Query 019169
Match_columns 345
No_of_seqs 152 out of 285
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 07:15:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019169.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019169hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0796 Spliceosome subunit [R 100.0 3.2E-86 7E-91 630.8 20.7 231 1-240 1-234 (319)
2 PF03194 LUC7: LUC7 N_terminus 100.0 3.9E-85 8.5E-90 617.8 23.2 235 1-241 1-239 (254)
3 COG5200 LUC7 U1 snRNP componen 100.0 9.4E-63 2E-67 444.5 14.9 226 2-237 3-230 (258)
4 KOG0796 Spliceosome subunit [R 98.4 2.6E-06 5.7E-11 82.8 12.7 146 84-247 73-234 (319)
5 PF03194 LUC7: LUC7 N_terminus 97.1 0.0027 5.8E-08 60.7 9.6 138 91-244 79-235 (254)
6 COG5200 LUC7 U1 snRNP componen 94.7 0.27 5.8E-06 46.0 9.7 144 92-243 80-229 (258)
7 KOG2888 Putative RNA binding p 93.6 0.043 9.2E-07 54.3 2.3 26 149-174 120-145 (453)
8 KOG4368 Predicted RNA binding 91.9 0.26 5.7E-06 51.9 5.4 17 158-174 257-273 (757)
9 KOG4676 Splicing factor, argin 91.6 0.14 2.9E-06 51.8 2.8 38 11-55 39-76 (479)
10 KOG4676 Splicing factor, argin 90.1 0.22 4.7E-06 50.4 2.7 7 218-224 215-221 (479)
11 PHA02562 46 endonuclease subun 87.9 8.7 0.00019 39.9 12.9 15 191-205 283-297 (562)
12 PRK01156 chromosome segregatio 87.4 9.6 0.00021 42.3 13.6 15 192-206 449-463 (895)
13 PF12171 zf-C2H2_jaz: Zinc-fin 86.9 0.26 5.7E-06 30.7 0.6 25 193-220 2-26 (27)
14 PRK02224 chromosome segregatio 86.7 15 0.00032 40.6 14.5 13 191-203 450-462 (880)
15 COG1579 Zn-ribbon protein, pos 86.3 4.9 0.00011 38.4 9.0 19 93-111 64-82 (239)
16 PF04012 PspA_IM30: PspA/IM30 86.1 7.7 0.00017 35.7 10.2 82 91-178 26-107 (221)
17 KOG0151 Predicted splicing reg 85.6 0.4 8.6E-06 51.7 1.5 9 3-11 431-439 (877)
18 TIGR02302 aProt_lowcomp conser 85.5 1.8 4E-05 48.1 6.6 35 138-172 570-604 (851)
19 PF12874 zf-met: Zinc-finger o 85.3 0.29 6.3E-06 29.5 0.2 24 194-220 2-25 (25)
20 smart00451 ZnF_U1 U1-like zinc 85.0 0.36 7.9E-06 31.3 0.6 28 193-223 4-31 (35)
21 PF13779 DUF4175: Domain of un 82.4 6.3 0.00014 43.9 9.1 35 135-169 537-571 (820)
22 COG0419 SbcC ATPase involved i 82.2 32 0.0007 38.6 14.7 24 192-216 457-480 (908)
23 PRK06835 DNA replication prote 80.4 11 0.00024 37.5 9.2 71 130-204 37-110 (329)
24 KOG2888 Putative RNA binding p 80.3 0.82 1.8E-05 45.5 1.3 10 89-98 174-183 (453)
25 PRK15058 cytochrome b562; Prov 76.1 9.7 0.00021 33.1 6.5 42 129-170 78-122 (128)
26 KOG4368 Predicted RNA binding 76.0 6.4 0.00014 42.0 6.3 8 49-56 129-136 (757)
27 PRK09720 cybC cytochrome b562; 75.6 11 0.00024 31.3 6.5 42 128-169 49-93 (100)
28 PF14282 FlxA: FlxA-like prote 75.3 11 0.00023 31.4 6.3 52 126-178 16-67 (106)
29 PF07361 Cytochrom_B562: Cytoc 74.1 27 0.00058 28.9 8.4 42 129-170 53-97 (103)
30 PF03962 Mnd1: Mnd1 family; I 73.1 75 0.0016 29.0 12.0 51 128-178 75-126 (188)
31 smart00356 ZnF_C3H1 zinc finge 71.8 2.3 5E-05 25.8 1.2 23 34-65 4-26 (27)
32 TIGR02977 phageshock_pspA phag 71.4 44 0.00095 31.0 10.2 79 91-175 27-105 (219)
33 KOG0687 26S proteasome regulat 70.7 38 0.00083 34.2 9.9 99 46-169 17-116 (393)
34 PF02403 Seryl_tRNA_N: Seryl-t 69.8 13 0.00028 30.4 5.6 50 127-178 41-90 (108)
35 PRK14143 heat shock protein Gr 69.6 32 0.00069 32.9 8.9 86 126-227 64-155 (238)
36 PRK03918 chromosome segregatio 69.6 44 0.00095 36.9 11.4 10 194-203 437-446 (880)
37 PF06220 zf-U1: U1 zinc finger 68.4 3 6.5E-05 28.5 1.3 32 193-225 4-35 (38)
38 PF13863 DUF4200: Domain of un 66.9 22 0.00048 29.6 6.6 51 92-148 50-100 (126)
39 PF12325 TMF_TATA_bd: TATA ele 65.7 86 0.0019 26.8 10.8 70 87-178 15-84 (120)
40 KOG1847 mRNA splicing factor [ 64.5 9.6 0.00021 41.2 4.6 13 292-304 765-777 (878)
41 PRK14158 heat shock protein Gr 63.8 59 0.0013 30.1 9.2 77 124-216 35-111 (194)
42 PRK14144 heat shock protein Gr 63.6 46 0.001 31.0 8.5 89 128-232 44-136 (199)
43 COG1675 TFA1 Transcription ini 63.4 25 0.00054 32.1 6.6 38 188-237 128-165 (176)
44 KOG0835 Cyclin L [General func 62.6 4.1 8.9E-05 40.6 1.5 17 221-237 234-250 (367)
45 PF10475 DUF2450: Protein of u 60.1 1.2E+02 0.0027 29.2 11.3 82 88-170 67-159 (291)
46 COG1842 PspA Phage shock prote 59.9 99 0.0021 29.2 10.2 82 91-178 27-108 (225)
47 PRK10246 exonuclease subunit S 59.0 40 0.00087 38.6 8.7 10 192-201 503-512 (1047)
48 PF02151 UVR: UvrB/uvrC motif; 58.6 31 0.00068 23.0 4.9 35 136-170 2-36 (36)
49 PRK10698 phage shock protein P 58.6 96 0.0021 29.0 9.9 76 92-173 28-110 (222)
50 PF01895 PhoU: PhoU domain; I 58.5 74 0.0016 23.7 7.7 82 131-216 1-82 (88)
51 PF04032 Rpr2: RNAse P Rpr2/Rp 57.5 26 0.00056 27.1 5.0 60 137-207 2-61 (85)
52 KOG3454 U1 snRNP-specific prot 57.3 9.4 0.0002 34.4 2.7 39 193-234 4-42 (165)
53 PRK14148 heat shock protein Gr 57.1 75 0.0016 29.5 8.7 72 129-216 40-111 (195)
54 PF13913 zf-C2HC_2: zinc-finge 56.4 7 0.00015 24.2 1.3 20 192-215 2-21 (25)
55 PF12998 ING: Inhibitor of gro 56.1 80 0.0017 25.1 7.9 76 93-169 20-96 (105)
56 PF10458 Val_tRNA-synt_C: Valy 55.7 48 0.001 25.0 6.1 59 91-149 7-66 (66)
57 PRK14162 heat shock protein Gr 55.3 68 0.0015 29.7 8.1 75 126-216 36-110 (194)
58 PF04645 DUF603: Protein of un 53.7 25 0.00055 32.0 4.9 69 131-208 107-176 (181)
59 PF04423 Rad50_zn_hook: Rad50 53.5 13 0.00029 26.8 2.6 10 194-203 22-31 (54)
60 PRK10884 SH3 domain-containing 52.1 1.1E+02 0.0023 28.6 9.0 55 92-148 90-144 (206)
61 KOG4302 Microtubule-associated 51.1 2.2E+02 0.0048 31.3 12.2 70 125-200 64-143 (660)
62 TIGR00570 cdk7 CDK-activating 50.7 69 0.0015 31.8 7.8 26 36-64 25-50 (309)
63 PRK11115 transcriptional regul 50.6 2E+02 0.0043 26.3 12.1 81 128-216 125-207 (236)
64 COG5136 U1 snRNP-specific prot 50.3 15 0.00033 33.2 2.8 31 193-224 4-34 (188)
65 PF07106 TBPIP: Tat binding pr 50.2 1.8E+02 0.0039 25.6 11.1 66 84-154 76-141 (169)
66 PF00642 zf-CCCH: Zinc finger 50.1 5.8 0.00013 24.8 0.2 24 34-66 3-27 (27)
67 PF02388 FemAB: FemAB family; 50.1 73 0.0016 32.4 8.2 22 127-148 247-268 (406)
68 PF03962 Mnd1: Mnd1 family; I 48.7 99 0.0022 28.2 8.1 79 89-168 70-148 (188)
69 COG3783 CybC Soluble cytochrom 48.2 1.3E+02 0.0028 25.1 7.7 27 143-169 67-93 (100)
70 PF07544 Med9: RNA polymerase 47.9 1.4E+02 0.003 23.6 8.0 57 92-151 25-81 (83)
71 PRK14154 heat shock protein Gr 47.7 91 0.002 29.2 7.7 70 130-215 53-122 (208)
72 KOG1666 V-SNARE [Intracellular 47.3 2.5E+02 0.0053 26.6 10.4 84 82-178 5-88 (220)
73 PRK11020 hypothetical protein; 47.1 1.3E+02 0.0028 25.8 7.7 21 129-149 31-51 (118)
74 PF10979 DUF2786: Protein of u 47.1 50 0.0011 23.2 4.5 35 134-170 3-37 (43)
75 PRK03918 chromosome segregatio 47.0 2.2E+02 0.0049 31.4 12.0 16 193-208 433-448 (880)
76 PRK14151 heat shock protein Gr 46.9 85 0.0018 28.5 7.3 88 127-230 18-111 (176)
77 PF04420 CHD5: CHD5-like prote 46.3 77 0.0017 28.1 6.8 54 125-178 36-89 (161)
78 PRK14163 heat shock protein Gr 46.0 1.1E+02 0.0025 28.8 8.1 85 129-231 40-124 (214)
79 TIGR01554 major_cap_HK97 phage 45.7 47 0.001 33.1 5.9 44 132-175 2-47 (378)
80 PF09969 DUF2203: Uncharacteri 44.9 80 0.0017 26.9 6.4 27 125-151 46-72 (120)
81 COG2093 DNA-directed RNA polym 44.7 8.2 0.00018 29.5 0.3 25 191-215 17-51 (64)
82 PRK10564 maltose regulon perip 44.3 27 0.00059 34.5 3.8 30 140-169 259-288 (303)
83 PF06632 XRCC4: DNA double-str 44.0 2.3E+02 0.0049 28.6 10.4 46 132-177 154-199 (342)
84 PF12854 PPR_1: PPR repeat 43.9 27 0.00059 22.6 2.7 21 143-163 12-32 (34)
85 PLN02678 seryl-tRNA synthetase 43.9 65 0.0014 33.5 6.8 49 128-178 46-94 (448)
86 COG4911 Uncharacterized conser 42.8 1.1E+02 0.0025 25.9 6.7 55 88-150 11-65 (123)
87 PF10367 Vps39_2: Vacuolar sor 42.8 47 0.001 26.3 4.5 12 192-203 78-89 (109)
88 PRK14147 heat shock protein Gr 42.2 1E+02 0.0022 28.0 6.9 68 133-216 22-89 (172)
89 PF00435 Spectrin: Spectrin re 42.1 1.5E+02 0.0032 22.3 8.1 83 94-178 7-96 (105)
90 KOG4552 Vitamin-D-receptor int 41.9 1.9E+02 0.0041 27.4 8.8 43 126-174 47-89 (272)
91 PRK05431 seryl-tRNA synthetase 41.5 74 0.0016 32.7 6.7 48 128-177 41-88 (425)
92 PF06156 DUF972: Protein of un 40.7 1.5E+02 0.0032 24.9 7.2 49 126-174 5-55 (107)
93 KOG4727 U1-like Zn-finger prot 40.7 11 0.00024 34.4 0.5 31 188-221 71-101 (193)
94 PF11931 DUF3449: Domain of un 40.1 9.5 0.00021 35.4 0.0 28 191-221 100-128 (196)
95 TIGR00414 serS seryl-tRNA synt 39.8 92 0.002 31.9 7.1 49 129-178 44-92 (418)
96 PRK12495 hypothetical protein; 39.1 34 0.00075 32.4 3.5 13 191-203 41-53 (226)
97 PRK00239 rpsT 30S ribosomal pr 38.8 72 0.0016 25.8 4.9 37 133-169 23-59 (88)
98 COG4467 Regulator of replicati 38.5 1.5E+02 0.0032 25.2 6.8 49 125-178 4-52 (114)
99 COG5187 RPN7 26S proteasome re 38.4 2.1E+02 0.0046 28.8 8.9 39 131-169 88-127 (412)
100 PF01025 GrpE: GrpE; InterPro 38.1 36 0.00079 29.7 3.4 35 198-232 64-103 (165)
101 PF14282 FlxA: FlxA-like prote 37.8 1.6E+02 0.0035 24.4 7.0 52 94-147 18-69 (106)
102 PF07743 HSCB_C: HSCB C-termin 37.7 1.8E+02 0.0039 22.1 8.1 48 125-172 27-74 (78)
103 PF11587 Prion_bPrPp: Major pr 37.6 8.3 0.00018 25.0 -0.5 23 40-62 4-26 (29)
104 PF03357 Snf7: Snf7; InterPro 37.5 1.6E+02 0.0034 25.3 7.4 52 126-177 12-63 (171)
105 KOG4765 Uncharacterized conser 36.7 30 0.00066 35.2 2.9 43 189-241 87-129 (419)
106 PRK14161 heat shock protein Gr 36.7 2.3E+02 0.0049 25.9 8.4 25 193-217 67-91 (178)
107 PF04111 APG6: Autophagy prote 36.5 92 0.002 30.7 6.3 22 58-79 4-25 (314)
108 TIGR02449 conserved hypothetic 36.3 98 0.0021 23.8 5.0 43 131-178 2-44 (65)
109 PRK14146 heat shock protein Gr 36.3 1.6E+02 0.0035 27.6 7.6 27 190-216 99-125 (215)
110 PF08317 Spc7: Spc7 kinetochor 35.7 3.3E+02 0.0071 26.8 10.0 23 85-108 140-162 (325)
111 PRK14141 heat shock protein Gr 35.2 1.8E+02 0.0038 27.3 7.6 26 191-216 77-102 (209)
112 KOG0978 E3 ubiquitin ligase in 35.2 1.6E+02 0.0035 32.4 8.3 20 188-207 674-693 (698)
113 TIGR03185 DNA_S_dndD DNA sulfu 35.2 5.1E+02 0.011 27.9 12.2 25 125-149 205-229 (650)
114 PRK14160 heat shock protein Gr 35.1 2.7E+02 0.0059 26.1 8.8 25 190-214 106-130 (211)
115 PF06005 DUF904: Protein of un 35.1 2.2E+02 0.0047 22.2 6.9 20 130-149 5-24 (72)
116 PRK14155 heat shock protein Gr 34.9 1.4E+02 0.003 28.0 6.8 70 131-216 15-84 (208)
117 TIGR00029 S20 ribosomal protei 34.2 1.1E+02 0.0023 24.8 5.2 37 133-169 23-59 (87)
118 PRK13169 DNA replication intia 33.9 2.2E+02 0.0047 24.1 7.2 46 125-175 4-49 (110)
119 PF08317 Spc7: Spc7 kinetochor 33.8 1.5E+02 0.0033 29.2 7.3 10 65-74 158-167 (325)
120 PF01649 Ribosomal_S20p: Ribos 33.8 1.1E+02 0.0025 24.4 5.3 37 133-169 22-58 (84)
121 PF12329 TMF_DNA_bd: TATA elem 33.5 2E+02 0.0044 22.3 6.5 44 129-177 5-48 (74)
122 KOG2751 Beclin-like protein [S 33.5 3.5E+02 0.0076 28.3 9.9 120 32-155 74-210 (447)
123 smart00787 Spc7 Spc7 kinetocho 33.2 2E+02 0.0044 28.5 8.1 35 67-105 120-154 (312)
124 smart00787 Spc7 Spc7 kinetocho 33.2 4.9E+02 0.011 25.7 10.9 20 129-148 211-230 (312)
125 PF05597 Phasin: Poly(hydroxya 33.1 2.3E+02 0.0049 24.6 7.4 23 128-150 108-130 (132)
126 TIGR02420 dksA RNA polymerase- 32.9 2.6E+02 0.0056 23.1 7.5 13 191-203 79-91 (110)
127 PF05529 Bap31: B-cell recepto 32.7 2.8E+02 0.0061 24.9 8.4 17 80-96 104-120 (192)
128 KOG4797 Transcriptional regula 32.6 1E+02 0.0022 26.2 5.0 52 99-158 45-96 (123)
129 PF07295 DUF1451: Protein of u 32.5 2.3E+02 0.0051 25.0 7.5 112 89-207 5-127 (146)
130 COG4477 EzrA Negative regulato 32.5 5.1E+02 0.011 27.9 11.1 151 66-238 232-392 (570)
131 PF14276 DUF4363: Domain of un 32.3 1.3E+02 0.0029 24.9 5.8 44 130-173 20-63 (121)
132 PF04108 APG17: Autophagy prot 31.6 4.4E+02 0.0096 26.9 10.5 20 46-65 124-143 (412)
133 PF05700 BCAS2: Breast carcino 31.6 2.1E+02 0.0045 26.6 7.5 78 90-175 138-216 (221)
134 PF07535 zf-DBF: DBF zinc fing 31.5 26 0.00057 25.4 1.1 41 190-236 3-43 (49)
135 cd00729 rubredoxin_SM Rubredox 31.1 19 0.00041 23.9 0.3 11 191-201 17-27 (34)
136 PRK06266 transcription initiat 31.0 23 0.00051 32.1 1.0 36 190-237 134-169 (178)
137 PF06160 EzrA: Septation ring 30.5 6.6E+02 0.014 26.8 11.9 160 66-239 229-390 (560)
138 PRK11637 AmiB activator; Provi 30.4 3.5E+02 0.0077 27.5 9.6 19 130-148 90-108 (428)
139 COG1592 Rubrerythrin [Energy p 30.2 3E+02 0.0065 24.9 7.9 9 191-199 133-141 (166)
140 PF13894 zf-C2H2_4: C2H2-type 29.9 24 0.00052 20.0 0.6 19 194-215 2-20 (24)
141 PRK06424 transcription factor; 29.8 20 0.00043 31.6 0.3 11 193-203 24-34 (144)
142 KOG2801 Probable Rab-GAPs [Int 29.7 19 0.00041 35.7 0.2 21 196-219 402-422 (559)
143 KOG4360 Uncharacterized coiled 29.7 2.2E+02 0.0047 30.4 7.8 137 35-178 141-284 (596)
144 PF06008 Laminin_I: Laminin Do 29.4 3.9E+02 0.0085 25.2 9.1 87 84-171 49-139 (264)
145 PF09237 GAGA: GAGA factor; I 29.2 19 0.00041 26.6 0.1 20 191-210 23-42 (54)
146 COG4499 Predicted membrane pro 29.1 2E+02 0.0044 29.7 7.2 75 93-169 335-409 (434)
147 PF03980 Nnf1: Nnf1 ; InterPr 28.7 3.2E+02 0.007 22.2 7.9 24 92-115 31-54 (109)
148 COG0172 SerS Seryl-tRNA synthe 28.6 1.6E+02 0.0034 30.7 6.6 50 128-178 42-91 (429)
149 PF15500 Toxin_39: Putative RN 28.5 63 0.0014 26.4 2.9 11 56-66 29-39 (96)
150 PRK14139 heat shock protein Gr 28.4 3.3E+02 0.0071 25.1 8.0 86 128-229 31-119 (185)
151 PF06632 XRCC4: DNA double-str 28.3 2.5E+02 0.0054 28.3 7.8 43 131-178 139-181 (342)
152 PLN00204 CP12 gene family prot 27.9 1.6E+02 0.0034 25.6 5.4 43 133-175 56-99 (126)
153 PRK14150 heat shock protein Gr 27.8 3E+02 0.0065 25.4 7.7 26 190-215 83-108 (193)
154 PLN03229 acetyl-coenzyme A car 27.6 3.8E+02 0.0082 30.0 9.5 41 66-108 439-479 (762)
155 TIGR01837 PHA_granule_1 poly(h 27.4 2.8E+02 0.006 23.4 6.9 30 69-101 25-54 (118)
156 TIGR00373 conserved hypothetic 27.2 29 0.00063 30.8 0.9 21 190-210 126-146 (158)
157 PF07106 TBPIP: Tat binding pr 27.2 2E+02 0.0043 25.3 6.3 50 129-178 72-132 (169)
158 KOG3032 Uncharacterized conser 27.2 2.2E+02 0.0048 27.4 6.7 34 145-178 194-227 (264)
159 PF05191 ADK_lid: Adenylate ki 26.9 26 0.00056 23.7 0.4 15 189-203 18-32 (36)
160 cd07973 Spt4 Transcription elo 26.9 23 0.0005 29.3 0.2 30 192-221 20-53 (98)
161 PRK14140 heat shock protein Gr 26.4 3.6E+02 0.0078 24.9 7.9 73 128-216 36-108 (191)
162 COG3809 Uncharacterized protei 26.3 24 0.00053 28.3 0.3 14 192-205 1-14 (88)
163 PF10146 zf-C4H2: Zinc finger- 26.1 5.3E+02 0.011 24.5 9.2 78 86-177 23-103 (230)
164 PF05852 DUF848: Gammaherpesvi 25.9 2.4E+02 0.0052 25.1 6.4 48 126-173 58-107 (146)
165 TIGR02135 phoU_full phosphate 25.8 3.7E+02 0.0081 23.4 7.9 35 128-162 11-45 (212)
166 PF01535 PPR: PPR repeat; Int 25.6 90 0.002 18.4 2.8 23 144-166 6-28 (31)
167 PRK01156 chromosome segregatio 25.5 6.6E+02 0.014 28.0 11.3 15 192-206 452-466 (895)
168 PF04880 NUDE_C: NUDE protein, 25.1 1.1E+02 0.0024 27.7 4.3 25 154-178 23-47 (166)
169 PF01396 zf-C4_Topoisom: Topoi 25.1 26 0.00057 23.9 0.2 13 193-205 2-14 (39)
170 PLN02943 aminoacyl-tRNA ligase 25.0 1.8E+02 0.0038 33.2 6.8 66 84-150 886-952 (958)
171 TIGR02135 phoU_full phosphate 24.5 4.7E+02 0.01 22.7 12.1 82 126-215 113-196 (212)
172 PRK14153 heat shock protein Gr 24.3 2.7E+02 0.0059 25.8 6.7 35 196-230 84-123 (194)
173 smart00150 SPEC Spectrin repea 24.3 3.1E+02 0.0066 20.5 6.3 50 128-178 44-93 (101)
174 KOG1510 RNA polymerase II holo 24.2 5E+02 0.011 22.9 9.9 43 125-172 87-129 (139)
175 PF06721 DUF1204: Protein of u 24.0 2.4E+02 0.0052 26.3 6.2 70 129-201 50-120 (228)
176 PF10883 DUF2681: Protein of u 23.5 2.1E+02 0.0046 23.2 5.2 30 130-159 24-53 (87)
177 PF03119 DNA_ligase_ZBD: NAD-d 23.5 25 0.00054 22.4 -0.1 12 195-206 2-13 (28)
178 COG3074 Uncharacterized protei 23.4 3.7E+02 0.0081 21.2 7.3 25 129-153 11-35 (79)
179 COG3058 FdhE Uncharacterized p 23.2 1.9E+02 0.0042 28.5 5.7 14 191-204 184-197 (308)
180 PRK13130 H/ACA RNA-protein com 22.9 28 0.00062 25.9 0.0 13 191-203 4-16 (56)
181 PF04102 SlyX: SlyX; InterPro 22.8 1.6E+02 0.0035 22.4 4.2 24 126-149 29-52 (69)
182 KOG1040 Polyadenylation factor 22.8 33 0.00072 34.2 0.5 16 31-46 74-89 (325)
183 CHL00102 rps20 ribosomal prote 22.7 1.9E+02 0.0041 23.7 4.8 36 134-169 24-66 (93)
184 smart00746 TRASH metallochaper 22.6 21 0.00045 21.6 -0.7 11 195-205 1-11 (39)
185 PF04065 Not3: Not1 N-terminal 22.6 5.7E+02 0.012 24.4 8.7 80 87-171 121-206 (233)
186 KOG4182 Uncharacterized conser 22.4 3.4E+02 0.0074 29.0 7.6 51 126-178 78-128 (828)
187 PF08898 DUF1843: Domain of un 22.3 2.1E+02 0.0046 21.2 4.5 34 137-176 18-52 (53)
188 TIGR00606 rad50 rad50. This fa 22.2 1.3E+03 0.029 27.2 13.8 120 89-221 578-706 (1311)
189 PRK04778 septation ring format 22.2 7.9E+02 0.017 26.1 10.7 87 87-173 104-212 (569)
190 PF15619 Lebercilin: Ciliary p 22.0 6.2E+02 0.014 23.2 9.3 39 140-178 103-141 (194)
191 PRK04406 hypothetical protein; 22.0 82 0.0018 24.7 2.5 16 130-145 40-55 (75)
192 PRK10778 dksA RNA polymerase-b 21.9 3.7E+02 0.0081 23.8 6.9 14 190-203 109-122 (151)
193 PF07967 zf-C3HC: C3HC zinc fi 21.8 31 0.00067 29.5 0.0 17 189-205 40-56 (133)
194 cd00350 rubredoxin_like Rubred 21.7 35 0.00076 22.3 0.3 11 191-201 16-26 (33)
195 PF05529 Bap31: B-cell recepto 21.6 2.9E+02 0.0063 24.8 6.4 14 160-173 159-172 (192)
196 PF06694 Plant_NMP1: Plant nuc 21.6 7E+02 0.015 25.0 9.2 81 122-203 168-253 (325)
197 PF00435 Spectrin: Spectrin re 21.6 3.5E+02 0.0076 20.2 7.9 50 129-178 8-57 (105)
198 COG5509 Uncharacterized small 21.5 1.2E+02 0.0025 23.2 3.0 21 130-150 26-46 (65)
199 PF14257 DUF4349: Domain of un 21.5 6.4E+02 0.014 23.6 9.0 54 125-178 128-185 (262)
200 PLN02320 seryl-tRNA synthetase 21.5 2.4E+02 0.0051 30.0 6.5 49 127-178 105-153 (502)
201 COG2178 Predicted RNA-binding 21.4 4.9E+02 0.011 24.5 7.7 50 127-176 18-67 (204)
202 PRK12496 hypothetical protein; 21.1 37 0.00079 30.4 0.4 12 193-204 144-155 (164)
203 KOG4722 Zn-finger protein [Gen 21.1 2.5E+02 0.0054 29.4 6.3 28 192-222 493-520 (672)
204 COG5188 PRP9 Splicing factor 3 21.0 38 0.00083 34.3 0.5 23 195-220 241-263 (470)
205 TIGR00270 conserved hypothetic 20.8 36 0.00079 30.2 0.3 7 195-201 3-9 (154)
206 PF04156 IncA: IncA protein; 20.8 5.9E+02 0.013 22.5 9.1 63 87-149 87-150 (191)
207 COG1340 Uncharacterized archae 20.8 8.3E+02 0.018 24.2 10.4 42 67-112 111-155 (294)
208 PF08792 A2L_zn_ribbon: A2L zi 20.7 33 0.00071 22.8 -0.0 14 191-204 2-15 (33)
209 PRK11020 hypothetical protein; 20.7 5.5E+02 0.012 22.0 8.6 17 125-141 34-50 (118)
210 PF10152 DUF2360: Predicted co 20.6 3.1E+02 0.0067 24.0 6.1 30 84-113 3-32 (148)
211 PRK13729 conjugal transfer pil 20.6 3.5E+02 0.0076 28.6 7.4 21 129-149 76-96 (475)
212 PHA03161 hypothetical protein; 20.5 3.4E+02 0.0074 24.3 6.3 48 125-172 57-106 (150)
213 PF05741 zf-nanos: Nanos RNA b 20.4 36 0.00078 25.3 0.1 12 191-202 32-43 (55)
214 KOG0250 DNA repair protein RAD 20.2 8.4E+02 0.018 28.5 10.6 86 87-181 695-780 (1074)
215 smart00355 ZnF_C2H2 zinc finge 20.1 54 0.0012 18.5 0.9 20 194-216 2-21 (26)
216 PF04100 Vps53_N: Vps53-like, 20.1 9.2E+02 0.02 24.4 13.6 23 89-111 26-48 (383)
217 PF01166 TSC22: TSC-22/dip/bun 20.1 66 0.0014 24.3 1.5 27 126-152 11-37 (59)
218 PF12729 4HB_MCP_1: Four helix 20.1 5E+02 0.011 21.3 9.5 33 129-161 112-144 (181)
219 KOG0113 U1 small nuclear ribon 20.0 82 0.0018 31.3 2.5 10 209-218 189-198 (335)
220 KOG0994 Extracellular matrix g 20.0 6.8E+02 0.015 29.8 9.7 69 48-116 1532-1605(1758)
No 1
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=100.00 E-value=3.2e-86 Score=630.78 Aligned_cols=231 Identities=43% Similarity=0.789 Sum_probs=206.3
Q ss_pred CHH-HHHHHHHhcCCCCCCChhhhhhccccCCCCCCCcchhhcCCChhHhhhhcccCCCCCCCCCcHHHHHHHhcCCCCC
Q 019169 1 MDA-QRALLDELMGAARNLTEEEKKEYKEIKWDDKEVCPFYMVRFCPHDLFVNTRSDLGPCPRIHDQKLKESFEKSPRHD 79 (345)
Q Consensus 1 md~-~RalLDeLMG~~Rn~~~~~~~~~~~~~~~D~~VCk~yL~g~CPhdLF~nTK~DlG~C~kiHd~~lK~~Ye~~~~~~ 79 (345)
|++ ||+|||||||++||..... ..+.|+||+||+||||||||||||+|||+|||+||+||+++||++|+.+++..
