588|consensus
Probab=97.74 E-value=0.00038 Score=64.94 Aligned_cols=42 Identities=36% Similarity=0.666 Sum_probs=35.7
Q ss_pred CcceEEEEEecC------CCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141 78 PGHVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119 (353)
Q Consensus 78 ~~~~t~~v~VP~------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~ 119 (353)
+-+.+.+|.||- ++||+|+|++|.++|+|+++|||+|.|-.+
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 445777788875 689999999999999999999999988543
No 75
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.72 E-value=6.1e-05 Score=80.48 Aligned_cols=96 Identities=21% Similarity=0.329 Sum_probs=68.6
Q ss_pred HHHHHHHHHHHHHHhhhhh-hhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141 40 EDVARAKREILSAADHFSA-LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118 (353)
Q Consensus 40 e~v~~Ak~~I~~i~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~ 118 (353)
+.++.|+.....+++.+.. +...+..- ....| ....+.||.+.++.+||+||.+||+|+++||+.|.+.
T Consensus 521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~-------~~~ap--~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~- 590 (693)
T PRK11824 521 EALEQAKEGRLHILGKMNEAISEPRAEL-------SPYAP--RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE- 590 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhhh-------cccCc--hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-
Confidence 4455566665555555433 22222211 12234 5567778999999999999999999999999988753
Q ss_pred CCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141 119 RDKEPVFEVTGA-PDSVEIARQEIESHIIR 147 (353)
Q Consensus 119 ~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~ 147 (353)
++..|.|.+. .+.+++|+++|+.++.+
T Consensus 591 --d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 --DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred --CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 3467888884 88999999999988864
No 76
>KOG1785|consensus
Probab=97.70 E-value=1.6e-05 Score=77.36 Aligned_cols=47 Identities=30% Similarity=0.833 Sum_probs=43.1
Q ss_pred cccccccccccccEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccccc
Q psy4141 301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQA 348 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~~~ 348 (353)
..|.||-++.++.-.-||||. +|..|+..|... ...||+||..|...
T Consensus 370 eLCKICaendKdvkIEPCGHL-lCt~CLa~WQ~sd~gq~CPFCRcEIKGt 418 (563)
T KOG1785|consen 370 ELCKICAENDKDVKIEPCGHL-LCTSCLAAWQDSDEGQTCPFCRCEIKGT 418 (563)
T ss_pred HHHHHhhccCCCcccccccch-HHHHHHHhhcccCCCCCCCceeeEeccc
Confidence 689999999999999999999 999999999865 67999999999765
No 77
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=2.2e-05 Score=74.09 Aligned_cols=47 Identities=23% Similarity=0.673 Sum_probs=40.0
Q ss_pred CCccccccccccc---ccEEeCCCCHhhhHHhHHHHhcc-CCCCCCcccccc
Q psy4141 299 GSRQCYLCNDREV---THALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVN 346 (353)
Q Consensus 299 ~~~~C~IC~~~~~---~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~ 346 (353)
...+|.||++.+. ..+.+||.|. |...|+.+|... ...||+||.++.
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 3489999999874 2456899999 999999999986 889999999874
No 78
>KOG4628|consensus
Probab=97.65 E-value=2.1e-05 Score=76.55 Aligned_cols=46 Identities=22% Similarity=0.665 Sum_probs=38.8
Q ss_pred ccccccccccccc---EEeCCCCHhhhHHhHHHHhccC-CCCCCccccccc
Q psy4141 301 RQCYLCNDREVTH---ALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQ 347 (353)
Q Consensus 301 ~~C~IC~~~~~~~---~llpCgH~~fC~~C~~~~~~~~-~~CP~Cr~~i~~ 347 (353)
..|.||+|.+... ..|||.|. |...|+..|..+. ..||+|+..+..
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~-FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHK-FHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCc-hhhccchhhHhhcCccCCCCCCcCCC
Confidence 5999999998643 34899999 9999999999995 569999987654
No 79
>KOG0802|consensus
Probab=97.61 E-value=2.2e-05 Score=81.76 Aligned_cols=47 Identities=28% Similarity=0.704 Sum_probs=42.7
Q ss_pred CCCcccccccccccc-----cEEeCCCCHhhhHHhHHHHhccCCCCCCccccc
Q psy4141 298 SGSRQCYLCNDREVT-----HALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~-----~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i 345 (353)
.....|.||.|.... +..+||+|. ||..|++.|.++...||+||..+
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 446899999999888 788999999 99999999999999999999944
No 80
>KOG4159|consensus
Probab=97.50 E-value=4.7e-05 Score=75.76 Aligned_cols=51 Identities=33% Similarity=0.879 Sum_probs=45.9
Q ss_pred CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
....+..|.||+..+..++.+||||. ||..|+.+...+...||.||.++..
T Consensus 80 ~~~sef~c~vc~~~l~~pv~tpcghs-~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 80 EIRSEFECCVCSRALYPPVVTPCGHS-FCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cccchhhhhhhHhhcCCCcccccccc-ccHHHHHHHhccCCCCccccccccc
Confidence 34667999999999999999999999 9999999987778999999998764
No 81
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.48 E-value=0.00027 Score=60.74 Aligned_cols=89 Identities=17% Similarity=0.169 Sum_probs=57.7
Q ss_pred eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT 82 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t 82 (353)
.||++|++|+.|++..|-+|++-.. +.. ++..|..++....- ..... ....+...
T Consensus 46 ~IG~~G~rI~~i~e~lgekIdVve~--------s~d------~~~fI~n~l~Pa~V------~~v~I-----~~~~~~~~ 100 (140)
T PRK08406 46 AIGKGGENVKRLEEKLGKDIELVEY--------SDD------PEEFIKNIFAPAAV------RSVTI-----KKKNGDKV 100 (140)
T ss_pred cCCcCchHHHHHHHHhCCceEEEEc--------CCC------HHHHHHHHcCCCEE------EEEEE-----EecCCcEE
Confidence 5899999999999998877764322 122 22333333221100 00000 00011356
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
..+.|+.+..|..|||+|++|+.+++.++-++.+
T Consensus 101 ~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 101 AYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 7788999999999999999999999999988854
No 82
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.40 E-value=0.00015 Score=69.56 Aligned_cols=57 Identities=28% Similarity=0.720 Sum_probs=47.9
Q ss_pred CCCCCCCCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccccc
Q psy4141 291 TSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVNQA 348 (353)
Q Consensus 291 ~~~~~~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~~~ 348 (353)
++..+..++...|.||-+...-..++||+|. .|--|+-++... .+.|++||.....+
T Consensus 52 sSaddtDEen~~C~ICA~~~TYs~~~PC~H~-~CH~Ca~RlRALY~~K~C~~CrTE~e~V 110 (493)
T COG5236 52 SSADDTDEENMNCQICAGSTTYSARYPCGHQ-ICHACAVRLRALYMQKGCPLCRTETEAV 110 (493)
T ss_pred ccccccccccceeEEecCCceEEEeccCCch-HHHHHHHHHHHHHhccCCCccccccceE
Confidence 3445566788999999999988899999999 999999998666 78999999876544
No 83
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.39 E-value=0.00017 Score=56.29 Aligned_cols=31 Identities=35% Similarity=0.730 Sum_probs=26.8
Q ss_pred EeCCCCHhhhHHhHHHHhcc---CCCCCCcccccc
Q psy4141 315 LIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN 346 (353)
Q Consensus 315 llpCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~ 346 (353)
+-.|+|. |.+.|+.+|.+. ...||+||++..
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 999999999997 578999999763
No 84
>KOG4692|consensus
Probab=97.38 E-value=7.6e-05 Score=71.81 Aligned_cols=49 Identities=22% Similarity=0.576 Sum_probs=44.8
Q ss_pred CCCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
.++..|+||+-.+.++++.||+|. -|..|+.++....+.|-.|+..+..
T Consensus 420 sEd~lCpICyA~pi~Avf~PC~H~-SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 420 SEDNLCPICYAGPINAVFAPCSHR-SCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred cccccCcceecccchhhccCCCCc-hHHHHHHHHHhcCCeeeEecceeee
Confidence 356899999999999999999999 9999999998889999999987764
No 85
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.36 E-value=4.5e-05 Score=56.15 Aligned_cols=46 Identities=30% Similarity=0.672 Sum_probs=25.7
Q ss_pred CCCcccccccccccccE-EeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141 298 SGSRQCYLCNDREVTHA-LIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~-llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~ 346 (353)
++-+.|.+|.+....++ +-.|.|+ ||..|+.... ...||+|+.+..
T Consensus 5 e~lLrCs~C~~~l~~pv~l~~CeH~-fCs~Ci~~~~--~~~CPvC~~Paw 51 (65)
T PF14835_consen 5 EELLRCSICFDILKEPVCLGGCEHI-FCSSCIRDCI--GSECPVCHTPAW 51 (65)
T ss_dssp HHTTS-SSS-S--SS-B---SSS---B-TTTGGGGT--TTB-SSS--B-S
T ss_pred HHhcCCcHHHHHhcCCceeccCccH-HHHHHhHHhc--CCCCCCcCChHH
Confidence 34578999999999996 5799999 9999997743 456999999874
No 86
>KOG2814|consensus
Probab=97.36 E-value=0.00027 Score=67.77 Aligned_cols=67 Identities=22% Similarity=0.371 Sum_probs=59.2
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCC-CCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-KEPVFEVTG-APDSVEIARQEIESHIIR 147 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~-~e~~v~I~G-~~e~V~~A~~~I~~~i~~ 147 (353)
....+.|+..++|.|||++|.|.++|+++|+++|.+|... +...|+|+| ..+.|.+|.+.|.-+|..
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence 5567889999999999999999999999999999999875 455677777 588999999999988887
No 87
>KOG2279|consensus
Probab=97.33 E-value=0.00036 Score=70.71 Aligned_cols=142 Identities=18% Similarity=0.241 Sum_probs=102.5
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhhhhh----------hhccCC---
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHFSAL----------RASRKS--- 65 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~----------~~~~~~--- 65 (353)
+|+||+|+++..|+.-++++|.+.+.+ ..+...|.+...-++.|+.++.+.+++.... +..+..
T Consensus 153 ~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n 232 (608)
T KOG2279|consen 153 RIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPIN 232 (608)
T ss_pred cccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCcc
Confidence 689999999999999999999988776 3477888888888889999998887765432 111110
Q ss_pred ----C-----CCCC------------CC-C---CCCC-----------------------CcceEEEEEecCCCccceec
Q psy4141 66 ----G-----ALSP------------LS-P---PTGV-----------------------PGHVTIEVRVPYKVVGLVVG 97 (353)
Q Consensus 66 ----g-----~~~~------------~~-~---~~~~-----------------------~~~~t~~v~VP~~~vG~IIG 97 (353)
+ .... ++ + .+.. ......+|.||..++|.|||
T Consensus 233 ~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig 312 (608)
T KOG2279|consen 233 VRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIG 312 (608)
T ss_pred ccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhh
Confidence 0 0000 00 0 0000 11234579999999999999
Q ss_pred cCChHHHHHHHHhCceEEcCCC---CCC---CeEEEEcCHHHHHHHHHHHHH
Q psy4141 98 PKGATIKRIQHQTNTYIVTPSR---DKE---PVFEVTGAPDSVEIARQEIES 143 (353)
Q Consensus 98 kgG~tIk~Iq~~Tga~I~ip~~---~~e---~~v~I~G~~e~V~~A~~~I~~ 143 (353)
+.|++|+.+...+++.+.|-.. ++- .++.+.|+..-+..+..||..
T Consensus 313 ~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n~vl~ml~~ 364 (608)
T KOG2279|consen 313 HAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHYENSVLEMLTV 364 (608)
T ss_pred hhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhHHHHHHHhhhhc
Confidence 9999999999999999865432 111 468899999999999888864
No 88
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.17 E-value=0.002 Score=66.73 Aligned_cols=66 Identities=24% Similarity=0.404 Sum_probs=53.1
Q ss_pred ceEEEEEecC-CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141 80 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-APDSVEIARQEIESHIIR 147 (353)
Q Consensus 80 ~~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-~~e~V~~A~~~I~~~i~~ 147 (353)
.....|.+|+ ++-|+|||+.|.|||-++..|||.|+|. |+...|+|+| .|---+.|+.-++.+|.+
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc--CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 3556688999 7789999999999999999999999887 4444788888 476667777777776664
No 89
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=97.17 E-value=0.0081 Score=54.75 Aligned_cols=116 Identities=16% Similarity=0.149 Sum_probs=87.6
Q ss_pred eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT 82 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t 82 (353)
|...+|..++.|....|++|.+... +..+.|+|++..++.+...|.+++... .+
T Consensus 40 Ll~~~~~~L~~l~~~~~~~I~~~~~--~~~i~I~g~k~~~~~i~~~i~~~l~~i------------------------~~ 93 (210)
T PF14611_consen 40 LLTGNGRILENLAARNGAKIEVSRS--ENRIRITGTKSTAEYIEASINEILSNI------------------------RT 93 (210)
T ss_pred eecCCchHHHHHHHhcCceEEEecC--CcEEEEEccHHHHHHHHHHHHHHHhhc------------------------EE
Confidence 5577888899998889999998643 567999999999999999999998865 56
Q ss_pred EEEEecCCCccceec----cCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-----CHHHHHHHHHHHHHHHH
Q psy4141 83 IEVRVPYKVVGLVVG----PKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-----APDSVEIARQEIESHII 146 (353)
Q Consensus 83 ~~v~VP~~~vG~IIG----kgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-----~~e~V~~A~~~I~~~i~ 146 (353)
.+|.++.-.--+..+ .....++.|++.|+++|....++. .+.|.. ....++.|++++...+.
T Consensus 94 ~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~~--~~~i~~~~~~~~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 94 EEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDGN--KLKISWLASPENEKRADRAKRLLLWALD 164 (210)
T ss_pred EEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCCC--eEEEEEEeeccccchHHHHHHHHHHhcc
Confidence 666666432222221 246789999999999997665433 355554 57899999999987775
No 90
>PRK12704 phosphodiesterase; Provisional
Probab=97.12 E-value=0.0023 Score=66.30 Aligned_cols=65 Identities=23% Similarity=0.399 Sum_probs=52.2
Q ss_pred eEEEEEecC-CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141 81 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-APDSVEIARQEIESHIIR 147 (353)
Q Consensus 81 ~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-~~e~V~~A~~~I~~~i~~ 147 (353)
.+..|.+|+ ++-|+|||+-|.|||.++..||+.|+|. |+..+|.|+| .|---+.|+.-++.++..
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid--dtp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID--DTPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc--CCCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 556688898 7889999999999999999999999887 4445788999 466656677777666553
No 91
>PRK00106 hypothetical protein; Provisional
Probab=97.12 E-value=0.0027 Score=65.76 Aligned_cols=66 Identities=27% Similarity=0.442 Sum_probs=53.7
Q ss_pred ceEEEEEecC-CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEc-CHHHHHHHHHHHHHHHHh
Q psy4141 80 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG-APDSVEIARQEIESHIIR 147 (353)
Q Consensus 80 ~~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G-~~e~V~~A~~~I~~~i~~ 147 (353)
.....|.+|+ ++-|+|||+-|.||+-++..||+.|+|. |+...|+|+| .|---+.|+.-++.+|.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid--dtp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID--DTPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc--CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 3556688999 7889999999999999999999999887 4445788998 577777777777776664
No 92
>KOG0311|consensus
Probab=97.09 E-value=8.2e-05 Score=71.71 Aligned_cols=51 Identities=22% Similarity=0.472 Sum_probs=42.6
Q ss_pred CCCCCcccccccccccccEE-eCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141 296 SISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 347 (353)
Q Consensus 296 ~~~~~~~C~IC~~~~~~~~l-lpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~ 347 (353)
.+..+..|.||++....... .-|.|. ||..|+..-... ...||-||+.+..
T Consensus 39 ~~~~~v~c~icl~llk~tmttkeClhr-fc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 39 MFDIQVICPICLSLLKKTMTTKECLHR-FCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred HhhhhhccHHHHHHHHhhcccHHHHHH-HHHHHHHHHHHhcCCCCchHHhhccc
Confidence 34567899999999876665 469999 999999998777 7899999998754
No 93
>KOG2879|consensus
Probab=97.05 E-value=0.00059 Score=63.83 Aligned_cols=49 Identities=27% Similarity=0.722 Sum_probs=41.1
Q ss_pred CCCcccccccccccccEEe-CCCCHhhhHHhHHHHhcc--CCCCCCccccccc
Q psy4141 298 SGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDF--DRTCPMCRVPVNQ 347 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~~ 347 (353)
..+.+|++|-+.+..+... +|+|. +|..|+..-... .-.||.|-.++..
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~Hi-yCY~Ci~ts~~~~asf~Cp~Cg~~~~~ 288 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCGHI-YCYYCIATSRLWDASFTCPLCGENVEP 288 (298)
T ss_pred cCCceeeccCCCCCCCeeeccccce-eehhhhhhhhcchhhcccCccCCCCcc
Confidence 3457999999999998876 59999 999999987665 4689999887753
No 94
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=97.04 E-value=0.00026 Score=63.14 Aligned_cols=49 Identities=27% Similarity=0.612 Sum_probs=43.7
Q ss_pred CcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccce
Q psy4141 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM 349 (353)
Q Consensus 300 ~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ 349 (353)
...|.||...+..++...|||. ||..|+.+-+.....|-+|.+......
T Consensus 196 PF~C~iCKkdy~spvvt~CGH~-FC~~Cai~~y~kg~~C~~Cgk~t~G~f 244 (259)
T COG5152 196 PFLCGICKKDYESPVVTECGHS-FCSLCAIRKYQKGDECGVCGKATYGRF 244 (259)
T ss_pred ceeehhchhhccchhhhhcchh-HHHHHHHHHhccCCcceecchhhccce
Confidence 3789999999999999999999 999999998888999999988765443
No 95
>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=96.86 E-value=0.00065 Score=65.26 Aligned_cols=30 Identities=30% Similarity=0.901 Sum_probs=26.6
Q ss_pred CCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141 317 PCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 347 (353)
Q Consensus 317 pCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~ 347 (353)
+|||. ||..|+.+++.. ...||.|+.++..
T Consensus 25 ~CGH~-~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 25 VCGHT-LCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCc-ccHHHHHHHhcCCCCCCCCCCCccch
Confidence 79999 999999999877 6789999998764
No 96
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.84 E-value=0.0027 Score=56.98 Aligned_cols=49 Identities=22% Similarity=0.294 Sum_probs=45.8
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD 54 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~ 54 (353)
+|||++|.+-+.|++-|+++|.+- +..|.|-|..++|+.|+++|..+++
T Consensus 115 RIIG~~GkTr~~IE~lt~~~I~V~----g~tVaiiG~~~~v~iAr~AVemli~ 163 (194)
T COG1094 115 RIIGREGKTRRAIEELTGVYISVY----GKTVAIIGGFEQVEIAREAVEMLIN 163 (194)
T ss_pred eeeCCCchHHHHHHHHhCCeEEEe----CcEEEEecChhhhHHHHHHHHHHHc
Confidence 699999999999999999999988 5678888999999999999999987
No 97
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.83 E-value=0.0017 Score=58.55 Aligned_cols=42 Identities=26% Similarity=0.616 Sum_probs=34.3
Q ss_pred CcceEEEEEecC------CCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141 78 PGHVTIEVRVPY------KVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119 (353)
Q Consensus 78 ~~~~t~~v~VP~------~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~ 119 (353)
|...+-++.||- ++||+|||+.|.|+|++++.|+|+|.|-..
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 334556666653 789999999999999999999999988654
No 98
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.80 E-value=0.0026 Score=59.36 Aligned_cols=63 Identities=22% Similarity=0.248 Sum_probs=54.2
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR 147 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~ 147 (353)
-..+.||..+++.+||++|.+|+.|.+.+++.|.+- .+..|-|.+. .+++++|+++|+++-++
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig---~NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG---QNGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc---CCcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 366899999999999999999999999999999764 3467999996 66999999999876554
No 99
>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=96.77 E-value=0.0039 Score=53.62 Aligned_cols=89 Identities=16% Similarity=0.179 Sum_probs=57.2
Q ss_pred eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT 82 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t 82 (353)
.||++|.+|+.|++..|-+|++= .-+.+++..- ..++. +.+-..... ...++...
T Consensus 47 ~IG~~G~rIk~i~el~gekIdVV--------eys~D~~~fI------~N~l~------PA~V~~V~i-----~~~~~~~~ 101 (141)
T TIGR01952 47 AIGKGGENVKRLEELIGKSIELI--------EYSENLEEFV------ANKLA------PAEVKNVTV-----SEFNGKKV 101 (141)
T ss_pred cCCCCchHHHHHHHhcCCeeEEE--------EcCCCHHHHH------HHcCC------CceEEEEEE-----EcCCCCEE
Confidence 58999999999998888777643 2333333321 11111 000000000 00122366
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
..+.||.+..++.|||+|.+|+...+.++-++.+
T Consensus 102 a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 102 AYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred EEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 7899999999999999999999999999888754
No 100
>KOG1039|consensus
Probab=96.72 E-value=0.00082 Score=65.75 Aligned_cols=50 Identities=30% Similarity=0.791 Sum_probs=41.1
Q ss_pred CCCcccccccccccccE-----E---eCCCCHhhhHHhHHHHhcc-------CCCCCCcccccccc
Q psy4141 298 SGSRQCYLCNDREVTHA-----L---IPCGHNFFCSECAERTCDF-------DRTCPMCRVPVNQA 348 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~-----l---lpCgH~~fC~~C~~~~~~~-------~~~CP~Cr~~i~~~ 348 (353)
..+..|-||++.....+ + .+|.|. ||..|+..|... .+.||.||.....+
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~-~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v 223 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHS-FCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV 223 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchh-hhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence 34689999999977766 4 679999 999999999843 47899999876654
No 101
>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=96.72 E-value=0.0026 Score=46.72 Aligned_cols=36 Identities=22% Similarity=0.308 Sum_probs=33.4
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
....+.|+.+.+|..|||+|.+|+.+++.+|-+|.+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 678899999999999999999999999999988854
No 102
>KOG1067|consensus
Probab=96.62 E-value=0.0041 Score=63.59 Aligned_cols=63 Identities=22% Similarity=0.298 Sum_probs=53.6
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHHh
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHIIR 147 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~~ 147 (353)
+...+.|+.+.+..+||++|...|+|+.+||+.-.+ ++..+.|... +...++|++.|..++..
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----De~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----DEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeee----cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 788999999999999999999999999999944442 3457888885 78889999999988765
No 103
>KOG0828|consensus
Probab=96.59 E-value=0.0011 Score=66.60 Aligned_cols=50 Identities=28% Similarity=0.671 Sum_probs=40.3
Q ss_pred CCCCcccccccccc-----------------cccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141 297 ISGSRQCYLCNDRE-----------------VTHALIPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 347 (353)
Q Consensus 297 ~~~~~~C~IC~~~~-----------------~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~ 347 (353)
.+....|.||+... .+..+.||.|. |...|+.+|... .-.||+||.++..
