Query 035172
Match_columns 71
No_of_seqs 100 out of 231
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 09:48:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035172.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035172hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00032 DNA-directed RNA poly 100.0 3E-48 6.6E-53 243.2 5.8 70 1-70 1-70 (71)
2 PRK04016 DNA-directed RNA poly 100.0 4.8E-46 1E-50 228.2 5.8 62 1-62 1-62 (62)
3 COG1644 RPB10 DNA-directed RNA 100.0 6.1E-46 1.3E-50 228.4 5.1 63 1-63 1-63 (63)
4 KOG3497 DNA-directed RNA polym 100.0 3.9E-45 8.4E-50 227.0 4.8 68 1-68 1-68 (69)
5 PF01194 RNA_pol_N: RNA polyme 100.0 4.4E-45 9.6E-50 222.6 4.6 60 1-60 1-60 (60)
6 PHA03082 DNA-dependent RNA pol 99.3 1.8E-13 3.9E-18 84.2 -0.1 49 1-54 1-49 (63)
7 PF05864 Chordopox_RPO7: Chord 99.3 2.2E-13 4.7E-18 83.9 0.1 49 1-54 1-49 (63)
8 PRK00418 DNA gyrase inhibitor; 87.2 0.18 3.8E-06 31.0 -0.1 14 1-14 3-16 (62)
9 COG3024 Uncharacterized protei 80.4 0.78 1.7E-05 28.6 0.7 13 2-14 5-17 (65)
10 PF06404 PSK: Phytosulfokine p 75.6 1.3 2.9E-05 28.0 0.8 11 46-56 64-74 (81)
11 PF00098 zf-CCHC: Zinc knuckle 74.8 1.6 3.4E-05 20.5 0.8 9 5-13 1-9 (18)
12 PF01807 zf-CHC2: CHC2 zinc fi 73.6 3.2 7E-05 26.1 2.2 29 6-37 56-84 (97)
13 PF00518 E6: Early Protein (E6 72.9 1.9 4.1E-05 28.2 1.1 14 3-16 70-83 (110)
14 smart00400 ZnF_CHCC zinc finge 72.4 5 0.00011 22.7 2.6 30 6-38 25-54 (55)
15 PF00653 BIR: Inhibitor of Apo 72.3 1.5 3.3E-05 25.8 0.4 14 5-19 37-50 (70)
16 PRK01343 zinc-binding protein; 70.6 1.2 2.7E-05 26.9 -0.2 13 4-16 9-21 (57)
17 PF04810 zf-Sec23_Sec24: Sec23 69.1 2.2 4.7E-05 23.3 0.6 13 4-16 2-14 (40)
18 PF13248 zf-ribbon_3: zinc-rib 68.5 2.3 4.9E-05 21.3 0.5 14 4-17 2-15 (26)
19 PF04423 Rad50_zn_hook: Rad50 68.4 3.5 7.6E-05 23.3 1.4 18 6-25 22-39 (54)
20 smart00238 BIR Baculoviral inh 65.6 1.6 3.4E-05 25.4 -0.5 16 4-20 36-51 (71)
21 PF02796 HTH_7: Helix-turn-hel 64.4 8.9 0.00019 20.9 2.5 27 16-42 9-35 (45)
22 PF03604 DNA_RNApol_7kD: DNA d 64.1 3.5 7.5E-05 22.1 0.8 11 4-14 17-27 (32)
23 KOG1101 Apoptosis inhibitor IA 62.6 4.1 8.9E-05 28.2 1.1 19 5-23 52-76 (147)
24 PF11023 DUF2614: Protein of u 60.8 3.6 7.9E-05 28.0 0.6 12 3-14 68-79 (114)
25 PF03884 DUF329: Domain of unk 60.6 3.4 7.3E-05 24.8 0.3 13 4-16 2-14 (57)
26 PF03918 CcmH: Cytochrome C bi 60.2 9.5 0.00021 26.2 2.5 34 5-38 41-83 (148)
27 TIGR02098 MJ0042_CXXC MJ0042 f 58.8 4.5 9.8E-05 21.1 0.6 10 5-14 26-35 (38)
28 smart00659 RPOLCX RNA polymera 56.9 5.1 0.00011 22.6 0.6 12 3-14 18-29 (44)
29 PF14392 zf-CCHC_4: Zinc knuck 56.4 4.7 0.0001 22.6 0.4 11 3-13 30-40 (49)
30 COG2051 RPS27A Ribosomal prote 56.3 4.5 9.7E-05 25.3 0.4 14 3-16 37-50 (67)
31 PRK02277 orotate phosphoribosy 53.8 10 0.00022 26.6 1.9 38 15-53 5-42 (200)
32 PTZ00172 40S ribosomal protein 53.4 5.6 0.00012 26.9 0.5 13 4-16 20-32 (108)
33 cd00022 BIR Baculoviral inhibi 52.2 3.7 8.1E-05 23.6 -0.4 15 5-20 35-49 (69)
34 PHA02779 E6 protein; Provision 52.1 9.9 0.00022 26.3 1.6 24 3-28 100-123 (150)
35 PHA02775 E6; Provisional 52.0 10 0.00022 26.7 1.6 24 3-28 115-138 (160)
36 PRK02935 hypothetical protein; 51.6 6.5 0.00014 26.7 0.6 13 3-15 69-81 (110)
37 PF08209 Sgf11: Sgf11 (transcr 51.1 6.7 0.00015 21.2 0.5 13 4-16 4-16 (33)
38 PRK09335 30S ribosomal protein 50.8 6.7 0.00015 26.0 0.5 13 4-16 20-32 (95)
39 PF08006 DUF1700: Protein of u 50.2 13 0.00028 25.2 1.9 31 17-47 28-59 (181)
40 PF04502 DUF572: Family of unk 50.0 7.8 0.00017 29.4 0.9 13 3-15 39-51 (324)
41 PRK00415 rps27e 30S ribosomal 49.8 7.3 0.00016 23.7 0.6 14 3-16 29-42 (59)
42 PLN00186 ribosomal protein S26 49.8 7 0.00015 26.5 0.5 13 4-16 20-32 (109)
43 COG4175 ProV ABC-type proline/ 49.5 20 0.00043 28.9 3.1 41 1-41 1-41 (386)
44 KOG4384 Uncharacterized SAM do 48.5 28 0.00061 27.8 3.8 42 19-60 228-278 (361)
45 PRK00398 rpoP DNA-directed RNA 47.6 9.2 0.0002 21.0 0.7 11 4-14 3-13 (46)
46 PF07754 DUF1610: Domain of un 47.1 9 0.0002 19.5 0.6 10 7-16 1-10 (24)
47 PF05443 ROS_MUCR: ROS/MUCR tr 47.1 20 0.00043 24.6 2.4 35 5-41 73-107 (132)
48 PF14410 GH-E: HNH/ENDO VII su 46.8 25 0.00055 21.4 2.7 35 5-39 6-51 (70)
49 COG2888 Predicted Zn-ribbon RN 45.5 9.9 0.00021 23.4 0.7 13 3-15 8-20 (61)
50 smart00132 LIM Zinc-binding do 45.1 9.8 0.00021 18.7 0.5 10 6-15 29-38 (39)
51 PRK11595 DNA utilization prote 45.1 10 0.00023 26.8 0.8 13 2-14 3-15 (227)
52 PF14149 YhfH: YhfH-like prote 45.1 6 0.00013 22.1 -0.3 21 4-24 13-33 (37)
53 PRK10144 formate-dependent nit 44.6 25 0.00054 24.1 2.6 34 5-38 41-83 (126)
54 PF10367 Vps39_2: Vacuolar sor 43.9 11 0.00024 22.7 0.7 11 6-16 80-90 (109)
55 PF08097 Toxin_26: Conotoxin T 43.8 6.9 0.00015 16.8 -0.1 6 40-45 5-10 (11)
56 smart00834 CxxC_CXXC_SSSS Puta 43.5 12 0.00026 19.3 0.7 11 4-14 26-36 (41)
57 PF10238 Eapp_C: E2F-associate 43.1 10 0.00022 26.1 0.5 14 3-16 108-121 (136)
58 PF06107 DUF951: Bacterial pro 42.3 23 0.00051 21.4 2.0 24 3-26 30-53 (57)
59 cd08576 GDPD_like_SMaseD_PLD G 42.1 23 0.0005 26.8 2.3 59 3-63 43-108 (265)
60 PF13240 zinc_ribbon_2: zinc-r 41.4 13 0.00029 18.2 0.7 11 6-16 1-11 (23)
61 PF06221 zf-C2HC5: Putative zi 40.7 11 0.00023 22.7 0.3 11 6-16 20-30 (57)
62 COG5134 Uncharacterized conser 40.7 9.3 0.0002 29.2 0.0 23 3-25 41-65 (272)
63 TIGR03147 cyt_nit_nrfF cytochr 40.6 31 0.00067 23.6 2.6 34 5-38 41-83 (126)
64 COG2442 Uncharacterized conser 40.5 26 0.00057 22.0 2.1 22 20-41 35-57 (79)
65 PRK14890 putative Zn-ribbon RN 39.1 16 0.00034 22.3 0.8 15 2-16 5-19 (59)
66 PF03226 Yippee-Mis18: Yippee 38.9 6.1 0.00013 24.4 -1.0 19 2-20 55-73 (96)
67 PF13894 zf-C2H2_4: C2H2-type 38.9 19 0.00041 15.8 0.9 14 6-19 2-15 (24)
68 COG4068 Uncharacterized protei 38.6 16 0.00034 22.7 0.8 18 1-18 4-22 (64)
69 cd02336 ZZ_RSC8 Zinc finger, Z 38.2 15 0.00033 20.8 0.7 16 6-23 2-17 (45)
70 PRK12899 secA preprotein trans 37.9 35 0.00076 30.4 3.1 36 14-49 42-78 (970)
71 PF12269 zf-CpG_bind_C: CpG bi 37.7 13 0.00028 27.9 0.4 16 2-17 82-97 (236)
72 smart00454 SAM Sterile alpha m 37.4 57 0.0012 17.5 2.9 28 30-57 39-66 (68)
73 PF08271 TF_Zn_Ribbon: TFIIB z 37.1 16 0.00034 19.8 0.6 12 5-16 20-31 (43)
74 PF09538 FYDLN_acid: Protein o 37.0 16 0.00034 24.1 0.7 13 4-16 26-38 (108)
75 TIGR01391 dnaG DNA primase, ca 36.8 37 0.0008 26.4 2.8 30 6-38 57-86 (415)
76 PF10571 UPF0547: Uncharacteri 36.6 16 0.00036 18.5 0.6 11 6-16 2-12 (26)
77 PF00096 zf-C2H2: Zinc finger, 36.1 21 0.00044 16.3 0.8 12 6-17 2-13 (23)
78 PF01283 Ribosomal_S26e: Ribos 36.1 13 0.00029 25.1 0.2 13 3-15 19-31 (113)
79 PF00412 LIM: LIM domain; Int 35.7 19 0.00041 19.5 0.8 12 5-16 27-38 (58)
