Query psy2248
Match_columns 102
No_of_seqs 100 out of 240
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 19:55:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2248.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2248hhsearch_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 99.9 5.1E-25 1.1E-29 167.3 9.0 84 14-101 121-207 (254)
2 KOG0796|consensus 99.9 7.7E-25 1.7E-29 170.0 8.6 85 12-101 118-203 (319)
3 COG5200 LUC7 U1 snRNP componen 99.7 2.5E-16 5.3E-21 117.6 7.1 83 15-101 120-202 (258)
4 PRK15058 cytochrome b562; Prov 90.0 1.9 4.2E-05 30.1 6.6 42 16-57 78-122 (128)
5 PF07361 Cytochrom_B562: Cytoc 89.3 1.9 4E-05 28.6 6.0 42 16-57 53-97 (103)
6 PRK09720 cybC cytochrome b562; 89.3 2.7 5.8E-05 28.2 6.6 42 15-56 49-93 (100)
7 PRK06835 DNA replication prote 87.3 3.6 7.8E-05 32.5 7.4 66 17-91 37-105 (329)
8 COG3783 CybC Soluble cytochrom 81.7 3.2 7E-05 27.8 4.1 27 30-56 67-93 (100)
9 PF12854 PPR_1: PPR repeat 79.6 3 6.4E-05 21.9 2.8 19 32-50 14-32 (34)
10 PF02151 UVR: UvrB/uvrC motif; 78.7 8.2 0.00018 20.7 5.0 35 23-57 2-36 (36)
11 COG1579 Zn-ribbon protein, pos 78.2 17 0.00036 27.9 7.5 18 84-101 221-238 (239)
12 PRK10246 exonuclease subunit S 77.0 12 0.00025 33.9 7.3 8 85-92 504-511 (1047)
13 PF04032 Rpr2: RNAse P Rpr2/Rp 75.2 11 0.00024 23.2 5.0 60 24-99 2-61 (85)
14 PRK10564 maltose regulon perip 74.4 4.8 0.0001 31.9 3.8 28 29-56 261-288 (303)
15 PF13779 DUF4175: Domain of un 73.4 7.8 0.00017 34.5 5.2 34 22-55 537-570 (820)
16 PF06156 DUF972: Protein of un 72.7 26 0.00056 23.5 7.9 52 11-62 3-56 (107)
17 TIGR02302 aProt_lowcomp conser 72.6 8.3 0.00018 34.5 5.2 34 23-56 568-601 (851)
18 PF03357 Snf7: Snf7; InterPro 72.1 28 0.00061 23.7 7.4 53 11-63 10-62 (171)
19 PF02403 Seryl_tRNA_N: Seryl-t 71.3 20 0.00042 23.2 5.7 50 14-65 41-90 (108)
20 PF14282 FlxA: FlxA-like prote 70.7 28 0.0006 23.0 6.3 47 15-61 18-70 (106)
21 TIGR00373 conserved hypothetic 68.3 1.5 3.2E-05 31.1 -0.2 17 84-100 128-144 (158)
22 PRK06266 transcription initiat 67.5 1.7 3.8E-05 31.5 -0.0 17 84-100 136-152 (178)
23 COG2093 DNA-directed RNA polym 66.5 1.5 3.2E-05 27.2 -0.4 9 84-92 18-26 (64)
24 PF04420 CHD5: CHD5-like prote 65.7 36 0.00078 24.1 6.5 54 12-65 36-89 (161)
25 PF05191 ADK_lid: Adenylate ki 65.6 1.9 4.1E-05 23.6 -0.1 16 80-95 17-32 (36)
26 PRK11020 hypothetical protein; 65.4 42 0.00091 23.1 7.9 49 15-63 4-52 (118)
27 PF03962 Mnd1: Mnd1 family; I 64.6 52 0.0011 23.9 7.7 53 13-65 73-126 (188)
28 cd00729 rubredoxin_SM Rubredox 64.5 2.2 4.7E-05 22.9 0.0 11 83-93 17-27 (34)
29 PF03119 DNA_ligase_ZBD: NAD-d 64.5 2.2 4.7E-05 22.0 0.0 14 87-100 2-15 (28)
30 PF10367 Vps39_2: Vacuolar sor 63.5 25 0.00054 22.1 4.9 13 84-96 78-90 (109)
31 TIGR01554 major_cap_HK97 phage 60.3 32 0.0007 27.1 5.9 35 20-54 3-39 (378)
32 PF01396 zf-C4_Topoisom: Topoi 58.5 2.8 6E-05 23.1 -0.3 13 85-97 2-14 (39)
33 PF04423 Rad50_zn_hook: Rad50 57.8 13 0.00027 21.5 2.5 10 86-95 22-31 (54)
34 PRK13130 H/ACA RNA-protein com 57.5 3 6.6E-05 25.1 -0.2 12 83-94 4-15 (56)
35 PLN00204 CP12 gene family prot 57.2 46 0.001 23.2 5.5 43 20-62 56-99 (126)
36 TIGR00029 S20 ribosomal protei 56.5 52 0.0011 21.3 5.7 38 19-56 22-59 (87)
37 PF05741 zf-nanos: Nanos RNA b 56.4 4 8.6E-05 24.5 0.1 9 85-93 34-42 (55)
38 PF02132 RecR: RecR protein; 56.2 14 0.0003 20.3 2.4 13 81-93 14-26 (41)
39 PF01535 PPR: PPR repeat; Int 55.7 21 0.00045 16.9 2.8 22 32-53 7-28 (31)
40 KOG4765|consensus 55.6 4.5 9.8E-05 33.2 0.4 16 82-97 88-103 (419)
41 PF08792 A2L_zn_ribbon: A2L zi 55.3 3.8 8.2E-05 22.0 -0.1 13 84-96 3-15 (33)
42 smart00531 TFIIE Transcription 55.1 3.3 7.1E-05 28.9 -0.4 16 85-100 124-139 (147)
43 PF14828 Amnionless: Amnionles 54.8 3.3 7.2E-05 34.1 -0.5 14 85-98 227-240 (437)
44 COG0419 SbcC ATPase involved i 54.7 68 0.0015 28.5 7.5 10 84-93 457-466 (908)
45 PF13913 zf-C2HC_2: zinc-finge 54.5 4.7 0.0001 20.1 0.2 9 84-92 2-10 (25)
46 PF07721 TPR_4: Tetratricopept 54.0 24 0.00052 17.1 2.9 21 29-49 5-25 (26)
47 COG1675 TFA1 Transcription ini 53.9 4.5 9.8E-05 29.6 0.1 19 83-101 131-149 (176)
48 PRK01156 chromosome segregatio 53.1 71 0.0015 28.0 7.3 10 86-95 451-460 (895)
49 COG1592 Rubrerythrin [Energy p 53.0 84 0.0018 22.8 6.6 8 84-91 134-141 (166)
50 cd00350 rubredoxin_like Rubred 52.7 4.6 9.9E-05 21.3 0.0 10 83-92 16-25 (33)
51 PF13790 DUF4182: Domain of un 52.2 4.1 8.8E-05 22.8 -0.3 18 85-102 4-21 (38)
52 PRK12496 hypothetical protein; 52.1 5 0.00011 28.7 0.1 12 85-96 144-155 (164)
53 PF13922 PHD_3: PHD domain of 51.8 3.6 7.8E-05 25.8 -0.6 13 81-93 40-52 (69)
54 PF13041 PPR_2: PPR repeat fam 51.5 29 0.00063 18.9 3.3 22 32-53 10-31 (50)
55 PHA02562 46 endonuclease subun 51.2 1.4E+02 0.0029 24.5 8.3 12 84-95 284-295 (562)
56 PRK02224 chromosome segregatio 51.0 1.2E+02 0.0025 26.5 8.3 12 84-95 451-462 (880)
57 PF09543 DUF2379: Protein of u 50.9 81 0.0017 21.9 5.9 40 12-51 61-100 (121)
58 PF14276 DUF4363: Domain of un 50.8 65 0.0014 21.2 5.4 38 17-54 20-57 (121)
59 TIGR00009 L28 ribosomal protei 50.3 5 0.00011 23.9 -0.1 10 85-94 3-12 (56)
60 PRK03954 ribonuclease P protei 49.2 36 0.00078 23.4 4.0 63 22-101 19-81 (121)
61 PF01649 Ribosomal_S20p: Ribos 49.0 69 0.0015 20.5 5.8 37 19-55 21-57 (84)
62 PF11931 DUF3449: Domain of un 48.9 5.7 0.00012 29.6 0.0 10 85-94 102-111 (196)
63 KOG3032|consensus 48.8 1E+02 0.0022 24.0 6.7 31 36-66 198-228 (264)
64 PF11781 RRN7: RNA polymerase 48.3 5.3 0.00012 21.7 -0.2 14 85-98 9-22 (36)
65 PRK00239 rpsT 30S ribosomal pr 47.9 74 0.0016 20.5 7.0 38 19-56 22-59 (88)
66 KOG4602|consensus 47.6 6.1 0.00013 31.0 -0.0 8 85-92 269-276 (318)
67 PRK13169 DNA replication intia 46.9 88 0.0019 21.1 7.5 51 11-61 3-55 (110)
68 KOG3576|consensus 46.5 6.3 0.00014 30.2 -0.1 12 81-92 209-220 (267)
69 PRK05431 seryl-tRNA synthetase 46.5 1E+02 0.0022 25.1 6.9 48 14-63 40-87 (425)
70 PF04645 DUF603: Protein of un 46.5 68 0.0015 23.7 5.2 46 17-62 106-151 (181)
71 COG1422 Predicted membrane pro 46.3 1.2E+02 0.0026 22.8 6.6 40 15-61 71-110 (201)
72 PF10979 DUF2786: Protein of u 45.9 54 0.0012 18.4 4.9 35 21-57 3-37 (43)
73 PF13894 zf-C2H2_4: C2H2-type 45.7 6.5 0.00014 17.9 -0.1 9 86-94 2-10 (24)
74 PF04216 FdhE: Protein involve 45.2 5.4 0.00012 30.6 -0.6 17 82-98 236-252 (290)
75 PLN02678 seryl-tRNA synthetase 44.9 1.1E+02 0.0024 25.4 6.9 47 15-63 46-92 (448)
76 COG5509 Uncharacterized small 44.8 36 0.00077 21.0 3.0 21 17-37 26-46 (65)
77 PRK00432 30S ribosomal protein 44.4 8.1 0.00018 22.5 0.2 16 83-98 19-35 (50)
78 PF14863 Alkyl_sulf_dimr: Alky 43.5 66 0.0014 22.4 4.7 52 3-54 48-99 (141)
79 PF09237 GAGA: GAGA factor; I 43.1 5.5 0.00012 23.8 -0.7 14 84-97 24-37 (54)
80 TIGR00414 serS seryl-tRNA synt 43.0 1.3E+02 0.0029 24.4 7.0 48 15-63 43-90 (418)
81 TIGR01206 lysW lysine biosynth 42.8 7.7 0.00017 23.1 -0.1 13 85-97 3-15 (54)
82 PF02591 DUF164: Putative zinc 42.7 7.5 0.00016 22.6 -0.2 13 82-94 44-56 (56)
83 PF00096 zf-C2H2: Zinc finger, 42.1 9.4 0.0002 17.7 0.2 10 86-95 2-11 (23)
84 TIGR00756 PPR pentatricopeptid 42.0 41 0.0009 15.9 3.4 21 32-52 7-27 (35)
85 PF08898 DUF1843: Domain of un 41.9 76 0.0016 18.9 4.2 33 25-63 19-52 (53)
86 PF08271 TF_Zn_Ribbon: TFIIB z 40.9 9.1 0.0002 21.1 0.0 13 86-98 2-14 (43)
87 PF12793 SgrR_N: Sugar transpo 39.8 54 0.0012 22.0 3.7 24 26-49 71-94 (115)
88 cd00730 rubredoxin Rubredoxin; 39.5 9.5 0.00021 22.3 -0.1 11 85-95 35-45 (50)
89 PF13432 TPR_16: Tetratricopep 38.8 48 0.001 18.6 2.9 25 30-54 2-26 (65)
90 smart00746 TRASH metallochaper 38.1 9.6 0.00021 18.3 -0.2 9 87-95 1-9 (39)
91 PF00301 Rubredoxin: Rubredoxi 38.0 11 0.00024 21.7 0.1 9 85-93 35-43 (47)
92 PRK03564 formate dehydrogenase 37.5 11 0.00024 29.8 0.0 17 83-99 251-267 (309)
93 PF06676 DUF1178: Protein of u 37.4 16 0.00034 26.0 0.8 15 79-93 27-41 (148)
94 PHA02768 hypothetical protein; 37.1 9.1 0.0002 22.9 -0.4 15 85-99 6-20 (55)
95 KOG2801|consensus 37.0 12 0.00026 30.4 0.1 12 88-99 402-413 (559)
96 PF06397 Desulfoferrod_N: Desu 36.9 9.1 0.0002 21.0 -0.4 16 82-97 4-19 (36)
97 PF08946 Osmo_CC: Osmosensory 36.5 88 0.0019 18.1 3.8 17 15-31 18-34 (46)
98 PF00435 Spectrin: Spectrin re 36.4 94 0.002 18.4 7.1 50 14-64 46-95 (105)
99 COG0268 RpsT Ribosomal protein 35.6 1.3E+02 0.0028 19.7 5.7 36 20-55 23-58 (88)
100 TIGR01562 FdhE formate dehydro 34.9 13 0.00029 29.3 0.1 18 82-99 250-267 (305)
101 TIGR02420 dksA RNA polymerase- 34.8 1.3E+02 0.0029 19.7 7.5 11 84-94 80-90 (110)
102 PF14257 DUF4349: Domain of un 34.3 2E+02 0.0042 21.5 7.7 52 13-64 129-184 (262)
103 PF12230 PRP21_like_P: Pre-mRN 34.2 13 0.00029 27.4 0.0 18 81-98 165-182 (229)
104 cd07973 Spt4 Transcription elo 34.2 16 0.00035 24.2 0.4 15 84-98 20-34 (98)
105 PF13248 zf-ribbon_3: zinc-rib 33.9 15 0.00033 18.2 0.2 8 85-92 17-24 (26)
106 PF04810 zf-Sec23_Sec24: Sec23 33.8 14 0.0003 20.3 0.0 11 86-96 4-14 (40)
107 PRK12495 hypothetical protein; 33.4 53 0.0011 25.1 3.1 12 85-96 43-54 (226)
108 smart00451 ZnF_U1 U1-like zinc 33.2 13 0.00028 18.9 -0.2 11 85-95 4-14 (35)
109 PF04012 PspA_IM30: PspA/IM30 33.1 1.9E+02 0.0041 20.9 8.4 53 12-64 54-106 (221)
110 PF13812 PPR_3: Pentatricopept 33.0 64 0.0014 15.5 3.4 22 32-53 8-29 (34)
111 PF12171 zf-C2H2_jaz: Zinc-fin 32.5 17 0.00037 17.8 0.2 11 85-95 2-12 (27)
112 KOG2034|consensus 32.5 1.6E+02 0.0035 26.9 6.3 12 85-96 818-829 (911)
113 PF13465 zf-H2C2_2: Zinc-finge 32.2 14 0.0003 18.2 -0.1 12 81-92 11-22 (26)
114 PF05852 DUF848: Gammaherpesvi 32.2 1.9E+02 0.0041 20.6 6.7 49 13-61 58-108 (146)
115 COG0172 SerS Seryl-tRNA synthe 31.9 2.2E+02 0.0047 23.7 6.6 49 15-64 42-90 (429)
116 PF13174 TPR_6: Tetratricopept 31.6 66 0.0014 15.2 3.3 24 28-51 3-26 (33)
117 PF09920 DUF2150: Uncharacteri 31.6 85 0.0018 23.3 3.9 31 22-52 115-145 (190)
118 PF14354 Lar_restr_allev: Rest 31.4 17 0.00037 21.1 0.1 9 83-91 2-10 (61)
119 COG2178 Predicted RNA-binding 31.2 1.9E+02 0.004 21.8 5.6 42 17-58 113-154 (204)
120 PF02672 CP12: CP12 domain; I 30.6 17 0.00036 22.7 0.0 41 21-61 1-43 (71)
121 PF01166 TSC22: TSC-22/dip/bun 30.4 28 0.00061 21.2 1.0 24 14-37 12-35 (59)
122 PF02150 RNA_POL_M_15KD: RNA p 30.1 18 0.0004 19.4 0.1 13 84-96 1-13 (35)
123 COG3461 Uncharacterized conser 30.1 1.3E+02 0.0028 20.1 4.1 26 11-36 9-34 (103)
124 PF07980 SusD: SusD family; I 30.0 1.2E+02 0.0026 21.5 4.5 26 27-52 135-160 (266)
125 COG2023 RPR2 RNase P subunit R 29.7 1.2E+02 0.0026 20.5 4.0 65 20-101 9-73 (105)
126 TIGR02795 tol_pal_ybgF tol-pal 29.7 1.2E+02 0.0025 18.4 3.9 28 26-53 3-30 (119)
127 PF12325 TMF_TATA_bd: TATA ele 29.4 1.9E+02 0.0041 19.7 5.8 26 40-65 59-84 (120)
128 PRK00398 rpoP DNA-directed RNA 29.1 17 0.00038 20.2 -0.1 17 84-100 21-37 (46)
129 PF07743 HSCB_C: HSCB C-termin 29.0 1.4E+02 0.003 18.0 8.4 42 13-54 28-69 (78)
130 PF01348 Intron_maturas2: Type 28.8 16 0.00034 25.4 -0.4 10 83-92 136-145 (146)
131 COG4338 Uncharacterized protei 28.4 19 0.00041 21.3 -0.0 9 85-93 13-21 (54)
132 PF11571 Med27: Mediator compl 28.2 26 0.00055 22.5 0.6 18 79-96 49-66 (90)
133 PRK06393 rpoE DNA-directed RNA 27.9 20 0.00043 22.2 0.0 8 85-92 18-25 (64)
134 PRK14892 putative transcriptio 27.4 19 0.00041 23.9 -0.1 12 84-95 42-53 (99)
135 TIGR03504 FimV_Cterm FimV C-te 27.3 1.2E+02 0.0027 16.9 3.3 24 29-52 3-26 (44)
136 PHA03161 hypothetical protein; 27.3 2.4E+02 0.0052 20.2 6.5 47 13-59 58-106 (150)
137 PF13428 TPR_14: Tetratricopep 27.2 1.1E+02 0.0023 16.2 4.0 25 29-53 5-29 (44)
138 PF06827 zf-FPG_IleRS: Zinc fi 27.2 23 0.00051 17.9 0.2 11 85-95 2-12 (30)
139 TIGR00618 sbcc exonuclease Sbc 27.1 2.7E+02 0.0059 25.2 6.9 11 82-92 499-509 (1042)
140 cd00176 SPEC Spectrin repeats, 26.5 2E+02 0.0044 19.2 6.4 49 15-64 46-94 (213)
141 PF13374 TPR_10: Tetratricopep 26.3 96 0.0021 15.4 4.9 29 28-56 5-33 (42)
142 TIGR03831 YgiT_finger YgiT-typ 26.1 23 0.00049 19.0 0.0 12 83-94 31-42 (46)
143 COG5319 Uncharacterized protei 26.1 29 0.00062 24.5 0.5 14 79-92 27-40 (142)
144 PF14446 Prok-RING_1: Prokaryo 25.9 21 0.00046 21.3 -0.1 8 85-92 22-29 (54)
145 PF09577 Spore_YpjB: Sporulati 25.7 1.7E+02 0.0036 22.3 4.7 30 24-53 4-33 (232)
146 COG1773 Rubredoxin [Energy pro 25.7 23 0.00049 21.3 -0.0 8 85-92 37-44 (55)
147 PF11062 DUF2863: Protein of u 25.5 22 0.00048 29.2 -0.1 13 83-95 363-375 (398)
148 smart00661 RPOL9 RNA polymeras 25.5 26 0.00057 19.5 0.2 13 86-98 2-14 (52)
149 PF05597 Phasin: Poly(hydroxya 25.4 1.2E+02 0.0027 21.0 3.6 22 15-36 108-129 (132)
150 PRK12286 rpmF 50S ribosomal pr 25.3 21 0.00046 21.3 -0.2 12 83-94 39-50 (57)
151 COG4467 Regulator of replicati 25.3 2.3E+02 0.005 19.4 7.6 48 11-63 3-50 (114)
152 COG5200 LUC7 U1 snRNP componen 25.1 3.2E+02 0.007 21.0 7.0 30 11-40 109-138 (258)
153 PF15188 CCDC-167: Coiled-coil 24.8 2E+02 0.0044 18.6 5.3 53 14-66 3-67 (85)
154 PF04981 NMD3: NMD3 family ; 24.7 22 0.00047 26.6 -0.3 15 82-96 33-47 (236)
155 KOG3231|consensus 24.6 3E+02 0.0064 20.4 6.7 47 15-61 28-74 (208)
156 TIGR01031 rpmF_bact ribosomal 24.5 24 0.00052 20.9 -0.1 12 83-94 25-36 (55)
157 COG0143 MetG Methionyl-tRNA sy 24.3 24 0.00052 30.1 -0.1 14 85-98 156-169 (558)
158 COG4499 Predicted membrane pro 24.2 2.1E+02 0.0046 23.8 5.2 45 12-56 365-409 (434)
159 PF07967 zf-C3HC: C3HC zinc fi 24.1 20 0.00043 24.4 -0.6 17 81-97 40-56 (133)
160 PF06721 DUF1204: Protein of u 24.0 3.2E+02 0.007 20.6 6.5 42 44-93 79-120 (228)
161 PF08274 PhnA_Zn_Ribbon: PhnA 24.0 29 0.00064 18.2 0.2 13 80-92 15-27 (30)
162 PRK06424 transcription factor; 24.0 27 0.00059 24.6 0.1 11 83-93 22-32 (144)
163 PRK06921 hypothetical protein; 23.9 86 0.0019 23.7 2.9 35 47-92 6-40 (266)
164 PF01783 Ribosomal_L32p: Ribos 23.8 20 0.00043 21.1 -0.6 12 83-94 25-36 (56)
165 PF04880 NUDE_C: NUDE protein, 23.7 1.8E+02 0.0038 21.1 4.3 23 41-63 23-45 (166)
166 PF10238 Eapp_C: E2F-associate 23.7 24 0.00052 24.8 -0.2 18 85-102 110-127 (136)
167 PLN02320 seryl-tRNA synthetase 23.6 3.5E+02 0.0076 23.0 6.6 47 15-64 106-152 (502)
168 PF09401 NSP10: RNA synthesis 23.6 28 0.00061 24.2 0.1 13 83-95 105-117 (124)
169 TIGR02986 restrict_Alw26I type 23.5 26 0.00055 29.0 -0.1 15 83-97 81-95 (424)
170 smart00668 CTLH C-terminal to 23.5 1.4E+02 0.0031 16.4 3.2 25 29-53 5-29 (58)
171 TIGR01837 PHA_granule_1 poly(h 23.2 1.4E+02 0.0031 20.0 3.6 19 17-35 97-115 (118)