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~Hi-fH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHI-FHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHH-HHHHHHHHHHhhhcccCCccCCCCCC
Confidence 34568899999852 24556799999 999999999986 6699999998753
No 104
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.42 E-value=0.004 Score=56.18 Aligned_cols=90 Identities=17% Similarity=0.163 Sum_probs=57.2
Q ss_pred eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceE
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVT 82 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t 82 (353)
.||++|.+|+.|.++.|-+|++- .-+.+-..-++..+. -.+ ..+... . . .+...
T Consensus 90 ~iG~~G~rvk~i~~eLgekIdVV----------e~s~d~~~fI~nal~-Pa~---------v~~V~~----~-~-~d~~~ 143 (190)
T COG0195 90 CIGKRGSRVKAVSEELGEKIDVV----------EWSEDPAEFIKNALA-PAE---------VLSVNI----K-E-DDGHV 143 (190)
T ss_pred hccCCChHHHHHHHHhCCceEEE----------EeCCCHHHHHHHhcC-cce---------EeEEEE----E-e-CCCcE
Confidence 58999999999999998555532 222111111111111 000 000000 0 0 01136
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~ 118 (353)
..+.||.+..+.+|||+|.+++.+.+.||-+|.+-.
T Consensus 144 ~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 144 AIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 788899999999999999999999999999997653
No 105
>KOG2660|consensus
Probab=96.36 E-value=0.0012 Score=63.46 Aligned_cols=51 Identities=24% Similarity=0.678 Sum_probs=44.8
Q ss_pred CCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141 297 ISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 348 (353)
Q Consensus 297 ~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~ 348 (353)
.....+|.+|...+.++..+ -|-|. ||..|+.+++.....||.|...+.+.
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 44568999999999998875 69999 99999999999999999999887654
No 106
>KOG1813|consensus
Probab=96.27 E-value=0.0013 Score=62.22 Aligned_cols=47 Identities=23% Similarity=0.671 Sum_probs=42.4
Q ss_pred cccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141 301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 348 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~ 348 (353)
..|.||...+.++|...|+|. ||..|+..-+.....|++|.+.+...
T Consensus 242 f~c~icr~~f~~pVvt~c~h~-fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVVTKCGHY-FCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred ccccccccccccchhhcCCce-eehhhhccccccCCcceecccccccc
Confidence 579999999999999999999 99999999888789999998876554
No 107
>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=96.23 E-value=0.0084 Score=63.91 Aligned_cols=52 Identities=17% Similarity=0.194 Sum_probs=43.8
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH 55 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~ 55 (353)
.|||.+|.+||.|.++||++|++.+. ..|.+..-+.+.+++|+..|..+...
T Consensus 591 ~vIG~gGk~I~~i~~~tg~~Idi~d~--G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 591 EVIGPKGKMINQIQDETGAEISIEDD--GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred heeCCCcHhHHHHHHHHCCEEEEecC--cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 48999999999999999999999853 34444445889999999999999773
No 108
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.22 E-value=0.0016 Score=46.46 Aligned_cols=45 Identities=27% Similarity=0.770 Sum_probs=37.2
Q ss_pred CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141 299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~ 346 (353)
....|..|.......+++||||. .|..|..-. .-..||+|..++.
T Consensus 6 ~~~~~~~~~~~~~~~~~~pCgH~-I~~~~f~~~--rYngCPfC~~~~~ 50 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTVLPCGHL-ICDNCFPGE--RYNGCPFCGTPFE 50 (55)
T ss_pred cceeEEEccccccccccccccce-eeccccChh--hccCCCCCCCccc
Confidence 34679999999888999999999 999997653 2468999999875
No 109
>KOG0297|consensus
Probab=96.19 E-value=0.0021 Score=64.38 Aligned_cols=52 Identities=27% Similarity=0.651 Sum_probs=46.4
Q ss_pred CCCCcccccccccccccEE-eCCCCHhhhHHhHHHHhccCCCCCCcccccccce
Q psy4141 297 ISGSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM 349 (353)
Q Consensus 297 ~~~~~~C~IC~~~~~~~~l-lpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ 349 (353)
+.++..|.+|.....+++. ..|||. ||..|+..+......||.|+..+.+..
T Consensus 18 ~~~~l~C~~C~~vl~~p~~~~~cgh~-fC~~C~~~~~~~~~~cp~~~~~~~~~~ 70 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQTTTCGHR-FCAGCLLESLSNHQKCPVCRQELTQAE 70 (391)
T ss_pred CcccccCccccccccCCCCCCCCCCc-ccccccchhhccCcCCcccccccchhh
Confidence 5677999999999999999 599999 999999999888899999998877653
No 110
>PRK12705 hypothetical protein; Provisional
Probab=96.18 E-value=0.013 Score=60.37 Aligned_cols=64 Identities=20% Similarity=0.326 Sum_probs=46.5
Q ss_pred eEEEEEecC-CCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcC-HHHHHHHHHHHHHHHH
Q psy4141 81 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGA-PDSVEIARQEIESHII 146 (353)
Q Consensus 81 ~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~-~e~V~~A~~~I~~~i~ 146 (353)
....|.+|+ ++-|+|||+-|.+||.++..||+.|+|.. ....|+|.+. |.--+.|+..+..+|.
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--TPEAVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--CccchhhcccCccchHHHHHHHHHHHh
Confidence 455678888 77899999999999999999999998873 3334666663 4444555555555444
No 111
>KOG2814|consensus
Probab=96.08 E-value=0.011 Score=56.92 Aligned_cols=56 Identities=23% Similarity=0.180 Sum_probs=48.6
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCC--cCeEEEecCHHHHHHHHHHHHHHHhhhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGE--EPVFVVTGRKEDVARAKREILSAADHFS 57 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e--~~vv~I~G~~e~v~~Ak~~I~~i~~~~~ 57 (353)
.|||++|.+-|+|+++|+++|.+|.+++ +.+.++.+..+.|-+|.+.|..+++.+.
T Consensus 70 ~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 70 WLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred hhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 4899999999999999999999998873 3555566789999999999999998763
No 112
>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=96.00 E-value=0.0091 Score=63.94 Aligned_cols=52 Identities=17% Similarity=0.159 Sum_probs=44.2
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH 55 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~ 55 (353)
.|||++|.+||.|+++||++|++.+. ..+.+.....+.+.+|++.|..+...
T Consensus 564 ~vIG~gGk~Ik~I~~~tg~~I~i~dd--G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 564 DVIGPGGKVIREITEETGAKIDIEDD--GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred hhcCCCcHHHHHHHHHHCCEEEEecC--eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 48999999999999999999999864 45556667889999999999888653
No 113
>KOG1002|consensus
Probab=95.97 E-value=0.0031 Score=63.87 Aligned_cols=48 Identities=29% Similarity=0.749 Sum_probs=41.9
Q ss_pred CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc-----CCCCCCcccccc
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF-----DRTCPMCRVPVN 346 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~-----~~~CP~Cr~~i~ 346 (353)
.++.+|.+|.+.-.+++...|.|. ||+.|+..+... ...||+|...+.
T Consensus 534 k~~~~C~lc~d~aed~i~s~ChH~-FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 534 KGEVECGLCHDPAEDYIESSCHHK-FCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred cCceeecccCChhhhhHhhhhhHH-HHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 456899999999999999999999 999999888775 568999987754
No 114
>KOG0804|consensus
Probab=95.93 E-value=0.0043 Score=61.81 Aligned_cols=45 Identities=29% Similarity=0.647 Sum_probs=35.3
Q ss_pred CCccccccccccccc----EEeCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141 299 GSRQCYLCNDREVTH----ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~----~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~ 346 (353)
+--+|+||+++.-.- +.+.|.|. |...|+..|+. ..||+||--..
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c~Hs-fh~~cl~~w~~--~scpvcR~~q~ 222 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILCNHS-FHCSCLMKWWD--SSCPVCRYCQS 222 (493)
T ss_pred cCCCcchhHhhcCccccceeeeecccc-cchHHHhhccc--CcChhhhhhcC
Confidence 446899999986432 34789999 99999999975 78999986443
No 115
>PRK00468 hypothetical protein; Provisional
Probab=95.78 E-value=0.011 Score=45.40 Aligned_cols=31 Identities=29% Similarity=0.468 Sum_probs=27.7
Q ss_pred ceEEEEEecCCCccceeccCChHHHHHHHHh
Q psy4141 80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T 110 (353)
....++.|..+.+|+||||+|.+|+.|+.--
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3678899999999999999999999998654
No 116
>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=95.77 E-value=0.011 Score=41.56 Aligned_cols=40 Identities=33% Similarity=0.775 Sum_probs=32.2
Q ss_pred ccccccc--cccccEEeCCC-----CHhhhHHhHHHHhcc--CCCCCCcc
Q psy4141 302 QCYLCND--REVTHALIPCG-----HNFFCSECAERTCDF--DRTCPMCR 342 (353)
Q Consensus 302 ~C~IC~~--~~~~~~llpCg-----H~~fC~~C~~~~~~~--~~~CP~Cr 342 (353)
.|.||++ ...++...||. |. +...|+.+|... ...||+|+
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 45566778995 66 999999999976 55899995
No 117
>KOG0336|consensus
Probab=95.67 E-value=0.017 Score=57.44 Aligned_cols=57 Identities=30% Similarity=0.260 Sum_probs=49.2
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhhhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSA 58 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~ 58 (353)
.+||++|++||.|+..|+++|++-....+-.++|-|..+--.+|+..|...++....
T Consensus 60 ~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~~k~e~ 116 (629)
T KOG0336|consen 60 KVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQDKDER 116 (629)
T ss_pred eeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhhhhhhh
Confidence 589999999999999999999998777677788999998888999988887765543
No 118
>PRK02821 hypothetical protein; Provisional
Probab=95.66 E-value=0.011 Score=45.48 Aligned_cols=33 Identities=30% Similarity=0.383 Sum_probs=29.1
Q ss_pred ceEEEEEecCCCccceeccCChHHHHHHHHhCc
Q psy4141 80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNT 112 (353)
Q Consensus 80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga 112 (353)
...+.+.|..+.+|+||||+|.+|+.|+.--.+
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 367889999999999999999999999877644
No 119
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.48 E-value=0.017 Score=44.32 Aligned_cols=32 Identities=41% Similarity=0.556 Sum_probs=28.2
Q ss_pred cceEEEEEecCCCccceeccCChHHHHHHHHh
Q psy4141 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 79 ~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T 110 (353)
.....++.|....+|.||||+|.+|+.|+.--
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 34778899999999999999999999998654
No 120
>KOG0825|consensus
Probab=95.42 E-value=0.0035 Score=66.01 Aligned_cols=50 Identities=24% Similarity=0.394 Sum_probs=41.9
Q ss_pred CCcccccccccccccEE---eCCCCHhhhHHhHHHHhccCCCCCCcccccccce
Q psy4141 299 GSRQCYLCNDREVTHAL---IPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM 349 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~l---lpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ 349 (353)
....|++|+....+... .+|+|- ||..|+..|+.-...||+||..|.+++
T Consensus 122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~-FC~~Ci~sWsR~aqTCPiDR~EF~~v~ 174 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQLEESEKHTAHY-FCEECVGSWSRCAQTCPVDRGEFGEVK 174 (1134)
T ss_pred hhhhhhHHHHHHHHHhhccccccccc-cHHHHhhhhhhhcccCchhhhhhheee
Confidence 45789999987655433 589999 999999999988999999999988764
No 121
>KOG1734|consensus
Probab=95.38 E-value=0.0095 Score=55.79 Aligned_cols=47 Identities=26% Similarity=0.641 Sum_probs=38.7
Q ss_pred CCcccccccccccc----------cEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141 299 GSRQCYLCNDREVT----------HALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN 346 (353)
Q Consensus 299 ~~~~C~IC~~~~~~----------~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~ 346 (353)
++..|.||-...-. .-.+.|+|. |...|++-|+.- .+.||.|+..+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHv-FHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHV-FHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccc-hHHHhhhhheeecCCCCCchHHHHhh
Confidence 45789999876533 335899999 999999999987 779999998774
No 122
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.37 E-value=0.042 Score=54.43 Aligned_cols=38 Identities=16% Similarity=0.064 Sum_probs=34.8
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~ 118 (353)
....+.||.++.++.|||+|.+++-..+.||.+|.|-+
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 56789999999999999999999999999999997643
No 123
>KOG0119|consensus
Probab=95.26 E-value=0.041 Score=55.57 Aligned_cols=53 Identities=21% Similarity=0.223 Sum_probs=42.0
Q ss_pred eecCCCchHHHHHHHcCceEEecCCC-------------------CcCeEEEe-cCHHHHHHHHHHHHHHHhh
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVRG-------------------EEPVFVVT-GRKEDVARAKREILSAADH 55 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~~-------------------e~~vv~I~-G~~e~v~~Ak~~I~~i~~~ 55 (353)
|||.+|.+.|+|+++|||+|.|-..+ |+--+.|+ -+.|.|.+|.+.|..+|++
T Consensus 158 iiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 158 IIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred EecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 89999999999999999999975311 12234444 5778999999999999885
No 124
>KOG0826|consensus
Probab=95.26 E-value=0.0095 Score=57.23 Aligned_cols=55 Identities=18% Similarity=0.451 Sum_probs=43.9
Q ss_pred CCCcccccccccccccEEeCC-CCHhhhHHhHHHHhccCCCCCCcc--cccccceeccC
Q psy4141 298 SGSRQCYLCNDREVTHALIPC-GHNFFCSECAERTCDFDRTCPMCR--VPVNQAMRIIS 353 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpC-gH~~fC~~C~~~~~~~~~~CP~Cr--~~i~~~~ri~~ 353 (353)
.+...|+||+...+++..+-- |-. ||..|+-.+......||+=. ..+.+++|+|+
T Consensus 298 ~~~~~CpvClk~r~Nptvl~vSGyV-fCY~Ci~~Yv~~~~~CPVT~~p~~v~~l~rl~~ 355 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPTVLEVSGYV-FCYPCIFSYVVNYGHCPVTGYPASVDHLIRLFN 355 (357)
T ss_pred CccccChhHHhccCCCceEEecceE-EeHHHHHHHHHhcCCCCccCCcchHHHHHHHhc
Confidence 456789999999988776654 777 99999999998899999744 44567777764
No 125
>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=95.24 E-value=0.005 Score=60.49 Aligned_cols=38 Identities=24% Similarity=0.301 Sum_probs=35.2
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~ 118 (353)
....+.||.+..+..|||+|.+++-..+.||.+|.+-+
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 57889999999999999999999999999999997754
No 126
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.04 E-value=0.063 Score=53.20 Aligned_cols=39 Identities=23% Similarity=0.220 Sum_probs=35.5
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~ 119 (353)
....+.||.+..++.|||+|.+++-..+.||.+|.+-..
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 568899999999999999999999999999999976543
No 127
>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=94.77 E-value=0.023 Score=49.33 Aligned_cols=53 Identities=25% Similarity=0.575 Sum_probs=38.6
Q ss_pred CCcccccccccccccEEeCCC-CHhhh-----------HHhHHHHhcc-------------------------------C
Q psy4141 299 GSRQCYLCNDREVTHALIPCG-HNFFC-----------SECAERTCDF-------------------------------D 335 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llpCg-H~~fC-----------~~C~~~~~~~-------------------------------~ 335 (353)
++..|+|||+.+-++|||-|. |.-.| .-|+.++... .
T Consensus 1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (162)
T PF07800_consen 1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPE 80 (162)
T ss_pred CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccccc
Confidence 357899999999999998764 22233 3677776542 2
Q ss_pred CCCCCcccccccceec
Q psy4141 336 RTCPMCRVPVNQAMRI 351 (353)
Q Consensus 336 ~~CP~Cr~~i~~~~ri 351 (353)
..||+||-.|..+..|
T Consensus 81 L~CPLCRG~V~GWtvv 96 (162)
T PF07800_consen 81 LACPLCRGEVKGWTVV 96 (162)
T ss_pred ccCccccCceeceEEc
Confidence 2599999999877654
No 128
>PRK01064 hypothetical protein; Provisional
Probab=94.67 E-value=0.038 Score=42.65 Aligned_cols=32 Identities=28% Similarity=0.428 Sum_probs=28.2
Q ss_pred ceEEEEEecCCCccceeccCChHHHHHHHHhC
Q psy4141 80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTN 111 (353)
Q Consensus 80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tg 111 (353)
....++.|.....|.+|||+|.+|+.|+.-..
T Consensus 29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred EEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 46788999999999999999999999987643
No 129
>KOG1001|consensus
Probab=94.53 E-value=0.016 Score=61.72 Aligned_cols=44 Identities=32% Similarity=0.892 Sum_probs=39.2
Q ss_pred cccccccccccccEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141 301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN 346 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~ 346 (353)
..|.+|.+ ...++..+|+|. ||.+|+...... ...||.||..+.
T Consensus 455 ~~c~ic~~-~~~~~it~c~h~-~c~~c~~~~i~~~~~~~~~~cr~~l~ 500 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRCGHD-FCVECLKKSIQQSENAPCPLCRNVLK 500 (674)
T ss_pred cccccccc-cccceeecccch-HHHHHHHhccccccCCCCcHHHHHHH
Confidence 78999999 788888999999 999999999888 457999998764
No 130
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.52 E-value=0.089 Score=53.09 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=34.9
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~ 118 (353)
....+.||.+..++.|||+|.+++-..+.||-+|.|-.
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 46789999999999999999999999999999997664
No 131
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.49 E-value=0.0067 Score=62.06 Aligned_cols=38 Identities=21% Similarity=0.282 Sum_probs=34.8
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~ 118 (353)
....+.||.+..+..|||+|.+|+...+.||.+|.+-.
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 47889999999999999999999999999999997654
No 132
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=94.32 E-value=0.08 Score=55.77 Aligned_cols=52 Identities=23% Similarity=0.245 Sum_probs=42.7
Q ss_pred eecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHF 56 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~ 56 (353)
+||++|.+|++|.++||++|++.+. ..+.+..-..+.+.+|+..|..+.++.
T Consensus 566 vIG~gGk~I~~I~eetg~~Idiedd--Gtv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 566 VIGPGGKTIKAITEETGVKIDIEDD--GTVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred ccCCcccchhhhhhhhCcEEEecCC--CcEEEEecchHHHHHHHHHHHHHHhhc
Confidence 7999999999999999999999833 244444445688999999999998765
No 133
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.13 E-value=0.028 Score=53.43 Aligned_cols=42 Identities=36% Similarity=0.739 Sum_probs=36.8
Q ss_pred cccccccccccccEEeC-CCCHhhhHHhHHHHhcc-CCCCCCccc
Q psy4141 301 RQCYLCNDREVTHALIP-CGHNFFCSECAERTCDF-DRTCPMCRV 343 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llp-CgH~~fC~~C~~~~~~~-~~~CP~Cr~ 343 (353)
+.|+.|.....+++..| |+|. ||.+|+...+.. ...||.|..
T Consensus 275 LkCplc~~Llrnp~kT~cC~~~-fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRNPMKTPCCGHT-FCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhCcccCccccch-HHHHHHhhhhhhccccCCCccc
Confidence 78999999999999885 7788 999999976665 889999977
No 134
>KOG3273|consensus
Probab=94.10 E-value=0.035 Score=49.98 Aligned_cols=125 Identities=18% Similarity=0.168 Sum_probs=75.8
Q ss_pred HHHcCceEEecCCC---CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhc---cCCCCCCCCCCCCCCCcceEEEEEec
Q psy4141 15 RAKTNTYIKTPVRG---EEPVFVVTGRKEDVARAKREILSAADHFSALRAS---RKSGALSPLSPPTGVPGHVTIEVRVP 88 (353)
Q Consensus 15 ~~~Tga~I~ip~~~---e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~---~~~g~~~~~~~~~~~~~~~t~~v~VP 88 (353)
-+..+.+|.+--.. +-|...-+-++.+++++...|...+-.|.--.+- +.... .-...++....+++=.=-
T Consensus 100 ve~lklqiRmNlK~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiALlrlddl---flesFEi~dVKtL~GdHl 176 (252)
T KOG3273|consen 100 VEHLKLQIRMNLKARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIALLRLDDL---FLESFEIKDVKTLKGDHL 176 (252)
T ss_pred HHhhhheeEeecccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHHHhhhhh---hheeeeecccccccchhH
Confidence 34445555543222 2244444567788888888887664433210000 00000 000001111112222223
Q ss_pred CCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHH
Q psy4141 89 YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHII 146 (353)
Q Consensus 89 ~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~ 146 (353)
.+.+|+|+||+|+|--.|...|.++|++. +..|.|-|..+++..|+..|..+|.
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla----d~kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA----DSKIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec----CceEEEeecchhhHHHHHhhHhhhc
Confidence 57799999999999999999999999865 3469999999999999999988775
No 135
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=94.08 E-value=0.038 Score=46.60 Aligned_cols=47 Identities=21% Similarity=0.784 Sum_probs=40.5
Q ss_pred cccccccccccccEEeC----CCCHhhhHHhHHHHhcc---CCCCCCcccccccc
Q psy4141 301 RQCYLCNDREVTHALIP----CGHNFFCSECAERTCDF---DRTCPMCRVPVNQA 348 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llp----CgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~~~ 348 (353)
-+|.||.|...+.-++. ||-+ .|..|-..+|.. .+.||+|+..+...
T Consensus 81 YeCnIC~etS~ee~FLKPneCCgY~-iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 81 YECNICKETSAEERFLKPNECCGYS-ICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred eeccCcccccchhhcCCcccccchH-HHHHHHHHHHHHcccCCCCCccccccccc
Confidence 57999999988877763 9999 999999999998 78999999988653
No 136
>KOG3002|consensus
Probab=94.07 E-value=0.027 Score=54.30 Aligned_cols=47 Identities=28% Similarity=0.711 Sum_probs=38.8
Q ss_pred CCCCCcccccccccccccEEeCC--CCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 296 SISGSRQCYLCNDREVTHALIPC--GHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 296 ~~~~~~~C~IC~~~~~~~~llpC--gH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
...+-++|+||++....+++ .| ||. .|..|-.++ ...||.||.++..
