Query 025496
Match_columns 252
No_of_seqs 110 out of 261
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 06:26:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025496.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025496hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03194 LUC7: LUC7 N_terminus 100.0 8.3E-88 1.8E-92 606.8 21.8 231 1-237 1-235 (254)
2 KOG0796 Spliceosome subunit [R 100.0 8.4E-82 1.8E-86 574.9 17.8 228 1-237 1-231 (319)
3 COG5200 LUC7 U1 snRNP componen 100.0 1.6E-67 3.5E-72 456.7 17.1 235 2-252 3-252 (258)
4 PF12171 zf-C2H2_jaz: Zinc-fin 89.2 0.2 4.2E-06 29.8 1.0 25 193-220 2-26 (27)
5 PF12874 zf-met: Zinc-finger o 88.0 0.22 4.7E-06 28.7 0.7 24 194-220 2-25 (25)
6 smart00451 ZnF_U1 U1-like zinc 87.6 0.33 7.1E-06 30.0 1.4 29 193-224 4-32 (35)
7 PF04012 PspA_IM30: PspA/IM30 87.4 7.3 0.00016 34.0 10.2 82 91-178 26-107 (221)
8 COG1579 Zn-ribbon protein, pos 83.4 5.2 0.00011 36.4 7.5 21 92-112 63-83 (239)
9 PHA02562 46 endonuclease subun 82.6 12 0.00026 36.9 10.4 15 191-205 283-297 (562)
10 TIGR02302 aProt_lowcomp conser 81.8 2.9 6.3E-05 44.4 6.0 31 138-168 570-600 (851)
11 COG0419 SbcC ATPase involved i 80.3 43 0.00093 35.7 14.1 24 192-216 457-480 (908)
12 PF13779 DUF4175: Domain of un 79.2 4.7 0.0001 42.7 6.5 34 135-168 537-570 (820)
13 PRK15058 cytochrome b562; Prov 78.8 20 0.00044 29.6 8.8 42 129-170 78-122 (128)
14 PRK06835 DNA replication prote 77.3 20 0.00043 33.8 9.6 67 130-200 37-106 (329)
15 PRK02224 chromosome segregatio 77.0 30 0.00065 36.3 11.7 12 192-203 451-462 (880)
16 PRK09720 cybC cytochrome b562; 76.2 12 0.00025 29.8 6.4 40 129-168 50-92 (100)
17 PF06220 zf-U1: U1 zinc finger 74.8 2.3 4.9E-05 27.8 1.8 32 193-225 4-35 (38)
18 smart00356 ZnF_C3H1 zinc finge 73.2 1.7 3.6E-05 25.2 0.8 23 34-65 4-26 (27)
19 PRK14143 heat shock protein Gr 72.9 28 0.0006 31.7 8.9 96 127-238 65-167 (238)
20 PF00642 zf-CCCH: Zinc finger 72.6 1.5 3.3E-05 26.2 0.5 24 33-65 2-26 (27)
21 TIGR02977 phageshock_pspA phag 71.8 51 0.0011 29.1 10.2 66 91-162 27-92 (219)
22 PF07361 Cytochrom_B562: Cytoc 70.2 10 0.00022 29.8 4.9 42 129-170 53-97 (103)
23 PF04423 Rad50_zn_hook: Rad50 69.2 8.4 0.00018 26.5 3.7 11 194-204 22-32 (54)
24 PRK14144 heat shock protein Gr 67.9 36 0.00078 30.2 8.3 95 128-238 44-143 (199)
25 KOG3454 U1 snRNP-specific prot 67.8 4.9 0.00011 34.6 2.7 33 193-226 4-36 (165)
26 PRK01156 chromosome segregatio 65.9 41 0.00088 35.5 9.7 14 193-206 450-463 (895)
27 PF13913 zf-C2HC_2: zinc-finge 64.1 4 8.7E-05 24.1 1.1 20 192-215 2-21 (25)
28 PRK14158 heat shock protein Gr 62.2 72 0.0016 28.1 9.1 99 124-238 35-138 (194)
29 COG1842 PspA Phage shock prote 60.3 1.1E+02 0.0025 27.4 10.2 82 91-178 27-108 (225)
30 PF02151 UVR: UvrB/uvrC motif; 59.9 31 0.00066 21.9 4.8 35 136-170 2-36 (36)
31 PRK14148 heat shock protein Gr 59.4 69 0.0015 28.3 8.5 93 129-237 40-138 (195)
32 PF02403 Seryl_tRNA_N: Seryl-t 59.1 31 0.00066 26.7 5.7 49 128-178 42-90 (108)
33 COG1675 TFA1 Transcription ini 57.6 31 0.00067 30.0 5.9 36 190-237 130-165 (176)
34 COG3783 CybC Soluble cytochrom 57.0 20 0.00044 28.3 4.2 26 143-168 67-92 (100)
35 PRK03918 chromosome segregatio 55.0 1.3E+02 0.0029 31.4 11.2 165 66-235 286-477 (880)
36 PF14282 FlxA: FlxA-like prote 54.5 51 0.0011 26.0 6.3 50 128-178 18-67 (106)
37 PF10367 Vps39_2: Vacuolar sor 54.3 29 0.00064 26.1 4.8 13 192-204 78-90 (109)
38 PF04032 Rpr2: RNAse P Rpr2/Rp 53.8 45 0.00098 24.4 5.6 60 137-207 2-61 (85)
39 PRK10246 exonuclease subunit S 53.5 49 0.0011 36.0 7.9 9 193-201 504-512 (1047)
40 PRK10698 phage shock protein P 53.1 1.7E+02 0.0036 26.1 10.2 63 91-159 27-89 (222)
41 PF13863 DUF4200: Domain of un 52.5 61 0.0013 25.5 6.5 50 92-147 50-99 (126)
42 PF12854 PPR_1: PPR repeat 52.0 17 0.00038 22.4 2.6 20 144-163 13-32 (34)
43 PF11931 DUF3449: Domain of un 51.7 4.9 0.00011 35.6 0.0 28 191-221 100-128 (196)
44 PF12325 TMF_TATA_bd: TATA ele 50.9 1.3E+02 0.0029 24.4 10.6 70 87-178 15-84 (120)
45 PF03962 Mnd1: Mnd1 family; I 50.7 86 0.0019 27.2 7.6 53 126-178 73-126 (188)
46 COG2093 DNA-directed RNA polym 50.1 5.7 0.00012 29.0 0.2 24 191-214 17-50 (64)
47 PF07544 Med9: RNA polymerase 49.9 1.1E+02 0.0024 23.0 7.9 56 92-150 25-80 (83)
48 PRK10884 SH3 domain-containing 49.9 1.3E+02 0.0029 26.5 8.8 56 91-148 89-144 (206)
49 PF09969 DUF2203: Uncharacteri 49.3 75 0.0016 25.7 6.6 28 124-151 45-72 (120)
50 PF07295 DUF1451: Protein of u 48.8 1.6E+02 0.0035 24.7 8.7 112 90-207 6-127 (146)
51 PRK14162 heat shock protein Gr 48.1 1.1E+02 0.0024 27.0 7.9 96 127-238 37-138 (194)
52 COG4911 Uncharacterized conser 45.2 1.1E+02 0.0025 24.8 6.8 54 88-149 11-64 (123)
53 PRK14154 heat shock protein Gr 45.2 1.3E+02 0.0028 26.9 7.9 93 130-238 53-152 (208)
54 PRK10564 maltose regulon perip 44.8 25 0.00055 33.1 3.6 27 142-168 261-287 (303)
55 PRK14151 heat shock protein Gr 44.5 1.3E+02 0.0028 26.0 7.7 95 128-238 19-120 (176)
56 COG1592 Rubrerythrin [Energy p 44.4 68 0.0015 27.7 5.9 17 192-209 134-150 (166)
57 PRK11020 hypothetical protein; 44.0 1.7E+02 0.0037 23.9 7.7 44 130-173 6-49 (118)
58 TIGR02420 dksA RNA polymerase- 43.8 1.5E+02 0.0032 23.3 7.4 13 191-203 79-91 (110)
59 PF03357 Snf7: Snf7; InterPro 43.6 1.2E+02 0.0027 24.6 7.3 52 126-177 12-63 (171)
60 PRK06266 transcription initiat 43.3 11 0.00025 32.4 1.0 33 191-235 135-167 (178)
61 PF09237 GAGA: GAGA factor; I 43.1 7 0.00015 27.6 -0.3 20 191-210 23-42 (54)
62 PF03962 Mnd1: Mnd1 family; I 43.0 2.2E+02 0.0048 24.6 10.9 78 90-168 71-148 (188)
63 PF12329 TMF_DNA_bd: TATA elem 42.6 1.4E+02 0.003 22.1 6.7 46 128-178 4-49 (74)
64 PF10458 Val_tRNA-synt_C: Valy 41.5 1.2E+02 0.0027 21.6 6.1 59 91-149 7-66 (66)
65 cd00729 rubredoxin_SM Rubredox 41.4 10 0.00022 24.0 0.3 11 191-201 17-27 (34)
66 PRK14160 heat shock protein Gr 40.4 2.4E+02 0.0052 25.2 8.9 95 128-238 60-157 (211)
67 TIGR00373 conserved hypothetic 40.3 13 0.00028 31.4 0.9 21 191-211 127-147 (158)
68 COG5136 U1 snRNP-specific prot 40.0 12 0.00026 32.3 0.6 30 193-223 4-33 (188)
69 PRK14147 heat shock protein Gr 39.9 1.2E+02 0.0026 26.0 6.8 89 133-237 22-114 (172)
70 KOG4727 U1-like Zn-finger prot 39.3 14 0.0003 32.2 0.9 33 186-221 69-101 (193)
71 PLN00204 CP12 gene family prot 39.1 90 0.0019 25.8 5.5 44 133-176 56-100 (126)
72 PRK14163 heat shock protein Gr 39.0 2.1E+02 0.0045 25.7 8.3 92 129-238 40-132 (214)
73 PF07535 zf-DBF: DBF zinc fing 38.5 17 0.00037 25.2 1.0 30 190-225 3-32 (49)
74 TIGR00570 cdk7 CDK-activating 37.3 1.2E+02 0.0026 28.7 6.8 25 36-63 25-49 (309)
75 PF02388 FemAB: FemAB family; 36.5 1.7E+02 0.0037 28.2 8.0 21 127-147 247-267 (406)
76 PRK14146 heat shock protein Gr 36.4 1.8E+02 0.004 25.9 7.6 91 131-237 56-152 (215)
77 PF13894 zf-C2H2_4: C2H2-type 36.3 18 0.00038 19.5 0.7 19 194-215 2-20 (24)
78 PF14282 FlxA: FlxA-like prote 36.2 2E+02 0.0043 22.6 7.0 52 94-147 18-69 (106)
79 PF06156 DUF972: Protein of un 36.1 2.2E+02 0.0048 22.6 7.5 49 126-174 5-55 (107)
80 COG1579 Zn-ribbon protein, pos 35.8 3.4E+02 0.0074 24.7 10.0 25 90-114 54-78 (239)
81 PF08317 Spc7: Spc7 kinetochor 35.8 3.7E+02 0.008 25.1 9.9 60 85-147 140-202 (325)
82 PF03119 DNA_ligase_ZBD: NAD-d 35.6 12 0.00027 22.7 -0.0 13 195-207 2-14 (28)
83 PF01895 PhoU: PhoU domain; I 35.5 1.6E+02 0.0034 20.6 6.7 82 131-216 1-82 (88)
84 PF04420 CHD5: CHD5-like prote 34.7 1.9E+02 0.0041 24.4 7.1 54 125-178 36-89 (161)
85 TIGR02449 conserved hypothetic 34.5 1.8E+02 0.004 21.2 6.4 43 131-178 2-44 (65)
86 PRK01156 chromosome segregatio 33.7 3.4E+02 0.0074 28.7 10.3 16 192-207 452-467 (895)
87 PRK14141 heat shock protein Gr 33.2 2.2E+02 0.0048 25.4 7.5 85 134-234 36-131 (209)
88 PF05597 Phasin: Poly(hydroxya 33.1 2.3E+02 0.0049 23.5 7.1 23 128-150 108-130 (132)
89 PRK11115 transcriptional regul 33.0 3.2E+02 0.007 23.5 11.5 81 128-216 125-207 (236)
90 cd07973 Spt4 Transcription elo 32.7 17 0.00036 28.7 0.3 23 192-214 20-42 (98)
91 COG4499 Predicted membrane pro 32.7 1.8E+02 0.0038 28.7 7.2 75 93-169 335-409 (434)
92 PF10979 DUF2786: Protein of u 32.6 1.4E+02 0.003 19.9 4.7 35 134-170 3-37 (43)
93 PF01025 GrpE: GrpE; InterPro 32.4 54 0.0012 27.1 3.4 37 199-235 65-106 (165)
94 TIGR03185 DNA_S_dndD DNA sulfu 31.7 5.6E+02 0.012 26.2 11.2 24 126-149 206-229 (650)
95 cd00350 rubredoxin_like Rubred 30.7 19 0.00041 22.4 0.2 11 191-201 16-26 (33)
96 PF11587 Prion_bPrPp: Major pr 30.6 13 0.00029 23.0 -0.4 23 40-62 4-26 (29)
97 PF05191 ADK_lid: Adenylate ki 30.5 20 0.00043 23.1 0.3 16 188-203 17-32 (36)
98 PF04645 DUF603: Protein of un 30.4 96 0.0021 27.1 4.6 49 127-175 110-158 (181)
99 PRK14139 heat shock protein Gr 30.2 3.4E+02 0.0073 23.7 8.1 94 129-238 32-129 (185)
100 PF06008 Laminin_I: Laminin Do 30.1 2.5E+02 0.0053 25.2 7.5 84 83-167 48-135 (264)
101 KOG2801 Probable Rab-GAPs [Int 30.1 19 0.00041 34.3 0.2 21 196-219 402-422 (559)
102 PF08209 Sgf11: Sgf11 (transcr 29.8 22 0.00048 22.6 0.5 22 191-216 3-24 (33)
103 KOG4809 Rab6 GTPase-interactin 29.7 3.8E+02 0.0082 27.7 9.1 125 97-235 396-525 (654)
104 PRK14161 heat shock protein Gr 29.5 3.5E+02 0.0076 23.4 8.0 93 130-238 20-120 (178)
105 PLN02678 seryl-tRNA synthetase 29.5 1.7E+02 0.0036 29.0 6.7 19 158-176 74-92 (448)
106 PRK05431 seryl-tRNA synthetase 29.4 1.7E+02 0.0036 28.6 6.7 17 160-176 71-87 (425)
107 PRK00239 rpsT 30S ribosomal pr 29.3 1.8E+02 0.0039 22.4 5.5 36 133-168 23-58 (88)
108 PF05700 BCAS2: Breast carcino 29.3 3.1E+02 0.0067 24.2 7.9 80 89-175 137-216 (221)
109 PRK14155 heat shock protein Gr 29.1 2.6E+02 0.0056 24.9 7.3 91 132-238 16-115 (208)
110 smart00746 TRASH metallochaper 29.0 12 0.00025 21.5 -0.9 11 195-205 1-11 (39)
111 PF05741 zf-nanos: Nanos RNA b 28.8 20 0.00043 25.5 0.1 10 192-201 33-42 (55)
112 COG5152 Uncharacterized conser 28.2 23 0.0005 31.7 0.5 25 32-65 139-164 (259)
113 PF05529 Bap31: B-cell recepto 28.0 3.8E+02 0.0082 22.8 8.4 18 161-178 174-191 (192)
114 PF07106 TBPIP: Tat binding pr 27.9 3.6E+02 0.0077 22.5 11.1 65 84-153 76-140 (169)
115 PRK14156 heat shock protein Gr 27.7 3E+02 0.0065 23.9 7.3 91 134-240 32-125 (177)
116 PF01535 PPR: PPR repeat; Int 27.6 82 0.0018 17.6 2.7 22 145-166 7-28 (31)
117 PF06005 DUF904: Protein of un 27.4 2.6E+02 0.0056 20.7 7.2 18 131-148 6-23 (72)
118 KOG3032 Uncharacterized conser 27.3 46 0.00099 30.5 2.2 37 189-235 32-68 (264)
119 PRK12495 hypothetical protein; 26.8 73 0.0016 28.8 3.3 13 192-204 42-54 (226)
120 COG0783 Dps DNA-binding ferrit 26.8 4E+02 0.0086 22.6 8.1 84 87-171 54-151 (156)
121 PF09543 DUF2379: Protein of u 26.7 2.1E+02 0.0045 23.5 5.7 40 125-164 61-100 (121)
122 PF01396 zf-C4_Topoisom: Topoi 26.6 23 0.00049 23.0 0.1 13 193-205 2-14 (39)
123 COG4477 EzrA Negative regulato 26.4 4.9E+02 0.011 26.7 9.3 110 125-241 277-395 (570)
124 TIGR00414 serS seryl-tRNA synt 26.4 2.2E+02 0.0047 27.7 6.9 21 157-177 71-91 (418)
125 PF05852 DUF848: Gammaherpesvi 26.2 2.6E+02 0.0056 23.7 6.4 51 126-176 58-110 (146)
126 PF11945 WASH_WAHD: WAHD domai 26.0 2.1E+02 0.0045 26.9 6.4 48 87-150 24-71 (297)
127 smart00531 TFIIE Transcription 26.0 27 0.0006 28.9 0.5 19 193-211 124-142 (147)
128 PF12907 zf-met2: Zinc-binding 26.0 33 0.00071 22.8 0.8 26 193-218 2-27 (40)
129 PF00435 Spectrin: Spectrin re 25.9 2.4E+02 0.0053 19.9 7.8 51 127-178 46-96 (105)
130 PF04111 APG6: Autophagy prote 25.8 2.2E+02 0.0048 26.7 6.6 23 58-80 4-26 (314)
131 PF12998 ING: Inhibitor of gro 25.7 2.9E+02 0.0062 20.7 7.9 71 93-167 20-94 (105)
132 PRK06424 transcription factor; 25.6 26 0.00056 29.4 0.3 9 193-201 24-32 (144)
133 TIGR00029 S20 ribosomal protei 25.5 2.3E+02 0.005 21.8 5.5 36 133-168 23-58 (87)
134 PRK13130 H/ACA RNA-protein com 25.4 25 0.00055 25.0 0.2 11 191-201 4-14 (56)
135 PRK14153 heat shock protein Gr 25.3 2.8E+02 0.0061 24.4 6.7 99 131-245 35-142 (194)
136 PF14276 DUF4363: Domain of un 25.2 1.8E+02 0.0038 22.9 5.1 38 130-167 20-57 (121)
137 PF08317 Spc7: Spc7 kinetochor 25.1 2.9E+02 0.0062 25.8 7.2 9 66-74 159-167 (325)
138 smart00787 Spc7 Spc7 kinetocho 25.0 5.8E+02 0.013 24.0 9.8 20 85-105 135-154 (312)
139 PF03194 LUC7: LUC7 N_terminus 24.6 2.1E+02 0.0046 26.0 6.1 81 88-169 90-170 (254)
140 PRK11637 AmiB activator; Provi 24.6 6.4E+02 0.014 24.3 9.9 19 129-147 89-107 (428)
141 PRK14140 heat shock protein Gr 24.5 4.6E+02 0.01 23.0 7.9 95 128-238 36-136 (191)
142 PF13647 Glyco_hydro_80: Glyco 24.4 32 0.00069 30.8 0.7 51 193-246 147-205 (308)
143 PF06103 DUF948: Bacterial pro 24.3 1.2E+02 0.0026 22.6 3.8 20 130-149 41-60 (90)
144 PF08792 A2L_zn_ribbon: A2L zi 24.0 19 0.00042 22.7 -0.6 13 192-204 3-15 (33)
145 PF06751 EutB: Ethanolamine am 24.0 27 0.00059 34.4 0.1 30 191-220 311-346 (444)
146 PRK12496 hypothetical protein; 23.8 33 0.00071 29.2 0.6 13 193-205 144-156 (164)
147 PRK13169 DNA replication intia 23.8 3.9E+02 0.0084 21.5 7.5 47 125-176 4-50 (110)
148 PF08898 DUF1843: Domain of un 23.7 1.9E+02 0.0041 20.5 4.3 33 138-176 19-52 (53)
149 PF07721 TPR_4: Tetratricopept 23.6 1.1E+02 0.0023 17.5 2.6 21 142-162 5-25 (26)
150 KOG4302 Microtubule-associated 23.5 8.8E+02 0.019 25.5 12.3 94 127-226 66-176 (660)
151 PF01649 Ribosomal_S20p: Ribos 23.3 2.4E+02 0.0052 21.4 5.2 35 133-167 22-56 (84)
152 PF04156 IncA: IncA protein; 23.1 4.5E+02 0.0098 22.0 9.3 64 86-149 86-150 (191)
153 PF02132 RecR: RecR protein; 23.1 92 0.002 20.3 2.5 12 190-201 15-26 (41)
154 KOG4602 Nanos and related prot 22.9 30 0.00065 32.1 0.2 9 193-201 269-277 (318)
155 COG5188 PRP9 Splicing factor 3 22.7 35 0.00076 33.1 0.6 31 192-225 238-268 (470)
156 KOG0250 DNA repair protein RAD 22.6 7.1E+02 0.015 27.7 10.2 28 219-246 529-558 (1074)
157 KOG0972 Huntingtin interacting 22.6 6.9E+02 0.015 23.9 9.3 12 224-235 338-349 (384)
158 PF05010 TACC: Transforming ac 22.5 5.5E+02 0.012 22.8 12.2 76 126-241 41-117 (207)
159 KOG0978 E3 ubiquitin ligase in 22.2 2.4E+02 0.0052 29.7 6.5 20 188-207 674-693 (698)
160 PRK04778 septation ring format 22.1 8.2E+02 0.018 24.7 10.5 78 86-167 103-206 (569)
161 COG3809 Uncharacterized protei 22.0 31 0.00067 26.5 0.1 13 192-204 1-13 (88)
162 KOG3032 Uncharacterized conser 22.0 3.3E+02 0.0071 25.1 6.6 30 149-178 198-227 (264)
163 PRK10778 dksA RNA polymerase-b 21.9 4.2E+02 0.0091 22.3 6.9 15 190-204 109-123 (151)
164 PF06246 Isy1: Isy1-like splic 21.8 2.6E+02 0.0057 25.7 6.1 45 86-144 42-86 (255)
165 PF14828 Amnionless: Amnionles 21.4 28 0.00061 34.3 -0.3 15 193-207 227-241 (437)
166 TIGR01206 lysW lysine biosynth 21.4 36 0.00079 23.9 0.3 14 193-206 3-16 (54)
167 PLN03229 acetyl-coenzyme A car 21.2 4.7E+02 0.01 27.9 8.4 50 123-172 559-614 (762)
168 PF10168 Nup88: Nuclear pore c 21.2 6E+02 0.013 26.8 9.3 22 220-241 681-702 (717)
169 PF13174 TPR_6: Tetratricopept 21.1 1.6E+02 0.0034 16.6 3.2 24 141-164 3-26 (33)
170 PLN02748 tRNA dimethylallyltra 21.1 46 0.001 33.2 1.1 29 191-221 417-445 (468)
171 CHL00112 rpl28 ribosomal prote 21.0 35 0.00075 24.8 0.2 14 193-206 3-16 (63)
172 PF07967 zf-C3HC: C3HC zinc fi 21.0 34 0.00074 27.7 0.1 17 189-205 40-56 (133)
173 PRK15067 ethanolamine ammonia 20.9 36 0.00079 33.7 0.3 10 211-220 347-356 (461)
174 smart00734 ZnF_Rad18 Rad18-lik 20.8 57 0.0012 19.4 1.1 20 193-216 2-21 (26)
175 PF13041 PPR_2: PPR repeat fam 20.5 1.4E+02 0.003 19.3 3.1 22 145-166 10-31 (50)
176 TIGR02284 conserved hypothetic 20.5 52 0.0011 27.0 1.1 17 215-231 66-82 (139)
177 PF11781 RRN7: RNA polymerase 20.4 26 0.00056 22.6 -0.6 20 193-212 9-28 (36)
178 COG5188 PRP9 Splicing factor 3 20.3 46 0.001 32.3 0.9 27 193-221 375-401 (470)
179 cd00730 rubredoxin Rubredoxin; 20.2 38 0.00082 23.4 0.2 11 193-203 35-45 (50)
No 1
>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=8.3e-88 Score=606.81 Aligned_cols=231 Identities=44% Similarity=0.806 Sum_probs=208.1
Q ss_pred CHHHHHHHHHhcCCCCCCChhhhhhhcccCCCCCCCcchhhcCCChhHhhhhcccCCCCCCccccHHHHHHhhcCCCCCC
Q 025496 1 MDAQRALLDELMGAARNLTEEEKKEYKEIKWDDKEVCPFYMVRFCPHDLFVNTRSDLGPCPRIHDQKLKESFEKSPRHDA 80 (252)
Q Consensus 1 md~~RalLDeLMG~~Rn~~~~~~~~~~~~~f~D~~VCk~yL~G~CPhdLF~nTK~DlG~C~kiHde~lk~~Ye~~~~~~~ 80 (252)
||+||+|||||||++||+++.++ .++|+||+|||||||||||||||+|||+||||||||||++||++|++++++++
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 MDEMRAMLDELMGSNRNGDPSKR----KVHFTDPDVCKYFLVGFCPHDLFVNTKSDLGPCPKIHDEALKAEYEKASKKEK 76 (254)
T ss_pred CHHHHHHHHHHcCCccCCCcccc----CCCCCCcccCHHHHhCCCcHHHHhhcccccchhhhhcCHHHHHHHHhCccccc
Confidence 89999999999999999876543 27999999999999999999999999999999999999999999999999888
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHH
Q 025496 81 YVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEAL 160 (252)
Q Consensus 81 ~~~gYE~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~ 160 (252)
+. |||++|+++|+++|++|||||++|++||+.++++.. ........++|.+|+++|+.++++||+||++|+||+|+++
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-GYEREFLRYLQRLIRDCDRRIERAKERLEQTQEEQA-KEADEEKAEKIDELDEKIGELLKEAEELGEEGDVDEAQKL 154 (254)
T ss_pred cc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccccc-cchhhhHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
Confidence 84 599999999999999999999999999998765432 2233335899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHh---hhhh-hhhhhhhhhccccccccchhhhcccChhhHhhhhhcchhhhcHHHHHHHHHHHHhh
Q 025496 161 MRKVEILNVEKTTLTQ---QSQN-DKVLMMAQEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKVC 236 (252)
Q Consensus 161 ~~~~e~Lk~ek~~l~~---~~~~-~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL~~~ 236 (252)
|.+||.|+.+++++++ ++.. ..++.++++|+|+||+|||||||++|||+||+|||+||||+||++||+++++|++.