80 PF01667 Ribosomal_S27e: Ribos 35.5 17 0.00037 21.7 0.6 14 3-16 25-38 (55)
81 PRK07218 replication factor A; 34.4 17 0.00037 29.0 0.6 14 3-16 296-309 (423)
82 COG4709 Predicted membrane pro 34.4 31 0.00068 25.4 2.0 23 19-41 31-53 (195)
83 PF06750 DiS_P_DiS: Bacterial 33.9 21 0.00045 22.6 0.9 13 6-18 60-72 (92)
84 PF03489 SapB_2: Saposin-like 33.7 26 0.00056 17.8 1.1 31 10-40 4-34 (35)
85 PF04161 Arv1: Arv1-like famil 33.6 16 0.00035 25.8 0.4 16 6-21 2-17 (208)
86 PF09706 Cas_CXXC_CXXC: CRISPR 33.5 20 0.00043 21.7 0.7 15 6-20 7-21 (69)
87 PRK00420 hypothetical protein; 33.5 30 0.00065 23.2 1.6 13 4-16 40-52 (112)
88 PF10122 Mu-like_Com: Mu-like 33.4 14 0.00031 21.9 0.0 16 1-16 1-16 (51)
89 smart00741 SapB Saposin (B) Do 33.1 29 0.00062 19.0 1.3 30 10-39 45-74 (76)
90 COG4416 Com Mu-like prophage p 33.1 9 0.00019 23.5 -0.9 16 1-16 1-16 (60)
91 PF13878 zf-C2H2_3: zinc-finge 32.6 21 0.00045 19.6 0.6 12 4-15 13-24 (41)
92 PF01286 XPA_N: XPA protein N- 32.1 14 0.0003 20.1 -0.1 15 4-18 3-17 (34)
93 PF13408 Zn_ribbon_recom: Reco 31.8 20 0.00044 19.5 0.5 12 5-16 6-17 (58)
94 PF07647 SAM_2: SAM domain (St 31.6 74 0.0016 17.6 2.9 24 32-55 41-64 (66)
95 PRK13832 plasmid partitioning 31.5 44 0.00096 27.8 2.6 35 16-50 106-141 (520)
96 PF12773 DZR: Double zinc ribb 31.0 22 0.00048 19.3 0.6 14 5-18 30-43 (50)
97 PLN00209 ribosomal protein S27 30.9 22 0.00047 23.2 0.6 14 3-16 54-67 (86)
98 PF01428 zf-AN1: AN1-like Zinc 30.3 23 0.00049 19.3 0.5 13 2-14 11-23 (43)
99 PF13717 zinc_ribbon_4: zinc-r 30.2 24 0.00052 18.8 0.6 9 5-13 26-34 (36)
100 PF04255 DUF433: Protein of un 29.7 47 0.001 18.9 1.8 23 19-41 22-45 (56)
101 PF13913 zf-C2HC_2: zinc-finge 29.7 26 0.00056 17.3 0.6 12 5-16 3-14 (25)
102 PLN00214 putative protein; Pro 29.4 62 0.0013 22.1 2.6 28 33-60 54-85 (115)
103 KOG3173 Predicted Zn-finger pr 29.0 18 0.00039 25.4 -0.1 14 3-16 104-117 (167)
104 smart00343 ZnF_C2HC zinc finge 28.9 25 0.00055 16.9 0.5 8 6-13 1-8 (26)
105 PF14690 zf-ISL3: zinc-finger 28.5 28 0.0006 18.5 0.7 11 4-14 2-12 (47)
106 PRK06386 replication factor A; 28.2 25 0.00054 27.6 0.6 13 4-16 236-248 (358)
107 PF13719 zinc_ribbon_5: zinc-r 27.2 29 0.00064 18.4 0.6 10 4-13 25-34 (37)
108 PF10013 DUF2256: Uncharacteri 27.1 29 0.00062 19.9 0.6 10 6-15 10-19 (42)
109 PF05515 Viral_NABP: Viral nuc 26.7 26 0.00056 24.1 0.4 24 5-28 63-96 (124)
110 COG5457 Uncharacterized conser 26.4 52 0.0011 20.1 1.6 27 17-43 24-51 (63)
111 cd00569 HTH_Hin_like Helix-tur 26.0 72 0.0016 13.8 2.6 27 17-43 10-36 (42)
112 COG5123 TOA2 Transcription ini 25.9 38 0.00083 23.0 1.1 23 15-38 2-24 (113)
113 PF14446 Prok-RING_1: Prokaryo 25.5 32 0.0007 20.5 0.6 10 5-14 22-31 (54)
114 PF06397 Desulfoferrod_N: Desu 25.4 28 0.00061 19.1 0.3 11 6-16 8-18 (36)
115 TIGR03793 TOMM_pelo TOMM prope 25.2 46 0.001 20.7 1.3 28 12-41 8-37 (77)
116 PTZ00083 40S ribosomal protein 25.2 32 0.00069 22.4 0.6 14 3-16 53-66 (85)
117 PRK08222 hydrogenase 4 subunit 25.1 55 0.0012 22.7 1.8 13 4-16 114-126 (181)
118 PF13451 zf-trcl: Probable zin 25.0 17 0.00036 21.3 -0.7 10 3-12 32-41 (49)
119 KOG1597 Transcription initiati 24.9 30 0.00064 27.2 0.5 13 5-17 22-34 (308)
120 COG1656 Uncharacterized conser 24.9 56 0.0012 23.4 1.8 20 6-25 132-153 (165)
121 COG4481 Uncharacterized protei 24.6 63 0.0014 19.8 1.8 23 3-25 33-55 (60)
122 PHA02562 46 endonuclease subun 24.4 49 0.0011 25.6 1.6 13 5-17 285-297 (562)
123 PF01927 Mut7-C: Mut7-C RNAse 24.2 34 0.00073 22.8 0.6 16 6-21 126-143 (147)
124 PF03119 DNA_ligase_ZBD: NAD-d 24.2 35 0.00077 17.4 0.5 10 6-15 1-10 (28)
125 PRK05667 dnaG DNA primase; Val 24.1 80 0.0017 26.0 2.8 30 6-38 59-88 (580)
126 PF01475 FUR: Ferric uptake re 24.0 60 0.0013 20.3 1.7 21 5-25 81-101 (120)
127 PF12171 zf-C2H2_jaz: Zinc-fin 23.9 47 0.001 16.0 1.0 11 6-16 3-13 (27)
128 PF07967 zf-C3HC: C3HC zinc fi 23.9 62 0.0013 21.2 1.8 56 4-61 43-124 (133)
129 cd00729 rubredoxin_SM Rubredox 23.8 39 0.00084 17.8 0.7 12 3-14 17-28 (34)
130 PF14319 Zn_Tnp_IS91: Transpos 23.8 47 0.001 21.6 1.2 17 7-23 63-79 (111)
131 smart00661 RPOL9 RNA polymeras 23.7 37 0.0008 18.3 0.6 11 6-16 2-12 (52)
132 COG0821 gcpE 1-hydroxy-2-methy 23.7 60 0.0013 26.0 2.0 20 4-23 261-280 (361)
133 smart00401 ZnF_GATA zinc finge 23.7 38 0.00083 19.3 0.7 16 3-18 2-17 (52)
134 PF07541 EIF_2_alpha: Eukaryot 23.5 61 0.0013 21.1 1.7 24 15-41 15-39 (114)
135 PF00482 T2SF: Type II secreti 23.2 55 0.0012 19.0 1.3 28 12-39 29-56 (124)
136 cd01775 CYR1_RA Ubiquitin doma 23.1 56 0.0012 21.6 1.5 37 5-41 48-88 (97)
137 PRK13130 H/ACA RNA-protein com 23.0 62 0.0013 19.3 1.5 23 5-27 18-50 (56)
138 PF02671 PAH: Paired amphipath 22.7 1.4E+02 0.003 16.0 3.6 40 16-62 2-45 (47)
139 PRK07956 ligA NAD-dependent DN 22.7 41 0.00088 28.2 0.9 13 2-14 402-414 (665)
140 TIGR02289 M3_not_pepF oligoend 22.6 89 0.0019 24.9 2.8 26 17-42 500-527 (549)
141 PRK03987 translation initiatio 22.5 71 0.0015 23.8 2.1 24 15-41 131-154 (262)
142 TIGR03652 FeS_repair_RIC iron- 22.4 64 0.0014 22.7 1.7 23 24-47 4-26 (216)
143 PF09597 IGR: IGR protein moti 22.3 1.6E+02 0.0035 17.5 3.3 24 30-54 29-52 (57)
144 PF06336 Corona_5a: Coronaviru 22.2 84 0.0018 19.4 2.0 32 32-64 23-60 (65)
145 KOG1885 Lysyl-tRNA synthetase 22.2 31 0.00068 29.0 0.2 54 8-64 470-553 (560)
146 COG1996 RPC10 DNA-directed RNA 22.2 41 0.0009 19.7 0.6 11 4-14 24-34 (49)
147 PF09889 DUF2116: Uncharacteri 22.2 41 0.00088 20.2 0.6 12 6-17 5-16 (59)
148 PF13342 Toprim_Crpt: C-termin 22.2 78 0.0017 18.8 1.9 20 10-31 12-31 (62)
149 TIGR02531 yecD_yerC TrpR-relat 22.1 1E+02 0.0022 19.5 2.5 26 19-44 41-66 (88)
150 PF15629 Perm-CXXC: Permuted s 22.0 32 0.0007 18.7 0.1 8 6-13 18-25 (32)
151 COG5216 Uncharacterized conser 21.8 28 0.0006 21.7 -0.2 16 5-20 45-60 (67)
152 PF09963 DUF2197: Uncharacteri 21.7 33 0.00071 20.6 0.1 11 4-14 2-12 (56)
153 cd00350 rubredoxin_like Rubred 21.5 43 0.00093 17.3 0.6 11 4-14 17-27 (33)
154 PF14353 CpXC: CpXC protein 21.5 44 0.00096 21.4 0.7 20 44-63 97-116 (128)
155 PF10083 DUF2321: Uncharacteri 21.4 59 0.0013 23.3 1.4 24 3-28 67-95 (158)
156 smart00547 ZnF_RBZ Zinc finger 21.4 44 0.00094 15.9 0.5 9 5-13 17-25 (26)
157 cd00435 ACBP Acyl CoA binding 21.3 1.6E+02 0.0034 18.3 3.2 29 17-61 54-82 (85)
158 smart00291 ZnF_ZZ Zinc-binding 21.2 56 0.0012 17.7 1.0 14 3-16 3-16 (44)
159 PF01258 zf-dskA_traR: Prokary 21.1 42 0.0009 17.5 0.5 11 6-16 5-15 (36)
160 COG0856 Orotate phosphoribosyl 21.0 76 0.0017 23.6 1.9 32 14-45 4-35 (203)
161 COG2093 DNA-directed RNA polym 21.0 18 0.00038 22.5 -1.2 33 7-41 21-54 (64)