T Consensus 44 ~~~~lleCPvC~~~l~~Pi~-QC~nGHl-aCssC~~~~---~~~CP~Cr~~~g~ 92 (299)
T KOG3002|consen 44 LDLDLLDCPVCFNPLSPPIF-QCDNGHL-ACSSCRTKV---SNKCPTCRLPIGN 92 (299)
T ss_pred cchhhccCchhhccCcccce-ecCCCcE-ehhhhhhhh---cccCCcccccccc
Confidence 34456899999999988876 66 799 999999765 6799999999873
No 137
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=94.00 E-value=0.018 Score=43.52 Aligned_cols=46 Identities=22% Similarity=0.577 Sum_probs=23.1
Q ss_pred Cccccccccccc-c---cEE----eCCCCHhhhHHhHHHHhcc---C--------CCCCCcccccc
Q psy4141 300 SRQCYLCNDREV-T---HAL----IPCGHNFFCSECAERTCDF---D--------RTCPMCRVPVN 346 (353)
Q Consensus 300 ~~~C~IC~~~~~-~---~~l----lpCgH~~fC~~C~~~~~~~---~--------~~CP~Cr~~i~ 346 (353)
+.+|.||+.... . +.+ -.|++. |...|+.+|... . ..||.|+.+|+
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 478999998754 1 111 268888 999999999875 1 15999999875
No 138
>KOG0824|consensus
Probab=93.85 E-value=0.032 Score=53.19 Aligned_cols=50 Identities=20% Similarity=0.505 Sum_probs=33.7
Q ss_pred CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141 299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 348 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~ 348 (353)
...+|.||+.....++.++|+|..+---=--.++..+..|++||.+|..-
T Consensus 6 ~~~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 6 KKKECLICYNTGNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST 55 (324)
T ss_pred cCCcceeeeccCCcCccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence 35789999999999999999999000000000111177799999999764
No 139
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.63 E-value=0.14 Score=53.10 Aligned_cols=52 Identities=17% Similarity=0.201 Sum_probs=41.5
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEec-CHHHHHHHHHHHHHHHhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAADH 55 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G-~~e~v~~Ak~~I~~i~~~ 55 (353)
+||||.|.||+.++.-||+.|-|.+. ..+|+|++ +|-.-+-|+..|..++.+
T Consensus 218 riigreGrnir~~e~~tgvd~iiddt--p~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 218 RIIGREGRNIRALETLTGVDLIIDDT--PEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred cccCCCcchHHHHHHHhCceEEEcCC--CCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 69999999999999999999998754 35667776 666667777777777653
No 140
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=93.61 E-value=0.048 Score=39.54 Aligned_cols=41 Identities=22% Similarity=0.344 Sum_probs=29.5
Q ss_pred CCcccccccccccccEE-eCCCCHhhhHHhHHHHhcc--CCCCCC
Q psy4141 299 GSRQCYLCNDREVTHAL-IPCGHNFFCSECAERTCDF--DRTCPM 340 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~l-lpCgH~~fC~~C~~~~~~~--~~~CP~ 340 (353)
-...|+|.+..+.+++. ..|+|. |..+.+..+... ...||+
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 35889999999999988 499999 999999999944 678998
No 141
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=93.59 E-value=0.055 Score=37.75 Aligned_cols=42 Identities=29% Similarity=0.768 Sum_probs=21.1
Q ss_pred cccccccc--cccEEe--CCCCHhhhHHhHHHHhcc-CCCCCCccccc
Q psy4141 303 CYLCNDRE--VTHALI--PCGHNFFCSECAERTCDF-DRTCPMCRVPV 345 (353)
Q Consensus 303 C~IC~~~~--~~~~ll--pCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i 345 (353)
|++|.+.. .+..+. +||+. .|..|..++.+. ...||-||.+.
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 55666654 222334 58899 999999999875 88999999875
No 142
>PRK12704 phosphodiesterase; Provisional
Probab=93.55 E-value=0.16 Score=52.89 Aligned_cols=53 Identities=17% Similarity=0.162 Sum_probs=43.0
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEec-CHHHHHHHHHHHHHHHhhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAADHF 56 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G-~~e~v~~Ak~~I~~i~~~~ 56 (353)
+||||.|.||+.|+.-||+.|-|.+. ..+|+++| ++-.-+-|+..+..++.+.
T Consensus 224 riigreGrnir~~e~~tgvd~iiddt--p~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 224 RIIGREGRNIRALETLTGVDLIIDDT--PEAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred ceeCCCcchHHHHHHHhCCeEEEcCC--CCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 69999999999999999999998854 35677887 5656567888888887654
No 143
>KOG3039|consensus
Probab=93.52 E-value=0.047 Score=50.65 Aligned_cols=48 Identities=25% Similarity=0.414 Sum_probs=41.1
Q ss_pred CCccccccccccccc----EEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 299 GSRQCYLCNDREVTH----ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~----~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
..-.|+||.+...+. +|-||||. ||++|++++......||+|-.++..
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 457899999987654 46799999 9999999999888899999988764
No 144
>PRK00106 hypothetical protein; Provisional
Probab=93.47 E-value=0.17 Score=52.56 Aligned_cols=52 Identities=21% Similarity=0.218 Sum_probs=42.4
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEec-CHHHHHHHHHHHHHHHhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTG-RKEDVARAKREILSAADH 55 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G-~~e~v~~Ak~~I~~i~~~ 55 (353)
+||||.|.||+.|+.-||+.|-|.+. ...|+|++ +|-.-+-|+..+..++.+
T Consensus 239 riIGreGrNir~~E~~tGvdliiddt--p~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 239 RIIGREGRNIRTLESLTGIDVIIDDT--PEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred ceeCCCcchHHHHHHHhCceEEEcCC--CCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 69999999999999999999998754 34566777 777777788888777663
No 145
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=93.40 E-value=0.051 Score=52.54 Aligned_cols=48 Identities=25% Similarity=0.626 Sum_probs=37.2
Q ss_pred CCccccccccccc--ccEE--eCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141 299 GSRQCYLCNDREV--THAL--IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 347 (353)
Q Consensus 299 ~~~~C~IC~~~~~--~~~l--lpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~ 347 (353)
++..|+.|++..- +.-+ -|||.. .|..|...+.+. ...||.||...+.
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 4456999999642 2223 478999 999999999887 7899999987653
No 146
>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=93.28 E-value=0.14 Score=44.01 Aligned_cols=35 Identities=31% Similarity=0.336 Sum_probs=30.8
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEE
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV 115 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ 115 (353)
.+-+|.|-.+.-|.+||++|.++++|.++||=.-.
T Consensus 76 ~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~ 110 (145)
T cd02410 76 DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPK 110 (145)
T ss_pred CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeE
Confidence 45688888899999999999999999999996654
No 147
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.19 E-value=0.048 Score=41.19 Aligned_cols=35 Identities=26% Similarity=0.302 Sum_probs=30.6
Q ss_pred ceEEEEEecCCCccceeccCChHHHHHHHHhCceE
Q psy4141 80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114 (353)
Q Consensus 80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I 114 (353)
.....+.+..+..|.||||+|+|++.||.-.+..+
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 36788999999999999999999999998876555
No 148
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=93.09 E-value=0.11 Score=56.95 Aligned_cols=51 Identities=22% Similarity=0.180 Sum_probs=42.5
Q ss_pred eeecCCCchHHHHHHHcCce-EEecCCCCcCeEEEecCHHHHHHHHHHHHHHHh
Q psy4141 2 KKISRSGCKIKALRAKTNTY-IKTPVRGEEPVFVVTGRKEDVARAKREILSAAD 54 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~-I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~ 54 (353)
.|||.+|.+||.|.++||+. |++.+. ..+.+..-+.+.+++|+..|..+..
T Consensus 698 ~vIG~GGktIk~I~eetg~~~Idi~dd--g~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 698 MIIGSGGKKVKSIIEETGVEAIDTQDD--GTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred HHhcCCchhHHHHHHHHCCCccCcCCC--eeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 37999999999999999999 887753 3555555688999999999988865
No 149
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.00 E-value=0.038 Score=59.72 Aligned_cols=49 Identities=22% Similarity=0.608 Sum_probs=38.2
Q ss_pred CCCCccccccccccc--ccE-----EeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141 297 ISGSRQCYLCNDREV--THA-----LIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN 346 (353)
Q Consensus 297 ~~~~~~C~IC~~~~~--~~~-----llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~ 346 (353)
.....+|.||+.... +.. .--|.|. |...|+-+|... ...||+||..++
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 346789999998643 111 2349999 999999999988 678999998775
No 150
>KOG4369|consensus
Probab=92.96 E-value=0.2 Score=55.50 Aligned_cols=67 Identities=21% Similarity=0.196 Sum_probs=57.0
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC----CCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS----RDKEPVFEVTGAPDSVEIARQEIESHIIR 147 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~----~~~e~~v~I~G~~e~V~~A~~~I~~~i~~ 147 (353)
....+.+|-....+|||++|.+|+.++.-||+.|.+.+ ...||.+.+.|.|+.+..|...|.-.|.+
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeec
Confidence 34568889999999999999999999999999997654 13478999999999999999988766654
No 151
>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=92.70 E-value=0.19 Score=36.41 Aligned_cols=34 Identities=29% Similarity=0.481 Sum_probs=27.8
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceE
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I 114 (353)
....+.+.....|.+||++|++|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666666789999999999999999998555
No 152
>KOG2874|consensus
Probab=92.63 E-value=0.21 Score=47.26 Aligned_cols=51 Identities=24% Similarity=0.434 Sum_probs=45.3
Q ss_pred cceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHh
Q psy4141 93 GLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR 147 (353)
Q Consensus 93 G~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~ 147 (353)
-++||++|.|+|.|+-.|.|+|.+.. .+|.+.|....++.++..+++-+.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG----~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG----NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC----cEEEeecCcchHHHHHHHHHHHHhc
Confidence 47999999999999999999998653 4799999999999999999887765
No 153
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=92.59 E-value=0.14 Score=39.43 Aligned_cols=30 Identities=30% Similarity=0.499 Sum_probs=27.0
Q ss_pred eCCCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141 316 IPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346 (353)
Q Consensus 316 lpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~ 346 (353)
--|.|. |...|+.+|+.....||++|++..
T Consensus 52 G~CnHa-FH~HCI~rWL~Tk~~CPld~q~w~ 81 (88)
T COG5194 52 GVCNHA-FHDHCIYRWLDTKGVCPLDRQTWV 81 (88)
T ss_pred EecchH-HHHHHHHHHHhhCCCCCCCCceeE
Confidence 469999 999999999999999999998753
No 154
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=92.53 E-value=0.26 Score=45.96 Aligned_cols=52 Identities=19% Similarity=0.225 Sum_probs=42.4
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH 55 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~ 55 (353)
++||++|.+|+.|.+++++.|.+-.. .++-+-.-+.+++.+|++.|..+-++
T Consensus 158 ~lig~~g~~i~~l~~~~~~~I~ig~N--G~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 158 RVIGKKGSMINMLKEETGCDIIVGQN--GRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred hhcCCCChhHhhhhhhhCcEEEEcCC--cEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 47999999999999999999998654 35555556777999999999887654
No 155
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=92.14 E-value=0.16 Score=54.65 Aligned_cols=52 Identities=19% Similarity=0.195 Sum_probs=41.9
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH 55 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~ 55 (353)
.+||.+|.+||.|.++||+.|++.+. ..+.+..-..+.+++|++.|..+..+
T Consensus 567 ~vIG~gg~~ik~I~~~~~~~idi~d~--G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 567 DVIGPGGKTIREITEETGAKIDIEDD--GTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred HHhcCCchhHHHHHHHHCCccccCCC--ceEEEEcccHHHHHHHHHHHHHhccc
Confidence 47999999999999999999887543 34444445789999999999888753
No 156
>KOG1814|consensus
Probab=92.01 E-value=0.081 Score=52.44 Aligned_cols=34 Identities=24% Similarity=0.774 Sum_probs=28.7
Q ss_pred Ccccccccccccc---cEEeCCCCHhhhHHhHHHHhcc
Q psy4141 300 SRQCYLCNDREVT---HALIPCGHNFFCSECAERTCDF 334 (353)
Q Consensus 300 ~~~C~IC~~~~~~---~~llpCgH~~fC~~C~~~~~~~ 334 (353)
...|.||++...- ..++||+|. ||..|+..+..-
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC~Hv-~Ck~C~kdY~~~ 220 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPCSHV-FCKSCLKDYFTI 220 (445)
T ss_pred cccceeeehhhcCcceeeecccchH-HHHHHHHHHHHH
Confidence 4789999998754 567999999 999999998764
No 157
>KOG1588|consensus
Probab=92.00 E-value=0.28 Score=46.11 Aligned_cols=26 Identities=23% Similarity=0.276 Sum_probs=23.8
Q ss_pred eeecCCCchHHHHHHHcCceEEecCC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVR 27 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~ 27 (353)
+|+|.+|.++|+|+++|+|+|-|-.+
T Consensus 111 RILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 111 RILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred ccccCCcchHHHHHHHHCCeEEEecC
Confidence 69999999999999999999998644
No 158
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=91.98 E-value=0.21 Score=42.96 Aligned_cols=36 Identities=25% Similarity=0.320 Sum_probs=32.2
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
..+-+.|+...+|..||++|++|+.|++..|-+|.+
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdV 67 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIEL 67 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEE
Confidence 567788899999999999999999999999988854
No 159
>KOG1493|consensus
Probab=91.98 E-value=0.074 Score=40.55 Aligned_cols=29 Identities=31% Similarity=0.675 Sum_probs=25.2
Q ss_pred CCCCHhhhHHhHHHHhcc---CCCCCCcccccc
Q psy4141 317 PCGHNFFCSECAERTCDF---DRTCPMCRVPVN 346 (353)
Q Consensus 317 pCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~ 346 (353)
-|.|. |-..|+.+|... ...||+||+.+.
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 69999 999999999887 568999998653
No 160
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=91.97 E-value=1.1 Score=40.66 Aligned_cols=71 Identities=11% Similarity=0.182 Sum_probs=57.8
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHhhhCCCCc
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVT 154 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~~~~ 154 (353)
...+.++....-++...+|..++.|....|++|.+..+. ..|.|+|+...++.+...|.+++..-.-.-++
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~--~~i~I~g~k~~~~~i~~~i~~~l~~i~~~~i~ 97 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRSE--NRIRITGTKSTAEYIEASINEILSNIRTEEID 97 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecCC--cEEEEEccHHHHHHHHHHHHHHHhhcEEEEEe
Confidence 445666788889999999999999989999999876544 37999999999999999999988874333333
No 161
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=91.95 E-value=0.23 Score=50.38 Aligned_cols=67 Identities=24% Similarity=0.252 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141 41 DVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119 (353)
Q Consensus 41 ~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~ 119 (353)
....|..+|.+.++.+-. ....-.+.+.....+.||...++.+|||+|.+|++|.++.|-+|.+-..
T Consensus 458 ~~~~a~~~i~~~i~r~~p------------~~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 458 ALKLAEEEIEREIKRYLP------------GDVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred hhHHHHHHHHHHHHHhCC------------CCceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 355677777777765510 0000011223557789999999999999999999999999999966443
No 162
>KOG2932|consensus
Probab=91.57 E-value=0.056 Score=51.68 Aligned_cols=45 Identities=36% Similarity=0.803 Sum_probs=30.7
Q ss_pred cccccccccccc-cEEeCCCCHhhhHHhHHHHhccCCCCCCcccccccc
Q psy4141 301 RQCYLCNDREVT-HALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 348 (353)
Q Consensus 301 ~~C~IC~~~~~~-~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~ 348 (353)
..|.-|--.... .-++||.|. ||.+|+..- ..+.||.|-.+|..+
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkHv-FCl~CAr~~--~dK~Cp~C~d~VqrI 136 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKHV-FCLECARSD--SDKICPLCDDRVQRI 136 (389)
T ss_pred EeecccCCcceeeecccccchh-hhhhhhhcC--ccccCcCcccHHHHH
Confidence 456556433222 224799999 999998874 257999998776543
No 163
>PF04641 Rtf2: Rtf2 RING-finger
Probab=91.24 E-value=0.19 Score=47.51 Aligned_cols=48 Identities=23% Similarity=0.480 Sum_probs=38.2
Q ss_pred CCCcccccccccc----cccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 298 SGSRQCYLCNDRE----VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 298 ~~~~~C~IC~~~~----~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
.....|+|....+ .-+++.||||. |+..++..+. ....||+|-.++..
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V-~s~~alke~k-~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCV-FSEKALKELK-KSKKCPVCGKPFTE 162 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCE-eeHHHHHhhc-ccccccccCCcccc
Confidence 4567899988765 33456799998 9999999994 35679999999875
No 164
>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=90.37 E-value=0.11 Score=36.07 Aligned_cols=47 Identities=26% Similarity=0.693 Sum_probs=27.6
Q ss_pred ccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccccee
Q psy4141 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR 350 (353)
Q Consensus 302 ~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~r 350 (353)
-|.-|.-... -++.|.....|..|+..+......||+|..++...+|
T Consensus 4 nCKsCWf~~k--~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtkir 50 (50)
T PF03854_consen 4 NCKSCWFANK--GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTKIR 50 (50)
T ss_dssp ---SS-S--S--SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----S-
T ss_pred cChhhhhcCC--CeeeecchhHHHHHHHHHhccccCCCcccCcCccccC
Confidence 4666765443 4677985559999999999889999999998876554
No 165
>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=90.35 E-value=0.24 Score=37.85 Aligned_cols=35 Identities=29% Similarity=0.478 Sum_probs=29.6
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEE
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV 115 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ 115 (353)
..+.+.|..+..|.+|||+|++++.||--++..+.
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 34667888899999999999999999988876654
No 166
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=90.13 E-value=0.29 Score=42.66 Aligned_cols=48 Identities=23% Similarity=0.567 Sum_probs=36.5
Q ss_pred CCCcccccccccccccEEeCCCCH----hhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHN----FFCSECAERTCDF--DRTCPMCRVPVN 346 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~----~fC~~C~~~~~~~--~~~CP~Cr~~i~ 346 (353)
..+..|.||++.... ...||.-. ....+|+++|... ...|++|+.++.
T Consensus 6 ~~~~~CRIC~~~~~~-~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~ 59 (162)
T PHA02825 6 LMDKCCWICKDEYDV-VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN 59 (162)
T ss_pred CCCCeeEecCCCCCC-ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence 456899999998653 34587743 1467999999988 678999998763
No 167
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=90.09 E-value=0.34 Score=49.52 Aligned_cols=119 Identities=9% Similarity=0.017 Sum_probs=78.1
Q ss_pred eecCCCchHHHHHHHcCceEEe--cCCCCcCeE-EEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCc
Q psy4141 3 KISRSGCKIKALRAKTNTYIKT--PVRGEEPVF-VVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPG 79 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~i--p~~~e~~vv-~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~ 79 (353)
|-||+.-++.+|++...+-+.+ -......+. .+.|..-+..++...+ . .+-|
T Consensus 394 l~gkkngK~TrIm~~v~c~~~~~i~~~~gs~~~~~~~g~~~~F~k~~~~~---~---------------------~EFp- 448 (657)
T COG5166 394 LRGKKNGKATRIMKGVSCSELSSIVSSTGSIVETNGIGEKMSFSKKLSIP---P---------------------TEFP- 448 (657)
T ss_pred hccccCcchhhhhhhcccceeeEEEecCCcEEEEeccCcchhhHHHhcCC---c---------------------ccCc-
Confidence 3477777788999888887553 222222322 2335554444322221 1 1123
Q ss_pred ceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC------CCCCeEEEEcCHH---HHHHHHHHHHHHHHh
Q psy4141 80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR------DKEPVFEVTGAPD---SVEIARQEIESHIIR 147 (353)
Q Consensus 80 ~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~------~~e~~v~I~G~~e---~V~~A~~~I~~~i~~ 147 (353)
..+.+.||...|..|||-||..|++++...++.|++... ...+-|.|.-+.. ++.-++.-+.++|.+
T Consensus 449 -ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 449 -AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred -hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 567889999999999999999999999999999987543 1123477777644 455577777788875
No 168
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=89.51 E-value=0.43 Score=48.87 Aligned_cols=33 Identities=36% Similarity=0.405 Sum_probs=29.6
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCce
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY 113 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~ 113 (353)
.+-+|.|-.+.=|+||||+|++.++|.++||-.
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~ 131 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWA 131 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCc
Confidence 556888999999999999999999999999844
No 169
>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=89.45 E-value=0.22 Score=37.87 Aligned_cols=34 Identities=26% Similarity=0.458 Sum_probs=28.8
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceE
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I 114 (353)
....+.+....-|.|||++|++|++|.+..+-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4467788889999999999999999988876555
No 170
>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=89.39 E-value=0.19 Score=42.66 Aligned_cols=33 Identities=27% Similarity=0.637 Sum_probs=26.7
Q ss_pred Ccccccccccccc---cEEeCCC------CHhhhHHhHHHHhc
Q psy4141 300 SRQCYLCNDREVT---HALIPCG------HNFFCSECAERTCD 333 (353)
Q Consensus 300 ~~~C~IC~~~~~~---~~llpCg------H~~fC~~C~~~~~~ 333 (353)
..+|.||++...+ .+.++|+ |. ||..|+++|..
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkm-fc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKM-FCADCDKRWRR 67 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHH-HHHHHHHHHHh
Confidence 4789999998765 5557888 66 99999999943
No 171
>KOG2874|consensus
Probab=89.25 E-value=0.65 Score=44.01 Aligned_cols=51 Identities=20% Similarity=0.296 Sum_probs=45.4
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHF 56 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~~ 56 (353)
++||.+|.++|+|+--|+|+|-+. ...|.+.|.-..+..+++-+.+.+...
T Consensus 162 RLiGpng~TLKAlelLT~CYilVq----G~TVsaiGpfkGlkevr~IV~DcM~Ni 212 (356)
T KOG2874|consen 162 RLIGPNGSTLKALELLTNCYILVQ----GNTVSAIGPFKGLKEVRKIVEDCMKNI 212 (356)
T ss_pred HhcCCCchhHHHHHHHhhcEEEee----CcEEEeecCcchHHHHHHHHHHHHhcc
Confidence 689999999999999999999987 456778899999999999999987754
No 172
>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=89.13 E-value=0.34 Score=35.39 Aligned_cols=23 Identities=13% Similarity=0.169 Sum_probs=20.5
Q ss_pred eeecCCCchHHHHHHHcCceEEe
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKT 24 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~i 24 (353)
..|||+|.+|+.+++-++-+|++
T Consensus 38 ~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 38 LAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred eeECCCCHHHHHHHHHHCCCeEE
Confidence 47999999999999999988764
No 173
>PRK13764 ATPase; Provisional
Probab=89.06 E-value=0.43 Score=50.47 Aligned_cols=67 Identities=24% Similarity=0.233 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCC
Q psy4141 41 DVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119 (353)
Q Consensus 41 ~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~ 119 (353)
.-..|.++|.+.++.+-. +. ..-.+.......|.||.+.++.+|||+|.+|++|.++.|..|.+-..