T Consensus 1 Msa~mR~mLdqLMGs~r~~~~~~----~~v~~~D~~VC~~fLvg~CPHDlF~nTk~dlg~C~kvHd~~lk~~Ye~~~k~~ 76 (319)
T KOG0796|consen 1 MSAQMRAMLDQLMGSNRDGDETR----QRVKFDDPDVCKSFLVGFCPHDLFQNTKMDLGPCPKVHDEALKADYERASKER 76 (319)
T ss_pred CchHHHHHHHHHhCCCcCCCccc----CCCCCCchhHHHHHHhCCCcHHHhhhhhcccCcccchhhHHHHHHHhhchHhh
Confidence 666 9999999999999865432 23799999999999999999999999999999999999999999999999999
Q ss_pred CChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHH
Q 019169 80 AYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEA 159 (345)
Q Consensus 80 ~~~~~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~ 159 (345)
++ +||++||.+|+.||.+|+++|+++++||+++.++.+ .....++++|..|+++|+.|+++||+||++|+|++||+
T Consensus 77 ~~--~~E~d~~~~l~~~v~d~~rri~~~kerL~e~~ee~~--~e~~~k~~~v~~l~e~I~~~l~~~E~LG~eG~Veeaq~ 152 (319)
T KOG0796|consen 77 DY--GYEWDALEILERFVADVDRRIEKAKERLAETVEERS--EEAARKAEKVHELEEKIGKLLEKAEELGEEGNVEEAQK 152 (319)
T ss_pred hh--hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh--hHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHH
Confidence 99 999999999999999999999999999999865333 33344578999999999999999999999999999999
Q ss_pred HHHHHHHHHH-HHHHHHhhhhhhhh-hhHHHhhcCcccccchhhhcccchHHHhhhhhccccccchHHHHHHHHHHHHHH
Q 019169 160 LMRKVEILNV-EKTTLTQQSQNDKV-LMMAQEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEAK 237 (345)
Q Consensus 160 l~~~ve~Lk~-ek~~le~~~~~~~~-~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eLk~~~ 237 (345)
+|.+||.|++ +++..+.++ .+.+ .+++++|||+||+||||||+++||++||||||+|||||||++||++|++|++++
T Consensus 153 ~~~e~E~lk~~e~e~~~~~~-~~~~~~~~~~~qkl~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~~iR~~l~eLk~~~ 231 (319)
T KOG0796|consen 153 AMKEVEELKAKEKEEAEESY-NTTMPGASAQQQKLRVCEVCGAFLSVNDADRRLADHFGGKLHLGYVLIREKLAELKKEK 231 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHH-ccCcchhhhhhhhhhHHHhhhHHHhccchHHHHHHhhcchHHHHHHHHHHHHHHHHHHH
Confidence 9999999997 555555444 3322 245689999999999999999999999999999999999999999999999987
Q ss_pred HHh
Q 019169 238 EKA 240 (345)
Q Consensus 238 ~~~ 240 (345)
.+.
T Consensus 232 ~~~ 234 (319)
T KOG0796|consen 232 AKR 234 (319)
T ss_pred hHH
Confidence 664
No 2
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=100.00 E-value=3.9e-85 Score=617.79 Aligned_cols=235 Identities=44% Similarity=0.824 Sum_probs=212.0
Q ss_pred CHHHHHHHHHhcCCCCCCChhhhhhccccCCCCCCCcchhhcCCChhHhhhhcccCCCCCCCCCcHHHHHHHhcCCCCCC
Q 019169 1 MDAQRALLDELMGAARNLTEEEKKEYKEIKWDDKEVCPFYMVRFCPHDLFVNTRSDLGPCPRIHDQKLKESFEKSPRHDA 80 (345)
Q Consensus 1 md~~RalLDeLMG~~Rn~~~~~~~~~~~~~~~D~~VCk~yL~g~CPhdLF~nTK~DlG~C~kiHd~~lK~~Ye~~~~~~~ 80 (345)
||+||||||||||++||+++..+. ++|+||+|||||||||||||||+|||+||||||||||++||++|++++++++
T Consensus 1 md~~Ra~LdeLMG~~Rn~~~~~~~----~~f~D~~VCk~~L~g~CPhdLF~nTK~DLG~C~kiHd~~lk~~Ye~~~~~~~ 76 (254)
T PF03194_consen 1 MDEMRAMLDELMGSNRNGDPSKRK----VHFTDPDVCKYFLVGFCPHDLFVNTKSDLGPCPKIHDEALKAEYEKASKKEK 76 (254)
T ss_pred CHHHHHHHHHHcCCccCCCccccC----CCCCCcccCHHHHhCCCcHHHHhhcccccchhhhhcCHHHHHHHHhCccccc
Confidence 899999999999999998765532 7999999999999999999999999999999999999999999999999998
Q ss_pred ChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHH
Q 019169 81 YVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEAL 160 (345)
Q Consensus 81 ~~~~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l 160 (345)
++ +||++|+.+|+.||.+||++|++|++||++++++.+. ......+++|..|+++|+.+|++||+||++|+|++||++
T Consensus 77 ~~-~YE~e~~~~L~~~i~d~drrI~~~k~RL~~~~~~~~~-~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~ 154 (254)
T PF03194_consen 77 YG-GYEREFLRYLQRLIRDCDRRIERAKERLEQTQEEQAK-EADEEKAEKIDELDEKIGELLKEAEELGEEGDVDEAQKL 154 (254)
T ss_pred cc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccccc-chhhhHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
Confidence 85 6999999999999999999999999999999865542 223335889999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhh--hh--hhhhHHHhhcCcccccchhhhcccchHHHhhhhhccccccchHHHHHHHHHHHHH
Q 019169 161 MRKVEILNVEKTTLTQQSQ--ND--KVLMMAQEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEA 236 (345)
Q Consensus 161 ~~~ve~Lk~ek~~le~~~~--~~--~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eLk~~ 236 (345)
|.+|+.|+.++++|++... .+ .++.++++|+|+||+|||||||++||++||+|||+|||||||++||++|++|++.
T Consensus 155 ~~~~e~Lk~ek~~le~~~~~~~~~~~~~~~~~~qkl~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~~IR~~l~el~e~ 234 (254)
T PF03194_consen 155 MEEVEKLKEEKEELEKELEEYRNSIENSAQSQQQKLEVCEVCGAFLSVGDNDRRLADHFGGKQHLGYAKIREKLKELKEK 234 (254)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhhhhhhhhcccccCccchhhhhhHHhccchHHHHHHHhccchhhhHHHHHHHHHHHHHH
Confidence 9999999999999998320 22 2223457999999999999999999999999999999999999999999999998
Q ss_pred HHHhH
Q 019169 237 KEKAR 241 (345)
Q Consensus 237 ~~~~~ 241 (345)
+.+..
T Consensus 235 ~~~~~ 239 (254)
T PF03194_consen 235 REERR 239 (254)
T ss_pred HHHHH
Confidence 76633
No 3
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=100.00 E-value=9.4e-63 Score=444.48 Aligned_cols=226 Identities=28% Similarity=0.476 Sum_probs=194.9
Q ss_pred HHHHHHHHHhcCCCCCCChhhhhhccccCCCCCCCcchhhcCCChhHhhhhcccCCCCCCCCCcHHHHHHHhcCCCCCCC
Q 019169 2 DAQRALLDELMGAARNLTEEEKKEYKEIKWDDKEVCPFYMVRFCPHDLFVNTRSDLGPCPRIHDQKLKESFEKSPRHDAY 81 (345)
Q Consensus 2 d~~RalLDeLMG~~Rn~~~~~~~~~~~~~~~D~~VCk~yL~g~CPhdLF~nTK~DlG~C~kiHd~~lK~~Ye~~~~~~~~ 81 (345)
++||++|+||||+++..-.. ...+||+|++||+||||||||||||+|||++||+||++|.+++|++|+...+...+
T Consensus 3 aeqRkv~eqLmG~~~s~f~~----~r~~hftd~kvC~s~Lvg~CP~dlF~nTk~slGkCp~~H~~k~K~~YeR~~~~~~~ 78 (258)
T COG5200 3 AEQRKVLEQLMGPERSTFDP----CRPTHFTDKKVCISMLVGFCPFDLFRNTKRSLGKCPTSHEEKYKAEYERNGRERAE 78 (258)
T ss_pred hHHHHHHHHHhCCCcccCCC----CCCccccchHHHHHHHHccCcHHHHhccccccCCCcchhHHHHHHHHhhhhhccch
Confidence 78999999999999863222 23468999999999999999999999999999999999999999999999988899
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHH
Q 019169 82 VPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALM 161 (345)
Q Consensus 82 ~~~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~ 161 (345)
+|||+|+..|..+|.+|+..|..|-.++..|+++- ..+.++.+.+..+.+.|+.|..+++.|...-.|+.|....
T Consensus 79 --~yEweyl~~L~r~V~~cn~~I~~a~~~~~~t~ee~---~kI~e~~e~~~~~d~sIg~lg~e~dalakrk~V~~a~~~f 153 (258)
T COG5200 79 --EYEWEYLRLLVRIVLSCNDGIRAAGLEDRTTPEEF---GKIKEKEELFNRVDESIGELGMEGDALAKRKLVERACSAF 153 (258)
T ss_pred --hhhHHHHHHHHHHHHHhcchhhhhhhhccCCHHHH---HhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999988887665332 2344555555555555555555555555555599999999
Q ss_pred HHHHHHHHHHHHHHhhhhh--hhhhhHHHhhcCcccccchhhhcccchHHHhhhhhccccccchHHHHHHHHHHHHHH
Q 019169 162 RKVEILNVEKTTLTQQSQN--DKVLMMAQEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEAK 237 (345)
Q Consensus 162 ~~ve~Lk~ek~~le~~~~~--~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eLk~~~ 237 (345)
.+++.|+.+++++...+ . ++|++++.+|||+||+|||||||.+|||+||||||.||+|+||+++|..|+.|-+..
T Consensus 154 ~el~rl~~~rkei~~~v-~sm~en~gq~thqklqvC~iCgayLsrlDtdrrladHf~GklHlGy~~~R~dl~~llk~~ 230 (258)
T COG5200 154 NELERLREERKEIKEAV-YSMVENNGQGTHQKLQVCGICGAYLSRLDTDRRLADHFNGKLHLGYLLVRSDLADLLKKF 230 (258)
T ss_pred HHHHHHHHHHHHHHHHH-HHHhhCcchhhhhhhhhhhhhhhHHHhcchhhHHHHHhccchhhhHHHHHHHHHHHHHHh
Confidence 99999999999999887 5 467788899999999999999999999999999999999999999999999887754
No 4
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=98.44 E-value=2.6e-06 Score=82.81 Aligned_cols=146 Identities=15% Similarity=0.101 Sum_probs=104.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHH
Q 019169 84 KFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRK 163 (345)
Q Consensus 84 ~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ 163 (345)
.++..++--.+ |+..|.+-|.-...+++...+....+ ..+..+......++|..|.++|+.|+++.+-.+.++.+.+
T Consensus 73 ~k~~~~~~E~d-~~~~l~~~v~d~~rri~~~kerL~e~--~ee~~~e~~~k~~~v~~l~e~I~~~l~~~E~LG~eG~Vee 149 (319)
T KOG0796|consen 73 SKERDYGYEWD-ALEILERFVADVDRRIEKAKERLAET--VEERSEEAARKAEKVHELEEKIGKLLEKAEELGEEGNVEE 149 (319)
T ss_pred hHhhhhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHhh--hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHH
Confidence 34455444444 89999999999999987654333211 1233344444477899999999999999999999999999
Q ss_pred HHHHHHHHHHHHh-hhhhhh----hhhHHHh-hcCcccccchhhhcccchHHHhhhhhccccccchH----------HHH
Q 019169 164 VEILNVEKTTLTQ-QSQNDK----VLMMAQE-KKMALCEICGSFLVANDAAERTQSHISGKQHIGYG----------MVR 227 (345)
Q Consensus 164 ve~Lk~ek~~le~-~~~~~~----~~~~~~~-qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~----------kIR 227 (345)
++.+..+.+.|.. +. ... +..+++. -+.+...||++|.+ .+-++.+ ||+
T Consensus 150 aq~~~~e~E~lk~~e~-e~~~~~~~~~~~~~~~~~qkl~VCeVCGa--------------~L~~~D~d~RlaDHf~GKlH 214 (319)
T KOG0796|consen 150 AQKAMKEVEELKAKEK-EEAEESYNTTMPGASAQQQKLRVCEVCGA--------------FLSVNDADRRLADHFGGKLH 214 (319)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHccCcchhhhhhhhhhHHHhhhH--------------HHhccchHHHHHHhhcchHH
Confidence 9999999999986 32 221 1122222 26788999999999 5566654 899
Q ss_pred HHHHHHHHHHHHhHHHHhhh
Q 019169 228 DFITEYKEAKEKAREEERLA 247 (345)
Q Consensus 228 e~l~eLk~~~~~~~e~~r~~ 247 (345)
-.|..+.+++.+..+.....
T Consensus 215 lGy~~iR~~l~eLk~~~~~~ 234 (319)
T KOG0796|consen 215 LGYVLIREKLAELKKEKAKR 234 (319)
T ss_pred HHHHHHHHHHHHHHHHHhHH
Confidence 99999999988765555443
No 5
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=97.14 E-value=0.0027 Score=60.75 Aligned_cols=138 Identities=15% Similarity=0.152 Sum_probs=101.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHH
Q 019169 91 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (345)
Q Consensus 91 ~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 170 (345)
.|-..|+..|.+-|...-.|++...+.....+........ ....++|..|..+|..|..+-+.-++++.+.+++.+..+
T Consensus 79 ~YE~e~~~~L~~~i~d~drrI~~~k~RL~~~~~~~~~~~~-~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~ 157 (254)
T PF03194_consen 79 GYEREFLRYLQRLIRDCDRRIERAKERLEQTQEEQAKEAD-EEKAEKIDELDEKIGELLKEAEELGEEGDVDEAQKLMEE 157 (254)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccccccchh-hhHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence 5889999999999999999998776433321111111111 112889999999999999999999999999999999999
Q ss_pred HHHHHhhhhhh-hh----hhH----HHhhcCcccccchhhhcccchHHHhhhhhccccccchH----------HHHHHHH
Q 019169 171 KTTLTQQSQND-KV----LMM----AQEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYG----------MVRDFIT 231 (345)
Q Consensus 171 k~~le~~~~~~-~~----~~~----~~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~----------kIRe~l~ 231 (345)
.+.|..+. .. .. ... +.....+-..||.++.+ .+-++.. ||+-.|.
T Consensus 158 ~e~Lk~ek-~~le~~~~~~~~~~~~~~~~~~qkl~VCeVCGA--------------~Ls~~D~d~RladH~~GK~HlGy~ 222 (254)
T PF03194_consen 158 VEKLKEEK-EELEKELEEYRNSIENSAQSQQQKLEVCEVCGA--------------FLSVGDNDRRLADHFGGKQHLGYA 222 (254)
T ss_pred HHHHHHHH-HHHHhhhhhhhhhhhhhhcccccCccchhhhhh--------------HHhccchHHHHHHHhccchhhhHH
Confidence 99998875 32 11 111 01245678899999998 5556554 8999999
Q ss_pred HHHHHHHHhHHHH
Q 019169 232 EYKEAKEKAREEE 244 (345)
Q Consensus 232 eLk~~~~~~~e~~ 244 (345)
.|++++++-.+..
T Consensus 223 ~IR~~l~el~e~~ 235 (254)
T PF03194_consen 223 KIREKLKELKEKR 235 (254)
T ss_pred HHHHHHHHHHHHH
Confidence 9999887754433
No 6
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=94.70 E-value=0.27 Score=45.98 Aligned_cols=144 Identities=13% Similarity=0.067 Sum_probs=91.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHH----HHHHH
Q 019169 92 FCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMR----KVEIL 167 (345)
Q Consensus 92 ~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~----~ve~L 167 (345)
|--.++..+.+-+.....++.....+ ...+++...+|+++++.|+-+-..|+.||.+|+.-.--++++ ...+|
T Consensus 80 yEweyl~~L~r~V~~cn~~I~~a~~~---~~~t~ee~~kI~e~~e~~~~~d~sIg~lg~e~dalakrk~V~~a~~~f~el 156 (258)
T COG5200 80 YEWEYLRLLVRIVLSCNDGIRAAGLE---DRTTPEEFGKIKEKEELFNRVDESIGELGMEGDALAKRKLVERACSAFNEL 156 (258)
T ss_pred hhHHHHHHHHHHHHHhcchhhhhhhh---ccCCHHHHHhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 67788888888888888887644211 135678889999999999999999999999987433333332 23333
Q ss_pred HHHHHHHHhhhhhhhhhh--HHHhhcCcccccchhhhcccchHHHhhhhhccccccchHHHHHHHHHHHHHHHHhHHH
Q 019169 168 NVEKTTLTQQSQNDKVLM--MAQEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEAKEKAREE 243 (345)
Q Consensus 168 k~ek~~le~~~~~~~~~~--~~~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eLk~~~~~~~e~ 243 (345)
+.-+...+.-+ .+-.++ ...|..-+..+|||.+.. +-.||+.---=--|.. .+|+-.|..+...+....+.
T Consensus 157 ~rl~~~rkei~-~~v~sm~en~gq~thqklqvC~iCga---yLsrlDtdrrladHf~-GklHlGy~~~R~dl~~llk~ 229 (258)
T COG5200 157 ERLREERKEIK-EAVYSMVENNGQGTHQKLQVCGICGA---YLSRLDTDRRLADHFN-GKLHLGYLLVRSDLADLLKK 229 (258)
T ss_pred HHHHHHHHHHH-HHHHHHhhCcchhhhhhhhhhhhhhh---HHHhcchhhHHHHHhc-cchhhhHHHHHHHHHHHHHH
Confidence 33333333322 111222 335667788999999977 4456543221111221 38888888888766555554
No 7
>KOG2888 consensus Putative RNA binding protein [General function prediction only]
Probab=93.61 E-value=0.043 Score=54.27 Aligned_cols=26 Identities=31% Similarity=0.442 Sum_probs=11.6
Q ss_pred hhcCCHHHHHHHHHHHHHHHHHHHHH
Q 019169 149 GEAGKVDEAEALMRKVEILNVEKTTL 174 (345)
Q Consensus 149 GeeG~VdeA~~l~~~ve~Lk~ek~~l 174 (345)
|+-|=|.-|.=|+=++=.|+--+++|
T Consensus 120 gaggivSTAyCLLYklftlklTrKQ~ 145 (453)
T KOG2888|consen 120 GAGGIVSTAYCLLYKLFTLKLTRKQL 145 (453)
T ss_pred CcCcchhhHHHHHHHHHHHHhHHHHH
Confidence 33344444444444444444444443
No 8
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=91.93 E-value=0.26 Score=51.94 Aligned_cols=17 Identities=12% Similarity=0.329 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHHH
Q 019169 158 EALMRKVEILNVEKTTL 174 (345)
Q Consensus 158 ~~l~~~ve~Lk~ek~~l 174 (345)
.++|..++.|+.+..+.
T Consensus 257 ~~~~~~~~~~~~qh~~~ 273 (757)
T KOG4368|consen 257 LAFQQQIQTLKTQHEEF 273 (757)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 35666777776665554
No 9
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=91.57 E-value=0.14 Score=51.79 Aligned_cols=38 Identities=13% Similarity=-0.010 Sum_probs=17.5
Q ss_pred hcCCCCCCChhhhhhccccCCCCCCCcchhhcCCChhHhhhhccc
Q 019169 11 LMGAARNLTEEEKKEYKEIKWDDKEVCPFYMVRFCPHDLFVNTRS 55 (345)
Q Consensus 11 LMG~~Rn~~~~~~~~~~~~~~~D~~VCk~yL~g~CPhdLF~nTK~ 55 (345)
||+...|++...-....-|.|+|+..- ---.+++||..
T Consensus 39 lyp~~~d~~~pv~sRtcyVkf~d~~sv-------~vaQhLtntvf 76 (479)
T KOG4676|consen 39 LYPNVDDSKIPVISRTCYVKFLDSQSV-------TVAQHLTNTVF 76 (479)
T ss_pred ccCCCCCccCcceeeeEEEeccCCcce-------eHHhhhcccee
Confidence 466555544322111233567666521 11345666654
No 10
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=90.08 E-value=0.22 Score=50.38 Aligned_cols=7 Identities=29% Similarity=0.349 Sum_probs=4.0
Q ss_pred ccccchH
Q 019169 218 KQHIGYG 224 (345)
Q Consensus 218 K~HlGy~ 224 (345)
-||.-|+
T Consensus 215 ~qhsr~a 221 (479)
T KOG4676|consen 215 RQHSRRA 221 (479)
T ss_pred hhhhhhh
Confidence 4566565
No 11
>PHA02562 46 endonuclease subunit; Provisional
Probab=87.88 E-value=8.7 Score=39.93 Aligned_cols=15 Identities=20% Similarity=0.503 Sum_probs=11.4
Q ss_pred cCcccccchhhhccc
Q 019169 191 KMALCEICGSFLVAN 205 (345)
Q Consensus 191 km~VCeVCGA~Ls~~ 205 (345)
.-.+|++|+.-+...
T Consensus 283 ~~~~Cp~C~~~~~~~ 297 (562)
T PHA02562 283 KGGVCPTCTQQISEG 297 (562)
T ss_pred CCCCCCCCCCcCCCc
Confidence 346999999887643
No 12
>PRK01156 chromosome segregation protein; Provisional
Probab=87.45 E-value=9.6 Score=42.33 Aligned_cols=15 Identities=7% Similarity=0.011 Sum_probs=12.1
Q ss_pred Ccccccchhhhcccc
Q 019169 192 MALCEICGSFLVAND 206 (345)
Q Consensus 192 m~VCeVCGA~Ls~~D 206 (345)
|.+|+||+.|+.-.+
T Consensus 449 l~~~~~Cp~c~~~~~ 463 (895)
T PRK01156 449 LNGQSVCPVCGTTLG 463 (895)
T ss_pred hccCCCCCCCCCcCC
Confidence 448999999988766
No 13
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=86.93 E-value=0.26 Score=30.67 Aligned_cols=25 Identities=20% Similarity=0.700 Sum_probs=21.3
Q ss_pred cccccchhhhcccchHHHhhhhhccccc
Q 019169 193 ALCEICGSFLVANDAAERTQSHISGKQH 220 (345)
Q Consensus 193 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~H 220 (345)
..|++|+..++ ++.=+..|+.||.|
T Consensus 2 ~~C~~C~k~f~---~~~~~~~H~~sk~H 26 (27)
T PF12171_consen 2 FYCDACDKYFS---SENQLKQHMKSKKH 26 (27)
T ss_dssp CBBTTTTBBBS---SHHHHHCCTTSHHH
T ss_pred CCcccCCCCcC---CHHHHHHHHccCCC
Confidence 47999997766 77779999999988
No 14
>PRK02224 chromosome segregation protein; Provisional
Probab=86.71 E-value=15 Score=40.62 Aligned_cols=13 Identities=23% Similarity=0.554 Sum_probs=10.3
Q ss_pred cCcccccchhhhc
Q 019169 191 KMALCEICGSFLV 203 (345)
Q Consensus 191 km~VCeVCGA~Ls 203 (345)
...+|++||..+.
T Consensus 450 ~~~~Cp~C~r~~~ 462 (880)
T PRK02224 450 EAGKCPECGQPVE 462 (880)
T ss_pred hcccCCCCCCcCC
Confidence 3579999998765
No 15
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=86.27 E-value=4.9 Score=38.37 Aligned_cols=19 Identities=26% Similarity=0.588 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 019169 93 CEKLVMDLDRRVRRGRERL 111 (345)
Q Consensus 93 L~~li~d~drkI~~~k~RL 111 (345)
++.=|.++..+|.++...|
T Consensus 64 ~e~ei~~~r~r~~~~e~kl 82 (239)
T COG1579 64 LESEIQEIRERIKRAEEKL 82 (239)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4555666667777776666
No 16
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=86.13 E-value=7.7 Score=35.71 Aligned_cols=82 Identities=22% Similarity=0.297 Sum_probs=67.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHH
Q 019169 91 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (345)
Q Consensus 91 ~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 170 (345)
..|..+|.+++.-|..++.-|.... ........++..+...|..+..+|+.....|+=+-|...+.....+..+
T Consensus 26 ~~l~q~ird~e~~l~~a~~~~a~~~------a~~~~le~~~~~~~~~~~~~~~~A~~Al~~g~edLAr~al~~k~~~e~~ 99 (221)
T PF04012_consen 26 KMLEQAIRDMEEQLRKARQALARVM------ANQKRLERKLDEAEEEAEKWEKQAELALAAGREDLAREALQRKADLEEQ 99 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 6789999999999999998886532 2334567789999999999999999999999999998888877777777
Q ss_pred HHHHHhhh
Q 019169 171 KTTLTQQS 178 (345)
Q Consensus 171 k~~le~~~ 178 (345)
...++..+
T Consensus 100 ~~~l~~~~ 107 (221)
T PF04012_consen 100 AERLEQQL 107 (221)
T ss_pred HHHHHHHH
Confidence 77776654
No 17
>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]
Probab=85.62 E-value=0.4 Score=51.71 Aligned_cols=9 Identities=44% Similarity=0.638 Sum_probs=3.8
Q ss_pred HHHHHHHHh
Q 019169 3 AQRALLDEL 11 (345)
Q Consensus 3 ~~RalLDeL 11 (345)
.||+-|+.|
T Consensus 431 ~qRdklE~l 439 (877)
T KOG0151|consen 431 LQRDKLEDL 439 (877)
T ss_pred HHHHHHHHH
Confidence 344444444
No 18
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=85.46 E-value=1.8 Score=48.08 Aligned_cols=35 Identities=23% Similarity=0.516 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHH
Q 019169 138 IKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKT 172 (345)
Q Consensus 138 I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~ 172 (345)
+..||.+||+|.+.|..++|+.++.+++.+.+-..
T Consensus 570 Lq~Mmd~ieela~~G~~~~A~qlL~qlq~mmenlq 604 (851)
T TIGR02302 570 LQNMMDQIENLARSGDRDQAKQLLSQLQQMMNNLQ 604 (851)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHh
Confidence 77999999999999999999999999988865443
No 19
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=85.33 E-value=0.29 Score=29.54 Aligned_cols=24 Identities=25% Similarity=0.699 Sum_probs=19.8
Q ss_pred ccccchhhhcccchHHHhhhhhccccc
Q 019169 194 LCEICGSFLVANDAAERTQSHISGKQH 220 (345)
Q Consensus 194 VCeVCGA~Ls~~D~d~Rl~dH~~GK~H 220 (345)
.|+||++-.. +..=+..|+.|+.|
T Consensus 2 ~C~~C~~~f~---s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 2 YCDICNKSFS---SENSLRQHLRSKKH 25 (25)
T ss_dssp EETTTTEEES---SHHHHHHHHTTHHH
T ss_pred CCCCCCCCcC---CHHHHHHHHCcCCC
Confidence 5999987665 66779999999987
No 20
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=85.03 E-value=0.36 Score=31.35 Aligned_cols=28 Identities=21% Similarity=0.538 Sum_probs=21.3
Q ss_pred cccccchhhhcccchHHHhhhhhccccccch
Q 019169 193 ALCEICGSFLVANDAAERTQSHISGKQHIGY 223 (345)
Q Consensus 193 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy 223 (345)
.-|++|+..+. +..=+..|+.||.|..-
T Consensus 4 ~~C~~C~~~~~---~~~~~~~H~~gk~H~~~ 31 (35)
T smart00451 4 FYCKLCNVTFT---DEISVEAHLKGKKHKKN 31 (35)
T ss_pred eEccccCCccC---CHHHHHHHHChHHHHHH
Confidence 45999999765 34445999999999643
No 21
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=82.40 E-value=6.3 Score=43.91 Aligned_cols=35 Identities=20% Similarity=0.588 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 135 EEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 135 ~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
...+..||.+||+|.++|..++|+.++.+++.+.+
T Consensus 537 ~~dL~~mmd~ie~la~~G~~~~A~q~L~qlq~mme 571 (820)
T PF13779_consen 537 QQDLQRMMDRIEELARSGRMDEARQLLEQLQQMME 571 (820)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 44567899999999999999999999999888765
No 22
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=82.23 E-value=32 Score=38.56 Aligned_cols=24 Identities=17% Similarity=0.340 Sum_probs=17.1
Q ss_pred CcccccchhhhcccchHHHhhhhhc
Q 019169 192 MALCEICGSFLVANDAAERTQSHIS 216 (345)
Q Consensus 192 m~VCeVCGA~Ls~~D~d~Rl~dH~~ 216 (345)
..+|+|||.-|- +.....+.+|+.