172 PRK08351 DNA-directed RNA poly 23.0 28 0.00062 21.2 0.1 9 86-94 17-25 (61)
173 PF09665 RE_Alw26IDE: Type II 23.0 27 0.00058 29.6 -0.1 15 83-97 81-95 (511)
174 smart00150 SPEC Spectrin repea 23.0 1.7E+02 0.0037 17.2 6.4 50 14-64 43-92 (101)
175 PF10602 RPN7: 26S proteasome 23.0 2.8E+02 0.0061 19.6 6.0 45 9-53 7-64 (177)
176 PF13181 TPR_8: Tetratricopept 22.9 1.1E+02 0.0023 14.7 4.8 27 29-55 5-31 (34)
177 PF01237 Oxysterol_BP: Oxyster 22.8 1.8E+02 0.0038 22.8 4.5 36 29-64 287-322 (354)
178 KOG3362|consensus 22.6 27 0.00059 25.1 -0.1 11 85-96 119-129 (156)
179 PF13424 TPR_12: Tetratricopep 22.4 1.7E+02 0.0037 16.8 4.7 32 25-56 46-77 (78)
180 COG1645 Uncharacterized Zn-fin 22.2 28 0.0006 24.4 -0.1 14 85-98 29-42 (131)
181 COG2178 Predicted RNA-binding 22.2 3.5E+02 0.0076 20.4 7.9 51 11-61 15-65 (204)
182 PF06694 Plant_NMP1: Plant nuc 22.2 4.2E+02 0.0091 21.3 6.5 58 7-64 166-223 (325)
183 PF14559 TPR_19: Tetratricopep 22.0 81 0.0017 17.6 1.9 19 35-53 1-19 (68)
184 PF14952 zf-tcix: Putative tre 22.0 30 0.00066 19.9 0.0 13 81-93 8-20 (44)
185 PF06008 Laminin_I: Laminin Do 21.9 3.5E+02 0.0075 20.2 7.2 42 13-54 91-135 (264)
186 PF06476 DUF1090: Protein of u 21.9 2.6E+02 0.0057 18.8 7.7 44 11-54 65-108 (115)
187 KOG2636|consensus 21.8 28 0.0006 29.3 -0.2 10 85-94 402-411 (497)
188 PF02388 FemAB: FemAB family; 21.7 4.1E+02 0.0088 21.4 6.4 22 16-37 242-263 (406)
189 CHL00102 rps20 ribosomal prote 21.7 2.4E+02 0.0053 18.4 6.8 38 19-56 22-66 (93)
190 PF06698 DUF1192: Protein of u 21.6 1.5E+02 0.0032 17.9 3.0 18 18-35 23-40 (59)
191 TIGR00319 desulf_FeS4 desulfof 21.5 22 0.00047 18.6 -0.6 16 83-98 6-21 (34)
192 PF04505 Dispanin: Interferon- 21.4 1.6E+02 0.0034 18.5 3.3 24 31-54 43-66 (82)
193 PF14149 YhfH: YhfH-like prote 21.3 46 0.001 18.4 0.7 14 81-94 10-23 (37)
194 PRK09591 celC cellobiose phosp 21.3 2.6E+02 0.0056 18.5 5.8 37 18-54 13-49 (104)
195 COG3183 Predicted restriction 21.3 29 0.00064 27.1 -0.2 7 85-91 196-202 (272)
196 PF05515 Viral_NABP: Viral nuc 21.3 32 0.00068 24.0 -0.0 16 81-96 59-74 (124)
197 PF12968 DUF3856: Domain of Un 21.1 3.1E+02 0.0068 19.4 5.2 36 24-59 99-134 (144)
198 PF13878 zf-C2H2_3: zinc-finge 21.0 35 0.00076 18.8 0.2 14 84-97 13-26 (41)
199 PF05605 zf-Di19: Drought indu 20.9 35 0.00076 19.5 0.1 14 82-95 29-42 (54)
200 COG0333 RpmF Ribosomal protein 20.9 33 0.00071 20.7 0.0 13 84-96 27-39 (57)
201 cd02336 ZZ_RSC8 Zinc finger, Z 20.8 32 0.00069 19.6 -0.1 10 86-95 2-11 (45)
202 PF14569 zf-UDP: Zinc-binding 20.6 38 0.00083 21.8 0.3 17 83-99 8-24 (80)
203 TIGR00823 EIIA-LAC phosphotran 20.6 2.6E+02 0.0056 18.3 5.8 35 20-54 12-46 (99)
204 PF07754 DUF1610: Domain of un 20.5 32 0.0007 17.2 -0.0 8 84-91 16-23 (24)
205 PF06677 Auto_anti-p27: Sjogre 20.4 30 0.00065 19.4 -0.2 12 85-96 18-29 (41)
206 COG1439 Predicted nucleic acid 20.4 36 0.00079 25.0 0.2 13 83-95 152-164 (177)
207 cd00974 DSRD Desulforedoxin (D 20.4 24 0.00053 18.4 -0.6 15 84-98 4-18 (34)
208 PF01258 zf-dskA_traR: Prokary 20.3 38 0.00083 17.8 0.2 10 85-94 4-13 (36)
209 PRK10778 dksA RNA polymerase-b 20.3 3.2E+02 0.007 19.2 7.3 12 83-94 110-121 (151)
210 PRK13844 recombination protein 20.1 1.6E+02 0.0035 21.9 3.6 14 80-93 53-66 (200)
211 TIGR02976 phageshock_pspB phag 20.1 2.3E+02 0.0051 17.7 3.8 19 45-63 45-63 (75)
212 TIGR02209 ftsL_broad cell divi 20.1 2E+02 0.0043 17.4 3.5 9 25-33 47-55 (85)
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=99.92 E-value=5.1e-25 Score=167.32 Aligned_cols=84 Identities=49% Similarity=0.749 Sum_probs=73.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHh---hcccccchhhhhhhhhhhhccccchhh
Q psy2248 14 NAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRK---QNDNNHWSQTVELAAAQEKQMEVCTVC 90 (102)
Q Consensus 14 ~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~---~~~~~~~~~~~~~~~~~~qkl~VCeVC 90 (102)
.+++|..|+++|+.++++||+||++|+||+|+++|.+++.|+.+++.++. .+.+. ..+...+++|+|+||+||
T Consensus 121 ~~~~i~~l~~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e~Lk~ek~~le~~~~~~~~~----~~~~~~~~~qkl~VCeVC 196 (254)
T PF03194_consen 121 KAEKIDELDEKIGELLKEAEELGEEGDVDEAQKLMEEVEKLKEEKEELEKELEEYRNS----IENSAQSQQQKLEVCEVC 196 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhh----hhhhhcccccCccchhhh
Confidence 47899999999999999999999999999999999999999999999998 33221 122234689999999999
Q ss_pred hhhhhcccccC
Q psy2248 91 GAFLIVGDAQS 101 (102)
Q Consensus 91 GA~Ls~~D~d~ 101 (102)
|||||++|||+
T Consensus 197 GA~Ls~~D~d~ 207 (254)
T PF03194_consen 197 GAFLSVGDNDR 207 (254)
T ss_pred hhHHhccchHH
Confidence 99999999985
No 2
>KOG0796|consensus
Probab=99.91 E-value=7.7e-25 Score=170.02 Aligned_cols=85 Identities=44% Similarity=0.659 Sum_probs=72.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH-HHHHHHhhcccccchhhhhhhhhhhhccccchhh
Q psy2248 12 NENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKE-EREMLRKQNDNNHWSQTVELAAAQEKQMEVCTVC 90 (102)
Q Consensus 12 ~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~-ek~~l~~~~~~~~~~~~~~~~~~~~qkl~VCeVC 90 (102)
..++++|..|+++|+.++++||+||++|+||+||++|.++|.|+. +++.....+.+ +.+.+.+++|||+||+||
T Consensus 118 ~~k~~~v~~l~e~I~~~l~~~E~LG~eG~Veeaq~~~~e~E~lk~~e~e~~~~~~~~-----~~~~~~~~~qkl~VCeVC 192 (319)
T KOG0796|consen 118 ARKAEKVHELEEKIGKLLEKAEELGEEGNVEEAQKAMKEVEELKAKEKEEAEESYNT-----TMPGASAQQQKLRVCEVC 192 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcc-----CcchhhhhhhhhhHHHhh
Confidence 344789999999999999999999999999999999999999997 55555444332 234566799999999999
Q ss_pred hhhhhcccccC
Q psy2248 91 GAFLIVGDAQS 101 (102)
Q Consensus 91 GA~Ls~~D~d~ 101 (102)
||||+++|+|+
T Consensus 193 Ga~L~~~D~d~ 203 (319)
T KOG0796|consen 193 GAFLSVNDADR 203 (319)
T ss_pred hHHHhccchHH
Confidence 99999999986
No 3
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=99.66 E-value=2.5e-16 Score=117.56 Aligned_cols=83 Identities=23% Similarity=0.380 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhhhhhhccccchhhhhhh
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQNDNNHWSQTVELAAAQEKQMEVCTVCGAFL 94 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~~~~~~~~~~~~~~~~~~qkl~VCeVCGA~L 94 (102)
.+.++.+++.|+.+..+++.|...-.|+.|...+.++++|+.+++++..++.++ ..+.+++.+|||+||+||||||
T Consensus 120 ~e~~~~~d~sIg~lg~e~dalakrk~V~~a~~~f~el~rl~~~rkei~~~v~sm----~en~gq~thqklqvC~iCgayL 195 (258)
T COG5200 120 EELFNRVDESIGELGMEGDALAKRKLVERACSAFNELERLREERKEIKEAVYSM----VENNGQGTHQKLQVCGICGAYL 195 (258)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----hhCcchhhhhhhhhhhhhhhHH
Confidence 334444445555555555555555559999999999999999999999887542 3456778999999999999999
Q ss_pred hcccccC
Q psy2248 95 IVGDAQS 101 (102)
Q Consensus 95 s~~D~d~ 101 (102)
|+.|+|+
T Consensus 196 srlDtdr 202 (258)
T COG5200 196 SRLDTDR 202 (258)
T ss_pred Hhcchhh
Confidence 9999986
No 4
>PRK15058 cytochrome b562; Provisional
Probab=90.00 E-value=1.9 Score=30.07 Aligned_cols=42 Identities=19% Similarity=0.251 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHhcCCHHHHHHHHHHHHHHHHH
Q psy2248 16 EQITLLSEKINNLVS---EAERVGMEGSVEKAQGLMKLCDQLKEE 57 (102)
Q Consensus 16 e~i~~l~~~I~~ll~---eaE~LGeeG~VdeA~~l~~~ve~Lk~e 57 (102)
.++..+.+-++.++. +++.|..+|++++|.....++..+|.+
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 455566666666554 556799999999999999998888754
No 5
>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=89.33 E-value=1.9 Score=28.64 Aligned_cols=42 Identities=24% Similarity=0.469 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHhcCCHHHHHHHHHHHHHHHHH
Q psy2248 16 EQITLLSEKINNLVS---EAERVGMEGSVEKAQGLMKLCDQLKEE 57 (102)
Q Consensus 16 e~i~~l~~~I~~ll~---eaE~LGeeG~VdeA~~l~~~ve~Lk~e 57 (102)
.++..+.+-++.++. .++.+.+.|++++|...+.++..||.+
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 344555555555544 566789999999999999999999865
No 6
>PRK09720 cybC cytochrome b562; Provisional
Probab=89.25 E-value=2.7 Score=28.22 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHH---HHHHHhcCCHHHHHHHHHHHHHHHH
Q psy2248 15 AEQITLLSEKINNLVSE---AERVGMEGSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~e---aE~LGeeG~VdeA~~l~~~ve~Lk~ 56 (102)
..++..+..-+..++.+ +..|..+|++++|.....++-.+|.
T Consensus 49 s~e~K~y~~Gld~lI~qID~A~~La~~GkL~eAK~~a~~l~~~Rn 93 (100)
T PRK09720 49 SPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRN 93 (100)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 34555666666666554 5569999999999988777766654
No 7
>PRK06835 DNA replication protein DnaC; Validated
Probab=87.34 E-value=3.6 Score=32.48 Aligned_cols=66 Identities=17% Similarity=0.252 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCC---HHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhhhhhhccccchhhh
Q psy2248 17 QITLLSEKINNLVSEAERVGMEGS---VEKAQGLMKLCDQLKEEREMLRKQNDNNHWSQTVELAAAQEKQMEVCTVCG 91 (102)
Q Consensus 17 ~i~~l~~~I~~ll~eaE~LGeeG~---VdeA~~l~~~ve~Lk~ek~~l~~~~~~~~~~~~~~~~~~~~qkl~VCeVCG 91 (102)
+|.+|+.+|..+--+.-...-.|+ -+.-..+-+++..|+.+|..|-.... ++ ...-..-..|+.|+
T Consensus 37 ~~~~id~~i~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~~lL~~~g---~~------~dyl~~~y~Cp~C~ 105 (329)
T PRK06835 37 EIAEIDDEIAKLGIKLSRAILKNPDKKEETLKELKEKITDLRVKKAELLVSNG---YP------PDYLEMKYTCPKCK 105 (329)
T ss_pred cHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHHHHcC---CC------hhhcCCCCCCCCCC
Confidence 456788888877555555444555 44556777888888888888765431 11 11122235799997
No 8
>COG3783 CybC Soluble cytochrome b562 [Energy production and conversion]
Probab=81.72 E-value=3.2 Score=27.80 Aligned_cols=27 Identities=19% Similarity=0.423 Sum_probs=22.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHHHHHH
Q psy2248 30 SEAERVGMEGSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 30 ~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 56 (102)
.++..|..+|++++|......+..++.
T Consensus 67 D~a~klaqeGnl~eAKaaak~l~d~Rn 93 (100)
T COG3783 67 DKADKLAQEGNLDEAKAAAKTLKDTRN 93 (100)
T ss_pred HHHHHHHHcCChHHHHHHHHHHHHHHH
Confidence 567789999999999999888877753
No 9
>PF12854 PPR_1: PPR repeat
Probab=79.58 E-value=3 Score=21.87 Aligned_cols=19 Identities=21% Similarity=0.219 Sum_probs=16.3
Q ss_pred HHHHHhcCCHHHHHHHHHH
Q psy2248 32 AERVGMEGSVEKAQGLMKL 50 (102)
Q Consensus 32 aE~LGeeG~VdeA~~l~~~ 50 (102)
+.-+...|+||+|..++.+
T Consensus 14 I~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 14 IDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHCCCHHHHHHHHHh
Confidence 5668899999999999875
No 10
>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=78.74 E-value=8.2 Score=20.70 Aligned_cols=35 Identities=26% Similarity=0.246 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q psy2248 23 EKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEE 57 (102)
Q Consensus 23 ~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 57 (102)
..|..+-.+.+.+.+..+.++|..+-.++..|+.+
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 56788888999999999999999998888888653
No 11
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=78.21 E-value=17 Score=27.89 Aligned_cols=18 Identities=22% Similarity=0.698 Sum_probs=13.8
Q ss_pred cccchhhhhhhhcccccC
Q psy2248 84 MEVCTVCGAFLIVGDAQS 101 (102)
Q Consensus 84 l~VCeVCGA~Ls~~D~d~ 101 (102)
+--|+-||+||...+++.
T Consensus 221 iv~CP~CgRILy~~e~~~ 238 (239)
T COG1579 221 IVFCPYCGRILYYDESEE 238 (239)
T ss_pred CccCCccchHHHhhhccc
Confidence 356999999998777653
No 12
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=77.02 E-value=12 Score=33.93 Aligned_cols=8 Identities=38% Similarity=1.352 Sum_probs=7.5
Q ss_pred ccchhhhh
Q psy2248 85 EVCTVCGA 92 (102)
Q Consensus 85 ~VCeVCGA 92 (102)
++|+|||+
T Consensus 504 ePCPVCGS 511 (1047)
T PRK10246 504 QPCPLCGS 511 (1047)
T ss_pred CCcCCCCc
Confidence 89999997
No 13
>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=75.15 E-value=11 Score=23.24 Aligned_cols=60 Identities=27% Similarity=0.435 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhhhhhhccccchhhhhhhhcccc
Q psy2248 24 KINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQNDNNHWSQTVELAAAQEKQMEVCTVCGAFLIVGDA 99 (102)
Q Consensus 24 ~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~~~~~~~~~~~~~~~~~~qkl~VCeVCGA~Ls~~D~ 99 (102)
+|+-|..-|-.+-..+..+-|..++.....+-.+- .+ ...+.-+...|.-||.+|+-+-|
T Consensus 2 Ri~~L~~~a~~~~~~~~~~lsr~y~~~~~~i~~k~-~~---------------~l~~~~kr~~Ck~C~~~liPG~~ 61 (85)
T PF04032_consen 2 RINFLYQAAHLLLADGSPSLSRHYMKLMRKISKKT-RI---------------RLPPEIKRTICKKCGSLLIPGVN 61 (85)
T ss_dssp HHHHHHHHHH-HHCCC-HHHHHHHHHHHHHHHHHC-T------------------STTCCCTB-TTT--B--CTTT
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHh-CC---------------CCChHHhcccccCCCCEEeCCCc
Confidence 45666666665667888888888887777764321 11 12244578999999999987765
No 14
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=74.38 E-value=4.8 Score=31.87 Aligned_cols=28 Identities=21% Similarity=0.298 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q psy2248 29 VSEAERVGMEGSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 29 l~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 56 (102)
...|++.-..|||++|++|+.++|+|--
T Consensus 261 ~~aI~~AVk~gDi~KAL~LldEAe~LG~ 288 (303)
T PRK10564 261 NQAIKQAVKKGDVDKALKLLDEAERLGS 288 (303)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence 4677888899999999999999999843
No 15
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=73.36 E-value=7.8 Score=34.47 Aligned_cols=34 Identities=15% Similarity=0.395 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q psy2248 22 SEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLK 55 (102)
Q Consensus 22 ~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk 55 (102)
...+..||..+++|.++|+.++|+.++.+++.+-
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 4567899999999999999999999999887764
No 16
>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=72.75 E-value=26 Score=23.51 Aligned_cols=52 Identities=21% Similarity=0.302 Sum_probs=36.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhc--CCHHHHHHHHHHHHHHHHHHHHHH
Q psy2248 11 QNENAEQITLLSEKINNLVSEAERVGME--GSVEKAQGLMKLCDQLKEEREMLR 62 (102)
Q Consensus 11 ~~~~~e~i~~l~~~I~~ll~eaE~LGee--G~VdeA~~l~~~ve~Lk~ek~~l~ 62 (102)
+.+....|..++.+|+.++.+++.|-.. .-+++-..|-.+-+.|+.....+.