T Consensus 453 ~~~~~~~~~~~~~~~~~~-------~~-----~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 453 VWRLAEKEIEREIKRYLP-------GP-----VEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred HHHHHHHHHHHHHHHhcC-------Cc-----eEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 345577777777776521 00 00011234667899999999999999999999999999999976443
No 174
>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=88.71 E-value=0.16 Score=47.07 Aligned_cols=46 Identities=26% Similarity=0.704 Sum_probs=34.4
Q ss_pred CCccccccccc-cc--ccEE--eC-CCCHhhhHHhHHHHhcc-CCCCC--Cccccc
Q psy4141 299 GSRQCYLCNDR-EV--THAL--IP-CGHNFFCSECAERTCDF-DRTCP--MCRVPV 345 (353)
Q Consensus 299 ~~~~C~IC~~~-~~--~~~l--lp-CgH~~fC~~C~~~~~~~-~~~CP--~Cr~~i 345 (353)
.++.|+||... +- +..+ -| |-|. +|..|..++... ...|| -|..-+
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 45799999864 22 2222 25 9999 999999999888 77899 786543
No 175
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=88.70 E-value=0.33 Score=36.54 Aligned_cols=35 Identities=31% Similarity=0.378 Sum_probs=27.2
Q ss_pred EEEEEecCCC-----ccceeccCChHHHHHHHHh-CceEEc
Q psy4141 82 TIEVRVPYKV-----VGLVVGPKGATIKRIQHQT-NTYIVT 116 (353)
Q Consensus 82 t~~v~VP~~~-----vG~IIGkgG~tIk~Iq~~T-ga~I~i 116 (353)
...+.|-... +|..||++|..||.|.++. |-+|.+
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence 3456666666 9999999999999999999 888854
No 176
>KOG3273|consensus
Probab=87.67 E-value=0.37 Score=43.54 Aligned_cols=49 Identities=16% Similarity=0.150 Sum_probs=44.3
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD 54 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~ 54 (353)
+|+||+|.+--.|+.-|.++|.+. +.-+.|-|.-+++..|+..|..++-
T Consensus 182 RiaGk~GkTkfaIEn~trtrIVla----d~kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 182 RIAGKGGKTKFAIENVTRTRIVLA----DSKIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HhhcCCCcceeeeeccceeEEEec----CceEEEeecchhhHHHHHhhHhhhc
Confidence 589999999999999999999988 4457888999999999999999865
No 177
>KOG1941|consensus
Probab=87.59 E-value=0.22 Score=49.10 Aligned_cols=46 Identities=28% Similarity=0.626 Sum_probs=36.5
Q ss_pred Cccccccccccc----ccEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141 300 SRQCYLCNDREV----THALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN 346 (353)
Q Consensus 300 ~~~C~IC~~~~~----~~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~ 346 (353)
+.-|-.|-+..- .--.+||.|. |...|+..+.++ .+.||-||+-..
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHI-fH~rCl~e~L~~n~~rsCP~CrklrS 416 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHI-FHLRCLQEILENNGTRSCPNCRKLRS 416 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHH-HHHHHHHHHHHhCCCCCCccHHHHHh
Confidence 578999988642 2224899999 999999999988 789999995433
No 178
>KOG4362|consensus
Probab=87.39 E-value=0.17 Score=53.62 Aligned_cols=49 Identities=18% Similarity=0.586 Sum_probs=41.8
Q ss_pred CCCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc---CCCCCCcccccc
Q psy4141 297 ISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVPVN 346 (353)
Q Consensus 297 ~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i~ 346 (353)
+....+|.||+.....++++.|-|. ||..|+...... ...||+|+..+.
T Consensus 18 ~~k~lEc~ic~~~~~~p~~~kc~~~-~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 18 MQKILECPICLEHVKEPSLLKCDHI-FLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred HhhhccCCceeEEeeccchhhhhHH-HHhhhhhceeeccCccccchhhhhhhh
Confidence 3456899999999999999999999 999999987776 457999996654
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=87.30 E-value=0.66 Score=39.92 Aligned_cols=35 Identities=20% Similarity=0.302 Sum_probs=31.0
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
.+-+.|....+|..||++|.+|+.|++..|-+|.+
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV 68 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL 68 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEE
Confidence 66678889999999999999999999999988853
No 180
>KOG1428|consensus
Probab=86.47 E-value=0.46 Score=53.87 Aligned_cols=48 Identities=23% Similarity=0.681 Sum_probs=38.1
Q ss_pred CCcccccccccc---cccEEeCCCCHhhhHHhHHHHhccCC----------CCCCccccccc
Q psy4141 299 GSRQCYLCNDRE---VTHALIPCGHNFFCSECAERTCDFDR----------TCPMCRVPVNQ 347 (353)
Q Consensus 299 ~~~~C~IC~~~~---~~~~llpCgH~~fC~~C~~~~~~~~~----------~CP~Cr~~i~~ 347 (353)
.+..|+||+... .-+..+.|+|. |...|..++++..+ .||+|..+|..
T Consensus 3485 ~DDmCmICFTE~L~AAP~IqL~C~Hi-FHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHI-FHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred cCceEEEEehhhhCCCcceecCCccc-hhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 458899999864 33456899999 99999999888622 69999988765
No 181
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=86.16 E-value=1.6 Score=40.67 Aligned_cols=56 Identities=27% Similarity=0.368 Sum_probs=42.7
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHH-HHHHHHHH
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDS-VEIARQEI 141 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~-V~~A~~~I 141 (353)
.-+.|+...|.++||++|..++-|.+.|+|.|.+-. ...|=|.|..+. ...|.+.|
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~---NG~IWV~~~~~~~e~~~~~aI 204 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ---NGRIWVDGENESLEELAIEAI 204 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec---CCEEEecCCCcchHHHHHHHH
Confidence 558899999999999999999999999999998653 345777776553 33333333
No 182
>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=86.16 E-value=5.5 Score=41.94 Aligned_cols=111 Identities=23% Similarity=0.315 Sum_probs=67.0
Q ss_pred CchHHHHHHHcC--ceEE---------ecCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCC
Q psy4141 8 GCKIKALRAKTN--TYIK---------TPVRG----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS 72 (353)
Q Consensus 8 G~~Ik~I~~~Tg--a~I~---------ip~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~ 72 (353)
|.+|+++..... +.|. .|..+ +.+++.+.|++++++++.+.+-..+.+. .
T Consensus 232 GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~~~~~--------~------- 296 (562)
T TIGR03802 232 GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEEVQEV--------E------- 296 (562)
T ss_pred CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCccCCc--------c-------
Confidence 778888876553 3332 12222 3478899999999987766543221110 0
Q ss_pred CCCCCCcceEEEEEecCCCccceeccCChHHHHHH------HHhCceEE-cCCCC------------CCCeEEEEcCHHH
Q psy4141 73 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQ------HQTNTYIV-TPSRD------------KEPVFEVTGAPDS 133 (353)
Q Consensus 73 ~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq------~~Tga~I~-ip~~~------------~e~~v~I~G~~e~ 133 (353)
..+.+ ....++.+|++ .++|| +|+++. ++.|+.|. +...+ ..+.+.+.|++++
T Consensus 297 -~~~~~-~~~e~VV~~~S---~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~ 368 (562)
T TIGR03802 297 -GLDVP-METKDVVLTNK---EYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQD 368 (562)
T ss_pred -ccCCc-eEEEEEEECCc---ccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHH
Confidence 00111 12445556654 66766 888886 36788883 32211 2368999999999
Q ss_pred HHHHHHHH
Q psy4141 134 VEIARQEI 141 (353)
Q Consensus 134 V~~A~~~I 141 (353)
++++.+.+
T Consensus 369 l~~~~~~l 376 (562)
T TIGR03802 369 VDRAAKQL 376 (562)
T ss_pred HHHHHHHc
Confidence 99987764
No 183
>PRK12705 hypothetical protein; Provisional
Probab=85.99 E-value=0.8 Score=47.45 Aligned_cols=51 Identities=16% Similarity=0.099 Sum_probs=36.7
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEe-cCHHHHHHHHHHHHHHHh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVT-GRKEDVARAKREILSAAD 54 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~-G~~e~v~~Ak~~I~~i~~ 54 (353)
+||||.|.||+.++..||+.|-|.+.. .+|++. =.+..-+.|+..+..++.
T Consensus 212 riIGreGrNir~~E~~tGvdliiddtp--~~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 212 RIIGREGRNIRAFEGLTGVDLIIDDTP--EAVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred cccCccchhHHHHHHhhCCceEecCCc--cchhhcccCccchHHHHHHHHHHHh
Confidence 699999999999999999999987553 333444 345555556666655544
No 184
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=85.73 E-value=1.2 Score=40.68 Aligned_cols=27 Identities=22% Similarity=0.263 Sum_probs=24.2
Q ss_pred eecCCCchHHHHHHHcCceEEecCCCC
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTPVRGE 29 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip~~~e 29 (353)
|||..|.+.|+|++.++|+|-|-..+.
T Consensus 168 liGPRG~Tlk~le~~s~akIaIRG~gs 194 (269)
T COG5176 168 LIGPRGSTLKQLERISRAKIAIRGSGS 194 (269)
T ss_pred EecCCcchHHHHHHHhCCeEEEecccc
Confidence 799999999999999999999875553
No 185
>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=85.40 E-value=1 Score=34.95 Aligned_cols=36 Identities=17% Similarity=0.202 Sum_probs=29.2
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
..++|.|-...-|.|||++|++|++|++.-.-...+
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 347788888899999999999999998876544433
No 186
>PHA02862 5L protein; Provisional
Probab=85.03 E-value=0.87 Score=39.12 Aligned_cols=45 Identities=24% Similarity=0.622 Sum_probs=35.0
Q ss_pred cccccccccccccEEeCCCCH----hhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141 301 RQCYLCNDREVTHALIPCGHN----FFCSECAERTCDF--DRTCPMCRVPVN 346 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llpCgH~----~fC~~C~~~~~~~--~~~CP~Cr~~i~ 346 (353)
..|-||++...+. .-||.-. ....+|+.+|... ...|++|+.++.
T Consensus 3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 5799999987554 4688742 2567999999987 678999998764
No 187
>KOG2930|consensus
Probab=84.68 E-value=0.7 Score=37.35 Aligned_cols=28 Identities=25% Similarity=0.481 Sum_probs=25.6
Q ss_pred eCCCCHhhhHHhHHHHhccCCCCCCcccc
Q psy4141 316 IPCGHNFFCSECAERTCDFDRTCPMCRVP 344 (353)
Q Consensus 316 lpCgH~~fC~~C~~~~~~~~~~CP~Cr~~ 344 (353)
--|.|. |..-|+.+|......||+|.+.
T Consensus 79 G~CNHa-FH~hCisrWlktr~vCPLdn~e 106 (114)
T KOG2930|consen 79 GVCNHA-FHFHCISRWLKTRNVCPLDNKE 106 (114)
T ss_pred eecchH-HHHHHHHHHHhhcCcCCCcCcc
Confidence 479999 9999999999999999999765
No 188
>PRK00468 hypothetical protein; Provisional
Probab=84.21 E-value=0.65 Score=35.59 Aligned_cols=16 Identities=38% Similarity=0.466 Sum_probs=14.3
Q ss_pred eeecCCCchHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAK 17 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~ 17 (353)
+||||+|.+|++||.-
T Consensus 43 rVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 43 KVIGKQGRIAKAIRTV 58 (75)
T ss_pred ceecCCChhHHHHHHH
Confidence 6999999999999953
No 189
>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=84.14 E-value=0.35 Score=38.68 Aligned_cols=33 Identities=30% Similarity=0.723 Sum_probs=26.0
Q ss_pred CCCCcccccccccccccEE--eCCCCHhhhHHhHHH
Q psy4141 297 ISGSRQCYLCNDREVTHAL--IPCGHNFFCSECAER 330 (353)
Q Consensus 297 ~~~~~~C~IC~~~~~~~~l--lpCgH~~fC~~C~~~ 330 (353)
+.+...|.+|.....+.++ .||||. |+..|+++
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 3456789999999876554 699998 99999764
No 190
>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=84.08 E-value=1.1 Score=44.27 Aligned_cols=48 Identities=23% Similarity=0.526 Sum_probs=32.7
Q ss_pred CCcccccccccccccEEe-CC---------------------CCHhhhHHhHHHHhcc-------------CCCCCCccc
Q psy4141 299 GSRQCYLCNDREVTHALI-PC---------------------GHNFFCSECAERTCDF-------------DRTCPMCRV 343 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~ll-pC---------------------gH~~fC~~C~~~~~~~-------------~~~CP~Cr~ 343 (353)
+...|.-|+....+..+. .| .-+ -|.+|+-+|... ...||.||+
T Consensus 270 e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPm-WC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa 348 (358)
T PF10272_consen 270 ELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPM-WCLECMGKWFASRQDQQHPETWLSGKCPCPTCRA 348 (358)
T ss_pred ccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccch-HHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcc
Confidence 446677787777666654 23 222 478999998764 336999999
Q ss_pred cccc
Q psy4141 344 PVNQ 347 (353)
Q Consensus 344 ~i~~ 347 (353)
.+.-
T Consensus 349 ~FCi 352 (358)
T PF10272_consen 349 KFCI 352 (358)
T ss_pred ccee
Confidence 8753
No 191
>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=83.91 E-value=0.33 Score=48.14 Aligned_cols=46 Identities=41% Similarity=0.889 Sum_probs=0.0
Q ss_pred Cccccccccc-------------------ccccEEeCCCCHhhhHHhHHHHhcc----------CCCCCCccccccc
Q psy4141 300 SRQCYLCNDR-------------------EVTHALIPCGHNFFCSECAERTCDF----------DRTCPMCRVPVNQ 347 (353)
Q Consensus 300 ~~~C~IC~~~-------------------~~~~~llpCgH~~fC~~C~~~~~~~----------~~~CP~Cr~~i~~ 347 (353)
.++|++|+.. ..+.++.||||. |.+=..++|.+ ...||+|-.++..
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 6899999863 245567899996 55544555554 2479999888864
No 192
>KOG3579|consensus
Probab=83.83 E-value=0.8 Score=43.51 Aligned_cols=34 Identities=26% Similarity=0.708 Sum_probs=29.6
Q ss_pred CcccccccccccccEEeCCC----CHhhhHHhHHHHhcc
Q psy4141 300 SRQCYLCNDREVTHALIPCG----HNFFCSECAERTCDF 334 (353)
Q Consensus 300 ~~~C~IC~~~~~~~~llpCg----H~~fC~~C~~~~~~~ 334 (353)
.+.|.+|.++..+.-++.|- |. ||..|-.....+
T Consensus 268 pLcCTLC~ERLEDTHFVQCPSVp~HK-FCFPCSResIK~ 305 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTHFVQCPSVPSHK-FCFPCSRESIKQ 305 (352)
T ss_pred ceeehhhhhhhccCceeecCCCcccc-eecccCHHHHHh
Confidence 48999999999999999995 88 999998876554
No 193
>KOG3842|consensus
Probab=83.56 E-value=0.8 Score=44.10 Aligned_cols=46 Identities=35% Similarity=0.777 Sum_probs=33.9
Q ss_pred CCcccccccccc-------------------cccEEeCCCCHhhhHHhHHHHhcc----------CCCCCCcccccc
Q psy4141 299 GSRQCYLCNDRE-------------------VTHALIPCGHNFFCSECAERTCDF----------DRTCPMCRVPVN 346 (353)
Q Consensus 299 ~~~~C~IC~~~~-------------------~~~~llpCgH~~fC~~C~~~~~~~----------~~~CP~Cr~~i~ 346 (353)
.+++|++|+..- .+.++-|||| +|.+=-..+|.+ ...||+|-..+.
T Consensus 340 ~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGH--v~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ 414 (429)
T KOG3842|consen 340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGH--VCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLA 414 (429)
T ss_pred ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCccc--ccchhhhhHhhcCcCCCccccccccCcchhhhhc
Confidence 468999998742 3445679999 577777777776 346999987764
No 194
>PRK02821 hypothetical protein; Provisional
Probab=83.50 E-value=0.73 Score=35.49 Aligned_cols=19 Identities=37% Similarity=0.441 Sum_probs=16.0
Q ss_pred eeecCCCchHHHHHHHcCc
Q psy4141 2 KKISRSGCKIKALRAKTNT 20 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga 20 (353)
+||||+|.+|++||.--.+
T Consensus 44 rVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 44 KVIGRGGRTATALRTVVAA 62 (77)
T ss_pred ceeCCCCchHHHHHHHHHH
Confidence 6999999999999965444
No 195
>KOG4445|consensus
Probab=83.31 E-value=0.46 Score=45.42 Aligned_cols=45 Identities=24% Similarity=0.599 Sum_probs=33.8
Q ss_pred cccccccccccc---cEEeCCCCHhhhHHhHHHHhcc-----------------------CCCCCCcccccc
Q psy4141 301 RQCYLCNDREVT---HALIPCGHNFFCSECAERTCDF-----------------------DRTCPMCRVPVN 346 (353)
Q Consensus 301 ~~C~IC~~~~~~---~~llpCgH~~fC~~C~~~~~~~-----------------------~~~CP~Cr~~i~ 346 (353)
..|+||+--+.+ ....+|-|. |...|+.+++.. ...||+||.+|.
T Consensus 116 gqCvICLygfa~~~~ft~T~C~Hy-~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~ 186 (368)
T KOG4445|consen 116 GQCVICLYGFASSPAFTVTACDHY-MHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK 186 (368)
T ss_pred CceEEEEEeecCCCceeeehhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence 568888876654 335799999 999999887651 236999999874
No 196
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=83.13 E-value=0.72 Score=35.42 Aligned_cols=16 Identities=38% Similarity=0.567 Sum_probs=14.4
Q ss_pred eeecCCCchHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAK 17 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~ 17 (353)
+||||+|.+|++||.-
T Consensus 43 kvIGk~GRti~AIRTl 58 (76)
T COG1837 43 KVIGKQGRTIQAIRTL 58 (76)
T ss_pred ceecCCChhHHHHHHH
Confidence 6999999999999954
No 197
>PHA03096 p28-like protein; Provisional
Probab=82.76 E-value=0.75 Score=44.17 Aligned_cols=43 Identities=14% Similarity=0.125 Sum_probs=30.8
Q ss_pred cccccccccccc--------cEEeCCCCHhhhHHhHHHHhcc---C---CCCCCcccc
Q psy4141 301 RQCYLCNDREVT--------HALIPCGHNFFCSECAERTCDF---D---RTCPMCRVP 344 (353)
Q Consensus 301 ~~C~IC~~~~~~--------~~llpCgH~~fC~~C~~~~~~~---~---~~CP~Cr~~ 344 (353)
..|-||++.... ..+-.|-|. ||..|+..|... . +.||.|+..
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~-fc~~ci~~wr~~~~~~e~~~~c~~~~~~ 235 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHE-FNIFCIKIWMTESLYKETEPENRRLNTV 235 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcH-HHHHHHHHHHHhhhhcccCccccchhhH
Confidence 689999997532 234579999 999999988765 3 345555443
No 198
>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=82.44 E-value=3.4 Score=44.09 Aligned_cols=36 Identities=33% Similarity=0.374 Sum_probs=31.5
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
.+-+|.|-.+.-|.||||+|.++++|-++||=.-.+
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~ 128 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKV 128 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeE
Confidence 557888989999999999999999999999966543
No 199
>KOG0827|consensus
Probab=82.18 E-value=0.78 Score=45.37 Aligned_cols=28 Identities=32% Similarity=0.929 Sum_probs=24.1
Q ss_pred CCCCHhhhHHhHHHHhcc---CCCCCCccccc
Q psy4141 317 PCGHNFFCSECAERTCDF---DRTCPMCRVPV 345 (353)
Q Consensus 317 pCgH~~fC~~C~~~~~~~---~~~CP~Cr~~i 345 (353)
.|||. |...|+.+|.+. .+.||+|+..+
T Consensus 25 ~cGhi-fh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 25 TCGHI-FHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred chhhH-HHHHHHHHHHccCCccCCCCceeecc
Confidence 59999 999999999998 35899999443
No 200
>PRK03818 putative transporter; Validated
Probab=81.67 E-value=9.8 Score=40.01 Aligned_cols=111 Identities=17% Similarity=0.254 Sum_probs=67.8
Q ss_pred CchHHHHHHHcCceEEe-----------cCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCC
Q psy4141 8 GCKIKALRAKTNTYIKT-----------PVRG----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS 72 (353)
Q Consensus 8 G~~Ik~I~~~Tga~I~i-----------p~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~ 72 (353)
|.++++++......+.+ |..+ +.+++.+.|++++++++...+-...+.. .
T Consensus 218 GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~~~~------------~--- 282 (552)
T PRK03818 218 GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEVDTS------------L--- 282 (552)
T ss_pred CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCccCcc------------c---
Confidence 77899988876654442 2221 3478999999999877765543211100 0
Q ss_pred CCCCCCcceEEEEEecCCCccceeccCChHHHHH--HHHhCceEE-cCCC--------C----CCCeEEEEcCHHHHHHH
Q psy4141 73 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRI--QHQTNTYIV-TPSR--------D----KEPVFEVTGAPDSVEIA 137 (353)
Q Consensus 73 ~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~I--q~~Tga~I~-ip~~--------~----~e~~v~I~G~~e~V~~A 137 (353)
...+ .......+.+|.. .++|| +|+++ +++.|+.|. +... + ..+.+.+.|+++++++.
T Consensus 283 ~~~~-~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l 355 (552)
T PRK03818 283 STRG-TDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGRPEAIDAV 355 (552)
T ss_pred cccC-cceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEECHHHHHHH
Confidence 0000 1124455555554 67766 77877 577888873 3211 1 13589999999999997
Q ss_pred HHH
Q psy4141 138 RQE 140 (353)
Q Consensus 138 ~~~ 140 (353)
.+.
T Consensus 356 ~~~ 358 (552)
T PRK03818 356 ANV 358 (552)
T ss_pred HHH
Confidence 774
No 201
>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=80.83 E-value=1.6 Score=35.64 Aligned_cols=31 Identities=26% Similarity=0.563 Sum_probs=25.8
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhCc
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNT 112 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga 112 (353)
.++|.|-...-|.|||++|++|++|++....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 3677777888999999999999999877643
No 202
>KOG0825|consensus
Probab=80.24 E-value=1.7 Score=46.58 Aligned_cols=51 Identities=20% Similarity=0.333 Sum_probs=34.5
Q ss_pred Ccccccccccccc----cEEeC---CCCHhhhHHhHHHHhcc------CCCCCCcccccccceec
Q psy4141 300 SRQCYLCNDREVT----HALIP---CGHNFFCSECAERTCDF------DRTCPMCRVPVNQAMRI 351 (353)
Q Consensus 300 ~~~C~IC~~~~~~----~~llp---CgH~~fC~~C~~~~~~~------~~~CP~Cr~~i~~~~ri 351 (353)
...|.+|...+.. .-..| |+|. +|..|+..|..+ ...|++|..-|..+-|+
T Consensus 96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~-~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~ 159 (1134)
T KOG0825|consen 96 SDTSPVCEKEHSPDVDSSNICPVQTHVEN-QCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC 159 (1134)
T ss_pred ccccchhheecCCcccccCcCchhhhhhh-hhhHHHHHHHHHhhccccccccccHHHHhhhhhhh
Confidence 3556666555544 11234 9999 999999999876 34688888766655443
No 203
>KOG4185|consensus
Probab=79.72 E-value=1 Score=43.09 Aligned_cols=31 Identities=32% Similarity=0.899 Sum_probs=26.6
Q ss_pred EEeCCCCHhhhHHhHHHHhcc-CCCCCCccccc
Q psy4141 314 ALIPCGHNFFCSECAERTCDF-DRTCPMCRVPV 345 (353)
Q Consensus 314 ~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i 345 (353)
..+.|||. +|..|+..+... ...||.||.+.