T Consensus 457 ~~~CPvCg~~l~-~~~~~~~~~~~~ 480 (908)
T COG0419 457 GEKCPVCGQELP-EEHEKELLELYE 480 (908)
T ss_pred CCCCCCCCCCCC-cHHHHHHHHHHH
Confidence 578999995544 333667888887
No 23
>PRK06835 DNA replication protein DnaC; Validated
Probab=80.38 E-value=11 Score=37.46 Aligned_cols=71 Identities=14% Similarity=0.128 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCC---HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcc
Q 019169 130 QLSVLEEKIKNLLEQVETLGEAGK---VDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVA 204 (345)
Q Consensus 130 ~i~~l~ekI~~ll~eaE~LGeeG~---VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~ 204 (345)
+|.+|+.+|..+-.++-...-.|+ -+....+-+++..|..++.+|-... .-+ ...-..-..|+.|+=-..+
T Consensus 37 ~~~~id~~i~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~~lL~~~-g~~---~dyl~~~y~Cp~C~dtG~i 110 (329)
T PRK06835 37 EIAEIDDEIAKLGIKLSRAILKNPDKKEETLKELKEKITDLRVKKAELLVSN-GYP---PDYLEMKYTCPKCKDTGFI 110 (329)
T ss_pred cHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHHHHc-CCC---hhhcCCCCCCCCCCCCCCc
Confidence 456667777666555544444555 4455567777888888877776543 110 0011222579999876555
No 24
>KOG2888 consensus Putative RNA binding protein [General function prediction only]
Probab=80.31 E-value=0.82 Score=45.48 Aligned_cols=10 Identities=20% Similarity=0.208 Sum_probs=4.1
Q ss_pred HHHHHHHHHH
Q 019169 89 LAQFCEKLVM 98 (345)
Q Consensus 89 ~~~~L~~li~ 98 (345)
|..+++.||.
T Consensus 174 Lw~WyEpyld 183 (453)
T KOG2888|consen 174 LWDWYEPYLD 183 (453)
T ss_pred HHHHhhhhcc
Confidence 3334444443
No 25
>PRK15058 cytochrome b562; Provisional
Probab=76.11 E-value=9.7 Score=33.06 Aligned_cols=42 Identities=19% Similarity=0.251 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHH---HHHHHhhcCCHHHHHHHHHHHHHHHHH
Q 019169 129 EQLSVLEEKIKNLLE---QVETLGEAGKVDEAEALMRKVEILNVE 170 (345)
Q Consensus 129 e~i~~l~ekI~~ll~---eaE~LGeeG~VdeA~~l~~~ve~Lk~e 170 (345)
.++..+.+-++.|+. +++.|.++|++++|.....++..|+.+
T Consensus 78 ~e~K~Y~~G~d~Li~qID~a~~la~~GkL~eAK~~a~~l~~lR~e 122 (128)
T PRK15058 78 PEMKDFRHGFDILVGQIDGALKLANEGKVKEAQAAAEQLKTTRNA 122 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 455555555555544 556799999999999999888888754
No 26
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=76.00 E-value=6.4 Score=41.97 Aligned_cols=8 Identities=38% Similarity=0.725 Sum_probs=4.0
Q ss_pred hhhhcccC
Q 019169 49 LFVNTRSD 56 (345)
Q Consensus 49 LF~nTK~D 56 (345)
+|.|.+++
T Consensus 129 ~f~~~~s~ 136 (757)
T KOG4368|consen 129 MFSNAKSP 136 (757)
T ss_pred hhhcCCCc
Confidence 35555544
No 27
>PRK09720 cybC cytochrome b562; Provisional
Probab=75.64 E-value=11 Score=31.33 Aligned_cols=42 Identities=24% Similarity=0.298 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHHH---HHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 128 SEQLSVLEEKIKNLLEQ---VETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~e---aE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
..++..+..-+..|+.+ +..|..+|+++||.....++-.++.
T Consensus 49 s~e~K~y~~Gld~lI~qID~A~~La~~GkL~eAK~~a~~l~~~Rn 93 (100)
T PRK09720 49 SPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRN 93 (100)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 34555666666655555 4569999999999987776666654
No 28
>PF14282 FlxA: FlxA-like protein
Probab=75.28 E-value=11 Score=31.43 Aligned_cols=52 Identities=27% Similarity=0.445 Sum_probs=35.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
.....|..|..+|..|.+++..|......+ +.....+++.|+.++..|+.++
T Consensus 16 ~~~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~-~e~k~~q~q~Lq~QI~~LqaQI 67 (106)
T PF14282_consen 16 SSDSQIEQLQKQIKQLQEQLQELSQDSDLD-AEQKQQQIQLLQAQIQQLQAQI 67 (106)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHcccCCC-HHHHHHHHHHHHHHHHHHHHHH
Confidence 347889999999999999999999954432 2223455555666666555554
No 29
>PF07361 Cytochrom_B562: Cytochrome b562; InterPro: IPR009155 Cytochrome b562 is a haem-containing protein that is expressed in the periplasm of Escherichia coli. In b-type cytochromes, the haem atom is not covalently attached to the polypeptide. Cytochrome b562 has a four-helical bundle structure that is structurally similar to that found in members of the cytochrome c family (IPR002321 from INTERPRO). Cytochrome b562 has a reduction potential of 167 mV, which sets the energy yield possible in metabolism and is also a key determinant of the rate at which redox reactions proceed [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0042597 periplasmic space; PDB: 4ER9_A 3IQ6_G 2QLA_B 3FOO_A 3M79_C 256B_A 3NMI_F 3HNK_A 3NMK_D 2BC5_A ....
Probab=74.09 E-value=27 Score=28.89 Aligned_cols=42 Identities=36% Similarity=0.597 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHH---HHHHHHhhcCCHHHHHHHHHHHHHHHHH
Q 019169 129 EQLSVLEEKIKNLL---EQVETLGEAGKVDEAEALMRKVEILNVE 170 (345)
Q Consensus 129 e~i~~l~ekI~~ll---~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 170 (345)
.++..+.+-++.|+ ..|+.|.+.|++++|...+.++..|+.+
T Consensus 53 ~~~~~Y~~Gl~~li~~id~a~~~~~~G~l~~AK~~l~~l~~lR~e 97 (103)
T PF07361_consen 53 AEVKDYQEGLDKLIDQIDKAEALAEAGKLDEAKAALKKLDDLRKE 97 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34455555555444 4567799999999999999999999864
No 30
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=73.05 E-value=75 Score=29.03 Aligned_cols=51 Identities=27% Similarity=0.421 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhc-CCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEA-GKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGee-G~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
..+|..+..+|..+-.+++.+... ++-++-..++++++.|+.+.+.|..++
T Consensus 75 ~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el 126 (188)
T PF03962_consen 75 QKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKEL 126 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444455555444444444222 122233445555555555555555443
No 31
>smart00356 ZnF_C3H1 zinc finger.
Probab=71.76 E-value=2.3 Score=25.81 Aligned_cols=23 Identities=30% Similarity=0.834 Sum_probs=17.1
Q ss_pred CCCcchhhcCCChhHhhhhcccCCCCCCCCCc
Q 019169 34 KEVCPFYMVRFCPHDLFVNTRSDLGPCPRIHD 65 (345)
Q Consensus 34 ~~VCk~yL~g~CPhdLF~nTK~DlG~C~kiHd 65 (345)
+.+|++|+.|.||+. ..|+-.|+
T Consensus 4 ~~~C~~~~~g~C~~g---------~~C~~~H~ 26 (27)
T smart00356 4 TELCKFFKRGYCPYG---------DRCKFAHP 26 (27)
T ss_pred CCcCcCccCCCCCCC---------CCcCCCCc
Confidence 358999999999752 25777775
No 32
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=71.38 E-value=44 Score=31.02 Aligned_cols=79 Identities=15% Similarity=0.190 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHH
Q 019169 91 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (345)
Q Consensus 91 ~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 170 (345)
..|..+|.+++.-|..++.=|+... ........++..+...|.....+++.....|+=+-|...+.+.......
T Consensus 27 ~~l~q~irem~~~l~~ar~~lA~~~------a~~k~~e~~~~~~~~~~~~~~~~A~~Al~~G~EdLAr~Al~~k~~~~~~ 100 (219)
T TIGR02977 27 KMIRLIIQEMEDTLVEVRTTSARTI------ADKKELERRVSRLEAQVADWQEKAELALSKGREDLARAALIEKQKAQEL 100 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4578888888888888877776432 1223456789999999999999999999999988887665444444433
Q ss_pred HHHHH
Q 019169 171 KTTLT 175 (345)
Q Consensus 171 k~~le 175 (345)
...|+
T Consensus 101 ~~~l~ 105 (219)
T TIGR02977 101 AEALE 105 (219)
T ss_pred HHHHH
Confidence 33333
No 33
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=70.72 E-value=38 Score=34.18 Aligned_cols=99 Identities=27% Similarity=0.411 Sum_probs=57.8
Q ss_pred hhHhhhhcccCCCCCCCC-CcHHHHHHHhcCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCc
Q 019169 46 PHDLFVNTRSDLGPCPRI-HDQKLKESFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPIS 124 (345)
Q Consensus 46 PhdLF~nTK~DlG~C~ki-Hd~~lK~~Ye~~~~~~~~~~~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~ 124 (345)
|+--.++|+..|-.-... -++++++.-..+-+...+.|-||. .+++++-++|. ..|.. ..
T Consensus 17 p~le~sq~~FlLt~p~~~~~~~~~~e~l~~~Ird~~Map~Ye~----lce~~~i~~D~------~~l~~---------m~ 77 (393)
T KOG0687|consen 17 PDLELSQLRFLLTHPEVLGQKAAAREKLLAAIRDEDMAPLYEY----LCESLVIKLDQ------DLLNS---------MK 77 (393)
T ss_pred cchhHHHHHHHHcCccccCcCHHHHHHHHHHHHhcccchHHHH----HHhhcceeccH------HHHHH---------HH
Confidence 455556666665433222 467777777666555556566765 23333333332 22321 22
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
+.+.++|.+|+++| +.+|+. .|+.+.+++.+.++|=+..
T Consensus 78 ~~neeki~eld~~i----edaeen--lGE~ev~ea~~~kaeYycq 116 (393)
T KOG0687|consen 78 KANEEKIKELDEKI----EDAEEN--LGESEVREAMLRKAEYYCQ 116 (393)
T ss_pred HhhHHHHHHHHHHH----HHHHHh--cchHHHHHHHHHHHHHHHH
Confidence 34456677766555 445554 6888999999999998874
No 34
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=69.80 E-value=13 Score=30.38 Aligned_cols=50 Identities=28% Similarity=0.375 Sum_probs=39.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 127 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 127 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
...++..|..+.+.+.++|-.+...| +++..+++++..++.+...++.++
T Consensus 41 l~~~~e~lr~~rN~~sk~I~~~~~~~--~~~~~l~~e~~~lk~~i~~le~~~ 90 (108)
T PF02403_consen 41 LQQELEELRAERNELSKEIGKLKKAG--EDAEELKAEVKELKEEIKELEEQL 90 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCHTT--CCTHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhHHHHHHHHHhhCc--ccHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567778888888888888888888 667788888888888888888765
No 35
>PRK14143 heat shock protein GrpE; Provisional
Probab=69.63 E-value=32 Score=32.86 Aligned_cols=86 Identities=15% Similarity=0.274 Sum_probs=55.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhccc
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVAN 205 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~ 205 (345)
....++..|..+|..|-+++++|- +.-+.+.+..+-++. ..+++. ....+.-++.+.-.+|-+.
T Consensus 64 ~~~~~~~~l~~el~~l~~e~~elk-----d~~lR~~AdfeN~RK---R~~kE~--------e~~~~~a~~~~~~~lLpV~ 127 (238)
T PRK14143 64 DNAARLAQLEQELESLKQELEELN-----SQYMRIAADFDNFRK---RTSREQ--------EDLRLQLKCNTLSEILPVV 127 (238)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH--------HHHHHHHHHHHHHHHHHHH
Confidence 345577888888888888888774 334455555555543 222211 0123446778889999999
Q ss_pred chHHHhhhhhcc------ccccchHHHH
Q 019169 206 DAAERTQSHISG------KQHIGYGMVR 227 (345)
Q Consensus 206 D~d~Rl~dH~~G------K~HlGy~kIR 227 (345)
|+-.|.-.|+.. .++-||..|.
T Consensus 128 DnLerAl~~~~~~~~~~~~l~~Gve~i~ 155 (238)
T PRK14143 128 DNFERARQQLKPEGEEAQALHRSYQGLY 155 (238)
T ss_pred hHHHHHHhcccccchhHHHHHHHHHHHH
Confidence 999998777743 3566776663
No 36
>PRK03918 chromosome segregation protein; Provisional
Probab=69.63 E-value=44 Score=36.88 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=5.1
Q ss_pred ccccchhhhc
Q 019169 194 LCEICGSFLV 203 (345)
Q Consensus 194 VCeVCGA~Ls 203 (345)
||+|||.-|.
T Consensus 437 ~Cp~c~~~L~ 446 (880)
T PRK03918 437 KCPVCGRELT 446 (880)
T ss_pred CCCCCCCcCC
Confidence 5555555444
No 37
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=68.39 E-value=3 Score=28.54 Aligned_cols=32 Identities=22% Similarity=0.441 Sum_probs=17.6
Q ss_pred cccccchhhhcccchHHHhhhhhccccccchHH
Q 019169 193 ALCEICGSFLVANDAAERTQSHISGKQHIGYGM 225 (345)
Q Consensus 193 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~k 225 (345)
.-|+.|..+|. +|+..=...|..|..|..=++
T Consensus 4 yyCdyC~~~~~-~d~~~~Rk~H~~G~kH~~nv~ 35 (38)
T PF06220_consen 4 YYCDYCKKYLT-HDSPSIRKQHERGWKHKENVK 35 (38)
T ss_dssp -B-TTT--B-S---SHHHHHHHT--THHHHHHH
T ss_pred eecccccceec-CCChHHHHHhhccHHHHHHHH
Confidence 57999999975 566555689999999986544
No 38
>PF13863 DUF4200: Domain of unknown function (DUF4200)
Probab=66.86 E-value=22 Score=29.63 Aligned_cols=51 Identities=18% Similarity=0.335 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 019169 92 FCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETL 148 (345)
Q Consensus 92 ~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~L 148 (345)
-+..||.+++.+..+|..+.+... .....+..+|..|..+|..|-.++..|
T Consensus 50 ~f~~flken~~k~~rA~k~a~~e~------k~~~~k~~ei~~l~~~l~~l~~~~~k~ 100 (126)
T PF13863_consen 50 KFDKFLKENEAKRERAEKRAEEEK------KKKEEKEAEIKKLKAELEELKSEISKL 100 (126)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788888888888877775432 122333444444444444444444443
No 39
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=65.70 E-value=86 Score=26.82 Aligned_cols=70 Identities=27% Similarity=0.326 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 019169 87 AELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEI 166 (345)
Q Consensus 87 ~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~ 166 (345)
--++..|+.-|..++--|...+..|+. ...+-..+.++|-.|+.+.+.+ .....++..
T Consensus 15 ~~~ve~L~s~lr~~E~E~~~l~~el~~-------------l~~~r~~l~~Eiv~l~~~~e~~---------~~~~~~~~~ 72 (120)
T PF12325_consen 15 VQLVERLQSQLRRLEGELASLQEELAR-------------LEAERDELREEIVKLMEENEEL---------RALKKEVEE 72 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHH
Confidence 346677888888888888887777742 2234456677777777777666 345555566
Q ss_pred HHHHHHHHHhhh
Q 019169 167 LNVEKTTLTQQS 178 (345)
Q Consensus 167 Lk~ek~~le~~~ 178 (345)
|+.+.+.|...+
T Consensus 73 L~~el~~l~~ry 84 (120)
T PF12325_consen 73 LEQELEELQQRY 84 (120)
T ss_pred HHHHHHHHHHHH
Confidence 666666666554
No 40
>KOG1847 consensus mRNA splicing factor [RNA processing and modification]
Probab=64.45 E-value=9.6 Score=41.18 Aligned_cols=13 Identities=31% Similarity=0.445 Sum_probs=7.3
Q ss_pred hhcccccccCCCC
Q 019169 292 RDRERSREWDGRS 304 (345)
Q Consensus 292 r~r~r~r~~~~r~ 304 (345)
..+.++|.+|+++
T Consensus 765 s~~k~~rhhRS~~ 777 (878)
T KOG1847|consen 765 SKDKRSRHHRSRK 777 (878)
T ss_pred ccccccccccCcc
Confidence 4455556666655
No 41
>PRK14158 heat shock protein GrpE; Provisional
Probab=63.76 E-value=59 Score=30.11 Aligned_cols=77 Identities=16% Similarity=0.111 Sum_probs=48.9
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhc
Q 019169 124 SAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLV 203 (345)
Q Consensus 124 ~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls 203 (345)
.....+.+..++++|..+.+++++|- +.-+.+.++.+-++. ..+.+. . ...+..+-.++-.+|-
T Consensus 35 ~~~~~~~~~~le~~l~~le~e~~el~-----d~~lR~~AefeN~Rk---R~~kE~-e-------~~~~~a~~~~~~~lLp 98 (194)
T PRK14158 35 PVAAADRIKELEEALAAKEAEAAANW-----DKYLRERADLENYRK---RVQKEK-E-------ELLKYGNESLILEILP 98 (194)
T ss_pred CCCchhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH-H-------HHHHHHHHHHHHHHHh
Confidence 44556678888989988888888884 333444444444432 222221 1 1233455568889999
Q ss_pred ccchHHHhhhhhc
Q 019169 204 ANDAAERTQSHIS 216 (345)
Q Consensus 204 ~~D~d~Rl~dH~~ 216 (345)
+.|+-.|.-.|..
T Consensus 99 V~DnLerAl~~~~ 111 (194)
T PRK14158 99 AVDNMERALDHAD 111 (194)
T ss_pred HHhHHHHHHhccC
Confidence 9999999767764
No 42
>PRK14144 heat shock protein GrpE; Provisional
Probab=63.58 E-value=46 Score=30.97 Aligned_cols=89 Identities=11% Similarity=0.180 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccch
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 207 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~ 207 (345)
..++..+.++|..+-+++++|- +..+.+.++.+-++. .++.+. . ...+..+=.++-++|-+.|+
T Consensus 44 ~~~~~~l~~~i~~le~e~~elk-----dk~lR~~AefeN~RK---R~~kE~-e-------~~~~~a~~~~~~~LLpV~Dn 107 (199)
T PRK14144 44 HPSYTALEEQLTLAEQKAHENW-----EKSVRALAELENVRR---RMEREV-A-------NAHKYGVEKLISALLPVVDS 107 (199)
T ss_pred chhHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH-H-------HHHHHHHHHHHHHHhhHHhH
Confidence 3556678888888888888773 555666666666543 222221 1 11122333477889999999
Q ss_pred HHHhhhhhc----cccccchHHHHHHHHH
Q 019169 208 AERTQSHIS----GKQHIGYGMVRDFITE 232 (345)
Q Consensus 208 d~Rl~dH~~----GK~HlGy~kIRe~l~e 232 (345)
-.|.-.|.. +.++-|+..|...+..
T Consensus 108 LerAl~~~~~~~~~~i~~Gv~mi~k~l~~ 136 (199)
T PRK14144 108 LEQALQLADKNSDPSMHEGLELTMKLFLD 136 (199)
T ss_pred HHHHHHcccccchhHHHHHHHHHHHHHHH
Confidence 999766653 3355566655444433
No 43
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=63.39 E-value=25 Score=32.11 Aligned_cols=38 Identities=21% Similarity=0.241 Sum_probs=28.1
Q ss_pred HhhcCcccccchhhhcccchHHHhhhhhccccccchHHHHHHHHHHHHHH
Q 019169 188 QEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEAK 237 (345)
Q Consensus 188 ~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eLk~~~ 237 (345)
+....++|+.||+-|--.|+.. .+..+...+++|.+.+
T Consensus 128 A~~~~F~Cp~Cg~~L~~~d~s~------------~i~~l~~~i~~l~~~l 165 (176)
T COG1675 128 AMELGFTCPKCGEDLEEYDSSE------------EIEELESELDELEEEL 165 (176)
T ss_pred HHHhCCCCCCCCchhhhccchH------------HHHHHHHHHHHHHHHH
Confidence 4456699999999999999887 4555666666666554
No 44
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=62.61 E-value=4.1 Score=40.63 Aligned_cols=17 Identities=12% Similarity=0.200 Sum_probs=8.4
Q ss_pred cchHHHHHHHHHHHHHH
Q 019169 221 IGYGMVRDFITEYKEAK 237 (345)
Q Consensus 221 lGy~kIRe~l~eLk~~~ 237 (345)
..|..|...++.++.+.
T Consensus 234 p~~~li~~~vd~~k~~~ 250 (367)
T KOG0835|consen 234 PDETLIEAFVDRLKRKF 250 (367)
T ss_pred cCHHHHHHHHHHhhHHH
Confidence 33445555555555544
No 45
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=60.06 E-value=1.2e+02 Score=29.15 Aligned_cols=82 Identities=17% Similarity=0.117 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCC--Cch---------hhHHHHHHHHHHHHHHHHHHHHHhhcCCHHH
Q 019169 88 ELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPP--ISA---------EKSEQLSVLEEKIKNLLEQVETLGEAGKVDE 156 (345)
Q Consensus 88 e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~--~~~---------e~~e~i~~l~ekI~~ll~eaE~LGeeG~Vde 156 (345)
.-+.-|+.-+..+-..|..+++.|....+...... +.. .....+..+ ..|..+...++.|.++|+..+
T Consensus 67 ~~v~el~~~l~~a~~~~~~~R~~L~~~~~~~~~~~L~Il~~~rkr~~l~~ll~~L~~i-~~v~~~~~~l~~ll~~~dy~~ 145 (291)
T PF10475_consen 67 SSVQELQDELEEALVICKNLRRNLKSADENLTKSGLEILRLQRKRQNLKKLLEKLEQI-KTVQQTQSRLQELLEEGDYPG 145 (291)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhcCCHHH
Confidence 44556677777777888888888876543221100 000 111122222 344567788899999999999
Q ss_pred HHHHHHHHHHHHHH
Q 019169 157 AEALMRKVEILNVE 170 (345)
Q Consensus 157 A~~l~~~ve~Lk~e 170 (345)
|..++.+++.+-.+
T Consensus 146 Al~li~~~~~~l~~ 159 (291)
T PF10475_consen 146 ALDLIEECQQLLEE 159 (291)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999988654
No 46
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=59.91 E-value=99 Score=29.22 Aligned_cols=82 Identities=18% Similarity=0.270 Sum_probs=64.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHH
Q 019169 91 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (345)
Q Consensus 91 ~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 170 (345)
..|+..|.+++.-+..++.=+++.. ........++..+...+..+-.+++.+...|+-+=|-..+.++..|...
T Consensus 27 ~~l~Q~ird~~~~l~~ar~~~A~~~------a~~k~~e~~~~~~~~~~~k~e~~A~~Al~~g~E~LAr~al~~~~~le~~ 100 (225)
T COG1842 27 KMLEQAIRDMESELAKARQALAQAI------ARQKQLERKLEEAQARAEKLEEKAELALQAGNEDLAREALEEKQSLEDL 100 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6788888888888888877776532 1334556789999999999999999999999988888888888888777
Q ss_pred HHHHHhhh
Q 019169 171 KTTLTQQS 178 (345)
Q Consensus 171 k~~le~~~ 178 (345)
.+.+...+
T Consensus 101 ~~~~~~~~ 108 (225)
T COG1842 101 AKALEAEL 108 (225)
T ss_pred HHHHHHHH
Confidence 77766654
No 47
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=59.00 E-value=40 Score=38.59 Aligned_cols=10 Identities=40% Similarity=0.863 Sum_probs=8.4
Q ss_pred Ccccccchhh
Q 019169 192 MALCEICGSF 201 (345)
Q Consensus 192 m~VCeVCGA~ 201 (345)
-++|+|||+.
T Consensus 503 GePCPVCGS~ 512 (1047)
T PRK10246 503 GQPCPLCGST 512 (1047)
T ss_pred CCCcCCCCcc
Confidence 3899999984
No 48
>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.
Probab=58.60 E-value=31 Score=22.96 Aligned_cols=35 Identities=26% Similarity=0.332 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHH
Q 019169 136 EKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (345)
Q Consensus 136 ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 170 (345)
+.|..|..+.+.+.+..+.++|..+-.++..|+.+
T Consensus 2 ~~i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~~q 36 (36)
T PF02151_consen 2 KLIKELEEKMEEAVENEDFEKAARLRDQIKALKKQ 36 (36)
T ss_dssp HHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHcC
Confidence 56788889999999999999999998888888753
No 49
>PRK10698 phage shock protein PspA; Provisional
Probab=58.56 E-value=96 Score=29.04 Aligned_cols=76 Identities=16% Similarity=0.162 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHH-------HHHHH
Q 019169 92 FCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEA-------LMRKV 164 (345)
Q Consensus 92 ~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~-------l~~~v 164 (345)
.|..+|.++..-+..++.=|+... ........++..+...|...-.+++.....|+=+-|-. ...++
T Consensus 28 ~l~q~i~em~~~l~~~r~alA~~~------A~~k~~er~~~~~~~~~~~~e~kA~~Al~~G~EdLAr~AL~~K~~~~~~~ 101 (222)
T PRK10698 28 LVRLMIQEMEDTLVEVRSTSARAL------AEKKQLTRRIEQAEAQQVEWQEKAELALRKEKEDLARAALIEKQKLTDLI 101 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455666666666666655444321 12234567888999999999999999999999888877 44444
Q ss_pred HHHHHHHHH
Q 019169 165 EILNVEKTT 173 (345)
Q Consensus 165 e~Lk~ek~~ 173 (345)
..|+.+.+.
T Consensus 102 ~~l~~~~~~ 110 (222)
T PRK10698 102 ATLEHEVTL 110 (222)
T ss_pred HHHHHHHHH
Confidence 444444443
No 50
>PF01895 PhoU: PhoU domain; InterPro: IPR008170 This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle []. The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect; suggesting that the protein has some secondary function []. ; PDB: 2I0M_A 1T72_B 1T8B_A 1SUM_B 1VCT_A 2BKN_A 2BKP_A 2BKO_A.
Probab=58.49 E-value=74 Score=23.66 Aligned_cols=82 Identities=13% Similarity=0.126 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccchHHH
Q 019169 131 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAER 210 (345)
Q Consensus 131 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~R 210 (345)
|..+.+.+..++..+-..-..++.+.|+.+...-+.+......+.... ... ....+.+.-=.-+-.++.+..+=+|
T Consensus 1 i~~m~~~~~~~l~~~~~~~~~~d~~~a~~i~~~e~~id~~~~~~~~~~-~~~---~~~~~~~~~~~~~~~~~~i~~~lER 76 (88)
T PF01895_consen 1 ISEMGELVEEMLDDAIEAFEERDSELAQEIIQLEEEIDELYREIRRQI-LKI---LKNQNPLEELRELVGLLRIARDLER 76 (88)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHH-HHH---HHHHCGHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhHHHHHHHHHHHHHHH-HHH---HhhCCCHHHHHHHHHHHHHHHHHHH
Confidence 456677788888888888888888777666655555544444443332 110 0011100000114556777788888
Q ss_pred hhhhhc
Q 019169 211 TQSHIS 216 (345)
Q Consensus 211 l~dH~~ 216 (345)
++||..