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 9999999999999998 3311 12233468999999999999999999999999999999999999999999999985
Q ss_pred c
Q 025496 237 Q 237 (252)
Q Consensus 237 ~ 237 (252)
.
T Consensus 235 ~ 235 (254)
T PF03194_consen 235 R 235 (254)
T ss_pred H
Confidence 4
No 2
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=100.00 E-value=8.4e-82 Score=574.91 Aligned_cols=228 Identities=43% Similarity=0.784 Sum_probs=203.9
Q ss_pred CHH-HHHHHHHhcCCCCCCChhhhhhhcccCCCCCCCcchhhcCCChhHhhhhcccCCCCCCccccHHHHHHhhcCCCCC
Q 025496 1 MDA-QRALLDELMGAARNLTEEEKKEYKEIKWDDKEVCPFYMVRFCPHDLFVNTRSDLGPCPRIHDQKLKESFEKSPRHD 79 (252)
Q Consensus 1 md~-~RalLDeLMG~~Rn~~~~~~~~~~~~~f~D~~VCk~yL~G~CPhdLF~nTK~DlG~C~kiHde~lk~~Ye~~~~~~ 79 (252)
|++ ||+|||||||++||+.... ..++|+||+||+||||||||||||+|||+|+|+||+|||++||++|+.+++..
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 655 9999999999999975432 23799999999999999999999999999999999999999999999999999
Q ss_pred CChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHH
Q 025496 80 AYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEA 159 (252)
Q Consensus 80 ~~~~gYE~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~ 159 (252)
++ |||++|+++|+++|.+|+++|+++++||+++.++. ......++++|..|+++|+.++++||+||++|+|++||+
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--GYEWDALEILERFVADVDRRIEKAKERLAETVEER--SEEAARKAEKVHELEEKIGKLLEKAEELGEEGNVEEAQK 152 (319)
T ss_pred hh--hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh--hhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHH
Confidence 99 99999999999999999999999999999874322 223334578999999999999999999999999999999
Q ss_pred HHHHHHHHHH-HHHHHHhhhhhhhh-hhhhhhccccccccchhhhcccChhhHhhhhhcchhhhcHHHHHHHHHHHHhhc
Q 025496 160 LMRKVEILNV-EKTTLTQQSQNDKV-LMMAQEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKVCQ 237 (252)
Q Consensus 160 ~~~~~e~Lk~-ek~~l~~~~~~~~~-~~~~~~qkl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL~~~~ 237 (252)
+|.+||.|++ +++..+.++ ...+ .+++++|||+||+||||||+++|||+||||||+||+|+||++||++|.+|++..
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 666666666 3333 345689999999999999999999999999999999999999999999998843
No 3
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=100.00 E-value=1.6e-67 Score=456.65 Aligned_cols=235 Identities=28% Similarity=0.494 Sum_probs=205.5
Q ss_pred HHHHHHHHHhcCCCCCCChhhhhhhcccCCCCCCCcchhhcCCChhHhhhhcccCCCCCCccccHHHHHHhhcCCCCCCC
Q 025496 2 DAQRALLDELMGAARNLTEEEKKEYKEIKWDDKEVCPFYMVRFCPHDLFVNTRSDLGPCPRIHDQKLKESFEKSPRHDAY 81 (252)
Q Consensus 2 d~~RalLDeLMG~~Rn~~~~~~~~~~~~~f~D~~VCk~yL~G~CPhdLF~nTK~DlG~C~kiHde~lk~~Ye~~~~~~~~ 81 (252)
+++|++|+||||++|..-. ..+.+||+||+||+||||||||||||+|||+|||+||++|.+.+|++|+.+...+++
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 AEQRKVLEQLMGPERSTFD----PCRPTHFTDKKVCISMLVGFCPFDLFRNTKRSLGKCPTSHEEKYKAEYERNGRERAE 78 (258)
T ss_pred hHHHHHHHHHhCCCcccCC----CCCCccccchHHHHHHHHccCcHHHHhccccccCCCcchhHHHHHHHHhhhhhccch
Confidence 7899999999999996322 223579999999999999999999999999999999999999999999999988899
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCC-------H
Q 025496 82 VPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGK-------V 154 (252)
Q Consensus 82 ~~gYE~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~-------V 154 (252)
+|||||++.|.++|.+|+.+|+.|-.++..+. +...+|+++++.|+-+-..++.+|.+|+ |
T Consensus 79 --~yEweyl~~L~r~V~~cn~~I~~a~~~~~~t~----------ee~~kI~e~~e~~~~~d~sIg~lg~e~dalakrk~V 146 (258)
T COG5200 79 --EYEWEYLRLLVRIVLSCNDGIRAAGLEDRTTP----------EEFGKIKEKEELFNRVDESIGELGMEGDALAKRKLV 146 (258)
T ss_pred --hhhHHHHHHHHHHHHHhcchhhhhhhhccCCH----------HHHHhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 99999999999999999999999987775432 3334555555555555555566666665 9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhh-hhhhhhhhhhccccccccchhhhcccChhhHhhhhhcchhhhcHHHHHHHHHHH
Q 025496 155 DEAEALMRKVEILNVEKTTLTQQSQ-NDKVLMMAQEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEY 233 (252)
Q Consensus 155 deA~~~~~~~e~Lk~ek~~l~~~~~-~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL 233 (252)
+.|+..+.+++.|+.+++++...+- .++|++++.+|||+||+|||||||+.|||+||||||.||+|+||+.+|+.|..|
T Consensus 147 ~~a~~~f~el~rl~~~rkei~~~v~sm~en~gq~thqklqvC~iCgayLsrlDtdrrladHf~GklHlGy~~~R~dl~~l 226 (258)
T COG5200 147 ERACSAFNELERLREERKEIKEAVYSMVENNGQGTHQKLQVCGICGAYLSRLDTDRRLADHFNGKLHLGYLLVRSDLADL 226 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcchhhhhhhhhhhhhhhHHHhcchhhHHHHHhccchhhhHHHHHHHHHHH
Confidence 9999999999999999999998871 256788889999999999999999999999999999999999999999999998
Q ss_pred Hh-------hccchhhhhhhhhhccC
Q 025496 234 KV-------CQLFIVDLLFQNLCIHF 252 (252)
Q Consensus 234 ~~-------~~~~~~~~~~~~~~~~~ 252 (252)
.+ +.+|.++|.|++|++|.
T Consensus 227 lk~~~~sr~~~~~k~~~sl~~~~~~~ 252 (258)
T COG5200 227 LKKFGISRVAEIFKEGFSLKCLRVHP 252 (258)
T ss_pred HHHhccchhhhcccccccchhhccCC
Confidence 76 46999999999999983
No 4
>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=89.17 E-value=0.2 Score=29.81 Aligned_cols=25 Identities=20% Similarity=0.700 Sum_probs=20.7
Q ss_pred cccccchhhhcccChhhHhhhhhcchhh
Q 025496 193 ALCEICGSFLVANDAAERTQSHISGKQH 220 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H 220 (252)
..|++|+...+ ++.-+..|+.||.|
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 57999996644 66779999999998
No 5
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=87.97 E-value=0.22 Score=28.68 Aligned_cols=24 Identities=25% Similarity=0.699 Sum_probs=19.5
Q ss_pred ccccchhhhcccChhhHhhhhhcchhh
Q 025496 194 LCEICGSFLVANDAAERTQSHISGKQH 220 (252)
Q Consensus 194 VCdVCGA~Ls~~D~d~Rl~dH~~GK~H 220 (252)
.|+||+...+ +..=+..|+.||.|
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 6999987644 56679999999988
No 6
>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=87.60 E-value=0.33 Score=30.05 Aligned_cols=29 Identities=21% Similarity=0.481 Sum_probs=21.7
Q ss_pred cccccchhhhcccChhhHhhhhhcchhhhcHH
Q 025496 193 ALCEICGSFLVANDAAERTQSHISGKQHIGYG 224 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~ 224 (252)
.-|++|+..+. +..-+..|+.||.|..-+
T Consensus 4 ~~C~~C~~~~~---~~~~~~~H~~gk~H~~~~ 32 (35)
T smart00451 4 FYCKLCNVTFT---DEISVEAHLKGKKHKKNV 32 (35)
T ss_pred eEccccCCccC---CHHHHHHHHChHHHHHHH
Confidence 45999998755 334459999999996543
No 7
>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=87.36 E-value=7.3 Score=34.05 Aligned_cols=82 Identities=22% Similarity=0.297 Sum_probs=65.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHH
Q 025496 91 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (252)
Q Consensus 91 ~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~e 170 (252)
..|..+|+|++.-|.+++.-++... ........++.++...|...-.+|+..-..|+=|-|...+.....+..+
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 6899999999999999998886432 1334567899999999999999999999999998887777766666666
Q ss_pred HHHHHhhh
Q 025496 171 KTTLTQQS 178 (252)
Q Consensus 171 k~~l~~~~ 178 (252)
...++..+
T Consensus 100 ~~~l~~~~ 107 (221)
T PF04012_consen 100 AERLEQQL 107 (221)
T ss_pred HHHHHHHH
Confidence 65555444
No 8
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=83.41 E-value=5.2 Score=36.41 Aligned_cols=21 Identities=29% Similarity=0.526 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhh
Q 025496 92 FCEKLVMDLDRRVRRGRERLS 112 (252)
Q Consensus 92 ~L~~~i~d~drkI~~~k~RL~ 112 (252)
-++.=|.++..||.++...+.
T Consensus 63 ~~e~ei~~~r~r~~~~e~kl~ 83 (239)
T COG1579 63 QLESEIQEIRERIKRAEEKLS 83 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 456667777777777777663
No 9
>PHA02562 46 endonuclease subunit; Provisional
Probab=82.61 E-value=12 Score=36.88 Aligned_cols=15 Identities=20% Similarity=0.503 Sum_probs=11.5
Q ss_pred cccccccchhhhccc
Q 025496 191 KMALCEICGSFLVAN 205 (252)
Q Consensus 191 kl~VCdVCGA~Ls~~ 205 (252)
.-.+|+.||.-+...
T Consensus 283 ~~~~Cp~C~~~~~~~ 297 (562)
T PHA02562 283 KGGVCPTCTQQISEG 297 (562)
T ss_pred CCCCCCCCCCcCCCc
Confidence 346999999887654
No 10
>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=81.83 E-value=2.9 Score=44.37 Aligned_cols=31 Identities=26% Similarity=0.619 Sum_probs=28.1
Q ss_pred HHHHHHHHHHhhhcCCHHHHHHHHHHHHHHH
Q 025496 138 IKNLLEQVETLGEAGKVDEAEALMRKVEILN 168 (252)
Q Consensus 138 I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk 168 (252)
++.+|..+|+|.++|..++|+.++.+++.+-
T Consensus 570 Lq~Mmd~ieela~~G~~~~A~qlL~qlq~mm 600 (851)
T TIGR02302 570 LQNMMDQIENLARSGDRDQAKQLLSQLQQMM 600 (851)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 7889999999999999999999999887754
No 11
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=80.26 E-value=43 Score=35.68 Aligned_cols=24 Identities=17% Similarity=0.303 Sum_probs=17.5
Q ss_pred ccccccchhhhcccChhhHhhhhhc
Q 025496 192 MALCEICGSFLVANDAAERTQSHIS 216 (252)
Q Consensus 192 l~VCdVCGA~Ls~~D~d~Rl~dH~~ 216 (252)
...|||||.-+--. .+..+.+|+.
T Consensus 457 ~~~CPvCg~~l~~~-~~~~~~~~~~ 480 (908)
T COG0419 457 GEKCPVCGQELPEE-HEKELLELYE 480 (908)
T ss_pred CCCCCCCCCCCCcH-HHHHHHHHHH
Confidence 47899999665433 3677888888
No 12
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=79.18 E-value=4.7 Score=42.72 Aligned_cols=34 Identities=21% Similarity=0.624 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHH
Q 025496 135 EEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 168 (252)
Q Consensus 135 ~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk 168 (252)
...++.+|.++|+|.++|+.++|+.++.+++.+-
T Consensus 537 ~~dL~~mmd~ie~la~~G~~~~A~q~L~qlq~mm 570 (820)
T PF13779_consen 537 QQDLQRMMDRIEELARSGRMDEARQLLEQLQQMM 570 (820)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 3457789999999999999999999998877654
No 13
>PRK15058 cytochrome b562; Provisional
Probab=78.79 E-value=20 Score=29.62 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHH---HHHHHhhhcCCHHHHHHHHHHHHHHHHH
Q 025496 129 EQLSVLEEKIKNLL---EQVETLGEAGKVDEAEALMRKVEILNVE 170 (252)
Q Consensus 129 ~~i~~l~~~I~~ll---~~aE~LGeeG~VdeA~~~~~~~e~Lk~e 170 (252)
.++..+.+-++.++ ..++.|.++|++++|.....++..++.+
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 34555555555544 4566799999999999988888887643
No 14
>PRK06835 DNA replication protein DnaC; Validated
Probab=77.35 E-value=20 Score=33.84 Aligned_cols=67 Identities=15% Similarity=0.172 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCC---HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchh
Q 025496 130 QLSVLEEKIKNLLEQVETLGEAGK---VDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGS 200 (252)
Q Consensus 130 ~i~~l~~~I~~ll~~aE~LGeeG~---VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA 200 (252)
+|.+|+.+|..+-.++-...-.|+ -+....+-+++..|+.++.+|.... +-. ...-..-..|+.|+=
T Consensus 37 ~~~~id~~i~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~~lL~~~-g~~---~dyl~~~y~Cp~C~d 106 (329)
T PRK06835 37 EIAEIDDEIAKLGIKLSRAILKNPDKKEETLKELKEKITDLRVKKAELLVSN-GYP---PDYLEMKYTCPKCKD 106 (329)
T ss_pred cHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHHHHc-CCC---hhhcCCCCCCCCCCC
Confidence 444555555544333333222344 4444566778888888888887654 211 111122357998874
No 15
>PRK02224 chromosome segregation protein; Provisional
Probab=77.04 E-value=30 Score=36.27 Aligned_cols=12 Identities=25% Similarity=0.567 Sum_probs=9.6
Q ss_pred ccccccchhhhc
Q 025496 192 MALCEICGSFLV 203 (252)
Q Consensus 192 l~VCdVCGA~Ls 203 (252)
-.+|++||..+.
T Consensus 451 ~~~Cp~C~r~~~ 462 (880)
T PRK02224 451 AGKCPECGQPVE 462 (880)
T ss_pred cccCCCCCCcCC
Confidence 478999998654
No 16
>PRK09720 cybC cytochrome b562; Provisional
Probab=76.22 E-value=12 Score=29.83 Aligned_cols=40 Identities=23% Similarity=0.312 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHH---HHHhhhcCCHHHHHHHHHHHHHHH
Q 025496 129 EQLSVLEEKIKNLLEQ---VETLGEAGKVDEAEALMRKVEILN 168 (252)
Q Consensus 129 ~~i~~l~~~I~~ll~~---aE~LGeeG~VdeA~~~~~~~e~Lk 168 (252)
.++..+..-++.++.+ +..|.++|+++||.....++-.++
T Consensus 50 ~e~K~y~~Gld~lI~qID~A~~La~~GkL~eAK~~a~~l~~~R 92 (100)
T PRK09720 50 PEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTR 92 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 4555666555555544 566999999999997766665554
No 17
>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=74.80 E-value=2.3 Score=27.78 Aligned_cols=32 Identities=22% Similarity=0.441 Sum_probs=17.5
Q ss_pred cccccchhhhcccChhhHhhhhhcchhhhcHHH
Q 025496 193 ALCEICGSFLVANDAAERTQSHISGKQHIGYGM 225 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~k 225 (252)
.-||.|..+|. +|+..=...|..|..|..=++
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 556555588999999986544
No 18
>smart00356 ZnF_C3H1 zinc finger.
Probab=73.18 E-value=1.7 Score=25.18 Aligned_cols=23 Identities=30% Similarity=0.834 Sum_probs=17.2
Q ss_pred CCCcchhhcCCChhHhhhhcccCCCCCCcccc
Q 025496 34 KEVCPFYMVRFCPHDLFVNTRSDLGPCPRIHD 65 (252)
Q Consensus 34 ~~VCk~yL~G~CPhdLF~nTK~DlG~C~kiHd 65 (252)
+.+|++|+.|.||+. ..|+-.|+
T Consensus 4 ~~~C~~~~~g~C~~g---------~~C~~~H~ 26 (27)
T smart00356 4 TELCKFFKRGYCPYG---------DRCKFAHP 26 (27)
T ss_pred CCcCcCccCCCCCCC---------CCcCCCCc
Confidence 458999999999862 25777775
No 19
>PRK14143 heat shock protein GrpE; Provisional
Probab=72.92 E-value=28 Score=31.67 Aligned_cols=96 Identities=15% Similarity=0.241 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccC
Q 025496 127 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVAND 206 (252)
Q Consensus 127 ~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D 206 (252)
...++..+..+|..+-+++++|- +.-+.+.++.+.+++-..+-... ..+.-++.+.-.+|-+.|
T Consensus 65 ~~~~~~~l~~el~~l~~e~~elk-----d~~lR~~AdfeN~RKR~~kE~e~-----------~~~~a~~~~~~~lLpV~D 128 (238)
T PRK14143 65 NAARLAQLEQELESLKQELEELN-----SQYMRIAADFDNFRKRTSREQED-----------LRLQLKCNTLSEILPVVD 128 (238)
T ss_pred chhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHh
Confidence 45678888999988888888875 66677777777776333221111 123356778889999999
Q ss_pred hhhHhhhhhcc------hhhhcHHHHHHHHHH-HHhhcc
Q 025496 207 AAERTQSHISG------KQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 207 ~d~Rl~dH~~G------K~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
|=.|.-.|+.. .++-||.-|.+.+.. |...|+
T Consensus 129 nLerAl~~~~~~~~~~~~l~~Gve~i~k~l~~~L~k~GV 167 (238)
T PRK14143 129 NFERARQQLKPEGEEAQALHRSYQGLYKQLVDVLKRLGV 167 (238)
T ss_pred HHHHHHhcccccchhHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 99997777642 478899888666554 444443
No 20
>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=72.63 E-value=1.5 Score=26.22 Aligned_cols=24 Identities=29% Similarity=0.787 Sum_probs=15.2
Q ss_pred CCCCcchhhc-CCChhHhhhhcccCCCCCCcccc
Q 025496 33 DKEVCPFYMV-RFCPHDLFVNTRSDLGPCPRIHD 65 (252)
Q Consensus 33 D~~VCk~yL~-G~CPhdLF~nTK~DlG~C~kiHd 65 (252)
...+|++|+. |.||+. ..|+-.|+
T Consensus 2 k~~~C~~f~~~g~C~~G---------~~C~f~H~ 26 (27)
T PF00642_consen 2 KTKLCRFFMRTGTCPFG---------DKCRFAHG 26 (27)
T ss_dssp TSSB-HHHHHTS--TTG---------GGSSSBSS
T ss_pred ccccChhhccCCccCCC---------CCcCccCC
Confidence 3568999999 999875 35666665
No 21
>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=71.80 E-value=51 Score=29.05 Aligned_cols=66 Identities=17% Similarity=0.237 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHH
Q 025496 91 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMR 162 (252)
Q Consensus 91 ~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~ 162 (252)
..|..+|++++.-|..++.-|+... ........++..+...|...-.+|+.+-..|+=+-|-..+.