T Consensus 23 ~~l~c~h~-~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 23 RVLKCGHT-ICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred cccccCce-ehHhHHHHHhcCceeeccCCCCcc
Confidence 34569999 999999999887 67899999974
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=79.19 E-value=1.5 Score=30.82 Aligned_cols=43 Identities=26% Similarity=0.468 Sum_probs=20.3
Q ss_pred cccccccccccccEE-eCCCCHhhhHH---hHHHHhcc-CCCCCCcccc
Q psy4141 301 RQCYLCNDREVTHAL-IPCGHNFFCSE---CAERTCDF-DRTCPMCRVP 344 (353)
Q Consensus 301 ~~C~IC~~~~~~~~l-lpCgH~~fC~~---C~~~~~~~-~~~CP~Cr~~ 344 (353)
+.|++.+.+...++. ..|.|. -|.+ -+...... ...||+|.++
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 579999999888886 689998 5532 12222222 5689999864
No 205
>KOG4369|consensus
Probab=78.68 E-value=0.76 Score=51.22 Aligned_cols=54 Identities=20% Similarity=0.149 Sum_probs=46.1
Q ss_pred eeecCCCchHHHHHHHcCceEEecC----CCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPV----RGEEPVFVVTGRKEDVARAKREILSAADH 55 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~----~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~ 55 (353)
++||++|.+|+.+|.-||+.|.+.. ...||.+.+.|+++.+.-|...|.-++.+
T Consensus 1353 RVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1353 RVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred hhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeec
Confidence 6899999999999999999999764 23578899999999999998888766543
No 206
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=78.49 E-value=3 Score=36.88 Aligned_cols=35 Identities=11% Similarity=0.128 Sum_probs=28.7
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
..+-+.|.... |.-|||+|.+|+++++..|-+|.+
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~Vev 95 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRV 95 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEE
Confidence 34456666666 999999999999999999988853
No 207
>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=78.10 E-value=2.6 Score=32.78 Aligned_cols=28 Identities=18% Similarity=0.400 Sum_probs=23.2
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHh
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~T 110 (353)
.++.|....-|.+||++|++|++|++.-
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 5566666888999999999999987664
No 208
>KOG3161|consensus
Probab=77.17 E-value=1.1 Score=47.01 Aligned_cols=39 Identities=26% Similarity=0.658 Sum_probs=30.5
Q ss_pred CCCccccccccccc----ccEEeCCCCHhhhHHhHHHHhccCCCCC
Q psy4141 298 SGSRQCYLCNDREV----THALIPCGHNFFCSECAERTCDFDRTCP 339 (353)
Q Consensus 298 ~~~~~C~IC~~~~~----~~~llpCgH~~fC~~C~~~~~~~~~~CP 339 (353)
.+-..|.||+..+. .++.+-|||. .|..|++.+.+ ..||
T Consensus 9 ~~~l~c~ic~n~f~~~~~~Pvsl~cght-ic~~c~~~lyn--~scp 51 (861)
T KOG3161|consen 9 VLLLLCDICLNLFVVQRLEPVSLQCGHT-ICGHCVQLLYN--ASCP 51 (861)
T ss_pred HHHhhchHHHHHHHHHhcCcccccccch-HHHHHHHhHhh--ccCC
Confidence 34578999977653 5667889999 99999999875 4566
No 209
>PRK01064 hypothetical protein; Provisional
Probab=75.12 E-value=1.9 Score=33.22 Aligned_cols=16 Identities=44% Similarity=0.594 Sum_probs=14.2
Q ss_pred eeecCCCchHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAK 17 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~ 17 (353)
++|||+|.+|++||.-
T Consensus 43 ~vIGk~G~~i~air~l 58 (78)
T PRK01064 43 KIIGKEGRTIKAIRTL 58 (78)
T ss_pred EEECCCCccHHHHHHH
Confidence 5899999999999964
No 210
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=75.01 E-value=12 Score=34.26 Aligned_cols=36 Identities=22% Similarity=0.370 Sum_probs=31.2
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
..+.+.|.....|.|||+.|+++..||-.++..+.-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 566788888889999999999999999999887753
No 211
>KOG1940|consensus
Probab=74.55 E-value=1.2 Score=42.45 Aligned_cols=45 Identities=27% Similarity=0.611 Sum_probs=36.1
Q ss_pred cccccccccc----cccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 301 RQCYLCNDRE----VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 301 ~~C~IC~~~~----~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
.-|++|.+.. ..+..++|||. .-..|.+......-.||+|.+ +..
T Consensus 159 ~ncPic~e~l~~s~~~~~~~~CgH~-~h~~cf~e~~~~~y~CP~C~~-~~d 207 (276)
T KOG1940|consen 159 FNCPICKEYLFLSFEDAGVLKCGHY-MHSRCFEEMICEGYTCPICSK-PGD 207 (276)
T ss_pred CCCchhHHHhccccccCCccCcccc-hHHHHHHHHhccCCCCCcccc-hHH
Confidence 3499999863 45566899999 779999998877889999988 443
No 212
>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=72.76 E-value=3 Score=29.89 Aligned_cols=21 Identities=24% Similarity=0.363 Sum_probs=18.4
Q ss_pred eeecCCCchHHHHHHHcCceE
Q psy4141 2 KKISRSGCKIKALRAKTNTYI 22 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I 22 (353)
.+|||+|++|+.|+..++-.+
T Consensus 38 ~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 38 LVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred eEECCCCccHHHHHHHHHHHc
Confidence 489999999999999988655
No 213
>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=72.28 E-value=4.5 Score=38.12 Aligned_cols=30 Identities=20% Similarity=0.331 Sum_probs=23.9
Q ss_pred eEEEEEecC-CCccceeccCChHHHHHHHHh
Q psy4141 81 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 81 ~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~T 110 (353)
+...|.|.. .+-+.|||++|++||+|....
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 455677776 667999999999999987654
No 214
>KOG2114|consensus
Probab=71.90 E-value=1.9 Score=46.64 Aligned_cols=46 Identities=24% Similarity=0.596 Sum_probs=35.6
Q ss_pred Cccccccccccccc-EEeCCCCHhhhHHhHHHHhccCCCCCCcccccccce
Q psy4141 300 SRQCYLCNDREVTH-ALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM 349 (353)
Q Consensus 300 ~~~C~IC~~~~~~~-~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~ 349 (353)
...|..|-...--| |...|||. |...|+.+ ....||-|+......+
T Consensus 840 ~skCs~C~~~LdlP~VhF~CgHs-yHqhC~e~---~~~~CP~C~~e~~~~m 886 (933)
T KOG2114|consen 840 VSKCSACEGTLDLPFVHFLCGHS-YHQHCLED---KEDKCPKCLPELRGVM 886 (933)
T ss_pred eeeecccCCccccceeeeecccH-HHHHhhcc---CcccCCccchhhhhhH
Confidence 46899998776544 45799999 99999993 4689999998655443
No 215
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=71.77 E-value=4.1 Score=37.86 Aligned_cols=30 Identities=27% Similarity=0.484 Sum_probs=25.4
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHh
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T 110 (353)
..++|.|....=|.|||++|+.|++|++..
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 457788888999999999999999886544
No 216
>KOG1812|consensus
Probab=70.65 E-value=1.8 Score=43.36 Aligned_cols=34 Identities=24% Similarity=0.832 Sum_probs=24.7
Q ss_pred Cccccccccccccc----EEeCCCCHhhhHHhHHHHhcc
Q psy4141 300 SRQCYLCNDREVTH----ALIPCGHNFFCSECAERTCDF 334 (353)
Q Consensus 300 ~~~C~IC~~~~~~~----~llpCgH~~fC~~C~~~~~~~ 334 (353)
..+|.||+...... ....|+|. ||..|..++.+.
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~-fC~~C~k~~iev 183 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHR-FCKDCVKQHIEV 183 (384)
T ss_pred cccCccCccccccHhhhHHHhcccch-hhhHHhHHHhhh
Confidence 46899999332221 24579999 999999988763
No 217
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=70.52 E-value=3 Score=31.33 Aligned_cols=23 Identities=26% Similarity=0.390 Sum_probs=18.3
Q ss_pred eecCCCchHHHHHHHc-CceEEec
Q psy4141 3 KISRSGCKIKALRAKT-NTYIKTP 25 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~T-ga~I~ip 25 (353)
.||++|.+||.|.++. |-+|++=
T Consensus 22 ~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 22 CIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp HH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred cCccccHHHHHHHHHhCCCeEEEE
Confidence 5899999999999999 8777754
No 218
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=70.02 E-value=2.9 Score=45.18 Aligned_cols=49 Identities=18% Similarity=0.567 Sum_probs=38.7
Q ss_pred CCCccccccccc--ccccEEeCCCCH----hhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141 298 SGSRQCYLCNDR--EVTHALIPCGHN----FFCSECAERTCDF--DRTCPMCRVPVN 346 (353)
Q Consensus 298 ~~~~~C~IC~~~--~~~~~llpCgH~----~fC~~C~~~~~~~--~~~CP~Cr~~i~ 346 (353)
++++.|.||... .-++.+.||... ....+|+-.|... ...|-+|+.++.
T Consensus 10 ~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 10 EDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred ccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 456899999875 457888899753 2567999999987 778999998763
No 219
>COG1159 Era GTPase [General function prediction only]
Probab=69.86 E-value=5.6 Score=38.34 Aligned_cols=30 Identities=27% Similarity=0.501 Sum_probs=23.9
Q ss_pred eEEEEEecC-CCccceeccCChHHHHHHHHh
Q psy4141 81 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 81 ~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~T 110 (353)
+...+.|+. .+-|-||||+|++||+|....
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 445577877 678999999999999986544
No 220
>PRK15494 era GTPase Era; Provisional
Probab=68.76 E-value=5.6 Score=38.98 Aligned_cols=30 Identities=20% Similarity=0.381 Sum_probs=23.5
Q ss_pred eEEEEEecC-CCccceeccCChHHHHHHHHh
Q psy4141 81 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 81 ~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~T 110 (353)
+...|.|.. .+-+.|||++|++||+|..+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 445677877 667999999999999986543
No 221
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=68.06 E-value=2.5 Score=29.22 Aligned_cols=39 Identities=28% Similarity=0.738 Sum_probs=24.5
Q ss_pred cccccccccc--cEEeCCCCH----hhhHHhHHHHhcc--CCCCCCc
Q psy4141 303 CYLCNDREVT--HALIPCGHN----FFCSECAERTCDF--DRTCPMC 341 (353)
Q Consensus 303 C~IC~~~~~~--~~llpCgH~----~fC~~C~~~~~~~--~~~CP~C 341 (353)
|.||++.... +...||.-. .....|+.+|... ...|++|
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 7889887543 456788733 1456899999886 5678887
No 222
>PRK00089 era GTPase Era; Reviewed
Probab=68.06 E-value=6.1 Score=37.45 Aligned_cols=30 Identities=23% Similarity=0.490 Sum_probs=22.9
Q ss_pred eEEEEEecC-CCccceeccCChHHHHHHHHh
Q psy4141 81 VTIEVRVPY-KVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 81 ~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~T 110 (353)
+...|.|.. .+-+.|||++|++||+|....
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 445566766 667999999999999986554
No 223
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=67.78 E-value=6.9 Score=34.38 Aligned_cols=61 Identities=16% Similarity=0.304 Sum_probs=39.9
Q ss_pred CCcceEEEEEecC--CCccceeccCChHHHHHHHHhCceEEc--------CCC------CCCCeEEEEcCHHHHHHHHHH
Q psy4141 77 VPGHVTIEVRVPY--KVVGLVVGPKGATIKRIQHQTNTYIVT--------PSR------DKEPVFEVTGAPDSVEIARQE 140 (353)
Q Consensus 77 ~~~~~t~~v~VP~--~~vG~IIGkgG~tIk~Iq~~Tga~I~i--------p~~------~~e~~v~I~G~~e~V~~A~~~ 140 (353)
+|+.....+.|-. .++|+=||- -+|+++|||.|+- ++. +..+++.+.|....+.+++.+
T Consensus 82 ~p~l~~~~~~i~~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f 156 (162)
T COG0490 82 LPGLIIEWFKIEAGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRF 156 (162)
T ss_pred cccchheeeeeecCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHH
Confidence 4444555555433 455555543 3689999999942 111 234699999999999999887
Q ss_pred HH
Q psy4141 141 IE 142 (353)
Q Consensus 141 I~ 142 (353)
..
T Consensus 157 ~~ 158 (162)
T COG0490 157 LL 158 (162)
T ss_pred hh
Confidence 64
No 224
>KOG1067|consensus
Probab=66.84 E-value=4.5 Score=42.16 Aligned_cols=51 Identities=16% Similarity=0.137 Sum_probs=39.5
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHHHHHhh
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADH 55 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~~~ 55 (353)
++||.+|.++|+|+.+||+.-.+. ++.+-+..-++...++|++.|..++..
T Consensus 610 ~lIGp~G~~~kki~~EtGai~~vD---e~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 610 TLIGPGGVLKKKIEVETGAISQVD---EGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred eeecCccceeeeEeeeccceeeec---CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 589999999999999999544433 334444456788899999999888764
No 225
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=66.29 E-value=6.3 Score=35.61 Aligned_cols=33 Identities=21% Similarity=0.345 Sum_probs=27.1
Q ss_pred EEEecCCCccceeccCChHHHHHHHHhCceEEc
Q psy4141 84 EVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVT 116 (353)
Q Consensus 84 ~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~i 116 (353)
...+-.+.+|..||++|.+|+.|+++.|=+|.+
T Consensus 79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred EeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 334445889999999999999999999977753
No 226
>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=65.75 E-value=6.3 Score=26.70 Aligned_cols=38 Identities=18% Similarity=0.572 Sum_probs=21.2
Q ss_pred cccccccccccEEeC---CCCHhhhHHhHHHHhccC--CCCCCc
Q psy4141 303 CYLCNDREVTHALIP---CGHNFFCSECAERTCDFD--RTCPMC 341 (353)
Q Consensus 303 C~IC~~~~~~~~llp---CgH~~fC~~C~~~~~~~~--~~CP~C 341 (353)
|.+|.+.......=+ |+=. +...|+..++... ..||.|
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 567777666655533 6656 7779999999883 379987
No 227
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=65.37 E-value=15 Score=36.28 Aligned_cols=58 Identities=17% Similarity=0.276 Sum_probs=47.7
Q ss_pred CCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHH--HHHHh-hhC
Q psy4141 89 YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIE--SHIIR-RTG 150 (353)
Q Consensus 89 ~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~--~~i~~-r~g 150 (353)
.+..-.|.|..|.+++.|.+.+|+.|... ...++|+|+...|+.|...+. +++.. +.|
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~r----G~~~~i~g~~~~v~~A~~~l~~l~~~~~~~~g 83 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVAR----GEAVRIIGARPLVDVATRVLLTLELLAEVRRG 83 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeC----CceEEEEechHHHHHHHHHHhHHHHHHHHhcc
Confidence 46677899999999999999999999833 346999999879999999888 55555 444
No 228
>KOG1423|consensus
Probab=64.94 E-value=6 Score=38.55 Aligned_cols=35 Identities=26% Similarity=0.445 Sum_probs=27.8
Q ss_pred ceEEEEEecC-CCccceeccCChHHHHHHHHhCceE
Q psy4141 80 HVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYI 114 (353)
Q Consensus 80 ~~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I 114 (353)
.+..++.+|. ++...||||||..|++|-++-+-.+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~dL 362 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANEDL 362 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHHH
Confidence 3566788898 6678999999999999987765443
No 229
>KOG2068|consensus
Probab=64.55 E-value=4.9 Score=39.13 Aligned_cols=46 Identities=30% Similarity=0.736 Sum_probs=35.4
Q ss_pred cccccccccc----cccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 301 RQCYLCNDRE----VTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 301 ~~C~IC~~~~----~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
..|++|.+.. .+.+-.||+|. .|..|+..++.....||.||.+...
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~-~~l~~~~t~~~~~~~~~~~rk~~~~ 299 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFR-LCLFCHKTISDGDGRCPGCRKPYER 299 (327)
T ss_pred CCCCCCCCccccccccccccccccc-chhhhhhcccccCCCCCccCCcccc
Confidence 4577777743 22223579999 9999999999999999999987654
No 230
>KOG3799|consensus
Probab=61.93 E-value=2.1 Score=36.35 Aligned_cols=42 Identities=33% Similarity=0.791 Sum_probs=27.5
Q ss_pred CCCcccccccccccccEEeCCCCHhhhHHhHHHHhcc------------CCCCCCcccc
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF------------DRTCPMCRVP 344 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~------------~~~CP~Cr~~ 344 (353)
.++.+|.||+... ..--|||+ |.+|-.+.|.. ...|-+|+..
T Consensus 63 ~ddatC~IC~KTK---FADG~GH~--C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 63 GDDATCGICHKTK---FADGCGHN--CSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred CcCcchhhhhhcc---cccccCcc--cchhhhhHHHhcCCeeeeccCceEEeccCCcHH
Confidence 5678999998632 22469997 56666665543 2358888764
No 231
>KOG2817|consensus
Probab=61.83 E-value=5.6 Score=39.62 Aligned_cols=44 Identities=20% Similarity=0.477 Sum_probs=34.2
Q ss_pred cccccccccc---cccEEeCCCCHhhhHHhHHHHhcc-C--CCCCCccccc
Q psy4141 301 RQCYLCNDRE---VTHALIPCGHNFFCSECAERTCDF-D--RTCPMCRVPV 345 (353)
Q Consensus 301 ~~C~IC~~~~---~~~~llpCgH~~fC~~C~~~~~~~-~--~~CP~Cr~~i 345 (353)
..|+|=.+.- --|+.+.|||. .|.+-+.++... . ..||.|....
T Consensus 335 F~CPVlKeqtsdeNPPm~L~CGHV-ISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 335 FICPVLKEQTSDENPPMMLICGHV-ISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred eecccchhhccCCCCCeeeeccce-ecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 5677765543 34677899999 999999999887 3 6899997654
No 232
>KOG3268|consensus
Probab=60.87 E-value=5.9 Score=35.27 Aligned_cols=49 Identities=22% Similarity=0.544 Sum_probs=36.4
Q ss_pred CCCcccccccccccccEE-------eCCCCHhhhHHhHHHHhcc---C--------CCCCCccccccc
Q psy4141 298 SGSRQCYLCNDREVTHAL-------IPCGHNFFCSECAERTCDF---D--------RTCPMCRVPVNQ 347 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~l-------lpCgH~~fC~~C~~~~~~~---~--------~~CP~Cr~~i~~ 347 (353)
.+-..|-||+...-+... ..||.. |..-|+..|+.. . ..||.|..+++-
T Consensus 163 d~~~~cgicyayqldGTipDqtCdN~qCgkp-FHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial 229 (234)
T KOG3268|consen 163 DELGACGICYAYQLDGTIPDQTCDNIQCGKP-FHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL 229 (234)
T ss_pred hhhhcccceeeeecCCccccccccccccCCc-HHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence 344678888876544332 579998 999999999886 1 269999998864
No 233
>KOG3970|consensus
Probab=59.70 E-value=7.7 Score=35.83 Aligned_cols=44 Identities=25% Similarity=0.549 Sum_probs=33.9
Q ss_pred cccccccccc--cccEEeCCCCHhhhHHhHHHHhcc--------CCCCCCccccc
Q psy4141 301 RQCYLCNDRE--VTHALIPCGHNFFCSECAERTCDF--------DRTCPMCRVPV 345 (353)
Q Consensus 301 ~~C~IC~~~~--~~~~llpCgH~~fC~~C~~~~~~~--------~~~CP~Cr~~i 345 (353)
--|..|.... .+.+-+-|-|. |...|+..+... ...||.|..+|
T Consensus 51 pNC~LC~t~La~gdt~RLvCyhl-fHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTRLVCYHL-FHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CCCceeCCccccCcceeehhhhh-HHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 4577777654 35667899999 999999998775 23799998775
No 234
>KOG1952|consensus
Probab=58.92 E-value=5.9 Score=43.06 Aligned_cols=48 Identities=23% Similarity=0.553 Sum_probs=36.4
Q ss_pred CCCcccccccccccccE--E--eCCCCHhhhHHhHHHHhcc-------CCCCCCcccccc
Q psy4141 298 SGSRQCYLCNDREVTHA--L--IPCGHNFFCSECAERTCDF-------DRTCPMCRVPVN 346 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~--l--lpCgH~~fC~~C~~~~~~~-------~~~CP~Cr~~i~ 346 (353)
...-+|+||++...... . -.|-|. |...|++.|... .+.||.|+....
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhV-FHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHV-FHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhh-hhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 35689999999864332 2 358899 999999999875 468999985443
No 235
>KOG1960|consensus
Probab=58.86 E-value=16 Score=36.59 Aligned_cols=142 Identities=16% Similarity=0.049 Sum_probs=83.0
Q ss_pred CCCchHHHHHHHcCceEEecCC---------C--Cc-CeEEEec-CHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCC
Q psy4141 6 RSGCKIKALRAKTNTYIKTPVR---------G--EE-PVFVVTG-RKEDVARAKREILSAADHFSALRASRKSGALSPLS 72 (353)
Q Consensus 6 k~G~~Ik~I~~~Tga~I~ip~~---------~--e~-~vv~I~G-~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~ 72 (353)
..|.....|+..+|+.|-+-.+ + ++ -+..|.+ ++|-+.+|...|--.+.....+...++.-+-....
T Consensus 111 TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~~~~~~n~~~V~i~~~~s 190 (531)
T KOG1960|consen 111 TRGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQDVEINNVRNVYILVRAS 190 (531)
T ss_pred ccchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceeecccccccceEEEeecCC
Confidence 3688899999999999984211 1 22 3667776 56778888888864443322111111100000000
Q ss_pred C---------------CCCCCcceEEEEEecC-CCccceeccCChHHHHHHHHhCceEEcCCC---------C---CCC-
Q psy4141 73 P---------------PTGVPGHVTIEVRVPY-KVVGLVVGPKGATIKRIQHQTNTYIVTPSR---------D---KEP- 123 (353)
Q Consensus 73 ~---------------~~~~~~~~t~~v~VP~-~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~---------~---~e~- 123 (353)
+ ...-+.+.-+.+.+|. .+-+.+=|++-.++..++.++++++.+..+ . .|+
T Consensus 191 P~~~i~~~V~~~~f~~G~~Y~~k~~v~~~~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPM 270 (531)
T KOG1960|consen 191 PLSEIENKVGVQLFSKGRYYPNKALATDKDPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPM 270 (531)
T ss_pred chhhhccccccccccccccchhheecccCCcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccccccCCce
Confidence 0 0000112333344555 344667778888999999999988755322 1 233
Q ss_pred eEEEE-cCHHHHHHHHHHHHHHHHh
Q psy4141 124 VFEVT-GAPDSVEIARQEIESHIIR 147 (353)
Q Consensus 124 ~v~I~-G~~e~V~~A~~~I~~~i~~ 147 (353)
-|.|+ |.++.+.+|++++.++.+.