T Consensus 77 igD~~~ 82 (88)
T PF01895_consen 77 IGDHAV 82 (88)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 888864
No 51
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=57.52 E-value=26 Score=27.13 Aligned_cols=60 Identities=20% Similarity=0.379 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccch
Q 019169 137 KIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 207 (345)
Q Consensus 137 kI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~ 207 (345)
.|+-|.+-|..+...+..+-|...+..+..+-.+. . ...+.+.+..+|.-||.+|+-+-|
T Consensus 2 Ri~~L~~~a~~~~~~~~~~lsr~y~~~~~~i~~k~--------~---~~l~~~~kr~~Ck~C~~~liPG~~ 61 (85)
T PF04032_consen 2 RINFLYQAAHLLLADGSPSLSRHYMKLMRKISKKT--------R---IRLPPEIKRTICKKCGSLLIPGVN 61 (85)
T ss_dssp HHHHHHHHHH-HHCCC-HHHHHHHHHHHHHHHHHC--------T------STTCCCTB-TTT--B--CTTT
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHh--------C---CCCChHHhcccccCCCCEEeCCCc
Confidence 46666666666678888888888887777665321 0 123355788999999999987654
No 52
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=57.32 E-value=9.4 Score=34.45 Aligned_cols=39 Identities=21% Similarity=0.576 Sum_probs=30.5
Q ss_pred cccccchhhhcccchHHHhhhhhccccccchHHHHHHHHHHH
Q 019169 193 ALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYK 234 (345)
Q Consensus 193 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eLk 234 (345)
.-||-|..||. +|+..=--.|.+|+.|+--++ ..|.+..
T Consensus 4 YyCDYCdt~Lt-hDslsvRK~H~~GrkH~~nvk--~YY~k~~ 42 (165)
T KOG3454|consen 4 YYCDYCDTYLT-HDSLSVRKTHCGGRKHKDNVK--DYYQKWM 42 (165)
T ss_pred chhhhhhhhhh-cccHHHHHhhhhhHHHHHHHH--HHHHHHH
Confidence 35999999986 999999999999999986543 4444443
No 53
>PRK14148 heat shock protein GrpE; Provisional
Probab=57.07 E-value=75 Score=29.46 Aligned_cols=72 Identities=21% Similarity=0.282 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccchH
Q 019169 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAA 208 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d 208 (345)
.++..++++|..+-+++++|- +.-+.+.++.+-++. .++.+. ....+.-++.+.-.+|-+.|+-
T Consensus 40 ~e~~~l~~~l~~l~~e~~elk-----d~~lR~~Ae~eN~rK---R~~rE~--------e~~~~~a~~~~~~~LLpV~Dnl 103 (195)
T PRK14148 40 EQLERAKDTIKELEDSCDQFK-----DEALRAKAEMENIRK---RAERDV--------SNARKFGIEKFAKELLPVIDSI 103 (195)
T ss_pred hHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH--------HHHHHHHHHHHHHHHhhHHhHH
Confidence 456677777777777777763 333444444444432 122111 1223445667888999999999
Q ss_pred HHhhhhhc
Q 019169 209 ERTQSHIS 216 (345)
Q Consensus 209 ~Rl~dH~~ 216 (345)
.|.-.|..
T Consensus 104 erAl~~~~ 111 (195)
T PRK14148 104 EQALKHEV 111 (195)
T ss_pred HHHHhccc
Confidence 99777764
No 54
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=56.35 E-value=7 Score=24.16 Aligned_cols=20 Identities=30% Similarity=0.684 Sum_probs=15.5
Q ss_pred CcccccchhhhcccchHHHhhhhh
Q 019169 192 MALCEICGSFLVANDAAERTQSHI 215 (345)
Q Consensus 192 m~VCeVCGA~Ls~~D~d~Rl~dH~ 215 (345)
|.+|.+||- .-+..+|+.|.
T Consensus 2 l~~C~~CgR----~F~~~~l~~H~ 21 (25)
T PF13913_consen 2 LVPCPICGR----KFNPDRLEKHE 21 (25)
T ss_pred CCcCCCCCC----EECHHHHHHHH
Confidence 689999994 44677888885
No 55
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=56.05 E-value=80 Score=25.12 Aligned_cols=76 Identities=20% Similarity=0.158 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcCCC-CCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 93 CEKLVMDLDRRVRRGRERLSQEVEP-APPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 93 L~~li~d~drkI~~~k~RL~~~~e~-~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
.-..|.++|.++......+...... ............+...+-.+|...+.++..|+++ +|.-|..+...|+.-..
T Consensus 20 ~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~l~de-Kv~lA~~~~d~v~~hi~ 96 (105)
T PF12998_consen 20 NLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERALELSDE-KVALAQQAYDLVDRHIR 96 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 3356667777666655555432100 0000010111235667778888888888888876 56666666655555443
No 56
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=55.74 E-value=48 Score=24.96 Aligned_cols=59 Identities=29% Similarity=0.416 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcC-CCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHh
Q 019169 91 QFCEKLVMDLDRRVRRGRERLSQEV-EPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLG 149 (345)
Q Consensus 91 ~~L~~li~d~drkI~~~k~RL~~~~-e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LG 149 (345)
.-|++=+..+...|.....+|.... -...|+.+.....+++..+..+|..+...++.|+
T Consensus 7 ~rL~Kel~kl~~~i~~~~~kL~n~~F~~kAP~eVve~er~kl~~~~~~~~~l~~~l~~Lk 66 (66)
T PF10458_consen 7 ERLEKELEKLEKEIERLEKKLSNENFVEKAPEEVVEKEREKLEELEEELEKLEEALEQLK 66 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCSTTHHHHS-CCHHHHHHHHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3467777888888999988886321 0122334556677889999999999988888774
No 57
>PRK14162 heat shock protein GrpE; Provisional
Probab=55.29 E-value=68 Score=29.69 Aligned_cols=75 Identities=20% Similarity=0.192 Sum_probs=46.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhccc
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVAN 205 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~ 205 (345)
+...++..|+.+|..+-+++++|- +.-+.+.++.+-++. ..+++. . ...+..+-.++-.+|-+.
T Consensus 36 ~~~~e~~~l~~~l~~l~~e~~elk-----d~~lR~~AEfeN~rk---R~~kE~-e-------~~~~~a~~~~~~~LLpV~ 99 (194)
T PRK14162 36 EKQNPVEDLEKEIADLKAKNKDLE-----DKYLRSQAEIQNMQN---RYAKER-A-------QLIKYESQSLAKDVLPAM 99 (194)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH-H-------HHHHHHHHHHHHHHhhHH
Confidence 345667788888888888888773 334455555555442 222221 0 112334455778999999
Q ss_pred chHHHhhhhhc
Q 019169 206 DAAERTQSHIS 216 (345)
Q Consensus 206 D~d~Rl~dH~~ 216 (345)
|+-.|.-.|..
T Consensus 100 DnLerAl~~~~ 110 (194)
T PRK14162 100 DNLERALAVKA 110 (194)
T ss_pred hHHHHHHhccc
Confidence 99999777754
No 58
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=53.74 E-value=25 Score=32.01 Aligned_cols=69 Identities=20% Similarity=0.288 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhh-cccchH
Q 019169 131 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFL-VANDAA 208 (345)
Q Consensus 131 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~L-s~~D~d 208 (345)
+..+..+|..|--+|+.|-.+++-..-+.+-.+++.|+-|...+..+. ....|+.|-.|=--| .++|.+
T Consensus 107 L~s~~~ei~~L~~kI~~L~~~in~~~k~~~n~~i~slk~EL~d~iKe~---------e~~emeLyyecMkkL~~a~~~e 176 (181)
T PF04645_consen 107 LKSIKKEIEILRLKISSLQKEINKNKKKDLNEEIESLKSELNDLIKER---------EIREMELYYECMKKLAKAHEVE 176 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHhhhhhhh
Confidence 444445555555555555555554444445555566665555555443 124455566665555 444444
No 59
>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=53.55 E-value=13 Score=26.81 Aligned_cols=10 Identities=40% Similarity=0.916 Sum_probs=5.5
Q ss_pred ccccchhhhc
Q 019169 194 LCEICGSFLV 203 (345)
Q Consensus 194 VCeVCGA~Ls 203 (345)
+|+|||.-|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 9999998877
No 60
>PRK10884 SH3 domain-containing protein; Provisional
Probab=52.13 E-value=1.1e+02 Score=28.57 Aligned_cols=55 Identities=20% Similarity=0.213 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 019169 92 FCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETL 148 (345)
Q Consensus 92 ~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~L 148 (345)
-+...|-.++..|...+.+|+...... ....++..+++...+..|..|.++-.+|
T Consensus 90 ~~~~rlp~le~el~~l~~~l~~~~~~~--~~~~~~l~~~~~~~~~~~~~L~~~n~~L 144 (206)
T PRK10884 90 SLRTRVPDLENQVKTLTDKLNNIDNTW--NQRTAEMQQKVAQSDSVINGLKEENQKL 144 (206)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556677778888888886543111 1233444555555555555555555555
No 61
>KOG4302 consensus Microtubule-associated protein essential for anaphase spindle elongation [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=51.08 E-value=2.2e+02 Score=31.28 Aligned_cols=70 Identities=20% Similarity=0.305 Sum_probs=41.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhcCC---------HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCccc
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGK---------VDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALC 195 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LGeeG~---------VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VC 195 (345)
+.+...|..++.+++.|+..+-..---|. ++.-..+...++.|..++++-.+++ .+ -..|..++|
T Consensus 64 ~~L~~~ia~~eael~~l~s~l~~~~~~~~~~~k~e~tLke~l~~l~~~le~lr~qk~eR~~ef-~e-----l~~qie~l~ 137 (660)
T KOG4302|consen 64 ARLLQEIAVIEAELNDLCSALGEPSIIGEISDKIEGTLKEQLESLKPYLEGLRKQKDERRAEF-KE-----LYHQIEKLC 137 (660)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCcccccccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHH-HH-----HHHHHHHHH
Confidence 34456677888888888777766544444 3444555556666666655555444 21 144555778
Q ss_pred c-cchh
Q 019169 196 E-ICGS 200 (345)
Q Consensus 196 e-VCGA 200 (345)
+ +||-
T Consensus 138 ~~l~g~ 143 (660)
T KOG4302|consen 138 EELGGP 143 (660)
T ss_pred HHhcCC
Confidence 7 5555
No 62
>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=50.68 E-value=69 Score=31.84 Aligned_cols=26 Identities=35% Similarity=0.722 Sum_probs=20.7
Q ss_pred CcchhhcCCChhHhhhhcccCCCCCCCCC
Q 019169 36 VCPFYMVRFCPHDLFVNTRSDLGPCPRIH 64 (345)
Q Consensus 36 VCk~yL~g~CPhdLF~nTK~DlG~C~kiH 64 (345)
+|.+-+|..|--.||.. .-++||..+
T Consensus 25 ~CGH~~C~sCv~~l~~~---~~~~CP~C~ 50 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVR---GSGSCPECD 50 (309)
T ss_pred CCCCcccHHHHHHHhcC---CCCCCCCCC
Confidence 79999999998888854 336899443
No 63
>PRK11115 transcriptional regulator PhoU; Provisional
Probab=50.58 E-value=2e+02 Score=26.25 Aligned_cols=81 Identities=17% Similarity=0.063 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccc--hhhhccc
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEIC--GSFLVAN 205 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVC--GA~Ls~~ 205 (345)
...|.++-+.+..++..+-..-..++++.|..+...-+.+......+.... .. .-.-..|.+- ..++.+.
T Consensus 125 ~~~l~~l~~~v~~~l~~a~~a~~~~d~~~a~~i~~~d~~Id~~~~~~~~~~-~~-------~l~~~~~~~~~~~~l~~i~ 196 (236)
T PRK11115 125 LVSLESLGRHTIQMLHDVLDAFARMDLDEAVRIYREDKKVDQEYEGIVRQL-MT-------YMMEDPRTIPSVLTVLWCA 196 (236)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH-HH-------HHHhCcccHHHHHHHHHHH
Confidence 356888888888999998888889999988887766666654433333322 11 0011467776 3333366
Q ss_pred chHHHhhhhhc
Q 019169 206 DAAERTQSHIS 216 (345)
Q Consensus 206 D~d~Rl~dH~~ 216 (345)
..-+|++||..
T Consensus 197 ~~lERigDh~~ 207 (236)
T PRK11115 197 RSIERIGDRCQ 207 (236)
T ss_pred HHHHHHHHHHH
Confidence 78889999964
No 64
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=50.29 E-value=15 Score=33.19 Aligned_cols=31 Identities=26% Similarity=0.462 Sum_probs=26.2
Q ss_pred cccccchhhhcccchHHHhhhhhccccccchH
Q 019169 193 ALCEICGSFLVANDAAERTQSHISGKQHIGYG 224 (345)
Q Consensus 193 ~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~ 224 (345)
..||-|..+|. +|+..=.-.|..|+-|+-..
T Consensus 4 Y~CeyC~~~Lt-hD~lsvRk~H~~G~~H~~~~ 34 (188)
T COG5136 4 YFCEYCNKMLT-HDRLSVRKMHCGGAKHGLMR 34 (188)
T ss_pred hHHHHHHHHHh-ccHHHHHHHhhhhHHHHHHH
Confidence 36999999986 88888889999999997543
No 65
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=50.18 E-value=1.8e+02 Score=25.62 Aligned_cols=66 Identities=26% Similarity=0.371 Sum_probs=47.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCH
Q 019169 84 KFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKV 154 (345)
Q Consensus 84 ~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~V 154 (345)
.++.+ +.-|..=+..+...+......|..-. . .+...+....|..|..+|..|..+++.|-..+..
T Consensus 76 ~ld~e-i~~L~~el~~l~~~~k~l~~eL~~L~--~--~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~ 141 (169)
T PF07106_consen 76 ELDAE-IKELREELAELKKEVKSLEAELASLS--S--EPTNEELREEIEELEEEIEELEEKLEKLRSGSKP 141 (169)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHh--c--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 34444 55566667777777777777775432 1 2456778899999999999999999999884433
No 66
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 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 C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=50.12 E-value=5.8 Score=24.80 Aligned_cols=24 Identities=29% Similarity=0.804 Sum_probs=14.8
Q ss_pred CCCcchhhc-CCChhHhhhhcccCCCCCCCCCcH
Q 019169 34 KEVCPFYMV-RFCPHDLFVNTRSDLGPCPRIHDQ 66 (345)
Q Consensus 34 ~~VCk~yL~-g~CPhdLF~nTK~DlG~C~kiHd~ 66 (345)
..+|++|+. |.||+. ..|+-+|++
T Consensus 3 ~~~C~~f~~~g~C~~G---------~~C~f~H~~ 27 (27)
T PF00642_consen 3 TKLCRFFMRTGTCPFG---------DKCRFAHGE 27 (27)
T ss_dssp SSB-HHHHHTS--TTG---------GGSSSBSSG
T ss_pred cccChhhccCCccCCC---------CCcCccCCC
Confidence 468999999 999864 356666653
No 67
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=50.08 E-value=73 Score=32.39 Aligned_cols=22 Identities=36% Similarity=0.463 Sum_probs=10.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH
Q 019169 127 KSEQLSVLEEKIKNLLEQVETL 148 (345)
Q Consensus 127 ~~e~i~~l~ekI~~ll~eaE~L 148 (345)
..++|..++.+|.+|.++.++.
T Consensus 247 l~~~~~~~~~~i~~l~~~l~~~ 268 (406)
T PF02388_consen 247 LQEKLEKLEKEIEKLEEKLEKN 268 (406)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHhC
Confidence 3444555555555554444433
No 68
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=48.65 E-value=99 Score=28.25 Aligned_cols=79 Identities=18% Similarity=0.293 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHH
Q 019169 89 LAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 168 (345)
Q Consensus 89 ~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk 168 (345)
.+.-|+.=|..+..+|...+..|+...........-....+++..|..++..|..+++.+.. .+.+.-..+-..+..++
T Consensus 70 ~~~~l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~~~~~-~Dp~~i~~~~~~~~~~~ 148 (188)
T PF03962_consen 70 KLEKLQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKELEKYSE-NDPEKIEKLKEEIKIAK 148 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHHH
Confidence 34455566666667777777777655322221122234567788888888888888886665 34444444444444443
No 69
>COG3783 CybC Soluble cytochrome b562 [Energy production and conversion]
Probab=48.23 E-value=1.3e+02 Score=25.06 Aligned_cols=27 Identities=22% Similarity=0.417 Sum_probs=22.4
Q ss_pred HHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 143 EQVETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 143 ~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
.++.+|..+|++++|.+...++..++.
T Consensus 67 D~a~klaqeGnl~eAKaaak~l~d~Rn 93 (100)
T COG3783 67 DKADKLAQEGNLDEAKAAAKTLKDTRN 93 (100)
T ss_pred HHHHHHHHcCChHHHHHHHHHHHHHHH
Confidence 566789999999999998888777654
No 70
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=47.88 E-value=1.4e+02 Score=23.63 Aligned_cols=57 Identities=18% Similarity=0.247 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 019169 92 FCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEA 151 (345)
Q Consensus 92 ~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGee 151 (345)
-+..-+..+-.||..++.-|..-+. .. ....+...+|..|+++|..+-+-+..+++.
T Consensus 25 d~~~~~~~lk~Klq~ar~~i~~lpg-i~--~s~eeq~~~i~~Le~~i~~k~~~L~~~~~~ 81 (83)
T PF07544_consen 25 DLDTATGSLKHKLQKARAAIRELPG-ID--RSVEEQEEEIEELEEQIRKKREVLQKFKER 81 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCC-cc--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3556677788899999888876542 21 344566778888888888777766666543
No 71
>PRK14154 heat shock protein GrpE; Provisional
Probab=47.75 E-value=91 Score=29.23 Aligned_cols=70 Identities=10% Similarity=0.045 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccchHH
Q 019169 130 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAE 209 (345)
Q Consensus 130 ~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~ 209 (345)
.+..|+.+|..+-+++++|- +.-+.+.++.+-++.-.+.-.+ ...+..+-.++-.+|-+.|+-.
T Consensus 53 ~~~~l~~el~~le~e~~elk-----d~~lRl~ADfeNyRKR~~kE~e-----------~~~~~a~e~~~~~LLpVlDnLe 116 (208)
T PRK14154 53 SREKLEGQLTRMERKVDEYK-----TQYLRAQAEMDNLRKRIEREKA-----------DIIKFGSKQLITDLLPVADSLI 116 (208)
T ss_pred chhhHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhHHhHHH
Confidence 35556666666667766663 3345555555555432211111 1123345567889999999999
Q ss_pred Hhhhhh
Q 019169 210 RTQSHI 215 (345)
Q Consensus 210 Rl~dH~ 215 (345)
|.-.|.
T Consensus 117 RAL~~~ 122 (208)
T PRK14154 117 HGLESP 122 (208)
T ss_pred HHHhcc
Confidence 976665
No 72
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.35 E-value=2.5e+02 Score=26.64 Aligned_cols=84 Identities=11% Similarity=0.202 Sum_probs=47.0
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHH
Q 019169 82 VPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALM 161 (345)
Q Consensus 82 ~~~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~ 161 (345)
|-+||.+|-.... ++-.+|..+ .+. + .......-.+|...-+++++|+.+++.-.-+--...=-.++
T Consensus 5 fe~yEqqy~~l~a----~it~k~~~~-----~~~---~-~~ekk~~l~~i~~~leEa~ell~qMdlEvr~lp~~~Rs~~~ 71 (220)
T KOG1666|consen 5 FEGYEQQYRELSA----EITKKIGRA-----LSL---P-GSEKKQLLSEIDSKLEEANELLDQMDLEVRELPPNFRSSYL 71 (220)
T ss_pred HHHHHHHHHHHHH----HHHHhHHHH-----hcC---C-chHHHHHHHHHHHhHHHHHHHHHHHHHHHHhCCchhhhHHH
Confidence 4588988876544 444555554 111 0 11222223344444555556666665554444444445677
Q ss_pred HHHHHHHHHHHHHHhhh
Q 019169 162 RKVEILNVEKTTLTQQS 178 (345)
Q Consensus 162 ~~ve~Lk~ek~~le~~~ 178 (345)
.++...+...+.+..++
T Consensus 72 ~KlR~yksdl~~l~~e~ 88 (220)
T KOG1666|consen 72 SKLREYKSDLKKLKREL 88 (220)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 88888888888877765
No 73
>PRK11020 hypothetical protein; Provisional
Probab=47.08 E-value=1.3e+02 Score=25.79 Aligned_cols=21 Identities=19% Similarity=0.309 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 019169 129 EQLSVLEEKIKNLLEQVETLG 149 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LG 149 (345)
+.|..+..+|..|.++|+.|-
T Consensus 31 ~~i~qf~~E~~~l~k~I~~lk 51 (118)
T PRK11020 31 EKYAQFEKEKATLEAEIARLK 51 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344445555555555555443
No 74
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=47.05 E-value=50 Score=23.17 Aligned_cols=35 Identities=37% Similarity=0.473 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHH
Q 019169 134 LEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (345)
Q Consensus 134 l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 170 (345)
+-.+|..||..++.-+ +.-.||+..+.+++.|..+
T Consensus 3 il~kI~kLLalA~~~~--~~~~EA~~A~~kAq~Lm~k 37 (43)
T PF10979_consen 3 ILEKIRKLLALAESTG--SNEHEAEAALAKAQRLMAK 37 (43)
T ss_pred HHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHHHH
Confidence 4467778887777322 6677999999999998754
No 75
>PRK03918 chromosome segregation protein; Provisional
Probab=46.98 E-value=2.2e+02 Score=31.36 Aligned_cols=16 Identities=6% Similarity=-0.176 Sum_probs=12.9
Q ss_pred cccccchhhhcccchH
Q 019169 193 ALCEICGSFLVANDAA 208 (345)
Q Consensus 193 ~VCeVCGA~Ls~~D~d 208 (345)
.+|+||+.|..-.+.+
T Consensus 433 ~~~~~Cp~c~~~L~~~ 448 (880)
T PRK03918 433 KAKGKCPVCGRELTEE 448 (880)
T ss_pred hcCCCCCCCCCcCCch
Confidence 5899999987766664
No 76
>PRK14151 heat shock protein GrpE; Provisional
Probab=46.94 E-value=85 Score=28.55 Aligned_cols=88 Identities=18% Similarity=0.215 Sum_probs=50.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccc
Q 019169 127 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVAND 206 (345)
Q Consensus 127 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D 206 (345)
.+..+..++++|..+-+++++|- +.-+.+.++.+-++. ..+++. . ...+.-+-.++-.+|-+.|
T Consensus 18 ~~~~~~~l~~~i~~le~e~~el~-----d~~lR~~Ae~eN~rk---R~~kE~-e-------~~~~~a~~~~~~~LLpv~D 81 (176)
T PRK14151 18 EAAAGDDLTARVQELEEQLAAAK-----DQSLRAAADLQNVRR---RAEQDV-E-------KAHKFALEKFAGDLLPVVD 81 (176)
T ss_pred cccchhhHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH-H-------HHHHHHHHHHHHHHhhHHh
Confidence 34556677777777777777774 334455555555532 222221 1 1123344457888999999
Q ss_pred hHHHhhhhhcc------ccccchHHHHHHH
Q 019169 207 AAERTQSHISG------KQHIGYGMVRDFI 230 (345)
Q Consensus 207 ~d~Rl~dH~~G------K~HlGy~kIRe~l 230 (345)
+-.|.-.|... .++-|+..|...+
T Consensus 82 nlerAl~~~~~~~~~~~~~~~Gv~mi~k~l 111 (176)
T PRK14151 82 SLERGLELSSADDEAIKPMREGVELTLKMF 111 (176)
T ss_pred HHHHHHhcccccchhHHHHHHHHHHHHHHH
Confidence 99997676531 2445555554443
No 77
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=46.31 E-value=77 Score=28.14 Aligned_cols=54 Identities=19% Similarity=0.267 Sum_probs=46.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
.....+...|..+|.++.+|....=...+....-++-.++++|.+|.+++.+..
T Consensus 36 ~~~~~~~~~l~~Ei~~l~~E~~~iS~qDeFAkwaKl~Rk~~kl~~el~~~~~~~ 89 (161)
T PF04420_consen 36 SKSSKEQRQLRKEILQLKRELNAISAQDEFAKWAKLNRKLDKLEEELEKLNKSL 89 (161)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTTS-TTTSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455678889999999999999999999999999999999999999998888765
No 78
>PRK14163 heat shock protein GrpE; Provisional
Probab=46.04 E-value=1.1e+02 Score=28.75 Aligned_cols=85 Identities=12% Similarity=0.158 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccchH
Q 019169 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAA 208 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d 208 (345)
..+..|.++|..+-+++++|- +.-+.+.++.+-++. .++.+. . ...+.-+=.+.-.+|-+.|+-
T Consensus 40 ~~~~~l~~~l~~l~~e~~el~-----d~~lR~~AEfeN~rk---R~~kE~-e-------~~~~~a~~~~~~~LLpVlDnL 103 (214)
T PRK14163 40 AATAGLTAQLDQVRTALGERT-----ADLQRLQAEYQNYRR---RVERDR-V-------TVKEIAVANLLSELLPVLDDV 103 (214)
T ss_pred hhhHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH-H-------HHHHHHHHHHHHHHhhhHhHH
Confidence 345677777888777877763 334445555554442 222221 1 112223334667889999999
Q ss_pred HHhhhhhccccccchHHHHHHHH
Q 019169 209 ERTQSHISGKQHIGYGMVRDFIT 231 (345)
Q Consensus 209 ~Rl~dH~~GK~HlGy~kIRe~l~ 231 (345)
.|.-.|. .++-|+..|...|.
T Consensus 104 erAl~~~--~l~~Gv~mi~k~l~ 124 (214)
T PRK14163 104 GRAREHG--ELVGGFKSVAESLE 124 (214)
T ss_pred HHHHhch--hHHHHHHHHHHHHH
Confidence 9987773 46666665555443
No 79
>TIGR01554 major_cap_HK97 phage major capsid protein, HK97 family. This family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease.
Probab=45.66 E-value=47 Score=33.11 Aligned_cols=44 Identities=20% Similarity=0.231 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHhh--cCCHHHHHHHHHHHHHHHHHHHHHH
Q 019169 132 SVLEEKIKNLLEQVETLGE--AGKVDEAEALMRKVEILNVEKTTLT 175 (345)
Q Consensus 132 ~~l~ekI~~ll~eaE~LGe--eG~VdeA~~l~~~ve~Lk~ek~~le 175 (345)
++|.++++.+.+++..|-+ +...+++.+...++++|+.+.+.++
T Consensus 2 ~el~~~~~~~~~~~r~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ 47 (378)
T TIGR01554 2 SELKEQREEIVAEIRSLLDKAEKLEKELTAAALEKEELETDVEKLK 47 (378)
T ss_pred hhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555555555554 4444555555544545554444443
No 80
>PF09969 DUF2203: Uncharacterized conserved protein (DUF2203); InterPro: IPR018699 This family has no known function.
Probab=44.90 E-value=80 Score=26.93 Aligned_cols=27 Identities=26% Similarity=0.546 Sum_probs=20.6
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhc
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLGEA 151 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LGee 151 (345)
.....++..+..+|..++.+|+++|-+
T Consensus 46 ~~~~~~~~~~~~~~~~~i~~i~~~Gv~ 72 (120)
T PF09969_consen 46 NGLEAELEELEARLRELIDEIEELGVE 72 (120)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHcCcE
Confidence 345667888888888888888888854
No 81
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=44.68 E-value=8.2 Score=29.50 Aligned_cols=25 Identities=24% Similarity=0.684 Sum_probs=17.3
Q ss_pred cCcccccchh---------hhcccchHHH-hhhhh
Q 019169 191 KMALCEICGS---------FLVANDAAER-TQSHI 215 (345)
Q Consensus 191 km~VCeVCGA---------~Ls~~D~d~R-l~dH~ 215 (345)
.-++|+|||. +|++.|.+.- +|+-+
T Consensus 17 d~e~CP~Cgs~~~te~W~G~~iIidpe~SeIAkrl 51 (64)
T COG2093 17 DTEICPVCGSTDLTEEWFGLLIIIDPEKSEIAKRL 51 (64)
T ss_pred CCccCCCCCCcccchhhccEEEEEcCcHHHHHHHh
Confidence 3478999998 5777787762 44433
No 82
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=44.26 E-value=27 Score=34.54 Aligned_cols=30 Identities=23% Similarity=0.309 Sum_probs=26.0
Q ss_pred HHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 140 NLLEQVETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 140 ~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
=-...|++....|+|+.|+.|+.|+|.|--
T Consensus 259 Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~ 288 (303)
T PRK10564 259 YFNQAIKQAVKKGDVDKALKLLDEAERLGS 288 (303)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence 345788899999999999999999999854
No 83
>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants. XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.
Probab=43.99 E-value=2.3e+02 Score=28.58 Aligned_cols=46 Identities=26% Similarity=0.343 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 019169 132 SVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 177 (345)
Q Consensus 132 ~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~ 177 (345)
..|...++.+++++|++..+-+--|..-+.+=+.-|+++|.+|...