T Consensus 3 k~~l~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~ 56 (107)
T PF06156_consen 3 KKELFDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELE 56 (107)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4467788899999999999999888764 345555556666666665555544
No 17
>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=72.60 E-value=8.3 Score=34.50 Aligned_cols=34 Identities=18% Similarity=0.412 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q psy2248 23 EKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 23 ~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 56 (102)
..+..||..+|+|.++|+-++|+.++.+++.+-+
T Consensus 568 ~dLq~Mmd~ieela~~G~~~~A~qlL~qlq~mme 601 (851)
T TIGR02302 568 QDLQNMMDQIENLARSGDRDQAKQLLSQLQQMMN 601 (851)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 3488999999999999999999999999888754
No 18
>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=72.07 E-value=28 Score=23.71 Aligned_cols=53 Identities=26% Similarity=0.291 Sum_probs=43.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q psy2248 11 QNENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRK 63 (102)
Q Consensus 11 ~~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~ 63 (102)
.......+..|+.+|..+..++-.+...|+.+.|..++...-.++.....+..
T Consensus 10 ~~~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~ 62 (171)
T PF03357_consen 10 IRRLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLN 62 (171)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567788999999999999999999999999999998888887776666544
No 19
>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=71.28 E-value=20 Score=23.24 Aligned_cols=50 Identities=28% Similarity=0.312 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy2248 14 NAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQN 65 (102)
Q Consensus 14 ~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~~ 65 (102)
...++..+..+-+.+-+++-.+-..| +++..+..++..++.+...++...
T Consensus 41 l~~~~e~lr~~rN~~sk~I~~~~~~~--~~~~~l~~e~~~lk~~i~~le~~~ 90 (108)
T PF02403_consen 41 LQQELEELRAERNELSKEIGKLKKAG--EDAEELKAEVKELKEEIKELEEQL 90 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCHTT--CCTHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhHHHHHHHHHhhCc--ccHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566777777777777777787777 667778888888888887777653
No 20
>PF14282 FlxA: FlxA-like protein
Probab=70.69 E-value=28 Score=23.04 Aligned_cols=47 Identities=23% Similarity=0.295 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCC--HHH----HHHHHHHHHHHHHHHHHH
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGS--VEK----AQGLMKLCDQLKEEREML 61 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~--Vde----A~~l~~~ve~Lk~ek~~l 61 (102)
...|..|..+|..|..++..|...++ -++ .+.|-.++..|..+...+
T Consensus 18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~ql 70 (106)
T PF14282_consen 18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQL 70 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999999433 222 233444444444444444
No 21
>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=68.26 E-value=1.5 Score=31.14 Aligned_cols=17 Identities=35% Similarity=0.489 Sum_probs=14.7
Q ss_pred cccchhhhhhhhccccc
Q psy2248 84 MEVCTVCGAFLIVGDAQ 100 (102)
Q Consensus 84 l~VCeVCGA~Ls~~D~d 100 (102)
-+.|++||+-|.-.||.
T Consensus 128 ~F~Cp~Cg~~L~~~dn~ 144 (158)
T TIGR00373 128 NFTCPRCGAMLDYLDNS 144 (158)
T ss_pred CCcCCCCCCEeeeccCH
Confidence 58999999999888875
No 22
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.46 E-value=1.7 Score=31.47 Aligned_cols=17 Identities=29% Similarity=0.401 Sum_probs=14.6
Q ss_pred cccchhhhhhhhccccc
Q psy2248 84 MEVCTVCGAFLIVGDAQ 100 (102)
Q Consensus 84 l~VCeVCGA~Ls~~D~d 100 (102)
-+.|++||..|.-.||.
T Consensus 136 ~F~Cp~Cg~~L~~~dn~ 152 (178)
T PRK06266 136 GFRCPQCGEMLEEYDNS 152 (178)
T ss_pred CCcCCCCCCCCeecccH
Confidence 48999999999888875
No 23
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=66.55 E-value=1.5 Score=27.17 Aligned_cols=9 Identities=56% Similarity=1.490 Sum_probs=7.8
Q ss_pred cccchhhhh
Q psy2248 84 MEVCTVCGA 92 (102)
Q Consensus 84 l~VCeVCGA 92 (102)
-++|+|||.
T Consensus 18 ~e~CP~Cgs 26 (64)
T COG2093 18 TEICPVCGS 26 (64)
T ss_pred CccCCCCCC
Confidence 478999997
No 24
>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=65.67 E-value=36 Score=24.06 Aligned_cols=54 Identities=24% Similarity=0.270 Sum_probs=45.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy2248 12 NENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQN 65 (102)
Q Consensus 12 ~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~~ 65 (102)
....++...+..+|.++.++....-.+.+.-+.-++-++++++..|.+.+.+..
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 345567788899999999999999999999999999999999999998887653
No 25
>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=65.57 E-value=1.9 Score=23.56 Aligned_cols=16 Identities=38% Similarity=0.681 Sum_probs=11.3
Q ss_pred hhhccccchhhhhhhh
Q psy2248 80 QEKQMEVCTVCGAFLI 95 (102)
Q Consensus 80 ~~qkl~VCeVCGA~Ls 95 (102)
+-+.--+||+||.-|+
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 3456689999998665
No 26
>PRK11020 hypothetical protein; Provisional
Probab=65.38 E-value=42 Score=23.12 Aligned_cols=49 Identities=20% Similarity=0.305 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRK 63 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~ 63 (102)
..+|..|+.+++.+-.+...+-..|+.+---.+..+++.|..+...+..
T Consensus 4 K~Eiq~L~drLD~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~lk~ 52 (118)
T PRK11020 4 KNEIKRLSDRLDAIRHKLAAASLRGDAEKYAQFEKEKATLEAEIARLKE 52 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578889999999999999999999999999999999999888888765
No 27
>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=64.60 E-value=52 Score=23.93 Aligned_cols=53 Identities=25% Similarity=0.310 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy2248 13 ENAEQITLLSEKINNLVSEAERVGME-GSVEKAQGLMKLCDQLKEEREMLRKQN 65 (102)
Q Consensus 13 ~~~e~i~~l~~~I~~ll~eaE~LGee-G~VdeA~~l~~~ve~Lk~ek~~l~~~~ 65 (102)
...+++..+..+|..+-.+++.+... ++-++=..++.+++.|+.+...|....
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 34566777777788877777776432 444567788999999998888887754
No 28
>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=64.50 E-value=2.2 Score=22.89 Aligned_cols=11 Identities=45% Similarity=0.929 Sum_probs=8.6
Q ss_pred ccccchhhhhh
Q psy2248 83 QMEVCTVCGAF 93 (102)
Q Consensus 83 kl~VCeVCGA~ 93 (102)
...+|+|||+-
T Consensus 17 ~p~~CP~Cg~~ 27 (34)
T cd00729 17 APEKCPICGAP 27 (34)
T ss_pred CCCcCcCCCCc
Confidence 34799999983
No 29
>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=64.50 E-value=2.2 Score=22.01 Aligned_cols=14 Identities=36% Similarity=0.954 Sum_probs=7.5
Q ss_pred chhhhhhhhccccc
Q psy2248 87 CTVCGAFLIVGDAQ 100 (102)
Q Consensus 87 CeVCGA~Ls~~D~d 100 (102)
|++||+-|...+.+
T Consensus 2 CP~C~s~l~~~~~e 15 (28)
T PF03119_consen 2 CPVCGSKLVREEGE 15 (28)
T ss_dssp -TTT--BEEE-CCT
T ss_pred cCCCCCEeEcCCCC
Confidence 99999998865543
No 30
>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=63.50 E-value=25 Score=22.11 Aligned_cols=13 Identities=38% Similarity=0.626 Sum_probs=10.1
Q ss_pred cccchhhhhhhhc
Q psy2248 84 MEVCTVCGAFLIV 96 (102)
Q Consensus 84 l~VCeVCGA~Ls~ 96 (102)
-..|.|||-.|..
T Consensus 78 ~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 78 STKCSVCGKPLGN 90 (109)
T ss_pred CCCccCcCCcCCC
Confidence 3779999987753
No 31
>TIGR01554 major_cap_HK97 phage major capsid protein, HK97 family. This family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease.
Probab=60.26 E-value=32 Score=27.05 Aligned_cols=35 Identities=17% Similarity=0.093 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHH
Q psy2248 20 LLSEKINNLVSEAERVGM--EGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 20 ~l~~~I~~ll~eaE~LGe--eG~VdeA~~l~~~ve~L 54 (102)
+|.++++.+-.++..|-+ +...+++-+...++..|
T Consensus 3 el~~~~~~~~~~~r~l~~~~~~~~~~~~~~~~~~~~l 39 (378)
T TIGR01554 3 ELKEQREEIVAEIRSLLDKAEKLEKELTAAALEKEEL 39 (378)
T ss_pred hHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHH
Confidence 344444444444444444 33344444443333333
No 32
>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=58.52 E-value=2.8 Score=23.10 Aligned_cols=13 Identities=38% Similarity=0.884 Sum_probs=10.4
Q ss_pred ccchhhhhhhhcc
Q psy2248 85 EVCTVCGAFLIVG 97 (102)
Q Consensus 85 ~VCeVCGA~Ls~~ 97 (102)
+.|+.||+.|+.-
T Consensus 2 ~~CP~Cg~~lv~r 14 (39)
T PF01396_consen 2 EKCPKCGGPLVLR 14 (39)
T ss_pred cCCCCCCceeEEE
Confidence 5799999988753
No 33
>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=57.76 E-value=13 Score=21.49 Aligned_cols=10 Identities=40% Similarity=0.909 Sum_probs=5.1
Q ss_pred cchhhhhhhh
Q psy2248 86 VCTVCGAFLI 95 (102)
Q Consensus 86 VCeVCGA~Ls 95 (102)
+|+|||.=|.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 9999997654
No 34
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=57.48 E-value=3 Score=25.09 Aligned_cols=12 Identities=25% Similarity=0.960 Sum_probs=8.7
Q ss_pred ccccchhhhhhh
Q psy2248 83 QMEVCTVCGAFL 94 (102)
Q Consensus 83 kl~VCeVCGA~L 94 (102)
+|++|.-||.|=
T Consensus 4 ~mr~C~~CgvYT 15 (56)
T PRK13130 4 KIRKCPKCGVYT 15 (56)
T ss_pred cceECCCCCCEE
Confidence 577888888763
No 35
>PLN00204 CP12 gene family protein; Provisional
Probab=57.16 E-value=46 Score=23.21 Aligned_cols=43 Identities=19% Similarity=0.228 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHHHHHHHHHH
Q psy2248 20 LLSEKINNLVSEAERVGMEG-SVEKAQGLMKLCDQLKEEREMLR 62 (102)
Q Consensus 20 ~l~~~I~~ll~eaE~LGeeG-~VdeA~~l~~~ve~Lk~ek~~l~ 62 (102)
.|+++|.+.+++|+.+-.+| .-.++-.....||+|..++.-..
T Consensus 56 ~L~e~Ie~aI~eArevCa~g~~S~eCaaAWDeVEELqAeasHqr 99 (126)
T PLN00204 56 GISEKVEKSIKEAEETCADDPASGECVAAWDEVEELSAAASHAR 99 (126)
T ss_pred cHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 58899999999999988876 44678889999999988775443
No 36
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=56.48 E-value=52 Score=21.28 Aligned_cols=38 Identities=16% Similarity=0.175 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q psy2248 19 TLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 19 ~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 56 (102)
..+-..|...+.+...+.+.|+.++|..++..+...-.
T Consensus 22 ~~~kS~~kT~iKk~~~ai~~~d~~~a~~~l~~a~s~iD 59 (87)
T TIGR00029 22 ASQKSKMKTIIKKVYAAIAAGDKDKAQEAFKEAAKKLD 59 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 36677888999999999999999999999988877643
No 37
>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=56.36 E-value=4 Score=24.51 Aligned_cols=9 Identities=56% Similarity=1.246 Sum_probs=3.0
Q ss_pred ccchhhhhh
Q psy2248 85 EVCTVCGAF 93 (102)
Q Consensus 85 ~VCeVCGA~ 93 (102)
.+|++|||-
T Consensus 34 y~Cp~CgAt 42 (55)
T PF05741_consen 34 YVCPICGAT 42 (55)
T ss_dssp ---TTT---
T ss_pred CcCCCCcCc
Confidence 799999984
No 38
>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=56.16 E-value=14 Score=20.34 Aligned_cols=13 Identities=23% Similarity=1.096 Sum_probs=6.0
Q ss_pred hhccccchhhhhh
Q psy2248 81 EKQMEVCTVCGAF 93 (102)
Q Consensus 81 ~qkl~VCeVCGA~ 93 (102)
..+.+.|.+||.|
T Consensus 14 ~~~i~~C~~C~nl 26 (41)
T PF02132_consen 14 KENIKFCSICGNL 26 (41)
T ss_dssp HHH-EE-SSS--E
T ss_pred HHcCCccCCCCCc
Confidence 3456778888865
No 39
>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=55.74 E-value=21 Score=16.93 Aligned_cols=22 Identities=14% Similarity=0.081 Sum_probs=17.7
Q ss_pred HHHHHhcCCHHHHHHHHHHHHH
Q psy2248 32 AERVGMEGSVEKAQGLMKLCDQ 53 (102)
Q Consensus 32 aE~LGeeG~VdeA~~l~~~ve~ 53 (102)
+..++..|++++|..++.+..+
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 7 ISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHccchHHHHHHHHHHHhH
Confidence 4678899999999999877543
No 40
>KOG4765|consensus
Probab=55.63 E-value=4.5 Score=33.17 Aligned_cols=16 Identities=44% Similarity=0.816 Sum_probs=13.1
Q ss_pred hccccchhhhhhhhcc
Q psy2248 82 KQMEVCTVCGAFLIVG 97 (102)
Q Consensus 82 qkl~VCeVCGA~Ls~~ 97 (102)
.-+-+|++||+||...
T Consensus 88 ~D~lkCe~C~a~L~~s 103 (419)
T KOG4765|consen 88 CDMLKCESCGAFLCAS 103 (419)
T ss_pred CCeeehhhhhhHHhcc
Confidence 4678999999999753
No 41
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=55.26 E-value=3.8 Score=21.96 Aligned_cols=13 Identities=38% Similarity=0.823 Sum_probs=10.1
Q ss_pred cccchhhhhhhhc
Q psy2248 84 MEVCTVCGAFLIV 96 (102)
Q Consensus 84 l~VCeVCGA~Ls~ 96 (102)
+..|.+||+.+++
T Consensus 3 ~~~C~~C~~~~i~ 15 (33)
T PF08792_consen 3 LKKCSKCGGNGIV 15 (33)
T ss_pred ceEcCCCCCCeEE
Confidence 4678888888776
No 42
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=55.05 E-value=3.3 Score=28.86 Aligned_cols=16 Identities=31% Similarity=0.501 Sum_probs=14.0
Q ss_pred ccchhhhhhhhccccc
Q psy2248 85 EVCTVCGAFLIVGDAQ 100 (102)
Q Consensus 85 ~VCeVCGA~Ls~~D~d 100 (102)
.+|+.||+-|...||.
T Consensus 124 f~Cp~Cg~~l~~~dn~ 139 (147)
T smart00531 124 FTCPRCGEELEEDDNS 139 (147)
T ss_pred EECCCCCCEEEEcCch
Confidence 8999999999888874
No 43
>PF14828 Amnionless: Amnionless
Probab=54.82 E-value=3.3 Score=34.08 Aligned_cols=14 Identities=29% Similarity=0.857 Sum_probs=11.2
Q ss_pred ccchhhhhhhhccc
Q psy2248 85 EVCTVCGAFLIVGD 98 (102)
Q Consensus 85 ~VCeVCGA~Ls~~D 98 (102)
.=|+||||+++..-
T Consensus 227 hCC~iCGa~v~~~~ 240 (437)
T PF14828_consen 227 HCCPICGAIVTLEY 240 (437)
T ss_pred CchhhcceEEEEee
Confidence 67999999887643
No 44
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=54.69 E-value=68 Score=28.47 Aligned_cols=10 Identities=50% Similarity=0.913 Sum_probs=7.9
Q ss_pred cccchhhhhh
Q psy2248 84 MEVCTVCGAF 93 (102)
Q Consensus 84 l~VCeVCGA~ 93 (102)
...|+|||.-
T Consensus 457 ~~~CPvCg~~ 466 (908)
T COG0419 457 GEKCPVCGQE 466 (908)
T ss_pred CCCCCCCCCC
Confidence 4789999943
No 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=54.48 E-value=4.7 Score=20.07 Aligned_cols=9 Identities=33% Similarity=1.158 Sum_probs=7.8
Q ss_pred cccchhhhh
Q psy2248 84 MEVCTVCGA 92 (102)
Q Consensus 84 l~VCeVCGA 92 (102)
|..|.+||-
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 678999995
No 46
>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=53.97 E-value=24 Score=17.06 Aligned_cols=21 Identities=19% Similarity=0.359 Sum_probs=17.1
Q ss_pred HHHHHHHHhcCCHHHHHHHHH
Q psy2248 29 VSEAERVGMEGSVEKAQGLMK 49 (102)
Q Consensus 29 l~eaE~LGeeG~VdeA~~l~~ 49 (102)
+.-+..+...|+.++|..++.
T Consensus 5 ~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 5 LALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHcCCHHHHHHHHh
Confidence 345778889999999998875
No 47
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=53.92 E-value=4.5 Score=29.58 Aligned_cols=19 Identities=26% Similarity=0.284 Sum_probs=16.2
Q ss_pred ccccchhhhhhhhcccccC
Q psy2248 83 QMEVCTVCGAFLIVGDAQS 101 (102)
Q Consensus 83 kl~VCeVCGA~Ls~~D~d~ 101 (102)
..+.|+.||+-|--.|+..
T Consensus 131 ~~F~Cp~Cg~~L~~~d~s~ 149 (176)
T COG1675 131 LGFTCPKCGEDLEEYDSSE 149 (176)
T ss_pred hCCCCCCCCchhhhccchH
Confidence 4499999999999888864
No 48
>PRK01156 chromosome segregation protein; Provisional
Probab=53.10 E-value=71 Score=28.05 Aligned_cols=10 Identities=20% Similarity=0.115 Sum_probs=5.5
Q ss_pred cchhhhhhhh
Q psy2248 86 VCTVCGAFLI 95 (102)
Q Consensus 86 VCeVCGA~Ls 95 (102)
+|+||+.-++
T Consensus 451 ~~~~Cp~c~~ 460 (895)
T PRK01156 451 GQSVCPVCGT 460 (895)
T ss_pred cCCCCCCCCC
Confidence 5666665444
No 49
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=52.97 E-value=84 Score=22.77 Aligned_cols=8 Identities=63% Similarity=1.406 Sum_probs=6.0
Q ss_pred cccchhhh
Q psy2248 84 MEVCTVCG 91 (102)
Q Consensus 84 l~VCeVCG 91 (102)
-.||.|||
T Consensus 134 ~~vC~vCG 141 (166)
T COG1592 134 VWVCPVCG 141 (166)
T ss_pred EEEcCCCC
Confidence 57777777
No 50
>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=52.72 E-value=4.6 Score=21.29 Aligned_cols=10 Identities=60% Similarity=1.066 Sum_probs=8.2
Q ss_pred ccccchhhhh
Q psy2248 83 QMEVCTVCGA 92 (102)
Q Consensus 83 kl~VCeVCGA 92 (102)
.-.+|++||+
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4479999997
No 51
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=52.22 E-value=4.1 Score=22.79 Aligned_cols=18 Identities=22% Similarity=0.375 Sum_probs=14.9
Q ss_pred ccchhhhhhhhcccccCC
Q psy2248 85 EVCTVCGAFLIVGDAQSV 102 (102)
Q Consensus 85 ~VCeVCGA~Ls~~D~d~~ 102 (102)
-||..|++.+-..|+++|
T Consensus 4 IvCq~C~~~Id~~e~ekV 21 (38)
T PF13790_consen 4 IVCQHCNETIDHFETEKV 21 (38)
T ss_pred EEeccccceeeeecCCcE
Confidence 689999998888877765
No 52
>PRK12496 hypothetical protein; Provisional
Probab=52.11 E-value=5 Score=28.66 Aligned_cols=12 Identities=33% Similarity=0.935 Sum_probs=9.0
Q ss_pred ccchhhhhhhhc
Q psy2248 85 EVCTVCGAFLIV 96 (102)
Q Consensus 85 ~VCeVCGA~Ls~ 96 (102)
.+|+|||.-|.+
T Consensus 144 ~~C~~CG~~~~r 155 (164)
T PRK12496 144 DVCEICGSPVKR 155 (164)
T ss_pred CcCCCCCChhhh
Confidence 679999986653
No 53
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=51.80 E-value=3.6 Score=25.77 Aligned_cols=13 Identities=54% Similarity=1.002 Sum_probs=11.3
Q ss_pred hhccccchhhhhh
Q psy2248 81 EKQMEVCTVCGAF 93 (102)
Q Consensus 81 ~qkl~VCeVCGA~ 93 (102)
-+-|-+|.-||||
T Consensus 40 LkAMi~Cq~CGAF 52 (69)
T PF13922_consen 40 LKAMIMCQGCGAF 52 (69)
T ss_pred hHHHHHHhhccch
Confidence 3578999999999
No 54
>PF13041 PPR_2: PPR repeat family
Probab=51.54 E-value=29 Score=18.93 Aligned_cols=22 Identities=23% Similarity=0.188 Sum_probs=17.9
Q ss_pred HHHHHhcCCHHHHHHHHHHHHH
Q psy2248 32 AERVGMEGSVEKAQGLMKLCDQ 53 (102)
Q Consensus 32 aE~LGeeG~VdeA~~l~~~ve~ 53 (102)
+.-+...|++++|.+++.+..+
T Consensus 10 i~~~~~~~~~~~a~~l~~~M~~ 31 (50)
T PF13041_consen 10 ISGYCKAGKFEEALKLFKEMKK 31 (50)
T ss_pred HHHHHHCcCHHHHHHHHHHHHH
Confidence 4567889999999999987654
No 55
>PHA02562 46 endonuclease subunit; Provisional
Probab=51.16 E-value=1.4e+02 Score=24.48 Aligned_cols=12 Identities=25% Similarity=0.537 Sum_probs=9.4
Q ss_pred cccchhhhhhhh
Q psy2248 84 MEVCTVCGAFLI 95 (102)
Q Consensus 84 l~VCeVCGA~Ls 95 (102)
-..|+.||.-+.