162 PF01450 IlvC: Acetohydroxy ac 20.9 47 0.001 22.6 0.8 30 7-36 14-43 (145)
163 PF12322 T4_baseplate: T4 bact 20.8 40 0.00086 24.3 0.4 11 2-13 182-192 (205)
164 COG1601 GCD7 Translation initi 20.7 42 0.00091 23.5 0.5 16 3-18 104-119 (151)
165 PF14787 zf-CCHC_5: GAG-polypr 20.7 44 0.00095 18.6 0.5 10 4-13 2-11 (36)
166 TIGR03826 YvyF flagellar opero 20.7 84 0.0018 21.6 2.0 37 5-41 19-59 (137)
167 PF09237 GAGA: GAGA factor; I 20.7 72 0.0016 19.2 1.5 13 4-16 24-36 (54)
168 PF11672 DUF3268: Protein of u 20.7 46 0.001 21.9 0.7 11 4-14 2-12 (102)
169 PF13384 HTH_23: Homeodomain-l 20.5 85 0.0018 16.5 1.7 26 21-46 10-35 (50)
170 COG4830 RPS26B Ribosomal prote 20.0 43 0.00093 22.7 0.4 14 3-16 19-32 (108)
No 1
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=3e-48 Score=243.21 Aligned_cols=70 Identities=94% Similarity=1.577 Sum_probs=67.6
Q ss_pred CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhccCcccccCC
Q 035172 1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLDKSDT 70 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y~~~~~~~~ 70 (71)
|||||||||||||||++||+|++++++|++|++|||+||++|||||||||||||+||+|++|++.++...
T Consensus 1 MiiPVRCFTCGkvig~~we~y~~~~~~g~~~~~~LD~LG~~RYCCRRMllsHvdlid~ll~y~~~~~~~~ 70 (71)
T PLN00032 1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYSEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLEKSEN 70 (71)
T ss_pred CCCceeecCCCCCcHHHHHHHHHHHhcCCCHHHHHHHhCchhhhhhhHHHHHHHHHHHHHccCchhhhcc
Confidence 9999999999999999999999999999999999999999999999999999999999999998877654
No 2
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=100.00 E-value=4.8e-46 Score=228.20 Aligned_cols=62 Identities=55% Similarity=1.195 Sum_probs=61.5
Q ss_pred CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhcc
Q 035172 1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNY 62 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y 62 (71)
||||||||||||+||++||+|++++++|++|++|||+||++|||||||||||||+||+|++|
T Consensus 1 MiiPvRCFTCGkvi~~~we~y~~~~~~g~~~~~vLd~Lg~~RyCCRRMllthvdlid~l~~y 62 (62)
T PRK04016 1 MMIPVRCFTCGKVIAEKWEEFKERVEAGEDPGKVLDDLGVKRYCCRRMLLSHVELIDEVIPY 62 (62)
T ss_pred CCCCeEecCCCCChHHHHHHHHHHHHcCCCHHHHHHHcCCcchhhhhHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999999999999999999999999999999999999998
No 3
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=100.00 E-value=6.1e-46 Score=228.43 Aligned_cols=63 Identities=60% Similarity=1.250 Sum_probs=62.2
Q ss_pred CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhccC
Q 035172 1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYN 63 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y~ 63 (71)
||||||||||||+||++|++|++++++|++|++|||+||++||||||||+||||+||++++|+
T Consensus 1 MiiPiRCFsCGkvi~~~w~~y~~rv~~ge~p~~vLDdLGv~RYCCRRM~lsHvd~id~~~~y~ 63 (63)
T COG1644 1 MIIPVRCFSCGKVIGHKWEEYKRRVEEGEDPGEVLDDLGVKRYCCRRMLLSHVDLIDELLPYD 63 (63)
T ss_pred CCCceEeecCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCcHHHHHHHHHHHHHHHHHhhccCC
Confidence 999999999999999999999999999999999999999999999999999999999999985
No 4
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=100.00 E-value=3.9e-45 Score=227.03 Aligned_cols=68 Identities=85% Similarity=1.509 Sum_probs=66.8
Q ss_pred CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhccCccccc
Q 035172 1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLDKS 68 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y~~~~~~ 68 (71)
||||||||||||+||+|||.|++++|+.+++++|||+||++|||||||+|||||+||+||+|++.+++
T Consensus 1 MIiPiRCFtCGKvig~KWe~Yl~lLq~d~~eg~ALd~LGl~RyCCRRM~l~HVDlieKlL~y~~lek~ 68 (69)
T KOG3497|consen 1 MIIPIRCFTCGKVIGDKWETYLELLQADYTEGDALDALGLKRYCCRRMLLTHVDLIEKLLNYNPLEKF 68 (69)
T ss_pred CeeeeEeeeccccccccHHHHHHHHHHhhccchHHHHhhhHHHHHHHHHHHHHHHHHHHHccCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999998875
No 5
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=100.00 E-value=4.4e-45 Score=222.64 Aligned_cols=60 Identities=75% Similarity=1.389 Sum_probs=51.4
Q ss_pred CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHh
Q 035172 1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLL 60 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll 60 (71)
||||||||||||+|||+||+|++++++|++|++|||+||++|||||||||||||+||+|+
T Consensus 1 MiiPVRCFTCGkvi~~~~e~y~~~~~~~~~~~~~Ld~LG~~ryCCRrmlLshvdli~~ll 60 (60)
T PF01194_consen 1 MIIPVRCFTCGKVIGNKWEEYLERLENGEDPGDALDDLGLKRYCCRRMLLSHVDLIDKLL 60 (60)
T ss_dssp ---SSS-STTTSBTCGHHHHHHHHHHTTS-HHHHHHHTT-SSHHHHHHHHTB--THHHHH
T ss_pred CCCceecCCCCCChhHhHHHHHHHHHcCCCHHHHHHHhCCceeehhhHHHHHHHHHHHhC
Confidence 999999999999999999999999999999999999999999999999999999999986
No 6
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=99.33 E-value=1.8e-13 Score=84.22 Aligned_cols=49 Identities=27% Similarity=0.575 Sum_probs=46.4
Q ss_pred CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHH
Q 035172 1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVD 54 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvd 54 (71)
|+||+.|.|||+.+|+ |+|..++ ...+.++||. ++++.|||-.|.||+|
T Consensus 1 MVf~lVCsTCGrDlSe--eRy~Lli-~~~~L~~Vl~--~v~~~CCRlKLsTQIE 49 (63)
T PHA03082 1 MVFQLVCSTCGRDLSE--ERYRLLI-KKKSLKKVLR--TVKNSCCRLKLSTQIE 49 (63)
T ss_pred CeeeeeecccCcchhH--HHHHHHH-HHhhHHHHHH--Hhhccceeeeeecccc
Confidence 8999999999999999 9999999 5589999999 9999999999999987
No 7
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 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. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=99.32 E-value=2.2e-13 Score=83.87 Aligned_cols=49 Identities=27% Similarity=0.603 Sum_probs=46.3
Q ss_pred CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHH
Q 035172 1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVD 54 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvd 54 (71)
|+||+.|.|||+.||+ |+|..++ +..+.++||. ++++.|||-.|.||+|
T Consensus 1 MVf~lvCSTCGrDlSe--eRy~Lli-~~~~Lk~Vl~--~v~n~CCRlKLsTQIE 49 (63)
T PF05864_consen 1 MVFQLVCSTCGRDLSE--ERYRLLI-KEMSLKKVLR--TVKNSCCRLKLSTQIE 49 (63)
T ss_pred CeeeeeecccCCcchH--HHHHHHH-HHhhHHHHHH--Hhhccceeeeeccccc
Confidence 8999999999999999 9999999 5589999999 9999999999999987
No 8
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=87.17 E-value=0.18 Score=31.01 Aligned_cols=14 Identities=50% Similarity=0.904 Sum_probs=11.5
Q ss_pred CcccccccCCCccc
Q 035172 1 MIIPVRCFTCGKVI 14 (71)
Q Consensus 1 MiiPvRCfTCGkvi 14 (71)
|...|+|++|||.+
T Consensus 3 ~~~~v~CP~C~k~~ 16 (62)
T PRK00418 3 ETITVNCPTCGKPV 16 (62)