T Consensus 154 erL~~e~~~~~~qlE~~v~~K~~~E~~L~~KF~~vLNeKK~KIR~l 199 (342)
T PF06632_consen 154 ERLESEANKLLKQLEKFVNAKEEHEEDLYAKFVLVLNEKKAKIREL 199 (342)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 4567777888888888888877777776666677777777776654
No 84
>PF12854 PPR_1: PPR repeat
Probab=43.95 E-value=27 Score=22.64 Aligned_cols=21 Identities=33% Similarity=0.487 Sum_probs=17.7
Q ss_pred HHHHHHhhcCCHHHHHHHHHH
Q 019169 143 EQVETLGEAGKVDEAEALMRK 163 (345)
Q Consensus 143 ~eaE~LGeeG~VdeA~~l~~~ 163 (345)
.=|..+...|+|++|..++.+
T Consensus 12 ~lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 12 TLIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHh
Confidence 446788999999999999875
No 85
>PLN02678 seryl-tRNA synthetase
Probab=43.92 E-value=65 Score=33.54 Aligned_cols=49 Identities=22% Similarity=0.263 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
..++..|..+++.+.++|-.+...+ +++..+++++..|+++...++.++
T Consensus 46 ~~~~e~lr~erN~~sk~I~~~k~~~--~~~~~l~~~~~~Lk~ei~~le~~~ 94 (448)
T PLN02678 46 QFELDSLRKEFNKLNKEVAKLKIAK--EDATELIAETKELKKEITEKEAEV 94 (448)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCC--CcHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566666666666665544333 334455566666666666655543
No 86
>COG4911 Uncharacterized conserved protein [Function unknown]
Probab=42.81 E-value=1.1e+02 Score=25.92 Aligned_cols=55 Identities=18% Similarity=0.146 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019169 88 ELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGE 150 (345)
Q Consensus 88 e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGe 150 (345)
+++..|.-++.++-.+.++-+.+.+.- . .++..-.|++++.++..++++|+++|-
T Consensus 11 e~~~el~P~l~d~~~~~r~~~n~~e~L----~----~qedk~~l~e~e~q~k~~l~~i~e~G~ 65 (123)
T COG4911 11 ETARELLPWLRDRLIQLRKIKNEIELL----L----VQEDKYALQEYESQTKKILDEIIEKGI 65 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh----c----ccccHHHHHHHHHHHHHHHHHHHHcCc
Confidence 566777777777776766666666531 1 122245688999999999999999884
No 87
>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=42.78 E-value=47 Score=26.34 Aligned_cols=12 Identities=33% Similarity=0.750 Sum_probs=9.8
Q ss_pred Ccccccchhhhc
Q 019169 192 MALCEICGSFLV 203 (345)
Q Consensus 192 m~VCeVCGA~Ls 203 (345)
..+|.|||-.|.
T Consensus 78 ~~~C~vC~k~l~ 89 (109)
T PF10367_consen 78 STKCSVCGKPLG 89 (109)
T ss_pred CCCccCcCCcCC
Confidence 367999998875
No 88
>PRK14147 heat shock protein GrpE; Provisional
Probab=42.17 E-value=1e+02 Score=27.96 Aligned_cols=68 Identities=15% Similarity=0.195 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccchHHHhh
Q 019169 133 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQ 212 (345)
Q Consensus 133 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~ 212 (345)
.+..+|..+-+++++|- +.-+.+.++.+-++. .++++. . ...+..+-.++..+|-+.|+-.|.-
T Consensus 22 ~l~~~l~~l~~e~~elk-----d~~lR~~Ad~eN~rk---R~~kE~-e-------~~~~~a~~~~~~~lLpv~DnlerAl 85 (172)
T PRK14147 22 PLKAEVESLRSEIALVK-----ADALRERADLENQRK---RIARDV-E-------QARKFANEKLLGELLPVFDSLDAGL 85 (172)
T ss_pred hHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH-H-------HHHHHHHHHHHHHHhhhhhHHHHHH
Confidence 45556666666666653 223344444444432 222222 1 1123344567889999999999966
Q ss_pred hhhc
Q 019169 213 SHIS 216 (345)
Q Consensus 213 dH~~ 216 (345)
.|..
T Consensus 86 ~~~~ 89 (172)
T PRK14147 86 TAAG 89 (172)
T ss_pred hccc
Confidence 6654
No 89
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=42.14 E-value=1.5e+02 Score=22.33 Aligned_cols=83 Identities=18% Similarity=0.202 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCCCCCCc-------hhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 019169 94 EKLVMDLDRRVRRGRERLSQEVEPAPPPPIS-------AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEI 166 (345)
Q Consensus 94 ~~li~d~drkI~~~k~RL~~~~e~~~~~~~~-------~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~ 166 (345)
..-+.++..=|......|....-+.. .... ......|......|..+...+..| ....-..+..+..+++.
T Consensus 7 ~~~~~~l~~Wl~~~e~~l~~~~~~~~-~~~~~~~~~~~~~~~~ei~~~~~~l~~l~~~~~~L-~~~~~~~~~~i~~~~~~ 84 (105)
T PF00435_consen 7 QQEADELLDWLQETEAKLSSSEPGSD-LEELEEQLKKHKELQEEIESRQERLESLNEQAQQL-IDSGPEDSDEIQEKLEE 84 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHCSCTHSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHTTHTTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH-HHcCCCcHHHHHHHHHH
Confidence 34455555566666666732210010 0111 123445666677777777777788 44446667778888888
Q ss_pred HHHHHHHHHhhh
Q 019169 167 LNVEKTTLTQQS 178 (345)
Q Consensus 167 Lk~ek~~le~~~ 178 (345)
|......|...+
T Consensus 85 l~~~w~~l~~~~ 96 (105)
T PF00435_consen 85 LNQRWEALCELV 96 (105)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 887777776654
No 90
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=41.87 E-value=1.9e+02 Score=27.43 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=25.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHH
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTL 174 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l 174 (345)
.+.+-+..-+.+|..||+-+++ .++|++++. .++.-.++++..
T Consensus 47 ~il~Ll~~kd~ef~~llkla~e---q~k~e~~m~---~Lea~VEkrD~~ 89 (272)
T KOG4552|consen 47 NILKLLDSKDDEFKTLLKLAPE---QQKREQLMR---TLEAHVEKRDEV 89 (272)
T ss_pred HHHHHHHhccHHHHHHHHHhHh---HHHHHHHHH---HHHHHHHHhHHH
Confidence 4455566677888888887765 455665443 334444444333
No 91
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=41.51 E-value=74 Score=32.69 Aligned_cols=48 Identities=25% Similarity=0.365 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 177 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~ 177 (345)
..++..|..+++.+.++|-.+...++ ++..+++++..|+++.+.++++
T Consensus 41 ~~~~~~lr~~rn~~sk~i~~~~~~~~--~~~~l~~~~~~l~~~~~~~~~~ 88 (425)
T PRK05431 41 QTELEELQAERNALSKEIGQAKRKGE--DAEALIAEVKELKEEIKALEAE 88 (425)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCC--cHHHHHHHHHHHHHHHHHHHHH
Confidence 34566666666666666655444441 2334555555555555555544
No 92
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=40.73 E-value=1.5e+02 Score=24.89 Aligned_cols=49 Identities=29% Similarity=0.346 Sum_probs=27.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhc--CCHHHHHHHHHHHHHHHHHHHHH
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLGEA--GKVDEAEALMRKVEILNVEKTTL 174 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LGee--G~VdeA~~l~~~ve~Lk~ek~~l 174 (345)
++...|..++++|+.|++++++|-.. .-+++-..|-.+-+.|++...++
T Consensus 5 ~l~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~ 55 (107)
T PF06156_consen 5 ELFDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEEL 55 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667778888888888888777653 12222333444444444444433
No 93
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=40.66 E-value=11 Score=34.36 Aligned_cols=31 Identities=29% Similarity=0.615 Sum_probs=24.1
Q ss_pred HhhcCcccccchhhhcccchHHHhhhhhcccccc
Q 019169 188 QEKKMALCEICGSFLVANDAAERTQSHISGKQHI 221 (345)
Q Consensus 188 ~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~Hl 221 (345)
+++.-.-|+||.+- +-|+-+ .-||+.||-|.
T Consensus 71 sq~~GyyCdVCdcv--vKDSin-flDHiNgKkHq 101 (193)
T KOG4727|consen 71 SQKGGYYCDVCDCV--VKDSIN-FLDHINGKKHQ 101 (193)
T ss_pred cccCceeeeeccee--ehhhHH-HHHHhccHHHH
Confidence 56667899999954 667655 55899999995
No 94
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=40.06 E-value=9.5 Score=35.41 Aligned_cols=28 Identities=25% Similarity=0.437 Sum_probs=0.0
Q ss_pred cCcccccchhhhcccchHHH-hhhhhcccccc
Q 019169 191 KMALCEICGSFLVANDAAER-TQSHISGKQHI 221 (345)
Q Consensus 191 km~VCeVCGA~Ls~~D~d~R-l~dH~~GK~Hl 221 (345)
+...|||||-+.-.+ +| ...||+.--|.
T Consensus 100 ~ey~CEICGN~~Y~G---rkaFekHF~E~rH~ 128 (196)
T PF11931_consen 100 VEYKCEICGNQSYKG---RKAFEKHFQEWRHA 128 (196)
T ss_dssp --------------------------------
T ss_pred CeeeeEeCCCcceec---HHHHHHhcChhHHH
Confidence 458999999875433 44 78999998885
No 95
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=39.79 E-value=92 Score=31.92 Aligned_cols=49 Identities=22% Similarity=0.289 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
.++..|..+.+.+.++|-.+...++ +++..+.+++..|+++.+.++++.
T Consensus 44 ~~~~~l~~erN~~sk~i~~~~~~~~-~~~~~l~~~~~~l~~~~~~~~~~~ 92 (418)
T TIGR00414 44 SEIEELQAKRNELSKQIGKAKGQKK-DKIEEIKKELKELKEELTELSAAL 92 (418)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCc-chHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666666666655554442 115566667777777776666553
No 96
>PRK12495 hypothetical protein; Provisional
Probab=39.07 E-value=34 Score=32.36 Aligned_cols=13 Identities=31% Similarity=0.708 Sum_probs=11.2
Q ss_pred cCcccccchhhhc
Q 019169 191 KMALCEICGSFLV 203 (345)
Q Consensus 191 km~VCeVCGA~Ls 203 (345)
..+.|++||..|.
T Consensus 41 sa~hC~~CG~PIp 53 (226)
T PRK12495 41 TNAHCDECGDPIF 53 (226)
T ss_pred chhhcccccCccc
Confidence 4489999999988
No 97
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=38.76 E-value=72 Score=25.80 Aligned_cols=37 Identities=16% Similarity=0.236 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 133 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 133 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
..-..|...+.+++.+.++|+.++|..++.++..+-.
T Consensus 23 ~~kS~~kT~iKk~~~ai~~~~~~~a~~~~~~a~s~iD 59 (88)
T PRK00239 23 SRKSRVRTAIKKVEAAIAAGDKEAAEEALKAAQSKID 59 (88)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 4455677788888899999999999999999888754
No 98
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=38.53 E-value=1.5e+02 Score=25.19 Aligned_cols=49 Identities=24% Similarity=0.328 Sum_probs=34.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
.++..+|..|+++|+.+++++..|-.. +..+|++--.|+-|-+.|...+
T Consensus 4 keiFd~v~~le~~l~~l~~el~~lK~~-----l~~lvEEN~~L~lENe~LR~RL 52 (114)
T COG4467 4 KEIFDQVDNLEEQLGVLLAELGGLKQH-----LGSLVEENTALRLENEKLRERL 52 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHhhHHHHhhHHHHHHHh
Confidence 467788999999999999998887653 4455666666665555555544
No 99
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=38.39 E-value=2.1e+02 Score=28.78 Aligned_cols=39 Identities=31% Similarity=0.291 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhc-CCHHHHHHHHHHHHHHHH
Q 019169 131 LSVLEEKIKNLLEQVETLGEA-GKVDEAEALMRKVEILNV 169 (345)
Q Consensus 131 i~~l~ekI~~ll~eaE~LGee-G~VdeA~~l~~~ve~Lk~ 169 (345)
++.-+++|.++-+.|+++-+. |+.+.|++....+|-...
T Consensus 88 ~kkneeki~Elde~i~~~eedngE~e~~ea~~n~aeyY~q 127 (412)
T COG5187 88 LKKNEEKIEELDERIREKEEDNGETEGSEADRNIAEYYCQ 127 (412)
T ss_pred HHhhHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHH
Confidence 444455555554444444332 788988888877776653
No 100
>PF01025 GrpE: GrpE; InterPro: IPR000740 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes the grpE protein. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. The X-ray crystal structure of GrpE in complex with the ATPase domain of DnaK revealed that GrpE is an asymmetric homodimer, bent in a manner that favours extensive contacts with only one DnaKATPase monomer []. GrpE does not actively compete for the atomic positions occupied by the nucleotide. GrpE and ADP mutually reduce one another's affinity for DnaK 200-fold, and ATP instantly dissociates GrpE from DnaK.; GO: 0000774 adenyl-nucleotide exchange factor activity, 0042803 protein homodimerization activity, 0051087 chaperone binding, 0006457 protein folding; PDB: 3A6M_A 4ANI_A 1DKG_B.
Probab=38.06 E-value=36 Score=29.67 Aligned_cols=35 Identities=17% Similarity=0.153 Sum_probs=20.3
Q ss_pred chhhhcccchHHHhhhhhc-----cccccchHHHHHHHHH
Q 019169 198 CGSFLVANDAAERTQSHIS-----GKQHIGYGMVRDFITE 232 (345)
Q Consensus 198 CGA~Ls~~D~d~Rl~dH~~-----GK~HlGy~kIRe~l~e 232 (345)
.-.+|-+.|+-.+...|+. ..++-||..+...+..
T Consensus 64 ~~~ll~v~D~l~~a~~~~~~~~~~~~~~~g~~~~~~~l~~ 103 (165)
T PF01025_consen 64 LKDLLPVLDNLERALEAAKSNEEEESLLEGLEMILKQLED 103 (165)
T ss_dssp HHHHHHHHHHHHHHHCC-SHHCTCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHHH
Confidence 3446777777788777764 3445555555444443
No 101
>PF14282 FlxA: FlxA-like protein
Probab=37.85 E-value=1.6e+02 Score=24.35 Aligned_cols=52 Identities=17% Similarity=0.362 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHH
Q 019169 94 EKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVET 147 (345)
Q Consensus 94 ~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~ 147 (345)
...|..+...|....+.|..-..... .....+..++..|..+|..|-.+|-.
T Consensus 18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~--~~~e~k~~q~q~Lq~QI~~LqaQI~q 69 (106)
T PF14282_consen 18 DSQIEQLQKQIKQLQEQLQELSQDSD--LDAEQKQQQIQLLQAQIQQLQAQIAQ 69 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccC--CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777777777777754321111 12234556677777777666666643
No 102
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=37.70 E-value=1.8e+02 Score=22.09 Aligned_cols=48 Identities=29% Similarity=0.346 Sum_probs=37.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHH
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKT 172 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~ 172 (345)
.....-...++..|..++.++..+-..++.+.|...+.++.=+..-.+
T Consensus 27 ~~L~~l~~~~~~~~~~~~~~l~~~f~~~d~~~A~~~~~kLky~~kl~~ 74 (78)
T PF07743_consen 27 AELEELKKEIEERIKELIKELAEAFDAKDWEEAKEALRKLKYLQKLLE 74 (78)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHHHHH
Confidence 556666778888899999999999999999999998888766554333
No 103
>PF11587 Prion_bPrPp: Major prion protein bPrPp - N terminal; PDB: 1SKH_A.
Probab=37.62 E-value=8.3 Score=25.04 Aligned_cols=23 Identities=35% Similarity=0.436 Sum_probs=20.7
Q ss_pred hhcCCChhHhhhhcccCCCCCCC
Q 019169 40 YMVRFCPHDLFVNTRSDLGPCPR 62 (345)
Q Consensus 40 yL~g~CPhdLF~nTK~DlG~C~k 62 (345)
..+||+---||+-|=+|+|-|.|
T Consensus 4 ~~lgcWilvLfvatwsdvglcKK 26 (29)
T PF11587_consen 4 SHLGCWILVLFVATWSDVGLCKK 26 (29)
T ss_dssp TTTTTHHHHHHHHHHHHHTTSSS
T ss_pred ccccHHHHHHHHHHHhhhccccC
Confidence 46789999999999999999987
No 104
>PF03357 Snf7: Snf7; InterPro: IPR005024 This is a family of eukaryotic proteins which are variously described as either hypothetical protein, developmental protein or related to yeast SNF7. The family contains human CHMP1. CHMP1 (CHromatin Modifying Protein; CHarged Multivesicular body Protein), is encoded by an alternative open reading frame in the PRSM1 gene [] and is conserved in both complex and simple eukaryotes. CHMP1 contains a predicted bipartite nuclear localisation signal and distributes as distinct forms to the cytoplasm and the nuclear matrix in all cell lines tested. Human CHMP1 is strongly implicated in multivesicular body formation. A multivesicular body is a vesicle-filled endosome that targets proteins to the interior of lysosomes. Immunocytochemistry and biochemical fractionation localise CHMP1 to early endosomes and CHMP1 physically interacts with SKD1/VPS4, a highly conserved protein directly linked to multivesicular body sorting in yeast. Similar to the action of a mutant SKD1 protein, over expression of a fusion derivative of human CHMP1 dilates endosomal compartments and disrupts the normal distribution of several endosomal markers. Genetic studies in Saccharomyces cerevisiae (Baker's yeast) further support a conserved role of CHMP1 in vesicle trafficking. Deletion of CHM1, the budding yeast homologue of CHMP1, results in defective sorting of carboxypeptidases S and Y and produces abnormal, multi-lamellar prevacuolar compartments. This phenotype classifies CHM1 as a member of the class E vacuolar protein sorting genes []. ; GO: 0015031 protein transport; PDB: 2V6X_B 2W2U_D 2GD5_D 3FRT_B 3FRV_A 4ABM_D 3EAB_H 3HTU_D.
Probab=37.52 E-value=1.6e+02 Score=25.32 Aligned_cols=52 Identities=23% Similarity=0.319 Sum_probs=42.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 177 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~ 177 (345)
.....+..|+.+|..+..+|-.+...|+...|..++...-.+......+...
T Consensus 12 ~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~~ 63 (171)
T PF03357_consen 12 RLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLNQ 63 (171)
T ss_dssp HHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456788899999999999999999999999999988888887777666554
No 105
>KOG4765 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.74 E-value=30 Score=35.24 Aligned_cols=43 Identities=28% Similarity=0.484 Sum_probs=30.2
Q ss_pred hhcCcccccchhhhcccchHHHhhhhhccccccchHHHHHHHHHHHHHHHHhH
Q 019169 189 EKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEAKEKAR 241 (345)
Q Consensus 189 ~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eLk~~~~~~~ 241 (345)
..-|-+|++||+||...=-+ +-+.|...-...++++++++.+.
T Consensus 87 d~D~lkCe~C~a~L~~s~pq----------~s~s~d~~n~~~ek~~kkLetaH 129 (419)
T KOG4765|consen 87 DCDMLKCESCGAFLCASLPQ----------QSFSFDRYNQRCEKFKKKLETAH 129 (419)
T ss_pred cCCeeehhhhhhHHhccCCc----------cccChHHHHhHHHHHHHHHHHHH
Confidence 35678999999999844211 14567777788888888776633
No 106
>PRK14161 heat shock protein GrpE; Provisional
Probab=36.72 E-value=2.3e+02 Score=25.88 Aligned_cols=25 Identities=20% Similarity=0.321 Sum_probs=19.0
Q ss_pred cccccchhhhcccchHHHhhhhhcc
Q 019169 193 ALCEICGSFLVANDAAERTQSHISG 217 (345)
Q Consensus 193 ~VCeVCGA~Ls~~D~d~Rl~dH~~G 217 (345)
.+=.++..+|-+.|+-.|.-.|...
T Consensus 67 a~~~~~~~LLpv~DnlerAl~~~~~ 91 (178)
T PRK14161 67 AIATFAKELLNVSDNLSRALAHKPA 91 (178)
T ss_pred HHHHHHHHHhhHHhHHHHHHhcCcc
Confidence 3445788899999999997677653
No 107
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=36.53 E-value=92 Score=30.73 Aligned_cols=22 Identities=14% Similarity=0.400 Sum_probs=0.0
Q ss_pred CCCCCCCcHHHHHHHhcCCCCC
Q 019169 58 GPCPRIHDQKLKESFEKSPRHD 79 (345)
Q Consensus 58 G~C~kiHd~~lK~~Ye~~~~~~ 79 (345)
..|..+=.+.|+.+|+.+.+..
T Consensus 4 ~eC~~~l~~~l~~~~~~~~~E~ 25 (314)
T PF04111_consen 4 QECTDLLLEQLDKQLEQAEKER 25 (314)
T ss_dssp ----------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666778888888775433
No 108
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=36.33 E-value=98 Score=23.82 Aligned_cols=43 Identities=23% Similarity=0.402 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 131 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 131 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
+..|+.+|..|+...+.|-.++.. +-.++..+..++..|....
T Consensus 2 L~~Le~kle~Li~~~~~L~~EN~~-----Lr~q~~~~~~ER~~L~ekn 44 (65)
T TIGR02449 2 LQALAAQVEHLLEYLERLKSENRL-----LRAQEKTWREERAQLLEKN 44 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999887654 6677777888887776653
No 109
>PRK14146 heat shock protein GrpE; Provisional
Probab=36.32 E-value=1.6e+02 Score=27.63 Aligned_cols=27 Identities=26% Similarity=0.319 Sum_probs=21.2
Q ss_pred hcCcccccchhhhcccchHHHhhhhhc
Q 019169 190 KKMALCEICGSFLVANDAAERTQSHIS 216 (345)
Q Consensus 190 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~ 216 (345)
.+..+-.++-.+|-+.|+-.|.-.|..
T Consensus 99 ~~~a~e~~~~~lLpv~DnlerAl~~~~ 125 (215)
T PRK14146 99 RKEAVKSLVSGFLNPIDNLERVGATQN 125 (215)
T ss_pred HHHHHHHHHHHHhhHHhHHHHHHhccc
Confidence 344566789999999999999766653
No 110
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=35.71 E-value=3.3e+02 Score=26.81 Aligned_cols=23 Identities=22% Similarity=0.225 Sum_probs=14.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Q 019169 85 FEAELAQFCEKLVMDLDRRVRRGR 108 (345)
Q Consensus 85 yE~e~~~~L~~li~d~drkI~~~k 108 (345)
||+. ++.++.|+..++..+..-+
T Consensus 140 YeWR-~~ll~gl~~~L~~~~~~L~ 162 (325)
T PF08317_consen 140 YEWR-MQLLEGLKEGLEENLELLQ 162 (325)
T ss_pred HHHH-HHHHHHHHHHHHHHHHHHH
Confidence 7776 5666777776666654433
No 111
>PRK14141 heat shock protein GrpE; Provisional
Probab=35.24 E-value=1.8e+02 Score=27.32 Aligned_cols=26 Identities=15% Similarity=0.263 Sum_probs=20.5
Q ss_pred cCcccccchhhhcccchHHHhhhhhc
Q 019169 191 KMALCEICGSFLVANDAAERTQSHIS 216 (345)
Q Consensus 191 km~VCeVCGA~Ls~~D~d~Rl~dH~~ 216 (345)
+..+-.++-.+|-+.|+-.|.-.|+.
T Consensus 77 ~~a~~~~~~dLLpViDnLerAl~~~~ 102 (209)
T PRK14141 77 AYGIAGFARDMLSVSDNLRRALDAIP 102 (209)
T ss_pred HHHHHHHHHHHhhhHhHHHHHHhccc
Confidence 33455688899999999999877764
No 112
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=35.18 E-value=1.6e+02 Score=32.45 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=16.3
Q ss_pred HhhcCcccccchhhhcccch
Q 019169 188 QEKKMALCEICGSFLVANDA 207 (345)
Q Consensus 188 ~~qkm~VCeVCGA~Ls~~D~ 207 (345)
..-.+.-|+.||+-.+.+|-
T Consensus 674 ~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 674 YETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred HHHhcCCCCCCCCCCCcccc
Confidence 45577999999998888873
No 113
>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Probab=35.15 E-value=5.1e+02 Score=27.94 Aligned_cols=25 Identities=24% Similarity=0.351 Sum_probs=15.6
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHh
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLG 149 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LG 149 (345)
....+++.+++.+|..+..+++.+-
T Consensus 205 ~~~~~~~~~le~el~~l~~~~e~l~ 229 (650)
T TIGR03185 205 SSILSEIEALEAELKEQSEKYEDLA 229 (650)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566677777766666666654
No 114
>PRK14160 heat shock protein GrpE; Provisional
Probab=35.13 E-value=2.7e+02 Score=26.13 Aligned_cols=25 Identities=20% Similarity=0.117 Sum_probs=19.5
Q ss_pred hcCcccccchhhhcccchHHHhhhh
Q 019169 190 KKMALCEICGSFLVANDAAERTQSH 214 (345)
Q Consensus 190 qkm~VCeVCGA~Ls~~D~d~Rl~dH 214 (345)
.+..+..+.-.+|-+.|+-.|.-.|
T Consensus 106 ~~~a~e~~~~~LLpVlDnLerAl~~ 130 (211)
T PRK14160 106 YSDACEDVLKELLPVLDNLERAAAV 130 (211)
T ss_pred HHHHHHHHHHHHhhHHhHHHHHHhc
Confidence 3445667888999999999996666
No 115
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=35.10 E-value=2.2e+02 Score=22.19 Aligned_cols=20 Identities=40% Similarity=0.512 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 019169 130 QLSVLEEKIKNLLEQVETLG 149 (345)
Q Consensus 130 ~i~~l~ekI~~ll~eaE~LG 149 (345)
.+..|+.+|+.++..|..|-
T Consensus 5 ~l~~LE~ki~~aveti~~Lq 24 (72)
T PF06005_consen 5 LLEQLEEKIQQAVETIALLQ 24 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555443
No 116
>PRK14155 heat shock protein GrpE; Provisional
Probab=34.85 E-value=1.4e+02 Score=27.97 Aligned_cols=70 Identities=19% Similarity=0.196 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccchHHH
Q 019169 131 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAER 210 (345)
Q Consensus 131 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~R 210 (345)
+..+..+|..+-+++++|- +..+.+.++.+-++. .++++. . ...+.-+=.++-.+|-+.|+-.|
T Consensus 15 ~~~l~~~l~~le~e~~elk-----d~~lR~~AefeN~RK---R~~kE~-e-------~~~~~a~~~~~~~LLpV~DnLer 78 (208)
T PRK14155 15 ADDAAQEIEALKAEVAALK-----DQALRYAAEAENTKR---RAEREM-N-------DARAYAIQKFARDLLGAADNLGR 78 (208)
T ss_pred ccchHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH-H-------HHHHHHHHHHHHHHhhHHhhHHH
Confidence 3455556666666666653 334455555555542 222221 1 11122233467789999999999
Q ss_pred hhhhhc
Q 019169 211 TQSHIS 216 (345)
Q Consensus 211 l~dH~~ 216 (345)
.-.|+.
T Consensus 79 Al~~~~ 84 (208)
T PRK14155 79 ATAASP 84 (208)
T ss_pred HHhccc
Confidence 777765
No 117
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=34.19 E-value=1.1e+02 Score=24.79 Aligned_cols=37 Identities=19% Similarity=0.220 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 133 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 133 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
..-..|...+.+++.+.++|+.++|+.++.++..+-.
T Consensus 23 ~~kS~~kT~iKk~~~ai~~~d~~~a~~~l~~a~s~iD 59 (87)
T TIGR00029 23 SQKSKMKTIIKKVYAAIAAGDKDKAQEAFKEAAKKLD 59 (87)
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4455677888999999999999999999988877653
No 118
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=33.91 E-value=2.2e+02 Score=24.07 Aligned_cols=46 Identities=24% Similarity=0.341 Sum_probs=28.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHH
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLT 175 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le 175 (345)
.++...|..|+++|+.+++++++|-.. ...++++-..|+.|=+.|.
T Consensus 4 ~elfd~l~~le~~l~~l~~el~~LK~~-----~~el~EEN~~L~iEN~~Lr 49 (110)
T PRK13169 4 KEIFDALDDLEQNLGVLLKELGALKKQ-----LAELLEENTALRLENDKLR 49 (110)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHH
Confidence 455677888888888888888877653 3445555555544433333
No 119
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=33.83 E-value=1.5e+02 Score=29.18 Aligned_cols=10 Identities=30% Similarity=0.451 Sum_probs=5.0
Q ss_pred cHHHHHHHhc
Q 019169 65 DQKLKESFEK 74 (345)
Q Consensus 65 d~~lK~~Ye~ 74 (345)
...|+.+|..
T Consensus 158 ~~~L~~D~~~ 167 (325)
T PF08317_consen 158 LELLQEDYAK 167 (325)
T ss_pred HHHHHHHHHH
Confidence 3455555544
No 120
>PF01649 Ribosomal_S20p: Ribosomal protein S20; InterPro: IPR002583 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1I94_T 1FJG_T 4DH9_T 3KNJ_T 3TVG_W 3UYF_W 3V28_T 3KIS_t 3HUY_T 1HNX_T ....
Probab=33.76 E-value=1.1e+02 Score=24.39 Aligned_cols=37 Identities=22% Similarity=0.280 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 133 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 133 ~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
..-..|...+.+++.+.+.|+.++|+.++..+..+-.