T Consensus 284 ~~~Cp~C~~~~~ 295 (562)
T PHA02562 284 GGVCPTCTQQIS 295 (562)
T ss_pred CCCCCCCCCcCC
Confidence 469999997664
No 56
>PRK02224 chromosome segregation protein; Provisional
Probab=51.00 E-value=1.2e+02 Score=26.53 Aligned_cols=12 Identities=25% Similarity=0.548 Sum_probs=9.1
Q ss_pred cccchhhhhhhh
Q psy2248 84 MEVCTVCGAFLI 95 (102)
Q Consensus 84 l~VCeVCGA~Ls 95 (102)
-.+|++||.-+.
T Consensus 451 ~~~Cp~C~r~~~ 462 (880)
T PRK02224 451 AGKCPECGQPVE 462 (880)
T ss_pred cccCCCCCCcCC
Confidence 478999997543
No 57
>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=50.91 E-value=81 Score=21.86 Aligned_cols=40 Identities=18% Similarity=0.174 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q psy2248 12 NENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLC 51 (102)
Q Consensus 12 ~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~v 51 (102)
.+....|.+=+.++..-+-.+-.+-..|++|.|-..|..+
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 3566778888888888899999999999999999988765
No 58
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=50.75 E-value=65 Score=21.20 Aligned_cols=38 Identities=13% Similarity=0.045 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q psy2248 17 QITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 17 ~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~L 54 (102)
-+......|...+..+++....++.++|.+.+.++...
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 44556788899999999999999999999998888776
No 59
>TIGR00009 L28 ribosomal protein L28. This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture and are not included.
Probab=50.33 E-value=5 Score=23.90 Aligned_cols=10 Identities=20% Similarity=0.341 Sum_probs=8.0
Q ss_pred ccchhhhhhh
Q psy2248 85 EVCTVCGAFL 94 (102)
Q Consensus 85 ~VCeVCGA~L 94 (102)
++|++||.--
T Consensus 3 ~~C~i~GK~~ 12 (56)
T TIGR00009 3 RKCQLTGKGP 12 (56)
T ss_pred CEeeeCCCcC
Confidence 6899999643
No 60
>PRK03954 ribonuclease P protein component 4; Validated
Probab=49.15 E-value=36 Score=23.44 Aligned_cols=63 Identities=25% Similarity=0.353 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhhhhhhccccchhhhhhhhcccccC
Q psy2248 22 SEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQNDNNHWSQTVELAAAQEKQMEVCTVCGAFLIVGDAQS 101 (102)
Q Consensus 22 ~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~~~~~~~~~~~~~~~~~~qkl~VCeVCGA~Ls~~D~d~ 101 (102)
.+.|+-|+.-|+.... ++-+-|-.....+..+-. |..+ ...++-|-.+|.-|.+||+-+-|-+
T Consensus 19 ~eRi~~L~~~A~~~~~-~~pelar~Yv~lar~Is~-K~ri---------------rlp~~~KR~~CK~C~t~LiPG~n~~ 81 (121)
T PRK03954 19 RERIDTLFTLAERVFP-YSPELANRYVELALAVQQ-KAKV---------------KLPRKWKRRYCKRCHSFLVPGVNAR 81 (121)
T ss_pred HHHHHHHHHHHHHHhh-cCHHHHHHHHHHHHHHHH-Hhcc---------------CCCHHHHHHHhhcCCCeeecCCceE
Confidence 4788999999988774 466777666665555432 1111 1123456789999999999776543
No 61
>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=49.05 E-value=69 Score=20.47 Aligned_cols=37 Identities=11% Similarity=0.119 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q psy2248 19 TLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLK 55 (102)
Q Consensus 19 ~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk 55 (102)
......|...+.+++.+.+.|+-++|..++..+...-
T Consensus 21 r~~kS~~rT~iKk~~~ai~~~~~~~a~~~l~~a~s~i 57 (84)
T PF01649_consen 21 RSRKSRVRTAIKKFREAIEAGDKEEAKELLRKAYSAI 57 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHH
Confidence 3667889999999999999999999999998888764
No 62
>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=48.95 E-value=5.7 Score=29.57 Aligned_cols=10 Identities=30% Similarity=0.773 Sum_probs=0.0
Q ss_pred ccchhhhhhh
Q psy2248 85 EVCTVCGAFL 94 (102)
Q Consensus 85 ~VCeVCGA~L 94 (102)
..|+|||-+-
T Consensus 102 y~CEICGN~~ 111 (196)
T PF11931_consen 102 YKCEICGNQS 111 (196)
T ss_dssp ----------
T ss_pred eeeEeCCCcc
Confidence 8999999763
No 63
>KOG3032|consensus
Probab=48.76 E-value=1e+02 Score=23.96 Aligned_cols=31 Identities=13% Similarity=0.169 Sum_probs=25.6
Q ss_pred HhcCCHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy2248 36 GMEGSVEKAQGLMKLCDQLKEEREMLRKQND 66 (102)
Q Consensus 36 GeeG~VdeA~~l~~~ve~Lk~ek~~l~~~~~ 66 (102)
.+.|++|+=+.....++.|+.++..|....+
T Consensus 198 reieeidEQi~~~kkvekl~~qK~ellnkkR 228 (264)
T KOG3032|consen 198 REIEEIDEQISYKKKVEKLKRQKMELLNKKR 228 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3457899999999999999999988877643
No 64
>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=48.33 E-value=5.3 Score=21.73 Aligned_cols=14 Identities=43% Similarity=0.883 Sum_probs=10.0
Q ss_pred ccchhhhhhhhccc
Q psy2248 85 EVCTVCGAFLIVGD 98 (102)
Q Consensus 85 ~VCeVCGA~Ls~~D 98 (102)
..|++||+.....|
T Consensus 9 ~~C~~C~~~~~~~~ 22 (36)
T PF11781_consen 9 EPCPVCGSRWFYSD 22 (36)
T ss_pred CcCCCCCCeEeEcc
Confidence 45999999854443
No 65
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=47.93 E-value=74 Score=20.54 Aligned_cols=38 Identities=13% Similarity=0.173 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q psy2248 19 TLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 19 ~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 56 (102)
..+-..|...+.+...+.+.|+.++|..++..+..+-.
T Consensus 22 ~~~kS~~kT~iKk~~~ai~~~~~~~a~~~~~~a~s~iD 59 (88)
T PRK00239 22 KSRKSRVRTAIKKVEAAIAAGDKEAAEEALKAAQSKID 59 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 36677888899999999999999999999998887643
No 66
>KOG4602|consensus
Probab=47.64 E-value=6.1 Score=31.03 Aligned_cols=8 Identities=63% Similarity=1.493 Sum_probs=7.2
Q ss_pred ccchhhhh
Q psy2248 85 EVCTVCGA 92 (102)
Q Consensus 85 ~VCeVCGA 92 (102)
.||.+|||
T Consensus 269 YVCPiCGA 276 (318)
T KOG4602|consen 269 YVCPICGA 276 (318)
T ss_pred hcCccccc
Confidence 79999998
No 67
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=46.88 E-value=88 Score=21.12 Aligned_cols=51 Identities=22% Similarity=0.247 Sum_probs=33.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhc--CCHHHHHHHHHHHHHHHHHHHHH
Q psy2248 11 QNENAEQITLLSEKINNLVSEAERVGME--GSVEKAQGLMKLCDQLKEEREML 61 (102)
Q Consensus 11 ~~~~~e~i~~l~~~I~~ll~eaE~LGee--G~VdeA~~l~~~ve~Lk~ek~~l 61 (102)
+.+....+..++..|+.++.+++.|-.. .-+++=..|-.+-+.|+.....+
T Consensus 3 k~elfd~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~ 55 (110)
T PRK13169 3 KKEIFDALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL 55 (110)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3566778899999999999999888653 33444444555555555544444
No 68
>KOG3576|consensus
Probab=46.52 E-value=6.3 Score=30.16 Aligned_cols=12 Identities=33% Similarity=0.816 Sum_probs=10.1
Q ss_pred hhccccchhhhh
Q psy2248 81 EKQMEVCTVCGA 92 (102)
Q Consensus 81 ~qkl~VCeVCGA 92 (102)
.-||.|||-||.
T Consensus 209 r~kl~vcedcg~ 220 (267)
T KOG3576|consen 209 RAKLYVCEDCGY 220 (267)
T ss_pred hhheeeecccCC
Confidence 348999999995
No 69
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=46.51 E-value=1e+02 Score=25.15 Aligned_cols=48 Identities=25% Similarity=0.306 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q psy2248 14 NAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRK 63 (102)
Q Consensus 14 ~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~ 63 (102)
...+++.|..+.+.+-+++-.+...+. ++..+..++..++.+.+.++.
T Consensus 40 l~~~~~~lr~~rn~~sk~i~~~~~~~~--~~~~l~~~~~~l~~~~~~~~~ 87 (425)
T PRK05431 40 LQTELEELQAERNALSKEIGQAKRKGE--DAEALIAEVKELKEEIKALEA 87 (425)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCC--cHHHHHHHHHHHHHHHHHHHH
Confidence 345666777777777777766544441 233455555555555544443
No 70
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=46.51 E-value=68 Score=23.65 Aligned_cols=46 Identities=20% Similarity=0.172 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Q psy2248 17 QITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLR 62 (102)
Q Consensus 17 ~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~ 62 (102)
++..+..+|..|=.+|+.|-.+++-..-.-+-..++.|+-+...+-
T Consensus 106 eL~s~~~ei~~L~~kI~~L~~~in~~~k~~~n~~i~slk~EL~d~i 151 (181)
T PF04645_consen 106 ELKSIKKEIEILRLKISSLQKEINKNKKKDLNEEIESLKSELNDLI 151 (181)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHHH
Confidence 4445566666666666666666655444444445555555554443
No 71
>COG1422 Predicted membrane protein [Function unknown]
Probab=46.26 E-value=1.2e+02 Score=22.78 Aligned_cols=40 Identities=18% Similarity=0.283 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREML 61 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l 61 (102)
.+++..+.+..++.-++.+++-++||- .++++|++++.+.
T Consensus 71 ~ekm~~~qk~m~efq~e~~eA~~~~d~-------~~lkkLq~~qmem 110 (201)
T COG1422 71 QEKMKELQKMMKEFQKEFREAQESGDM-------KKLKKLQEKQMEM 110 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCH-------HHHHHHHHHHHHH
Confidence 467788888888888888888888874 4455565555444
No 72
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=45.91 E-value=54 Score=18.38 Aligned_cols=35 Identities=23% Similarity=0.317 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Q psy2248 21 LSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEE 57 (102)
Q Consensus 21 l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~e 57 (102)
+-.+|.+|+..++.- .+.-.||...+.++.+|..+
T Consensus 3 il~kI~kLLalA~~~--~~~~~EA~~A~~kAq~Lm~k 37 (43)
T PF10979_consen 3 ILEKIRKLLALAEST--GSNEHEAEAALAKAQRLMAK 37 (43)
T ss_pred HHHHHHHHHHHhhCC--CCCHHHHHHHHHHHHHHHHH
Confidence 446778888777632 26667999999999988654
No 73
>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=45.70 E-value=6.5 Score=17.87 Aligned_cols=9 Identities=33% Similarity=1.113 Sum_probs=5.4
Q ss_pred cchhhhhhh
Q psy2248 86 VCTVCGAFL 94 (102)
Q Consensus 86 VCeVCGA~L 94 (102)
.|++||.-.
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 699999754
No 74
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=45.23 E-value=5.4 Score=30.57 Aligned_cols=17 Identities=41% Similarity=0.901 Sum_probs=13.8
Q ss_pred hccccchhhhhhhhccc
Q psy2248 82 KQMEVCTVCGAFLIVGD 98 (102)
Q Consensus 82 qkl~VCeVCGA~Ls~~D 98 (102)
-+.+||+.||.|+=+.|
T Consensus 236 ~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 236 YRVEVCESCGSYLKTVD 252 (290)
T ss_dssp EEEEEETTTTEEEEEEE
T ss_pred EEEEECCcccchHHHHh
Confidence 46689999999987776
No 75
>PLN02678 seryl-tRNA synthetase
Probab=44.92 E-value=1.1e+02 Score=25.38 Aligned_cols=47 Identities=21% Similarity=0.261 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRK 63 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~ 63 (102)
..++..|..+++.+-+++-.+-..+ +++..+.+++..|+.+...++.
T Consensus 46 ~~~~e~lr~erN~~sk~I~~~k~~~--~~~~~l~~~~~~Lk~ei~~le~ 92 (448)
T PLN02678 46 QFELDSLRKEFNKLNKEVAKLKIAK--EDATELIAETKELKKEITEKEA 92 (448)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCC--CcHHHHHHHHHHHHHHHHHHHH
Confidence 4456667777777777665544444 3444555555555555555443
No 76
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=44.81 E-value=36 Score=21.00 Aligned_cols=21 Identities=33% Similarity=0.430 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q psy2248 17 QITLLSEKINNLVSEAERVGM 37 (102)
Q Consensus 17 ~i~~l~~~I~~ll~eaE~LGe 37 (102)
-+.+|+++|..+..+|+.|-.
T Consensus 26 sV~El~eRIalLq~EIeRlkA 46 (65)
T COG5509 26 SVAELEERIALLQAEIERLKA 46 (65)
T ss_pred hHHHHHHHHHHHHHHHHHHHH
Confidence 356788888888777776643
No 77
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=44.44 E-value=8.1 Score=22.48 Aligned_cols=16 Identities=25% Similarity=0.648 Sum_probs=12.6
Q ss_pred ccccchhhhh-hhhccc
Q psy2248 83 QMEVCTVCGA-FLIVGD 98 (102)
Q Consensus 83 kl~VCeVCGA-~Ls~~D 98 (102)
..+.|+.||+ ||....
T Consensus 19 ~~~fCP~Cg~~~m~~~~ 35 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL 35 (50)
T ss_pred ccCcCcCCCcchheccC
Confidence 4579999999 887654
No 78
>PF14863 Alkyl_sulf_dimr: Alkyl sulfatase dimerisation; PDB: 2YHE_C 2CG2_A 2CG3_A 2CFU_A 2CFZ_A.
Probab=43.49 E-value=66 Score=22.45 Aligned_cols=52 Identities=17% Similarity=0.189 Sum_probs=40.5
Q ss_pred CCccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q psy2248 3 PSRLSQSQQNENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 3 ~~~~~~~~~~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~L 54 (102)
|..+.+..+.+.++++.++---...+++.++++-.+|+..-|..+...+-..
T Consensus 48 P~~L~pl~p~~~A~~~v~l~GG~d~vl~~A~~~~~~gd~~wA~~L~d~l~~a 99 (141)
T PF14863_consen 48 PANLNPLPPEEEAKRYVELAGGADKVLERAQAALAAGDYQWAAELLDHLVFA 99 (141)
T ss_dssp GGGTS---HHHHHHHHHHHTTCHHHHHHHHHHHHHCT-HHHHHHHHHHHHHH
T ss_pred ccccCCCChHHHHHHHHHHcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence 4556677777888899888888899999999999999999999988776543
No 79
>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=5.5 Score=23.84 Aligned_cols=14 Identities=29% Similarity=0.766 Sum_probs=7.7
Q ss_pred cccchhhhhhhhcc
Q psy2248 84 MEVCTVCGAFLIVG 97 (102)
Q Consensus 84 l~VCeVCGA~Ls~~ 97 (102)
--.|.+||+.++..
T Consensus 24 PatCP~C~a~~~~s 37 (54)
T PF09237_consen 24 PATCPICGAVIRQS 37 (54)
T ss_dssp -EE-TTT--EESSH
T ss_pred CCCCCcchhhccch
Confidence 36899999987654
No 80
>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=43.02 E-value=1.3e+02 Score=24.43 Aligned_cols=48 Identities=25% Similarity=0.249 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRK 63 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~ 63 (102)
..+++.|..+.|..-+++-.+...|+ +++..+..++..++.+...++.
T Consensus 43 ~~~~~~l~~erN~~sk~i~~~~~~~~-~~~~~l~~~~~~l~~~~~~~~~ 90 (418)
T TIGR00414 43 LSEIEELQAKRNELSKQIGKAKGQKK-DKIEEIKKELKELKEELTELSA 90 (418)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCc-chHHHHHHHHHHHHHHHHHHHH
Confidence 44556666666666666655544442 2155666666666666666544
No 81
>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=42.81 E-value=7.7 Score=23.08 Aligned_cols=13 Identities=31% Similarity=0.529 Sum_probs=6.4
Q ss_pred ccchhhhhhhhcc
Q psy2248 85 EVCTVCGAFLIVG 97 (102)
Q Consensus 85 ~VCeVCGA~Ls~~ 97 (102)
..|.+||+-+.+.
T Consensus 3 ~~CP~CG~~iev~ 15 (54)
T TIGR01206 3 FECPDCGAEIELE 15 (54)
T ss_pred cCCCCCCCEEecC
Confidence 3455555544443
No 82
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=42.66 E-value=7.5 Score=22.63 Aligned_cols=13 Identities=31% Similarity=0.892 Sum_probs=11.0
Q ss_pred hccccchhhhhhh
Q psy2248 82 KQMEVCTVCGAFL 94 (102)
Q Consensus 82 qkl~VCeVCGA~L 94 (102)
..+..|+-||.+|
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 4678999999886
No 83
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=42.08 E-value=9.4 Score=17.70 Aligned_cols=10 Identities=30% Similarity=0.936 Sum_probs=7.4
Q ss_pred cchhhhhhhh
Q psy2248 86 VCTVCGAFLI 95 (102)
Q Consensus 86 VCeVCGA~Ls 95 (102)
+|++||....
T Consensus 2 ~C~~C~~~f~ 11 (23)
T PF00096_consen 2 KCPICGKSFS 11 (23)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCccC
Confidence 7999996543
No 84
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=41.99 E-value=41 Score=15.93 Aligned_cols=21 Identities=29% Similarity=0.240 Sum_probs=17.0
Q ss_pred HHHHHhcCCHHHHHHHHHHHH
Q psy2248 32 AERVGMEGSVEKAQGLMKLCD 52 (102)
Q Consensus 32 aE~LGeeG~VdeA~~l~~~ve 52 (102)
+..+...|++++|..++.+..
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~ 27 (35)
T TIGR00756 7 IDGLCKAGRVEEALELFKEML 27 (35)
T ss_pred HHHHHHCCCHHHHHHHHHHHH
Confidence 456788999999999987764
No 85
>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=41.92 E-value=76 Score=18.92 Aligned_cols=33 Identities=27% Similarity=0.441 Sum_probs=19.2
Q ss_pred HHHHHHHHHH-HHhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q psy2248 25 INNLVSEAER-VGMEGSVEKAQGLMKLCDQLKEEREMLRK 63 (102)
Q Consensus 25 I~~ll~eaE~-LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~ 63 (102)
.+.+...+|+ |.+.|+|-.| ++.|+.|..+|+.
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 3445556654 5666666544 4566777766653
No 86
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=40.89 E-value=9.1 Score=21.11 Aligned_cols=13 Identities=46% Similarity=0.710 Sum_probs=6.9
Q ss_pred cchhhhhhhhccc
Q psy2248 86 VCTVCGAFLIVGD 98 (102)
Q Consensus 86 VCeVCGA~Ls~~D 98 (102)
+|+.||+--++.|
T Consensus 2 ~Cp~Cg~~~~~~D 14 (43)
T PF08271_consen 2 KCPNCGSKEIVFD 14 (43)
T ss_dssp SBTTTSSSEEEEE
T ss_pred CCcCCcCCceEEc
Confidence 4666665444444
No 87
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=39.81 E-value=54 Score=22.01 Aligned_cols=24 Identities=29% Similarity=0.324 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHH
Q psy2248 26 NNLVSEAERVGMEGSVEKAQGLMK 49 (102)
Q Consensus 26 ~~ll~eaE~LGeeG~VdeA~~l~~ 49 (102)
..+...++.+-++|+++.|..++.