T Consensus 27 ~~l~q~irem~~~l~~ar~~lA~~~------a~~k~~e~~~~~~~~~~~~~~~~A~~Al~~G~EdLAr~Al~ 92 (219)
T TIGR02977 27 KMIRLIIQEMEDTLVEVRTTSARTI------ADKKELERRVSRLEAQVADWQEKAELALSKGREDLARAALI 92 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence 4688899999998888887776432 12334567899999999999999999999998887766543
No 22
>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=70.20 E-value=10 Score=29.81 Aligned_cols=42 Identities=36% Similarity=0.597 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHH---HHHHHhhhcCCHHHHHHHHHHHHHHHHH
Q 025496 129 EQLSVLEEKIKNLL---EQVETLGEAGKVDEAEALMRKVEILNVE 170 (252)
Q Consensus 129 ~~i~~l~~~I~~ll---~~aE~LGeeG~VdeA~~~~~~~e~Lk~e 170 (252)
.++..+.+-++.++ ..++.+.+.|++++|...+.++..|+.+
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 34555555555544 4567789999999999999999998754
No 23
>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=69.16 E-value=8.4 Score=26.50 Aligned_cols=11 Identities=36% Similarity=0.833 Sum_probs=5.8
Q ss_pred ccccchhhhcc
Q 025496 194 LCEICGSFLVA 204 (252)
Q Consensus 194 VCdVCGA~Ls~ 204 (252)
+|+|||.-|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 99999988653
No 24
>PRK14144 heat shock protein GrpE; Provisional
Probab=67.93 E-value=36 Score=30.16 Aligned_cols=95 Identities=11% Similarity=0.148 Sum_probs=62.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccCh
Q 025496 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 207 (252)
Q Consensus 128 ~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~ 207 (252)
..++..+.++|..+-+++++|- +..+.+.++.+.++.--+.-.... .+.-+=.++-++|-+.||
T Consensus 44 ~~~~~~l~~~i~~le~e~~elk-----dk~lR~~AefeN~RKR~~kE~e~~-----------~~~a~~~~~~~LLpV~Dn 107 (199)
T PRK14144 44 HPSYTALEEQLTLAEQKAHENW-----EKSVRALAELENVRRRMEREVANA-----------HKYGVEKLISALLPVVDS 107 (199)
T ss_pred chhHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHhhHHhH
Confidence 3566778888888888888874 777888888887753221111111 111223467889999999
Q ss_pred hhHhhhhhc----chhhhcHHHHHHHHHH-HHhhcc
Q 025496 208 AERTQSHIS----GKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 208 d~Rl~dH~~----GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
=.|.-+|.. +.++-|+..|++.+.. |...++
T Consensus 108 LerAl~~~~~~~~~~i~~Gv~mi~k~l~~~L~k~GV 143 (199)
T PRK14144 108 LEQALQLADKNSDPSMHEGLELTMKLFLDALQKFDV 143 (199)
T ss_pred HHHHHHcccccchhHHHHHHHHHHHHHHHHHHHCCC
Confidence 999766643 4588899999766655 455443
No 25
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=67.83 E-value=4.9 Score=34.58 Aligned_cols=33 Identities=21% Similarity=0.520 Sum_probs=28.1
Q ss_pred cccccchhhhcccChhhHhhhhhcchhhhcHHHH
Q 025496 193 ALCEICGSFLVANDAAERTQSHISGKQHIGYGMV 226 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~kI 226 (252)
.-||-|-.||. +|+.+=.-.|.+|+.|+--++.
T Consensus 4 YyCDYCdt~Lt-hDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 4 YYCDYCDTYLT-HDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred chhhhhhhhhh-cccHHHHHhhhhhHHHHHHHHH
Confidence 45999999986 8999989999999999875444
No 26
>PRK01156 chromosome segregation protein; Provisional
Probab=65.91 E-value=41 Score=35.51 Aligned_cols=14 Identities=7% Similarity=-0.054 Sum_probs=9.0
Q ss_pred cccccchhhhcccC
Q 025496 193 ALCEICGSFLVAND 206 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D 206 (252)
.+|+|||.-++-.+
T Consensus 450 ~~~~~Cp~c~~~~~ 463 (895)
T PRK01156 450 NGQSVCPVCGTTLG 463 (895)
T ss_pred ccCCCCCCCCCcCC
Confidence 36777777666555
No 27
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=64.09 E-value=4 Score=24.08 Aligned_cols=20 Identities=30% Similarity=0.684 Sum_probs=15.8
Q ss_pred ccccccchhhhcccChhhHhhhhh
Q 025496 192 MALCEICGSFLVANDAAERTQSHI 215 (252)
Q Consensus 192 l~VCdVCGA~Ls~~D~d~Rl~dH~ 215 (252)
|..|++||- .-+..|+..|.
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 678999994 34778888885
No 28
>PRK14158 heat shock protein GrpE; Provisional
Probab=62.24 E-value=72 Score=28.10 Aligned_cols=99 Identities=15% Similarity=0.078 Sum_probs=65.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhc
Q 025496 124 SAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLV 203 (252)
Q Consensus 124 ~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls 203 (252)
.....+.+..++++|..+-.++++|- +.-+.+.++.+.++.-.+.-... ..+.-+-.+.-.+|.
T Consensus 35 ~~~~~~~~~~le~~l~~le~e~~el~-----d~~lR~~AefeN~RkR~~kE~e~-----------~~~~a~~~~~~~lLp 98 (194)
T PRK14158 35 PVAAADRIKELEEALAAKEAEAAANW-----DKYLRERADLENYRKRVQKEKEE-----------LLKYGNESLILEILP 98 (194)
T ss_pred CCCchhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHh
Confidence 34455678899999999888888884 55667777777765322211111 122344567788999
Q ss_pred ccChhhHhhhhhc----chhhhcHHHHHHHHHH-HHhhcc
Q 025496 204 ANDAAERTQSHIS----GKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 204 ~~D~d~Rl~dH~~----GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
+.||=.|.-.|.. ..++-|+..|.+.+.. |...|+
T Consensus 99 V~DnLerAl~~~~~~~~~~i~~Gv~mi~k~l~~vLek~Gv 138 (194)
T PRK14158 99 AVDNMERALDHADEESMSAIIEGIRMTLSMLLSTLKKFGV 138 (194)
T ss_pred HHhHHHHHHhccCcchHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 9999999666753 3478898888777554 555554
No 29
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=60.30 E-value=1.1e+02 Score=27.39 Aligned_cols=82 Identities=18% Similarity=0.270 Sum_probs=61.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHH
Q 025496 91 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (252)
Q Consensus 91 ~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~e 170 (252)
..|++.|+|++.-...++.-+++.. ........++..+...+.++-.+++.+-..|+=+-|-..+.+...|...
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 6888999999999888887776432 1334566789999999999999999999999877776666666666555
Q ss_pred HHHHHhhh
Q 025496 171 KTTLTQQS 178 (252)
Q Consensus 171 k~~l~~~~ 178 (252)
.+.+...+
T Consensus 101 ~~~~~~~~ 108 (225)
T COG1842 101 AKALEAEL 108 (225)
T ss_pred HHHHHHHH
Confidence 55554433
No 30
>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=59.95 E-value=31 Score=21.90 Aligned_cols=35 Identities=26% Similarity=0.332 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHH
Q 025496 136 EKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (252)
Q Consensus 136 ~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~e 170 (252)
+.|..+-.+.+.+.+..+.++|..+-.++..|+.+
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 46777888889999999999999988888887653
No 31
>PRK14148 heat shock protein GrpE; Provisional
Probab=59.41 E-value=69 Score=28.26 Aligned_cols=93 Identities=18% Similarity=0.233 Sum_probs=61.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChh
Q 025496 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAA 208 (252)
Q Consensus 129 ~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d 208 (252)
.++..++.+|..+-+++++|- +.-+.+.++.+.++.-.++-.. ...+.-+..+.-.+|-+.|+=
T Consensus 40 ~e~~~l~~~l~~l~~e~~elk-----d~~lR~~Ae~eN~rKR~~rE~e-----------~~~~~a~~~~~~~LLpV~Dnl 103 (195)
T PRK14148 40 EQLERAKDTIKELEDSCDQFK-----DEALRAKAEMENIRKRAERDVS-----------NARKFGIEKFAKELLPVIDSI 103 (195)
T ss_pred hHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhHHhHH
Confidence 567788888888888888874 5666777777776532221111 112334566788899999999
Q ss_pred hHhhhhhcc-----hhhhcHHHHHHHHHH-HHhhc
Q 025496 209 ERTQSHISG-----KQHIGYGMVRDFITE-YKVCQ 237 (252)
Q Consensus 209 ~Rl~dH~~G-----K~H~Gy~kIR~~l~e-L~~~~ 237 (252)
.|.-.|... .++-|+..|.+.+.. |...|
T Consensus 104 erAl~~~~~~~~~~~l~~Gv~mi~k~l~~vL~k~G 138 (195)
T PRK14148 104 EQALKHEVKLEEAIAMKEGIELTAKMLVDILKKNG 138 (195)
T ss_pred HHHHhccccchhHHHHHHHHHHHHHHHHHHHHHCC
Confidence 997666543 477898888766655 44444
No 32
>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=59.09 E-value=31 Score=26.69 Aligned_cols=49 Identities=29% Similarity=0.397 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (252)
Q Consensus 128 ~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~ 178 (252)
..++..+..+-+.+-+++-.+...| +++..+..++..++.+...++.+.
T Consensus 42 ~~~~e~lr~~rN~~sk~I~~~~~~~--~~~~~l~~e~~~lk~~i~~le~~~ 90 (108)
T PF02403_consen 42 QQELEELRAERNELSKEIGKLKKAG--EDAEELKAEVKELKEEIKELEEQL 90 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCHTT--CCTHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhHHHHHHHHHhhCc--ccHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566666666666666666666 566677777888888777777665
No 33
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=57.61 E-value=31 Score=30.00 Aligned_cols=36 Identities=19% Similarity=0.201 Sum_probs=29.1
Q ss_pred ccccccccchhhhcccChhhHhhhhhcchhhhcHHHHHHHHHHHHhhc
Q 025496 190 KKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKVCQ 237 (252)
Q Consensus 190 qkl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL~~~~ 237 (252)
...++|+.||+.|--.|+.. .+..+.+.+++|.+..
T Consensus 130 ~~~F~Cp~Cg~~L~~~d~s~------------~i~~l~~~i~~l~~~l 165 (176)
T COG1675 130 ELGFTCPKCGEDLEEYDSSE------------EIEELESELDELEEEL 165 (176)
T ss_pred HhCCCCCCCCchhhhccchH------------HHHHHHHHHHHHHHHH
Confidence 34599999999999999988 6677778888777643
No 34
>COG3783 CybC Soluble cytochrome b562 [Energy production and conversion]
Probab=57.03 E-value=20 Score=28.35 Aligned_cols=26 Identities=23% Similarity=0.461 Sum_probs=21.7
Q ss_pred HHHHHhhhcCCHHHHHHHHHHHHHHH
Q 025496 143 EQVETLGEAGKVDEAEALMRKVEILN 168 (252)
Q Consensus 143 ~~aE~LGeeG~VdeA~~~~~~~e~Lk 168 (252)
.++.+|..+|++++|.....++..++
T Consensus 67 D~a~klaqeGnl~eAKaaak~l~d~R 92 (100)
T COG3783 67 DKADKLAQEGNLDEAKAAAKTLKDTR 92 (100)
T ss_pred HHHHHHHHcCChHHHHHHHHHHHHHH
Confidence 56778999999999999888777665
No 35
>PRK03918 chromosome segregation protein; Provisional
Probab=55.02 E-value=1.3e+02 Score=31.37 Aligned_cols=165 Identities=18% Similarity=0.230 Sum_probs=0.0
Q ss_pred HHHHHHhhcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHH
Q 025496 66 QKLKESFEKSPRHDAYVPKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQV 145 (252)
Q Consensus 66 e~lk~~Ye~~~~~~~~~~gYE~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~a 145 (252)
+.+++.|+...........|...+ .-|..-+...+..+.....++.+-..... ...+...++..+.+....+....
T Consensus 286 ~~l~~~~~~~~~l~~~~~~l~~~~-~~l~~~~~~l~~~~~~l~~~l~~~e~~~~---~~~e~~~~~~~~~~~~~~l~~~~ 361 (880)
T PRK03918 286 KELKEKAEEYIKLSEFYEEYLDEL-REIEKRLSRLEEEINGIEERIKELEEKEE---RLEELKKKLKELEKRLEELEERH 361 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred HHhhhcCCHHHHHHHHHH---------------------------HHHHHHHHHHHHhhhhhhhhhhhhhhccccccccc
Q 025496 146 ETLGEAGKVDEAEALMRK---------------------------VEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEIC 198 (252)
Q Consensus 146 E~LGeeG~VdeA~~~~~~---------------------------~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVC 198 (252)
+.+-.--........+.. +..++.++..+......-......-...--||++|
T Consensus 362 ~~l~~~~~~~~~l~~l~~~l~~~~~~~l~~~l~~l~~~~~~l~~~i~~l~~~~~~~~~~i~eL~~~l~~L~~~~~~Cp~c 441 (880)
T PRK03918 362 ELYEEAKAKKEELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGKCPVC 441 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q ss_pred hhhhcccChhhHhhhhhcchhhhcHHHHHHHHHHHHh
Q 025496 199 GSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKV 235 (252)
Q Consensus 199 GA~Ls~~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL~~ 235 (252)
|.-|+ .+.-..+-+++...+--=-..|+..-+++..
T Consensus 442 ~~~L~-~~~~~el~~~~~~ei~~l~~~~~~l~~~~~~ 477 (880)
T PRK03918 442 GRELT-EEHRKELLEEYTAELKRIEKELKEIEEKERK 477 (880)
T ss_pred CCcCC-chhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 36
>PF14282 FlxA: FlxA-like protein
Probab=54.50 E-value=51 Score=25.97 Aligned_cols=50 Identities=28% Similarity=0.460 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (252)
Q Consensus 128 ~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~ 178 (252)
...|..|..+|..|..++.+|...+..+ +.....++..|+.++..|+.++
T Consensus 18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~-~e~k~~q~q~Lq~QI~~LqaQI 67 (106)
T PF14282_consen 18 DSQIEQLQKQIKQLQEQLQELSQDSDLD-AEQKQQQIQLLQAQIQQLQAQI 67 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccCCC-HHHHHHHHHHHHHHHHHHHHHH
Confidence 6788888888888888888888843321 1122344444555554444443
No 37
>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=54.33 E-value=29 Score=26.11 Aligned_cols=13 Identities=31% Similarity=0.685 Sum_probs=10.3
Q ss_pred ccccccchhhhcc
Q 025496 192 MALCEICGSFLVA 204 (252)
Q Consensus 192 l~VCdVCGA~Ls~ 204 (252)
..+|.|||-.|..
T Consensus 78 ~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 78 STKCSVCGKPLGN 90 (109)
T ss_pred CCCccCcCCcCCC
Confidence 3679999988754
No 38
>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=53.83 E-value=45 Score=24.40 Aligned_cols=60 Identities=20% Similarity=0.351 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccCh
Q 025496 137 KIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 207 (252)
Q Consensus 137 ~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~ 207 (252)
+|+-|...|..+-..+..+-|...+..+..+-.+- . . ..++.-+...|.-||.+|+-+-|
T Consensus 2 Ri~~L~~~a~~~~~~~~~~lsr~y~~~~~~i~~k~-~----~------~l~~~~kr~~Ck~C~~~liPG~~ 61 (85)
T PF04032_consen 2 RINFLYQAAHLLLADGSPSLSRHYMKLMRKISKKT-R----I------RLPPEIKRTICKKCGSLLIPGVN 61 (85)
T ss_dssp HHHHHHHHHH-HHCCC-HHHHHHHHHHHHHHHHHC-T-------------STTCCCTB-TTT--B--CTTT
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHh-C----C------CCChHHhcccccCCCCEEeCCCc
Confidence 56667777776677888888888887777764321 1 1 12245678999999999998765
No 39
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=53.47 E-value=49 Score=36.00 Aligned_cols=9 Identities=44% Similarity=1.088 Sum_probs=8.0
Q ss_pred cccccchhh
Q 025496 193 ALCEICGSF 201 (252)
Q Consensus 193 ~VCdVCGA~ 201 (252)
.+|+|||+.
T Consensus 504 ePCPVCGS~ 512 (1047)
T PRK10246 504 QPCPLCGST 512 (1047)
T ss_pred CCcCCCCcc
Confidence 899999973
No 40
>PRK10698 phage shock protein PspA; Provisional
Probab=53.07 E-value=1.7e+02 Score=26.07 Aligned_cols=63 Identities=13% Similarity=0.153 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHH
Q 025496 91 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEA 159 (252)
Q Consensus 91 ~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~ 159 (252)
..|..+|.+++.-+...+.-++... ........++..+...|...-.+|+.+-..|+=+-|-.
T Consensus 27 k~l~q~i~em~~~l~~~r~alA~~~------A~~k~~er~~~~~~~~~~~~e~kA~~Al~~G~EdLAr~ 89 (222)
T PRK10698 27 KLVRLMIQEMEDTLVEVRSTSARAL------AEKKQLTRRIEQAEAQQVEWQEKAELALRKEKEDLARA 89 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence 3566667777666666655554321 12334567888899999999999999999998888877
No 41
>PF13863 DUF4200: Domain of unknown function (DUF4200)
Probab=52.45 E-value=61 Score=25.51 Aligned_cols=50 Identities=16% Similarity=0.315 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 025496 92 FCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVET 147 (252)
Q Consensus 92 ~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~ 147 (252)
-...||.+++.+..+|..+.+... .....+..+|..|...|+.+-.++..
T Consensus 50 ~f~~flken~~k~~rA~k~a~~e~------k~~~~k~~ei~~l~~~l~~l~~~~~k 99 (126)
T PF13863_consen 50 KFDKFLKENEAKRERAEKRAEEEK------KKKEEKEAEIKKLKAELEELKSEISK 99 (126)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788888888888887775432 12233444555555555554444444
No 42
>PF12854 PPR_1: PPR repeat
Probab=52.04 E-value=17 Score=22.42 Aligned_cols=20 Identities=35% Similarity=0.513 Sum_probs=16.5
Q ss_pred HHHHhhhcCCHHHHHHHHHH
Q 025496 144 QVETLGEAGKVDEAEALMRK 163 (252)
Q Consensus 144 ~aE~LGeeG~VdeA~~~~~~ 163 (252)
-+..+...|+|++|.+++.+
T Consensus 13 lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 13 LIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHHCCCHHHHHHHHHh
Confidence 35568899999999999875
No 43
>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=51.70 E-value=4.9 Score=35.56 Aligned_cols=28 Identities=25% Similarity=0.437 Sum_probs=0.0
Q ss_pred cccccccchhhhcccChhhH-hhhhhcchhhh
Q 025496 191 KMALCEICGSFLVANDAAER-TQSHISGKQHI 221 (252)
Q Consensus 191 kl~VCdVCGA~Ls~~D~d~R-l~dH~~GK~H~ 221 (252)
+...|+|||-+.-.+ +| .+.||+.--|.
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 348999999885554 55 78999999885
No 44
>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=50.90 E-value=1.3e+02 Score=24.38 Aligned_cols=70 Identities=27% Similarity=0.326 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHH
Q 025496 87 AELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEI 166 (252)
Q Consensus 87 ~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~ 166 (252)
--++..|++-|+..|--|...+.+++. ....-+.+.++|-.++.+.+++ .....++..
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 456778888888888888888877753 2234456677777777776664 344555556
Q ss_pred HHHHHHHHHhhh
Q 025496 167 LNVEKTTLTQQS 178 (252)
Q Consensus 167 Lk~ek~~l~~~~ 178 (252)
|+.+.+++...+
T Consensus 73 L~~el~~l~~ry 84 (120)
T PF12325_consen 73 LEQELEELQQRY 84 (120)
T ss_pred HHHHHHHHHHHH
Confidence 666666665555
No 45
>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=50.73 E-value=86 Score=27.23 Aligned_cols=53 Identities=26% Similarity=0.399 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhc-CCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 126 EKSEQLSVLEEKIKNLLEQVETLGEA-GKVDEAEALMRKVEILNVEKTTLTQQS 178 (252)
Q Consensus 126 ~~~~~i~~l~~~I~~ll~~aE~LGee-G~VdeA~~~~~~~e~Lk~ek~~l~~~~ 178 (252)
...+++..+..+|..+-.+++.+... ++-++-..++++++.|+.+.+.+..++
T Consensus 73 ~l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el 126 (188)
T PF03962_consen 73 KLQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKEL 126 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556667777777777777766432 334556778899999998888888776
No 46
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=50.10 E-value=5.7 Score=29.00 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=17.3
Q ss_pred cccccccchh---------hhcccChhhH-hhhh
Q 025496 191 KMALCEICGS---------FLVANDAAER-TQSH 214 (252)
Q Consensus 191 kl~VCdVCGA---------~Ls~~D~d~R-l~dH 214 (252)
.-++|+|||. ++++.|.+.- +|+-
T Consensus 17 d~e~CP~Cgs~~~te~W~G~~iIidpe~SeIAkr 50 (64)
T COG2093 17 DTEICPVCGSTDLTEEWFGLLIIIDPEKSEIAKR 50 (64)
T ss_pred CCccCCCCCCcccchhhccEEEEEcCcHHHHHHH
Confidence 3478999998 5778888872 4443
No 47
>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=49.93 E-value=1.1e+02 Score=23.02 Aligned_cols=56 Identities=18% Similarity=0.239 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 92 FCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGE 150 (252)
Q Consensus 92 ~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGe 150 (252)
.+..-+..+-.||.+++.-+..-+ .......+...+|..|+++|..+-.-...+++
T Consensus 25 d~~~~~~~lk~Klq~ar~~i~~lp---gi~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~ 80 (83)
T PF07544_consen 25 DLDTATGSLKHKLQKARAAIRELP---GIDRSVEEQEEEIEELEEQIRKKREVLQKFKE 80 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCC---CccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455667788889999998886543 23345566778888888888877776666654
No 48
>PRK10884 SH3 domain-containing protein; Provisional
Probab=49.85 E-value=1.3e+02 Score=26.54 Aligned_cols=56 Identities=20% Similarity=0.199 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHh
Q 025496 91 QFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETL 148 (252)
Q Consensus 91 ~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~L 148 (252)
..+..-+..+++.+...+.+|++... .......+.++++...+..|..+-.+-++|
T Consensus 89 p~~~~rlp~le~el~~l~~~l~~~~~--~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L 144 (206)
T PRK10884 89 PSLRTRVPDLENQVKTLTDKLNNIDN--TWNQRTAEMQQKVAQSDSVINGLKEENQKL 144 (206)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHh--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556667788888888888865331 122234445555556565555555555444
No 49
>PF09969 DUF2203: Uncharacterized conserved protein (DUF2203); InterPro: IPR018699 This family has no known function.