T Consensus 22 ~~kS~~rT~iKk~~~ai~~~~~~~a~~~l~~a~s~iD 58 (84)
T PF01649_consen 22 SRKSRVRTAIKKFREAIEAGDKEEAKELLRKAYSAID 58 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHH
Confidence 4456777889999999999999999999988887643
No 121
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=33.52 E-value=2e+02 Score=22.31 Aligned_cols=44 Identities=25% Similarity=0.353 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 019169 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 177 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~ 177 (345)
..|.+-+++|..|+.+.|.|-.. =+.+...+-.|+.+...++..
T Consensus 5 ~~l~EKDe~Ia~L~eEGekLSk~-----el~~~~~IKKLr~~~~e~e~~ 48 (74)
T PF12329_consen 5 KKLAEKDEQIAQLMEEGEKLSKK-----ELKLNNTIKKLRAKIKELEKQ 48 (74)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHH-----HHhhHHHHHHHHHHHHHHHHH
Confidence 44555666666666666665433 233445555555555555443
No 122
>KOG2751 consensus Beclin-like protein [Signal transduction mechanisms]
Probab=33.49 E-value=3.5e+02 Score=28.25 Aligned_cols=120 Identities=21% Similarity=0.231 Sum_probs=69.2
Q ss_pred CCCCCcchhhcCCChhHhhhhcccCCCCCCCCCcHH---------HHHHHhcC-CCCCCChh---hhHHHHHHHHHHHHH
Q 019169 32 DDKEVCPFYMVRFCPHDLFVNTRSDLGPCPRIHDQK---------LKESFEKS-PRHDAYVP---KFEAELAQFCEKLVM 98 (345)
Q Consensus 32 ~D~~VCk~yL~g~CPhdLF~nTK~DlG~C~kiHd~~---------lK~~Ye~~-~~~~~~~~---~yE~e~~~~L~~li~ 98 (345)
.+.-||++|.--+=-++.=.+|+.+++.|-++|..- +-..|..+ ....-..| .-+.-++..|...+.
T Consensus 74 ~~~~~~~~~~~p~r~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~f~i~~~qt~~d~PlC~eC~d~l~~~ld~e~~ 153 (447)
T KOG2751|consen 74 QESSVVVYFSPPVRDSDTEHNLSFELGENGSDGSNTKTLSATINVLTRLFDILSSQTQVDHPLCEECMDVLLNKLDKEVE 153 (447)
T ss_pred hhccceecccCcccccccccccccccccccchhhhhHHHHHHHHHHHHHHHHhhccCCcccchHHHHHHHHHHHHHHHHH
Confidence 345688888877777888889999999888777531 11122222 12222211 234456666677777
Q ss_pred HHHHHHHHHH---HhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhc-CCHH
Q 019169 99 DLDRRVRRGR---ERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEA-GKVD 155 (345)
Q Consensus 99 d~drkI~~~k---~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGee-G~Vd 155 (345)
+++.-+..=+ .+|+++. .. ...+....++.++..+=..|+++++.|-++ -+|+
T Consensus 154 ~~~~e~~~Y~~~l~~Le~~~--~~--~~~~~~~~e~~~l~~eE~~L~q~lk~le~~~~~l~ 210 (447)
T KOG2751|consen 154 DAEDEVDTYKACLQRLEQQN--QD--VSEEDLLKELKNLKEEEERLLQQLEELEKEEAELD 210 (447)
T ss_pred HHHHHHHHHHHHHHHHhhcC--cc--cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7766665444 4454432 11 133445556666666666777777775443 3344
No 123
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=33.21 E-value=2e+02 Score=28.45 Aligned_cols=35 Identities=20% Similarity=0.371 Sum_probs=18.2
Q ss_pred HHHHHHhcCCCCCCChhhhHHHHHHHHHHHHHHHHHHHH
Q 019169 67 KLKESFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVR 105 (345)
Q Consensus 67 ~lK~~Ye~~~~~~~~~~~yE~e~~~~L~~li~d~drkI~ 105 (345)
.+-..|-...-+..| |||. ++.|+.|+..++..+.
T Consensus 120 ~lvK~~aRl~ak~~W---YeWR-~kllegLk~~L~~~~~ 154 (312)
T smart00787 120 QLVKTFARLEAKKMW---YEWR-MKLLEGLKEGLDENLE 154 (312)
T ss_pred HHHHHHHHHHHHHHH---HHHH-HHHHHHHHHHHHHHHH
Confidence 444555444333344 6774 3446666666665543
No 124
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=33.20 E-value=4.9e+02 Score=25.75 Aligned_cols=20 Identities=30% Similarity=0.386 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 019169 129 EQLSVLEEKIKNLLEQVETL 148 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~L 148 (345)
++|..+..+|..+..+++++
T Consensus 211 ~~l~~~~~ei~~~~~~l~e~ 230 (312)
T smart00787 211 EKLKKLLQEIMIKVKKLEEL 230 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44444454554444444444
No 125
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=33.09 E-value=2.3e+02 Score=24.64 Aligned_cols=23 Identities=30% Similarity=0.489 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGE 150 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGe 150 (345)
...|..|..+|..|..+++.|..
T Consensus 108 ~~dv~~L~~rId~L~~~v~~l~~ 130 (132)
T PF05597_consen 108 RKDVEALSARIDQLTAQVERLAN 130 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 46788888888888888887754
No 126
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=32.90 E-value=2.6e+02 Score=23.09 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=10.1
Q ss_pred cCcccccchhhhc
Q 019169 191 KMALCEICGSFLV 203 (345)
Q Consensus 191 km~VCeVCGA~Ls 203 (345)
.--+|+.||--+.
T Consensus 79 ~yG~C~~Cge~I~ 91 (110)
T TIGR02420 79 EYGYCEECGEEIG 91 (110)
T ss_pred CCCchhccCCccc
Confidence 3469999998754
No 127
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=32.73 E-value=2.8e+02 Score=24.88 Aligned_cols=17 Identities=18% Similarity=0.370 Sum_probs=8.2
Q ss_pred CChhhhHHHHHHHHHHH
Q 019169 80 AYVPKFEAELAQFCEKL 96 (345)
Q Consensus 80 ~~~~~yE~e~~~~L~~l 96 (345)
-|..||=.=+.=.|..+
T Consensus 104 ~YIsGf~LfL~l~I~r~ 120 (192)
T PF05529_consen 104 MYISGFALFLSLVIRRV 120 (192)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 35566665444333333
No 128
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=32.61 E-value=1e+02 Score=26.17 Aligned_cols=52 Identities=17% Similarity=0.305 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHH
Q 019169 99 DLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAE 158 (345)
Q Consensus 99 d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~ 158 (345)
-+|.||+.|-.=+ ++. ..-.+.+++..|.++|.+|.+....|-.|..+-...
T Consensus 45 aIDNKIeQAMDLV-KtH-------LmfAVREEVe~Lk~qI~eL~er~~~Le~EN~lLk~~ 96 (123)
T KOG4797|consen 45 AIDNKIEQAMDLV-KTH-------LMFAVREEVEVLKEQIRELEERNSALERENSLLKTL 96 (123)
T ss_pred eechHHHHHHHHH-HHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4667777764333 221 234567788888888888888877777665554433
No 129
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=32.54 E-value=2.3e+02 Score=24.98 Aligned_cols=112 Identities=19% Similarity=0.165 Sum_probs=56.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchh-hHHHHHHHHHHHHHHHHHHHHHhhcCCHHH-------HHHH
Q 019169 89 LAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAE-KSEQLSVLEEKIKNLLEQVETLGEAGKVDE-------AEAL 160 (345)
Q Consensus 89 ~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e-~~e~i~~l~ekI~~ll~eaE~LGeeG~Vde-------A~~l 160 (345)
+...++.=...++.-|..+++.+....+ .+.+ .+.-..-|...|..+....+.+...-.++- ...+
T Consensus 5 l~e~~~~~~~~L~~~le~a~e~~~~~~e------lT~eEl~lv~~ylkRDl~~~a~~~~~~~~~~~~~~~lie~slw~~L 78 (146)
T PF07295_consen 5 LEEALEHSEEELQEALEKAKEYLVAAGE------LTREELALVSAYLKRDLEEFARYYEELREWLSPDLQLIEESLWDEL 78 (146)
T ss_pred HHHHHhcCHHHHHHHHHHHHHHHHHHhh------cCHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccHHHHHHHHHHHH
Confidence 3444555567777888888888865431 2222 222222334444444444444222222211 1344
Q ss_pred HHHHHHHHHHHHHHHhhhhhhhh---hhHHHhhcCcccccchhhhcccch
Q 019169 161 MRKVEILNVEKTTLTQQSQNDKV---LMMAQEKKMALCEICGSFLVANDA 207 (345)
Q Consensus 161 ~~~ve~Lk~ek~~le~~~~~~~~---~~~~~~qkm~VCeVCGA~Ls~~D~ 207 (345)
..-+++-+-|..+|.+.+ .... +|.-.....-||.-||.-+....+
T Consensus 79 ~~ItDkTqvEw~el~~d~-~h~g~Y~sGE~~g~G~l~C~~Cg~~~~~~~~ 127 (146)
T PF07295_consen 79 SSITDKTQVEWAELAQDL-EHHGVYHSGEVVGPGTLVCENCGHEVELTHP 127 (146)
T ss_pred HhhhchhHHHHHHHHHHH-HhcCCeecCcEecCceEecccCCCEEEecCC
Confidence 445555566666666554 2210 111123567899999988776653
No 130
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=32.51 E-value=5.1e+02 Score=27.88 Aligned_cols=151 Identities=21% Similarity=0.226 Sum_probs=76.6
Q ss_pred HHHHHHHhcCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHH
Q 019169 66 QKLKESFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQV 145 (345)
Q Consensus 66 ~~lK~~Ye~~~~~~~~~~~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~ea 145 (345)
..||.-|......+.+++.+ .+|.++..-+..|........ .-...+..++|..++++|..|.+-.
T Consensus 232 ~~Lk~Gyr~m~~~gY~l~~~-------------~id~~~~~L~~~l~~~~~~l~-~Leld~aeeel~~I~e~ie~lYd~l 297 (570)
T COG4477 232 QDLKAGYRDMKEEGYHLEHV-------------NIDSRLERLKEQLVENSELLT-QLELDEAEEELGLIQEKIESLYDLL 297 (570)
T ss_pred HHHHHHHHHHHHccCCcccc-------------cHHHHHHHHHHHHHHHHhHHH-HhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 57888887765555543322 334444444444433221010 0112344578889999999999998
Q ss_pred HHHhhcCCHHHHH---------HHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhh-cCcccccchhhhcccchHHHhhhhh
Q 019169 146 ETLGEAGKVDEAE---------ALMRKVEILNVEKTTLTQQSQNDKVLMMAQEK-KMALCEICGSFLVANDAAERTQSHI 215 (345)
Q Consensus 146 E~LGeeG~VdeA~---------~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~q-km~VCeVCGA~Ls~~D~d~Rl~dH~ 215 (345)
|-=.+.+++-+.. .+-..-+.|+++.+.+.+.+.-+..-..+..+ .-+.=++=.++..+. -.
T Consensus 298 E~EveA~~~V~~~~~~l~~~l~k~ke~n~~L~~Eie~V~~sY~l~e~e~~~vr~~e~eL~el~~~~~~i~--------~~ 369 (570)
T COG4477 298 EREVEAKNVVEENLPILPDYLEKAKENNEHLKEEIERVKESYRLAETELGSVRKFEKELKELESVLDEIL--------EN 369 (570)
T ss_pred HHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHHHhccChhHHHHHHHHHHHHHHHHHHHHHHH--------HH
Confidence 8888777765441 22222334444444444433000000010100 001111112222222 23
Q ss_pred ccccccchHHHHHHHHHHHHHHH
Q 019169 216 SGKQHIGYGMVRDFITEYKEAKE 238 (345)
Q Consensus 216 ~GK~HlGy~kIRe~l~eLk~~~~ 238 (345)
.+.+|+.|.-+.++++++.+++.
T Consensus 370 ~~~~~~~yS~lq~~l~~~~~~l~ 392 (570)
T COG4477 370 IEAQEVAYSELQDNLEEIEKALT 392 (570)
T ss_pred hhcccccHHHHHHHHHHHHHHHH
Confidence 46889999999999988887663
No 131
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=32.27 E-value=1.3e+02 Score=24.88 Aligned_cols=44 Identities=20% Similarity=0.118 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHH
Q 019169 130 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTT 173 (345)
Q Consensus 130 ~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~ 173 (345)
-+......|...+..+++....++-++|...+.++...-.+...
T Consensus 20 ~l~~~~~~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~ 63 (121)
T PF14276_consen 20 YLNNSTDSIEEQLEQIEEAIENEDWEKAYKETEELEKEWDKNKK 63 (121)
T ss_pred hhhhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhch
Confidence 34556778888999999999999999999999888888665544
No 132
>PF04108 APG17: Autophagy protein Apg17 ; InterPro: IPR007240 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Autophagy protein 17 (Apg17) is required for activating Apg1 protein kinases. This entry also contains Autophagy protein 11 which is involved in cytoplasm to vacuole transport (Cvt) and pexophagy. ; GO: 0006914 autophagy
Probab=31.64 E-value=4.4e+02 Score=26.92 Aligned_cols=20 Identities=15% Similarity=0.096 Sum_probs=16.0
Q ss_pred hhHhhhhcccCCCCCCCCCc
Q 019169 46 PHDLFVNTRSDLGPCPRIHD 65 (345)
Q Consensus 46 PhdLF~nTK~DlG~C~kiHd 65 (345)
-+.|+.|-+..+..||+||.
T Consensus 124 v~~L~~~l~~~i~~~~~~~~ 143 (412)
T PF04108_consen 124 VEILRENLKISIDELQAIQE 143 (412)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 38888888888899986664
No 133
>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].
Probab=31.59 E-value=2.1e+02 Score=26.64 Aligned_cols=78 Identities=21% Similarity=0.298 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcC-CCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHH
Q 019169 90 AQFCEKLVMDLDRRVRRGRERLSQEV-EPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 168 (345)
Q Consensus 90 ~~~L~~li~d~drkI~~~k~RL~~~~-e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk 168 (345)
...|+.++..++..+...++.++.-. ..+ ..-.....+|..|+.+-..++.+.=++..+ +..+-.+|..|+
T Consensus 138 n~~Le~~~~~le~~l~~~k~~ie~vN~~RK---~~Q~~~~~~L~~Le~~W~~~v~kn~eie~a-----~~~Le~ei~~l~ 209 (221)
T PF05700_consen 138 NEQLEAMLKRLEKELAKLKKEIEEVNRERK---RRQEEAGEELRYLEQRWKELVSKNLEIEVA-----CEELEQEIEQLK 209 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHhHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHH
Confidence 34555666666666666555554211 000 001123345666666666666665555432 344555555555
Q ss_pred HHHHHHH
Q 019169 169 VEKTTLT 175 (345)
Q Consensus 169 ~ek~~le 175 (345)
.+..+++
T Consensus 210 ~~~~~~~ 216 (221)
T PF05700_consen 210 RKAAELK 216 (221)
T ss_pred HHHHHHh
Confidence 5544443
No 134
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=31.51 E-value=26 Score=25.40 Aligned_cols=41 Identities=22% Similarity=0.318 Sum_probs=29.3
Q ss_pred hcCcccccchhhhcccchHHHhhhhhccccccchHHHHHHHHHHHHH
Q 019169 190 KKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEA 236 (345)
Q Consensus 190 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eLk~~ 236 (345)
++--.||+|.+--- =|..|+.+.+|..|+.=-.-+..|-..
T Consensus 3 ~k~GYCE~C~~ky~------~l~~Hi~s~~Hr~FA~~~~Nf~~lD~l 43 (49)
T PF07535_consen 3 KKPGYCENCRVKYD------DLEEHIQSEKHRKFAENDSNFKELDSL 43 (49)
T ss_pred CCCccCccccchhh------hHHHHhCCHHHHHHHcCcccHHHHHHH
Confidence 45568999986432 288999999999998655555555443
No 135
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.13 E-value=19 Score=23.92 Aligned_cols=11 Identities=36% Similarity=0.772 Sum_probs=8.8
Q ss_pred cCcccccchhh
Q 019169 191 KMALCEICGSF 201 (345)
Q Consensus 191 km~VCeVCGA~ 201 (345)
...+|+||||-
T Consensus 17 ~p~~CP~Cg~~ 27 (34)
T cd00729 17 APEKCPICGAP 27 (34)
T ss_pred CCCcCcCCCCc
Confidence 45799999984
No 136
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=31.01 E-value=23 Score=32.10 Aligned_cols=36 Identities=25% Similarity=0.362 Sum_probs=25.2
Q ss_pred hcCcccccchhhhcccchHHHhhhhhccccccchHHHHHHHHHHHHHH
Q 019169 190 KKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKEAK 237 (345)
Q Consensus 190 qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy~kIRe~l~eLk~~~ 237 (345)
.-...|++||..|.-.||..-+ ..|.+.+++|++.+
T Consensus 134 ~~~F~Cp~Cg~~L~~~dn~~~~------------~~l~~~I~~l~~~~ 169 (178)
T PRK06266 134 EYGFRCPQCGEMLEEYDNSELI------------KELKEQIKELEEEL 169 (178)
T ss_pred hcCCcCCCCCCCCeecccHHHH------------HHHHHHHHHHHHHh
Confidence 3469999999999987776543 34566666665543
No 137
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=30.47 E-value=6.6e+02 Score=26.77 Aligned_cols=160 Identities=16% Similarity=0.208 Sum_probs=0.0
Q ss_pred HHHHHHHhcCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHH
Q 019169 66 QKLKESFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQV 145 (345)
Q Consensus 66 ~~lK~~Ye~~~~~~~~~~~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~ea 145 (345)
..|+.-|......+.+++..+ +..-|..+...|..+...|... ...+..+.+..+.++|..|...+
T Consensus 229 ~eL~~gy~~m~~~gy~l~~~~------i~~~i~~i~~~l~~~~~~L~~l--------~l~~~~~~~~~i~~~Id~lYd~l 294 (560)
T PF06160_consen 229 EELKEGYREMEEEGYYLEHLD------IEEEIEQIEEQLEEALALLKNL--------ELDEVEEENEEIEERIDQLYDIL 294 (560)
T ss_pred HHHHHHHHHHHHCCCCCCCCC------HHHHHHHHHHHHHHHHHHHHcC--------CHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred HHHhhcCCHHHH--HHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccchHHHhhhhhccccccch
Q 019169 146 ETLGEAGKVDEA--EALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQSHISGKQHIGY 223 (345)
Q Consensus 146 E~LGeeG~VdeA--~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlGy 223 (345)
|.-......-+- ..+...++.++..-..|..++..-..+..-.+.-+..=.....-|......--...+-....++-|
T Consensus 295 e~E~~Ak~~V~~~~~~l~~~l~~~~~~~~~l~~e~~~v~~sY~L~~~e~~~~~~l~~~l~~l~~~~~~~~~~i~~~~~~y 374 (560)
T PF06160_consen 295 EKEVEAKKYVEKNLKELYEYLEHAKEQNKELKEELERVSQSYTLNHNELEIVRELEKQLKELEKRYEDLEERIEEQQVPY 374 (560)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcCH
Q ss_pred HHHHHHHHHHHHHHHH
Q 019169 224 GMVRDFITEYKEAKEK 239 (345)
Q Consensus 224 ~kIRe~l~eLk~~~~~ 239 (345)
..|.+.+.++.+.+..
T Consensus 375 S~i~~~l~~~~~~l~~ 390 (560)
T PF06160_consen 375 SEIQEELEEIEEQLEE 390 (560)
T ss_pred HHHHHHHHHHHHHHHH
No 138
>PRK11637 AmiB activator; Provisional
Probab=30.36 E-value=3.5e+02 Score=27.46 Aligned_cols=19 Identities=21% Similarity=0.417 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 019169 130 QLSVLEEKIKNLLEQVETL 148 (345)
Q Consensus 130 ~i~~l~ekI~~ll~eaE~L 148 (345)
+|..++.+|..+-.+|+.|
T Consensus 90 ~i~~~~~~i~~~~~ei~~l 108 (428)
T PRK11637 90 KLRETQNTLNQLNKQIDEL 108 (428)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444333
No 139
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=30.17 E-value=3e+02 Score=24.94 Aligned_cols=9 Identities=44% Similarity=1.302 Sum_probs=7.0
Q ss_pred cCcccccch
Q 019169 191 KMALCEICG 199 (345)
Q Consensus 191 km~VCeVCG 199 (345)
+.-||.|||
T Consensus 133 ~~~vC~vCG 141 (166)
T COG1592 133 KVWVCPVCG 141 (166)
T ss_pred CEEEcCCCC
Confidence 378888887
No 140
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=29.86 E-value=24 Score=19.96 Aligned_cols=19 Identities=26% Similarity=0.684 Sum_probs=10.4
Q ss_pred ccccchhhhcccchHHHhhhhh
Q 019169 194 LCEICGSFLVANDAAERTQSHI 215 (345)
Q Consensus 194 VCeVCGA~Ls~~D~d~Rl~dH~ 215 (345)
+|++||.-.. +..-|..|+
T Consensus 2 ~C~~C~~~~~---~~~~l~~H~ 20 (24)
T PF13894_consen 2 QCPICGKSFR---SKSELRQHM 20 (24)
T ss_dssp E-SSTS-EES---SHHHHHHHH
T ss_pred CCcCCCCcCC---cHHHHHHHH
Confidence 6999997654 444455554
No 141
>PRK06424 transcription factor; Provisional
Probab=29.79 E-value=20 Score=31.60 Aligned_cols=11 Identities=27% Similarity=0.806 Sum_probs=5.4
Q ss_pred cccccchhhhc
Q 019169 193 ALCEICGSFLV 203 (345)
Q Consensus 193 ~VCeVCGA~Ls 203 (345)
.||+-|.-|.-
T Consensus 24 ~vC~~Ca~~G~ 34 (144)
T PRK06424 24 NVCDDCAKFGT 34 (144)
T ss_pred ehhHHHHHcCC
Confidence 45555554444
No 142
>KOG2801 consensus Probable Rab-GAPs [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.72 E-value=19 Score=35.68 Aligned_cols=21 Identities=29% Similarity=0.697 Sum_probs=15.2
Q ss_pred ccchhhhcccchHHHhhhhhcccc
Q 019169 196 EICGSFLVANDAAERTQSHISGKQ 219 (345)
Q Consensus 196 eVCGA~Ls~~D~d~Rl~dH~~GK~ 219 (345)
+||||||+..= --.+.|+||+
T Consensus 402 evcgaylstdw---sernkfggkl 422 (559)
T KOG2801|consen 402 EVCGAYLSTDW---SERNKFGGKL 422 (559)
T ss_pred HHhhHhcccch---hhhcccCcee
Confidence 79999999432 2346899984
No 143
>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]
Probab=29.68 E-value=2.2e+02 Score=30.43 Aligned_cols=137 Identities=19% Similarity=0.179 Sum_probs=74.8
Q ss_pred CCcchhhcCCChhHhhhhcccCCCCCCCCCcHHHHHHHhc---C--CCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 019169 35 EVCPFYMVRFCPHDLFVNTRSDLGPCPRIHDQKLKESFEK---S--PRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRE 109 (345)
Q Consensus 35 ~VCk~yL~g~CPhdLF~nTK~DlG~C~kiHd~~lK~~Ye~---~--~~~~~~~~~yE~e~~~~L~~li~d~drkI~~~k~ 109 (345)
.||.-=|+.-=-.-+|.| -.+---|+|+-++.=+..-.. . ....-.++..|.-++..|.+=+++.+-+|....+
T Consensus 141 ~v~~~P~~~~~s~S~~~~-~~~EaL~ekLk~~~een~~lr~k~~llk~Et~~~~~keq~~y~~~~KelrdtN~q~~s~~e 219 (596)
T KOG4360|consen 141 SVCSTPLVSNESRSAFQR-ELLEALQEKLKPLEEENTQLRSKAMLLKTETLTYEEKEQQLYGDCVKELRDTNTQARSGQE 219 (596)
T ss_pred ccccCCCccCcchhhHHH-HHHHHHHhhcCChHHHHHHHHHHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 477766654444556666 334466877776532221111 1 2233445567888888899999999999999988
Q ss_pred hhhhcCCCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHH-HHHHHHHHHHHhhh
Q 019169 110 RLSQEVEPAP-PPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKV-EILNVEKTTLTQQS 178 (345)
Q Consensus 110 RL~~~~e~~~-~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~v-e~Lk~ek~~le~~~ 178 (345)
-|+.-.++.. ..+.......+|..++++|..+.-+.|+|++ -+.++..+ +++..|.++++.++
T Consensus 220 el~~kt~el~~q~Ee~skLlsql~d~qkk~k~~~~Ekeel~~------~Lq~~~da~~ql~aE~~EleDky 284 (596)
T KOG4360|consen 220 ELQSKTKELSRQQEENSKLLSQLVDLQKKIKYLRHEKEELDE------HLQAYKDAQRQLTAELEELEDKY 284 (596)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH------HHHHHHhhHHHHHHHHHHHHHHH
Confidence 7764221110 0011223334555555555555555555544 23333333 34555666665554
No 144
>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells. Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex
Probab=29.40 E-value=3.9e+02 Score=25.25 Aligned_cols=87 Identities=18% Similarity=0.227 Sum_probs=49.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHhh---cCCHHHHHH
Q 019169 84 KFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAP-PPPISAEKSEQLSVLEEKIKNLLEQVETLGE---AGKVDEAEA 159 (345)
Q Consensus 84 ~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~-~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGe---eG~VdeA~~ 159 (345)
.+|.+ +.-|..=+..+..++..+......-..... .-.........|..+...|..++.++..|+. .+-......
T Consensus 49 ~~e~~-l~~L~~d~~~L~~k~~~~~~~~~~l~~~t~~t~~~a~~L~~~i~~l~~~i~~l~~~~~~l~~~~~~~~~~~l~~ 127 (264)
T PF06008_consen 49 PLEKE-LESLEQDVENLQEKATKVSRKAQQLNNNTERTLQRAQDLEQFIQNLQDNIQELIEQVESLNENGDQLPSEDLQR 127 (264)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccCCCCHHHHHH
Confidence 45555 444555555666666655544432210000 0012234566788999999999999999999 444444455
Q ss_pred HHHHHHHHHHHH
Q 019169 160 LMRKVEILNVEK 171 (345)
Q Consensus 160 l~~~ve~Lk~ek 171 (345)
.+++|+.+-.+.
T Consensus 128 ~l~ea~~mL~em 139 (264)
T PF06008_consen 128 ALAEAQRMLEEM 139 (264)
T ss_pred HHHHHHHHHHHH
Confidence 555555554443
No 145
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=29.20 E-value=19 Score=26.64 Aligned_cols=20 Identities=30% Similarity=0.655 Sum_probs=11.9
Q ss_pred cCcccccchhhhcccchHHH
Q 019169 191 KMALCEICGSFLVANDAAER 210 (345)
Q Consensus 191 km~VCeVCGA~Ls~~D~d~R 210 (345)
+--.|+||||.+...-|-+|
T Consensus 23 ~PatCP~C~a~~~~srnLrR 42 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRR 42 (54)
T ss_dssp --EE-TTT--EESSHHHHHH
T ss_pred CCCCCCcchhhccchhhHHH
Confidence 44689999999997766666
No 146
>COG4499 Predicted membrane protein [Function unknown]
Probab=29.06 E-value=2e+02 Score=29.65 Aligned_cols=75 Identities=12% Similarity=0.096 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 019169 93 CEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 169 (345)
Q Consensus 93 L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 169 (345)
|.+.+.|.+--.=..-.++++.. ........+..+.|.+++.+|..++.+.+++..+-+-+++...-.+-|+++.
T Consensus 335 IAr~L~D~d~~~~Al~k~~eevk--sn~~lsg~~r~e~lk~~n~~lqd~~k~~~e~k~e~das~~aeaka~eek~~~ 409 (434)
T COG4499 335 IARNLDDNDLTLLALTKLYEEVK--SNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQ 409 (434)
T ss_pred HHHhCCcchhHHHHHHHHHHHHh--cccCCCchHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhHhhhhhhhhhh
Confidence 44455555554444445555443 2122344678889999999999999999999987665554444444444443
No 147
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=28.74 E-value=3.2e+02 Score=22.22 Aligned_cols=24 Identities=17% Similarity=0.223 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcC
Q 019169 92 FCEKLVMDLDRRVRRGRERLSQEV 115 (345)
Q Consensus 92 ~L~~li~d~drkI~~~k~RL~~~~ 115 (345)
-|..-++++|.-|..|+.|.....
T Consensus 31 ~v~~kLneLd~Li~eA~~r~~~~~ 54 (109)
T PF03980_consen 31 DVVEKLNELDKLIEEAKERKNSGE 54 (109)
T ss_pred hHHHHHHHHHHHHHHHHHhHhccc
Confidence 356778889999999999987543
No 148
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=28.56 E-value=1.6e+02 Score=30.66 Aligned_cols=50 Identities=20% Similarity=0.244 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
..++..|..+.+.+.++|-..+..|+- .++.+++++..|+.+.+.++.+.