T Consensus 71 ~~~~~~~~~~l~~g~~~~a~~ll~ 94 (115)
T PF12793_consen 71 ELLEQQAEELLEQGKYEQALQLLD 94 (115)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHH
Confidence 445678999999999999999987
No 88
>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=39.49 E-value=9.5 Score=22.27 Aligned_cols=11 Identities=55% Similarity=0.712 Sum_probs=8.7
Q ss_pred ccchhhhhhhh
Q psy2248 85 EVCTVCGAFLI 95 (102)
Q Consensus 85 ~VCeVCGA~Ls 95 (102)
.+|.+|||=-+
T Consensus 35 w~CP~C~a~K~ 45 (50)
T cd00730 35 WVCPVCGAGKD 45 (50)
T ss_pred CCCCCCCCcHH
Confidence 69999998543
No 89
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=38.81 E-value=48 Score=18.64 Aligned_cols=25 Identities=12% Similarity=0.086 Sum_probs=19.1
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHHHH
Q psy2248 30 SEAERVGMEGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 30 ~eaE~LGeeG~VdeA~~l~~~ve~L 54 (102)
..+..+-..|++++|...+.++-..
T Consensus 2 ~~a~~~~~~g~~~~A~~~~~~~l~~ 26 (65)
T PF13432_consen 2 ALARALYQQGDYDEAIAAFEQALKQ 26 (65)
T ss_dssp HHHHHHHHCTHHHHHHHHHHHHHCC
T ss_pred hHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 4567788889999998888776553
No 90
>smart00746 TRASH metallochaperone-like domain.
Probab=38.12 E-value=9.6 Score=18.25 Aligned_cols=9 Identities=33% Similarity=1.051 Sum_probs=7.5
Q ss_pred chhhhhhhh
Q psy2248 87 CTVCGAFLI 95 (102)
Q Consensus 87 CeVCGA~Ls 95 (102)
|++||..+.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 889998875
No 91
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=38.01 E-value=11 Score=21.69 Aligned_cols=9 Identities=67% Similarity=1.140 Sum_probs=6.1
Q ss_pred ccchhhhhh
Q psy2248 85 EVCTVCGAF 93 (102)
Q Consensus 85 ~VCeVCGA~ 93 (102)
-+|.+|||=
T Consensus 35 w~CP~C~a~ 43 (47)
T PF00301_consen 35 WVCPVCGAP 43 (47)
T ss_dssp -B-TTTSSB
T ss_pred CcCcCCCCc
Confidence 699999974
No 92
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=37.50 E-value=11 Score=29.82 Aligned_cols=17 Identities=29% Similarity=0.634 Sum_probs=12.5
Q ss_pred ccccchhhhhhhhcccc
Q psy2248 83 QMEVCTVCGAFLIVGDA 99 (102)
Q Consensus 83 kl~VCeVCGA~Ls~~D~ 99 (102)
+.+||+.|+.||=+.|.
T Consensus 251 r~e~C~~C~~YlK~~~~ 267 (309)
T PRK03564 251 KAESCGDCGTYLKILYQ 267 (309)
T ss_pred Eeeecccccccceeccc
Confidence 56888888888876543
No 93
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=37.36 E-value=16 Score=26.04 Aligned_cols=15 Identities=33% Similarity=0.802 Sum_probs=11.9
Q ss_pred hhhhccccchhhhhh
Q psy2248 79 AQEKQMEVCTVCGAF 93 (102)
Q Consensus 79 ~~~qkl~VCeVCGA~ 93 (102)
...+.|--|.|||..
T Consensus 27 Q~~~glv~CP~Cgs~ 41 (148)
T PF06676_consen 27 QQARGLVSCPVCGST 41 (148)
T ss_pred HHHcCCccCCCCCCC
Confidence 345789999999974
No 94
>PHA02768 hypothetical protein; Provisional
Probab=37.08 E-value=9.1 Score=22.95 Aligned_cols=15 Identities=27% Similarity=0.713 Sum_probs=11.9
Q ss_pred ccchhhhhhhhcccc
Q psy2248 85 EVCTVCGAFLIVGDA 99 (102)
Q Consensus 85 ~VCeVCGA~Ls~~D~ 99 (102)
..|+.||-..+..|+
T Consensus 6 y~C~~CGK~Fs~~~~ 20 (55)
T PHA02768 6 YECPICGEIYIKRKS 20 (55)
T ss_pred cCcchhCCeeccHHH
Confidence 589999998777654
No 95
>KOG2801|consensus
Probab=37.00 E-value=12 Score=30.38 Aligned_cols=12 Identities=42% Similarity=0.753 Sum_probs=9.4
Q ss_pred hhhhhhhhcccc
Q psy2248 88 TVCGAFLIVGDA 99 (102)
Q Consensus 88 eVCGA~Ls~~D~ 99 (102)
+|||||||..=+
T Consensus 402 evcgaylstdws 413 (559)
T KOG2801|consen 402 EVCGAYLSTDWS 413 (559)
T ss_pred HHhhHhcccchh
Confidence 799999996533
No 96
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=36.89 E-value=9.1 Score=21.03 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=8.9
Q ss_pred hccccchhhhhhhhcc
Q psy2248 82 KQMEVCTVCGAFLIVG 97 (102)
Q Consensus 82 qkl~VCeVCGA~Ls~~ 97 (102)
.+...|++||...-+.
T Consensus 4 ~~~YkC~~CGniVev~ 19 (36)
T PF06397_consen 4 GEFYKCEHCGNIVEVV 19 (36)
T ss_dssp TEEEE-TTT--EEEEE
T ss_pred ccEEEccCCCCEEEEE
Confidence 3568899999876544
No 97
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=36.48 E-value=88 Score=18.11 Aligned_cols=17 Identities=24% Similarity=0.403 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy2248 15 AEQITLLSEKINNLVSE 31 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~e 31 (102)
..+|.+++++|..|-++
T Consensus 18 Eqkiedid~qIaeLe~K 34 (46)
T PF08946_consen 18 EQKIEDIDEQIAELEAK 34 (46)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHhHHHHHHHHHHHHHH
Confidence 34455555555444433
No 98
>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=36.38 E-value=94 Score=18.40 Aligned_cols=50 Identities=18% Similarity=0.314 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q psy2248 14 NAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64 (102)
Q Consensus 14 ~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~ 64 (102)
....|.....+|+.+...+..| ....-..+..+...++.|......|...
T Consensus 46 ~~~ei~~~~~~l~~l~~~~~~L-~~~~~~~~~~i~~~~~~l~~~w~~l~~~ 95 (105)
T PF00435_consen 46 LQEEIESRQERLESLNEQAQQL-IDSGPEDSDEIQEKLEELNQRWEALCEL 95 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH-HHTTHTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhHHHHHHHHHHHHHHHHHHH-HHcCCCcHHHHHHHHHHHHHHHHHHHHH
Confidence 4556677777888888888888 4444777788888888888777777654
No 99
>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]
Probab=35.56 E-value=1.3e+02 Score=19.69 Aligned_cols=36 Identities=14% Similarity=0.121 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q psy2248 20 LLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLK 55 (102)
Q Consensus 20 ~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk 55 (102)
.....+...+.+.+...+.|+.|.|..++..+...-
T Consensus 23 ~~kS~~rT~iKk~~~ai~~gd~~~A~~~l~~a~~~i 58 (88)
T COG0268 23 SRKSALRTAIKKVEAAIEAGDKEAAKAALKEAQKKI 58 (88)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 667788899999999999999999999998887753
No 100
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=34.93 E-value=13 Score=29.29 Aligned_cols=18 Identities=22% Similarity=0.492 Sum_probs=14.1
Q ss_pred hccccchhhhhhhhcccc
Q psy2248 82 KQMEVCTVCGAFLIVGDA 99 (102)
Q Consensus 82 qkl~VCeVCGA~Ls~~D~ 99 (102)
-+.+||+.|+.||=+.|.
T Consensus 250 ~r~e~C~~C~~YlK~~~~ 267 (305)
T TIGR01562 250 LKAETCDSCQGYLKILYQ 267 (305)
T ss_pred eEEeeccccccchhhhcc
Confidence 366899999999877654
No 101
>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=34.76 E-value=1.3e+02 Score=19.67 Aligned_cols=11 Identities=27% Similarity=0.739 Sum_probs=8.4
Q ss_pred cccchhhhhhh
Q psy2248 84 MEVCTVCGAFL 94 (102)
Q Consensus 84 l~VCeVCGA~L 94 (102)
.-+|+.||--+
T Consensus 80 yG~C~~Cge~I 90 (110)
T TIGR02420 80 YGYCEECGEEI 90 (110)
T ss_pred CCchhccCCcc
Confidence 36999999643
No 102
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=34.31 E-value=2e+02 Score=21.46 Aligned_cols=52 Identities=27% Similarity=0.333 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH----HHhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q psy2248 13 ENAEQITLLSEKINNLVSEAER----VGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64 (102)
Q Consensus 13 ~~~e~i~~l~~~I~~ll~eaE~----LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~ 64 (102)
++..+..+++.+|..+-.+.+. |...+.+++-.++-.++...+.+.+.++.+
T Consensus 129 DvT~~y~D~~arl~~l~~~~~rl~~ll~ka~~~~d~l~ie~~L~~v~~eIe~~~~~ 184 (262)
T PF14257_consen 129 DVTEQYVDLEARLKNLEAEEERLLELLEKAKTVEDLLEIERELSRVRSEIEQLEGQ 184 (262)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666666666555544 334579999999999988888888877664
No 103
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=34.23 E-value=13 Score=27.43 Aligned_cols=18 Identities=17% Similarity=0.632 Sum_probs=0.0
Q ss_pred hhccccchhhhhhhhccc
Q psy2248 81 EKQMEVCTVCGAFLIVGD 98 (102)
Q Consensus 81 ~qkl~VCeVCGA~Ls~~D 98 (102)
..+|.+|++||-.+-+++
T Consensus 165 ~~~~~~cPitGe~IP~~e 182 (229)
T PF12230_consen 165 KEKMIICPITGEMIPADE 182 (229)
T ss_dssp ------------------
T ss_pred cccccccccccccccccc
Confidence 457899999998765543
No 104
>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=34.22 E-value=16 Score=24.22 Aligned_cols=15 Identities=20% Similarity=0.539 Sum_probs=11.4
Q ss_pred cccchhhhhhhhccc
Q psy2248 84 MEVCTVCGAFLIVGD 98 (102)
Q Consensus 84 l~VCeVCGA~Ls~~D 98 (102)
-..|+.||.||...+
T Consensus 20 ~~gCpnC~~~l~~~g 34 (98)
T cd07973 20 RDGCPNCEGYLDMKG 34 (98)
T ss_pred CCCCCCCcchhccCC
Confidence 378999998885543
No 105
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=33.93 E-value=15 Score=18.21 Aligned_cols=8 Identities=50% Similarity=1.298 Sum_probs=3.7
Q ss_pred ccchhhhh
Q psy2248 85 EVCTVCGA 92 (102)
Q Consensus 85 ~VCeVCGA 92 (102)
+.|..||+
T Consensus 17 ~fC~~CG~ 24 (26)
T PF13248_consen 17 KFCPNCGA 24 (26)
T ss_pred ccChhhCC
Confidence 44444443
No 106
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=33.84 E-value=14 Score=20.26 Aligned_cols=11 Identities=36% Similarity=0.748 Sum_probs=5.6
Q ss_pred cchhhhhhhhc
Q psy2248 86 VCTVCGAFLIV 96 (102)
Q Consensus 86 VCeVCGA~Ls~ 96 (102)
.|.-|+|||+-
T Consensus 4 rC~~C~aylNp 14 (40)
T PF04810_consen 4 RCRRCRAYLNP 14 (40)
T ss_dssp B-TTT--BS-T
T ss_pred ccCCCCCEECC
Confidence 58999999864
No 107
>PRK12495 hypothetical protein; Provisional
Probab=33.38 E-value=53 Score=25.08 Aligned_cols=12 Identities=25% Similarity=0.650 Sum_probs=9.3
Q ss_pred ccchhhhhhhhc
Q psy2248 85 EVCTVCGAFLIV 96 (102)
Q Consensus 85 ~VCeVCGA~Ls~ 96 (102)
+.|++||.-|-.
T Consensus 43 ~hC~~CG~PIpa 54 (226)
T PRK12495 43 AHCDECGDPIFR 54 (226)
T ss_pred hhcccccCcccC
Confidence 889999986643
No 108
>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=33.20 E-value=13 Score=18.94 Aligned_cols=11 Identities=18% Similarity=0.594 Sum_probs=8.7
Q ss_pred ccchhhhhhhh
Q psy2248 85 EVCTVCGAFLI 95 (102)
Q Consensus 85 ~VCeVCGA~Ls 95 (102)
.-|++|+.++.
T Consensus 4 ~~C~~C~~~~~ 14 (35)
T smart00451 4 FYCKLCNVTFT 14 (35)
T ss_pred eEccccCCccC
Confidence 45999998765
No 109
>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=33.14 E-value=1.9e+02 Score=20.89 Aligned_cols=53 Identities=19% Similarity=0.191 Sum_probs=42.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q psy2248 12 NENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64 (102)
Q Consensus 12 ~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~ 64 (102)
.....++..+...|...-.+|+.+-..|+=|-|...+.....+..+...+...
T Consensus 54 ~~le~~~~~~~~~~~~~~~~A~~Al~~g~edLAr~al~~k~~~e~~~~~l~~~ 106 (221)
T PF04012_consen 54 KRLERKLDEAEEEAEKWEKQAELALAAGREDLAREALQRKADLEEQAERLEQQ 106 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567888999999999999999999999999988777777766666665543
No 110
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=33.03 E-value=64 Score=15.48 Aligned_cols=22 Identities=14% Similarity=0.149 Sum_probs=17.5
Q ss_pred HHHHHhcCCHHHHHHHHHHHHH
Q psy2248 32 AERVGMEGSVEKAQGLMKLCDQ 53 (102)
Q Consensus 32 aE~LGeeG~VdeA~~l~~~ve~ 53 (102)
+..++..|+++.|..++....+
T Consensus 8 l~a~~~~g~~~~a~~~~~~M~~ 29 (34)
T PF13812_consen 8 LRACAKAGDPDAALQLFDEMKE 29 (34)
T ss_pred HHHHHHCCCHHHHHHHHHHHHH
Confidence 4567889999999998877654
No 111
>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=32.49 E-value=17 Score=17.80 Aligned_cols=11 Identities=18% Similarity=0.700 Sum_probs=8.5
Q ss_pred ccchhhhhhhh
Q psy2248 85 EVCTVCGAFLI 95 (102)
Q Consensus 85 ~VCeVCGA~Ls 95 (102)
..|++|+...+
T Consensus 2 ~~C~~C~k~f~ 12 (27)
T PF12171_consen 2 FYCDACDKYFS 12 (27)
T ss_dssp CBBTTTTBBBS
T ss_pred CCcccCCCCcC
Confidence 47999997654
No 112
>KOG2034|consensus
Probab=32.48 E-value=1.6e+02 Score=26.86 Aligned_cols=12 Identities=33% Similarity=0.966 Sum_probs=10.1
Q ss_pred ccchhhhhhhhc
Q psy2248 85 EVCTVCGAFLIV 96 (102)
Q Consensus 85 ~VCeVCGA~Ls~ 96 (102)
..|++||-+|..
T Consensus 818 d~C~~C~~~ll~ 829 (911)
T KOG2034|consen 818 DSCDHCGRPLLI 829 (911)
T ss_pred cchHHhcchhhc
Confidence 899999988764
No 113
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=32.24 E-value=14 Score=18.20 Aligned_cols=12 Identities=25% Similarity=0.647 Sum_probs=9.5
Q ss_pred hhccccchhhhh
Q psy2248 81 EKQMEVCTVCGA 92 (102)
Q Consensus 81 ~qkl~VCeVCGA 92 (102)
..+...|+.||.
T Consensus 11 ~~k~~~C~~C~k 22 (26)
T PF13465_consen 11 GEKPYKCPYCGK 22 (26)
T ss_dssp SSSSEEESSSSE
T ss_pred CCCCCCCCCCcC
Confidence 456799999984
No 114
>PF05852 DUF848: Gammaherpesvirus protein of unknown function (DUF848); InterPro: IPR008566 This family consists of several uncharacterised proteins from the Gammaherpesvirinae.
Probab=32.22 E-value=1.9e+02 Score=20.61 Aligned_cols=49 Identities=24% Similarity=0.278 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--hcCCHHHHHHHHHHHHHHHHHHHHH
Q psy2248 13 ENAEQITLLSEKINNLVSEAERVG--MEGSVEKAQGLMKLCDQLKEEREML 61 (102)
Q Consensus 13 ~~~e~i~~l~~~I~~ll~eaE~LG--eeG~VdeA~~l~~~ve~Lk~ek~~l 61 (102)
.....+..+...|.....+...|- .-.+|+.+.+|...++.|+.+.+.-
T Consensus 58 ~~~~~v~~~~~~i~~k~~El~~L~~~d~~kv~~~E~L~d~v~eLkeel~~e 108 (146)
T PF05852_consen 58 EIKNKVSSLETEISEKKKELSHLKKFDRKKVEDLEKLTDRVEELKEELEFE 108 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455677888889999888888875 4588999999999999999877543
No 115
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=31.87 E-value=2.2e+02 Score=23.72 Aligned_cols=49 Identities=24% Similarity=0.267 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~ 64 (102)
..++..|..+.|.+-+++-..+..|.= .+..++.++..++.+.+.++..
T Consensus 42 ~~~~e~l~~~rn~~sk~ig~~~~~~~~-~~~~l~~e~~~l~~~l~~~e~~ 90 (429)
T COG0172 42 LRELEELQAERNELSKEIGRALKRGED-DAEELIAEVKELKEKLKELEAA 90 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccch-hHHHHHHHHHHHHHHHHhccHH
Confidence 345556666666666666655555443 7788888888888777766553
No 116
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=31.62 E-value=66 Score=15.23 Aligned_cols=24 Identities=17% Similarity=0.005 Sum_probs=16.6
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHH
Q psy2248 28 LVSEAERVGMEGSVEKAQGLMKLC 51 (102)
Q Consensus 28 ll~eaE~LGeeG~VdeA~~l~~~v 51 (102)
++..+......|+.++|...+.++
T Consensus 3 ~~~~a~~~~~~g~~~~A~~~~~~~ 26 (33)
T PF13174_consen 3 LYRLARCYYKLGDYDEAIEYFQRL 26 (33)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccCHHHHHHHHHHH
Confidence 344555566678899998877655
No 117
>PF09920 DUF2150: Uncharacterized protein conserved in archaea (DUF2150); InterPro: IPR014518 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=31.55 E-value=85 Score=23.33 Aligned_cols=31 Identities=26% Similarity=0.276 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q psy2248 22 SEKINNLVSEAERVGMEGSVEKAQGLMKLCD 52 (102)
Q Consensus 22 ~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve 52 (102)
...|..+++++-..-++|+.|.|+..+.++=
T Consensus 115 ~~~i~~lvk~A~~aE~~edle~Al~~~a~~G 145 (190)
T PF09920_consen 115 EADIEELVKAAVEAEAEEDLEAALGYAAQIG 145 (190)
T ss_pred cCCHHHHHHHHHHHhhccCHHHHHHHHHHhC
Confidence 4567788888888888888888888876653
No 118
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=31.35 E-value=17 Score=21.12 Aligned_cols=9 Identities=33% Similarity=1.246 Sum_probs=5.3
Q ss_pred ccccchhhh
Q psy2248 83 QMEVCTVCG 91 (102)
Q Consensus 83 kl~VCeVCG 91 (102)
+|..|+-||
T Consensus 2 ~LkPCPFCG 10 (61)
T PF14354_consen 2 ELKPCPFCG 10 (61)
T ss_pred CCcCCCCCC
Confidence 355666666
No 119
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=31.21 E-value=1.9e+02 Score=21.83 Aligned_cols=42 Identities=26% Similarity=0.336 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Q psy2248 17 QITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEER 58 (102)
Q Consensus 17 ~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek 58 (102)
=|..+-.-|++|...+=.++.+|+++.|.....=+|.+=...
T Consensus 113 YilGl~D~vGELrR~~le~l~~~~~~~Ae~~~~~ME~lY~~L 154 (204)
T COG2178 113 YILGLADAVGELRRHVLELLRKGSFEEAERFLKFMEKLYEEL 154 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Confidence 566788899999999999999999999999988888775543
No 120
>PF02672 CP12: CP12 domain; InterPro: IPR003823 This entry represents an uncharacterised domain in proteins of unknown function. This domain is found associated with CBS domains in some proteins IPR000644 from INTERPRO.; PDB: 3B1K_I 3B1J_D 3RVD_N 3QV1_I 2LJ9_A.