T ss_pred CCccccCCCCCCcc
Confidence 34568999999997
No 9
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.36 E-value=0.78 Score=28.60 Aligned_cols=13 Identities=54% Similarity=0.948 Sum_probs=10.8
Q ss_pred cccccccCCCccc
Q 035172 2 IIPVRCFTCGKVI 14 (71)
Q Consensus 2 iiPvRCfTCGkvi 14 (71)
++-|-|+||||++
T Consensus 5 ~~~v~CP~Cgkpv 17 (65)
T COG3024 5 RITVPCPTCGKPV 17 (65)
T ss_pred cccccCCCCCCcc
Confidence 3557799999998
No 10
>PF06404 PSK: Phytosulfokine precursor protein (PSK); InterPro: IPR009438 This family consists of several plant specific phytosulfokine precursor proteins. Phytosulfokines, are active as either a pentapeptide or a C-terminally truncated tetrapeptide. These compounds were first isolated because of their ability to stimulate cell division in somatic embryo cultures of Asparagus officinalis [].; GO: 0008083 growth factor activity, 0008283 cell proliferation, 0005576 extracellular region
Probab=75.65 E-value=1.3 Score=27.97 Aligned_cols=11 Identities=55% Similarity=0.884 Sum_probs=10.4
Q ss_pred hhHHHHhHHHH
Q 035172 46 RRMLMTHVDLI 56 (71)
Q Consensus 46 Rrmllthvdli 56 (71)
||||.+|.|.|
T Consensus 64 RRtL~AHlDYI 74 (81)
T PF06404_consen 64 RRTLAAHLDYI 74 (81)
T ss_pred HHHHHHHhhhe
Confidence 99999999997
No 11
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=74.84 E-value=1.6 Score=20.50 Aligned_cols=9 Identities=44% Similarity=1.376 Sum_probs=7.3
Q ss_pred ccccCCCcc
Q 035172 5 VRCFTCGKV 13 (71)
Q Consensus 5 vRCfTCGkv 13 (71)
.+||.||+.
T Consensus 1 ~~C~~C~~~ 9 (18)
T PF00098_consen 1 RKCFNCGEP 9 (18)
T ss_dssp SBCTTTSCS
T ss_pred CcCcCCCCc
Confidence 479999974
No 12
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=73.56 E-value=3.2 Score=26.15 Aligned_cols=29 Identities=28% Similarity=0.560 Sum_probs=13.8
Q ss_pred cccCCCccccchHHHHHHHHHccCChhhHHHh
Q 035172 6 RCFTCGKVIGNKWDTYLDLLQADYPEGDALDA 37 (71)
Q Consensus 6 RCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~ 37 (71)
+||+||+- |+.++ |...+ +|.+-.+|+..
T Consensus 56 ~Cf~Cg~~-Gd~i~-~v~~~-~~~~f~eAv~~ 84 (97)
T PF01807_consen 56 KCFGCGKG-GDVID-FVMKY-EGCSFKEAVKW 84 (97)
T ss_dssp EETTT--E-E-HHH-HHHHH-HT--HHHHHHH
T ss_pred EECCCCCC-CcHHh-HHHHH-hCCCHHHHHHH
Confidence 69999973 55444 34444 45565555553
No 13
>PF00518 E6: Early Protein (E6); InterPro: IPR001334 The papillomavirus E6 oncoproteins are small zinc-binding proteins that share a conserved zinc-binding CXXC motif and do not have identified intrinsic enzymatic activity. E6 proteins are thought to act as adapter proteins, thereby altering the function of E6-associated cellular proteins. This model for E6 function is best supported by observations of human papillomavirus type 16 (HPV-16) E6 (16E6), which can alter the metabolism of the p53 tumor suppressor through association with a cellular E3 ubiquitin ligase called E6AP. HPV-16 E6 interacts with an 18-amino-acid sequence in E6AP, and in an as yet ill-defined fashion the E6AP-16E6 complex binds to p53, inducing the ubiquitin-dependent degradation of the trimolecular complex. 16E6 apparently functions as an adapter protein in the complex with p53, since E6AP does not interact with p53 in the absence of E6 and since the degradation of p53 requires both E6 and E6AP. Despite the similarity in structure of the E6 oncoproteins, studies have indicated surprising biochemical diversity among E6 oncoproteins of different papillomavirus types. E6 from the cancer-associated human papillomaviruses (HPVs) complex with a cellular protein termed E6-AP and together with E6-AP bind to the p53 tumor suppressor protein thereby degrading p53 through ubiquitin-mediated proteolysis. E6 from the non-cancer-associated HPV types do not bind E6-AP or degrade p53. Bovine papilloma virus E6 (BE6) binds E6-AP but fails either to complex with p53 or to degrade associated proteins, implying that BE6 might transform cells through a mechanism different from that of the HPVs. In addition to targeting p53, E6 of both cancer-associated HPVs and BPV-1 have been shown to associate with a cellular-calcium-binding protein localized to the endoplasmic reticulum [, ].; GO: 0003677 DNA binding, 0042025 host cell nucleus; PDB: 2LJY_B 2LJX_A 2LJZ_A 2FK4_A 3PY7_A.
Probab=72.91 E-value=1.9 Score=28.19 Aligned_cols=14 Identities=36% Similarity=0.790 Sum_probs=9.1
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
|+|||..|+|+++.
T Consensus 70 i~iRC~~C~k~L~~ 83 (110)
T PF00518_consen 70 IIIRCYYCLKPLTP 83 (110)
T ss_dssp SEEEETTT--B--H
T ss_pred EEEEhHHcCCcCCH
Confidence 68999999999976
No 14
>smart00400 ZnF_CHCC zinc finger.
Probab=72.44 E-value=5 Score=22.67 Aligned_cols=30 Identities=30% Similarity=0.512 Sum_probs=19.6
Q ss_pred cccCCCccccchHHHHHHHHHccCChhhHHHhc
Q 035172 6 RCFTCGKVIGNKWDTYLDLLQADYPEGDALDAL 38 (71)
Q Consensus 6 RCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~L 38 (71)
.||.||+ =|+. -.|...+ .|.+-.+|++.|
T Consensus 25 ~Cf~cg~-gGd~-i~fv~~~-~~~sf~eA~~~L 54 (55)
T smart00400 25 HCFGCGA-GGNV-ISFLMKY-DKLSFVEAVKKL 54 (55)
T ss_pred EEeCCCC-CCCH-HHHHHHH-HCcCHHHHHHHh
Confidence 6999985 3333 4444445 467888888765
No 15
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=72.32 E-value=1.5 Score=25.82 Aligned_cols=14 Identities=50% Similarity=1.412 Sum_probs=10.8
Q ss_pred ccccCCCccccchHH
Q 035172 5 VRCFTCGKVIGNKWD 19 (71)
Q Consensus 5 vRCfTCGkvi~~~~e 19 (71)
|+||.||..|. .|+
T Consensus 37 v~C~~C~~~l~-~w~ 50 (70)
T PF00653_consen 37 VRCFYCGLELD-NWE 50 (70)
T ss_dssp EEETTTTEEEE-S-S
T ss_pred EEEeccCCEEe-CCC
Confidence 78999999995 353
No 16
>PRK01343 zinc-binding protein; Provisional
Probab=70.61 E-value=1.2 Score=26.87 Aligned_cols=13 Identities=31% Similarity=0.557 Sum_probs=10.7
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
.++|.+|||+..+
T Consensus 9 ~~~CP~C~k~~~~ 21 (57)
T PRK01343 9 TRPCPECGKPSTR 21 (57)
T ss_pred CCcCCCCCCcCcC
Confidence 5679999999754
No 17
>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=69.08 E-value=2.2 Score=23.26 Aligned_cols=13 Identities=38% Similarity=0.899 Sum_probs=6.7
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
|+||..|+..|..
T Consensus 2 p~rC~~C~aylNp 14 (40)
T PF04810_consen 2 PVRCRRCRAYLNP 14 (40)
T ss_dssp S-B-TTT--BS-T
T ss_pred ccccCCCCCEECC
Confidence 8999999988743
No 18
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=68.48 E-value=2.3 Score=21.27 Aligned_cols=14 Identities=29% Similarity=0.610 Sum_probs=11.0
Q ss_pred cccccCCCccccch
Q 035172 4 PVRCFTCGKVIGNK 17 (71)
Q Consensus 4 PvRCfTCGkvi~~~ 17 (71)
++.|..||+.+...