T Consensus 42 ~~~~e~l~~~rn~~sk~ig~~~~~~~~-~~~~l~~e~~~l~~~l~~~e~~~ 91 (429)
T COG0172 42 LRELEELQAERNELSKEIGRALKRGED-DAEELIAEVKELKEKLKELEAAL 91 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccch-hHHHHHHHHHHHHHHHHhccHHH
Confidence 345666777777777777755555544 67788888888888887777654
No 149
>PF15500 Toxin_39: Putative RNase-like toxin
Probab=28.49 E-value=63 Score=26.41 Aligned_cols=11 Identities=36% Similarity=0.748 Sum_probs=8.4
Q ss_pred CCCCCCCCCcH
Q 019169 56 DLGPCPRIHDQ 66 (345)
Q Consensus 56 DlG~C~kiHd~ 66 (345)
+--|||.||-+
T Consensus 29 SppPCPvi~ve 39 (96)
T PF15500_consen 29 SPPPCPVIRVE 39 (96)
T ss_pred CCCCCCchhHH
Confidence 66789988854
No 150
>PRK14139 heat shock protein GrpE; Provisional
Probab=28.37 E-value=3.3e+02 Score=25.06 Aligned_cols=86 Identities=17% Similarity=0.180 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccch
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 207 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~ 207 (345)
..++..+..+|..+-+++++|- +.-+.+.++.+-++. .++++. .. ..+.-+=.++-.+|-+.|+
T Consensus 31 ~~e~~~l~~~l~~le~e~~elk-----d~~lR~~AefeN~rK---R~~kE~-e~-------~~~~a~~~~~~~LLpv~Dn 94 (185)
T PRK14139 31 EDAAPALEAELAEAEAKAAELQ-----DSFLRAKAETENVRR---RAQEDV-AK-------AHKFAIESFAESLLPVKDS 94 (185)
T ss_pred chhHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH-HH-------HHHHHHHHHHHHHhhHHhH
Confidence 3457778888888888888774 344555555555542 222221 10 1111222355678889999
Q ss_pred HHHhhhhhcc---ccccchHHHHHH
Q 019169 208 AERTQSHISG---KQHIGYGMVRDF 229 (345)
Q Consensus 208 d~Rl~dH~~G---K~HlGy~kIRe~ 229 (345)
-.|.-.|... .++-|+..|...
T Consensus 95 LerAl~~~~~~~~~l~~Gv~mi~k~ 119 (185)
T PRK14139 95 LEAALADESGDLEKLREGVELTLKQ 119 (185)
T ss_pred HHHHHhcccchHHHHHHHHHHHHHH
Confidence 9986566542 234444444333
No 151
>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants. XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.
Probab=28.34 E-value=2.5e+02 Score=28.28 Aligned_cols=43 Identities=23% Similarity=0.264 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 131 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 131 i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
+..|.+++..|..+.+.|- .++..+.+++|++...|++++..+
T Consensus 139 ~~~l~~~~~~L~~enerL~-----~e~~~~~~qlE~~v~~K~~~E~~L 181 (342)
T PF06632_consen 139 NSRLQAENEHLQKENERLE-----SEANKLLKQLEKFVNAKEEHEEDL 181 (342)
T ss_dssp HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555553 345677777888888887777765
No 152
>PLN00204 CP12 gene family protein; Provisional
Probab=27.90 E-value=1.6e+02 Score=25.59 Aligned_cols=43 Identities=19% Similarity=0.202 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHhhcCC-HHHHHHHHHHHHHHHHHHHHHH
Q 019169 133 VLEEKIKNLLEQVETLGEAGK-VDEAEALMRKVEILNVEKTTLT 175 (345)
Q Consensus 133 ~l~ekI~~ll~eaE~LGeeG~-VdeA~~l~~~ve~Lk~ek~~le 175 (345)
.|+++|.+.+++++++-.+|. -.++.....+||+|.+++.-..
T Consensus 56 ~L~e~Ie~aI~eArevCa~g~~S~eCaaAWDeVEELqAeasHqr 99 (126)
T PLN00204 56 GISEKVEKSIKEAEETCADDPASGECVAAWDEVEELSAAASHAR 99 (126)
T ss_pred cHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 578888889999999877763 3567778888888887765443
No 153
>PRK14150 heat shock protein GrpE; Provisional
Probab=27.76 E-value=3e+02 Score=25.35 Aligned_cols=26 Identities=27% Similarity=0.293 Sum_probs=19.5
Q ss_pred hcCcccccchhhhcccchHHHhhhhh
Q 019169 190 KKMALCEICGSFLVANDAAERTQSHI 215 (345)
Q Consensus 190 qkm~VCeVCGA~Ls~~D~d~Rl~dH~ 215 (345)
++..+-.++-.+|-+.|+-.|.-.|.
T Consensus 83 ~~~a~~~~~~~lL~v~DnlerAl~~~ 108 (193)
T PRK14150 83 HKFALEKFANELLPVIDNLERALQAA 108 (193)
T ss_pred HHHHHHHHHHHHHhHHhHHHHHHhcc
Confidence 34455667888999999999965664
No 154
>PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional
Probab=27.62 E-value=3.8e+02 Score=29.95 Aligned_cols=41 Identities=27% Similarity=0.295 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 019169 66 QKLKESFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGR 108 (345)
Q Consensus 66 ~~lK~~Ye~~~~~~~~~~~yE~e~~~~L~~li~d~drkI~~~k 108 (345)
++||+++-+++..... --+.-+..-|++|-.++|..+..|-
T Consensus 439 ekLk~eilKAk~s~~~--~~~~~L~e~IeKLk~E~d~e~S~A~ 479 (762)
T PLN03229 439 EKLKEQILKAKESSSK--PSELALNEMIEKLKKEIDLEYTEAV 479 (762)
T ss_pred HHHHHHHHhcccccCC--CCChHHHHHHHHHHHHHHHHHHHhh
Confidence 5888888777433333 3477788899999999999988763
No 155
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=27.44 E-value=2.8e+02 Score=23.39 Aligned_cols=30 Identities=10% Similarity=0.036 Sum_probs=16.5
Q ss_pred HHHHhcCCCCCCChhhhHHHHHHHHHHHHHHHH
Q 019169 69 KESFEKSPRHDAYVPKFEAELAQFCEKLVMDLD 101 (345)
Q Consensus 69 K~~Ye~~~~~~~~~~~yE~e~~~~L~~li~d~d 101 (345)
..-|+..-+.+.. ++.+.-.+++.++..+.
T Consensus 25 ~k~~~~LVkkGe~---~~ee~k~~~~e~~~~~~ 54 (118)
T TIGR01837 25 SKFFNRLVKEGEL---AEKRGQKRFDESVDAAR 54 (118)
T ss_pred HHHHHHHHHhccc---cHHHHHHHHHHHHHHHH
Confidence 4444444444443 56666666666665555
No 156
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=27.19 E-value=29 Score=30.82 Aligned_cols=21 Identities=29% Similarity=0.431 Sum_probs=17.1
Q ss_pred hcCcccccchhhhcccchHHH
Q 019169 190 KKMALCEICGSFLVANDAAER 210 (345)
Q Consensus 190 qkm~VCeVCGA~Ls~~D~d~R 210 (345)
.-...|++||+.|.-.||..-
T Consensus 126 ~~~F~Cp~Cg~~L~~~dn~~~ 146 (158)
T TIGR00373 126 ELNFTCPRCGAMLDYLDNSEA 146 (158)
T ss_pred HcCCcCCCCCCEeeeccCHHH
Confidence 356999999999998887654
No 157
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=27.18 E-value=2e+02 Score=25.33 Aligned_cols=50 Identities=34% Similarity=0.395 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCHHHH-----------HHHHHHHHHHHHHHHHHHhhh
Q 019169 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEA-----------EALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA-----------~~l~~~ve~Lk~ek~~le~~~ 178 (345)
+++..|+.+|..|.+++.+|..+-..-.+ ..+...++.|+.+...++..+
T Consensus 72 eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL 132 (169)
T PF07106_consen 72 EELAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKL 132 (169)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555666666666555555544322222 234555556666665555544
No 158
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.16 E-value=2.2e+02 Score=27.38 Aligned_cols=34 Identities=26% Similarity=0.303 Sum_probs=25.9
Q ss_pred HHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 145 VETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 145 aE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
+..-.+.++|++-+....+|+.|+.++.+|.+..
T Consensus 194 ~~l~reieeidEQi~~~kkvekl~~qK~ellnkk 227 (264)
T KOG3032|consen 194 AALTREIEEIDEQISYKKKVEKLKRQKMELLNKK 227 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333455678888888999999999998888765
No 159
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=26.91 E-value=26 Score=23.67 Aligned_cols=15 Identities=40% Similarity=0.771 Sum_probs=11.9
Q ss_pred hhcCcccccchhhhc
Q 019169 189 EKKMALCEICGSFLV 203 (345)
Q Consensus 189 ~qkm~VCeVCGA~Ls 203 (345)
-+.-.||++||.-|+
T Consensus 18 P~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 18 PKVEGVCDNCGGELV 32 (36)
T ss_dssp -SSTTBCTTTTEBEB
T ss_pred CCCCCccCCCCCeeE
Confidence 456789999999776
No 160
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=26.88 E-value=23 Score=29.33 Aligned_cols=30 Identities=20% Similarity=0.360 Sum_probs=21.6
Q ss_pred CcccccchhhhcccchHHHhhh----hhcccccc
Q 019169 192 MALCEICGSFLVANDAAERTQS----HISGKQHI 221 (345)
Q Consensus 192 m~VCeVCGA~Ls~~D~d~Rl~d----H~~GK~Hl 221 (345)
-..|++||.||-..++..++.| .|.|-+-|
T Consensus 20 ~~gCpnC~~~l~~~g~~~~v~~~tT~~f~G~i~i 53 (98)
T cd07973 20 RDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIAL 53 (98)
T ss_pred CCCCCCCcchhccCCCccccccccCCCcceEEEE
Confidence 4799999999887777665544 56666554
No 161
>PRK14140 heat shock protein GrpE; Provisional
Probab=26.35 E-value=3.6e+02 Score=24.92 Aligned_cols=73 Identities=19% Similarity=0.202 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhhhcccch
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 207 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~Ls~~D~ 207 (345)
.+.|.++..+|..+-+++.+|- +.-+.+.+..+-++. ..+.+. . ...+..+=.++..+|-+.|+
T Consensus 36 ~~~~~~l~~~i~~l~~ei~elk-----d~~lR~~Ae~eN~rk---R~~rE~-~-------~~~~~a~~~~~~~LLpvlDn 99 (191)
T PRK14140 36 AELLDEEQAKIAELEAKLDELE-----ERYLRLQADFENYKR---RIQKEN-E-------AAEKYRAQSLASDLLPALDN 99 (191)
T ss_pred hhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH---HHHHHH-H-------HHHHHHHHHHHHHHHHHHHH
Confidence 4567777777777777776663 222333333333321 222211 0 12233344577889999999
Q ss_pred HHHhhhhhc
Q 019169 208 AERTQSHIS 216 (345)
Q Consensus 208 d~Rl~dH~~ 216 (345)
-.|.-.|..
T Consensus 100 LerAl~~~~ 108 (191)
T PRK14140 100 FERALQIEA 108 (191)
T ss_pred HHHHHhccC
Confidence 999777754
No 162
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.33 E-value=24 Score=28.26 Aligned_cols=14 Identities=57% Similarity=1.020 Sum_probs=11.2
Q ss_pred Ccccccchhhhccc
Q 019169 192 MALCEICGSFLVAN 205 (345)
Q Consensus 192 m~VCeVCGA~Ls~~ 205 (345)
|-+|+|||+-|...
T Consensus 1 ~llCP~C~v~l~~~ 14 (88)
T COG3809 1 MLLCPICGVELVMS 14 (88)
T ss_pred CcccCcCCceeeee
Confidence 56899999988744
No 163
>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=26.06 E-value=5.3e+02 Score=24.47 Aligned_cols=78 Identities=18% Similarity=0.243 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhc--CCHHHHHHHHH
Q 019169 86 EAELAQFCEKLVMDLDRRVRRG-RERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEA--GKVDEAEALMR 162 (345)
Q Consensus 86 E~e~~~~L~~li~d~drkI~~~-k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGee--G~VdeA~~l~~ 162 (345)
|.+++.-.+.+|.++..-+..- .+| ....++|..+...|+.|-..|..+-.+ --.+.+..++.
T Consensus 23 e~~~~e~ee~~L~e~~kE~~~L~~Er--------------~~h~eeLrqI~~DIn~lE~iIkqa~~er~~~~~~i~r~~e 88 (230)
T PF10146_consen 23 EVESLENEEKCLEEYRKEMEELLQER--------------MAHVEELRQINQDINTLENIIKQAESERNKRQEKIQRLYE 88 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555666666665554322 111 222344444455555444444333222 13455677777
Q ss_pred HHHHHHHHHHHHHhh
Q 019169 163 KVEILNVEKTTLTQQ 177 (345)
Q Consensus 163 ~ve~Lk~ek~~le~~ 177 (345)
++..|+.+..++..+
T Consensus 89 ey~~Lk~~in~~R~e 103 (230)
T PF10146_consen 89 EYKPLKDEINELRKE 103 (230)
T ss_pred HHHHHHHHHHHHHHH
Confidence 777777777777666
No 164
>PF05852 DUF848: Gammaherpesvirus protein of unknown function (DUF848); InterPro: IPR008566 This family consists of several uncharacterised proteins from the Gammaherpesvirinae.
Probab=25.85 E-value=2.4e+02 Score=25.10 Aligned_cols=48 Identities=29% Similarity=0.357 Sum_probs=36.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHh--hcCCHHHHHHHHHHHHHHHHHHHH
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLG--EAGKVDEAEALMRKVEILNVEKTT 173 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LG--eeG~VdeA~~l~~~ve~Lk~ek~~ 173 (345)
.....|..++..|.....++..|- .-.+|+.+.+|...|..|+++.+.
T Consensus 58 ~~~~~v~~~~~~i~~k~~El~~L~~~d~~kv~~~E~L~d~v~eLkeel~~ 107 (146)
T PF05852_consen 58 EIKNKVSSLETEISEKKKELSHLKKFDRKKVEDLEKLTDRVEELKEELEF 107 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345567777888888888877764 457889999999999999876643
No 165
>TIGR02135 phoU_full phosphate transport system regulatory protein PhoU. This model describes PhoU, a regulatory protein of unknown mechanism for high-affinity phosphate ABC transporter systems. The protein consists of two copies of the domain described by Pfam model pfam01895. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect and so likely has some second function.
Probab=25.77 E-value=3.7e+02 Score=23.39 Aligned_cols=35 Identities=14% Similarity=0.126 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHH
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMR 162 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~ 162 (345)
..+|..+...+..++..+..+-..++.+.|+.+..
T Consensus 11 ~~el~~m~~~~~~ml~~~~~~~~~~d~~~~~~i~~ 45 (212)
T TIGR02135 11 REELLEMGGLVEEQLEDAVRALTEKDRELARKVIE 45 (212)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHH
Confidence 34555555666666666666666666554444443
No 166
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=25.58 E-value=90 Score=18.41 Aligned_cols=23 Identities=13% Similarity=0.245 Sum_probs=18.4
Q ss_pred HHHHHhhcCCHHHHHHHHHHHHH
Q 019169 144 QVETLGEAGKVDEAEALMRKVEI 166 (345)
Q Consensus 144 eaE~LGeeG~VdeA~~l~~~ve~ 166 (345)
=+..++..|++++|..++.+..+
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHccchHHHHHHHHHHHhH
Confidence 36778999999999998877643
No 167
>PRK01156 chromosome segregation protein; Provisional
Probab=25.50 E-value=6.6e+02 Score=28.03 Aligned_cols=15 Identities=27% Similarity=0.789 Sum_probs=10.3
Q ss_pred Ccccccchhhhcccc
Q 019169 192 MALCEICGSFLVAND 206 (345)
Q Consensus 192 m~VCeVCGA~Ls~~D 206 (345)
--||+|||.-+--.=
T Consensus 452 ~~~Cp~c~~~~~~e~ 466 (895)
T PRK01156 452 QSVCPVCGTTLGEEK 466 (895)
T ss_pred CCCCCCCCCcCChhh
Confidence 478999988665444
No 168
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=25.11 E-value=1.1e+02 Score=27.67 Aligned_cols=25 Identities=36% Similarity=0.391 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 154 VDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 154 VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
|+|=..|..+++.|+.|...|.+++
T Consensus 23 LdEKE~L~~~~QRLkDE~RDLKqEl 47 (166)
T PF04880_consen 23 LDEKENLREEVQRLKDELRDLKQEL 47 (166)
T ss_dssp HHHHHHHHHCH--------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555556666666666666666554
No 169
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=25.06 E-value=26 Score=23.89 Aligned_cols=13 Identities=38% Similarity=0.718 Sum_probs=10.6
Q ss_pred cccccchhhhccc
Q 019169 193 ALCEICGSFLVAN 205 (345)
Q Consensus 193 ~VCeVCGA~Ls~~ 205 (345)
..|+.||+.|+.-
T Consensus 2 ~~CP~Cg~~lv~r 14 (39)
T PF01396_consen 2 EKCPKCGGPLVLR 14 (39)
T ss_pred cCCCCCCceeEEE
Confidence 5799999998853
No 170
>PLN02943 aminoacyl-tRNA ligase
Probab=24.95 E-value=1.8e+02 Score=33.24 Aligned_cols=66 Identities=21% Similarity=0.195 Sum_probs=44.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC-CCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019169 84 KFEAELAQFCEKLVMDLDRRVRRGRERLSQEV-EPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGE 150 (345)
Q Consensus 84 ~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~-e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGe 150 (345)
.++.+.-+ |++-+..++..|.+.+.+|.... ..+.++.+.....+++.+++++|..+.+.+..|++
T Consensus 886 D~~~E~~r-L~K~l~klekei~~~~~kLsN~~F~~KAP~evv~~e~~kl~~~~~~l~~~~~~l~~l~~ 952 (958)
T PLN02943 886 DISAEVER-LSKRLSKMQTEYDALAARLSSPKFVEKAPEDVVRGVREKAAEAEEKIKLTKNRLAFLKS 952 (958)
T ss_pred cHHHHHHH-HHHHHHHHHHHHHHHHHHhCCchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 46666555 88888899999999999996432 11222233444556777777777777777777663
No 171
>TIGR02135 phoU_full phosphate transport system regulatory protein PhoU. This model describes PhoU, a regulatory protein of unknown mechanism for high-affinity phosphate ABC transporter systems. The protein consists of two copies of the domain described by Pfam model pfam01895. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect and so likely has some second function.
Probab=24.49 E-value=4.7e+02 Score=22.73 Aligned_cols=82 Identities=13% Similarity=0.059 Sum_probs=53.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccc--cchhhhc
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCE--ICGSFLV 203 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCe--VCGA~Ls 203 (345)
+...+|..+-..+..++..+-.+-..++.+.|..+...-+.+...-.++.+.. .. .. +. ..|+ .+-.|+.
T Consensus 113 ~~~~el~~m~~~v~~~l~~a~~al~~~d~~~~~~i~~~e~~id~l~~~i~~~~-~~---~~-~~---~~~~~~~~~~~~~ 184 (212)
T TIGR02135 113 KHLEELEKMGKLALKMLKDALDAFLNKDAELARQVAEMDERVDELYRQIFREL-VT---YM-KE---NPENIEAALDVLL 184 (212)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH-HH---HH-HH---CcccHHHHHHHHH
Confidence 44567888888888888988888888888766665555444443333333222 11 01 11 3466 5667778
Q ss_pred ccchHHHhhhhh
Q 019169 204 ANDAAERTQSHI 215 (345)
Q Consensus 204 ~~D~d~Rl~dH~ 215 (345)
+..+=+|+.||.
T Consensus 185 i~~~lERigD~~ 196 (212)
T TIGR02135 185 IARYLERIGDHA 196 (212)
T ss_pred HHHHHHHHHHHH
Confidence 888999999996
No 172
>PRK14153 heat shock protein GrpE; Provisional
Probab=24.28 E-value=2.7e+02 Score=25.78 Aligned_cols=35 Identities=20% Similarity=0.172 Sum_probs=22.4
Q ss_pred ccchhhhcccchHHHhhhhhc-----cccccchHHHHHHH
Q 019169 196 EICGSFLVANDAAERTQSHIS-----GKQHIGYGMVRDFI 230 (345)
Q Consensus 196 eVCGA~Ls~~D~d~Rl~dH~~-----GK~HlGy~kIRe~l 230 (345)
.++-.+|-+.|+-.|.-.|.. ..++-|+..|...+
T Consensus 84 ~~~~~LLpv~DnLerAl~~~~~~~~~~~l~~Gvemi~k~~ 123 (194)
T PRK14153 84 QVLLDLLEVTDNFERALESARTAEDMNSIVEGIEMVSKQF 123 (194)
T ss_pred HHHHHHhhHHhHHHHHHhcccccchHHHHHHHHHHHHHHH
Confidence 466788999999999766653 12444554444333
No 173
>smart00150 SPEC Spectrin repeats.
Probab=24.27 E-value=3.1e+02 Score=20.46 Aligned_cols=50 Identities=30% Similarity=0.356 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 128 ~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
..+|......|..+...++.|...|.. .+..+...++.|......|....
T Consensus 44 ~~e~~~~~~~v~~~~~~~~~L~~~~~~-~~~~i~~~~~~l~~~w~~l~~~~ 93 (101)
T smart00150 44 EAELEAHEERVEALNELGEQLIEEGHP-DAEEIEERLEELNERWEELKELA 93 (101)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556666667777777777777543 45567777777777776665543
No 174
>KOG1510 consensus RNA polymerase II holoenzyme and mediator subcomplex, subunit SURB7/SRB7 [Transcription]
Probab=24.19 E-value=5e+02 Score=22.91 Aligned_cols=43 Identities=21% Similarity=0.287 Sum_probs=29.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHH
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKT 172 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~ 172 (345)
....++|..|++++.+...+.+++... +..++.+|+.+-+...
T Consensus 87 e~Ql~~i~kLq~en~e~~~el~~~v~~-----~e~Ll~~vq~~le~~a 129 (139)
T KOG1510|consen 87 EAQLEKIKKLQEENEEVALELEELVSK-----GEKLLEQVQSLLEDIA 129 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHH
Confidence 345567888888888877777776554 4457777777655443
No 175
>PF06721 DUF1204: Protein of unknown function (DUF1204); InterPro: IPR009596 This family represents the C terminus of a number of Arabidopsis thaliana hypothetical proteins of unknown function. Family members contain a conserved DFD motif.
Probab=24.05 E-value=2.4e+02 Score=26.33 Aligned_cols=70 Identities=13% Similarity=0.233 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHHH-HhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhHHHhhcCcccccchhh
Q 019169 129 EQLSVLEEKIKNLLEQVET-LGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSF 201 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~-LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~~~~~qkm~VCeVCGA~ 201 (345)
.+..+|+..|.......+. -.+..+..-..++..-++.+++..+.+...+ ... ....-+-|+.|+|||..
T Consensus 50 ~K~deLedr~~se~KRLRsrR~~~AEn~rrs~L~kv~~l~QARidRvK~Hi-Ddk--ia~ePkFle~nQV~Gni 120 (228)
T PF06721_consen 50 VKFDELEDRISSEQKRLRSRRINYAENNRRSALEKVASLYQARIDRVKAHI-DDK--IADEPKFLEFNQVKGNI 120 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hhh--hhcchHHHHHHHhhchH
Confidence 3444555555544444443 1112222234556666667777777777765 332 12233567789999974
No 176
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=23.53 E-value=2.1e+02 Score=23.23 Aligned_cols=30 Identities=17% Similarity=0.214 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCHHHHHH
Q 019169 130 QLSVLEEKIKNLLEQVETLGEAGKVDEAEA 159 (345)
Q Consensus 130 ~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~ 159 (345)
++..+..+|..|.++.+.|-.+-.|.+++-
T Consensus 24 k~~ka~~~~~kL~~en~qlk~Ek~~~~~qv 53 (87)
T PF10883_consen 24 KVKKAKKQNAKLQKENEQLKTEKAVAETQV 53 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445556667777777777766655544443
No 177
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=23.48 E-value=25 Score=22.40 Aligned_cols=12 Identities=50% Similarity=1.151 Sum_probs=6.5
Q ss_pred cccchhhhcccc
Q 019169 195 CEICGSFLVAND 206 (345)
Q Consensus 195 CeVCGA~Ls~~D 206 (345)
|+|||+-|+..+
T Consensus 2 CP~C~s~l~~~~ 13 (28)
T PF03119_consen 2 CPVCGSKLVREE 13 (28)
T ss_dssp -TTT--BEEE-C
T ss_pred cCCCCCEeEcCC
Confidence 999999988443
No 178
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.40 E-value=3.7e+02 Score=21.16 Aligned_cols=25 Identities=20% Similarity=0.242 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCC
Q 019169 129 EQLSVLEEKIKNLLEQVETLGEAGK 153 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LGeeG~ 153 (345)
.+|..-=..|..|--+||+|-+..+
T Consensus 11 ~KiqqAvdTI~LLQmEieELKEknn 35 (79)
T COG3074 11 AKVQQAIDTITLLQMEIEELKEKNN 35 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3444444455566667777776655
No 179
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=23.23 E-value=1.9e+02 Score=28.53 Aligned_cols=14 Identities=43% Similarity=0.897 Sum_probs=10.8
Q ss_pred cCcccccchhhhcc
Q 019169 191 KMALCEICGSFLVA 204 (345)
Q Consensus 191 km~VCeVCGA~Ls~ 204 (345)
...+|+|||..=++
T Consensus 184 ~~~~CPvCGS~Pva 197 (308)
T COG3058 184 SRQYCPVCGSMPVA 197 (308)
T ss_pred ccccCCCcCCCCcc
Confidence 55799999986553
No 180
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=22.90 E-value=28 Score=25.94 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=8.1
Q ss_pred cCcccccchhhhc
Q 019169 191 KMALCEICGSFLV 203 (345)
Q Consensus 191 km~VCeVCGA~Ls 203 (345)
+|.+|+.||+|-.
T Consensus 4 ~mr~C~~CgvYTL 16 (56)
T PRK13130 4 KIRKCPKCGVYTL 16 (56)
T ss_pred cceECCCCCCEEc
Confidence 5667777766633
No 181
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=22.84 E-value=1.6e+02 Score=22.42 Aligned_cols=24 Identities=25% Similarity=0.445 Sum_probs=10.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHh
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLG 149 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LG 149 (345)
....+|..|..+|..|..++..+.
T Consensus 29 ~Qq~~I~~L~~~l~~L~~rl~~~~ 52 (69)
T PF04102_consen 29 EQQRQIDRLQRQLRLLRERLRELE 52 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHT-----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 334555566666666666555554
No 182
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=22.84 E-value=33 Score=34.22 Aligned_cols=16 Identities=25% Similarity=0.600 Sum_probs=12.9
Q ss_pred CCCCCCcchhhcCCCh
Q 019169 31 WDDKEVCPFYMVRFCP 46 (345)
Q Consensus 31 ~~D~~VCk~yL~g~CP 46 (345)
..-..|||+||=|+|=
T Consensus 74 ~~~~~vcK~~l~glC~ 89 (325)
T KOG1040|consen 74 SRGKVVCKHWLRGLCK 89 (325)
T ss_pred cCCceeehhhhhhhhh
Confidence 4455799999999993
No 183
>CHL00102 rps20 ribosomal protein S20
Probab=22.68 E-value=1.9e+02 Score=23.70 Aligned_cols=36 Identities=11% Similarity=0.052 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHhhc-------CCHHHHHHHHHHHHHHHH
Q 019169 134 LEEKIKNLLEQVETLGEA-------GKVDEAEALMRKVEILNV 169 (345)
Q Consensus 134 l~ekI~~ll~eaE~LGee-------G~VdeA~~l~~~ve~Lk~ 169 (345)
.-..|..++.+++.+.+. |++++|+.++..+..+-.
T Consensus 24 ~kS~~rT~iKk~~~ai~~~~~~~~~~d~~~a~~~l~~a~s~iD 66 (93)
T CHL00102 24 YKSSVKTLIKKYLKNLEDYKTSPNSNNKKKVQETLSSVYSKID 66 (93)
T ss_pred HHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHH
Confidence 344555667777777776 999999999998887754
No 184
>smart00746 TRASH metallochaperone-like domain.
Probab=22.62 E-value=21 Score=21.56 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=8.5
Q ss_pred cccchhhhccc
Q 019169 195 CEICGSFLVAN 205 (345)
Q Consensus 195 CeVCGA~Ls~~ 205 (345)
|++||..+...