Probab=49.28 E-value=75 Score=25.75 Aligned_cols=28 Identities=25% Similarity=0.515 Sum_probs=22.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 025496 124 SAEKSEQLSVLEEKIKNLLEQVETLGEA 151 (252)
Q Consensus 124 ~~~~~~~i~~l~~~I~~ll~~aE~LGee 151 (252)
......++..+..+|...+.+++++|-+
T Consensus 45 ~~~~~~~~~~~~~~~~~~i~~i~~~Gv~ 72 (120)
T PF09969_consen 45 VNGLEAELEELEARLRELIDEIEELGVE 72 (120)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHHcCcE
Confidence 3445678888899999999999998843
No 50
>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=48.75 E-value=1.6e+02 Score=24.73 Aligned_cols=112 Identities=18% Similarity=0.167 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCH-----HHH--HHHHH
Q 025496 90 AQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKV-----DEA--EALMR 162 (252)
Q Consensus 90 ~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~V-----deA--~~~~~ 162 (252)
...++.=..++++-|+.+++++....+ ....+.+.-..-+..-|.......+.+...-.+ +++ ..++.
T Consensus 6 ~e~~~~~~~~L~~~le~a~e~~~~~~e-----lT~eEl~lv~~ylkRDl~~~a~~~~~~~~~~~~~~~lie~slw~~L~~ 80 (146)
T PF07295_consen 6 EEALEHSEEELQEALEKAKEYLVAAGE-----LTREELALVSAYLKRDLEEFARYYEELREWLSPDLQLIEESLWDELSS 80 (146)
T ss_pred HHHHhcCHHHHHHHHHHHHHHHHHHhh-----cCHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccHHHHHHHHHHHHHh
Confidence 344555567778888888888864321 112222222233444444444444442222222 222 34555
Q ss_pred HHHHHHHHHHHHHhhhhhhh--h-hhhhhhccccccccchhhhcccCh
Q 025496 163 KVEILNVEKTTLTQQSQNDK--V-LMMAQEKKMALCEICGSFLVANDA 207 (252)
Q Consensus 163 ~~e~Lk~ek~~l~~~~~~~~--~-~~~~~~qkl~VCdVCGA~Ls~~D~ 207 (252)
-.++-+.+..++.+.+ ... + +|--......||+-||.-+....+
T Consensus 81 ItDkTqvEw~el~~d~-~h~g~Y~sGE~~g~G~l~C~~Cg~~~~~~~~ 127 (146)
T PF07295_consen 81 ITDKTQVEWAELAQDL-EHHGVYHSGEVVGPGTLVCENCGHEVELTHP 127 (146)
T ss_pred hhchhHHHHHHHHHHH-HhcCCeecCcEecCceEecccCCCEEEecCC
Confidence 5666777777777665 211 1 121123467899999988877654
No 51
>PRK14162 heat shock protein GrpE; Provisional
Probab=48.15 E-value=1.1e+02 Score=26.98 Aligned_cols=96 Identities=19% Similarity=0.155 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccC
Q 025496 127 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVAND 206 (252)
Q Consensus 127 ~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D 206 (252)
...++..++.+|..+-+++++|- +.-+.+.++.+.++..-+.-... ..+.-+-.+.-.+|.+.|
T Consensus 37 ~~~e~~~l~~~l~~l~~e~~elk-----d~~lR~~AEfeN~rkR~~kE~e~-----------~~~~a~~~~~~~LLpV~D 100 (194)
T PRK14162 37 KQNPVEDLEKEIADLKAKNKDLE-----DKYLRSQAEIQNMQNRYAKERAQ-----------LIKYESQSLAKDVLPAMD 100 (194)
T ss_pred cchhHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHhhHHh
Confidence 34577788888888888888774 56677777777765322211111 112234456788999999
Q ss_pred hhhHhhhhhc-----chhhhcHHHHHHHHHH-HHhhcc
Q 025496 207 AAERTQSHIS-----GKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 207 ~d~Rl~dH~~-----GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
|=.|--.|.. ..++-|+..|.+.+.. |...|+
T Consensus 101 nLerAl~~~~~~~~~~~l~~Gvemi~k~l~~vL~~~GV 138 (194)
T PRK14162 101 NLERALAVKADDEAAKQLKKGVQMTLDHLVKALKDHGV 138 (194)
T ss_pred HHHHHHhccccchhHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 9999766753 2467899888776665 444443
No 52
>COG4911 Uncharacterized conserved protein [Function unknown]
Probab=45.22 E-value=1.1e+02 Score=24.78 Aligned_cols=54 Identities=19% Similarity=0.191 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhh
Q 025496 88 ELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLG 149 (252)
Q Consensus 88 e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LG 149 (252)
++.+.|..+..|+-.+.++-+.+.+.-. ..+..-.+.+++.++..++++++++|
T Consensus 11 e~~~el~P~l~d~~~~~r~~~n~~e~L~--------~qedk~~l~e~e~q~k~~l~~i~e~G 64 (123)
T COG4911 11 ETARELLPWLRDRLIQLRKIKNEIELLL--------VQEDKYALQEYESQTKKILDEIIEKG 64 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhc--------ccccHHHHHHHHHHHHHHHHHHHHcC
Confidence 6777888888887777777776665321 11123578999999999999999988
No 53
>PRK14154 heat shock protein GrpE; Provisional
Probab=45.16 E-value=1.3e+02 Score=26.89 Aligned_cols=93 Identities=10% Similarity=0.077 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChhh
Q 025496 130 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAE 209 (252)
Q Consensus 130 ~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~ 209 (252)
.+..++.+|..+-+++++|- +.-+.+.++.+.++.-.++-.+.. .+.-+-.+...+|-+.|+=.
T Consensus 53 ~~~~l~~el~~le~e~~elk-----d~~lRl~ADfeNyRKR~~kE~e~~-----------~~~a~e~~~~~LLpVlDnLe 116 (208)
T PRK14154 53 SREKLEGQLTRMERKVDEYK-----TQYLRAQAEMDNLRKRIEREKADI-----------IKFGSKQLITDLLPVADSLI 116 (208)
T ss_pred chhhHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHhhHHhHHH
Confidence 45566666777777777663 566777777777763322222111 12234457788999999999
Q ss_pred Hhhhhhc------chhhhcHHHHHHHHHH-HHhhcc
Q 025496 210 RTQSHIS------GKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 210 Rl~dH~~------GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
|.-.|.. ..+.-|+..|.+.+.. |...++
T Consensus 117 RAL~~~~~~~~~~~~l~eGvemi~k~l~~vL~k~GV 152 (208)
T PRK14154 117 HGLESPASEDPQVKSMRDGMSLTLDLLHNTLAKHGV 152 (208)
T ss_pred HHHhcccccchhHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 9665542 3477888888666655 444443
No 54
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=44.84 E-value=25 Score=33.09 Aligned_cols=27 Identities=26% Similarity=0.348 Sum_probs=23.8
Q ss_pred HHHHHHhhhcCCHHHHHHHHHHHHHHH
Q 025496 142 LEQVETLGEAGKVDEAEALMRKVEILN 168 (252)
Q Consensus 142 l~~aE~LGeeG~VdeA~~~~~~~e~Lk 168 (252)
...|++.-+.|+|++|+.++.|+|+|-
T Consensus 261 ~~aI~~AVk~gDi~KAL~LldEAe~LG 287 (303)
T PRK10564 261 NQAIKQAVKKGDVDKALKLLDEAERLG 287 (303)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence 467778888999999999999999985
No 55
>PRK14151 heat shock protein GrpE; Provisional
Probab=44.47 E-value=1.3e+02 Score=26.03 Aligned_cols=95 Identities=20% Similarity=0.230 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccCh
Q 025496 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 207 (252)
Q Consensus 128 ~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~ 207 (252)
+..+..++++|..+-++++++- +.-+.+.++.+.++.-. +++. . ...+.-+-.++..+|-+.||
T Consensus 19 ~~~~~~l~~~i~~le~e~~el~-----d~~lR~~Ae~eN~rkR~---~kE~-e-------~~~~~a~~~~~~~LLpv~Dn 82 (176)
T PRK14151 19 AAAGDDLTARVQELEEQLAAAK-----DQSLRAAADLQNVRRRA---EQDV-E-------KAHKFALEKFAGDLLPVVDS 82 (176)
T ss_pred ccchhhHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHH---HHHH-H-------HHHHHHHHHHHHHHhhHHhH
Confidence 3456667777777777777764 55667777777764222 2211 0 01122334577889999999
Q ss_pred hhHhhhhhc------chhhhcHHHHHHHHHH-HHhhcc
Q 025496 208 AERTQSHIS------GKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 208 d~Rl~dH~~------GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
=.|.-.|.. ..++-|+..|.+.+.. |...|+
T Consensus 83 lerAl~~~~~~~~~~~~~~~Gv~mi~k~l~~~L~k~Gv 120 (176)
T PRK14151 83 LERGLELSSADDEAIKPMREGVELTLKMFQDTLKRYQL 120 (176)
T ss_pred HHHHHhcccccchhHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 999766653 3478899888777655 444443
No 56
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=44.38 E-value=68 Score=27.67 Aligned_cols=17 Identities=29% Similarity=0.710 Sum_probs=9.9
Q ss_pred ccccccchhhhcccChhh
Q 025496 192 MALCEICGSFLVANDAAE 209 (252)
Q Consensus 192 l~VCdVCGA~Ls~~D~d~ 209 (252)
..||.|||= +..+.++.
T Consensus 134 ~~vC~vCGy-~~~ge~P~ 150 (166)
T COG1592 134 VWVCPVCGY-THEGEAPE 150 (166)
T ss_pred EEEcCCCCC-cccCCCCC
Confidence 788888873 33334443
No 57
>PRK11020 hypothetical protein; Provisional
Probab=43.96 E-value=1.7e+02 Score=23.89 Aligned_cols=44 Identities=9% Similarity=0.253 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHH
Q 025496 130 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTT 173 (252)
Q Consensus 130 ~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~ 173 (252)
+|..|+.+++..-.+...+-..|+.+---.+..+++.|..++..
T Consensus 6 Eiq~L~drLD~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~ 49 (118)
T PRK11020 6 EIKRLSDRLDAIRHKLAAASLRGDAEKYAQFEKEKATLEAEIAR 49 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 33334444444433333344444444333333444444333333
No 58
>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=43.80 E-value=1.5e+02 Score=23.31 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=10.2
Q ss_pred cccccccchhhhc
Q 025496 191 KMALCEICGSFLV 203 (252)
Q Consensus 191 kl~VCdVCGA~Ls 203 (252)
.--+|+.||.-+.
T Consensus 79 ~yG~C~~Cge~I~ 91 (110)
T TIGR02420 79 EYGYCEECGEEIG 91 (110)
T ss_pred CCCchhccCCccc
Confidence 3469999998765
No 59
>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=43.64 E-value=1.2e+02 Score=24.58 Aligned_cols=52 Identities=23% Similarity=0.319 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q 025496 126 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQ 177 (252)
Q Consensus 126 ~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~ 177 (252)
.+...+..|+.+|..+..++-.+...|+.+.|..++...-.++.....+...
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 3446778888888888899999999999999988888887777766666543
No 60
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.32 E-value=11 Score=32.45 Aligned_cols=33 Identities=24% Similarity=0.349 Sum_probs=26.4
Q ss_pred cccccccchhhhcccChhhHhhhhhcchhhhcHHHHHHHHHHHHh
Q 025496 191 KMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKV 235 (252)
Q Consensus 191 kl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL~~ 235 (252)
--+.|++||..|.-.||...+ ..|++.++.|.+
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~------------~~l~~~I~~l~~ 167 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELI------------KELKEQIKELEE 167 (178)
T ss_pred cCCcCCCCCCCCeecccHHHH------------HHHHHHHHHHHH
Confidence 359999999999999998865 357777777765
No 61
>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=43.08 E-value=7 Score=27.59 Aligned_cols=20 Identities=30% Similarity=0.655 Sum_probs=11.7
Q ss_pred cccccccchhhhcccChhhH
Q 025496 191 KMALCEICGSFLVANDAAER 210 (252)
Q Consensus 191 kl~VCdVCGA~Ls~~D~d~R 210 (252)
+--.|++|||.++..-|-+|
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 34789999999987665555
No 62
>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=42.98 E-value=2.2e+02 Score=24.64 Aligned_cols=78 Identities=18% Similarity=0.306 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHH
Q 025496 90 AQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 168 (252)
Q Consensus 90 ~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk 168 (252)
+.-|..=+.++..+|...+.+++....+...........+++.+|..++..+..+.+.+.. .+.+.-..+-.++..++
T Consensus 71 ~~~l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~~~~~-~Dp~~i~~~~~~~~~~~ 148 (188)
T PF03962_consen 71 LEKLQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKELEKYSE-NDPEKIEKLKEEIKIAK 148 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHHH
Confidence 4455566666677777777777644221111112334567788888888888888886554 34444333333333333
No 63
>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=42.61 E-value=1.4e+02 Score=22.09 Aligned_cols=46 Identities=24% Similarity=0.333 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (252)
Q Consensus 128 ~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~ 178 (252)
...|.+-+++|..|+.+.|.|- ..=.+....+-.|+.+..+++...
T Consensus 4 ~~~l~EKDe~Ia~L~eEGekLS-----k~el~~~~~IKKLr~~~~e~e~~~ 49 (74)
T PF12329_consen 4 EKKLAEKDEQIAQLMEEGEKLS-----KKELKLNNTIKKLRAKIKELEKQI 49 (74)
T ss_pred HHHHHhHHHHHHHHHHHHHHHH-----HHHHhhHHHHHHHHHHHHHHHHHH
Confidence 4567777888888888888776 223345566666666666665443
No 64
>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=41.50 E-value=1.2e+02 Score=21.56 Aligned_cols=59 Identities=29% Similarity=0.416 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcc-CCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhh
Q 025496 91 QFCEKLVMDLDRRVRRGRERLSQEV-EPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLG 149 (252)
Q Consensus 91 ~~L~~~i~d~drkI~~~k~RL~~~~-~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LG 149 (252)
.-|++=+..+...|.+...+|.... -...+........+++.++..+|..+...++.|+
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 3566777788888999998986320 0011233455667888899988888888877764
No 65
>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=41.38 E-value=10 Score=24.04 Aligned_cols=11 Identities=36% Similarity=0.772 Sum_probs=8.8
Q ss_pred cccccccchhh
Q 025496 191 KMALCEICGSF 201 (252)
Q Consensus 191 kl~VCdVCGA~ 201 (252)
...+|+||||-
T Consensus 17 ~p~~CP~Cg~~ 27 (34)
T cd00729 17 APEKCPICGAP 27 (34)
T ss_pred CCCcCcCCCCc
Confidence 34799999984
No 66
>PRK14160 heat shock protein GrpE; Provisional
Probab=40.43 E-value=2.4e+02 Score=25.23 Aligned_cols=95 Identities=15% Similarity=0.100 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccCh
Q 025496 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 207 (252)
Q Consensus 128 ~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~ 207 (252)
++++..+..+|..+-.+++.|- +.-+.+.++.+.++.--++-.. ...+.-+..+.-.+|-+.|+
T Consensus 60 ~~e~~~l~~~l~~l~~e~~elk-----d~~lR~~AefeN~RKR~~kE~e-----------~~~~~a~e~~~~~LLpVlDn 123 (211)
T PRK14160 60 KDENNKLKEENKKLENELEALK-----DRLLRTVAEYDNYRKRTAKEKE-----------GIYSDACEDVLKELLPVLDN 123 (211)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhHHhH
Confidence 3455555555555555555553 4445555555555421111111 11233455677889999999
Q ss_pred hhHhhhhhc--chhhhcHHHHHHHHHH-HHhhcc
Q 025496 208 AERTQSHIS--GKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 208 d~Rl~dH~~--GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
=.|.-.|.. ..++-|+..|...+.. |...|+
T Consensus 124 LerAl~~~~~~~~l~~Gv~mi~kql~~vL~k~GV 157 (211)
T PRK14160 124 LERAAAVEGSVEDLKKGIEMTVKQFKTSLEKLGV 157 (211)
T ss_pred HHHHHhcccchhHHHHHHHHHHHHHHHHHHHCCC
Confidence 999655533 2477888888665544 555454
No 67
>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=40.35 E-value=13 Score=31.42 Aligned_cols=21 Identities=29% Similarity=0.403 Sum_probs=17.9
Q ss_pred cccccccchhhhcccChhhHh
Q 025496 191 KMALCEICGSFLVANDAAERT 211 (252)
Q Consensus 191 kl~VCdVCGA~Ls~~D~d~Rl 211 (252)
--+.|++||+.|.-.||..-+
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i 147 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAI 147 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHH
Confidence 359999999999999998754
No 68
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=39.97 E-value=12 Score=32.34 Aligned_cols=30 Identities=27% Similarity=0.489 Sum_probs=25.9
Q ss_pred cccccchhhhcccChhhHhhhhhcchhhhcH
Q 025496 193 ALCEICGSFLVANDAAERTQSHISGKQHIGY 223 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy 223 (252)
.-||-|..+|. +|+.+=...|.+|+-|+-.
T Consensus 4 Y~CeyC~~~Lt-hD~lsvRk~H~~G~~H~~~ 33 (188)
T COG5136 4 YFCEYCNKMLT-HDRLSVRKMHCGGAKHGLM 33 (188)
T ss_pred hHHHHHHHHHh-ccHHHHHHHhhhhHHHHHH
Confidence 46999999986 8888888899999999864
No 69
>PRK14147 heat shock protein GrpE; Provisional
Probab=39.87 E-value=1.2e+02 Score=26.05 Aligned_cols=89 Identities=12% Similarity=0.134 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChhhHhh
Q 025496 133 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQ 212 (252)
Q Consensus 133 ~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~Rl~ 212 (252)
.+..+|..+-+++++|- +.-+.+.++.+.++.- ..++. . ...+.-+-.++..+|-+.|+=.|--
T Consensus 22 ~l~~~l~~l~~e~~elk-----d~~lR~~Ad~eN~rkR---~~kE~-e-------~~~~~a~~~~~~~lLpv~DnlerAl 85 (172)
T PRK14147 22 PLKAEVESLRSEIALVK-----ADALRERADLENQRKR---IARDV-E-------QARKFANEKLLGELLPVFDSLDAGL 85 (172)
T ss_pred hHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHH---HHHHH-H-------HHHHHHHHHHHHHHhhhhhHHHHHH
Confidence 34555555556666553 4455666666666422 22211 0 0112233467888999999999965
Q ss_pred hhhc---chhhhcHHHHHHHHHHH-Hhhc
Q 025496 213 SHIS---GKQHIGYGMVRDFITEY-KVCQ 237 (252)
Q Consensus 213 dH~~---GK~H~Gy~kIR~~l~eL-~~~~ 237 (252)
.|.. ..++-|+..|.+.+... ...|
T Consensus 86 ~~~~~~~~~l~~Gv~mi~k~l~~~L~~~G 114 (172)
T PRK14147 86 TAAGTEPSPLRDGLELTYKQLLKVAADNG 114 (172)
T ss_pred hcccchHHHHHHHHHHHHHHHHHHHHHCC
Confidence 5654 34778888887766654 4444
No 70
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=39.33 E-value=14 Score=32.22 Aligned_cols=33 Identities=27% Similarity=0.548 Sum_probs=24.8
Q ss_pred hhhhccccccccchhhhcccChhhHhhhhhcchhhh
Q 025496 186 MAQEKKMALCEICGSFLVANDAAERTQSHISGKQHI 221 (252)
Q Consensus 186 ~~~~qkl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~ 221 (252)
+..++.-.-|+||.+. +-|+-+ .-||+.||-|.
T Consensus 69 p~sq~~GyyCdVCdcv--vKDSin-flDHiNgKkHq 101 (193)
T KOG4727|consen 69 PRSQKGGYYCDVCDCV--VKDSIN-FLDHINGKKHQ 101 (193)
T ss_pred cccccCceeeeeccee--ehhhHH-HHHHhccHHHH
Confidence 3355666899999954 667655 55899999995
No 71
>PLN00204 CP12 gene family protein; Provisional
Probab=39.12 E-value=90 Score=25.81 Aligned_cols=44 Identities=18% Similarity=0.213 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHhhhcCCH-HHHHHHHHHHHHHHHHHHHHHh
Q 025496 133 VLEEKIKNLLEQVETLGEAGKV-DEAEALMRKVEILNVEKTTLTQ 176 (252)
Q Consensus 133 ~l~~~I~~ll~~aE~LGeeG~V-deA~~~~~~~e~Lk~ek~~l~~ 176 (252)
.|+++|.+.+++|++.-.+|.. .++.....+||+|+.+..-...
T Consensus 56 ~L~e~Ie~aI~eArevCa~g~~S~eCaaAWDeVEELqAeasHqr~ 100 (126)
T PLN00204 56 GISEKVEKSIKEAEETCADDPASGECVAAWDEVEELSAAASHARD 100 (126)
T ss_pred cHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 5788889999999999888744 4667779999999988765443
No 72
>PRK14163 heat shock protein GrpE; Provisional
Probab=39.02 E-value=2.1e+02 Score=25.72 Aligned_cols=92 Identities=13% Similarity=0.151 Sum_probs=58.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChh
Q 025496 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAA 208 (252)
Q Consensus 129 ~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d 208 (252)
..+..+..+|..+-+++++|- +.-+.+.++.+.++.--.+-.... .+.-+=.+.-.+|-+.|+=
T Consensus 40 ~~~~~l~~~l~~l~~e~~el~-----d~~lR~~AEfeN~rkR~~kE~e~~-----------~~~a~~~~~~~LLpVlDnL 103 (214)
T PRK14163 40 AATAGLTAQLDQVRTALGERT-----ADLQRLQAEYQNYRRRVERDRVTV-----------KEIAVANLLSELLPVLDDV 103 (214)
T ss_pred hhhHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHhhhHhHH
Confidence 345677777888777777763 666677777777653221111111 1112224566889999999
Q ss_pred hHhhhhhcchhhhcHHHHHHHHHH-HHhhcc
Q 025496 209 ERTQSHISGKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 209 ~Rl~dH~~GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
.|--.| +.++-|+..|++.+.. |...++
T Consensus 104 erAl~~--~~l~~Gv~mi~k~l~~~L~k~Gv 132 (214)
T PRK14163 104 GRAREH--GELVGGFKSVAESLETTVAKLGL 132 (214)
T ss_pred HHHHhc--hhHHHHHHHHHHHHHHHHHHCCC
Confidence 997777 4688899999776665 444443
No 73
>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=38.47 E-value=17 Score=25.15 Aligned_cols=30 Identities=30% Similarity=0.512 Sum_probs=23.1
Q ss_pred ccccccccchhhhcccChhhHhhhhhcchhhhcHHH
Q 025496 190 KKMALCEICGSFLVANDAAERTQSHISGKQHIGYGM 225 (252)
Q Consensus 190 qkl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~k 225 (252)
++--.|++|..- .| -+..|+.++.|..|+.