Probab=30.58 E-value=17 Score=22.70 Aligned_cols=41 Identities=24% Similarity=0.332 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHHHHH
Q psy2248 21 LSEKINNLVSEAERVGMEG--SVEKAQGLMKLCDQLKEEREML 61 (102)
Q Consensus 21 l~~~I~~ll~eaE~LGeeG--~VdeA~~l~~~ve~Lk~ek~~l 61 (102)
|+++|..-+.++..+-..+ +-.++-.....|+.|..++...
T Consensus 1 l~e~Ie~~i~eA~~~c~~~g~~s~ec~~AWdeVEELqa~~~h~ 43 (71)
T PF02672_consen 1 LEEKIEKAIEEAREACAEGGANSAECRHAWDEVEELQAEASHQ 43 (71)
T ss_dssp -------------------------------------------
T ss_pred ChHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHc
Confidence 5678888899999988888 7778888888899988776544
No 121
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=30.37 E-value=28 Score=21.21 Aligned_cols=24 Identities=21% Similarity=0.338 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q psy2248 14 NAEQITLLSEKINNLVSEAERVGM 37 (102)
Q Consensus 14 ~~e~i~~l~~~I~~ll~eaE~LGe 37 (102)
+.+++..|.++|.++..+..+|-.
T Consensus 12 VrEEVevLK~~I~eL~~~n~~Le~ 35 (59)
T PF01166_consen 12 VREEVEVLKEQIAELEERNSQLEE 35 (59)
T ss_dssp -TTSHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677777777777766665543
No 122
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=30.14 E-value=18 Score=19.36 Aligned_cols=13 Identities=38% Similarity=0.917 Sum_probs=6.4
Q ss_pred cccchhhhhhhhc
Q psy2248 84 MEVCTVCGAFLIV 96 (102)
Q Consensus 84 l~VCeVCGA~Ls~ 96 (102)
|+-|+-||.+|..
T Consensus 1 m~FCp~C~nlL~p 13 (35)
T PF02150_consen 1 MRFCPECGNLLYP 13 (35)
T ss_dssp --BETTTTSBEEE
T ss_pred CeeCCCCCccceE
Confidence 3456666666543
No 123
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=30.09 E-value=1.3e+02 Score=20.08 Aligned_cols=26 Identities=27% Similarity=0.282 Sum_probs=21.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy2248 11 QNENAEQITLLSEKINNLVSEAERVG 36 (102)
Q Consensus 11 ~~~~~e~i~~l~~~I~~ll~eaE~LG 36 (102)
..+..++|..+..-++.|+.+||..+
T Consensus 9 ~eeLs~kirdf~Ra~~SLiEEiEA~~ 34 (103)
T COG3461 9 PEELSEKIRDFSRARQSLIEEIEAMM 34 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34677888899999999999998765
No 124
>PF07980 SusD: SusD family; InterPro: IPR012944 This domain occurs in several hypothetical proteins. It also occurs in RagB, Q9ZA59 from SWISSPROT, a protein involved in signalling [] and SusD, Q8A1G2 from SWISSPROT, an outer membrane protein involved in nutrient binding [].; PDB: 3IHV_A 3LEW_A 3JQ1_A 3JQ0_A 3NQP_B 3SNX_A 3L22_A 3OTN_A 3IV0_A 3QNK_C ....
Probab=30.00 E-value=1.2e+02 Score=21.52 Aligned_cols=26 Identities=15% Similarity=0.114 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHH
Q psy2248 27 NLVSEAERVGMEGSVEKAQGLMKLCD 52 (102)
Q Consensus 27 ~ll~eaE~LGeeG~VdeA~~l~~~ve 52 (102)
-+|-.||.+...|++++|...+.+|.
T Consensus 135 vyL~~AEA~~~~g~~~~A~~~lN~vR 160 (266)
T PF07980_consen 135 VYLIYAEALARLGNTAEALEYLNQVR 160 (266)
T ss_dssp HHHHHHHHHHHTTSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 35779999999999999887776653
No 125
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=29.73 E-value=1.2e+02 Score=20.47 Aligned_cols=65 Identities=23% Similarity=0.325 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhhhhhhccccchhhhhhhhcccc
Q psy2248 20 LLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQNDNNHWSQTVELAAAQEKQMEVCTVCGAFLIVGDA 99 (102)
Q Consensus 20 ~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~~~~~~~~~~~~~~~~~~qkl~VCeVCGA~Ls~~D~ 99 (102)
.-.+.|+-|..-|+.....| -|-|-..+..++..-. .+.. .-..+=|=..|.-|.+||.-+=|
T Consensus 9 ia~eRi~~L~~lA~~~~~~~-~~laRrYv~la~~Is~-------K~rv---------~lp~~iKR~~CkkC~t~Lvpg~n 71 (105)
T COG2023 9 IAAERIDYLYSLAEETFRTG-PDLARRYVKLARRISM-------KYRV---------RLPREIKRTICKKCYTPLVPGKN 71 (105)
T ss_pred HHHHHHHHHHHHHHHHHhcC-cHHHHHHHHHHHHHHH-------hhcc---------ccCHHHHHHhccccCcccccCcc
Confidence 34678999999999999999 5777777766655432 1111 11133455789999999987766
Q ss_pred cC
Q psy2248 100 QS 101 (102)
Q Consensus 100 d~ 101 (102)
-+
T Consensus 72 ~r 73 (105)
T COG2023 72 AR 73 (105)
T ss_pred eE
Confidence 54
No 126
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=29.69 E-value=1.2e+02 Score=18.37 Aligned_cols=28 Identities=14% Similarity=-0.016 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q psy2248 26 NNLVSEAERVGMEGSVEKAQGLMKLCDQ 53 (102)
Q Consensus 26 ~~ll~eaE~LGeeG~VdeA~~l~~~ve~ 53 (102)
+.....+..+...|+.++|...+.++-.
T Consensus 3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~ 30 (119)
T TIGR02795 3 EAYYDAALLVLKAGDYADAIQAFQAFLK 30 (119)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 3445566666666777777666666543
No 127
>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=29.37 E-value=1.9e+02 Score=19.72 Aligned_cols=26 Identities=27% Similarity=0.360 Sum_probs=16.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy2248 40 SVEKAQGLMKLCDQLKEEREMLRKQN 65 (102)
Q Consensus 40 ~VdeA~~l~~~ve~Lk~ek~~l~~~~ 65 (102)
..|+......++..|+.+.+.|...+
T Consensus 59 ~~e~~~~~~~~~~~L~~el~~l~~ry 84 (120)
T PF12325_consen 59 ENEELRALKKEVEELEQELEELQQRY 84 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555566666677777777776655
No 128
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=29.06 E-value=17 Score=20.19 Aligned_cols=17 Identities=18% Similarity=0.438 Sum_probs=12.3
Q ss_pred cccchhhhhhhhccccc
Q psy2248 84 MEVCTVCGAFLIVGDAQ 100 (102)
Q Consensus 84 l~VCeVCGA~Ls~~D~d 100 (102)
...|+-||.-+...|..
T Consensus 21 ~~~Cp~CG~~~~~~~~~ 37 (46)
T PRK00398 21 GVRCPYCGYRILFKERP 37 (46)
T ss_pred ceECCCCCCeEEEccCC
Confidence 57888888877666554
No 129
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=29.04 E-value=1.4e+02 Score=18.03 Aligned_cols=42 Identities=21% Similarity=0.184 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q psy2248 13 ENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 13 ~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~L 54 (102)
....-...++.+|..+..++..+-..++.+.|...+.++-=+
T Consensus 28 ~L~~l~~~~~~~~~~~~~~l~~~f~~~d~~~A~~~~~kLky~ 69 (78)
T PF07743_consen 28 ELEELKKEIEERIKELIKELAEAFDAKDWEEAKEALRKLKYL 69 (78)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHH
Confidence 444455678888888889999988999999998887766443
No 130
>PF01348 Intron_maturas2: Type II intron maturase; InterPro: IPR002866 Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA []. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. These introns are found in plant organelles []. Maturases in higher plants are encoded for in the nuclear genes [] but are otherwise encoded by organellar introns. The Maturase-related, N-terminal domain is found in plant potential maturases, which probably assists in the splicing of chloroplast group II introns []. The function of this region is, however, unknown It has been shown that a specific region of the aI2 intron is needed for the maturase function []. This C-terminal region was found to be conserved in group II introns and called domain X [].; GO: 0006397 mRNA processing, 0009507 chloroplast
Probab=28.76 E-value=16 Score=25.42 Aligned_cols=10 Identities=30% Similarity=1.062 Sum_probs=8.1
Q ss_pred ccccchhhhh
Q psy2248 83 QMEVCTVCGA 92 (102)
Q Consensus 83 kl~VCeVCGA 92 (102)
+-.+|++||+
T Consensus 136 ~~~~C~lCg~ 145 (146)
T PF01348_consen 136 KARKCELCGS 145 (146)
T ss_pred CCCEEEEeee
Confidence 4479999995
No 131
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.42 E-value=19 Score=21.32 Aligned_cols=9 Identities=33% Similarity=0.940 Sum_probs=7.4
Q ss_pred ccchhhhhh
Q psy2248 85 EVCTVCGAF 93 (102)
Q Consensus 85 ~VCeVCGA~ 93 (102)
.+|+|||--
T Consensus 13 KICpvCqRP 21 (54)
T COG4338 13 KICPVCQRP 21 (54)
T ss_pred hhhhhhcCc
Confidence 799999853
No 132
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=28.16 E-value=26 Score=22.48 Aligned_cols=18 Identities=22% Similarity=0.427 Sum_probs=13.2
Q ss_pred hhhhccccchhhhhhhhc
Q psy2248 79 AQEKQMEVCTVCGAFLIV 96 (102)
Q Consensus 79 ~~~qkl~VCeVCGA~Ls~ 96 (102)
...=.-..|..||.+|+.
T Consensus 49 Y~~lfs~pC~~C~klL~~ 66 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLLSS 66 (90)
T ss_pred HhhhccchhhHHHhHhhh
Confidence 334455899999999943
No 133
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=27.92 E-value=20 Score=22.16 Aligned_cols=8 Identities=38% Similarity=0.883 Sum_probs=7.0
Q ss_pred ccchhhhh
Q psy2248 85 EVCTVCGA 92 (102)
Q Consensus 85 ~VCeVCGA 92 (102)
.+|++||.
T Consensus 18 ~~Cp~Cgs 25 (64)
T PRK06393 18 KTCPVHGD 25 (64)
T ss_pred CcCCCCCC
Confidence 48999997
No 134
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.42 E-value=19 Score=23.93 Aligned_cols=12 Identities=25% Similarity=0.722 Sum_probs=9.4
Q ss_pred cccchhhhhhhh
Q psy2248 84 MEVCTVCGAFLI 95 (102)
Q Consensus 84 l~VCeVCGA~Ls 95 (102)
..+|.+||.|-.
T Consensus 42 h~~C~~CG~y~~ 53 (99)
T PRK14892 42 IITCGNCGLYTE 53 (99)
T ss_pred eEECCCCCCccC
Confidence 478999998743
No 135
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=27.31 E-value=1.2e+02 Score=16.92 Aligned_cols=24 Identities=21% Similarity=0.113 Sum_probs=20.0
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHH
Q psy2248 29 VSEAERVGMEGSVEKAQGLMKLCD 52 (102)
Q Consensus 29 l~eaE~LGeeG~VdeA~~l~~~ve 52 (102)
+.-|....+-|+.+.|-.++.++-
T Consensus 3 LdLA~ayie~Gd~e~Ar~lL~evl 26 (44)
T TIGR03504 3 LDLARAYIEMGDLEGARELLEEVI 26 (44)
T ss_pred hHHHHHHHHcCChHHHHHHHHHHH
Confidence 456788889999999999888776
No 136
>PHA03161 hypothetical protein; Provisional
Probab=27.25 E-value=2.4e+02 Score=20.24 Aligned_cols=47 Identities=15% Similarity=0.098 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHHHHHHH
Q psy2248 13 ENAEQITLLSEKINNLVSEAERVGM--EGSVEKAQGLMKLCDQLKEERE 59 (102)
Q Consensus 13 ~~~e~i~~l~~~I~~ll~eaE~LGe--eG~VdeA~~l~~~ve~Lk~ek~ 59 (102)
.....|..++..|...-.+.+.|-. -++|+.+.++-..|+.|+.+..
T Consensus 58 ~i~~~v~~l~~~I~~k~kE~~~L~~fd~kkl~~~E~L~drv~eLkeel~ 106 (150)
T PHA03161 58 SIEGMLQAVDLSIQEKKKELSLLKAFDRHKLSAAEDLQDKILELKEDIH 106 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556777888899999999888864 4789999999999999987764
No 137
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=27.16 E-value=1.1e+02 Score=16.21 Aligned_cols=25 Identities=16% Similarity=0.153 Sum_probs=19.6
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHH
Q psy2248 29 VSEAERVGMEGSVEKAQGLMKLCDQ 53 (102)
Q Consensus 29 l~eaE~LGeeG~VdeA~~l~~~ve~ 53 (102)
+.-+..+-..|+.|+|...+.++=+
T Consensus 5 ~~la~~~~~~G~~~~A~~~~~~~l~ 29 (44)
T PF13428_consen 5 LALARAYRRLGQPDEAERLLRRALA 29 (44)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 4457778899999999998876544
No 138
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=27.15 E-value=23 Score=17.86 Aligned_cols=11 Identities=27% Similarity=0.724 Sum_probs=6.1
Q ss_pred ccchhhhhhhh
Q psy2248 85 EVCTVCGAFLI 95 (102)
Q Consensus 85 ~VCeVCGA~Ls 95 (102)
+.|+.||.++.
T Consensus 2 ~~C~rC~~~~~ 12 (30)
T PF06827_consen 2 EKCPRCWNYIE 12 (30)
T ss_dssp SB-TTT--BBE
T ss_pred CcCccCCCcce
Confidence 57999998864
No 139
>TIGR00618 sbcc exonuclease SbcC. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.13 E-value=2.7e+02 Score=25.19 Aligned_cols=11 Identities=45% Similarity=0.999 Sum_probs=8.8
Q ss_pred hccccchhhhh
Q psy2248 82 KQMEVCTVCGA 92 (102)
Q Consensus 82 qkl~VCeVCGA 92 (102)
..-++|++||+
T Consensus 499 ~~~~~cplcgs 509 (1042)
T TIGR00618 499 LQEEPCPLCGS 509 (1042)
T ss_pred CCCCCCCCCCC
Confidence 34489999997
No 140
>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here
Probab=26.53 E-value=2e+02 Score=19.21 Aligned_cols=49 Identities=20% Similarity=0.304 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~ 64 (102)
...|......++.+...++.|...+. ..+..+...++.++.....|...
T Consensus 46 ~~e~~~~~~~~~~l~~~~~~L~~~~~-~~~~~i~~~~~~l~~~w~~l~~~ 94 (213)
T cd00176 46 EAELAAHEERVEALNELGEQLIEEGH-PDAEEIQERLEELNQRWEELREL 94 (213)
T ss_pred HHHHHHCHHHHHHHHHHHHHHHhcCC-CChHHHHHHHHHHHHHHHHHHHH
Confidence 34455557777888888888888887 66777778888887776666543
No 141
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=26.30 E-value=96 Score=15.35 Aligned_cols=29 Identities=24% Similarity=0.279 Sum_probs=21.3
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q psy2248 28 LVSEAERVGMEGSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 28 ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 56 (102)
+..-+..+...|+.++|..+..++=....
T Consensus 5 ~~~la~~~~~~g~~~~A~~~~~~al~~~~ 33 (42)
T PF13374_consen 5 LNNLANAYRAQGRYEEALELLEEALEIRE 33 (42)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHhhhhcchhhHHHHHHHHHHH
Confidence 34456678889999999999988876654
No 142
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=26.07 E-value=23 Score=19.01 Aligned_cols=12 Identities=33% Similarity=0.667 Sum_probs=9.0
Q ss_pred ccccchhhhhhh
Q psy2248 83 QMEVCTVCGAFL 94 (102)
Q Consensus 83 kl~VCeVCGA~L 94 (102)
.-.+|+.||-.+
T Consensus 31 p~~~C~~CGE~~ 42 (46)
T TIGR03831 31 PALVCPQCGEEY 42 (46)
T ss_pred CccccccCCCEe
Confidence 347899999654
No 143
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.07 E-value=29 Score=24.53 Aligned_cols=14 Identities=36% Similarity=0.992 Sum_probs=11.4
Q ss_pred hhhhccccchhhhh
Q psy2248 79 AQEKQMEVCTVCGA 92 (102)
Q Consensus 79 ~~~qkl~VCeVCGA 92 (102)
..+..|--|+|||.
T Consensus 27 Q~~rgLv~CPvCgs 40 (142)
T COG5319 27 QRERGLVTCPVCGS 40 (142)
T ss_pred HHHcCceeCCCCCc
Confidence 34678899999996
No 144
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=25.90 E-value=21 Score=21.32 Aligned_cols=8 Identities=63% Similarity=1.319 Sum_probs=6.6
Q ss_pred ccchhhhh
Q psy2248 85 EVCTVCGA 92 (102)
Q Consensus 85 ~VCeVCGA 92 (102)
=||+.|||
T Consensus 22 VvCp~Cga 29 (54)
T PF14446_consen 22 VVCPECGA 29 (54)
T ss_pred EECCCCCC
Confidence 58999987
No 145
>PF09577 Spore_YpjB: Sporulation protein YpjB (SpoYpjB); InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon []. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Probab=25.75 E-value=1.7e+02 Score=22.29 Aligned_cols=30 Identities=23% Similarity=0.408 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q psy2248 24 KINNLVSEAERVGMEGSVEKAQGLMKLCDQ 53 (102)
Q Consensus 24 ~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~ 53 (102)
+++.+..++=+|-.+|+.++|..++....+
T Consensus 4 eLd~~sd~~lqlvk~~~yeeA~q~l~~fs~ 33 (232)
T PF09577_consen 4 ELDQLSDEALQLVKQGKYEEAKQLLEYFSE 33 (232)
T ss_pred HHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence 455666777889999999999999887765
No 146
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.67 E-value=23 Score=21.29 Aligned_cols=8 Identities=50% Similarity=1.124 Sum_probs=7.3
Q ss_pred ccchhhhh
Q psy2248 85 EVCTVCGA 92 (102)
Q Consensus 85 ~VCeVCGA 92 (102)
-+|.+||+
T Consensus 37 w~CP~Cg~ 44 (55)
T COG1773 37 WVCPECGV 44 (55)
T ss_pred cCCCCCCC
Confidence 79999996
No 147
>PF11062 DUF2863: Protein of unknown function (DUF2863); InterPro: IPR021292 This bacterial family of proteins have no known function.
Probab=25.52 E-value=22 Score=29.24 Aligned_cols=13 Identities=46% Similarity=0.761 Sum_probs=9.4
Q ss_pred ccccchhhhhhhh
Q psy2248 83 QMEVCTVCGAFLI 95 (102)
Q Consensus 83 kl~VCeVCGA~Ls 95 (102)
.|+-||-|||=|-
T Consensus 363 ~~E~CdDCGaPly 375 (398)
T PF11062_consen 363 PPEFCDDCGAPLY 375 (398)
T ss_pred CchhcccCCCCCC
Confidence 5678888887654
No 148
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=25.46 E-value=26 Score=19.50 Aligned_cols=13 Identities=38% Similarity=0.953 Sum_probs=9.9
Q ss_pred cchhhhhhhhccc
Q psy2248 86 VCTVCGAFLIVGD 98 (102)
Q Consensus 86 VCeVCGA~Ls~~D 98 (102)
-|+-||.+|...+
T Consensus 2 FCp~Cg~~l~~~~ 14 (52)
T smart00661 2 FCPKCGNMLIPKE 14 (52)
T ss_pred CCCCCCCcccccc
Confidence 4889999887654
No 149
>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=25.38 E-value=1.2e+02 Score=20.99 Aligned_cols=22 Identities=27% Similarity=0.555 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q psy2248 15 AEQITLLSEKINNLVSEAERVG 36 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LG 36 (102)
.+.|..|+.+|..|-.+++.|.
T Consensus 108 ~~dv~~L~~rId~L~~~v~~l~ 129 (132)
T PF05597_consen 108 RKDVEALSARIDQLTAQVERLA 129 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3466666777777666666664
No 150
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=25.28 E-value=21 Score=21.29 Aligned_cols=12 Identities=33% Similarity=0.883 Sum_probs=8.1
Q ss_pred ccccchhhhhhh
Q psy2248 83 QMEVCTVCGAFL 94 (102)
Q Consensus 83 kl~VCeVCGA~L 94 (102)
.-.||..||-|-
T Consensus 39 ~H~vC~~CG~Y~ 50 (57)
T PRK12286 39 PHRVCPSCGYYK 50 (57)
T ss_pred CeEECCCCCcCC
Confidence 347888888663
No 151
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=25.27 E-value=2.3e+02 Score=19.39 Aligned_cols=48 Identities=25% Similarity=0.311 Sum_probs=32.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHh
Q psy2248 11 QNENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRK 63 (102)
Q Consensus 11 ~~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~ 63 (102)
+.++..++..++..|+.+++++..|-. -...++.+=-.|+-|-+.|..