T Consensus 1 c~~C~~~~~~~ 11 (39)
T smart00746 1 CSFCGKDIYNP 11 (39)
T ss_pred CCCCCCCccCC
Confidence 88999887633
No 185
>PF04065 Not3: Not1 N-terminal domain, CCR4-Not complex component ; InterPro: IPR007207 The Ccr4-Not complex (Not1, Not2, Not3, Not4 and Not5) is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID []. This domain is the N-terminal region of the Not proteins.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.57 E-value=5.7e+02 Score=24.38 Aligned_cols=80 Identities=18% Similarity=0.263 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHH------HHHHHHHHHhhcCCHHHHHHH
Q 019169 87 AELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIK------NLLEQVETLGEAGKVDEAEAL 160 (345)
Q Consensus 87 ~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~------~ll~eaE~LGeeG~VdeA~~l 160 (345)
.+...||..+|..+...|.....-++.-..........+.....|..|...|. ..|+.+=.|.+.|.|+-
T Consensus 121 ~e~~~wl~~~Id~L~~QiE~~E~E~E~L~~~~kKkk~~~~~~~r~~~l~~~ierhk~Hi~kLE~lLR~L~N~~l~~---- 196 (233)
T PF04065_consen 121 EEARDWLKDSIDELNRQIEQLEAEIESLSSQKKKKKKDSTKQERIEELESRIERHKFHIEKLELLLRLLDNDELDP---- 196 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCccCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCH----
Confidence 56888999999999999998877665321000000111234455556665555 44566666778888853
Q ss_pred HHHHHHHHHHH
Q 019169 161 MRKVEILNVEK 171 (345)
Q Consensus 161 ~~~ve~Lk~ek 171 (345)
..|+.++.-.
T Consensus 197 -e~V~~ikedi 206 (233)
T PF04065_consen 197 -EQVEDIKEDI 206 (233)
T ss_pred -HHHHHHHHHH
Confidence 4455555433
No 186
>KOG4182 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.39 E-value=3.4e+02 Score=29.04 Aligned_cols=51 Identities=12% Similarity=0.186 Sum_probs=36.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
........|.+++..++.++- ..+|+..++++.++.++..+.+.+...+.+
T Consensus 78 ~Lq~Da~~Lq~kma~il~el~--~aegesadCiAaLaRldn~kQkleaA~esL 128 (828)
T KOG4182|consen 78 ALQADAHRLQEKMAAILLELA--AAEGESADCIAALARLDNKKQKLEAAKESL 128 (828)
T ss_pred HHHHHHHHHHHHHHHHHHHHH--HHhCChHHHHHHHHHhccHHHHHHHHHHHH
Confidence 345667788888888887654 467888888888888777766555444433
No 187
>PF08898 DUF1843: Domain of unknown function (DUF1843); InterPro: IPR014994 This domain is found in functionally uncharacterised proteins. It can be found independently or at the C terminus of the protein.
Probab=22.25 E-value=2.1e+02 Score=21.20 Aligned_cols=34 Identities=35% Similarity=0.493 Sum_probs=20.3
Q ss_pred HHHHHHHHHHH-HhhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q 019169 137 KIKNLLEQVET-LGEAGKVDEAEALMRKVEILNVEKTTLTQ 176 (345)
Q Consensus 137 kI~~ll~eaE~-LGeeG~VdeA~~l~~~ve~Lk~ek~~le~ 176 (345)
+++.|+.++|+ |.+.|+|.. .++.|+.|+..|+.
T Consensus 18 ~MK~l~~~aeq~L~~~~~i~~------al~~Lk~EIaklE~ 52 (53)
T PF08898_consen 18 QMKALAAQAEQQLAEAGDIAA------ALEKLKAEIAKLEA 52 (53)
T ss_pred HHHHHHHHHHHHHccchHHHH------HHHHHHHHHHHHhc
Confidence 34466666665 555566543 45566777766653
No 188
>TIGR00606 rad50 rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.20 E-value=1.3e+03 Score=27.16 Aligned_cols=120 Identities=13% Similarity=0.145 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHH
Q 019169 89 LAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 168 (345)
Q Consensus 89 ~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk 168 (345)
++.-+..-|.++...+..+...+..-. ........++..+..++......|. +...++. .-..++.++
T Consensus 578 ~~~~~~~el~~~~~~~~~~~~el~~~e------~~l~~~~~~l~~~~~eL~~~~~~i~---~~~~~~~---~~~~L~~~~ 645 (1311)
T TIGR00606 578 WLHSKSKEINQTRDRLAKLNKELASLE------QNKNHINNELESKEEQLSSYEDKLF---DVCGSQD---EESDLERLK 645 (1311)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHh---cCCCchh---HHHHHHHHH
Confidence 444455555555555555555553211 1112333445555555554444444 3333333 233444444
Q ss_pred HHHHHHHhhhhhh-hh------hhHHHh--hcCcccccchhhhcccchHHHhhhhhcccccc
Q 019169 169 VEKTTLTQQSQND-KV------LMMAQE--KKMALCEICGSFLVANDAAERTQSHISGKQHI 221 (345)
Q Consensus 169 ~ek~~le~~~~~~-~~------~~~~~~--qkm~VCeVCGA~Ls~~D~d~Rl~dH~~GK~Hl 221 (345)
.+.+.+...+ .. .. ...... ..-..|++|.--+...+.-..+-.++..++--
T Consensus 646 ~~l~~~~~~~-~~~~~~~~~~~k~ie~a~~~~~~~C~LC~R~f~~eee~~~f~~~L~~~~~~ 706 (1311)
T TIGR00606 646 EEIEKSSKQR-AMLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEFISDLQSKLRL 706 (1311)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHHhhccCCcCCCCCCCCCChhHHHHHHHHHHHHHhc
Confidence 4444444332 11 00 011122 45569999998765444334555555554443
No 189
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=22.18 E-value=7.9e+02 Score=26.15 Aligned_cols=87 Identities=16% Similarity=0.129 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhc--CCCCCCCCC--------------------chhhHHHHHHHHHHHHHHHHH
Q 019169 87 AELAQFCEKLVMDLDRRVRRGRERLSQE--VEPAPPPPI--------------------SAEKSEQLSVLEEKIKNLLEQ 144 (345)
Q Consensus 87 ~e~~~~L~~li~d~drkI~~~k~RL~~~--~e~~~~~~~--------------------~~e~~e~i~~l~ekI~~ll~e 144 (345)
...+..+..+|..++..|..-..-|.+= .++..-... -+.-...|...=..|.....+
T Consensus 104 ~~~~~~~~~~l~~~e~~~~~i~~~l~~l~~~e~~nr~~v~~l~~~y~~~rk~ll~~~~~~G~a~~~le~~l~~~e~~f~~ 183 (569)
T PRK04778 104 KHEINEIESLLDLIEEDIEQILEELQELLESEEKNREEVEQLKDLYRELRKSLLANRFSFGPALDELEKQLENLEEEFSQ 183 (569)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHH
Confidence 3456677788888888877766666431 100000000 000011122222334466788
Q ss_pred HHHHhhcCCHHHHHHHHHHHHHHHHHHHH
Q 019169 145 VETLGEAGKVDEAEALMRKVEILNVEKTT 173 (345)
Q Consensus 145 aE~LGeeG~VdeA~~l~~~ve~Lk~ek~~ 173 (345)
.+.|.+.|+..+|..++.+++.--.....
T Consensus 184 f~~l~~~Gd~~~A~e~l~~l~~~~~~l~~ 212 (569)
T PRK04778 184 FVELTESGDYVEAREILDQLEEELAALEQ 212 (569)
T ss_pred HHHHhcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999888777665544443
No 190
>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease
Probab=22.04 E-value=6.2e+02 Score=23.25 Aligned_cols=39 Identities=23% Similarity=0.316 Sum_probs=29.3
Q ss_pred HHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 140 NLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 140 ~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
.-+.....|.+.++..+...+..+++.+..+........
T Consensus 103 ~~l~~L~~L~~dknL~eReeL~~kL~~~~~~l~~~~~ki 141 (194)
T PF15619_consen 103 DELKHLKKLSEDKNLAEREELQRKLSQLEQKLQEKEKKI 141 (194)
T ss_pred HHHHHHHHHHHcCCchhHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566778888999988888888888887766655443
No 191
>PRK04406 hypothetical protein; Provisional
Probab=21.96 E-value=82 Score=24.69 Aligned_cols=16 Identities=13% Similarity=0.453 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 019169 130 QLSVLEEKIKNLLEQV 145 (345)
Q Consensus 130 ~i~~l~ekI~~ll~ea 145 (345)
+|..|..++..|..++
T Consensus 40 ~I~~L~~ql~~L~~rl 55 (75)
T PRK04406 40 LITKMQDQMKYVVGKV 55 (75)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333333333333333
No 192
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=21.86 E-value=3.7e+02 Score=23.76 Aligned_cols=14 Identities=29% Similarity=0.710 Sum_probs=10.8
Q ss_pred hcCcccccchhhhc
Q 019169 190 KKMALCEICGSFLV 203 (345)
Q Consensus 190 qkm~VCeVCGA~Ls 203 (345)
-.--+|+.||-.+.
T Consensus 109 gtYG~Ce~CGe~I~ 122 (151)
T PRK10778 109 EDFGYCESCGVEIG 122 (151)
T ss_pred CCCceeccCCCccc
Confidence 35579999998755
No 193
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 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 zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=21.82 E-value=31 Score=29.49 Aligned_cols=17 Identities=41% Similarity=0.767 Sum_probs=14.9
Q ss_pred hhcCcccccchhhhccc
Q 019169 189 EKKMALCEICGSFLVAN 205 (345)
Q Consensus 189 ~qkm~VCeVCGA~Ls~~ 205 (345)
.+-+-.|+.||+.|++.
T Consensus 40 ~~d~l~C~~C~~~l~~~ 56 (133)
T PF07967_consen 40 SKDMLKCESCGARLCVK 56 (133)
T ss_pred CCCEEEeCCCCCEEEEe
Confidence 46778999999999988
No 194
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=21.69 E-value=35 Score=22.25 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=8.7
Q ss_pred cCcccccchhh
Q 019169 191 KMALCEICGSF 201 (345)
Q Consensus 191 km~VCeVCGA~ 201 (345)
.-.+|+|||+-
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 45799999984
No 195
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=21.60 E-value=2.9e+02 Score=24.77 Aligned_cols=14 Identities=29% Similarity=0.321 Sum_probs=5.6
Q ss_pred HHHHHHHHHHHHHH
Q 019169 160 LMRKVEILNVEKTT 173 (345)
Q Consensus 160 l~~~ve~Lk~ek~~ 173 (345)
.-++++.|+.|.+.
T Consensus 159 ~~~ei~~lk~el~~ 172 (192)
T PF05529_consen 159 LSEEIEKLKKELEK 172 (192)
T ss_pred hHHHHHHHHHHHHH
Confidence 33444444443333
No 196
>PF06694 Plant_NMP1: Plant nuclear matrix protein 1 (NMP1); InterPro: IPR010604 This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm [].
Probab=21.57 E-value=7e+02 Score=24.98 Aligned_cols=81 Identities=20% Similarity=0.162 Sum_probs=56.4
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhh-----HHHhhcCcccc
Q 019169 122 PISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLM-----MAQEKKMALCE 196 (345)
Q Consensus 122 ~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~~~~~~~~-----~~~~qkm~VCe 196 (345)
+-..+...++..+..++..+.++++.|...+.+..=+.-...+..|+.+.+.+.+.+ ..=+.. -+=...|.|=.
T Consensus 168 PD~seLe~~~s~~sk~Lq~lqq~v~~Lask~~y~pd~~~~e~~~~Lr~~L~tflq~~-~~F~~~Y~~EIrpWch~~~~P~ 246 (325)
T PF06694_consen 168 PDVSELEKKASELSKQLQSLQQQVAELASKHPYNPDEEYVEKESQLRLELETFLQTA-AGFNHCYEKEIRPWCHMMEVPQ 246 (325)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhhHHHHHHHHHHHHHHHHHH-HHHHHHHHhcchhhhccCccch
Confidence 455677889999999999999999999999888776666777777888777777654 221100 11124557777
Q ss_pred cchhhhc
Q 019169 197 ICGSFLV 203 (345)
Q Consensus 197 VCGA~Ls 203 (345)
.||-=..
T Consensus 247 L~gLGPA 253 (325)
T PF06694_consen 247 LHGLGPA 253 (325)
T ss_pred hhcccHH
Confidence 7884333
No 197
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=21.56 E-value=3.5e+02 Score=20.16 Aligned_cols=50 Identities=12% Similarity=0.162 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
..+..+..=|......+......+.++.+..++.+.+.+..+.......+
T Consensus 8 ~~~~~l~~Wl~~~e~~l~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~l 57 (105)
T PF00435_consen 8 QEADELLDWLQETEAKLSSSEPGSDLEELEEQLKKHKELQEEIESRQERL 57 (105)
T ss_dssp HHHHHHHHHHHHHHHHHCSCTHSSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence 34555555555555555445557888999999999999988777655544
No 198
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=21.54 E-value=1.2e+02 Score=23.21 Aligned_cols=21 Identities=33% Similarity=0.464 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 019169 130 QLSVLEEKIKNLLEQVETLGE 150 (345)
Q Consensus 130 ~i~~l~ekI~~ll~eaE~LGe 150 (345)
-+.+|++.|..|..+|+-|-.
T Consensus 26 sV~El~eRIalLq~EIeRlkA 46 (65)
T COG5509 26 SVAELEERIALLQAEIERLKA 46 (65)
T ss_pred hHHHHHHHHHHHHHHHHHHHH
Confidence 366788888888777776643
No 199
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=21.53 E-value=6.4e+02 Score=23.65 Aligned_cols=54 Identities=28% Similarity=0.324 Sum_probs=37.6
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHH----HhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVET----LGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~----LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
..++++...++.+|..+-++.+. |...+.|++.+.+-.++..++.+++.++.+.
T Consensus 128 ~DvT~~y~D~~arl~~l~~~~~rl~~ll~ka~~~~d~l~ie~~L~~v~~eIe~~~~~~ 185 (262)
T PF14257_consen 128 EDVTEQYVDLEARLKNLEAEEERLLELLEKAKTVEDLLEIERELSRVRSEIEQLEGQL 185 (262)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555666666655544443 2245689999999999999999999888765
No 200
>PLN02320 seryl-tRNA synthetase
Probab=21.53 E-value=2.4e+02 Score=29.98 Aligned_cols=49 Identities=14% Similarity=0.136 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 127 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (345)
Q Consensus 127 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~~~ 178 (345)
...++..|..+.+.+.++|-.. ..+ ++++.+.+++..|+++...|++++
T Consensus 105 ~~~~~~~lr~ern~~sk~i~~~-~~~--~~~~~l~~~~k~lk~~i~~le~~~ 153 (502)
T PLN02320 105 LQKEVERLRAERNAVANKMKGK-LEP--SERQALVEEGKNLKEGLVTLEEDL 153 (502)
T ss_pred HHHHHHHHHHHHHHHHHHHHhh-hCC--CCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445666666676666666542 112 345677777777777777777654
No 201
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=21.38 E-value=4.9e+02 Score=24.45 Aligned_cols=50 Identities=22% Similarity=0.169 Sum_probs=38.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q 019169 127 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQ 176 (345)
Q Consensus 127 ~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~le~ 176 (345)
..+++-.|.-+|..+-..+=.+.-.|++++|...++++..+-.+.+.+-+
T Consensus 18 ~REE~l~lsRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~ 67 (204)
T COG2178 18 AREEALKLSREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRLLA 67 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45677778888888888888888889999998888888777766664443
No 202
>PRK12496 hypothetical protein; Provisional
Probab=21.13 E-value=37 Score=30.40 Aligned_cols=12 Identities=50% Similarity=1.016 Sum_probs=9.9
Q ss_pred cccccchhhhcc
Q 019169 193 ALCEICGSFLVA 204 (345)
Q Consensus 193 ~VCeVCGA~Ls~ 204 (345)
.+|+|||.-|..
T Consensus 144 ~~C~~CG~~~~r 155 (164)
T PRK12496 144 DVCEICGSPVKR 155 (164)
T ss_pred CcCCCCCChhhh
Confidence 679999988764
No 203
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=21.09 E-value=2.5e+02 Score=29.39 Aligned_cols=28 Identities=21% Similarity=0.532 Sum_probs=23.0
Q ss_pred CcccccchhhhcccchHHHhhhhhccccccc
Q 019169 192 MALCEICGSFLVANDAAERTQSHISGKQHIG 222 (345)
Q Consensus 192 m~VCeVCGA~Ls~~D~d~Rl~dH~~GK~HlG 222 (345)
-..|..|.+++| ++-=|-.|+-|.-|.-
T Consensus 493 kkqcslcnvlis---sevylfshvkgrkhqq 520 (672)
T KOG4722|consen 493 KKQCSLCNVLIS---SEVYLFSHVKGRKHQQ 520 (672)
T ss_pred hhccchhhhhhh---hhhhhhhhhcchhHHH
Confidence 378999999888 5667889999998864
No 204
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=21.04 E-value=38 Score=34.33 Aligned_cols=23 Identities=30% Similarity=0.668 Sum_probs=0.0
Q ss_pred cccchhhhcccchHHHhhhhhccccc
Q 019169 195 CEICGSFLVANDAAERTQSHISGKQH 220 (345)
Q Consensus 195 CeVCGA~Ls~~D~d~Rl~dH~~GK~H 220 (345)
|++||-+.+ .-.=...|+.||.|
T Consensus 241 C~~C~r~f~---~~~VFe~Hl~gK~H 263 (470)
T COG5188 241 CVKCGREFS---RSKVFEYHLEGKRH 263 (470)
T ss_pred eHhhhhHhh---hhHHHHHHHhhhhh
No 205
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.80 E-value=36 Score=30.23 Aligned_cols=7 Identities=71% Similarity=1.602 Sum_probs=4.1
Q ss_pred cccchhh
Q 019169 195 CEICGSF 201 (345)
Q Consensus 195 CeVCGA~ 201 (345)
||+||+-
T Consensus 3 CEiCG~~ 9 (154)
T TIGR00270 3 CEICGRK 9 (154)
T ss_pred cccCCCc
Confidence 6666653
No 206
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=20.78 E-value=5.9e+02 Score=22.48 Aligned_cols=63 Identities=21% Similarity=0.246 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCC-CCCchhhHHHHHHHHHHHHHHHHHHHHHh
Q 019169 87 AELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPP-PPISAEKSEQLSVLEEKIKNLLEQVETLG 149 (345)
Q Consensus 87 ~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~-~~~~~e~~e~i~~l~ekI~~ll~eaE~LG 149 (345)
...+..+..-+.+.+.++......+..-.+.... ........+++..++..+..+.+++..|-
T Consensus 87 ~~~l~~l~~el~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~e~~~l~ 150 (191)
T PF04156_consen 87 QQQLQQLQEELDQLQERIQELESELEKLKEDLQELRELLKSVEERLDSLDESIKELEKEIRELQ 150 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566666666666666666432211000 01223556788899999999999999888
No 207
>COG1340 Uncharacterized archaeal coiled-coil protein [Function unknown]
Probab=20.78 E-value=8.3e+02 Score=24.20 Aligned_cols=42 Identities=21% Similarity=0.364 Sum_probs=22.8
Q ss_pred HHHHHHhcC---CCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 019169 67 KLKESFEKS---PRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLS 112 (345)
Q Consensus 67 ~lK~~Ye~~---~~~~~~~~~yE~e~~~~L~~li~d~drkI~~~k~RL~ 112 (345)
.+...++.. .......|..|.++++.|.. +...+..++.-++
T Consensus 111 ~ler~i~~Le~~~~T~~L~~e~E~~lvq~I~~----L~k~le~~~k~~e 155 (294)
T COG1340 111 SLEREIERLEKKQQTSVLTPEEERELVQKIKE----LRKELEDAKKALE 155 (294)
T ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence 455555443 23344555677777766555 4555555555554
No 208
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=20.70 E-value=33 Score=22.77 Aligned_cols=14 Identities=21% Similarity=0.593 Sum_probs=11.3
Q ss_pred cCcccccchhhhcc
Q 019169 191 KMALCEICGSFLVA 204 (345)
Q Consensus 191 km~VCeVCGA~Ls~ 204 (345)
++.+|.+||+.+++
T Consensus 2 ~~~~C~~C~~~~i~ 15 (33)
T PF08792_consen 2 NLKKCSKCGGNGIV 15 (33)
T ss_pred CceEcCCCCCCeEE
Confidence 35789999998887
No 209
>PRK11020 hypothetical protein; Provisional
Probab=20.67 E-value=5.5e+02 Score=22.04 Aligned_cols=17 Identities=29% Similarity=0.386 Sum_probs=8.7
Q ss_pred hhhHHHHHHHHHHHHHH
Q 019169 125 AEKSEQLSVLEEKIKNL 141 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~l 141 (345)
++...+|..|+.+|..+
T Consensus 34 ~qf~~E~~~l~k~I~~l 50 (118)
T PRK11020 34 AQFEKEKATLEAEIARL 50 (118)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 44445555555555543
No 210
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=20.63 E-value=3.1e+02 Score=24.04 Aligned_cols=30 Identities=17% Similarity=0.317 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 019169 84 KFEAELAQFCEKLVMDLDRRVRRGRERLSQ 113 (345)
Q Consensus 84 ~yE~e~~~~L~~li~d~drkI~~~k~RL~~ 113 (345)
.|=.-..+||.+|...|+.|+.....||.+
T Consensus 3 ~Fi~~tv~fLN~F~~~cE~kL~~~e~~Lq~ 32 (148)
T PF10152_consen 3 HFIVHTVQFLNRFASVCEEKLSDMEQRLQR 32 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355667899999999999999998888853
No 211
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=20.61 E-value=3.5e+02 Score=28.56 Aligned_cols=21 Identities=5% Similarity=0.267 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 019169 129 EQLSVLEEKIKNLLEQVETLG 149 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LG 149 (345)
.++.+|+++|..|-.+.+.|.
T Consensus 76 ~kasELEKqLaaLrqElq~~s 96 (475)
T PRK13729 76 VTAAQMQKQYEEIRRELDVLN 96 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 345555666665555555333
No 212
>PHA03161 hypothetical protein; Provisional
Probab=20.47 E-value=3.4e+02 Score=24.27 Aligned_cols=48 Identities=19% Similarity=0.207 Sum_probs=37.6
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHh--hcCCHHHHHHHHHHHHHHHHHHH
Q 019169 125 AEKSEQLSVLEEKIKNLLEQVETLG--EAGKVDEAEALMRKVEILNVEKT 172 (345)
Q Consensus 125 ~e~~e~i~~l~ekI~~ll~eaE~LG--eeG~VdeA~~l~~~ve~Lk~ek~ 172 (345)
..+...|..++..|...-.+++.|- .-.+|+.+.++...|+.|+.+..
T Consensus 57 ~~i~~~v~~l~~~I~~k~kE~~~L~~fd~kkl~~~E~L~drv~eLkeel~ 106 (150)
T PHA03161 57 KSIEGMLQAVDLSIQEKKKELSLLKAFDRHKLSAAEDLQDKILELKEDIH 106 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455677888888888888888875 45788999999999999887654
No 213
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=20.41 E-value=36 Score=25.35 Aligned_cols=12 Identities=33% Similarity=0.791 Sum_probs=4.1
Q ss_pred cCcccccchhhh
Q 019169 191 KMALCEICGSFL 202 (345)
Q Consensus 191 km~VCeVCGA~L 202 (345)
.-.||++|||-.
T Consensus 32 r~y~Cp~CgAtG 43 (55)
T PF05741_consen 32 RKYVCPICGATG 43 (55)
T ss_dssp GG---TTT---G
T ss_pred hcCcCCCCcCcC
Confidence 337999999863
No 214
>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]
Probab=20.16 E-value=8.4e+02 Score=28.48 Aligned_cols=86 Identities=16% Similarity=0.218 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 019169 87 AELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEI 166 (345)
Q Consensus 87 ~e~~~~L~~li~d~drkI~~~k~RL~~~~e~~~~~~~~~e~~e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~~~ve~ 166 (345)
...++.|...+...+++|.+....+.+.. ... .........|..+...|...+++|++.-.. .+.+-.+++.
T Consensus 695 ~~~~~~l~~~~~q~~~~~~~~~~em~el~--n~~-e~~~~~~~~~~~l~~ei~~~~~eIe~~~~~-----~e~l~~e~e~ 766 (1074)
T KOG0250|consen 695 EKKLRELSEHIEQIKRRIRKKRAEMTELK--NTA-EEKQVDISKLEDLAREIKKKEKEIEEKEAP-----LEKLKEELEH 766 (1074)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh--hhh-hhhhcchhhhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHH
Q ss_pred HHHHHHHHHhhhhhh
Q 019169 167 LNVEKTTLTQQSQND 181 (345)
Q Consensus 167 Lk~ek~~le~~~~~~ 181 (345)
+..+..+++..+ .+
T Consensus 767 ~~~e~~e~~~~~-~~ 780 (1074)
T KOG0250|consen 767 IELEAQELEEYY-AA 780 (1074)
T ss_pred HHHHHHHHHHHH-HH
No 215
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.13 E-value=54 Score=18.49 Aligned_cols=20 Identities=20% Similarity=0.562 Sum_probs=13.6
Q ss_pred ccccchhhhcccchHHHhhhhhc
Q 019169 194 LCEICGSFLVANDAAERTQSHIS 216 (345)
Q Consensus 194 VCeVCGA~Ls~~D~d~Rl~dH~~ 216 (345)
.|++|+.-.. +..-+..|+.
T Consensus 2 ~C~~C~~~f~---~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFK---SKSALKEHMR 21 (26)
T ss_pred CCCCCcchhC---CHHHHHHHHH
Confidence 6999996654 4555667765
No 216
>PF04100 Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007234 Vps53 complexes with Vps52 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=20.10 E-value=9.2e+02 Score=24.43 Aligned_cols=23 Identities=17% Similarity=0.170 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q 019169 89 LAQFCEKLVMDLDRRVRRGRERL 111 (345)
Q Consensus 89 ~~~~L~~li~d~drkI~~~k~RL 111 (345)
++..|...|..+|..|..+.+-.
T Consensus 26 ~i~~l~~~i~~ld~eI~~~v~~q 48 (383)
T PF04100_consen 26 LIAKLRKEIRELDEEIKELVREQ 48 (383)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555556666665554444
No 217
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=20.09 E-value=66 Score=24.32 Aligned_cols=27 Identities=33% Similarity=0.434 Sum_probs=19.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhcC
Q 019169 126 EKSEQLSVLEEKIKNLLEQVETLGEAG 152 (345)
Q Consensus 126 e~~e~i~~l~ekI~~ll~eaE~LGeeG 152 (345)
.+.+++..|.++|..|..++.+|-.+.
T Consensus 11 AVrEEVevLK~~I~eL~~~n~~Le~EN 37 (59)
T PF01166_consen 11 AVREEVEVLKEQIAELEERNSQLEEEN 37 (59)
T ss_dssp T-TTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455778888888888888777765543
No 218
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=20.07 E-value=5e+02 Score=21.33 Aligned_cols=33 Identities=30% Similarity=0.427 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHH
Q 019169 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALM 161 (345)
Q Consensus 129 e~i~~l~ekI~~ll~eaE~LGeeG~VdeA~~l~ 161 (345)
.++...-........++-.|...|+.++|..++
T Consensus 112 ~~~~~~~~~y~~~~~~~~~~~~~~~~~~a~~~~ 144 (181)
T PF12729_consen 112 EEFKEAWKAYRKLRDQVIELAKSGDNDEARAIL 144 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 344444444455566666666777777665544
No 219
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=20.04 E-value=82 Score=31.30 Aligned_cols=10 Identities=20% Similarity=0.478 Sum_probs=4.1
Q ss_pred HHhhhhhccc
Q 019169 209 ERTQSHISGK 218 (345)
Q Consensus 209 ~Rl~dH~~GK 218 (345)
+||--=|+|+
T Consensus 189 RRLGGGLGg~ 198 (335)
T KOG0113|consen 189 RRLGGGLGGR 198 (335)
T ss_pred ccccCCcCCc
Confidence 3444444443
No 220
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=20.00 E-value=6.8e+02 Score=29.81 Aligned_cols=69 Identities=12% Similarity=0.159 Sum_probs=35.9
Q ss_pred HhhhhcccCCCCCCCCCcHHHHHHHhcCCCCCCC---hh--hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC
Q 019169 48 DLFVNTRSDLGPCPRIHDQKLKESFEKSPRHDAY---VP--KFEAELAQFCEKLVMDLDRRVRRGRERLSQEVE 116 (345)
Q Consensus 48 dLF~nTK~DlG~C~kiHd~~lK~~Ye~~~~~~~~---~~--~yE~e~~~~L~~li~d~drkI~~~k~RL~~~~e 116 (345)
.++..||.|+-.-..+-.++-++.=.+..-+... +. .-=...+..-+..|...+.-|+-+++.|.+-++
T Consensus 1532 ~IL~~T~~di~ra~~L~s~A~~a~~~A~~v~~~ae~V~eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~ 1605 (1758)
T KOG0994|consen 1532 AILSRTKGDIARAENLQSEAERARSRAEDVKGQAEDVVEALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQE 1605 (1758)
T ss_pred HHHHhhhhhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 4788899887655444444333222111001111 00 001123445567788888888888888876543
Done!