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 2 EMFCPNCGAEIDPD 15 (26)
T ss_pred cCCCcccCCcCCcc
Confidence 57899999987653
No 19
>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=68.44 E-value=3.5 Score=23.35 Aligned_cols=18 Identities=22% Similarity=0.658 Sum_probs=10.5
Q ss_pred cccCCCccccchHHHHHHHH
Q 035172 6 RCFTCGKVIGNKWDTYLDLL 25 (71)
Q Consensus 6 RCfTCGkvi~~~~e~y~~~v 25 (71)
+|+-||++++. +...+++
T Consensus 22 ~CPlC~r~l~~--e~~~~li 39 (54)
T PF04423_consen 22 CCPLCGRPLDE--EHRQELI 39 (54)
T ss_dssp E-TTT--EE-H--HHHHHHH
T ss_pred cCCCCCCCCCH--HHHHHHH
Confidence 79999999988 5555555
No 20
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=65.64 E-value=1.6 Score=25.42 Aligned_cols=16 Identities=44% Similarity=1.263 Sum_probs=12.6
Q ss_pred cccccCCCccccchHHH
Q 035172 4 PVRCFTCGKVIGNKWDT 20 (71)
Q Consensus 4 PvRCfTCGkvi~~~~e~ 20 (71)
.|+||-||..+.+ |++
T Consensus 36 ~v~C~~C~~~l~~-w~~ 51 (71)
T smart00238 36 EVKCFFCGGELDN-WEP 51 (71)
T ss_pred EEEeCCCCCCcCC-CCC
Confidence 3899999999876 543
No 21
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=64.42 E-value=8.9 Score=20.86 Aligned_cols=27 Identities=11% Similarity=0.250 Sum_probs=21.2
Q ss_pred chHHHHHHHHHccCChhhHHHhcCCcc
Q 035172 16 NKWDTYLDLLQADYPEGDALDALGLVR 42 (71)
Q Consensus 16 ~~~e~y~~~v~~~~~~~~vLd~Lg~~r 42 (71)
+.+++-.++.++|.+..++-..+|+.|
T Consensus 9 ~~~~~i~~l~~~G~si~~IA~~~gvsr 35 (45)
T PF02796_consen 9 EQIEEIKELYAEGMSIAEIAKQFGVSR 35 (45)
T ss_dssp CCHHHHHHHHHTT--HHHHHHHTTS-H
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCcCH
Confidence 367888999999999999999999975
No 22
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=64.09 E-value=3.5 Score=22.06 Aligned_cols=11 Identities=55% Similarity=1.322 Sum_probs=8.6
Q ss_pred cccccCCCccc
Q 035172 4 PVRCFTCGKVI 14 (71)
Q Consensus 4 PvRCfTCGkvi 14 (71)
||||.-||--|
T Consensus 17 ~irC~~CG~RI 27 (32)
T PF03604_consen 17 PIRCPECGHRI 27 (32)
T ss_dssp TSSBSSSS-SE
T ss_pred cEECCcCCCeE
Confidence 78999999765
No 23
>KOG1101 consensus Apoptosis inhibitor IAP1 and related BIR domain proteins [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=62.63 E-value=4.1 Score=28.20 Aligned_cols=19 Identities=26% Similarity=0.847 Sum_probs=13.7
Q ss_pred ccccCCCcccc------chHHHHHH
Q 035172 5 VRCFTCGKVIG------NKWDTYLD 23 (71)
Q Consensus 5 vRCfTCGkvi~------~~~e~y~~ 23 (71)
++||+||.-|. +.|++=.+
T Consensus 52 ~~Cf~C~~~L~~We~~DDPW~EH~k 76 (147)
T KOG1101|consen 52 VKCFFCSGGLDDWEPGDDPWEEHAK 76 (147)
T ss_pred eECcccCcccccCCCCCCcHHHHHh
Confidence 68999998775 56665443
No 24
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=60.77 E-value=3.6 Score=28.03 Aligned_cols=12 Identities=42% Similarity=0.947 Sum_probs=10.2
Q ss_pred ccccccCCCccc
Q 035172 3 IPVRCFTCGKVI 14 (71)
Q Consensus 3 iPvRCfTCGkvi 14 (71)
.+|+|++|||+.
T Consensus 68 v~V~CP~C~K~T 79 (114)
T PF11023_consen 68 VQVECPNCGKQT 79 (114)
T ss_pred eeeECCCCCChH
Confidence 478999999875
No 25
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=60.61 E-value=3.4 Score=24.83 Aligned_cols=13 Identities=38% Similarity=0.808 Sum_probs=7.2
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
-|+|++|||.+.-
T Consensus 2 ~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 2 TVKCPICGKPVEW 14 (57)
T ss_dssp EEE-TTT--EEE-
T ss_pred cccCCCCCCeecc
Confidence 3789999999844
No 26
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=60.20 E-value=9.5 Score=26.25 Aligned_cols=34 Identities=18% Similarity=0.445 Sum_probs=19.8
Q ss_pred ccccCC-CccccchH--------HHHHHHHHccCChhhHHHhc
Q 035172 5 VRCFTC-GKVIGNKW--------DTYLDLLQADYPEGDALDAL 38 (71)
Q Consensus 5 vRCfTC-Gkvi~~~~--------e~y~~~v~~~~~~~~vLd~L 38 (71)
+||..| |..|++-- ++=.+++++|++.+++++.+
T Consensus 41 LrCp~Cq~qsi~~s~a~~A~dmR~~I~~~l~~G~s~~eI~~~~ 83 (148)
T PF03918_consen 41 LRCPVCQNQSIADSNAPIARDMRREIREMLAEGKSDEEIIDYF 83 (148)
T ss_dssp CE-TTTTS-CTTT--SHHHHHHHHHHHHHHHHT--HHHHHHHH
T ss_pred ccCCCCCCCchhhcCcHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 688888 45555432 34456778999999998854
No 27
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=58.83 E-value=4.5 Score=21.13 Aligned_cols=10 Identities=60% Similarity=1.159 Sum_probs=8.0
Q ss_pred ccccCCCccc
Q 035172 5 VRCFTCGKVI 14 (71)
Q Consensus 5 vRCfTCGkvi 14 (71)
++|..||.++
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 6888888775
No 28
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=56.86 E-value=5.1 Score=22.58 Aligned_cols=12 Identities=50% Similarity=0.797 Sum_probs=9.8
Q ss_pred ccccccCCCccc
Q 035172 3 IPVRCFTCGKVI 14 (71)
Q Consensus 3 iPvRCfTCGkvi 14 (71)
-||||.-||.-|
T Consensus 18 ~~irC~~CG~rI 29 (44)
T smart00659 18 DVVRCRECGYRI 29 (44)
T ss_pred CceECCCCCceE
Confidence 378999999766
No 29
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=56.44 E-value=4.7 Score=22.61 Aligned_cols=11 Identities=45% Similarity=1.431 Sum_probs=8.9
Q ss_pred ccccccCCCcc
Q 035172 3 IPVRCFTCGKV 13 (71)
Q Consensus 3 iPvRCfTCGkv 13 (71)
+|..||.||.+
T Consensus 30 lp~~C~~C~~~ 40 (49)
T PF14392_consen 30 LPRFCFHCGRI 40 (49)
T ss_pred cChhhcCCCCc
Confidence 57889999964
No 30
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=56.33 E-value=4.5 Score=25.34 Aligned_cols=14 Identities=29% Similarity=0.859 Sum_probs=11.3
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
..|+|-+||++|..
T Consensus 37 t~V~C~~CG~~l~~ 50 (67)
T COG2051 37 TVVTCLICGTTLAE 50 (67)
T ss_pred eEEEecccccEEEe
Confidence 36889999998865
No 31
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=53.84 E-value=10 Score=26.57 Aligned_cols=38 Identities=18% Similarity=0.246 Sum_probs=25.8
Q ss_pred cchHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhH
Q 035172 15 GNKWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHV 53 (71)
Q Consensus 15 ~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthv 53 (71)
-+..++=.++-++|.+.++..|+|++.+.| -.-|+++-
T Consensus 5 ~~l~~~a~~l~~~~~~~~~ia~el~vs~~t-~~~l~~~~ 42 (200)
T PRK02277 5 EELIEKAAELKNKGLSTGEIADELNVSRET-ATWLLTRA 42 (200)
T ss_pred HHHHHHHHHHHHcCCChhhhhhhhcchHHH-HHHHHhcc
Confidence 344566667777888888888888887775 34455543
No 32
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=53.40 E-value=5.6 Score=26.87 Aligned_cols=13 Identities=46% Similarity=1.229 Sum_probs=11.2
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
||+|..||+.+-.