T Consensus 3 KkeiFd~v~~le~~l~~l~~el~~lK~-----~l~~lvEEN~~L~lENe~LR~ 50 (114)
T COG4467 3 KKEIFDQVDNLEEQLGVLLAELGGLKQ-----HLGSLVEENTALRLENEKLRE 50 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHhhHHHHhhHHHHHH
Confidence 567788999999999999999988765 233444444445444444443
No 152
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=25.07 E-value=3.2e+02 Score=21.03 Aligned_cols=30 Identities=27% Similarity=0.329 Sum_probs=26.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy2248 11 QNENAEQITLLSEKINNLVSEAERVGMEGS 40 (102)
Q Consensus 11 ~~~~~e~i~~l~~~I~~ll~eaE~LGeeG~ 40 (102)
.++...+|.++.+.|+-+-.-++.+|.+|+
T Consensus 109 t~ee~~kI~e~~e~~~~~d~sIg~lg~e~d 138 (258)
T COG5200 109 TPEEFGKIKEKEELFNRVDESIGELGMEGD 138 (258)
T ss_pred CHHHHHhHHHHHHHHHHHHHHHHHHHHhHH
Confidence 456678999999999999999999999987
No 153
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=24.82 E-value=2e+02 Score=18.59 Aligned_cols=53 Identities=25% Similarity=0.260 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH------------HhcCCHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy2248 14 NAEQITLLSEKINNLVSEAERV------------GMEGSVEKAQGLMKLCDQLKEEREMLRKQND 66 (102)
Q Consensus 14 ~~e~i~~l~~~I~~ll~eaE~L------------GeeG~VdeA~~l~~~ve~Lk~ek~~l~~~~~ 66 (102)
++.+|+.++++|.......|.. +..+--++-..++..+...-.+...|....+
T Consensus 3 V~~eId~lEekl~~cr~~le~ve~rL~~~eLs~e~R~~lE~E~~~l~~~l~~~E~eL~~LrkENr 67 (85)
T PF15188_consen 3 VAKEIDGLEEKLAQCRRRLEAVESRLRRRELSPEARRSLEKELNELKEKLENNEKELKLLRKENR 67 (85)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHcccCCChHHHHHHHHHHHHHHHHhhccHHHHHHHHHhhh
Confidence 4678888999988888777763 2223335556666666666666666666543
No 154
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=24.74 E-value=22 Score=26.55 Aligned_cols=15 Identities=27% Similarity=0.782 Sum_probs=12.7
Q ss_pred hccccchhhhhhhhc
Q psy2248 82 KQMEVCTVCGAFLIV 96 (102)
Q Consensus 82 qkl~VCeVCGA~Ls~ 96 (102)
-...+|..||+|+..
T Consensus 33 i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 33 IEVTICPKCGRYRIG 47 (236)
T ss_pred cCceECCCCCCEECC
Confidence 367999999999875
No 155
>KOG3231|consensus
Probab=24.56 E-value=3e+02 Score=20.44 Aligned_cols=47 Identities=13% Similarity=0.176 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREML 61 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l 61 (102)
...-..++.+-..|-.++..+..-|+-|.|--|..++=.|+.++.+-
T Consensus 28 erdRr~me~~Ek~LElEIkk~Aa~GnndAcr~LAKQLV~lRkQKtrt 74 (208)
T KOG3231|consen 28 ERDRRAMEKQEKQLELEIKKMAAIGNNDACRVLAKQLVHLRKQKTRT 74 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHhhhhh
Confidence 33445677778888889999999999999999999999998887654
No 156
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=24.53 E-value=24 Score=20.88 Aligned_cols=12 Identities=42% Similarity=1.018 Sum_probs=8.3
Q ss_pred ccccchhhhhhh
Q psy2248 83 QMEVCTVCGAFL 94 (102)
Q Consensus 83 kl~VCeVCGA~L 94 (102)
.+-+|..||.|.
T Consensus 25 ~l~~C~~cG~~~ 36 (55)
T TIGR01031 25 TLVVCPNCGEFK 36 (55)
T ss_pred cceECCCCCCcc
Confidence 456788887764
No 157
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.25 E-value=24 Score=30.12 Aligned_cols=14 Identities=29% Similarity=0.612 Sum_probs=10.4
Q ss_pred ccchhhhhhhhccc
Q psy2248 85 EVCTVCGAFLIVGD 98 (102)
Q Consensus 85 ~VCeVCGA~Ls~~D 98 (102)
--||+||+.+...|
T Consensus 156 D~Ce~Cg~~~~P~~ 169 (558)
T COG0143 156 DQCENCGRTLDPTE 169 (558)
T ss_pred chhhhccCcCCchh
Confidence 35888888887665
No 158
>COG4499 Predicted membrane protein [Function unknown]
Probab=24.24 E-value=2.1e+02 Score=23.84 Aligned_cols=45 Identities=13% Similarity=0.181 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q psy2248 12 NENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 12 ~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 56 (102)
.++.+.+.+++.+|.+.+++..++..+-+-+++-..=.+=|+++.
T Consensus 365 ~~r~e~lk~~n~~lqd~~k~~~e~k~e~das~~aeaka~eek~~~ 409 (434)
T COG4499 365 DKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQ 409 (434)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhHhhhhhhhhhh
Confidence 466789999999999999999999987665555444444444443
No 159
>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=24.13 E-value=20 Score=24.38 Aligned_cols=17 Identities=47% Similarity=0.726 Sum_probs=14.5
Q ss_pred hhccccchhhhhhhhcc
Q psy2248 81 EKQMEVCTVCGAFLIVG 97 (102)
Q Consensus 81 ~qkl~VCeVCGA~Ls~~ 97 (102)
.+.+-.|+.||++|++.
T Consensus 40 ~~d~l~C~~C~~~l~~~ 56 (133)
T PF07967_consen 40 SKDMLKCESCGARLCVK 56 (133)
T ss_pred CCCEEEeCCCCCEEEEe
Confidence 36778999999999876
No 160
>PF06721 DUF1204: Protein of unknown function (DUF1204); InterPro: IPR009596 This family represents the C terminus of a number of Arabidopsis thaliana hypothetical proteins of unknown function. Family members contain a conserved DFD motif.
Probab=24.05 E-value=3.2e+02 Score=20.63 Aligned_cols=42 Identities=19% Similarity=0.263 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcccccchhhhhhhhhhhhccccchhhhhh
Q psy2248 44 AQGLMKLCDQLKEEREMLRKQNDNNHWSQTVELAAAQEKQMEVCTVCGAF 93 (102)
Q Consensus 44 A~~l~~~ve~Lk~ek~~l~~~~~~~~~~~~~~~~~~~~qkl~VCeVCGA~ 93 (102)
..++-.-++.++...+++.....+. .....+-|+.|+|||..
T Consensus 79 rs~L~kv~~l~QARidRvK~HiDdk--------ia~ePkFle~nQV~Gni 120 (228)
T PF06721_consen 79 RSALEKVASLYQARIDRVKAHIDDK--------IADEPKFLEFNQVKGNI 120 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhh--------hhcchHHHHHHHhhchH
Confidence 3444445555666666665543221 11223567789999974
No 161
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=24.03 E-value=29 Score=18.17 Aligned_cols=13 Identities=31% Similarity=0.907 Sum_probs=9.5
Q ss_pred hhhccccchhhhh
Q psy2248 80 QEKQMEVCTVCGA 92 (102)
Q Consensus 80 ~~qkl~VCeVCGA 92 (102)
.+.-+.||+.||.
T Consensus 15 ~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 15 EDGELLVCPECGH 27 (30)
T ss_dssp E-SSSEEETTTTE
T ss_pred ccCCEEeCCcccc
Confidence 4556799999984
No 162
>PRK06424 transcription factor; Provisional
Probab=23.98 E-value=27 Score=24.56 Aligned_cols=11 Identities=36% Similarity=0.981 Sum_probs=9.1
Q ss_pred ccccchhhhhh
Q psy2248 83 QMEVCTVCGAF 93 (102)
Q Consensus 83 kl~VCeVCGA~ 93 (102)
.|.||+-|.-|
T Consensus 22 ~l~vC~~Ca~~ 32 (144)
T PRK06424 22 ILNVCDDCAKF 32 (144)
T ss_pred eeehhHHHHHc
Confidence 58999999876
No 163
>PRK06921 hypothetical protein; Provisional
Probab=23.93 E-value=86 Score=23.74 Aligned_cols=35 Identities=9% Similarity=0.107 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHhhcccccchhhhhhhhhhhhccccchhhhh
Q psy2248 47 LMKLCDQLKEEREMLRKQNDNNHWSQTVELAAAQEKQMEVCTVCGA 92 (102)
Q Consensus 47 l~~~ve~Lk~ek~~l~~~~~~~~~~~~~~~~~~~~qkl~VCeVCGA 92 (102)
+..+...|..++..|..... + + ....-..|+.|+-
T Consensus 6 ~~~~~~~l~~~~~~~l~~~g---~-------~-~~~~~~~Cp~C~d 40 (266)
T PRK06921 6 IEEKAAELLMRERPSTTTKP---E-------E-SDAERYDCPKCKD 40 (266)
T ss_pred HHHHHHHHHHHHHHHHHhCC---C-------C-CcCCCCCCCCCCC
Confidence 55667777777766654321 1 1 1122367999984
No 164
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=23.75 E-value=20 Score=21.14 Aligned_cols=12 Identities=25% Similarity=0.598 Sum_probs=8.6
Q ss_pred ccccchhhhhhh
Q psy2248 83 QMEVCTVCGAFL 94 (102)
Q Consensus 83 kl~VCeVCGA~L 94 (102)
.+.+|..||++-
T Consensus 25 ~l~~c~~cg~~~ 36 (56)
T PF01783_consen 25 NLVKCPNCGEPK 36 (56)
T ss_dssp SEEESSSSSSEE
T ss_pred ceeeeccCCCEe
Confidence 567788888753
No 165
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=23.75 E-value=1.8e+02 Score=21.09 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q psy2248 41 VEKAQGLMKLCDQLKEEREMLRK 63 (102)
Q Consensus 41 VdeA~~l~~~ve~Lk~ek~~l~~ 63 (102)
+||=..|..++.+||.|...|..
T Consensus 23 LdEKE~L~~~~QRLkDE~RDLKq 45 (166)
T PF04880_consen 23 LDEKENLREEVQRLKDELRDLKQ 45 (166)
T ss_dssp HHHHHHHHHCH------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35555555666666555555544
No 166
>PF10238 Eapp_C: E2F-associated phosphoprotein; InterPro: IPR019370 This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis [].
Probab=23.68 E-value=24 Score=24.77 Aligned_cols=18 Identities=28% Similarity=0.469 Sum_probs=15.6
Q ss_pred ccchhhhhhhhcccccCC
Q psy2248 85 EVCTVCGAFLIVGDAQSV 102 (102)
Q Consensus 85 ~VCeVCGA~Ls~~D~d~~ 102 (102)
=-|.+|+.-+.+.|.|.|
T Consensus 110 V~Cs~C~TeVaV~D~DEV 127 (136)
T PF10238_consen 110 VKCSECSTEVAVYDKDEV 127 (136)
T ss_pred eecccCCCEEEEEeccCc
Confidence 359999999999998875
No 167
>PLN02320 seryl-tRNA synthetase
Probab=23.64 E-value=3.5e+02 Score=22.96 Aligned_cols=47 Identities=19% Similarity=0.256 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q psy2248 15 AEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64 (102)
Q Consensus 15 ~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~ 64 (102)
..+++.+..+.+.+-+++-. ...+ +++.++..++..|+.+...|+..
T Consensus 106 ~~~~~~lr~ern~~sk~i~~-~~~~--~~~~~l~~~~k~lk~~i~~le~~ 152 (502)
T PLN02320 106 QKEVERLRAERNAVANKMKG-KLEP--SERQALVEEGKNLKEGLVTLEED 152 (502)
T ss_pred HHHHHHHHHHHHHHHHHHHh-hhCC--CCHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666666666655544 1122 34566777777777766666553
No 168
>PF09401 NSP10: RNA synthesis protein NSP10; InterPro: IPR018995 Non-structural protein 10 (NSP10) is involved in RNA synthesis. It is synthesised as part of a replicase polyprotein, whose cleavage generates many non-structural proteins []. NSP10 contains two zinc binding motifs and forms two anti-parallel helices which are stacked against an irregular beta sheet []. A cluster of basic residues on the protein surface suggests a nucleic acid-binding function. ; GO: 0003723 RNA binding, 0008270 zinc ion binding, 0019079 viral genome replication, 0048471 perinuclear region of cytoplasm; PDB: 2XYQ_B 2XYR_B 2XYV_B 3R24_B 2GA6_I 2G9T_V 2FYG_A.
Probab=23.55 E-value=28 Score=24.19 Aligned_cols=13 Identities=62% Similarity=1.211 Sum_probs=8.5
Q ss_pred ccccchhhhhhhh
Q psy2248 83 QMEVCTVCGAFLI 95 (102)
Q Consensus 83 kl~VCeVCGA~Ls 95 (102)
+-+||-|||.+|.
T Consensus 105 ~n~vC~vCg~W~~ 117 (124)
T PF09401_consen 105 ENEVCTVCGCWLN 117 (124)
T ss_dssp H--B-TTTSSBTT
T ss_pred ccceeeeeceEec
Confidence 3489999999876
No 169
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family. Members of this family are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterized specificities of three members are GGTCTC, CGTCTC, and the shared subsequence GTCTC.
Probab=23.53 E-value=26 Score=29.02 Aligned_cols=15 Identities=27% Similarity=0.809 Sum_probs=11.9
Q ss_pred ccccchhhhhhhhcc
Q psy2248 83 QMEVCTVCGAFLIVG 97 (102)
Q Consensus 83 kl~VCeVCGA~Ls~~ 97 (102)
+-+||.+||-.+++.
T Consensus 81 ~~kpC~~CG~~m~i~ 95 (424)
T TIGR02986 81 GVKPCQTCGKTMSLG 95 (424)
T ss_pred CCcchHhcCCeeeee
Confidence 348999999987753
No 170
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=23.53 E-value=1.4e+02 Score=16.36 Aligned_cols=25 Identities=8% Similarity=0.097 Sum_probs=19.6
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHH
Q psy2248 29 VSEAERVGMEGSVEKAQGLMKLCDQ 53 (102)
Q Consensus 29 l~eaE~LGeeG~VdeA~~l~~~ve~ 53 (102)
+..+..+...|+++.|.+.......
T Consensus 5 ~~~i~~~i~~g~~~~a~~~~~~~~~ 29 (58)
T smart00668 5 RKRIRELILKGDWDEALEWLSSLKP 29 (58)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHcCH
Confidence 4567778889999999998866544
No 171
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=23.16 E-value=1.4e+02 Score=19.96 Aligned_cols=19 Identities=37% Similarity=0.529 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy2248 17 QITLLSEKINNLVSEAERV 35 (102)
Q Consensus 17 ~i~~l~~~I~~ll~eaE~L 35 (102)
+|..|..+|..|-.+++.|
T Consensus 97 ev~~L~~RI~~Le~~l~~l 115 (118)
T TIGR01837 97 EIEALSAKIEQLAVQVEEL 115 (118)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444443
No 172
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=23.04 E-value=28 Score=21.23 Aligned_cols=9 Identities=44% Similarity=0.925 Sum_probs=7.3
Q ss_pred cchhhhhhh
Q psy2248 86 VCTVCGAFL 94 (102)
Q Consensus 86 VCeVCGA~L 94 (102)
+|++||...
T Consensus 17 ~CP~Cgs~~ 25 (61)
T PRK08351 17 RCPVCGSRD 25 (61)
T ss_pred cCCCCcCCc
Confidence 799999854
No 173
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=23.04 E-value=27 Score=29.57 Aligned_cols=15 Identities=20% Similarity=0.673 Sum_probs=11.9
Q ss_pred ccccchhhhhhhhcc
Q psy2248 83 QMEVCTVCGAFLIVG 97 (102)
Q Consensus 83 kl~VCeVCGA~Ls~~ 97 (102)
+-+||.+||-.+++.
T Consensus 81 ~~kpCk~CG~~m~i~ 95 (511)
T PF09665_consen 81 KQKPCKTCGKIMSIY 95 (511)
T ss_pred CCcchHhcCCeeeee
Confidence 448999999887753
No 174
>smart00150 SPEC Spectrin repeats.
Probab=23.03 E-value=1.7e+02 Score=17.15 Aligned_cols=50 Identities=20% Similarity=0.258 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q psy2248 14 NAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64 (102)
Q Consensus 14 ~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~ 64 (102)
....|......|+.+...++.|...|.. .+..+-..++.|......|...
T Consensus 43 ~~~e~~~~~~~v~~~~~~~~~L~~~~~~-~~~~i~~~~~~l~~~w~~l~~~ 92 (101)
T smart00150 43 LEAELEAHEERVEALNELGEQLIEEGHP-DAEEIEERLEELNERWEELKEL 92 (101)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566667777777777777777543 4566667777777766666543
No 175
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=23.00 E-value=2.8e+02 Score=19.59 Aligned_cols=45 Identities=20% Similarity=0.262 Sum_probs=31.8
Q ss_pred hhhhHHHHHHHHHHHHHHH-------------HHHHHHHHHhcCCHHHHHHHHHHHHH
Q psy2248 9 SQQNENAEQITLLSEKINN-------------LVSEAERVGMEGSVEKAQGLMKLCDQ 53 (102)
Q Consensus 9 ~~~~~~~e~i~~l~~~I~~-------------ll~eaE~LGeeG~VdeA~~l~~~ve~ 53 (102)
.......+++..|+.+|+. +...++-.-.-|+.+.|.+....+-.
T Consensus 7 ~~~~~~~~~~~~Le~elk~~~~n~~kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~ 64 (177)
T PF10602_consen 7 ETKAKNAEELEKLEAELKDAKSNLGKESIRMALEDLADHYCKIGDLEEALKAYSRARD 64 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhh
Confidence 3445566777888887774 44666777778999999888776544
No 176
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=22.91 E-value=1.1e+02 Score=14.75 Aligned_cols=27 Identities=15% Similarity=0.065 Sum_probs=21.3
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHH
Q psy2248 29 VSEAERVGMEGSVEKAQGLMKLCDQLK 55 (102)
Q Consensus 29 l~eaE~LGeeG~VdeA~~l~~~ve~Lk 55 (102)
...+...-..|+.++|...+.++-++.
T Consensus 5 ~~lg~~y~~~~~~~~A~~~~~~a~~~~ 31 (34)
T PF13181_consen 5 YNLGKIYEQLGDYEEALEYFEKALELN 31 (34)
T ss_dssp HHHHHHHHHTTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence 445666778899999999998887664
No 177
>PF01237 Oxysterol_BP: Oxysterol-binding protein ; InterPro: IPR000648 A number of eukaryotic proteins that seem to be involved with sterol synthesis and/or its regulation have been found [] to be evolutionary related. These include mammalian oxysterol-binding protein (OSBP), a protein of about 800 amino-acid residues that binds a variety of oxysterols (oxygenated derivatives of cholesterol); yeast OSH1, a protein of 859 residues that also plays a role in ergosterol synthesis; yeast proteins HES1 and KES1, highly related proteins of 434 residues that seem to play a role in ergosterol synthesis; and yeast hypothetical proteins YHR001w, YHR073w and YKR003w.; PDB: 3SPW_A 1ZI7_C 1ZHW_A 1ZHX_A 1ZHY_A 1ZHZ_A 1ZHT_A.
Probab=22.83 E-value=1.8e+02 Score=22.84 Aligned_cols=36 Identities=22% Similarity=0.213 Sum_probs=27.7
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q psy2248 29 VSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64 (102)
Q Consensus 29 l~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~ 64 (102)
...--.+-+.|++|.|++.=..+|..++.+.+++++
T Consensus 287 ~R~d~~al~~gd~~~A~~eK~~lEe~QR~~rk~R~~ 322 (354)
T PF01237_consen 287 WRPDQRALENGDIDKAQEEKKRLEEKQRADRKERKE 322 (354)
T ss_dssp HHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455678999999999999999998887777654
No 178
>KOG3362|consensus
Probab=22.59 E-value=27 Score=25.10 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=8.7
Q ss_pred ccchhhhhhhhc
Q psy2248 85 EVCTVCGAFLIV 96 (102)
Q Consensus 85 ~VCeVCGA~Ls~ 96 (102)
.-|-||| |-|.