T Consensus 3 ~k~GYCE~C~~k---y~---~l~~Hi~s~~Hr~FA~ 32 (49)
T PF07535_consen 3 KKPGYCENCRVK---YD---DLEEHIQSEKHRKFAE 32 (49)
T ss_pred CCCccCccccch---hh---hHHHHhCCHHHHHHHc
Confidence 455689999864 22 2788999999999984
No 74
>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=37.33 E-value=1.2e+02 Score=28.74 Aligned_cols=25 Identities=36% Similarity=0.745 Sum_probs=20.4
Q ss_pred CcchhhcCCChhHhhhhcccCCCCCCcc
Q 025496 36 VCPFYMVRFCPHDLFVNTRSDLGPCPRI 63 (252)
Q Consensus 36 VCk~yL~G~CPhdLF~nTK~DlG~C~ki 63 (252)
.|-|-+|.-|--.+|.. .-|+||..
T Consensus 25 ~CGH~~C~sCv~~l~~~---~~~~CP~C 49 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVR---GSGSCPEC 49 (309)
T ss_pred CCCCcccHHHHHHHhcC---CCCCCCCC
Confidence 79999999999999965 34689843
No 75
>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=36.47 E-value=1.7e+02 Score=28.16 Aligned_cols=21 Identities=38% Similarity=0.533 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 025496 127 KSEQLSVLEEKIKNLLEQVET 147 (252)
Q Consensus 127 ~~~~i~~l~~~I~~ll~~aE~ 147 (252)
..+++..++.+|.++-.+.++
T Consensus 247 l~~~~~~~~~~i~~l~~~l~~ 267 (406)
T PF02388_consen 247 LQEKLEKLEKEIEKLEEKLEK 267 (406)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 344444555555554444333
No 76
>PRK14146 heat shock protein GrpE; Provisional
Probab=36.40 E-value=1.8e+02 Score=25.93 Aligned_cols=91 Identities=15% Similarity=0.130 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChhhH
Q 025496 131 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAER 210 (252)
Q Consensus 131 i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~R 210 (252)
+..+..+|..+-+++++|- +..+.+.++.+.++.--+.-.. ...+.-+-.++..+|-+.||=.|
T Consensus 56 ~~~l~~~l~~l~~e~~el~-----d~~lR~~AdfeN~rkR~~kE~e-----------~~~~~a~e~~~~~lLpv~Dnler 119 (215)
T PRK14146 56 ETSLQKELDNAKKEIESLK-----DSWARERAEFQNFKRRSAQEFV-----------SIRKEAVKSLVSGFLNPIDNLER 119 (215)
T ss_pred hhhHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhHHhHHHH
Confidence 4444555555555555553 4555566666655422111111 11233455678899999999999
Q ss_pred hhhhhc-----chhhhcHHHHHHHHHH-HHhhc
Q 025496 211 TQSHIS-----GKQHIGYGMVRDFITE-YKVCQ 237 (252)
Q Consensus 211 l~dH~~-----GK~H~Gy~kIR~~l~e-L~~~~ 237 (252)
.-.|.. ..++-|+..|.+.+.. |...|
T Consensus 120 Al~~~~~~~~~~~l~~Gv~mi~k~l~~~L~k~G 152 (215)
T PRK14146 120 VGATQNQSEELKPFVEGVKMILKEFYSVLEKSN 152 (215)
T ss_pred HHhcccccchhhHHHHHHHHHHHHHHHHHHHCc
Confidence 766653 3367888888776655 44444
No 77
>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=36.28 E-value=18 Score=19.50 Aligned_cols=19 Identities=26% Similarity=0.684 Sum_probs=11.1
Q ss_pred ccccchhhhcccChhhHhhhhh
Q 025496 194 LCEICGSFLVANDAAERTQSHI 215 (252)
Q Consensus 194 VCdVCGA~Ls~~D~d~Rl~dH~ 215 (252)
.|++||.-.. +...+..|+
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 6999997643 445566665
No 78
>PF14282 FlxA: FlxA-like protein
Probab=36.18 E-value=2e+02 Score=22.55 Aligned_cols=52 Identities=17% Similarity=0.357 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 025496 94 EKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVET 147 (252)
Q Consensus 94 ~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~ 147 (252)
...|..+.++|..-++.|..-... .......+..++..|..+|..|-.++-.
T Consensus 18 ~~~I~~L~~Qi~~Lq~ql~~l~~~--~~~~~e~k~~q~q~Lq~QI~~LqaQI~q 69 (106)
T PF14282_consen 18 DSQIEQLQKQIKQLQEQLQELSQD--SDLDAEQKQQQIQLLQAQIQQLQAQIAQ 69 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcc--cCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788888888888888643321 1223445677778888777777666643
No 79
>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=36.10 E-value=2.2e+02 Score=22.62 Aligned_cols=49 Identities=29% Similarity=0.346 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhc--CCHHHHHHHHHHHHHHHHHHHHH
Q 025496 126 EKSEQLSVLEEKIKNLLEQVETLGEA--GKVDEAEALMRKVEILNVEKTTL 174 (252)
Q Consensus 126 ~~~~~i~~l~~~I~~ll~~aE~LGee--G~VdeA~~~~~~~e~Lk~ek~~l 174 (252)
++-..|..++++|+.+++++++|-.. .-++|-..+-.+-+.|++...++
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 45567888888888888888887632 23344444555555555444444
No 80
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=35.79 E-value=3.4e+02 Score=24.72 Aligned_cols=25 Identities=24% Similarity=0.335 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhc
Q 025496 90 AQFCEKLVMDLDRRVRRGRERLSQE 114 (252)
Q Consensus 90 ~~~L~~~i~d~drkI~~~k~RL~~~ 114 (252)
+.-|+.-|...+-.|+...+|+...
T Consensus 54 ~e~le~qv~~~e~ei~~~r~r~~~~ 78 (239)
T COG1579 54 LEDLENQVSQLESEIQEIRERIKRA 78 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445666666777777777777543
No 81
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=35.76 E-value=3.7e+02 Score=25.08 Aligned_cols=60 Identities=23% Similarity=0.292 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhh---hccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHH
Q 025496 85 FEAELAQFCEKLVMDLDRRVRRGRERLS---QEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVET 147 (252)
Q Consensus 85 YE~e~~~~L~~~i~d~drkI~~~k~RL~---~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~ 147 (252)
|||. +..++.+...++..+..-+.-.+ ... .......+...+.-..|..+|..+-+.+.+
T Consensus 140 YeWR-~~ll~gl~~~L~~~~~~L~~D~~~L~~~~--~~l~~~~~~l~~~~~~L~~e~~~Lk~~~~e 202 (325)
T PF08317_consen 140 YEWR-MQLLEGLKEGLEENLELLQEDYAKLDKQL--EQLDELLPKLRERKAELEEELENLKQLVEE 202 (325)
T ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 8887 56677777777766554432222 111 000112333444555566666655554444
No 82
>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=35.59 E-value=12 Score=22.70 Aligned_cols=13 Identities=46% Similarity=1.076 Sum_probs=7.1
Q ss_pred cccchhhhcccCh
Q 025496 195 CEICGSFLVANDA 207 (252)
Q Consensus 195 CdVCGA~Ls~~D~ 207 (252)
|++||+-|...+.
T Consensus 2 CP~C~s~l~~~~~ 14 (28)
T PF03119_consen 2 CPVCGSKLVREEG 14 (28)
T ss_dssp -TTT--BEEE-CC
T ss_pred cCCCCCEeEcCCC
Confidence 9999999985544
No 83
>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=35.46 E-value=1.6e+02 Score=20.65 Aligned_cols=82 Identities=15% Similarity=0.131 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChhhH
Q 025496 131 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAER 210 (252)
Q Consensus 131 i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~R 210 (252)
|..+.+.+..++..+-..-..++.+.|..+...-+.+..-...+.... ... . ..++.+.-=.-.-.++.+..+=.|
T Consensus 1 i~~m~~~~~~~l~~~~~~~~~~d~~~a~~i~~~e~~id~~~~~~~~~~-~~~-~--~~~~~~~~~~~~~~~~~i~~~lER 76 (88)
T PF01895_consen 1 ISEMGELVEEMLDDAIEAFEERDSELAQEIIQLEEEIDELYREIRRQI-LKI-L--KNQNPLEELRELVGLLRIARDLER 76 (88)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHH-HHH-H--HHHCGHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhHHHHHHHHHHHHHHH-HHH-H--hhCCCHHHHHHHHHHHHHHHHHHH
Confidence 456677778888888888888888777666555444444444443332 110 0 000100000113456666777888
Q ss_pred hhhhhc
Q 025496 211 TQSHIS 216 (252)
Q Consensus 211 l~dH~~ 216 (252)
++||..
T Consensus 77 igD~~~ 82 (88)
T PF01895_consen 77 IGDHAV 82 (88)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 888864
No 84
>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=34.66 E-value=1.9e+02 Score=24.38 Aligned_cols=54 Identities=19% Similarity=0.267 Sum_probs=44.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (252)
Q Consensus 125 ~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~ 178 (252)
....++...+..+|.++.+|....=.+.+.-+.-++-.+++++.+|.+.+.+..
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 345577788899999999999999999999998999999999988888887654
No 85
>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=34.46 E-value=1.8e+02 Score=21.22 Aligned_cols=43 Identities=26% Similarity=0.383 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 131 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (252)
Q Consensus 131 i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~ 178 (252)
+..|+.+|+.++...++|-. +-..+-.++..+..++..+....
T Consensus 2 L~~Le~kle~Li~~~~~L~~-----EN~~Lr~q~~~~~~ER~~L~ekn 44 (65)
T TIGR02449 2 LQALAAQVEHLLEYLERLKS-----ENRLLRAQEKTWREERAQLLEKN 44 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 56889999999999999984 44566777778888887776543
No 86
>PRK01156 chromosome segregation protein; Provisional
Probab=33.69 E-value=3.4e+02 Score=28.69 Aligned_cols=16 Identities=25% Similarity=0.762 Sum_probs=11.6
Q ss_pred ccccccchhhhcccCh
Q 025496 192 MALCEICGSFLVANDA 207 (252)
Q Consensus 192 l~VCdVCGA~Ls~~D~ 207 (252)
--||+|||.-+.-.=.
T Consensus 452 ~~~Cp~c~~~~~~e~~ 467 (895)
T PRK01156 452 QSVCPVCGTTLGEEKS 467 (895)
T ss_pred CCCCCCCCCcCChhhH
Confidence 4799999986654443
No 87
>PRK14141 heat shock protein GrpE; Provisional
Probab=33.19 E-value=2.2e+02 Score=25.36 Aligned_cols=85 Identities=14% Similarity=0.154 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChhhHhhh
Q 025496 134 LEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQS 213 (252)
Q Consensus 134 l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~Rl~d 213 (252)
++.+|..+-+++++|- +.-+.+.++.+.++.-. +++. . ...+.-+-.++-.+|-+.|+=.|.-.
T Consensus 36 ~~~~i~~le~e~~elk-----d~~lR~~Ae~eN~RKR~---~kE~-e-------~~~~~a~~~~~~dLLpViDnLerAl~ 99 (209)
T PRK14141 36 EPDPLEALKAENAELK-----DRMLRLAAEMENLRKRT---QRDV-A-------DARAYGIAGFARDMLSVSDNLRRALD 99 (209)
T ss_pred hHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHH---HHHH-H-------HHHHHHHHHHHHHHhhhHhHHHHHHh
Confidence 3334444444444442 44566666677665322 1111 0 11223445678899999999999777
Q ss_pred hhc-----------chhhhcHHHHHHHHHHHH
Q 025496 214 HIS-----------GKQHIGYGMVRDFITEYK 234 (252)
Q Consensus 214 H~~-----------GK~H~Gy~kIR~~l~eL~ 234 (252)
|+. -.++-|+..|+..+...-
T Consensus 100 ~~~~~~~~~~~~~~~~l~eGv~mi~k~l~~vL 131 (209)
T PRK14141 100 AIPAEARAAADAGLKALIEGVEMTERAMLNAL 131 (209)
T ss_pred ccccccccccchhHHHHHHHHHHHHHHHHHHH
Confidence 763 247789988877665543
No 88
>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=23.46 Aligned_cols=23 Identities=30% Similarity=0.489 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Q 025496 128 SEQLSVLEEKIKNLLEQVETLGE 150 (252)
Q Consensus 128 ~~~i~~l~~~I~~ll~~aE~LGe 150 (252)
...|..|..+|+.|-++++.|..
T Consensus 108 ~~dv~~L~~rId~L~~~v~~l~~ 130 (132)
T PF05597_consen 108 RKDVEALSARIDQLTAQVERLAN 130 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 36888888888888888888754
No 89
>PRK11115 transcriptional regulator PhoU; Provisional
Probab=33.00 E-value=3.2e+02 Score=23.55 Aligned_cols=81 Identities=17% Similarity=0.065 Sum_probs=52.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccc--hhhhccc
Q 025496 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEIC--GSFLVAN 205 (252)
Q Consensus 128 ~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVC--GA~Ls~~ 205 (252)
...|.++.+.+..++..+-..-..++++.|..+...-+.+......+.... ... -.-..|.+- ..++.+.
T Consensus 125 ~~~l~~l~~~v~~~l~~a~~a~~~~d~~~a~~i~~~d~~Id~~~~~~~~~~-~~~-------l~~~~~~~~~~~~l~~i~ 196 (236)
T PRK11115 125 LVSLESLGRHTIQMLHDVLDAFARMDLDEAVRIYREDKKVDQEYEGIVRQL-MTY-------MMEDPRTIPSVLTVLWCA 196 (236)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH-HHH-------HHhCcccHHHHHHHHHHH
Confidence 356888899999999999888889999998887776666654443333322 110 011457765 2333355
Q ss_pred ChhhHhhhhhc
Q 025496 206 DAAERTQSHIS 216 (252)
Q Consensus 206 D~d~Rl~dH~~ 216 (252)
.+=.|++||..
T Consensus 197 ~~lERigDh~~ 207 (236)
T PRK11115 197 RSIERIGDRCQ 207 (236)
T ss_pred HHHHHHHHHHH
Confidence 67789999863
No 90
>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=32.75 E-value=17 Score=28.74 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=17.6
Q ss_pred ccccccchhhhcccChhhHhhhh
Q 025496 192 MALCEICGSFLVANDAAERTQSH 214 (252)
Q Consensus 192 l~VCdVCGA~Ls~~D~d~Rl~dH 214 (252)
-..|++||.+|..-++..|+.|-
T Consensus 20 ~~gCpnC~~~l~~~g~~~~v~~~ 42 (98)
T cd07973 20 RDGCPNCEGYLDMKGNHERVYDC 42 (98)
T ss_pred CCCCCCCcchhccCCCccccccc
Confidence 46899999999887777665543
No 91
>COG4499 Predicted membrane protein [Function unknown]
Probab=32.67 E-value=1.8e+02 Score=28.70 Aligned_cols=75 Identities=12% Similarity=0.096 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHH
Q 025496 93 CEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNV 169 (252)
Q Consensus 93 L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ 169 (252)
|.+.+.|.|--.=..-.++++.. +.+...-.++.+.+++++.+|+..+++.+++..+-+-+++...-.+=|+++.
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 44555666655544445555432 2233455678899999999999999999999987666555444444444443
No 92
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=32.58 E-value=1.4e+02 Score=19.89 Aligned_cols=35 Identities=37% Similarity=0.473 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHH
Q 025496 134 LEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVE 170 (252)
Q Consensus 134 l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~e 170 (252)
+-++|.+|+..++.-| +.-.||+..+.++..|..+
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 3467778888777433 6667898888888888643
No 93
>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=32.44 E-value=54 Score=27.11 Aligned_cols=37 Identities=16% Similarity=0.116 Sum_probs=26.5
Q ss_pred hhhhcccChhhHhhhhhc-----chhhhcHHHHHHHHHHHHh
Q 025496 199 GSFLVANDAAERTQSHIS-----GKQHIGYGMVRDFITEYKV 235 (252)
Q Consensus 199 GA~Ls~~D~d~Rl~dH~~-----GK~H~Gy~kIR~~l~eL~~ 235 (252)
-.+|.+.|+=.|...|+. +..+-||..+.+.+..+-+
T Consensus 65 ~~ll~v~D~l~~a~~~~~~~~~~~~~~~g~~~~~~~l~~~L~ 106 (165)
T PF01025_consen 65 KDLLPVLDNLERALEAAKSNEEEESLLEGLEMILKQLEDILE 106 (165)
T ss_dssp HHHHHHHHHHHHHHCC-SHHCTCHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHHHHHH
Confidence 346777777777777763 5778899999888777544
No 94
>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=31.67 E-value=5.6e+02 Score=26.22 Aligned_cols=24 Identities=25% Similarity=0.350 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Q 025496 126 EKSEQLSVLEEKIKNLLEQVETLG 149 (252)
Q Consensus 126 ~~~~~i~~l~~~I~~ll~~aE~LG 149 (252)
...+++.+++.+|..+..+.+.+.
T Consensus 206 ~~~~~~~~le~el~~l~~~~e~l~ 229 (650)
T TIGR03185 206 SILSEIEALEAELKEQSEKYEDLA 229 (650)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566666666666666666543
No 95
>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=30.68 E-value=19 Score=22.44 Aligned_cols=11 Identities=27% Similarity=0.754 Sum_probs=8.8
Q ss_pred cccccccchhh
Q 025496 191 KMALCEICGSF 201 (252)
Q Consensus 191 kl~VCdVCGA~ 201 (252)
.-.+|++||+-
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 45799999983
No 96
>PF11587 Prion_bPrPp: Major prion protein bPrPp - N terminal; PDB: 1SKH_A.
Probab=30.57 E-value=13 Score=23.05 Aligned_cols=23 Identities=35% Similarity=0.436 Sum_probs=20.4
Q ss_pred hhcCCChhHhhhhcccCCCCCCc
Q 025496 40 YMVRFCPHDLFVNTRSDLGPCPR 62 (252)
Q Consensus 40 yL~G~CPhdLF~nTK~DlG~C~k 62 (252)
..+||+---||.-|=+|.|-|.|
T Consensus 4 ~~lgcWilvLfvatwsdvglcKK 26 (29)
T PF11587_consen 4 SHLGCWILVLFVATWSDVGLCKK 26 (29)
T ss_dssp TTTTTHHHHHHHHHHHHHTTSSS
T ss_pred ccccHHHHHHHHHHHhhhccccC
Confidence 35788889999999999999987
No 97
>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=30.45 E-value=20 Score=23.09 Aligned_cols=16 Identities=38% Similarity=0.719 Sum_probs=11.5
Q ss_pred hhccccccccchhhhc
Q 025496 188 QEKKMALCEICGSFLV 203 (252)
Q Consensus 188 ~~qkl~VCdVCGA~Ls 203 (252)
+-+.-.|||+||.-|+
T Consensus 17 pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 17 PPKVEGVCDNCGGELV 32 (36)
T ss_dssp --SSTTBCTTTTEBEB
T ss_pred CCCCCCccCCCCCeeE
Confidence 3456689999998765
No 98
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=30.37 E-value=96 Score=27.07 Aligned_cols=49 Identities=18% Similarity=0.234 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHH
Q 025496 127 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLT 175 (252)
Q Consensus 127 ~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~ 175 (252)
+..+|..|+-+|..+-.++..--..|--.+-..+-.++..++.+++..+
T Consensus 110 ~~~ei~~L~~kI~~L~~~in~~~k~~~n~~i~slk~EL~d~iKe~e~~e 158 (181)
T PF04645_consen 110 IKKEIEILRLKISSLQKEINKNKKKDLNEEIESLKSELNDLIKEREIRE 158 (181)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 4445555555555555554442222211222334444444444444333
No 99
>PRK14139 heat shock protein GrpE; Provisional
Probab=30.24 E-value=3.4e+02 Score=23.73 Aligned_cols=94 Identities=16% Similarity=0.170 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChh
Q 025496 129 EQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAA 208 (252)
Q Consensus 129 ~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d 208 (252)
..+..+..+|..+-+++++|- +.-+.+.++.+.++.-.++-.... .+.-+=.+.-.+|-+.|+=
T Consensus 32 ~e~~~l~~~l~~le~e~~elk-----d~~lR~~AefeN~rKR~~kE~e~~-----------~~~a~~~~~~~LLpv~DnL 95 (185)
T PRK14139 32 DAAPALEAELAEAEAKAAELQ-----DSFLRAKAETENVRRRAQEDVAKA-----------HKFAIESFAESLLPVKDSL 95 (185)
T ss_pred hhHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHhhHHhHH
Confidence 466777888888888888774 666777777777653222111111 0111123455788889988
Q ss_pred hHhhhhhc---chhhhcHHHHHHHHHH-HHhhcc
Q 025496 209 ERTQSHIS---GKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 209 ~Rl~dH~~---GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
.|--.|.. ..++-|+..|.+.+.. |...++
T Consensus 96 erAl~~~~~~~~~l~~Gv~mi~k~l~~vL~k~Gv 129 (185)
T PRK14139 96 EAALADESGDLEKLREGVELTLKQLTSAFEKGRV 129 (185)
T ss_pred HHHHhcccchHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 88655554 4577899888777754 455443
No 100
>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=30.07 E-value=2.5e+02 Score=25.24 Aligned_cols=84 Identities=18% Similarity=0.239 Sum_probs=49.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCC-CCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhh---cCCHHHHH
Q 025496 83 PKFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEP-APPPPISAEKSEQLSVLEEKIKNLLEQVETLGE---AGKVDEAE 158 (252)
Q Consensus 83 ~gYE~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~-~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGe---eG~VdeA~ 158 (252)
..+|.+ +.-|..=+....+++.++..+-..-... ..+..........|..+...|..++.++..+|. .+....-.