T Consensus 271 YI~i~h~~~~g~~~A~r~~~nl~~~ 295 (531)
T KOG1960|consen 271 YIFSTHGNGNGENGAPRRKWNLEEK 295 (531)
T ss_pred eEEeecCCchhhccchhHHHhHHHH
Confidence 35555 4799999999999988765
No 236
>PRK04972 putative transporter; Provisional
Probab=58.59 E-value=69 Score=33.77 Aligned_cols=113 Identities=17% Similarity=0.188 Sum_probs=63.8
Q ss_pred CchHHHHHHHcCceEEe-----------cCCC----CcCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCC
Q psy4141 8 GCKIKALRAKTNTYIKT-----------PVRG----EEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLS 72 (353)
Q Consensus 8 G~~Ik~I~~~Tga~I~i-----------p~~~----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~ 72 (353)
|.+|+++.......+.+ |..+ ..+++.+.|++++++++.+.+ .+-++. ...
T Consensus 230 Gktl~el~~~~~~~v~I~~I~R~g~~~~p~~dt~L~~GDiL~V~G~~e~l~~l~~~~-~lg~e~-------------~~~ 295 (558)
T PRK04972 230 GKNLRELGIYRQTGCYIERIRRNGILANPDGDAVLQMGDEIALVGYPDAHARLDPSF-RNGKEV-------------FDR 295 (558)
T ss_pred CCCHHHHHhhcCCCEEEEEEEECCEEecCCCCCEeCCCCEEEEEECHHHHHHHHHhh-cCCCcc-------------cCc
Confidence 78899988766433331 2221 347888999999887665443 000110 000
Q ss_pred CCCCCCcceEEEEEecCCCccceeccCChHHHHHH-HHhCceEE-cCCC--------C----CCCeEEEEcCHHHHHHHH
Q psy4141 73 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQ-HQTNTYIV-TPSR--------D----KEPVFEVTGAPDSVEIAR 138 (353)
Q Consensus 73 ~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq-~~Tga~I~-ip~~--------~----~e~~v~I~G~~e~V~~A~ 138 (353)
...+.+ .....+.+|.+ .++|| +|+++. ++.|+.|. +... + ..+++.+.|+++++++..
T Consensus 296 ~~~~~~-~~~E~vVv~~s---~liGk---TL~eL~~r~~gv~Vl~I~R~g~~~~~~~~~~L~~GD~LlVvG~~~~i~~l~ 368 (558)
T PRK04972 296 DLLDMR-IVTEEIVVKNH---NAVGK---RLSQLKLTDHGCFLNRVIRSQIEMPIDDNVVLNKGDVLQVSGDARRVKTIA 368 (558)
T ss_pred cccCcc-eEEEEEEEcCc---ccCCC---CHHHhCCccCCeEEEEEecCCcccCCCCCCEecCCCEEEEEECHHHHHHHH
Confidence 000111 13445555543 67766 677773 23788873 3221 1 135899999999999876
Q ss_pred HHH
Q psy4141 139 QEI 141 (353)
Q Consensus 139 ~~I 141 (353)
+.+
T Consensus 369 ~~l 371 (558)
T PRK04972 369 DRI 371 (558)
T ss_pred HHh
Confidence 655
No 237
>KOG1815|consensus
Probab=58.38 E-value=6.8 Score=39.98 Aligned_cols=36 Identities=28% Similarity=0.556 Sum_probs=30.6
Q ss_pred CCCcccccccccccc-cEEeCCCCHhhhHHhHHHHhcc
Q psy4141 298 SGSRQCYLCNDREVT-HALIPCGHNFFCSECAERTCDF 334 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~-~~llpCgH~~fC~~C~~~~~~~ 334 (353)
.....|-||.+.... .+.+.|+|. ||..|...+...
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 345789999999985 777899999 999999997765
No 238
>KOG1645|consensus
Probab=58.30 E-value=5.1 Score=40.09 Aligned_cols=32 Identities=31% Similarity=0.710 Sum_probs=27.1
Q ss_pred EEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141 314 ALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN 346 (353)
Q Consensus 314 ~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~ 346 (353)
+.+.|||. |-..|+++|..+ ...||.|....+
T Consensus 23 vsl~cghl-Fgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 23 VSLQCGHL-FGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred eeeccccc-ccHHHHHHHHhhhhhhhCcccCChhH
Confidence 45789999 999999999976 668999987654
No 239
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=58.08 E-value=22 Score=33.23 Aligned_cols=48 Identities=25% Similarity=0.256 Sum_probs=34.9
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHH-HHHHHHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKE-DVARAKREILSA 52 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e-~v~~Ak~~I~~i 52 (353)
++|||+|..++.|.++|++.|-+-.+| .|-|.+..+ ....|...|..+
T Consensus 159 Rvig~~~sm~~~l~~~~~~~I~VG~NG---~IWV~~~~~~~e~~~~~aI~~i 207 (239)
T COG1097 159 RVIGKKGSMLNMLKEKTGCEIIVGQNG---RIWVDGENESLEELAIEAIRKI 207 (239)
T ss_pred eEecCCCcHHHHhhhhcCeEEEEecCC---EEEecCCCcchHHHHHHHHHHH
Confidence 589999999999999999999987654 355666555 344455555444
No 240
>KOG0298|consensus
Probab=57.03 E-value=3.6 Score=46.62 Aligned_cols=46 Identities=28% Similarity=0.617 Sum_probs=38.7
Q ss_pred CCccccccccccc-ccEEeCCCCHhhhHHhHHHHhccCCCCCCccccc
Q psy4141 299 GSRQCYLCNDREV-THALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345 (353)
Q Consensus 299 ~~~~C~IC~~~~~-~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i 345 (353)
+...|.+|.+... .....-|||- +|..|...|......||+|....
T Consensus 1152 ~~~~c~ic~dil~~~~~I~~cgh~-~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIAGCGHE-PCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred cccchHHHHHHHHhcCCeeeechh-HhhhHHHHHHHHhccCcchhhhh
Confidence 4468999999876 4556789998 99999999999999999997543
No 241
>CHL00048 rps3 ribosomal protein S3
Probab=54.16 E-value=14 Score=34.11 Aligned_cols=31 Identities=23% Similarity=0.228 Sum_probs=25.5
Q ss_pred eEEEEEecCCCccceeccCChHHHHHHHHhC
Q psy4141 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTN 111 (353)
Q Consensus 81 ~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tg 111 (353)
...+|.|-...-|.|||++|++|++|++.-.
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 3467777778889999999999999987663
No 242
>KOG3053|consensus
Probab=53.56 E-value=8.3 Score=36.33 Aligned_cols=52 Identities=23% Similarity=0.542 Sum_probs=37.3
Q ss_pred CCCCCCcccccccccccccEE----eCCCCH----hhhHHhHHHHhcc--------CCCCCCcccccc
Q psy4141 295 GSISGSRQCYLCNDREVTHAL----IPCGHN----FFCSECAERTCDF--------DRTCPMCRVPVN 346 (353)
Q Consensus 295 ~~~~~~~~C~IC~~~~~~~~l----lpCgH~----~fC~~C~~~~~~~--------~~~CP~Cr~~i~ 346 (353)
.+.+.++.|-||+....+..+ -||... +....|+.+|... ...||.|+....
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 345678999999998765443 477621 2677999999875 236999987653
No 243
>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=53.36 E-value=4.2 Score=30.72 Aligned_cols=21 Identities=24% Similarity=0.460 Sum_probs=17.6
Q ss_pred eecCCCchHHHHHHHcCceEE
Q psy4141 3 KISRSGCKIKALRAKTNTYIK 23 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ 23 (353)
|||++|++|++|+.+.+-.+.
T Consensus 39 vIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 39 VIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp HHTGGGHHHHHHHHHHHHHHH
T ss_pred hHHhhhHHHHHHHHHHHHHHh
Confidence 799999999999988766554
No 244
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=53.25 E-value=8 Score=39.64 Aligned_cols=28 Identities=29% Similarity=0.332 Sum_probs=24.5
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGE 29 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e 29 (353)
++|||+|.+|++|+++.|..|++-..++
T Consensus 499 ~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 499 KVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred HHhhcccchHHHHHHHhCCceEEEEccc
Confidence 5799999999999999999999865543
No 245
>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=53.08 E-value=9.1 Score=29.04 Aligned_cols=22 Identities=23% Similarity=0.291 Sum_probs=18.0
Q ss_pred eeecCCCchHHHHHHHcCceEE
Q psy4141 2 KKISRSGCKIKALRAKTNTYIK 23 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ 23 (353)
.+|||+|+++++||-=++..++
T Consensus 37 ~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 37 LLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred eEECCCCccHHHHHHHHHHHHh
Confidence 4899999999999977665555
No 246
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=52.95 E-value=1.6e+02 Score=25.97 Aligned_cols=95 Identities=16% Similarity=0.205 Sum_probs=55.5
Q ss_pred eEEEec--CHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHH
Q psy4141 32 VFVVTG--RKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQ 109 (353)
Q Consensus 32 vv~I~G--~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~ 109 (353)
-++++| +.+++..|.+.+.++++++... .. ..+ ...++-.|-.-..++=| .+++|...
T Consensus 57 KivitGaks~~~~~~a~~~~~~~L~~~g~~-----------~~---~~~-~~~v~NIvas~~l~~~i-----~L~~la~~ 116 (174)
T cd00652 57 KMVITGAKSEEDAKLAARKYARILQKLGFP-----------VE---KFP-EFKVQNIVASCDLGFPI-----RLEELALK 116 (174)
T ss_pred EEEEEecCCHHHHHHHHHHHHHHHHHcCCC-----------cc---ccC-ceEEEEEEEEEECCCcc-----cHHHHHhh
Confidence 366677 6899999999999998875210 00 001 13333333222233333 46777666
Q ss_pred hCceEEcCCC----------C--------CCCeEEEEcC--HHHHHHHHHHHHHHHH
Q psy4141 110 TNTYIVTPSR----------D--------KEPVFEVTGA--PDSVEIARQEIESHII 146 (353)
Q Consensus 110 Tga~I~ip~~----------~--------~e~~v~I~G~--~e~V~~A~~~I~~~i~ 146 (353)
.+-++....+ + ....|+|+|. ++.+++|.+.|..+|.
T Consensus 117 ~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i~~~L~ 173 (174)
T cd00652 117 HPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPILK 173 (174)
T ss_pred hhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 5533322111 0 1247999995 7899999999988775
No 247
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=52.08 E-value=15 Score=33.56 Aligned_cols=30 Identities=17% Similarity=0.370 Sum_probs=23.9
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHhCc
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNT 112 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga 112 (353)
..+.|-...-|.+||++|++|+++++.-.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 556666688899999999999998876543
No 248
>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=50.91 E-value=17 Score=33.01 Aligned_cols=30 Identities=23% Similarity=0.376 Sum_probs=25.0
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhC
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTN 111 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tg 111 (353)
..+|.|....-|.|||++|+.|++|++.-.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 467788888889999999999999876653
No 249
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=50.76 E-value=11 Score=33.27 Aligned_cols=23 Identities=26% Similarity=0.304 Sum_probs=20.4
Q ss_pred eecCCCchHHHHHHHcCceEEec
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTP 25 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip 25 (353)
.|||+|.+|+++++..|-+|.+-
T Consensus 74 aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 74 PIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred cccccchHHHHHHHHhCCcEEEE
Confidence 48999999999999999888754
No 250
>KOG2034|consensus
Probab=49.70 E-value=9.2 Score=41.86 Aligned_cols=29 Identities=31% Similarity=0.775 Sum_probs=13.3
Q ss_pred ccccccccccccc--EEeCCCCHhhhHHhHHH
Q psy4141 301 RQCYLCNDREVTH--ALIPCGHNFFCSECAER 330 (353)
Q Consensus 301 ~~C~IC~~~~~~~--~llpCgH~~fC~~C~~~ 330 (353)
..|-+|....... .+.||||. |...|+.+
T Consensus 818 d~C~~C~~~ll~~pF~vf~CgH~-FH~~Cl~~ 848 (911)
T KOG2034|consen 818 DSCDHCGRPLLIKPFYVFPCGHC-FHRDCLIR 848 (911)
T ss_pred cchHHhcchhhcCcceeeeccch-HHHHHHHH
Confidence 4455555443221 12355555 55555544
No 251
>KOG3039|consensus
Probab=49.67 E-value=11 Score=35.24 Aligned_cols=36 Identities=22% Similarity=0.121 Sum_probs=31.0
Q ss_pred CCCCCcccccccccccccEEeCCCCHhhhHHhHHHHh
Q psy4141 296 SISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTC 332 (353)
Q Consensus 296 ~~~~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~ 332 (353)
+...-..|..|+....+++..|=||. ||++|+-.+.
T Consensus 39 siK~FdcCsLtLqPc~dPvit~~Gyl-fdrEaILe~i 74 (303)
T KOG3039|consen 39 SIKPFDCCSLTLQPCRDPVITPDGYL-FDREAILEYI 74 (303)
T ss_pred ccCCcceeeeecccccCCccCCCCee-eeHHHHHHHH
Confidence 34455789999999999999999999 9999998764
No 252
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=49.21 E-value=18 Score=33.47 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=24.9
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHhC
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTN 111 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tg 111 (353)
.++|.|-...-|.|||++|..|++|++.-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 367777778889999999999999876654
No 253
>PRK13764 ATPase; Provisional
Probab=48.63 E-value=10 Score=40.25 Aligned_cols=28 Identities=29% Similarity=0.327 Sum_probs=24.5
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCC
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGE 29 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e 29 (353)
++|||+|.+|++|+++.|..|++-...+
T Consensus 494 ~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 494 KVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred HHhccCcchHHHHHHHhCCceEEEEccc
Confidence 4799999999999999999999865543
No 254
>KOG3899|consensus
Probab=48.50 E-value=12 Score=35.97 Aligned_cols=28 Identities=25% Similarity=0.634 Sum_probs=20.2
Q ss_pred CCCHhhhHHhHHHHhcc-------------CCCCCCcccccc
Q psy4141 318 CGHNFFCSECAERTCDF-------------DRTCPMCRVPVN 346 (353)
Q Consensus 318 CgH~~fC~~C~~~~~~~-------------~~~CP~Cr~~i~ 346 (353)
|.-. -|.+|+.+|... ...||+||+.+.
T Consensus 325 crp~-wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc 365 (381)
T KOG3899|consen 325 CRPL-WCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC 365 (381)
T ss_pred cccH-HHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence 3344 678999987642 457999999874
No 255
>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=48.40 E-value=10 Score=29.35 Aligned_cols=23 Identities=17% Similarity=0.361 Sum_probs=18.0
Q ss_pred eecCCCchHHHHHHHcCceEEec
Q psy4141 3 KISRSGCKIKALRAKTNTYIKTP 25 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I~ip 25 (353)
|||++|.+|++|+++-.....++
T Consensus 44 vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 44 VLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred EECCCchhHHHHHHHHHHHhCCC
Confidence 78999999999888766666554
No 256
>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=48.23 E-value=25 Score=25.38 Aligned_cols=41 Identities=24% Similarity=0.390 Sum_probs=29.3
Q ss_pred CchHHH--HHHHcCceEE---------ecCCC----CcCeEEEecCHHHHHHHHHH
Q psy4141 8 GCKIKA--LRAKTNTYIK---------TPVRG----EEPVFVVTGRKEDVARAKRE 48 (353)
Q Consensus 8 G~~Ik~--I~~~Tga~I~---------ip~~~----e~~vv~I~G~~e~v~~Ak~~ 48 (353)
|.+|+. +++.+++.|- .|..+ +..++.+.|.+++++++.+.
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~ 69 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFREL 69 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHH
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHh
Confidence 667888 7787788877 22222 34688889999999887765
No 257
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=48.15 E-value=44 Score=32.54 Aligned_cols=80 Identities=13% Similarity=0.122 Sum_probs=58.5
Q ss_pred ccceeccCChHHHHHHHHhCc--eEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHHHhhhCCCCccCccccCCCCccchH
Q psy4141 92 VGLVVGPKGATIKRIQHQTNT--YIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSADL 169 (353)
Q Consensus 92 vG~IIGkgG~tIk~Iq~~Tga--~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i~~r~g~~~~~~d~~~~~~~~~~~~ 169 (353)
-..|+|---+.|+++-++.+- .|.+.+.+....+.|+|.+++|++|...+.+.=..|.=.......||...-++..+-
T Consensus 133 Maav~gl~~e~v~~~~~~~~~~~~v~iaN~N~~~QiVIsG~~~ale~a~~~~~~~g~kr~i~l~vs~pfHs~lm~pa~~~ 212 (310)
T COG0331 133 MAAVLGLDDEQVEKACEEAAQGTVVEIANYNSPGQIVISGTKEALEKAAEILKEAGAKRAIPLPVSGPFHSPLMKPAADE 212 (310)
T ss_pred HHHHcCCCHHHHHHHHHHhccCCeEEEeeeCCCCcEEEECCHHHHHHHHHHHHHhhhhhhcccCCCchhhhhhhHHHHHH
Confidence 346778788899998888864 355555555578999999999999999888766444333444568888877776666
Q ss_pred HH
Q psy4141 170 LA 171 (353)
Q Consensus 170 ~~ 171 (353)
+.
T Consensus 213 ~~ 214 (310)
T COG0331 213 LA 214 (310)
T ss_pred HH
Confidence 55
No 258
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=48.13 E-value=45 Score=32.95 Aligned_cols=45 Identities=16% Similarity=0.156 Sum_probs=39.3
Q ss_pred eeecCCCchHHHHHHHcCceEEecCCCCcCeEEEecCHHHHHHHHHHHH
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREIL 50 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~ 50 (353)
.+.|..+.+++.|++.+|+.|... ...+.|.|....++.|.+.+.
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 468999999999999999999866 456889999889999998887
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=44.89 E-value=5.4 Score=38.20 Aligned_cols=50 Identities=20% Similarity=0.352 Sum_probs=26.7
Q ss_pred CcccccccccccccEEeCC-----CCHhhhHHhHHHHhccCCCCCCccccccccee
Q psy4141 300 SRQCYLCNDREVTHALIPC-----GHNFFCSECAERTCDFDRTCPMCRVPVNQAMR 350 (353)
Q Consensus 300 ~~~C~IC~~~~~~~~llpC-----gH~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~r 350 (353)
...|+||-....-.++..= .|. +|..|...|......||.|-..-...+.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L-~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~ 226 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYL-HCSLCGTEWRFVRIKCPYCGNTDHEKLE 226 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEE-EETTT--EEE--TTS-TTT---SS-EEE
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEE-EcCCCCCeeeecCCCCcCCCCCCCccee
Confidence 3689999999888777654 465 9999999997778899999765444333
No 260
>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=44.59 E-value=14 Score=34.40 Aligned_cols=23 Identities=22% Similarity=0.741 Sum_probs=20.4
Q ss_pred hhHHhHHHHhccCCCCCCccccc
Q psy4141 323 FCSECAERTCDFDRTCPMCRVPV 345 (353)
Q Consensus 323 fC~~C~~~~~~~~~~CP~Cr~~i 345 (353)
.|..|-+.+....+.||+|++.-
T Consensus 196 ~C~sC~qqIHRNAPiCPlCK~Ks 218 (230)
T PF10146_consen 196 TCQSCHQQIHRNAPICPLCKAKS 218 (230)
T ss_pred hhHhHHHHHhcCCCCCccccccc
Confidence 89999999988899999998754
No 261
>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=43.20 E-value=17 Score=26.29 Aligned_cols=42 Identities=29% Similarity=0.506 Sum_probs=30.0
Q ss_pred ChHHHH--HHHHhCceEEc---------CCCC----CCCeEEEEcCHHHHHHHHHHH
Q psy4141 100 GATIKR--IQHQTNTYIVT---------PSRD----KEPVFEVTGAPDSVEIARQEI 141 (353)
Q Consensus 100 G~tIk~--Iq~~Tga~I~i---------p~~~----~e~~v~I~G~~e~V~~A~~~I 141 (353)
|++|++ +.+.+++.|.- |..+ ..+.+.|.|.+++++++.+++
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 447888 78888998842 2221 235899999999999987754
No 262
>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=41.67 E-value=77 Score=28.01 Aligned_cols=57 Identities=18% Similarity=0.303 Sum_probs=43.8
Q ss_pred CcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHH
Q psy4141 78 PGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESH 144 (353)
Q Consensus 78 ~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~ 144 (353)
++..+++|.++...+- +.+++|.+-.|+-|.+ +.+..|.|-|..+.|.+|.+.+.-+
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Ef---ee~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEF---EEDDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEe---cCCcEEEEeccHHHHHHHHHHHHHH
Confidence 3456778888776653 3567888888988877 4445799999999999999987543
No 263
>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=41.30 E-value=1.8 Score=32.64 Aligned_cols=41 Identities=24% Similarity=0.615 Sum_probs=22.4
Q ss_pred cccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
..|+.|....... . +|. .|..|...+ .....||-|..++..
T Consensus 2 ~~CP~C~~~L~~~---~-~~~-~C~~C~~~~-~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 2 NTCPKCQQELEWQ---G-GHY-HCEACQKDY-KKEAFCPDCGQPLEV 42 (70)
T ss_dssp -B-SSS-SBEEEE---T-TEE-EETTT--EE-EEEEE-TTT-SB-EE
T ss_pred CcCCCCCCccEEe---C-CEE-ECccccccc-eecccCCCcccHHHH
Confidence 5789998763322 1 677 999998875 226789999887754
No 264
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=38.38 E-value=33 Score=31.51 Aligned_cols=28 Identities=29% Similarity=0.579 Sum_probs=23.7
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHh
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~T 110 (353)
++|.|-...-|.|||++|+.|++|++.-
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 5677777778999999999999998655
No 265
>KOG4185|consensus
Probab=37.33 E-value=6.5 Score=37.53 Aligned_cols=44 Identities=23% Similarity=0.618 Sum_probs=34.6
Q ss_pred Cccccccccccc-c-----cEEeC--------CCCHhhhHHhHHHHhcc-CCCCCCcccc
Q psy4141 300 SRQCYLCNDREV-T-----HALIP--------CGHNFFCSECAERTCDF-DRTCPMCRVP 344 (353)
Q Consensus 300 ~~~C~IC~~~~~-~-----~~llp--------CgH~~fC~~C~~~~~~~-~~~CP~Cr~~ 344 (353)
...|.+|...+. + +.++. |+|. .|..|+..+..+ ...||.|+..