T Consensus 20 ~V~C~nCgr~vPK 32 (108)
T PTZ00172 20 PVRCSNCGRCVPK 32 (108)
T ss_pred cEEeCCccccccc
Confidence 7999999998764
No 33
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=52.24 E-value=3.7 Score=23.63 Aligned_cols=15 Identities=47% Similarity=1.309 Sum_probs=12.1
Q ss_pred ccccCCCccccchHHH
Q 035172 5 VRCFTCGKVIGNKWDT 20 (71)
Q Consensus 5 vRCfTCGkvi~~~~e~ 20 (71)
|+|+-||..+.+ |++
T Consensus 35 v~C~~C~~~~~~-w~~ 49 (69)
T cd00022 35 VKCFFCGLELKN-WEP 49 (69)
T ss_pred EEeCCCCCCccC-CCC
Confidence 899999999865 543
No 34
>PHA02779 E6 protein; Provisional
Probab=52.11 E-value=9.9 Score=26.30 Aligned_cols=24 Identities=17% Similarity=0.487 Sum_probs=16.8
Q ss_pred ccccccCCCccccchHHHHHHHHHcc
Q 035172 3 IPVRCFTCGKVIGNKWDTYLDLLQAD 28 (71)
Q Consensus 3 iPvRCfTCGkvi~~~~e~y~~~v~~~ 28 (71)
|+|||..|+|+++. .|=...+..+
T Consensus 100 i~IRC~~C~k~L~~--~EK~~~~~~~ 123 (150)
T PHA02779 100 VRIRCYLCHKPLCP--VEKVNHILKK 123 (150)
T ss_pred EEEEHhHcCCcCCH--HHHHHHHHcC
Confidence 68999999999976 4433344344
No 35
>PHA02775 E6; Provisional
Probab=52.01 E-value=10 Score=26.72 Aligned_cols=24 Identities=21% Similarity=0.325 Sum_probs=16.9
Q ss_pred ccccccCCCccccchHHHHHHHHHcc
Q 035172 3 IPVRCFTCGKVIGNKWDTYLDLLQAD 28 (71)
Q Consensus 3 iPvRCfTCGkvi~~~~e~y~~~v~~~ 28 (71)
|.|||..|+|+++. .|=...+..+
T Consensus 115 i~IRC~~C~k~L~~--~EK~~~~~~~ 138 (160)
T PHA02775 115 CEVRCVRCLALLQS--VEKDFIARED 138 (160)
T ss_pred EEEEHhHcCCcCCH--HHHHHHHHcC
Confidence 68999999999976 4444444344
No 36
>PRK02935 hypothetical protein; Provisional
Probab=51.64 E-value=6.5 Score=26.72 Aligned_cols=13 Identities=31% Similarity=0.603 Sum_probs=10.8
Q ss_pred ccccccCCCcccc
Q 035172 3 IPVRCFTCGKVIG 15 (71)
Q Consensus 3 iPvRCfTCGkvi~ 15 (71)
++|.|++|+|+..
T Consensus 69 vqV~CP~C~K~TK 81 (110)
T PRK02935 69 VQVICPSCEKPTK 81 (110)
T ss_pred eeeECCCCCchhh
Confidence 5789999999863
No 37
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=51.11 E-value=6.7 Score=21.17 Aligned_cols=13 Identities=31% Similarity=0.800 Sum_probs=9.9
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
.+.|..||+.|+.
T Consensus 4 ~~~C~nC~R~v~a 16 (33)
T PF08209_consen 4 YVECPNCGRPVAA 16 (33)
T ss_dssp EEE-TTTSSEEEG
T ss_pred eEECCCCcCCcch
Confidence 4679999999875
No 38
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=50.81 E-value=6.7 Score=25.96 Aligned_cols=13 Identities=31% Similarity=0.766 Sum_probs=11.2
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
||+|..||+.+--
T Consensus 20 ~V~C~nCgr~vPK 32 (95)
T PRK09335 20 YVQCDNCGRRVPR 32 (95)
T ss_pred cEEeCCCCCcCcC
Confidence 7999999998753
No 39
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=50.20 E-value=13 Score=25.24 Aligned_cols=31 Identities=19% Similarity=0.346 Sum_probs=22.1
Q ss_pred hHHHHHH-HHHccCChhhHHHhcCCcchhhhh
Q 035172 17 KWDTYLD-LLQADYPEGDALDALGLVRYCCRR 47 (71)
Q Consensus 17 ~~e~y~~-~v~~~~~~~~vLd~Lg~~ryCCRr 47 (71)
.|++|-+ ..++|++++++..+||=.+---|.
T Consensus 28 ~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~ 59 (181)
T PF08006_consen 28 YYEEYFDDAGEEGKSEEEIIAELGSPKEIARE 59 (181)
T ss_pred HHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHH
Confidence 4555544 456889999999999977655444
No 40
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=49.98 E-value=7.8 Score=29.36 Aligned_cols=13 Identities=38% Similarity=0.787 Sum_probs=9.1
Q ss_pred ccccccCCCcccc
Q 035172 3 IPVRCFTCGKVIG 15 (71)
Q Consensus 3 iPvRCfTCGkvi~ 15 (71)
|.|+|-|||..|+
T Consensus 39 f~i~C~~C~~~I~ 51 (324)
T PF04502_consen 39 FNIWCNTCGEYIY 51 (324)
T ss_pred ccCcCCCCccccc
Confidence 5677777777764
No 41
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=49.83 E-value=7.3 Score=23.71 Aligned_cols=14 Identities=43% Similarity=1.063 Sum_probs=11.3
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
.+|+|-.||+.|+.
T Consensus 29 t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 29 TVVRCLVCGKTLAE 42 (59)
T ss_pred cEEECcccCCCccc
Confidence 47889999998865
No 42
>PLN00186 ribosomal protein S26; Provisional
Probab=49.80 E-value=7 Score=26.46 Aligned_cols=13 Identities=38% Similarity=1.017 Sum_probs=11.3
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
||+|..||+.+-.
T Consensus 20 ~V~C~nCgr~vPK 32 (109)
T PLN00186 20 RIRCSNCGKCVPK 32 (109)
T ss_pred ceeeCCCcccccc
Confidence 7999999998863
No 43
>COG4175 ProV ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]
Probab=49.51 E-value=20 Score=28.88 Aligned_cols=41 Identities=24% Similarity=0.371 Sum_probs=36.2
Q ss_pred CcccccccCCCccccchHHHHHHHHHccCChhhHHHhcCCc
Q 035172 1 MIIPVRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLV 41 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ 41 (71)
|..-+.|-.+-|+.|..+++....+++|.+..+++.+-|..
T Consensus 1 ~~~~i~i~nv~kiFG~~~~~a~~~~~~G~~k~ei~~~tg~v 41 (386)
T COG4175 1 MMVKIEIKNVYKIFGKNPKRALKLLDQGKSKAEILKKTGLV 41 (386)
T ss_pred CCceEEeecceeecccCHHHHHHHHHcCCcHHHHHHhhCcE
Confidence 45667788899999999999999999999999999987764
No 44
>KOG4384 consensus Uncharacterized SAM domain protein [General function prediction only]
Probab=48.52 E-value=28 Score=27.81 Aligned_cols=42 Identities=26% Similarity=0.568 Sum_probs=32.4
Q ss_pred HHHHH-HHHccCC--------hhhHHHhcCCcchhhhhHHHHhHHHHHHHh
Q 035172 19 DTYLD-LLQADYP--------EGDALDALGLVRYCCRRMLMTHVDLIEKLL 60 (71)
Q Consensus 19 e~y~~-~v~~~~~--------~~~vLd~Lg~~ryCCRrmllthvdlid~ll 60 (71)
|+|.+ +|++|++ ..+=|++||+..-=-|+.||+.|++..+.-
T Consensus 228 e~y~~~~L~nGYd~le~~k~i~e~dL~~lgI~nP~Hr~kLL~av~~~~e~d 278 (361)
T KOG4384|consen 228 EEYIETLLENGYDTLEDLKDITEEDLEELGIDNPDHRKKLLSAVELLKEID 278 (361)
T ss_pred HHHHHHHHHcchHHHHHHHhccHHHHHHhCCCCHHHHHHHHHHHHHHHhcc
Confidence 56654 3467775 245589999999999999999999876654
No 45
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=47.58 E-value=9.2 Score=20.96 Aligned_cols=11 Identities=27% Similarity=0.972 Sum_probs=5.9
Q ss_pred cccccCCCccc
Q 035172 4 PVRCFTCGKVI 14 (71)
Q Consensus 4 PvRCfTCGkvi 14 (71)
..+|..||..+
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 44555555554
No 46
>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=47.12 E-value=9 Score=19.49 Aligned_cols=10 Identities=40% Similarity=1.112 Sum_probs=8.0
Q ss_pred ccCCCccccc
Q 035172 7 CFTCGKVIGN 16 (71)
Q Consensus 7 CfTCGkvi~~ 16 (71)
|.|||..|+.
T Consensus 1 C~sC~~~i~~ 10 (24)
T PF07754_consen 1 CTSCGRPIAP 10 (24)
T ss_pred CccCCCcccC
Confidence 7889888875
No 47
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=47.08 E-value=20 Score=24.57 Aligned_cols=35 Identities=20% Similarity=0.329 Sum_probs=22.3
Q ss_pred ccccCCCccccchHHHHHHHHHccCChhhHHHhcCCc
Q 035172 5 VRCFTCGKVIGNKWDTYLDLLQADYPEGDALDALGLV 41 (71)
Q Consensus 5 vRCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~~ 41 (71)
|.|+-|||..... .+.+..- -|.+|++--...|+.
T Consensus 73 i~clecGk~~k~L-krHL~~~-~gltp~eYR~kwGlp 107 (132)
T PF05443_consen 73 IICLECGKKFKTL-KRHLRTH-HGLTPEEYRAKWGLP 107 (132)
T ss_dssp EE-TBT--EESBH-HHHHHHT-T-S-HHHHHHHTT-G
T ss_pred eEEccCCcccchH-HHHHHHc-cCCCHHHHHHHhCcC
Confidence 6799999999887 6665532 389999999888885
No 48
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=46.78 E-value=25 Score=21.38 Aligned_cols=35 Identities=29% Similarity=0.264 Sum_probs=23.8
Q ss_pred ccccCCCccc------cchH-HHHHHHHH----ccCChhhHHHhcC
Q 035172 5 VRCFTCGKVI------GNKW-DTYLDLLQ----ADYPEGDALDALG 39 (71)
Q Consensus 5 vRCfTCGkvi------~~~~-e~y~~~v~----~~~~~~~vLd~Lg 39 (71)
++|..||++| ||+. .+|..++. -|.+.++++|...