T Consensus 48 ~~~e~~-l~~L~~d~~~L~~k~~~~~~~~~~l~~~t~~t~~~a~~L~~~i~~l~~~i~~l~~~~~~l~~~~~~~~~~~l~ 126 (264)
T PF06008_consen 48 DPLEKE-LESLEQDVENLQEKATKVSRKAQQLNNNTERTLQRAQDLEQFIQNLQDNIQELIEQVESLNENGDQLPSEDLQ 126 (264)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccCCCCHHHHH
Confidence 356666 5555666666666666655444321000 011113345667888999999999999999999 33333344
Q ss_pred HHHHHHHHH
Q 025496 159 ALMRKVEIL 167 (252)
Q Consensus 159 ~~~~~~e~L 167 (252)
..+++++.+
T Consensus 127 ~~l~ea~~m 135 (264)
T PF06008_consen 127 RALAEAQRM 135 (264)
T ss_pred HHHHHHHHH
Confidence 444444443
No 101
>KOG2801 consensus Probable Rab-GAPs [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.06 E-value=19 Score=34.28 Aligned_cols=21 Identities=33% Similarity=0.770 Sum_probs=15.4
Q ss_pred ccchhhhcccChhhHhhhhhcchh
Q 025496 196 EICGSFLVANDAAERTQSHISGKQ 219 (252)
Q Consensus 196 dVCGA~Ls~~D~d~Rl~dH~~GK~ 219 (252)
+|||||||..=++ | +.|+||+
T Consensus 402 evcgaylstdwse-r--nkfggkl 422 (559)
T KOG2801|consen 402 EVCGAYLSTDWSE-R--NKFGGKL 422 (559)
T ss_pred HHhhHhcccchhh-h--cccCcee
Confidence 6999999954333 3 6799984
No 102
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=29.82 E-value=22 Score=22.61 Aligned_cols=22 Identities=27% Similarity=0.531 Sum_probs=16.2
Q ss_pred cccccccchhhhcccChhhHhhhhhc
Q 025496 191 KMALCEICGSFLVANDAAERTQSHIS 216 (252)
Q Consensus 191 kl~VCdVCGA~Ls~~D~d~Rl~dH~~ 216 (252)
...+|+.||-.++. .|.|-|+.
T Consensus 3 ~~~~C~nC~R~v~a----~RfA~HLe 24 (33)
T PF08209_consen 3 PYVECPNCGRPVAA----SRFAPHLE 24 (33)
T ss_dssp -EEE-TTTSSEEEG----GGHHHHHH
T ss_pred CeEECCCCcCCcch----hhhHHHHH
Confidence 34789999988765 68999985
No 103
>KOG4809 consensus Rab6 GTPase-interacting protein involved in endosome-to-TGN transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.72 E-value=3.8e+02 Score=27.70 Aligned_cols=125 Identities=14% Similarity=0.253 Sum_probs=70.0
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q 025496 97 VMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQ 176 (252)
Q Consensus 97 i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~ 176 (252)
+.++++...+|++++... ...++..+.|..++..|+..-.+.-.. +..|++-..++++|+.+|.-+...-.
T Consensus 396 c~kme~qLkkAh~~~dda-------r~~pe~~d~i~~le~e~~~y~de~~ka--qaevdrlLeilkeveneKnDkdkkia 466 (654)
T KOG4809|consen 396 CSKMEAQLKKAHNIEDDA-------RMNPEFADQIKQLEKEASYYRDECGKA--QAEVDRLLEILKEVENEKNDKDKKIA 466 (654)
T ss_pred HHHHHHHHHHHHHhhHhh-------hcChhhHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHhhhccccchhh
Confidence 456677777777777432 133455577777777777655444332 23589999999999999865443322
Q ss_pred hhh---hhhhhhhh--hhccccccccchhhhcccChhhHhhhhhcchhhhcHHHHHHHHHHHHh
Q 025496 177 QSQ---NDKVLMMA--QEKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKV 235 (252)
Q Consensus 177 ~~~---~~~~~~~~--~~qkl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL~~ 235 (252)
++. .+.|...+ .++. ++=--=.|.+++ ..-+|-+.|..--+|+- |++.+.+|..
T Consensus 467 eler~~kdqnkkvaNlkHk~-q~Ekkk~aq~le-e~rrred~~~d~sqhlq---~eel~~alek 525 (654)
T KOG4809|consen 467 ELERHMKDQNKKVANLKHKQ-QLEKKKNAQLLE-EVRRREDSMADNSQHLQ---IEELMNALEK 525 (654)
T ss_pred hcCchhhhhhhHHhhHHHHH-HHHHHHHHHHHH-HHHHHHhhhcchHHHHH---HHHHHHHHHH
Confidence 220 11111111 1110 111111233332 24566788888888875 7887777765
No 104
>PRK14161 heat shock protein GrpE; Provisional
Probab=29.52 E-value=3.5e+02 Score=23.39 Aligned_cols=93 Identities=15% Similarity=0.224 Sum_probs=54.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChhh
Q 025496 130 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAE 209 (252)
Q Consensus 130 ~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~ 209 (252)
-+....++|..+-++++++- +.-+.+.++.+.++.--++-... ..+.-+=.+...+|-+.|+=.
T Consensus 20 ~~~~~~~ei~~l~~e~~elk-----d~~lR~~AefeN~rkR~~ke~~~-----------~~~~a~~~~~~~LLpv~Dnle 83 (178)
T PRK14161 20 IVETANPEITALKAEIEELK-----DKLIRTTAEIDNTRKRLEKARDE-----------AKDYAIATFAKELLNVSDNLS 83 (178)
T ss_pred hhhhhHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHhhHHhHHH
Confidence 34455556666666666653 55566666666665322111111 111223346778899999999
Q ss_pred Hhhhhhc-------chhhhcHHHHHHHHHH-HHhhcc
Q 025496 210 RTQSHIS-------GKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 210 Rl~dH~~-------GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
|--.|.. ....-|+..|.+.+.. |...|+
T Consensus 84 rAl~~~~~~~~~~~~~~~~Gv~mi~k~l~~vL~~~Gv 120 (178)
T PRK14161 84 RALAHKPANSDVEVTNIIAGVQMTKDELDKVFHKHHI 120 (178)
T ss_pred HHHhcCccccchhHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 9666654 3577888888666555 566554
No 105
>PLN02678 seryl-tRNA synthetase
Probab=29.45 E-value=1.7e+02 Score=29.05 Aligned_cols=19 Identities=21% Similarity=0.179 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q 025496 158 EALMRKVEILNVEKTTLTQ 176 (252)
Q Consensus 158 ~~~~~~~e~Lk~ek~~l~~ 176 (252)
..+.+++..|+++...++.
T Consensus 74 ~~l~~~~~~Lk~ei~~le~ 92 (448)
T PLN02678 74 TELIAETKELKKEITEKEA 92 (448)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444443
No 106
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=29.44 E-value=1.7e+02 Score=28.60 Aligned_cols=17 Identities=29% Similarity=0.350 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHHHHh
Q 025496 160 LMRKVEILNVEKTTLTQ 176 (252)
Q Consensus 160 ~~~~~e~Lk~ek~~l~~ 176 (252)
+.+++..++++.+.+++
T Consensus 71 l~~~~~~l~~~~~~~~~ 87 (425)
T PRK05431 71 LIAEVKELKEEIKALEA 87 (425)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 44444444444444443
No 107
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=29.30 E-value=1.8e+02 Score=22.37 Aligned_cols=36 Identities=17% Similarity=0.269 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHH
Q 025496 133 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 168 (252)
Q Consensus 133 ~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk 168 (252)
..-..|...+.+++.+.++|+.++|..++..+..+-
T Consensus 23 ~~kS~~kT~iKk~~~ai~~~~~~~a~~~~~~a~s~i 58 (88)
T PRK00239 23 SRKSRVRTAIKKVEAAIAAGDKEAAEEALKAAQSKI 58 (88)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 445566677788888888899999999998887764
No 108
>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=29.28 E-value=3.1e+02 Score=24.19 Aligned_cols=80 Identities=18% Similarity=0.248 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHH
Q 025496 89 LAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 168 (252)
Q Consensus 89 ~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk 168 (252)
+...|+.++..+++.+...++.++.-. ..-.........+|..|+.+-..++.+.=+++ -.+..+-.++..++
T Consensus 137 ~n~~Le~~~~~le~~l~~~k~~ie~vN--~~RK~~Q~~~~~~L~~Le~~W~~~v~kn~eie-----~a~~~Le~ei~~l~ 209 (221)
T PF05700_consen 137 HNEQLEAMLKRLEKELAKLKKEIEEVN--RERKRRQEEAGEELRYLEQRWKELVSKNLEIE-----VACEELEQEIEQLK 209 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHH
Confidence 345566666666666666666554211 00000011233566677777777766666554 33455556666666
Q ss_pred HHHHHHH
Q 025496 169 VEKTTLT 175 (252)
Q Consensus 169 ~ek~~l~ 175 (252)
.+..+++
T Consensus 210 ~~~~~~~ 216 (221)
T PF05700_consen 210 RKAAELK 216 (221)
T ss_pred HHHHHHh
Confidence 5555444
No 109
>PRK14155 heat shock protein GrpE; Provisional
Probab=29.09 E-value=2.6e+02 Score=24.87 Aligned_cols=91 Identities=18% Similarity=0.174 Sum_probs=54.7
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChhhHh
Q 025496 132 SVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERT 211 (252)
Q Consensus 132 ~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~Rl 211 (252)
.++..+|..+-++++++- +.-+.+.++.+.++.--++-.+.. .+.-+=.++-.+|-+.|+=.|-
T Consensus 16 ~~l~~~l~~le~e~~elk-----d~~lR~~AefeN~RKR~~kE~e~~-----------~~~a~~~~~~~LLpV~DnLerA 79 (208)
T PRK14155 16 DDAAQEIEALKAEVAALK-----DQALRYAAEAENTKRRAEREMNDA-----------RAYAIQKFARDLLGAADNLGRA 79 (208)
T ss_pred cchHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHhhHHhhHHHH
Confidence 455555666666666653 556777777777753222111111 1112224667889999999997
Q ss_pred hhhhc--------chhhhcHHHHHHHHHH-HHhhcc
Q 025496 212 QSHIS--------GKQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 212 ~dH~~--------GK~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
-.|.. ..++-|+..|++.+.. |...++
T Consensus 80 l~~~~~~~~~~~~~~i~~Gvemi~k~~~~~L~k~GV 115 (208)
T PRK14155 80 TAASPKDSADPAVKNFIIGVEMTEKELLGAFERNGL 115 (208)
T ss_pred HhcccccccchHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 77764 3578899998777655 444443
No 110
>smart00746 TRASH metallochaperone-like domain.
Probab=28.99 E-value=12 Score=21.54 Aligned_cols=11 Identities=27% Similarity=0.815 Sum_probs=8.5
Q ss_pred cccchhhhccc
Q 025496 195 CEICGSFLVAN 205 (252)
Q Consensus 195 CdVCGA~Ls~~ 205 (252)
|++||..+...
T Consensus 1 c~~C~~~~~~~ 11 (39)
T smart00746 1 CSFCGKDIYNP 11 (39)
T ss_pred CCCCCCCccCC
Confidence 88999887643
No 111
>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=28.82 E-value=20 Score=25.49 Aligned_cols=10 Identities=40% Similarity=1.006 Sum_probs=3.3
Q ss_pred ccccccchhh
Q 025496 192 MALCEICGSF 201 (252)
Q Consensus 192 l~VCdVCGA~ 201 (252)
-.||++|||-
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 3799999985
No 112
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=28.18 E-value=23 Score=31.72 Aligned_cols=25 Identities=28% Similarity=0.696 Sum_probs=19.8
Q ss_pred CCCCCcchh-hcCCChhHhhhhcccCCCCCCcccc
Q 025496 32 DDKEVCPFY-MVRFCPHDLFVNTRSDLGPCPRIHD 65 (252)
Q Consensus 32 ~D~~VCk~y-L~G~CPhdLF~nTK~DlG~C~kiHd 65 (252)
+.|+|||.| +.|.|-|. ..|.-+|+
T Consensus 139 ~qpdVCKdyk~TGYCGYG---------DsCKflH~ 164 (259)
T COG5152 139 TQPDVCKDYKETGYCGYG---------DSCKFLHD 164 (259)
T ss_pred cCcccccchhhcccccCC---------chhhhhhh
Confidence 379999965 78999653 58999997
No 113
>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=28.04 E-value=3.8e+02 Score=22.79 Aligned_cols=18 Identities=17% Similarity=0.313 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 025496 161 MRKVEILNVEKTTLTQQS 178 (252)
Q Consensus 161 ~~~~e~Lk~ek~~l~~~~ 178 (252)
-.+++.||.+.+.+.++|
T Consensus 174 ~~~~~~LkkQ~~~l~~ey 191 (192)
T PF05529_consen 174 EKEIEALKKQSEGLQKEY 191 (192)
T ss_pred HHHHHHHHHHHHHHHhhc
Confidence 344555555555555443
No 114
>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=27.86 E-value=3.6e+02 Score=22.47 Aligned_cols=65 Identities=26% Similarity=0.382 Sum_probs=49.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 025496 84 KFEAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGK 153 (252)
Q Consensus 84 gYE~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~ 153 (252)
.++.+ +.-|+.=+.++...+......|..-. ..+...+....|..+..+|..+-.+.+.|...+.
T Consensus 76 ~ld~e-i~~L~~el~~l~~~~k~l~~eL~~L~----~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~ 140 (169)
T PF07106_consen 76 ELDAE-IKELREELAELKKEVKSLEAELASLS----SEPTNEELREEIEELEEEIEELEEKLEKLRSGSK 140 (169)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHh----cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 44555 66777777778888888777776433 2335678889999999999999999999988443
No 115
>PRK14156 heat shock protein GrpE; Provisional
Probab=27.69 E-value=3e+02 Score=23.87 Aligned_cols=91 Identities=12% Similarity=0.096 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChhhHhhh
Q 025496 134 LEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAERTQS 213 (252)
Q Consensus 134 l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~Rl~d 213 (252)
+..+|..+-+++++|. +.-+.+.++.+.++.-..+-.... .+.-.=.++-.+|-+.|+=.|--.
T Consensus 32 ~~~~l~~l~~e~~elk-----d~~lR~~AEfeN~rKR~~rE~e~~-----------~~~a~~~~~~~LLpVlDnLerAl~ 95 (177)
T PRK14156 32 EKSELELANERADEFE-----NKYLRAHAEMQNIQRRANEERQQL-----------QRYRSQDLAKAILPSLDNLERALA 95 (177)
T ss_pred cHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHhhHHhHHHHHHh
Confidence 4455555556666654 455666666666652221111111 111222466788999999988655
Q ss_pred hhc--chhhhcHHHHHHHH-HHHHhhccch
Q 025496 214 HIS--GKQHIGYGMVRDFI-TEYKVCQLFI 240 (252)
Q Consensus 214 H~~--GK~H~Gy~kIR~~l-~eL~~~~~~~ 240 (252)
|.. +.++-|+..|++.+ +-|...|+..
T Consensus 96 ~~~~~~~l~~Gv~mi~k~l~~~L~~~GV~~ 125 (177)
T PRK14156 96 VEGLTDDVKKGLEMVQESLIQALKEEGVEE 125 (177)
T ss_pred CcccchhHHHHHHHHHHHHHHHHHHCCCee
Confidence 543 34788999998777 5566666543
No 116
>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=27.56 E-value=82 Score=17.63 Aligned_cols=22 Identities=14% Similarity=0.280 Sum_probs=17.6
Q ss_pred HHHhhhcCCHHHHHHHHHHHHH
Q 025496 145 VETLGEAGKVDEAEALMRKVEI 166 (252)
Q Consensus 145 aE~LGeeG~VdeA~~~~~~~e~ 166 (252)
+..++..|++++|..+..+..+
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 7 ISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHccchHHHHHHHHHHHhH
Confidence 4678889999999998877643
No 117
>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=27.38 E-value=2.6e+02 Score=20.68 Aligned_cols=18 Identities=44% Similarity=0.617 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 025496 131 LSVLEEKIKNLLEQVETL 148 (252)
Q Consensus 131 i~~l~~~I~~ll~~aE~L 148 (252)
++.|+.+|+.++..+..|
T Consensus 6 l~~LE~ki~~aveti~~L 23 (72)
T PF06005_consen 6 LEQLEEKIQQAVETIALL 23 (72)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344444444444444433
No 118
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.29 E-value=46 Score=30.46 Aligned_cols=37 Identities=24% Similarity=0.476 Sum_probs=29.0
Q ss_pred hccccccccchhhhcccChhhHhhhhhcchhhhcHHHHHHHHHHHHh
Q 025496 189 EKKMALCEICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKV 235 (252)
Q Consensus 189 ~qkl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL~~ 235 (252)
.-..-||-||.+.+= +.=-.-|..||+| |+.++.|+.
T Consensus 32 ~sgql~C~vCn~piK----p~lW~vHvnsKkH------re~id~lKs 68 (264)
T KOG3032|consen 32 ESGQLVCRVCNVPIK----PSLWDVHVNSKKH------REAIDSLKS 68 (264)
T ss_pred CCCCeeEEEecCccc----HHHHHHHhccHHH------HHHHHHHHh
Confidence 345589999998754 4556789999999 788888883
No 119
>PRK12495 hypothetical protein; Provisional
Probab=26.78 E-value=73 Score=28.85 Aligned_cols=13 Identities=31% Similarity=0.690 Sum_probs=10.5
Q ss_pred ccccccchhhhcc
Q 025496 192 MALCEICGSFLVA 204 (252)
Q Consensus 192 l~VCdVCGA~Ls~ 204 (252)
.+.|++||..|-.
T Consensus 42 a~hC~~CG~PIpa 54 (226)
T PRK12495 42 NAHCDECGDPIFR 54 (226)
T ss_pred hhhcccccCcccC
Confidence 3899999998873
No 120
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=26.77 E-value=4e+02 Score=22.62 Aligned_cols=84 Identities=19% Similarity=0.162 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH--------Hhhhhc--cCCCCCCCCc----hHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 025496 87 AELAQFCEKLVMDLDRRVRRGR--------ERLSQE--VEPAPPPPIS----AEKSEQLSVLEEKIKNLLEQVETLGEAG 152 (252)
Q Consensus 87 ~e~~~~L~~~i~d~drkI~~~k--------~RL~~~--~~~~~~~~~~----~~~~~~i~~l~~~I~~ll~~aE~LGeeG 152 (252)
.+++..+...++++-.||..-- +=++.. .+.+. .... ..+.+....+...+-+.+.-++++|..|
T Consensus 54 ee~y~el~~~~DeiAERi~~LGg~p~~t~~~~~~~s~ike~~~-~~~~~~~l~~l~~~~~~l~~~~r~~~~~a~e~gD~~ 132 (156)
T COG0783 54 EELYEELAEHVDEIAERIRALGGVPLGTLSEYLKLSSIKEEPG-DYTAREMLKELVEDYEYLIKELRKGIELADEAGDEV 132 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCcccHHHHHHhCCCcccCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCChh
Confidence 3567788888999988886421 111111 11111 1111 1233444455666666667777777777
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q 025496 153 KVDEAEALMRKVEILNVEK 171 (252)
Q Consensus 153 ~VdeA~~~~~~~e~Lk~ek 171 (252)
=.+-....+...|+...-.
T Consensus 133 Tadl~~~~~~~~EK~~Wml 151 (156)
T COG0783 133 TADLLTDIIRELEKTLWML 151 (156)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 7777777777777765443
No 121
>PF09543 DUF2379: Protein of unknown function (DUF2379); InterPro: IPR011753 This family consists of at least 7 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown.
Probab=26.72 E-value=2.1e+02 Score=23.55 Aligned_cols=40 Identities=25% Similarity=0.346 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHH
Q 025496 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKV 164 (252)
Q Consensus 125 ~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~ 164 (252)
.++...|.+=+.++...+-.+-.+-+.|++|.|-..|..+
T Consensus 61 ~ei~rRIr~GS~RL~~al~r~~~~~daGD~dgARq~m~dv 100 (121)
T PF09543_consen 61 REIRRRIRDGSRRLSRALHRMYRLRDAGDLDGARQEMRDV 100 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccCHHHHHHHHHHH
Confidence 4566777777888888888899999999999999887765
No 122
>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=26.58 E-value=23 Score=23.04 Aligned_cols=13 Identities=38% Similarity=0.718 Sum_probs=10.7
Q ss_pred cccccchhhhccc
Q 025496 193 ALCEICGSFLVAN 205 (252)
Q Consensus 193 ~VCdVCGA~Ls~~ 205 (252)
+.|+.||+.|+.-
T Consensus 2 ~~CP~Cg~~lv~r 14 (39)
T PF01396_consen 2 EKCPKCGGPLVLR 14 (39)
T ss_pred cCCCCCCceeEEE
Confidence 5799999988764
No 123
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=26.43 E-value=4.9e+02 Score=26.73 Aligned_cols=110 Identities=21% Similarity=0.180 Sum_probs=58.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHH---------HHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhcccccc
Q 025496 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEA---------EALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALC 195 (252)
Q Consensus 125 ~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA---------~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VC 195 (252)
.+..+++..++++|+.+.+-.|.=.+.+++-+. .+.-..-+.|+.+.+.+...|.-+.+-.. ..++.
T Consensus 277 d~aeeel~~I~e~ie~lYd~lE~EveA~~~V~~~~~~l~~~l~k~ke~n~~L~~Eie~V~~sY~l~e~e~~-~vr~~--- 352 (570)
T COG4477 277 DEAEEELGLIQEKIESLYDLLEREVEAKNVVEENLPILPDYLEKAKENNEHLKEEIERVKESYRLAETELG-SVRKF--- 352 (570)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHHHhccChhHHH-HHHHH---
Confidence 344577888888888888888876666655433 22223334466666666665521111000 11110
Q ss_pred ccchhhhcccChhhHhhhhhcchhhhcHHHHHHHHHHHHhhccchh
Q 025496 196 EICGSFLVANDAAERTQSHISGKQHIGYGMVRDFITEYKVCQLFIV 241 (252)
Q Consensus 196 dVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL~~~~~~~~ 241 (252)
+.-|...+..==--.--.+.+|+.|.-++++++++......++
T Consensus 353 ---e~eL~el~~~~~~i~~~~~~~~~~yS~lq~~l~~~~~~l~~i~ 395 (570)
T COG4477 353 ---EKELKELESVLDEILENIEAQEVAYSELQDNLEEIEKALTDIE 395 (570)
T ss_pred ---HHHHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHHHh
Confidence 0111111111111123457889999999999888877555444
No 124
>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=26.36 E-value=2.2e+02 Score=27.73 Aligned_cols=21 Identities=24% Similarity=0.324 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 025496 157 AEALMRKVEILNVEKTTLTQQ 177 (252)
Q Consensus 157 A~~~~~~~e~Lk~ek~~l~~~ 177 (252)
+..+.+++..|+++...++++
T Consensus 71 ~~~l~~~~~~l~~~~~~~~~~ 91 (418)
T TIGR00414 71 IEEIKKELKELKEELTELSAA 91 (418)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555555555443
No 125
>PF05852 DUF848: Gammaherpesvirus protein of unknown function (DUF848); InterPro: IPR008566 This family consists of several uncharacterised proteins from the Gammaherpesvirinae.