T Consensus 119 ~fCaVCG-~~S~ 129 (156)
T KOG3362|consen 119 KFCAVCG-YDSK 129 (156)
T ss_pred hhhhhcC-CCch
Confidence 6799999 6654
No 179
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=22.37 E-value=1.7e+02 Score=16.83 Aligned_cols=32 Identities=22% Similarity=0.067 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Q psy2248 25 INNLVSEAERVGMEGSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 25 I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ 56 (102)
+..+..-+.-....|+.++|...+.++-++.+
T Consensus 46 a~~~~~lg~~~~~~g~~~~A~~~~~~al~i~~ 77 (78)
T PF13424_consen 46 ANTLNNLGECYYRLGDYEEALEYYQKALDIFE 77 (78)
T ss_dssp HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhc
Confidence 44455566677888999999999998877754
No 180
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.22 E-value=28 Score=24.42 Aligned_cols=14 Identities=36% Similarity=0.729 Sum_probs=11.7
Q ss_pred ccchhhhhhhhccc
Q psy2248 85 EVCTVCGAFLIVGD 98 (102)
Q Consensus 85 ~VCeVCGA~Ls~~D 98 (102)
.-|+.||.-|...|
T Consensus 29 ~hCp~Cg~PLF~Kd 42 (131)
T COG1645 29 KHCPKCGTPLFRKD 42 (131)
T ss_pred hhCcccCCcceeeC
Confidence 67999999887755
No 181
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=22.20 E-value=3.5e+02 Score=20.38 Aligned_cols=51 Identities=25% Similarity=0.248 Sum_probs=40.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Q psy2248 11 QNENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREML 61 (102)
Q Consensus 11 ~~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l 61 (102)
.....+++-.|+.+|--.-..+=.+.-.|+.++|.....++.++-.+.+++
T Consensus 15 ~d~~REE~l~lsRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~ 65 (204)
T COG2178 15 KDKAREEALKLSREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRL 65 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHH
Confidence 445667777888888888888888999999999998888887766555543
No 182
>PF06694 Plant_NMP1: Plant nuclear matrix protein 1 (NMP1); InterPro: IPR010604 This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm [].
Probab=22.20 E-value=4.2e+02 Score=21.33 Aligned_cols=58 Identities=14% Similarity=0.176 Sum_probs=43.9
Q ss_pred chhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhh
Q psy2248 7 SQSQQNENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64 (102)
Q Consensus 7 ~~~~~~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~~l~~~ 64 (102)
.++...+...++..++.++..+.+..+.|...+.+.-=+.....+.+|+.....+.+.
T Consensus 166 ~lPD~seLe~~~s~~sk~Lq~lqq~v~~Lask~~y~pd~~~~e~~~~Lr~~L~tflq~ 223 (325)
T PF06694_consen 166 PLPDVSELEKKASELSKQLQSLQQQVAELASKHPYNPDEEYVEKESQLRLELETFLQT 223 (325)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhhHHHHHHHHHHHHHHHHH
Confidence 4445567788899999999999999999999988766556666666677766666553
No 183
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=22.00 E-value=81 Score=17.64 Aligned_cols=19 Identities=21% Similarity=0.219 Sum_probs=13.5
Q ss_pred HHhcCCHHHHHHHHHHHHH
Q psy2248 35 VGMEGSVEKAQGLMKLCDQ 53 (102)
Q Consensus 35 LGeeG~VdeA~~l~~~ve~ 53 (102)
|-.+|+.++|..++.++=.
T Consensus 1 ll~~~~~~~A~~~~~~~l~ 19 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQ 19 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHH
T ss_pred ChhccCHHHHHHHHHHHHH
Confidence 3467888888888777644
No 184
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=21.96 E-value=30 Score=19.86 Aligned_cols=13 Identities=23% Similarity=0.866 Sum_probs=10.5
Q ss_pred hhccccchhhhhh
Q psy2248 81 EKQMEVCTVCGAF 93 (102)
Q Consensus 81 ~qkl~VCeVCGA~ 93 (102)
-.-++-|.-||+|
T Consensus 8 lRGirkCp~CGt~ 20 (44)
T PF14952_consen 8 LRGIRKCPKCGTY 20 (44)
T ss_pred HhccccCCcCcCc
Confidence 3456899999987
No 185
>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=21.92 E-value=3.5e+02 Score=20.22 Aligned_cols=42 Identities=17% Similarity=0.249 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh---cCCHHHHHHHHHHHHHH
Q psy2248 13 ENAEQITLLSEKINNLVSEAERVGM---EGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 13 ~~~e~i~~l~~~I~~ll~eaE~LGe---eG~VdeA~~l~~~ve~L 54 (102)
.....|..+...|..++.++..||. .+....-...+.+++.+
T Consensus 91 ~L~~~i~~l~~~i~~l~~~~~~l~~~~~~~~~~~l~~~l~ea~~m 135 (264)
T PF06008_consen 91 DLEQFIQNLQDNIQELIEQVESLNENGDQLPSEDLQRALAEAQRM 135 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHHHHH
Confidence 4556777888889999999998888 44444444455555544
No 186
>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli.
Probab=21.91 E-value=2.6e+02 Score=18.81 Aligned_cols=44 Identities=16% Similarity=0.182 Sum_probs=32.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q psy2248 11 QNENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 11 ~~~~~e~i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~L 54 (102)
..+...+|.....+|.+.-.+..++-..|+-|.--+--.++.+-
T Consensus 65 ~~e~q~ki~~~~~kV~ere~eL~eA~~~G~~~KI~K~~~KL~ea 108 (115)
T PF06476_consen 65 KAERQQKIAEKQQKVAEREAELKEAQAKGDSDKIAKRQKKLAEA 108 (115)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 45667788888999999999999999999886555444443333
No 187
>KOG2636|consensus
Probab=21.77 E-value=28 Score=29.33 Aligned_cols=10 Identities=30% Similarity=1.142 Sum_probs=8.3
Q ss_pred ccchhhhhhh
Q psy2248 85 EVCTVCGAFL 94 (102)
Q Consensus 85 ~VCeVCGA~L 94 (102)
.-|+|||-|-
T Consensus 402 y~CEICGNy~ 411 (497)
T KOG2636|consen 402 YNCEICGNYV 411 (497)
T ss_pred cceeeccCcc
Confidence 7899999663
No 188
>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=21.66 E-value=4.1e+02 Score=21.36 Aligned_cols=22 Identities=32% Similarity=0.430 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q psy2248 16 EQITLLSEKINNLVSEAERVGM 37 (102)
Q Consensus 16 e~i~~l~~~I~~ll~eaE~LGe 37 (102)
+-+..++.+|..+..++++|.+
T Consensus 242 ~~~~~l~~~~~~~~~~i~~l~~ 263 (406)
T PF02388_consen 242 EYLESLQEKLEKLEKEIEKLEE 263 (406)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555666666666655555
No 189
>CHL00102 rps20 ribosomal protein S20
Probab=21.65 E-value=2.4e+02 Score=18.38 Aligned_cols=38 Identities=8% Similarity=0.049 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHHHhc-------CCHHHHHHHHHHHHHHHH
Q psy2248 19 TLLSEKINNLVSEAERVGME-------GSVEKAQGLMKLCDQLKE 56 (102)
Q Consensus 19 ~~l~~~I~~ll~eaE~LGee-------G~VdeA~~l~~~ve~Lk~ 56 (102)
...-..+...+.+...+.+. |+.++|+.++..+...-.
T Consensus 22 ~~~kS~~rT~iKk~~~ai~~~~~~~~~~d~~~a~~~l~~a~s~iD 66 (93)
T CHL00102 22 KAYKSSVKTLIKKYLKNLEDYKTSPNSNNKKKVQETLSSVYSKID 66 (93)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHH
Confidence 35667778888888888887 999999999998887643
No 190
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=21.62 E-value=1.5e+02 Score=17.90 Aligned_cols=18 Identities=33% Similarity=0.444 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy2248 18 ITLLSEKINNLVSEAERV 35 (102)
Q Consensus 18 i~~l~~~I~~ll~eaE~L 35 (102)
+.+|+++|..|-.+|+.+
T Consensus 23 v~EL~~RIa~L~aEI~R~ 40 (59)
T PF06698_consen 23 VEELEERIALLEAEIARL 40 (59)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 446666666666555544
No 191
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=21.48 E-value=22 Score=18.56 Aligned_cols=16 Identities=38% Similarity=0.667 Sum_probs=12.2
Q ss_pred ccccchhhhhhhhccc
Q psy2248 83 QMEVCTVCGAFLIVGD 98 (102)
Q Consensus 83 kl~VCeVCGA~Ls~~D 98 (102)
+...|+.||-+..+.+
T Consensus 6 ~~ykC~~Cgniv~v~~ 21 (34)
T TIGR00319 6 QVYKCEVCGNIVEVLH 21 (34)
T ss_pred cEEEcCCCCcEEEEEE
Confidence 3578999998876554
No 192
>PF04505 Dispanin: Interferon-induced transmembrane protein; InterPro: IPR007593 This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [].; GO: 0009607 response to biotic stimulus, 0016021 integral to membrane
Probab=21.44 E-value=1.6e+02 Score=18.51 Aligned_cols=24 Identities=13% Similarity=0.086 Sum_probs=19.7
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHHH
Q psy2248 31 EAERVGMEGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 31 eaE~LGeeG~VdeA~~l~~~ve~L 54 (102)
+++.+-..||+++|+...+++-.+
T Consensus 43 kv~~~~~~Gd~~~A~~aS~~Ak~~ 66 (82)
T PF04505_consen 43 KVRSRYAAGDYEGARRASRKAKKW 66 (82)
T ss_pred hhHHHHHCCCHHHHHHHHHHhHHH
Confidence 677888899999999988776655
No 193
>PF14149 YhfH: YhfH-like protein
Probab=21.30 E-value=46 Score=18.41 Aligned_cols=14 Identities=29% Similarity=0.581 Sum_probs=10.3
Q ss_pred hhccccchhhhhhh
Q psy2248 81 EKQMEVCTVCGAFL 94 (102)
Q Consensus 81 ~qkl~VCeVCGA~L 94 (102)
.=..++|..||-.+
T Consensus 10 nLp~K~C~~CG~~i 23 (37)
T PF14149_consen 10 NLPPKKCTECGKEI 23 (37)
T ss_pred hCCCcccHHHHHHH
Confidence 33568999999754
No 194
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=21.29 E-value=2.6e+02 Score=18.50 Aligned_cols=37 Identities=24% Similarity=0.187 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q psy2248 18 ITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 18 i~~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~L 54 (102)
|....-.-....-+|=....+|+.++|..++.+.+..
T Consensus 13 II~~aG~Ars~~~eAl~~ak~gdf~~A~~~l~eA~~~ 49 (104)
T PRK09591 13 IILHSGNARTEVHEAFAAMREGNFDLAEQKLNQSNEE 49 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 3344444556666777788999999999999999885
No 195
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=21.29 E-value=29 Score=27.12 Aligned_cols=7 Identities=57% Similarity=1.374 Sum_probs=6.4
Q ss_pred ccchhhh
Q psy2248 85 EVCTVCG 91 (102)
Q Consensus 85 ~VCeVCG 91 (102)
-||+|||
T Consensus 196 ~vC~vC~ 202 (272)
T COG3183 196 TVCDVCE 202 (272)
T ss_pred ceeeecC
Confidence 6999998
No 196
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=21.28 E-value=32 Score=23.95 Aligned_cols=16 Identities=31% Similarity=0.692 Sum_probs=13.5
Q ss_pred hhccccchhhhhhhhc
Q psy2248 81 EKQMEVCTVCGAFLIV 96 (102)
Q Consensus 81 ~qkl~VCeVCGA~Ls~ 96 (102)
.+.|-+|--||+||.-
T Consensus 59 AkR~~~C~~CG~~l~~ 74 (124)
T PF05515_consen 59 AKRYNRCFKCGRYLHN 74 (124)
T ss_pred HHHhCccccccceeec
Confidence 4689999999999863
No 197
>PF12968 DUF3856: Domain of Unknown Function (DUF3856); InterPro: IPR024552 This domain of unknown function is found in a small group of tetratricopeptide-like proteins, which includes the uncharacterised protein Q8KAL8 from SWISSPROT. The structure of Q8KAL8 is known and belongs to the SCOP all alpha class, TPR-like superfamily, CT2138-like family.; PDB: 2HR2_D.
Probab=21.14 E-value=3.1e+02 Score=19.42 Aligned_cols=36 Identities=22% Similarity=0.233 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Q psy2248 24 KINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEERE 59 (102)
Q Consensus 24 ~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~Lk~ek~ 59 (102)
=|.....++-.|-.-|.-++|.+.+..+-++-.||+
T Consensus 99 WIaaVfsra~Al~~~Gr~~eA~~~fr~agEMiaERK 134 (144)
T PF12968_consen 99 WIAAVFSRAVALEGLGRKEEALKEFRMAGEMIAERK 134 (144)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHc
Confidence 377788899999999999999999999988887764
No 198
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=21.05 E-value=35 Score=18.83 Aligned_cols=14 Identities=29% Similarity=0.790 Sum_probs=9.9
Q ss_pred cccchhhhhhhhcc
Q psy2248 84 MEVCTVCGAFLIVG 97 (102)
Q Consensus 84 l~VCeVCGA~Ls~~ 97 (102)
...|.+||-.-+.+
T Consensus 13 ~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 13 ATTCPTCGMLYSPG 26 (41)
T ss_pred CcCCCCCCCEECCC
Confidence 57999999644443
No 199
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=20.87 E-value=35 Score=19.50 Aligned_cols=14 Identities=21% Similarity=0.634 Sum_probs=10.4
Q ss_pred hccccchhhhhhhh
Q psy2248 82 KQMEVCTVCGAFLI 95 (102)
Q Consensus 82 qkl~VCeVCGA~Ls 95 (102)
.+.-||+||.+...
T Consensus 29 ~~~v~CPiC~~~~~ 42 (54)
T PF05605_consen 29 SKNVVCPICSSRVT 42 (54)
T ss_pred CCCccCCCchhhhh
Confidence 34689999998543
No 200
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=20.87 E-value=33 Score=20.70 Aligned_cols=13 Identities=31% Similarity=0.971 Sum_probs=8.4
Q ss_pred cccchhhhhhhhc
Q psy2248 84 MEVCTVCGAFLIV 96 (102)
Q Consensus 84 l~VCeVCGA~Ls~ 96 (102)
|.+|..||-|...
T Consensus 27 ~~~c~~cG~~~l~ 39 (57)
T COG0333 27 LSVCPNCGEYKLP 39 (57)
T ss_pred ceeccCCCCcccC
Confidence 6677777766543
No 201
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=20.82 E-value=32 Score=19.57 Aligned_cols=10 Identities=30% Similarity=0.617 Sum_probs=7.6
Q ss_pred cchhhhhhhh
Q psy2248 86 VCTVCGAFLI 95 (102)
Q Consensus 86 VCeVCGA~Ls 95 (102)
+|++||.=++
T Consensus 2 ~C~~Cg~D~t 11 (45)
T cd02336 2 HCFTCGNDCT 11 (45)
T ss_pred cccCCCCccC
Confidence 7999997543
No 202
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=20.62 E-value=38 Score=21.83 Aligned_cols=17 Identities=18% Similarity=0.595 Sum_probs=6.7
Q ss_pred ccccchhhhhhhhcccc
Q psy2248 83 QMEVCTVCGAFLIVGDA 99 (102)
Q Consensus 83 kl~VCeVCGA~Ls~~D~ 99 (102)
.-++|.|||--+..+.+
T Consensus 8 ~~qiCqiCGD~VGl~~~ 24 (80)
T PF14569_consen 8 NGQICQICGDDVGLTEN 24 (80)
T ss_dssp SS-B-SSS--B--B-SS
T ss_pred CCcccccccCccccCCC
Confidence 34899999976655443
No 203
>TIGR00823 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. operon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family.
Probab=20.58 E-value=2.6e+02 Score=18.28 Aligned_cols=35 Identities=17% Similarity=0.184 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q psy2248 20 LLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQL 54 (102)
Q Consensus 20 ~l~~~I~~ll~eaE~LGeeG~VdeA~~l~~~ve~L 54 (102)
...-.-..+.-+|=....+|++++|..++.+.+..
T Consensus 12 ~~aG~Ars~~~eAl~~a~~gdfe~A~~~l~eA~~~ 46 (99)
T TIGR00823 12 AYAGDARSKALEALKAAKAGDFAKARALVEQAGMC 46 (99)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 33334445556677788999999999999999885
No 204
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=20.52 E-value=32 Score=17.19 Aligned_cols=8 Identities=38% Similarity=0.808 Sum_probs=6.7
Q ss_pred cccchhhh
Q psy2248 84 MEVCTVCG 91 (102)
Q Consensus 84 l~VCeVCG 91 (102)
-.+|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 47899998
No 205
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=20.44 E-value=30 Score=19.37 Aligned_cols=12 Identities=42% Similarity=0.825 Sum_probs=10.2
Q ss_pred ccchhhhhhhhc
Q psy2248 85 EVCTVCGAFLIV 96 (102)
Q Consensus 85 ~VCeVCGA~Ls~ 96 (102)
+.|+.||.-|..
T Consensus 18 ~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 18 EHCPDCGTPLMR 29 (41)
T ss_pred CccCCCCCeeEE
Confidence 789999988876
No 206
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=20.41 E-value=36 Score=25.00 Aligned_cols=13 Identities=31% Similarity=0.851 Sum_probs=9.9
Q ss_pred ccccchhhhhhhh
Q psy2248 83 QMEVCTVCGAFLI 95 (102)
Q Consensus 83 kl~VCeVCGA~Ls 95 (102)
...+|++||.-+.
T Consensus 152 ~~~~Cp~CG~~~~ 164 (177)
T COG1439 152 PKDFCPICGSPLK 164 (177)
T ss_pred CCCcCCCCCCceE
Confidence 4589999997653
No 207
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=20.35 E-value=24 Score=18.42 Aligned_cols=15 Identities=27% Similarity=0.685 Sum_probs=11.5
Q ss_pred cccchhhhhhhhccc
Q psy2248 84 MEVCTVCGAFLIVGD 98 (102)
Q Consensus 84 l~VCeVCGA~Ls~~D 98 (102)
...|+.||-+..+.+
T Consensus 4 ~ykC~~CGniv~v~~ 18 (34)
T cd00974 4 VYKCEICGNIVEVLN 18 (34)
T ss_pred EEEcCCCCcEEEEEE
Confidence 478999998876554
No 208
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=20.28 E-value=38 Score=17.84 Aligned_cols=10 Identities=30% Similarity=0.929 Sum_probs=6.7
Q ss_pred ccchhhhhhh
Q psy2248 85 EVCTVCGAFL 94 (102)
Q Consensus 85 ~VCeVCGA~L 94 (102)
.+|+.||..+
T Consensus 4 g~C~~CGe~I 13 (36)
T PF01258_consen 4 GICEDCGEPI 13 (36)
T ss_dssp SB-TTTSSBE
T ss_pred CCccccCChH
Confidence 4599999754
No 209
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=20.27 E-value=3.2e+02 Score=19.22 Aligned_cols=12 Identities=25% Similarity=0.780 Sum_probs=9.3
Q ss_pred ccccchhhhhhh
Q psy2248 83 QMEVCTVCGAFL 94 (102)
Q Consensus 83 kl~VCeVCGA~L 94 (102)
..-+|+.||--+
T Consensus 110 tYG~Ce~CGe~I 121 (151)
T PRK10778 110 DFGYCESCGVEI 121 (151)
T ss_pred CCceeccCCCcc
Confidence 457999999754
No 210
>PRK13844 recombination protein RecR; Provisional
Probab=20.15 E-value=1.6e+02 Score=21.93 Aligned_cols=14 Identities=21% Similarity=0.650 Sum_probs=10.4
Q ss_pred hhhccccchhhhhh
Q psy2248 80 QEKQMEVCTVCGAF 93 (102)
Q Consensus 80 ~~qkl~VCeVCGA~ 93 (102)
...+.+.|.+||.|
T Consensus 53 ~~~~i~~C~~C~~l 66 (200)
T PRK13844 53 ATANIKKCVYCQAL 66 (200)
T ss_pred HHHhCCcCCCCCCC
Confidence 34567888888876
No 211
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=20.13 E-value=2.3e+02 Score=17.75 Aligned_cols=19 Identities=32% Similarity=0.455 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q psy2248 45 QGLMKLCDQLKEEREMLRK 63 (102)
Q Consensus 45 ~~l~~~ve~Lk~ek~~l~~ 63 (102)
+.+...+++|.+-.+.|+.
T Consensus 45 ~~L~~~a~rm~eRI~tLE~ 63 (75)
T TIGR02976 45 QELYAKADRLEERIDTLER 63 (75)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444443
No 212
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=20.08 E-value=2e+02 Score=17.42 Aligned_cols=9 Identities=22% Similarity=0.180 Sum_probs=3.2
Q ss_pred HHHHHHHHH
Q psy2248 25 INNLVSEAE 33 (102)
Q Consensus 25 I~~ll~eaE 33 (102)
.+.|..++.
T Consensus 47 n~~L~~ei~ 55 (85)
T TIGR02209 47 WRDLQLEVA 55 (85)
T ss_pred HHHHHHHHH
Confidence 333333333
Done!