T Consensus 6 ~~~~~~~~~i~~~~dmgH~~~~e~~~~~~~~~~~~~t~ke~~d~~n 51 (70)
T PF14410_consen 6 VRDPNTGYPIEGPWDMGHKPGVEYWRLVGRAEEGGITRKEFLDWYN 51 (70)
T ss_pred EecCCCCCCCCCCCCccCchHHHHHHHHHHHHhcCCCHHHHHHHHh
Confidence 5788999999 3432 35555554 4578889988654
No 49
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=45.47 E-value=9.9 Score=23.45 Aligned_cols=13 Identities=38% Similarity=0.876 Sum_probs=10.3
Q ss_pred ccccccCCCcccc
Q 035172 3 IPVRCFTCGKVIG 15 (71)
Q Consensus 3 iPvRCfTCGkvi~ 15 (71)
.|-+|-|||.+|+
T Consensus 8 ~~~~CtSCg~~i~ 20 (61)
T COG2888 8 DPPVCTSCGREIA 20 (61)
T ss_pred CCceeccCCCEec
Confidence 4678999999983
No 50
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=45.10 E-value=9.8 Score=18.68 Aligned_cols=10 Identities=50% Similarity=1.345 Sum_probs=5.6
Q ss_pred cccCCCcccc
Q 035172 6 RCFTCGKVIG 15 (71)
Q Consensus 6 RCfTCGkvi~ 15 (71)
+|.+||++++
T Consensus 29 ~C~~C~~~L~ 38 (39)
T smart00132 29 KCSKCGKPLG 38 (39)
T ss_pred CCcccCCcCc
Confidence 4556666554
No 51
>PRK11595 DNA utilization protein GntX; Provisional
Probab=45.10 E-value=10 Score=26.83 Aligned_cols=13 Identities=23% Similarity=0.731 Sum_probs=8.9
Q ss_pred cccccccCCCccc
Q 035172 2 IIPVRCFTCGKVI 14 (71)
Q Consensus 2 iiPvRCfTCGkvi 14 (71)
++|.||.-||+++
T Consensus 3 ~~P~~C~~C~~~~ 15 (227)
T PRK11595 3 TVPGLCWLCRMPL 15 (227)
T ss_pred CCCCcCccCCCcc
Confidence 5677777777665
No 52
>PF14149 YhfH: YhfH-like protein
Probab=45.07 E-value=6 Score=22.13 Aligned_cols=21 Identities=33% Similarity=0.702 Sum_probs=16.9
Q ss_pred cccccCCCccccchHHHHHHH
Q 035172 4 PVRCFTCGKVIGNKWDTYLDL 24 (71)
Q Consensus 4 PvRCfTCGkvi~~~~e~y~~~ 24 (71)
+-.|..||+.|.+.-|-|...
T Consensus 13 ~K~C~~CG~~i~EQ~E~Y~n~ 33 (37)
T PF14149_consen 13 PKKCTECGKEIEEQAECYGNE 33 (37)
T ss_pred CcccHHHHHHHHHHHHHHhCc
Confidence 345999999999988888653
No 53
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=44.55 E-value=25 Score=24.09 Aligned_cols=34 Identities=12% Similarity=0.286 Sum_probs=23.9
Q ss_pred ccccCCCcc-c-------cc-hHHHHHHHHHccCChhhHHHhc
Q 035172 5 VRCFTCGKV-I-------GN-KWDTYLDLLQADYPEGDALDAL 38 (71)
Q Consensus 5 vRCfTCGkv-i-------~~-~~e~y~~~v~~~~~~~~vLd~L 38 (71)
+||..|.+- | +. .=.+=.+++++|++.++++|-+
T Consensus 41 LRC~vCqnqsiadSna~iA~dmR~~Vr~~i~~G~sd~eI~~~~ 83 (126)
T PRK10144 41 LRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGKSEVEIIGWM 83 (126)
T ss_pred CCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 689999653 2 22 2245567788999999999854
No 54
>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=43.89 E-value=11 Score=22.70 Aligned_cols=11 Identities=55% Similarity=1.334 Sum_probs=10.1
Q ss_pred cccCCCccccc
Q 035172 6 RCFTCGKVIGN 16 (71)
Q Consensus 6 RCfTCGkvi~~ 16 (71)
.|..|||.|++
T Consensus 80 ~C~vC~k~l~~ 90 (109)
T PF10367_consen 80 KCSVCGKPLGN 90 (109)
T ss_pred CccCcCCcCCC
Confidence 59999999988
No 55
>PF08097 Toxin_26: Conotoxin T-superfamily; InterPro: IPR012631 This family consists of the T-superfamily of conotoxins. Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding types of Conus, suggesting that the T-superfamily is a large and diverse group of peptides, widely distributed in the 500 different Conus species [].; GO: 0005576 extracellular region
Probab=43.78 E-value=6.9 Score=16.78 Aligned_cols=6 Identities=67% Similarity=2.239 Sum_probs=4.4
Q ss_pred Ccchhh
Q 035172 40 LVRYCC 45 (71)
Q Consensus 40 ~~ryCC 45 (71)
+-||||
T Consensus 5 virycc 10 (11)
T PF08097_consen 5 VIRYCC 10 (11)
T ss_pred hhheec
Confidence 458888
No 56
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=43.50 E-value=12 Score=19.35 Aligned_cols=11 Identities=27% Similarity=0.679 Sum_probs=7.5
Q ss_pred cccccCCCccc
Q 035172 4 PVRCFTCGKVI 14 (71)
Q Consensus 4 PvRCfTCGkvi 14 (71)
+++|+.||..+
T Consensus 26 ~~~CP~Cg~~~ 36 (41)
T smart00834 26 LATCPECGGDV 36 (41)
T ss_pred CCCCCCCCCcc
Confidence 46788888743
No 57
>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=43.05 E-value=10 Score=26.12 Aligned_cols=14 Identities=29% Similarity=0.752 Sum_probs=12.1
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
=||.|..|+..||=
T Consensus 108 hPV~Cs~C~TeVaV 121 (136)
T PF10238_consen 108 HPVKCSECSTEVAV 121 (136)
T ss_pred eceecccCCCEEEE
Confidence 49999999999873
No 58
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=42.33 E-value=23 Score=21.39 Aligned_cols=24 Identities=25% Similarity=0.596 Sum_probs=18.5
Q ss_pred ccccccCCCccccchHHHHHHHHH
Q 035172 3 IPVRCFTCGKVIGNKWDTYLDLLQ 26 (71)
Q Consensus 3 iPvRCfTCGkvi~~~~e~y~~~v~ 26 (71)
|-++|-+||..|-=.=.+|...++
T Consensus 30 ikikC~gCg~~imlpR~~feK~~K 53 (57)
T PF06107_consen 30 IKIKCLGCGRQIMLPRSKFEKRLK 53 (57)
T ss_pred EEEEECCCCCEEEEeHHHHHHHHH
Confidence 668999999998766667766663
No 59
>cd08576 GDPD_like_SMaseD_PLD Glycerophosphodiester phosphodiesterase-like domain of spider venom sphingomyelinases D, bacterial phospholipase D, and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase-like domain (GDPD-like) present in sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.4) from spider venom, the Corynebacterium pseudotuberculosis Phospholipase D (PLD)-like protein from pathogenic bacteria, and the Ajellomyces capsulatus H143 PLD-like protein from ascomycetes. Spider SMases D and bacterial PLD proteins catalyze the Mg2+-dependent hydrolysis of sphingomyelin producing choline and ceramide 1-phosphate (C1P), which possess a number of biological functions, such as regulating cell proliferation and apoptosis, participating in inflammatory responses, and playing a key role in phagocytosis. In the presence of Mg2+, SMases D can function as lysophospholipase D and hydrolyze lysophosphatidylcholine (LPC) to choline
Probab=42.13 E-value=23 Score=26.78 Aligned_cols=59 Identities=25% Similarity=0.349 Sum_probs=44.5
Q ss_pred cccccc-CCCccccchHHHHHHHHHccCChhh----HH--HhcCCcchhhhhHHHHhHHHHHHHhccC
Q 035172 3 IPVRCF-TCGKVIGNKWDTYLDLLQADYPEGD----AL--DALGLVRYCCRRMLMTHVDLIEKLLNYN 63 (71)
Q Consensus 3 iPvRCf-TCGkvi~~~~e~y~~~v~~~~~~~~----vL--d~Lg~~ryCCRrmllthvdlid~ll~y~ 63 (71)
+|--|| .|.+-- ..++|++.++++.+|+= +| =+|-...+|=....=+..|+.++||++.
T Consensus 43 ~pcdc~r~c~~~~--~f~~~l~~~r~~ttpg~~~~l~lv~lDlK~~~~~~~~~~~ag~~la~~ll~~~ 108 (265)
T cd08576 43 VPCDCFRGCTARE--MFDEILDYRRNGTTPGFRENLIFVWLDLKNPDLCGECSINAGRDLARKLLEPY 108 (265)
T ss_pred CccccccCCcHHH--HHHHHHHHHHhcCCCCccceeEEEEEEcCCCCcCHHHHHHHHHHHHHHHHHHh
Confidence 467788 888755 67899999988887761 11 1345568888888888999999999874
No 60
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=41.39 E-value=13 Score=18.23 Aligned_cols=11 Identities=36% Similarity=0.836 Sum_probs=8.5
Q ss_pred cccCCCccccc
Q 035172 6 RCFTCGKVIGN 16 (71)
Q Consensus 6 RCfTCGkvi~~ 16 (71)
+|..||+.|.+
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 48888888865
No 61
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=40.72 E-value=11 Score=22.67 Aligned_cols=11 Identities=45% Similarity=1.259 Sum_probs=9.1
Q ss_pred cccCCCccccc
Q 035172 6 RCFTCGKVIGN 16 (71)
Q Consensus 6 RCfTCGkvi~~ 16 (71)
-|.+|||+|-.