Probab=26.17 E-value=2.6e+02 Score=23.69 Aligned_cols=51 Identities=27% Similarity=0.320 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh--hcCCHHHHHHHHHHHHHHHHHHHHHHh
Q 025496 126 EKSEQLSVLEEKIKNLLEQVETLG--EAGKVDEAEALMRKVEILNVEKTTLTQ 176 (252)
Q Consensus 126 ~~~~~i~~l~~~I~~ll~~aE~LG--eeG~VdeA~~~~~~~e~Lk~ek~~l~~ 176 (252)
.....|..++..|.....+...|- .-.+|+.+.++...++.|+++.+.--.
T Consensus 58 ~~~~~v~~~~~~i~~k~~El~~L~~~d~~kv~~~E~L~d~v~eLkeel~~el~ 110 (146)
T PF05852_consen 58 EIKNKVSSLETEISEKKKELSHLKKFDRKKVEDLEKLTDRVEELKEELEFELE 110 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677788888888888887764 457899999999999999877654443
No 126
>PF11945 WASH_WAHD: WAHD domain of WASH complex; InterPro: IPR021854 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. This entry represents the WASH subunit of the WASH complex. WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires probably vary extensively among individuals []. It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7 transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene.
Probab=26.02 E-value=2.1e+02 Score=26.86 Aligned_cols=48 Identities=21% Similarity=0.411 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 87 AELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGE 150 (252)
Q Consensus 87 ~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGe 150 (252)
.+.|++|.+.++++=.||.. |++ ...++|..|+.+|...-+++++|..
T Consensus 24 ~~aL~~L~~v~~diF~rI~~---Rv~-------------~~~~~l~~i~~Ri~~~qaKi~~l~g 71 (297)
T PF11945_consen 24 ADALEYLDKVSNDIFSRISA---RVE-------------RNRERLQAIQQRIEVAQAKIEKLQG 71 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHH-------------HHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 46778888888888777754 332 2235667777777777777777643
No 127
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.01 E-value=27 Score=28.88 Aligned_cols=19 Identities=32% Similarity=0.550 Sum_probs=16.2
Q ss_pred cccccchhhhcccChhhHh
Q 025496 193 ALCEICGSFLVANDAAERT 211 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl 211 (252)
.+|+.||+-|...||..-+
T Consensus 124 f~Cp~Cg~~l~~~dn~~~~ 142 (147)
T smart00531 124 FTCPRCGEELEEDDNSEPI 142 (147)
T ss_pred EECCCCCCEEEEcCchhhH
Confidence 8999999999999886543
No 128
>PF12907 zf-met2: Zinc-binding
Probab=26.00 E-value=33 Score=22.78 Aligned_cols=26 Identities=19% Similarity=0.529 Sum_probs=18.9
Q ss_pred cccccchhhhcccChhhHhhhhhcch
Q 025496 193 ALCEICGSFLVANDAAERTQSHISGK 218 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl~dH~~GK 218 (252)
.+|.||=.-....-+..-|.+|+..|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enK 27 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENK 27 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHcc
Confidence 47999985444454666799999876
No 129
>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=25.93 E-value=2.4e+02 Score=19.91 Aligned_cols=51 Identities=22% Similarity=0.299 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 127 KSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (252)
Q Consensus 127 ~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~ 178 (252)
....|.....+|+.+...+..|. ...-..+..+...++.|......+....
T Consensus 46 ~~~ei~~~~~~l~~l~~~~~~L~-~~~~~~~~~i~~~~~~l~~~w~~l~~~~ 96 (105)
T PF00435_consen 46 LQEEIESRQERLESLNEQAQQLI-DSGPEDSDEIQEKLEELNQRWEALCELV 96 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH-HTTHTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhHHHHHHHHHHHHHHHHHHHH-HcCCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566677777778888888884 3336667777888888877777776544
No 130
>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=25.83 E-value=2.2e+02 Score=26.66 Aligned_cols=23 Identities=13% Similarity=0.378 Sum_probs=0.0
Q ss_pred CCCCccccHHHHHHhhcCCCCCC
Q 025496 58 GPCPRIHDQKLKESFEKSPRHDA 80 (252)
Q Consensus 58 G~C~kiHde~lk~~Ye~~~~~~~ 80 (252)
..|...=-+.++.+|+.+.+..+
T Consensus 4 ~eC~~~l~~~l~~~~~~~~~E~~ 26 (314)
T PF04111_consen 4 QECTDLLLEQLDKQLEQAEKERD 26 (314)
T ss_dssp -----------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666666788888877754444
No 131
>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=25.74 E-value=2.9e+02 Score=20.67 Aligned_cols=71 Identities=24% Similarity=0.276 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhhc----cCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHH
Q 025496 93 CEKLVMDLDRRVRRGRERLSQE----VEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEIL 167 (252)
Q Consensus 93 L~~~i~d~drkI~~~k~RL~~~----~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~L 167 (252)
.-..|+++|.++......+... .......+.++ .+...+-.+|...+.++..++++ +|.-|......|+.-
T Consensus 20 ~l~~irelD~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~I~~~~~~~~~l~de-Kv~lA~~~~d~v~~h 94 (105)
T PF12998_consen 20 NLTLIRELDAKSQDLLEELDQQIQKFIKNHGSPSLSP---EKRRELLKEIQEEYERALELSDE-KVALAQQAYDLVDRH 94 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTS--S-H---HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHhhcccccCCh---HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 3356777777766666555432 11111001111 25566777888888888888754 355555555554443
No 132
>PRK06424 transcription factor; Provisional
Probab=25.59 E-value=26 Score=29.39 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=4.3
Q ss_pred cccccchhh
Q 025496 193 ALCEICGSF 201 (252)
Q Consensus 193 ~VCdVCGA~ 201 (252)
.||+-|.-|
T Consensus 24 ~vC~~Ca~~ 32 (144)
T PRK06424 24 NVCDDCAKF 32 (144)
T ss_pred ehhHHHHHc
Confidence 455555433
No 133
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=25.49 E-value=2.3e+02 Score=21.76 Aligned_cols=36 Identities=19% Similarity=0.253 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHH
Q 025496 133 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILN 168 (252)
Q Consensus 133 ~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk 168 (252)
..-..|...+.+.+.+.++|+.++|..++.++...=
T Consensus 23 ~~kS~~kT~iKk~~~ai~~~d~~~a~~~l~~a~s~i 58 (87)
T TIGR00029 23 SQKSKMKTIIKKVYAAIAAGDKDKAQEAFKEAAKKL 58 (87)
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 445566777888888899999999999988877653
No 134
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=25.40 E-value=25 Score=24.98 Aligned_cols=11 Identities=36% Similarity=1.032 Sum_probs=6.1
Q ss_pred cccccccchhh
Q 025496 191 KMALCEICGSF 201 (252)
Q Consensus 191 kl~VCdVCGA~ 201 (252)
+|++|+.||.|
T Consensus 4 ~mr~C~~CgvY 14 (56)
T PRK13130 4 KIRKCPKCGVY 14 (56)
T ss_pred cceECCCCCCE
Confidence 45555555554
No 135
>PRK14153 heat shock protein GrpE; Provisional
Probab=25.26 E-value=2.8e+02 Score=24.43 Aligned_cols=99 Identities=15% Similarity=0.137 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccChhhH
Q 025496 131 LSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDAAER 210 (252)
Q Consensus 131 i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~d~R 210 (252)
+..++.+|..+-+++++|- +.-+.+.++.+.++.-.+.-.... .+.-+=.+.-.+|-+.|+=.|
T Consensus 35 ~~~~~~ei~~l~~e~~elk-----d~~lR~~AEfeN~rKR~~kE~e~~-----------~~~a~~~~~~~LLpv~DnLer 98 (194)
T PRK14153 35 DSTADSETEKCREEIESLK-----EQLFRLAAEFDNFRKRTAREMEEN-----------RKFVLEQVLLDLLEVTDNFER 98 (194)
T ss_pred cccchHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHhhHHhHHHH
Confidence 4566667777777777664 555666777777653322111111 011112456788999999999
Q ss_pred hhhhhc-----chhhhcHHHHHHHHHH-HHhhc---cchhhhhh
Q 025496 211 TQSHIS-----GKQHIGYGMVRDFITE-YKVCQ---LFIVDLLF 245 (252)
Q Consensus 211 l~dH~~-----GK~H~Gy~kIR~~l~e-L~~~~---~~~~~~~~ 245 (252)
.-+|.. ..++-|+..|...+.. |...+ +-+.|=.|
T Consensus 99 Al~~~~~~~~~~~l~~Gvemi~k~~~~vL~k~Gv~~I~~~G~~F 142 (194)
T PRK14153 99 ALESARTAEDMNSIVEGIEMVSKQFFSILEKYGLERIECEGEEF 142 (194)
T ss_pred HHhcccccchHHHHHHHHHHHHHHHHHHHHHCCCeeeCCCCCCC
Confidence 766653 3578899888776665 44444 33444444
No 136
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=25.22 E-value=1.8e+02 Score=22.88 Aligned_cols=38 Identities=24% Similarity=0.174 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHH
Q 025496 130 QLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEIL 167 (252)
Q Consensus 130 ~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~L 167 (252)
.+......|...+..+++....++.++|.+.+.+++..
T Consensus 20 ~l~~~~~~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~ 57 (121)
T PF14276_consen 20 YLNNSTDSIEEQLEQIEEAIENEDWEKAYKETEELEKE 57 (121)
T ss_pred hhhhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 44556778888999999999999999999988777765
No 137
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=25.11 E-value=2.9e+02 Score=25.81 Aligned_cols=9 Identities=33% Similarity=0.648 Sum_probs=3.8
Q ss_pred HHHHHHhhc
Q 025496 66 QKLKESFEK 74 (252)
Q Consensus 66 e~lk~~Ye~ 74 (252)
+.|+.+|..
T Consensus 159 ~~L~~D~~~ 167 (325)
T PF08317_consen 159 ELLQEDYAK 167 (325)
T ss_pred HHHHHHHHH
Confidence 344444433
No 138
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=25.01 E-value=5.8e+02 Score=23.97 Aligned_cols=20 Identities=25% Similarity=0.414 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 025496 85 FEAELAQFCEKLVMDLDRRVR 105 (252)
Q Consensus 85 YE~e~~~~L~~~i~d~drkI~ 105 (252)
|||.. ..|+.+...+++.+.
T Consensus 135 YeWR~-kllegLk~~L~~~~~ 154 (312)
T smart00787 135 YEWRM-KLLEGLKEGLDENLE 154 (312)
T ss_pred HHHHH-HHHHHHHHHHHHHHH
Confidence 88764 346666666665543
No 139
>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=24.62 E-value=2.1e+02 Score=26.01 Aligned_cols=81 Identities=19% Similarity=0.239 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHH
Q 025496 88 ELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEIL 167 (252)
Q Consensus 88 e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~L 167 (252)
.+++.+.+-|.-.-.|.+...+....... .........+.++|..+-.++..+-.+-+.=.++.-+.++..+-.+-+.|
T Consensus 90 ~~i~d~drrI~~~k~RL~~~~~~~~~~~~-~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l 168 (254)
T PF03194_consen 90 RLIRDCDRRIERAKERLEQTQEEQAKEAD-EEKAEKIDELDEKIGELLKEAEELGEEGDVDEAQKLMEEVEKLKEEKEEL 168 (254)
T ss_pred HHHHHHHHHHHHHHHHHHhCccccccchh-hhHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444454444555444433322110 00122445566777777777766655444444444456666666666665
Q ss_pred HH
Q 025496 168 NV 169 (252)
Q Consensus 168 k~ 169 (252)
..
T Consensus 169 e~ 170 (254)
T PF03194_consen 169 EK 170 (254)
T ss_pred Hh
Confidence 55
No 140
>PRK11637 AmiB activator; Provisional
Probab=24.60 E-value=6.4e+02 Score=24.27 Aligned_cols=19 Identities=16% Similarity=0.354 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 025496 129 EQLSVLEEKIKNLLEQVET 147 (252)
Q Consensus 129 ~~i~~l~~~I~~ll~~aE~ 147 (252)
.+|..++.+|..+-.+++.
T Consensus 89 ~~i~~~~~~i~~~~~ei~~ 107 (428)
T PRK11637 89 RKLRETQNTLNQLNKQIDE 107 (428)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444444433333
No 141
>PRK14140 heat shock protein GrpE; Provisional
Probab=24.52 E-value=4.6e+02 Score=22.98 Aligned_cols=95 Identities=20% Similarity=0.154 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhccccccccchhhhcccCh
Q 025496 128 SEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALCEICGSFLVANDA 207 (252)
Q Consensus 128 ~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VCdVCGA~Ls~~D~ 207 (252)
.+.|.++..+|..+-+++.+|- +.-..+.++.+.++.-.++-... ..+.-+=.+...+|-+.|+
T Consensus 36 ~~~~~~l~~~i~~l~~ei~elk-----d~~lR~~Ae~eN~rkR~~rE~~~-----------~~~~a~~~~~~~LLpvlDn 99 (191)
T PRK14140 36 AELLDEEQAKIAELEAKLDELE-----ERYLRLQADFENYKRRIQKENEA-----------AEKYRAQSLASDLLPALDN 99 (191)
T ss_pred hhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHH
Confidence 4567777888887777777763 44555666666654222111111 1122233467788999999
Q ss_pred hhHhhhhhcc-----hhhhcHHHHHHHHHH-HHhhcc
Q 025496 208 AERTQSHISG-----KQHIGYGMVRDFITE-YKVCQL 238 (252)
Q Consensus 208 d~Rl~dH~~G-----K~H~Gy~kIR~~l~e-L~~~~~ 238 (252)
=.|.-.|... .+.-|+..|.+.+.. |...|+
T Consensus 100 LerAl~~~~~~~~~~~i~~Gv~mi~k~l~~~L~k~GV 136 (191)
T PRK14140 100 FERALQIEADDEQTKSLLKGVEMVHRQLLEALKKEGV 136 (191)
T ss_pred HHHHHhccCccchHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 9997666543 356788888777665 444443
No 142
>PF13647 Glyco_hydro_80: Glycosyl hydrolase family 80 of chitosanase A
Probab=24.38 E-value=32 Score=30.82 Aligned_cols=51 Identities=27% Similarity=0.376 Sum_probs=39.6
Q ss_pred cccccchhhhcccChhhH--hhhhhcchhhhcHHHHHHHHHHHHhhcc------chhhhhhh
Q 025496 193 ALCEICGSFLVANDAAER--TQSHISGKQHIGYGMVRDFITEYKVCQL------FIVDLLFQ 246 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~R--l~dH~~GK~H~Gy~kIR~~l~eL~~~~~------~~~~~~~~ 246 (252)
-.-.||||+.|..|+.+- +-.|+ .|+.--++--.|+.|+..+. -|+|+-||
T Consensus 147 altkic~alqs~fd~~q~~yvmshy---ahid~dkl~pvl~alk~~gft~f~~ynlvglafq 205 (308)
T PF13647_consen 147 ALTKICQALQSDFDNQQDQYVMSHY---AHIDQDKLVPVLNALKKIGFTSFDQYNLVGLAFQ 205 (308)
T ss_pred HHHHHHHHHHhhhhhhhhHHHHHhh---hhccccchhHHHHHHhhcCcceecccceeeEEEE
Confidence 445799999999998765 67777 48888888888999998663 46777776
No 143
>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins.
Probab=24.25 E-value=1.2e+02 Score=22.60 Aligned_cols=20 Identities=25% Similarity=0.415 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHHHHhh
Q 025496 130 QLSVLEEKIKNLLEQVETLG 149 (252)
Q Consensus 130 ~i~~l~~~I~~ll~~aE~LG 149 (252)
+++.+..+++.++.++..+-
T Consensus 41 ~~~~i~~e~~~ll~~~n~l~ 60 (90)
T PF06103_consen 41 QVDPITKEINDLLHNTNELL 60 (90)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444443
No 144
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=24.02 E-value=19 Score=22.75 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=10.0
Q ss_pred ccccccchhhhcc
Q 025496 192 MALCEICGSFLVA 204 (252)
Q Consensus 192 l~VCdVCGA~Ls~ 204 (252)
+..|.+||+.+++
T Consensus 3 ~~~C~~C~~~~i~ 15 (33)
T PF08792_consen 3 LKKCSKCGGNGIV 15 (33)
T ss_pred ceEcCCCCCCeEE
Confidence 4678888887776
No 145
>PF06751 EutB: Ethanolamine ammonia lyase large subunit (EutB); InterPro: IPR010628 This family consists of several bacterial ethanolamine ammonia lyase large subunit (EutB) proteins. Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia. The enzyme is a heterodimer composed of subunits of Mr approximately 55,000 (EutB) and 35,000 (EutC) [].; GO: 0008851 ethanolamine ammonia-lyase activity, 0006520 cellular amino acid metabolic process; PDB: 3ABQ_C 3ABS_C 3AO0_A 3ABR_A 3ABO_C 3ANY_A 2QEZ_B.
Probab=24.01 E-value=27 Score=34.36 Aligned_cols=30 Identities=20% Similarity=0.281 Sum_probs=18.3
Q ss_pred cccccccchhh--hcccChhh--H--hhhhhcchhh
Q 025496 191 KMALCEICGSF--LVANDAAE--R--TQSHISGKQH 220 (252)
Q Consensus 191 kl~VCdVCGA~--Ls~~D~d~--R--l~dH~~GK~H 220 (252)
.+-|=.|-|=+ =-..|..| | |+|||.||+|
T Consensus 311 P~lVNtVvGFIGPEylyd~kQiiRAgLEDhF~GKL~ 346 (444)
T PF06751_consen 311 PFLVNTVVGFIGPEYLYDGKQIIRAGLEDHFMGKLL 346 (444)
T ss_dssp ESEEEEECCCSSTTTSSBCHHHHHHHHHHHHHHHHC
T ss_pred ceeEeecceecccceeeccchheecchHhhhhhhhc
Confidence 34566666631 01345555 3 7999999987
No 146
>PRK12496 hypothetical protein; Provisional
Probab=23.83 E-value=33 Score=29.21 Aligned_cols=13 Identities=46% Similarity=0.958 Sum_probs=9.8
Q ss_pred cccccchhhhccc
Q 025496 193 ALCEICGSFLVAN 205 (252)
Q Consensus 193 ~VCdVCGA~Ls~~ 205 (252)
.+|+|||.-|.+-
T Consensus 144 ~~C~~CG~~~~r~ 156 (164)
T PRK12496 144 DVCEICGSPVKRK 156 (164)
T ss_pred CcCCCCCChhhhc
Confidence 6788998877654
No 147
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=23.81 E-value=3.9e+02 Score=21.47 Aligned_cols=47 Identities=23% Similarity=0.355 Sum_probs=30.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q 025496 125 AEKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQ 176 (252)
Q Consensus 125 ~~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~ 176 (252)
.++-..+..++.+|+.+++++++|- .....++++-..|+.|=+.|..
T Consensus 4 ~elfd~l~~le~~l~~l~~el~~LK-----~~~~el~EEN~~L~iEN~~Lr~ 50 (110)
T PRK13169 4 KEIFDALDDLEQNLGVLLKELGALK-----KQLAELLEENTALRLENDKLRE 50 (110)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH
Confidence 3456778888888888888888876 3444555555555555444433
No 148
>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=23.68 E-value=1.9e+02 Score=20.45 Aligned_cols=33 Identities=39% Similarity=0.521 Sum_probs=20.3
Q ss_pred HHHHHHHHHH-hhhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q 025496 138 IKNLLEQVET-LGEAGKVDEAEALMRKVEILNVEKTTLTQ 176 (252)
Q Consensus 138 I~~ll~~aE~-LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~ 176 (252)
+..+..++|+ |.+.|+|-.| ++.|+.|+.++|.
T Consensus 19 MK~l~~~aeq~L~~~~~i~~a------l~~Lk~EIaklE~ 52 (53)
T PF08898_consen 19 MKALAAQAEQQLAEAGDIAAA------LEKLKAEIAKLEA 52 (53)
T ss_pred HHHHHHHHHHHHccchHHHHH------HHHHHHHHHHHhc
Confidence 3455566665 5666666554 5667777776653
No 149
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=23.58 E-value=1.1e+02 Score=17.52 Aligned_cols=21 Identities=43% Similarity=0.531 Sum_probs=17.1
Q ss_pred HHHHHHhhhcCCHHHHHHHHH
Q 025496 142 LEQVETLGEAGKVDEAEALMR 162 (252)
Q Consensus 142 l~~aE~LGeeG~VdeA~~~~~ 162 (252)
+.-+..+...|+.++|..++.
T Consensus 5 ~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 5 LALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHcCCHHHHHHHHh
Confidence 456778889999999988764
No 150
>KOG4302 consensus Microtubule-associated protein essential for anaphase spindle elongation [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=23.54 E-value=8.8e+02 Score=25.51 Aligned_cols=94 Identities=17% Similarity=0.244 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCC---------HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhcccccc-c
Q 025496 127 KSEQLSVLEEKIKNLLEQVETLGEAGK---------VDEAEALMRKVEILNVEKTTLTQQSQNDKVLMMAQEKKMALC-E 196 (252)
Q Consensus 127 ~~~~i~~l~~~I~~ll~~aE~LGeeG~---------VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~~~~~~~~qkl~VC-d 196 (252)
+...|..++.+++.+....-..---|. ++.=..+...++.|+.++.+..+++ .. -.+|..++| +
T Consensus 66 L~~~ia~~eael~~l~s~l~~~~~~~~~~~k~e~tLke~l~~l~~~le~lr~qk~eR~~ef-~e-----l~~qie~l~~~ 139 (660)
T KOG4302|consen 66 LLQEIAVIEAELNDLCSALGEPSIIGEISDKIEGTLKEQLESLKPYLEGLRKQKDERRAEF-KE-----LYHQIEKLCEE 139 (660)
T ss_pred HHHHHHHHHHHHHHHHHHhCCcccccccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHH-HH-----HHHHHHHHHHH
Confidence 334566666666666655544333333 3444556666677766666666554 21 134555778 4
Q ss_pred cchh-----hhcccChhh--HhhhhhcchhhhcHHHH
Q 025496 197 ICGS-----FLVANDAAE--RTQSHISGKQHIGYGMV 226 (252)
Q Consensus 197 VCGA-----~Ls~~D~d~--Rl~dH~~GK~H~Gy~kI 226 (252)
+||- ++++..+|= +--++|.++++.=-...