T Consensus 207 ~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~ht-lc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 207 EKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHT-LCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHH-HHhcchHHHHHHhhhcCCcccce
Confidence 477999988765 2 22345 9999 999999999877 6789999864
No 266
>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=37.07 E-value=1.2e+02 Score=23.41 Aligned_cols=47 Identities=15% Similarity=0.251 Sum_probs=36.7
Q ss_pred hHHHHHHHcCceEEecCC-C-----CcCeEEEecCHHHHHHHHHHHHHHHhhh
Q psy4141 10 KIKALRAKTNTYIKTPVR-G-----EEPVFVVTGRKEDVARAKREILSAADHF 56 (353)
Q Consensus 10 ~Ik~I~~~Tga~I~ip~~-~-----e~~vv~I~G~~e~v~~Ak~~I~~i~~~~ 56 (353)
-++++-++.+..++.... | .+.++.+.|+..++..|.+.++.+++++
T Consensus 35 ~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~~ 87 (88)
T PF02749_consen 35 EAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQRL 87 (88)
T ss_dssp HHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHHh
Confidence 355666777888886533 2 2579999999999999999999998875
No 267
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=36.70 E-value=2.8e+02 Score=24.31 Aligned_cols=115 Identities=17% Similarity=0.220 Sum_probs=67.5
Q ss_pred HHHHHHHcCceEE----ecCCCCc---CeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCC-cceE
Q psy4141 11 IKALRAKTNTYIK----TPVRGEE---PVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP-GHVT 82 (353)
Q Consensus 11 Ik~I~~~Tga~I~----ip~~~e~---~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~t 82 (353)
|-.+-.+.|..|. .|...++ -++++.|+.+.+++..++|.++++-..- .. . ...+.+. .-.-
T Consensus 19 I~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~~~~~~i~qi~kQl~KLidV~~V----~~----~--~~~~~v~rEl~L 88 (161)
T PRK11895 19 VAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTSGDEQVIEQITKQLNKLIDVLKV----VD----L--TEEAHVERELAL 88 (161)
T ss_pred HHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEECCHHHHHHHHHHHhccccEEEE----Ee----c--CCcchhheEEEE
Confidence 4445557777775 2222111 2466679999999999999888663211 00 0 0000010 0111
Q ss_pred EEEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHH
Q psy4141 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESH 144 (353)
Q Consensus 83 ~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~ 144 (353)
++|..+.. ....|.+|-+.++++|.--.. +.-+++++|.++.++.-.+++...
T Consensus 89 iKv~~~~~--------~r~~i~~i~~~f~a~ivdv~~-~~~~iE~tG~~~ki~~~~~~l~~~ 141 (161)
T PRK11895 89 VKVRASGE--------NRAEILRLADIFRAKIVDVTP-ESLTIEVTGDSDKIDAFIDLLRPY 141 (161)
T ss_pred EEEECCcc--------cHHHHHHHHHHhCCEEEEecC-CEEEEEEeCCHHHHHHHHHHhhhc
Confidence 22333222 245788999999999963322 233799999999999888888653
No 268
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=36.23 E-value=29 Score=34.58 Aligned_cols=27 Identities=30% Similarity=0.465 Sum_probs=23.8
Q ss_pred CCccceeccCChHHHHHHHHh-CceEEc
Q psy4141 90 KVVGLVVGPKGATIKRIQHQT-NTYIVT 116 (353)
Q Consensus 90 ~~vG~IIGkgG~tIk~Iq~~T-ga~I~i 116 (353)
+-+|..||++|.+|+.|+++. |=+|.+
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdi 272 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDI 272 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEE
Confidence 678999999999999999888 777754
No 269
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=36.20 E-value=73 Score=28.51 Aligned_cols=50 Identities=22% Similarity=0.317 Sum_probs=32.3
Q ss_pred ccCChHHHHHHHHh----CceE--EcCCCCCCC-eEEEEcCHHHHHH-HHHHHHHHHH
Q psy4141 97 GPKGATIKRIQHQT----NTYI--VTPSRDKEP-VFEVTGAPDSVEI-ARQEIESHII 146 (353)
Q Consensus 97 GkgG~tIk~Iq~~T----ga~I--~ip~~~~e~-~v~I~G~~e~V~~-A~~~I~~~i~ 146 (353)
|++-+.|.+|.+.. |+++ +++..+..| ++|+.|.++.|.. |..++...++
T Consensus 12 gR~~~~ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~vG~p~~v~~a~~~~~~~A~~ 69 (178)
T PF07837_consen 12 GRDKEVIEAIAKAARNVPGVKLLDVFSDADYNRSVITLVGEPEAVAEAAFAAIRKALE 69 (178)
T ss_dssp SSSHHHHHHHHHHCCTSTTEEEEEEEEETTTTEEEEEEEE-HHHHHHHHHHHHHHHHC
T ss_pred CCCHHHHHHHHHHHHcCCCCEEEecCCCCCCCCCeEEEeeChHHHHHHHHHHHHHHHH
Confidence 67777788876654 5677 344445554 7999999998866 4555555433
No 270
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=35.79 E-value=6.8 Score=22.90 Aligned_cols=22 Identities=32% Similarity=0.940 Sum_probs=12.5
Q ss_pred hhHHhHHHHhccCCCCCCcccc
Q psy4141 323 FCSECAERTCDFDRTCPMCRVP 344 (353)
Q Consensus 323 fC~~C~~~~~~~~~~CP~Cr~~ 344 (353)
||..|-..+......||.|-.+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 3555555554445667777554
No 271
>KOG2807|consensus
Probab=35.69 E-value=21 Score=34.86 Aligned_cols=44 Identities=27% Similarity=0.691 Sum_probs=32.0
Q ss_pred CCcccccccccccccE---EeCCCCHhhhHHhHHHHhccCCCCCCccc
Q psy4141 299 GSRQCYLCNDREVTHA---LIPCGHNFFCSECAERTCDFDRTCPMCRV 343 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~---llpCgH~~fC~~C~~~~~~~~~~CP~Cr~ 343 (353)
..+.|..|.+...... --.|.|. ||.+|-.-+-+..-.||-|..
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 3456999955543322 2468898 999998888777889999963
No 272
>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=34.02 E-value=16 Score=29.12 Aligned_cols=37 Identities=32% Similarity=0.893 Sum_probs=28.2
Q ss_pred CCcccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCcccc
Q psy4141 299 GSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 344 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~ 344 (353)
....|..|.+..+..+. |. .|..|+... ..|+-|..+
T Consensus 54 ~p~kC~~C~qktVk~AY----h~-iC~~Ca~~~----~vCaKC~k~ 90 (92)
T PF10217_consen 54 QPKKCNKCQQKTVKHAY----HV-ICDPCAKEL----KVCAKCGKP 90 (92)
T ss_pred CCccccccccchHHHHH----HH-HHHHHHHhh----ccCcccCCC
Confidence 34678888877665543 88 999999996 889999654
No 273
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=33.66 E-value=35 Score=26.34 Aligned_cols=47 Identities=21% Similarity=0.609 Sum_probs=19.2
Q ss_pred Ccccccccccccc----cEE---eCCCCHhhhHHhHHHHhcc-CCCCCCccccccc
Q psy4141 300 SRQCYLCNDREVT----HAL---IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQ 347 (353)
Q Consensus 300 ~~~C~IC~~~~~~----~~l---lpCgH~~fC~~C~~~~~~~-~~~CP~Cr~~i~~ 347 (353)
...|.||-+..-. -++ .-|+-- .|+.|..--... ...||.|+.+...
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 4689999886321 123 356665 899998755444 7899999987753
No 274
>COG2985 Predicted permease [General function prediction only]
Probab=33.60 E-value=1.4e+02 Score=31.10 Aligned_cols=89 Identities=19% Similarity=0.214 Sum_probs=57.4
Q ss_pred cCeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHH-H
Q psy4141 30 EPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQ-H 108 (353)
Q Consensus 30 ~~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq-~ 108 (353)
...+.+.|.++.++++...+-+.++... ..+ ..-.+.++.|.++ .+.|| +|++|. .
T Consensus 253 Gd~l~lVG~~~~l~r~~~~~G~evd~~~----------------~~~-~~l~~~rivVtn~---~vlGk---~l~~L~~~ 309 (544)
T COG2985 253 GDELHLVGYPDALARLDLRIGKEVDDRL----------------LLD-TRLRTERVVVTNE---NVLGK---RLRDLNLT 309 (544)
T ss_pred CcEEEecCChHHHHHHHHhccccccccc----------------ccc-cceeeEEEEeech---hhhcc---chhhcCcc
Confidence 4678888999999999855544443210 001 1236788889887 45555 556654 3
Q ss_pred HhCceEE-cCCC--------C----CCCeEEEEcCHHHHHHHHHHH
Q psy4141 109 QTNTYIV-TPSR--------D----KEPVFEVTGAPDSVEIARQEI 141 (353)
Q Consensus 109 ~Tga~I~-ip~~--------~----~e~~v~I~G~~e~V~~A~~~I 141 (353)
+.|+.|. +... + ..+++.+.|.++.|+.+.+.+
T Consensus 310 ~~g~~I~Ri~Ra~iElv~~~d~~lq~gDvl~vvg~~~~v~~~~~~l 355 (544)
T COG2985 310 EYGVFINRINRADIELVASDDVVLQKGDVLQVVGRARRVKAVADVL 355 (544)
T ss_pred ccceeeeehhhcCccccCCcchhhhhcceeeeccchHHHHHHHHHh
Confidence 3777773 2221 1 236899999999999877766
No 275
>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=33.41 E-value=35 Score=33.72 Aligned_cols=27 Identities=37% Similarity=0.551 Sum_probs=23.8
Q ss_pred CCccceeccCChHHHHHHHHh-CceEEc
Q psy4141 90 KVVGLVVGPKGATIKRIQHQT-NTYIVT 116 (353)
Q Consensus 90 ~~vG~IIGkgG~tIk~Iq~~T-ga~I~i 116 (353)
+-+|..||++|.+|+.|.++. |=+|.+
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idi 270 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDI 270 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEE
Confidence 678999999999999999988 777754
No 276
>KOG0824|consensus
Probab=33.06 E-value=12 Score=36.07 Aligned_cols=51 Identities=25% Similarity=0.656 Sum_probs=40.9
Q ss_pred CCCCCcccccccccccccEEe-CCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 296 SISGSRQCYLCNDREVTHALI-PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 296 ~~~~~~~C~IC~~~~~~~~ll-pCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
....+..|.+|+.....+.+. -|+|. ||..|...+.+....||.|+..+..
T Consensus 101 ~~~~~~~~~~~~g~l~vpt~~qg~w~q-f~~~~p~~~~~~~~~~~d~~~~~~p 152 (324)
T KOG0824|consen 101 FQQDHDICYICYGKLTVPTRIQGCWHQ-FCYVCPKSNFAMGNDCPDCRGKISP 152 (324)
T ss_pred ccCCccceeeeeeeEEecccccCceee-eeecCCchhhhhhhccchhhcCcCc
Confidence 345678999999998777665 49999 9999998887778889988876554
No 277
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.89 E-value=26 Score=26.57 Aligned_cols=23 Identities=35% Similarity=0.885 Sum_probs=16.7
Q ss_pred CHhhhHHhHHHHhccCCCCCCccccc
Q psy4141 320 HNFFCSECAERTCDFDRTCPMCRVPV 345 (353)
Q Consensus 320 H~~fC~~C~~~~~~~~~~CP~Cr~~i 345 (353)
|. ||..|+...+ ...||-|--.+
T Consensus 29 cT-FCadCae~~l--~g~CPnCGGel 51 (84)
T COG3813 29 CT-FCADCAENRL--HGLCPNCGGEL 51 (84)
T ss_pred ee-hhHhHHHHhh--cCcCCCCCchh
Confidence 44 9999999643 57899885443
No 278
>KOG4451|consensus
Probab=32.85 E-value=27 Score=32.39 Aligned_cols=28 Identities=18% Similarity=0.551 Sum_probs=22.1
Q ss_pred CCCHhhhHHhHHHHhccCCCCCCcccccc
Q psy4141 318 CGHNFFCSECAERTCDFDRTCPMCRVPVN 346 (353)
Q Consensus 318 CgH~~fC~~C~~~~~~~~~~CP~Cr~~i~ 346 (353)
=-.. .|..|-+++....+.||+|+..-.
T Consensus 247 ppMK-~ClsChqqIHRNAPiCPlCKaKsR 274 (286)
T KOG4451|consen 247 PPMK-VCLSCHQQIHRNAPICPLCKAKSR 274 (286)
T ss_pred Ccch-HHHHHHHHHhcCCCCCcchhhccc
Confidence 3344 889999999888999999987543
No 279
>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=32.83 E-value=31 Score=24.38 Aligned_cols=25 Identities=28% Similarity=0.812 Sum_probs=16.8
Q ss_pred CCCCHhhhHHhHHHHhccCCCCCCcc
Q psy4141 317 PCGHNFFCSECAERTCDFDRTCPMCR 342 (353)
Q Consensus 317 pCgH~~fC~~C~~~~~~~~~~CP~Cr 342 (353)
.|.+. ||.+|-.=+-+..-.||-|.
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 99999877766678999984
No 280
>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=32.81 E-value=8.9 Score=37.23 Aligned_cols=44 Identities=23% Similarity=0.403 Sum_probs=32.8
Q ss_pred CcccccccccccccEEeC----CC--CHhhhHHhHHHHhccCCCCCCcccc
Q psy4141 300 SRQCYLCNDREVTHALIP----CG--HNFFCSECAERTCDFDRTCPMCRVP 344 (353)
Q Consensus 300 ~~~C~IC~~~~~~~~llp----Cg--H~~fC~~C~~~~~~~~~~CP~Cr~~ 344 (353)
...|+||-....-.++.. =| |. +|..|...|......||.|-..
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL-~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYL-SCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEE-EcCCCCCcccccCccCCCCCCC
Confidence 468999999886554433 22 44 8999999987778889999764
No 281
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=31.94 E-value=3.7e+02 Score=23.89 Aligned_cols=104 Identities=21% Similarity=0.299 Sum_probs=60.3
Q ss_pred eEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCC-cceEEEEEecCCCccceeccCChHHHHHHHHh
Q psy4141 32 VFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVP-GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 32 vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T 110 (353)
.+++.|..+.+++-.+++.++++...-. .. ...+.+. .-.-++|.++. ....-|.+|-+.+
T Consensus 47 TIvv~~~~~~ieqL~kQL~KLidVl~V~---~~-------~~~~~v~rEl~LiKv~~~~--------~~r~ei~~~~~~f 108 (174)
T CHL00100 47 TMVVPGDDRTIEQLTKQLYKLVNILKVQ---DI-------TNIPCVERELMLIKINVNS--------QTRPEILEIAQIF 108 (174)
T ss_pred EEEEECCHHHHHHHHHHHHHHhHhhEEE---ec-------CCccceeeEEEEEEEecCC--------cCHHHHHHHHHHh
Confidence 4666787666777777777776643210 00 0000000 00111222222 2456688999999
Q ss_pred CceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHH-HHh--hhCCCCc
Q psy4141 111 NTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESH-IIR--RTGSCVT 154 (353)
Q Consensus 111 ga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~-i~~--r~g~~~~ 154 (353)
+++|.--..+. -+|+++|.++.++.-.+++... |.+ |+|..--
T Consensus 109 ~a~ivdv~~~~-~~ie~tG~~~ki~a~~~~l~~~gi~e~~RtG~val 154 (174)
T CHL00100 109 RAKVVDLSEES-LILEVTGDPGKIVAIEQLLEKFGIIEIARTGKIAL 154 (174)
T ss_pred CCEEEEecCCE-EEEEEcCCHHHHHHHHHHhhhcCCEEEEccCceeE
Confidence 99996333222 4799999999999988888763 222 6665443
No 282
>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=31.76 E-value=42 Score=27.26 Aligned_cols=42 Identities=24% Similarity=0.715 Sum_probs=26.4
Q ss_pred cccccccccccccEE--------eCC---CCHhhhHHhHHHHhcc---------CCCCCCccc
Q psy4141 301 RQCYLCNDREVTHAL--------IPC---GHNFFCSECAERTCDF---------DRTCPMCRV 343 (353)
Q Consensus 301 ~~C~IC~~~~~~~~l--------lpC---gH~~fC~~C~~~~~~~---------~~~CP~Cr~ 343 (353)
..|..|.....+... -.| .=. ||..|+...+.. ...||.||-
T Consensus 8 ~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~-fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 8 KTCHQCRQKTLDFKTICTGHWKNSSCRGCRGK-FCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCchhhcCCCCCCceEcCCCCCCCCCccCcce-ehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 457777765543331 234 434 999997765542 467999986
No 283
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=31.46 E-value=34 Score=34.96 Aligned_cols=27 Identities=22% Similarity=0.434 Sum_probs=23.8
Q ss_pred CCccceeccCChHHHHHHHHh-CceEEc
Q psy4141 90 KVVGLVVGPKGATIKRIQHQT-NTYIVT 116 (353)
Q Consensus 90 ~~vG~IIGkgG~tIk~Iq~~T-ga~I~i 116 (353)
+-+|..||++|.+|+.|.++. |=+|.+
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDV 304 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDV 304 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEE
Confidence 668999999999999999998 777753
No 284
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=30.90 E-value=16 Score=35.61 Aligned_cols=44 Identities=16% Similarity=0.331 Sum_probs=32.7
Q ss_pred CCcccccccccccccEEeC---C--CCHhhhHHhHHHHhccCCCCCCccc
Q psy4141 299 GSRQCYLCNDREVTHALIP---C--GHNFFCSECAERTCDFDRTCPMCRV 343 (353)
Q Consensus 299 ~~~~C~IC~~~~~~~~llp---C--gH~~fC~~C~~~~~~~~~~CP~Cr~ 343 (353)
....|+||-....-.++.. = .|. +|..|...|......||.|-.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL-~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYL-HCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEE-EcCCCCCcccccCccCCCCCC
Confidence 4578999999886554422 2 244 899999998777888999975
No 285
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=29.85 E-value=3.8e+02 Score=23.37 Aligned_cols=115 Identities=17% Similarity=0.191 Sum_probs=64.7
Q ss_pred HHHHHHHcCceEE----ecCCCCc--C-eEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEE
Q psy4141 11 IKALRAKTNTYIK----TPVRGEE--P-VFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTI 83 (353)
Q Consensus 11 Ik~I~~~Tga~I~----ip~~~e~--~-vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~ 83 (353)
|-.+-.+-|..|. .|...++ + ++++.|+.+.+++..++|.++++-..- ... ...+.+. ..-.
T Consensus 18 I~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~~d~~~i~qi~kQl~Kli~V~~V----~~~------~~~~~v~-rEl~ 86 (157)
T TIGR00119 18 VAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVVGDDKVLEQITKQLNKLVDVIKV----SDL------TESAIVE-RELC 86 (157)
T ss_pred HHHHHHhCCceEEEEEEeecCCCCEEEEEEEEECCHHHHHHHHHHHhcCccEEEE----Eec------CCCccee-eEEE
Confidence 3344556777775 2322111 2 456668888888888888777653211 000 0000000 0111
Q ss_pred EEEecCCCccceeccCChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHH
Q psy4141 84 EVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIES 143 (353)
Q Consensus 84 ~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~ 143 (353)
-+.|.... .....|.+|-+.++++|.--.. +.-+++++|.++.++.-.+++..
T Consensus 87 LiKv~~~~------~~r~~i~~i~~~f~a~ivdv~~-~~~~ie~tG~~~ki~~~~~~l~~ 139 (157)
T TIGR00119 87 LVKVSAPG------EGRDEIIRLTNIFRGRIVDVSP-DSYTVEVTGDSDKIDAFLELLRP 139 (157)
T ss_pred EEEEECCc------cCHHHHHHHHHHhCCEEEEecC-CEEEEEEcCCHHHHHHHHHHhhh
Confidence 12222211 3456788999999999963322 22379999999999988888765
No 286
>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=29.77 E-value=26 Score=24.59 Aligned_cols=39 Identities=21% Similarity=0.521 Sum_probs=23.6
Q ss_pred CcccccccccccccEEeCCCCHhhhHHhHHHHhcc--CCCCCCcccccc
Q psy4141 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDF--DRTCPMCRVPVN 346 (353)
Q Consensus 300 ~~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~--~~~CP~Cr~~i~ 346 (353)
...|+.|...+... . ++.-|....... ...||+|...+.
T Consensus 2 ~f~CP~C~~~~~~~-------~-L~~H~~~~H~~~~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 2 SFTCPYCGKGFSES-------S-LVEHCEDEHRSESKNVVCPICSSRVT 42 (54)
T ss_pred CcCCCCCCCccCHH-------H-HHHHHHhHCcCCCCCccCCCchhhhh
Confidence 46799998833322 1 444555554443 457999987654
No 287
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=29.73 E-value=34 Score=31.87 Aligned_cols=20 Identities=25% Similarity=0.468 Sum_probs=15.8
Q ss_pred eecCCCchHHHHHHHcCceE
Q psy4141 3 KISRSGCKIKALRAKTNTYI 22 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~I 22 (353)
||||+|.+|++|+++....+
T Consensus 65 VIGk~G~~I~~L~~~l~k~~ 84 (233)
T COG0092 65 VIGKKGSNIEKLRKELEKLF 84 (233)
T ss_pred eEcCCCccHHHHHHHHHHHh
Confidence 79999999999887654333
No 288
>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=29.64 E-value=1.5e+02 Score=21.96 Aligned_cols=32 Identities=25% Similarity=0.407 Sum_probs=23.2
Q ss_pred CceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHH
Q psy4141 111 NTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESH 144 (353)
Q Consensus 111 ga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~ 144 (353)
+.+|... +....+.|.|+++.+++.+++|..+
T Consensus 45 ~~~i~~d--~~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 45 SGRIVAD--ERTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTEEEEE--CTTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CeEEEEE--CCCCEEEEEeCHHHHHHHHHHHHHH
Confidence 3455433 3345799999999999999988654
No 289
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=29.30 E-value=98 Score=32.30 Aligned_cols=53 Identities=19% Similarity=0.299 Sum_probs=35.9
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHh----CceEEcCCCCCCCeEEEEcCHHHHH
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQT----NTYIVTPSRDKEPVFEVTGAPDSVE 135 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T----ga~I~ip~~~~e~~v~I~G~~e~V~ 135 (353)
.+-+..|..-++.|+|++......++++. ...|.|-... .+.+++-|-..-+.
T Consensus 498 NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~~~-~sI~~v~~~~~~I~ 554 (657)
T COG5166 498 NVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCPQS-TSIFTVDIYSDEIE 554 (657)
T ss_pred ceEEECCccCccchhcccccHHHHHhhhcccccccceEEcCCc-eEEEEEcccccHHH
Confidence 35677899999999999999988888665 4445444322 23677766544433
No 290
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=28.86 E-value=35 Score=33.24 Aligned_cols=43 Identities=21% Similarity=0.419 Sum_probs=32.5
Q ss_pred ccccccccc---ccccEEeCCCCHhhhHHhHHHHhcc---CCCCCCcccc
Q psy4141 301 RQCYLCNDR---EVTHALIPCGHNFFCSECAERTCDF---DRTCPMCRVP 344 (353)
Q Consensus 301 ~~C~IC~~~---~~~~~llpCgH~~fC~~C~~~~~~~---~~~CP~Cr~~ 344 (353)
..|+|=.+. +-.++.+.|||. .-.+-+.++... ...||.|...
T Consensus 337 FiCPVlKe~~t~ENpP~ml~CgHV-Iskeal~~LS~nG~~~FKCPYCP~~ 385 (396)
T COG5109 337 FICPVLKELCTDENPPVMLECGHV-ISKEALSVLSQNGVLSFKCPYCPEM 385 (396)
T ss_pred eeccccHhhhcccCCCeeeeccce-eeHHHHHHHhhcCcEEeeCCCCCcc
Confidence 567665543 345777899999 999999998776 5689999654
No 291
>KOG3113|consensus
Probab=28.85 E-value=41 Score=31.74 Aligned_cols=36 Identities=19% Similarity=0.361 Sum_probs=28.4
Q ss_pred cccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccccc
Q psy4141 309 REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347 (353)
Q Consensus 309 ~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i~~ 347 (353)
.+.-.++.+|||. |-..-++++. ...|++|.+.+..
T Consensus 124 ~~~F~~l~~CGcV-~SerAlKeik--as~C~~C~a~y~~ 159 (293)
T KOG3113|consen 124 KYRFCALRCCGCV-FSERALKEIK--ASVCHVCGAAYQE 159 (293)
T ss_pred eEEEEEEecccee-ccHHHHHHhh--hccccccCCcccc
Confidence 3455567899999 9888888874 5789999998754
No 292
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=28.47 E-value=37 Score=33.94 Aligned_cols=27 Identities=26% Similarity=0.410 Sum_probs=23.8
Q ss_pred CCccceeccCChHHHHHHHHh-CceEEc
Q psy4141 90 KVVGLVVGPKGATIKRIQHQT-NTYIVT 116 (353)
Q Consensus 90 ~~vG~IIGkgG~tIk~Iq~~T-ga~I~i 116 (353)
+-+|..||++|.+|+.|.++. |=+|.+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDv 278 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDC 278 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEE
Confidence 668999999999999999988 777754
No 293
>TIGR02024 FtcD glutamate formiminotransferase. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism.
Probab=28.43 E-value=1.7e+02 Score=28.43 Aligned_cols=50 Identities=22% Similarity=0.275 Sum_probs=32.2
Q ss_pred ccCChHHHHHHHHh----CceE--EcCCCCCCC-eEEEEcCHHHHHH-HHHHHHHHHH
Q psy4141 97 GPKGATIKRIQHQT----NTYI--VTPSRDKEP-VFEVTGAPDSVEI-ARQEIESHII 146 (353)
Q Consensus 97 GkgG~tIk~Iq~~T----ga~I--~ip~~~~e~-~v~I~G~~e~V~~-A~~~I~~~i~ 146 (353)
||+=+.|.+|.+.. |+++ .++..+..| ++|+.|.|+.|.. |..++...++
T Consensus 14 GR~~~vie~I~~a~~~~~gv~lld~~~D~d~NRsv~Tlvg~pe~v~eaa~~~~~~A~e 71 (298)
T TIGR02024 14 GRNKEVIEKIVDAIIKTDNVKLLDVDMDPDHNRSVITFVGEPECVVNAALKLAKKAAE 71 (298)
T ss_pred CCCHHHHHHHHHHHhcCCCcEEEeCCCCCCCCceEEEEecChHHHHHHHHHHHHHHHH
Confidence 56666676665444 7888 334444444 8999999998866 4555554333
No 294
>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=28.38 E-value=32 Score=27.97 Aligned_cols=21 Identities=24% Similarity=0.408 Sum_probs=17.1
Q ss_pred eeecCCCchHHHHHHHcCceE
Q psy4141 2 KKISRSGCKIKALRAKTNTYI 22 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I 22 (353)
.|||++|++|++|++.....+
T Consensus 74 ~vIG~~G~~i~~L~~~l~~~~ 94 (109)
T cd02412 74 IIIGKKGAGIEKLRKELQKLL 94 (109)
T ss_pred cccCCchHHHHHHHHHHHHHh
Confidence 379999999999998865543
No 295
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=27.94 E-value=58 Score=30.35 Aligned_cols=29 Identities=28% Similarity=0.571 Sum_probs=23.2
Q ss_pred EEEEEecCCCccceeccCChHHHHHHHHh
Q psy4141 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 82 t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T 110 (353)
.++|.|-...-|.|||++|..|++|++..
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 35666666777999999999999987665
No 296
>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=27.78 E-value=20 Score=35.90 Aligned_cols=33 Identities=30% Similarity=0.581 Sum_probs=0.0
Q ss_pred cccEEeCCCCHhhhHHhHHHHhc---cCCCCCCcccc
Q psy4141 311 VTHALIPCGHNFFCSECAERTCD---FDRTCPMCRVP 344 (353)
Q Consensus 311 ~~~~llpCgH~~fC~~C~~~~~~---~~~~CP~Cr~~ 344 (353)
.--+.+.|||. +=..=.-.-.. ....||+||..
T Consensus 302 qP~VYl~CGHV-hG~h~Wg~~~~~~~~~r~CPlCr~~ 337 (416)
T PF04710_consen 302 QPWVYLNCGHV-HGYHNWGQDSDRDPRSRTCPLCRQV 337 (416)
T ss_dssp -------------------------------------
T ss_pred Cceeeccccce-eeecccccccccccccccCCCcccc
Confidence 34467899997 33221111111 15789999874
No 297
>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=26.65 E-value=26 Score=24.60 Aligned_cols=11 Identities=36% Similarity=1.226 Sum_probs=5.8
Q ss_pred CCCCCcccccc
Q psy4141 336 RTCPMCRVPVN 346 (353)
Q Consensus 336 ~~CP~Cr~~i~ 346 (353)
..||+|..++.
T Consensus 21 ~~CPlC~r~l~ 31 (54)
T PF04423_consen 21 GCCPLCGRPLD 31 (54)
T ss_dssp EE-TTT--EE-
T ss_pred CcCCCCCCCCC
Confidence 38999999875
No 298
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=26.47 E-value=1.1e+02 Score=29.66 Aligned_cols=51 Identities=12% Similarity=0.154 Sum_probs=38.5
Q ss_pred eecCCCchHHHHHHHcCce--EEecCCCCcCeEEEecCHHHHHHHHHHHHHHH
Q psy4141 3 KISRSGCKIKALRAKTNTY--IKTPVRGEEPVFVVTGRKEDVARAKREILSAA 53 (353)
Q Consensus 3 IIGk~G~~Ik~I~~~Tga~--I~ip~~~e~~vv~I~G~~e~v~~Ak~~I~~i~ 53 (353)
|+|---+.|+++-++.+-. |.+-..+.+..++|+|.+++|++|...+.++-
T Consensus 136 v~gl~~e~v~~~~~~~~~~~~v~iaN~N~~~QiVIsG~~~ale~a~~~~~~~g 188 (310)
T COG0331 136 VLGLDDEQVEKACEEAAQGTVVEIANYNSPGQIVISGTKEALEKAAEILKEAG 188 (310)
T ss_pred HcCCCHHHHHHHHHHhccCCeEEEeeeCCCCcEEEECCHHHHHHHHHHHHHhh
Confidence 4454556788888887753 66666666688999999999999988886664
No 299
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=26.43 E-value=98 Score=23.33 Aligned_cols=43 Identities=21% Similarity=0.339 Sum_probs=30.4
Q ss_pred ChHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHH
Q psy4141 100 GATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIES 143 (353)
Q Consensus 100 G~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~ 143 (353)
-..|.+|-+.++++|+--..+ .-+|.++|+++.++...+++..
T Consensus 16 r~ei~~l~~~f~a~ivd~~~~-~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVSPD-SIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEETT-EEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHHhCCEEEEECCC-EEEEEEcCCHHHHHHHHHHhhh
Confidence 346778889999999633222 2379999999999988887754
No 300
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=26.01 E-value=46 Score=34.34 Aligned_cols=27 Identities=30% Similarity=0.429 Sum_probs=23.6
Q ss_pred CCccceeccCChHHHHHHHHh-CceEEc
Q psy4141 90 KVVGLVVGPKGATIKRIQHQT-NTYIVT 116 (353)
Q Consensus 90 ~~vG~IIGkgG~tIk~Iq~~T-ga~I~i 116 (353)
+-+|..||++|.+|+.|.++. |=+|.+
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idi 272 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDI 272 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEE
Confidence 568999999999999999888 788853
No 301
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.55 E-value=2e+02 Score=24.97 Aligned_cols=42 Identities=21% Similarity=0.241 Sum_probs=32.1
Q ss_pred hHHHHHHHHhCceEEcCCCCCCCeEEEEcCHHHHHHHHHHHHHHH
Q psy4141 101 ATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHI 145 (353)
Q Consensus 101 ~tIk~Iq~~Tga~I~ip~~~~e~~v~I~G~~e~V~~A~~~I~~~i 145 (353)
+.++.|.+-.|+-|.+. ..+.|.|-|..+.|.+|.+.|..+-
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 35566767777777654 3458999999999999999987653
No 302
>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=24.61 E-value=8.6 Score=24.09 Aligned_cols=23 Identities=39% Similarity=0.924 Sum_probs=11.3
Q ss_pred CHhhhHHhHHHHhcc----CCCCCCccc
Q psy4141 320 HNFFCSECAERTCDF----DRTCPMCRV 343 (353)
Q Consensus 320 H~~fC~~C~~~~~~~----~~~CP~Cr~ 343 (353)
|. ||..|-...... ...||.|..
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 55 777777665443 346888764
No 303
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.24 E-value=39 Score=29.52 Aligned_cols=27 Identities=33% Similarity=0.972 Sum_probs=21.5
Q ss_pred CHhhhHHhHHHHhccCCCCCCccccccccee
Q psy4141 320 HNFFCSECAERTCDFDRTCPMCRVPVNQAMR 350 (353)
Q Consensus 320 H~~fC~~C~~~~~~~~~~CP~Cr~~i~~~~r 350 (353)
+. ||..|-.... ..||-|..+|..-..
T Consensus 28 ~~-fC~kCG~~tI---~~Cp~C~~~IrG~y~ 54 (158)
T PF10083_consen 28 EK-FCSKCGAKTI---TSCPNCSTPIRGDYH 54 (158)
T ss_pred HH-HHHHhhHHHH---HHCcCCCCCCCCcee
Confidence 45 9999988863 689999999876543
No 304
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=24.14 E-value=5e+02 Score=22.91 Aligned_cols=94 Identities=13% Similarity=0.159 Sum_probs=52.8
Q ss_pred EEEec--CHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCCCCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHh
Q psy4141 33 FVVTG--RKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 110 (353)
Q Consensus 33 v~I~G--~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~T 110 (353)
++++| +.+++.+|.+.+.++++++... ....+ ..+++-.|-.-..++=| .+.+|....
T Consensus 58 iviTGaks~~~~~~a~~~~~~~l~~~g~~--------------~~~~~-~f~v~nIvat~~~~~~i-----~L~~la~~~ 117 (174)
T cd04517 58 ITITGATSEEEAKQAARRAARLLQKLGFK--------------VVRFS-NFRVVNVLATCSMPFPI-----RLDELAAKN 117 (174)
T ss_pred EEEEccCCHHHHHHHHHHHHHHHHHcCCC--------------cccCC-ceEEEEEEEEEeCCCcc-----cHHHHHHhc
Confidence 56666 4788999999998888765210 00011 23333333333233323 366665544
Q ss_pred CceEEcCCC----------C--------CCCeEEEEcC--HHHHHHHHHHHHHHHH
Q psy4141 111 NTYIVTPSR----------D--------KEPVFEVTGA--PDSVEIARQEIESHII 146 (353)
Q Consensus 111 ga~I~ip~~----------~--------~e~~v~I~G~--~e~V~~A~~~I~~~i~ 146 (353)
.-++...++ + ....|+|+|. ++.+++|.+.|..++.
T Consensus 118 ~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~pil~ 173 (174)
T cd04517 118 RSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIYPIVF 173 (174)
T ss_pred hhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 333322111 0 1247999994 7899999999887764
No 305
>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=23.69 E-value=84 Score=27.19 Aligned_cols=24 Identities=17% Similarity=0.213 Sum_probs=21.1
Q ss_pred eeecCCCchHHHHHHHcCceEEec
Q psy4141 2 KKISRSGCKIKALRAKTNTYIKTP 25 (353)
Q Consensus 2 ~IIGk~G~~Ik~I~~~Tga~I~ip 25 (353)
.+|||+|.++++|..+||=+-++-
T Consensus 89 ~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 89 LVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred EEEecCchhHHHHHHHhCCeeEEE
Confidence 479999999999999999887753
No 306
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=23.22 E-value=45 Score=24.87 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=8.7
Q ss_pred hhHHhHHHHhcc
Q psy4141 323 FCSECAERTCDF 334 (353)
Q Consensus 323 fC~~C~~~~~~~ 334 (353)
||+-|+.+|...
T Consensus 12 FCRNCLskWy~~ 23 (68)
T PF06844_consen 12 FCRNCLSKWYRE 23 (68)
T ss_dssp --HHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 999999999764
No 307
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=22.63 E-value=88 Score=23.18 Aligned_cols=45 Identities=11% Similarity=0.161 Sum_probs=31.9
Q ss_pred ChHHHHHHHHhCceEEcCCCC-----C----CCeEEEEcCHHHHHHHHHHHHHH
Q psy4141 100 GATIKRIQHQTNTYIVTPSRD-----K----EPVFEVTGAPDSVEIARQEIESH 144 (353)
Q Consensus 100 G~tIk~Iq~~Tga~I~ip~~~-----~----e~~v~I~G~~e~V~~A~~~I~~~ 144 (353)
.--|.++.+++++.+.|-... . .-.+.+.|..+++++|.+.+.++
T Consensus 16 ~piis~l~~~~~v~~nIl~g~i~~i~~~~~G~l~l~l~g~~~~~~~a~~~L~~~ 69 (76)
T PF09383_consen 16 EPIISQLIREFGVDVNILHGNIEEIQGTPFGILILELPGDDEEIEKAIAYLREQ 69 (76)
T ss_dssp SCHHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHT
T ss_pred chHHHHHHHHhCCCEEEEEEEeEEcCCeeEEEEEEEEECCHHHHHHHHHHHHHC
Confidence 345789999999998654331 1 12789999999999999988753
No 308
>PLN00062 TATA-box-binding protein; Provisional
Probab=22.59 E-value=5.5e+02 Score=22.83 Aligned_cols=25 Identities=20% Similarity=0.219 Sum_probs=21.3
Q ss_pred CeEEEEcC--HHHHHHHHHHHHHHHHh
Q psy4141 123 PVFEVTGA--PDSVEIARQEIESHIIR 147 (353)
Q Consensus 123 ~~v~I~G~--~e~V~~A~~~I~~~i~~ 147 (353)
..|.|+|. .+.+++|.+.|...|.+
T Consensus 147 GkvvitGaks~~~~~~ai~~i~p~L~~ 173 (179)
T PLN00062 147 GKIVITGAKVREEIYTAFENIYPVLTE 173 (179)
T ss_pred CEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 47899995 78999999999998876
No 309
>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=21.65 E-value=6.4 Score=32.54 Aligned_cols=44 Identities=23% Similarity=0.578 Sum_probs=28.5
Q ss_pred CCcccccccccc-----cccEEeCCCCHhhhHHhHHHHhcc-CCCCCCccc
Q psy4141 299 GSRQCYLCNDRE-----VTHALIPCGHNFFCSECAERTCDF-DRTCPMCRV 343 (353)
Q Consensus 299 ~~~~C~IC~~~~-----~~~~llpCgH~~fC~~C~~~~~~~-~~~CP~Cr~ 343 (353)
.+..|.+|...+ ....-.-|.|. +|..|-...... ...|-+|+.
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 457899998753 23444678898 999887663222 567888865
No 310
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.56 E-value=64 Score=26.66 Aligned_cols=41 Identities=24% Similarity=0.570 Sum_probs=30.0
Q ss_pred ccccccccccccc--------------EEeCCCCHhhhHHhHHHHhccCCCCCCcc
Q psy4141 301 RQCYLCNDREVTH--------------ALIPCGHNFFCSECAERTCDFDRTCPMCR 342 (353)
Q Consensus 301 ~~C~IC~~~~~~~--------------~llpCgH~~fC~~C~~~~~~~~~~CP~Cr 342 (353)
..|..|...+... .--.|.+. ||.+|-.=+-+..-.||-|.
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 4577787765432 12468888 99999888777778899995
No 311
>KOG1960|consensus
Probab=21.29 E-value=35 Score=34.28 Aligned_cols=117 Identities=21% Similarity=0.250 Sum_probs=72.7
Q ss_pred cCCCchHHHHHHHcCceEEec---------CCCC---c--CeEEEecCHHHHHHHHHHHHHHHhhhhhhhhccCCCCCCC
Q psy4141 5 SRSGCKIKALRAKTNTYIKTP---------VRGE---E--PVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSP 70 (353)
Q Consensus 5 Gk~G~~Ik~I~~~Tga~I~ip---------~~~e---~--~vv~I~G~~e~v~~Ak~~I~~i~~~~~~~~~~~~~g~~~~ 70 (353)
|++-..+..++.++++.+-+. ..++ | .++++-+.++.+.+|++++.++.+.... .-+|-+
T Consensus 231 ~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~-~~sr~~----- 304 (531)
T KOG1960|consen 231 NRKDLTLALQEIESWINPLIDGRRSGRREPNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYI-NLSRGF----- 304 (531)
T ss_pred CccchhhhhhhhhhhhhhhhccccccccCcccccccCCceeEEeecCCchhhccchhHHHhHHHHHHH-Hhhhhh-----
Confidence 445556777777887764432 1222 2 4666678999999999999999775311 001100
Q ss_pred CCCCCCCCcceEEEEEecCCCccceeccCChHHHHHHHHhCceEEcCC---------C--C-CC--CeEEEEcCHHHHHH
Q psy4141 71 LSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS---------R--D-KE--PVFEVTGAPDSVEI 136 (353)
Q Consensus 71 ~~~~~~~~~~~t~~v~VP~~~vG~IIGkgG~tIk~Iq~~Tga~I~ip~---------~--~-~e--~~v~I~G~~e~V~~ 136 (353)
.--.++|+.|...|.|++.+-.++.+.. . + ++ .+..|.-.+.+++.
T Consensus 305 --------------------~~~~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p~~~~~~~~p~~~~~~~~~~~~~~~ 364 (531)
T KOG1960|consen 305 --------------------HRQAIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEPSTNRESDEPIHLCIMSHDPNAIQR 364 (531)
T ss_pred --------------------hhcccccCCcccccccCCCCCcceeccCccceeecCCCCCCCCCCcccccccCChhhhhh
Confidence 0014667777778888877777665422 1 1 12 25677778888888
Q ss_pred HHHHHHHHHHh
Q psy4141 137 ARQEIESHIIR 147 (353)
Q Consensus 137 A~~~I~~~i~~ 147 (353)
|+-++.+.|.-
T Consensus 365 ~~~~~~~~i~~ 375 (531)
T KOG1960|consen 365 AKVLCEDLIAS 375 (531)
T ss_pred hhhcccccCCc
Confidence 88877766654
No 312
>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=21.26 E-value=47 Score=26.34 Aligned_cols=35 Identities=26% Similarity=0.807 Sum_probs=26.7
Q ss_pred cccccccccccccEEeCCCCHhhhHHhHHHHhccCCCCCCccccc
Q psy4141 301 RQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345 (353)
Q Consensus 301 ~~C~IC~~~~~~~~llpCgH~~fC~~C~~~~~~~~~~CP~Cr~~i 345 (353)
..|.+|..... .=||. ||..|+-. ...|.+|-..+
T Consensus 45 ~~C~~CK~~v~-----q~g~~-YCq~CAYk----kGiCamCGKki 79 (90)
T PF10235_consen 45 SKCKICKTKVH-----QPGAK-YCQTCAYK----KGICAMCGKKI 79 (90)
T ss_pred ccccccccccc-----cCCCc-cChhhhcc----cCcccccCCee
Confidence 56999986433 23777 99999877 47999997766
No 313
>KOG0006|consensus
Probab=20.23 E-value=62 Score=31.59 Aligned_cols=34 Identities=24% Similarity=0.580 Sum_probs=29.0
Q ss_pred CcccccccccccccEEeCCC--CHhhhHHhHHHHhcc
Q psy4141 300 SRQCYLCNDREVTHALIPCG--HNFFCSECAERTCDF 334 (353)
Q Consensus 300 ~~~C~IC~~~~~~~~llpCg--H~~fC~~C~~~~~~~ 334 (353)
...|..|-+.......++|. |. .|.+|...++..
T Consensus 221 ni~C~~Ctdv~~~vlvf~Cns~Hv-tC~dCFr~yc~~ 256 (446)
T KOG0006|consen 221 NITCITCTDVRSPVLVFQCNSRHV-TCLDCFRLYCVT 256 (446)
T ss_pred cceeEEecCCccceEEEecCCcee-ehHHhhhhHhhh
Confidence 47899999999988889999 98 999998876553
No 314
>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=20.19 E-value=3.2e+02 Score=20.93 Aligned_cols=48 Identities=10% Similarity=0.111 Sum_probs=38.5
Q ss_pred CChHHHHHHHHhCceEEcCCCC------CCCeEEEEcCHHHHHHHHHHHHHHHH
Q psy4141 99 KGATIKRIQHQTNTYIVTPSRD------KEPVFEVTGAPDSVEIARQEIESHII 146 (353)
Q Consensus 99 gG~tIk~Iq~~Tga~I~ip~~~------~e~~v~I~G~~e~V~~A~~~I~~~i~ 146 (353)
|-.-+++|-+..|+++....+| .+..++|.|+..++..|-+.++.++.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 5567788888999999765433 34689999999999999999988775
No 315
>KOG4621|consensus
Probab=20.14 E-value=27 Score=29.64 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=25.2
Q ss_pred CCCcccccccccccccEEeCCCCHhhhHH
Q psy4141 298 SGSRQCYLCNDREVTHALIPCGHNFFCSE 326 (353)
Q Consensus 298 ~~~~~C~IC~~~~~~~~llpCgH~~fC~~ 326 (353)
.+.+-|..|.+..+...+.|-||.|||+.
T Consensus 79 q~~Lhcdlceeplk~ccfspnghhcfcrt 107 (167)
T KOG4621|consen 79 QDKLHCDLCEEPLKSCCFSPNGHHCFCRT 107 (167)
T ss_pred CCceehHHHHhHHHHhccCCCCccccccC
Confidence 45688999999999999999999999974
Done!