T Consensus 140 l~g~~~~~~~~~~D~~dlsl~kLeelr~~L~~L~~ek 176 (660)
T KOG4302|consen 140 LGGPEDLPSFLIADESDLSLEKLEELREHLNELQKEK 176 (660)
T ss_pred hcCCccCCcccccCcccccHHHHHHHHHHHHHHHHHH
Confidence 5554 333333221 33467877766543333
No 151
>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=23.31 E-value=2.4e+02 Score=21.41 Aligned_cols=35 Identities=23% Similarity=0.350 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHH
Q 025496 133 VLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEIL 167 (252)
Q Consensus 133 ~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~L 167 (252)
.....|-..+.+++.+.+.|+-++|+.++..+...
T Consensus 22 ~~kS~~rT~iKk~~~ai~~~~~~~a~~~l~~a~s~ 56 (84)
T PF01649_consen 22 SRKSRVRTAIKKFREAIEAGDKEEAKELLRKAYSA 56 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHH
Confidence 45567778889999999999999999998888765
No 152
>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=23.13 E-value=4.5e+02 Score=22.01 Aligned_cols=64 Identities=20% Similarity=0.216 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCC-CCCCCchHHHHHHHHHHHHHHHHHHHHHHhh
Q 025496 86 EAELAQFCEKLVMDLDRRVRRGRERLSQEVEPA-PPPPISAEKSEQLSVLEEKIKNLLEQVETLG 149 (252)
Q Consensus 86 E~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~-~~~~~~~~~~~~i~~l~~~I~~ll~~aE~LG 149 (252)
....+..+..-+.+.+.++......+....+.. ..........+++..+++.+..+.++...+-
T Consensus 86 ~~~~l~~l~~el~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~e~~~l~ 150 (191)
T PF04156_consen 86 LQQQLQQLQEELDQLQERIQELESELEKLKEDLQELRELLKSVEERLDSLDESIKELEKEIRELQ 150 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555566666667777777666664321110 0011233566788899999999999998887
No 153
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=23.12 E-value=92 Score=20.25 Aligned_cols=12 Identities=33% Similarity=1.187 Sum_probs=5.6
Q ss_pred ccccccccchhh
Q 025496 190 KKMALCEICGSF 201 (252)
Q Consensus 190 qkl~VCdVCGA~ 201 (252)
.+...|.+||.+
T Consensus 15 ~~i~~C~~C~nl 26 (41)
T PF02132_consen 15 ENIKFCSICGNL 26 (41)
T ss_dssp HH-EE-SSS--E
T ss_pred HcCCccCCCCCc
Confidence 456778888865
No 154
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=22.90 E-value=30 Score=32.12 Aligned_cols=9 Identities=44% Similarity=1.169 Sum_probs=7.9
Q ss_pred cccccchhh
Q 025496 193 ALCEICGSF 201 (252)
Q Consensus 193 ~VCdVCGA~ 201 (252)
.||++|||-
T Consensus 269 YVCPiCGAT 277 (318)
T KOG4602|consen 269 YVCPICGAT 277 (318)
T ss_pred hcCcccccc
Confidence 799999984
No 155
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.72 E-value=35 Score=33.08 Aligned_cols=31 Identities=26% Similarity=0.488 Sum_probs=23.8
Q ss_pred ccccccchhhhcccChhhHhhhhhcchhhhcHHH
Q 025496 192 MALCEICGSFLVANDAAERTQSHISGKQHIGYGM 225 (252)
Q Consensus 192 l~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~Gy~k 225 (252)
-.-|++||.+.+.. .=...|+.||.|.-=.+
T Consensus 238 ~~YC~~C~r~f~~~---~VFe~Hl~gK~H~k~~~ 268 (470)
T COG5188 238 KVYCVKCGREFSRS---KVFEYHLEGKRHCKEGQ 268 (470)
T ss_pred ceeeHhhhhHhhhh---HHHHHHHhhhhhhhhhh
Confidence 36799999998753 44678999999975433
No 156
>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]
Probab=22.62 E-value=7.1e+02 Score=27.68 Aligned_cols=28 Identities=21% Similarity=0.221 Sum_probs=13.7
Q ss_pred hhhcHHHHHHHHHHHHhhc--cchhhhhhh
Q 025496 219 QHIGYGMVRDFITEYKVCQ--LFIVDLLFQ 246 (252)
Q Consensus 219 ~H~Gy~kIR~~l~eL~~~~--~~~~~~~~~ 246 (252)
-|.-=.-+|.....++--+ +.+..+.|-
T Consensus 529 sh~D~~~Lr~i~~~~~~~~~~ptIvvs~~~ 558 (1074)
T KOG0250|consen 529 SHKDARILRAIMRRLKIPGNRPTIVVSSFT 558 (1074)
T ss_pred CHhhHHHHHHHHHHcCCCCCCCcEEEecCC
Confidence 3444445555555554433 555544443
No 157
>KOG0972 consensus Huntingtin interacting protein 1 (Hip1) interactor Hippi [Signal transduction mechanisms]
Probab=22.58 E-value=6.9e+02 Score=23.93 Aligned_cols=12 Identities=8% Similarity=0.191 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHh
Q 025496 224 GMVRDFITEYKV 235 (252)
Q Consensus 224 ~kIR~~l~eL~~ 235 (252)
++||..+..|++
T Consensus 338 vkIkqavsKLk~ 349 (384)
T KOG0972|consen 338 VKIKQAVSKLKE 349 (384)
T ss_pred HHHHHHHHHHHH
Confidence 566666666665
No 158
>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].
Probab=22.50 E-value=5.5e+02 Score=22.80 Aligned_cols=76 Identities=17% Similarity=0.185 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhh-hhhhhhhccccccccchhhhcc
Q 025496 126 EKSEQLSVLEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKTTLTQQSQNDK-VLMMAQEKKMALCEICGSFLVA 204 (252)
Q Consensus 126 ~~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~~~~~-~~~~~~~qkl~VCdVCGA~Ls~ 204 (252)
+...-|.+++..|..++.+.+.- ....-.++..+..+++.+...+ .+. .+++
T Consensus 41 ~m~~i~~e~Ek~i~~~i~e~~~~--------~~~~~~~i~~~~~erdq~~~dL-~s~E~sfs------------------ 93 (207)
T PF05010_consen 41 EMRKIMEEYEKTIAQMIEEKQKQ--------KELSEAEIQKLLKERDQAYADL-NSLEKSFS------------------ 93 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhh--------HHhHHHHHHHHHhhHHHHHHHH-HHHHhhHH------------------
Confidence 34456677777777777775553 1222344555555665555444 211 1111
Q ss_pred cChhhHhhhhhcchhhhcHHHHHHHHHHHHhhccchh
Q 025496 205 NDAAERTQSHISGKQHIGYGMVRDFITEYKVCQLFIV 241 (252)
Q Consensus 205 ~D~d~Rl~dH~~GK~H~Gy~kIR~~l~eL~~~~~~~~ 241 (252)
-+|..|.++|+.+..++.+.-+|.
T Consensus 94 -------------dl~~ryek~K~vi~~~k~NEE~Lk 117 (207)
T PF05010_consen 94 -------------DLHKRYEKQKEVIEGYKKNEETLK 117 (207)
T ss_pred -------------HHHHHHHHHHHHHHHHHHhHHHHH
Confidence 567777777777777776554444
No 159
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=22.15 E-value=2.4e+02 Score=29.75 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=15.8
Q ss_pred hhccccccccchhhhcccCh
Q 025496 188 QEKKMALCEICGSFLVANDA 207 (252)
Q Consensus 188 ~~qkl~VCdVCGA~Ls~~D~ 207 (252)
..-.++-||.||+--+.+|-
T Consensus 674 ~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 674 YETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred HHHhcCCCCCCCCCCCcccc
Confidence 34467999999999888873
No 160
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=22.15 E-value=8.2e+02 Score=24.67 Aligned_cols=78 Identities=21% Similarity=0.191 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhc--cCC------------------------CCCCCCchHHHHHHHHHHHHHH
Q 025496 86 EAELAQFCEKLVMDLDRRVRRGRERLSQE--VEP------------------------APPPPISAEKSEQLSVLEEKIK 139 (252)
Q Consensus 86 E~e~~~~L~~~i~d~drkI~~~k~RL~~~--~~~------------------------~~~~~~~~~~~~~i~~l~~~I~ 139 (252)
=+..+..+..+|+.++.+|..-..-|.+- ++. ..-.+..+.+.+++. .|.
T Consensus 103 a~~~~~~~~~~l~~~e~~~~~i~~~l~~l~~~e~~nr~~v~~l~~~y~~~rk~ll~~~~~~G~a~~~le~~l~----~~e 178 (569)
T PRK04778 103 AKHEINEIESLLDLIEEDIEQILEELQELLESEEKNREEVEQLKDLYRELRKSLLANRFSFGPALDELEKQLE----NLE 178 (569)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHH----HHH
Confidence 34567778888888888887777666421 000 000001122233333 344
Q ss_pred HHHHHHHHhhhcCCHHHHHHHHHHHHHH
Q 025496 140 NLLEQVETLGEAGKVDEAEALMRKVEIL 167 (252)
Q Consensus 140 ~ll~~aE~LGeeG~VdeA~~~~~~~e~L 167 (252)
....+-+.|.+.|+..+|...+.+++.-
T Consensus 179 ~~f~~f~~l~~~Gd~~~A~e~l~~l~~~ 206 (569)
T PRK04778 179 EEFSQFVELTESGDYVEAREILDQLEEE 206 (569)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 5667788999999999998887666543
No 161
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.03 E-value=31 Score=26.45 Aligned_cols=13 Identities=62% Similarity=1.076 Sum_probs=8.9
Q ss_pred ccccccchhhhcc
Q 025496 192 MALCEICGSFLVA 204 (252)
Q Consensus 192 l~VCdVCGA~Ls~ 204 (252)
|-+|++||+-|..
T Consensus 1 ~llCP~C~v~l~~ 13 (88)
T COG3809 1 MLLCPICGVELVM 13 (88)
T ss_pred CcccCcCCceeee
Confidence 4578888876543
No 162
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.96 E-value=3.3e+02 Score=25.05 Aligned_cols=30 Identities=30% Similarity=0.370 Sum_probs=24.8
Q ss_pred hhcCCHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025496 149 GEAGKVDEAEALMRKVEILNVEKTTLTQQS 178 (252)
Q Consensus 149 GeeG~VdeA~~~~~~~e~Lk~ek~~l~~~~ 178 (252)
.+.|++||-+.....++.|+.++..+.+..
T Consensus 198 reieeidEQi~~~kkvekl~~qK~ellnkk 227 (264)
T KOG3032|consen 198 REIEEIDEQISYKKKVEKLKRQKMELLNKK 227 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345778898999999999999998888765
No 163
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=21.90 E-value=4.2e+02 Score=22.27 Aligned_cols=15 Identities=27% Similarity=0.645 Sum_probs=11.4
Q ss_pred ccccccccchhhhcc
Q 025496 190 KKMALCEICGSFLVA 204 (252)
Q Consensus 190 qkl~VCdVCGA~Ls~ 204 (252)
...-+|+.||-.+..
T Consensus 109 gtYG~Ce~CGe~I~~ 123 (151)
T PRK10778 109 EDFGYCESCGVEIGI 123 (151)
T ss_pred CCCceeccCCCcccH
Confidence 345799999988653
No 164
>PF06246 Isy1: Isy1-like splicing family; InterPro: IPR009360 Isy1 protein is important in the optimisation of splicing [].; PDB: 1X4T_A.
Probab=21.82 E-value=2.6e+02 Score=25.65 Aligned_cols=45 Identities=18% Similarity=0.350 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCCchHHHHHHHHHHHHHHHHHHH
Q 025496 86 EAELAQFCEKLVMDLDRRVRRGRERLSQEVEPAPPPPISAEKSEQLSVLEEKIKNLLEQ 144 (252)
Q Consensus 86 E~e~~~~L~~~i~d~drkI~~~k~RL~~~~~~~~~~~~~~~~~~~i~~l~~~I~~ll~~ 144 (252)
-.+...+...+|.++-++|.+-+ ++ ... .-+|.+|+.+|+.|+.+
T Consensus 42 l~~ae~WR~~ii~EIs~kv~~Iq-----d~-------~L~--E~~IRdLNDeINkL~rE 86 (255)
T PF06246_consen 42 LPEAEKWRRQIIKEISRKVTRIQ-----DP-------SLG--EFQIRDLNDEINKLIRE 86 (255)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH-----H---------S---HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-----hc-------CCC--HHHHHHHHHHHHHHHHH
Confidence 45666778888888888887754 21 111 25899999999999976
No 165
>PF14828 Amnionless: Amnionless
Probab=21.42 E-value=28 Score=34.27 Aligned_cols=15 Identities=27% Similarity=0.727 Sum_probs=12.4
Q ss_pred cccccchhhhcccCh
Q 025496 193 ALCEICGSFLVANDA 207 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~ 207 (252)
.=|+||||+++..-+
T Consensus 227 hCC~iCGa~v~~~~~ 241 (437)
T PF14828_consen 227 HCCPICGAIVTLEYS 241 (437)
T ss_pred CchhhcceEEEEeec
Confidence 679999999887654
No 166
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=21.39 E-value=36 Score=23.95 Aligned_cols=14 Identities=21% Similarity=0.482 Sum_probs=8.8
Q ss_pred cccccchhhhcccC
Q 025496 193 ALCEICGSFLVAND 206 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D 206 (252)
..|++||+-+.+.|
T Consensus 3 ~~CP~CG~~iev~~ 16 (54)
T TIGR01206 3 FECPDCGAEIELEN 16 (54)
T ss_pred cCCCCCCCEEecCC
Confidence 46777777665544
No 167
>PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional
Probab=21.20 E-value=4.7e+02 Score=27.88 Aligned_cols=50 Identities=24% Similarity=0.346 Sum_probs=34.2
Q ss_pred CchHHHHHHHH------HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHH
Q 025496 123 ISAEKSEQLSV------LEEKIKNLLEQVETLGEAGKVDEAEALMRKVEILNVEKT 172 (252)
Q Consensus 123 ~~~~~~~~i~~------l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~ 172 (252)
...++.++|.+ +.+++..+++++...|..--.+--..+-++|++++++.+
T Consensus 559 Lk~ei~kki~e~~~~~~~kek~ea~~aev~~~g~s~~~~~~~~lkeki~~~~~Ei~ 614 (762)
T PLN03229 559 LKAEINKKFKEVMDRPEIKEKMEALKAEVASSGASSGDELDDDLKEKVEKMKKEIE 614 (762)
T ss_pred hhHHHHHHHHHhcccHHHHHHHHHHHHHHHhcCccccCCCCHHHHHHHHHHHHHHH
Confidence 35567777777 888888888888777755333444566777777777554
No 168
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=21.18 E-value=6e+02 Score=26.77 Aligned_cols=22 Identities=14% Similarity=-0.153 Sum_probs=9.9
Q ss_pred hhcHHHHHHHHHHHHhhccchh
Q 025496 220 HIGYGMVRDFITEYKVCQLFIV 241 (252)
Q Consensus 220 H~Gy~kIR~~l~eL~~~~~~~~ 241 (252)
.++-.+.|...+-|++.+--|+
T Consensus 681 ~L~~~Q~~~I~~iL~~~~~~I~ 702 (717)
T PF10168_consen 681 VLSESQKRTIKEILKQQGEEID 702 (717)
T ss_pred cCCHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444443333
No 169
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=21.07 E-value=1.6e+02 Score=16.61 Aligned_cols=24 Identities=21% Similarity=0.285 Sum_probs=16.9
Q ss_pred HHHHHHHhhhcCCHHHHHHHHHHH
Q 025496 141 LLEQVETLGEAGKVDEAEALMRKV 164 (252)
Q Consensus 141 ll~~aE~LGeeG~VdeA~~~~~~~ 164 (252)
++..+......|+.++|...+.++
T Consensus 3 ~~~~a~~~~~~g~~~~A~~~~~~~ 26 (33)
T PF13174_consen 3 LYRLARCYYKLGDYDEAIEYFQRL 26 (33)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccCHHHHHHHHHHH
Confidence 445566666678888888877655
No 170
>PLN02748 tRNA dimethylallyltransferase
Probab=21.06 E-value=46 Score=33.15 Aligned_cols=29 Identities=24% Similarity=0.541 Sum_probs=21.2
Q ss_pred cccccccchhhhcccChhhHhhhhhcchhhh
Q 025496 191 KMALCEICGSFLVANDAAERTQSHISGKQHI 221 (252)
Q Consensus 191 kl~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~ 221 (252)
+..+|+|||.-..+++ .=-.-|+.|+.|-
T Consensus 417 ~~~~Ce~C~~~~~~G~--~eW~~Hlksr~Hk 445 (468)
T PLN02748 417 TQYVCEACGNKVLRGA--HEWEQHKQGRGHR 445 (468)
T ss_pred ccccccCCCCcccCCH--HHHHHHhcchHHH
Confidence 5678999996433444 4466799999995
No 171
>CHL00112 rpl28 ribosomal protein L28; Provisional
Probab=20.98 E-value=35 Score=24.78 Aligned_cols=14 Identities=14% Similarity=0.247 Sum_probs=10.6
Q ss_pred cccccchhhhcccC
Q 025496 193 ALCEICGSFLVAND 206 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D 206 (252)
++|++||---..+-
T Consensus 3 r~C~i~GK~~~~Gn 16 (63)
T CHL00112 3 KKCQLTGKKANNGY 16 (63)
T ss_pred CeeccCCCcCccCc
Confidence 69999997665553
No 172
>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=20.96 E-value=34 Score=27.73 Aligned_cols=17 Identities=41% Similarity=0.767 Sum_probs=14.9
Q ss_pred hccccccccchhhhccc
Q 025496 189 EKKMALCEICGSFLVAN 205 (252)
Q Consensus 189 ~qkl~VCdVCGA~Ls~~ 205 (252)
.+.+-.|+.||+.|++.
T Consensus 40 ~~d~l~C~~C~~~l~~~ 56 (133)
T PF07967_consen 40 SKDMLKCESCGARLCVK 56 (133)
T ss_pred CCCEEEeCCCCCEEEEe
Confidence 36778999999999998
No 173
>PRK15067 ethanolamine ammonia lyase large subunit; Provisional
Probab=20.89 E-value=36 Score=33.68 Aligned_cols=10 Identities=30% Similarity=0.428 Sum_probs=9.3
Q ss_pred hhhhhcchhh
Q 025496 211 TQSHISGKQH 220 (252)
Q Consensus 211 l~dH~~GK~H 220 (252)
|+|||.||+|
T Consensus 347 LEDhf~GKLl 356 (461)
T PRK15067 347 LEDHFMGKLL 356 (461)
T ss_pred hHhhhhhhhh
Confidence 7999999987
No 174
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=20.84 E-value=57 Score=19.35 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=13.3
Q ss_pred cccccchhhhcccChhhHhhhhhc
Q 025496 193 ALCEICGSFLVANDAAERTQSHIS 216 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl~dH~~ 216 (252)
-.|+||+..+ ....+.+|+-
T Consensus 2 v~CPiC~~~v----~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV----PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc----cHHHHHHHHH
Confidence 4699999876 3345666654
No 175
>PF13041 PPR_2: PPR repeat family
Probab=20.48 E-value=1.4e+02 Score=19.27 Aligned_cols=22 Identities=27% Similarity=0.447 Sum_probs=17.7
Q ss_pred HHHhhhcCCHHHHHHHHHHHHH
Q 025496 145 VETLGEAGKVDEAEALMRKVEI 166 (252)
Q Consensus 145 aE~LGeeG~VdeA~~~~~~~e~ 166 (252)
+..+...|++++|.+++++..+
T Consensus 10 i~~~~~~~~~~~a~~l~~~M~~ 31 (50)
T PF13041_consen 10 ISGYCKAGKFEEALKLFKEMKK 31 (50)
T ss_pred HHHHHHCcCHHHHHHHHHHHHH
Confidence 4567889999999999877653
No 176
>TIGR02284 conserved hypothetical protein. Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.
Probab=20.48 E-value=52 Score=27.03 Aligned_cols=17 Identities=29% Similarity=0.499 Sum_probs=15.2
Q ss_pred hcchhhhcHHHHHHHHH
Q 025496 215 ISGKQHIGYGMVRDFIT 231 (252)
Q Consensus 215 ~~GK~H~Gy~kIR~~l~ 231 (252)
+.|++|-+|..||..+.
T Consensus 66 ~~g~lhr~w~~lks~~~ 82 (139)
T TIGR02284 66 MVGSLHQFWGKIRATLT 82 (139)
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 68999999999999875
No 177
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=20.35 E-value=26 Score=22.56 Aligned_cols=20 Identities=25% Similarity=0.366 Sum_probs=13.7
Q ss_pred cccccchhhhcccChhhHhh
Q 025496 193 ALCEICGSFLVANDAAERTQ 212 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl~ 212 (252)
..|++||+.....|.-.+.-
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC 28 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYC 28 (36)
T ss_pred CcCCCCCCeEeEccCCEEEh
Confidence 45999999876666544443
No 178
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=20.28 E-value=46 Score=32.32 Aligned_cols=27 Identities=33% Similarity=0.751 Sum_probs=20.6
Q ss_pred cccccchhhhcccChhhHhhhhhcchhhh
Q 025496 193 ALCEICGSFLVANDAAERTQSHISGKQHI 221 (252)
Q Consensus 193 ~VCdVCGA~Ls~~D~d~Rl~dH~~GK~H~ 221 (252)
..|+|||-|.-- --.|.+.||.---|+
T Consensus 375 f~CEICgNyvy~--GR~~FdrHF~E~rHi 401 (470)
T COG5188 375 FECEICGNYVYY--GRDRFDRHFEEDRHI 401 (470)
T ss_pred eeeeeccccccc--chHHHHhhhhhhhhh
Confidence 789999988443 346688899877774
No 179
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=20.19 E-value=38 Score=23.41 Aligned_cols=11 Identities=27% Similarity=0.646 Sum_probs=8.6
Q ss_pred cccccchhhhc
Q 025496 193 ALCEICGSFLV 203 (252)
Q Consensus 193 ~VCdVCGA~Ls 203 (252)
.+|++|||--+
T Consensus 35 w~CP~C~a~K~ 45 (50)
T cd00730 35 WVCPVCGAGKD 45 (50)
T ss_pred CCCCCCCCcHH
Confidence 69999998543
Done!