T Consensus 20 NCl~CGkIiC~ 30 (57)
T PF06221_consen 20 NCLNCGKIICE 30 (57)
T ss_pred cccccChhhcc
Confidence 48999999866
No 62
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=40.68 E-value=9.3 Score=29.24 Aligned_cols=23 Identities=26% Similarity=0.771 Sum_probs=14.4
Q ss_pred ccccccCCCcccc--chHHHHHHHH
Q 035172 3 IPVRCFTCGKVIG--NKWDTYLDLL 25 (71)
Q Consensus 3 iPvRCfTCGkvi~--~~~e~y~~~v 25 (71)
|||||-+||.-|- ..+..-.+.+
T Consensus 41 F~~RCL~C~~YI~K~~rfNavkE~~ 65 (272)
T COG5134 41 FPVRCLNCENYIQKGTRFNAVKEEI 65 (272)
T ss_pred cceeecchhhhhhcccchhHHHHHh
Confidence 6889999987662 3334444444
No 63
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=40.59 E-value=31 Score=23.58 Aligned_cols=34 Identities=12% Similarity=0.316 Sum_probs=23.6
Q ss_pred ccccCCCcc-ccc--------hHHHHHHHHHccCChhhHHHhc
Q 035172 5 VRCFTCGKV-IGN--------KWDTYLDLLQADYPEGDALDAL 38 (71)
Q Consensus 5 vRCfTCGkv-i~~--------~~e~y~~~v~~~~~~~~vLd~L 38 (71)
+||..|.+- |++ .=.+=.+++++|++.++++|-+
T Consensus 41 LRC~vCqnqsiadS~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~ 83 (126)
T TIGR03147 41 LRCPQCQNQNLVESNSPIAYDLRHEVYSMVNEGKSNQQIIDFM 83 (126)
T ss_pred CCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 689998653 222 2245567788999999998843
No 64
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=40.50 E-value=26 Score=21.95 Aligned_cols=22 Identities=23% Similarity=0.259 Sum_probs=18.1
Q ss_pred HHHHHHHccCChhhHHHhcC-Cc
Q 035172 20 TYLDLLQADYPEGDALDALG-LV 41 (71)
Q Consensus 20 ~y~~~v~~~~~~~~vLd~Lg-~~ 41 (71)
.=++.+++|.+++++|++++ ++
T Consensus 35 ~Il~~l~~G~s~eeil~dyp~Lt 57 (79)
T COG2442 35 DILEMLAAGESIEEILADYPDLT 57 (79)
T ss_pred HHHHHHHCCCCHHHHHHhCCCCC
Confidence 34667889999999999988 65
No 65
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=39.14 E-value=16 Score=22.33 Aligned_cols=15 Identities=33% Similarity=0.817 Sum_probs=10.7
Q ss_pred cccccccCCCccccc
Q 035172 2 IIPVRCFTCGKVIGN 16 (71)
Q Consensus 2 iiPvRCfTCGkvi~~ 16 (71)
+-|..|-|||..|+.
T Consensus 5 ~~~~~CtSCg~~i~~ 19 (59)
T PRK14890 5 MEPPKCTSCGIEIAP 19 (59)
T ss_pred ccCccccCCCCcccC
Confidence 345578888888863
No 66
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=38.91 E-value=6.1 Score=24.40 Aligned_cols=19 Identities=21% Similarity=0.677 Sum_probs=15.9
Q ss_pred cccccccCCCccccchHHH
Q 035172 2 IIPVRCFTCGKVIGNKWDT 20 (71)
Q Consensus 2 iiPvRCfTCGkvi~~~~e~ 20 (71)
+-++.|-+||..||-+|+.
T Consensus 55 ~~~l~C~~C~~~lGwkY~~ 73 (96)
T PF03226_consen 55 VRDLFCSGCNTILGWKYES 73 (96)
T ss_pred EEEeEcccCChhHCcEEEE
Confidence 4578999999999998854
No 67
>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=38.86 E-value=19 Score=15.82 Aligned_cols=14 Identities=36% Similarity=0.771 Sum_probs=9.3
Q ss_pred cccCCCccccchHH
Q 035172 6 RCFTCGKVIGNKWD 19 (71)
Q Consensus 6 RCfTCGkvi~~~~e 19 (71)
.|.-||+...++++
T Consensus 2 ~C~~C~~~~~~~~~ 15 (24)
T PF13894_consen 2 QCPICGKSFRSKSE 15 (24)
T ss_dssp E-SSTS-EESSHHH
T ss_pred CCcCCCCcCCcHHH
Confidence 48889999888664
No 68
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=38.64 E-value=16 Score=22.74 Aligned_cols=18 Identities=39% Similarity=0.809 Sum_probs=13.4
Q ss_pred Cccccc-ccCCCccccchH
Q 035172 1 MIIPVR-CFTCGKVIGNKW 18 (71)
Q Consensus 1 MiiPvR-CfTCGkvi~~~~ 18 (71)
|+.|-| |.-||+.|-..-
T Consensus 4 ~v~PH~HC~VCg~aIp~de 22 (64)
T COG4068 4 GVVPHRHCVVCGKAIPPDE 22 (64)
T ss_pred CCCCCccccccCCcCCCcc
Confidence 355666 999999997644
No 69
>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=38.19 E-value=15 Score=20.78 Aligned_cols=16 Identities=38% Similarity=0.848 Sum_probs=12.2
Q ss_pred cccCCCccccchHHHHHH
Q 035172 6 RCFTCGKVIGNKWDTYLD 23 (71)
Q Consensus 6 RCfTCGkvi~~~~e~y~~ 23 (71)
.|++||..+.. -+|..
T Consensus 2 ~C~~Cg~D~t~--vryh~ 17 (45)
T cd02336 2 HCFTCGNDCTR--VRYHN 17 (45)
T ss_pred cccCCCCccCc--eEEEe
Confidence 59999999986 44543
No 70
>PRK12899 secA preprotein translocase subunit SecA; Reviewed
Probab=37.93 E-value=35 Score=30.39 Aligned_cols=36 Identities=28% Similarity=0.399 Sum_probs=31.6
Q ss_pred ccchHHHHHHHHHccCChhhHH-HhcCCcchhhhhHH
Q 035172 14 IGNKWDTYLDLLQADYPEGDAL-DALGLVRYCCRRML 49 (71)
Q Consensus 14 i~~~~e~y~~~v~~~~~~~~vL-d~Lg~~ryCCRrml 49 (71)
+.++..+|+.++++|++..+.| .++++.|--|+|-+
T Consensus 42 L~~kt~~~k~~l~~~~~ld~~l~eafal~re~~~r~l 78 (970)
T PRK12899 42 LRNKTAELKQRYQDGESLDKLLPEAYGVVKNVCRRLA 78 (970)
T ss_pred HHHHHHHHHHHHHcCCchHHHHHHHhCCCHHHHHHHh
Confidence 3456788999999999988887 88999999999999
No 71
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=37.69 E-value=13 Score=27.89 Aligned_cols=16 Identities=38% Similarity=0.794 Sum_probs=13.3
Q ss_pred cccccccCCCccccch
Q 035172 2 IIPVRCFTCGKVIGNK 17 (71)
Q Consensus 2 iiPvRCfTCGkvi~~~ 17 (71)
..++-|+|||..|..+
T Consensus 82 ~~~~~Cv~Cg~~i~~~ 97 (236)
T PF12269_consen 82 DLSIYCVTCGHEIPSK 97 (236)
T ss_pred ceeeeeeeCCCcCCHH
Confidence 3578899999999875
No 72
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=37.38 E-value=57 Score=17.48 Aligned_cols=28 Identities=14% Similarity=0.430 Sum_probs=22.6
Q ss_pred ChhhHHHhcCCcchhhhhHHHHhHHHHH
Q 035172 30 PEGDALDALGLVRYCCRRMLMTHVDLIE 57 (71)
Q Consensus 30 ~~~~vLd~Lg~~ryCCRrmllthvdlid 57 (71)
+..+.|.++|++...-|..++..++-+.
T Consensus 39 ~~~~~l~~lgi~~~~~r~~ll~~i~~l~ 66 (68)
T smart00454 39 TSEEDLKELGITKLGHRKKILKAIQKLK 66 (68)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHHHHH
Confidence 3367788999999999999998877543
No 73
>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=37.09 E-value=16 Score=19.80 Aligned_cols=12 Identities=33% Similarity=0.841 Sum_probs=8.0
Q ss_pred ccccCCCccccc
Q 035172 5 VRCFTCGKVIGN 16 (71)
Q Consensus 5 vRCfTCGkvi~~ 16 (71)
+.|..||.||.+
T Consensus 20 ~vC~~CG~Vl~e 31 (43)
T PF08271_consen 20 LVCPNCGLVLEE 31 (43)
T ss_dssp EEETTT-BBEE-
T ss_pred EECCCCCCEeec
Confidence 468899988875
No 74
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=37.04 E-value=16 Score=24.11 Aligned_cols=13 Identities=31% Similarity=0.802 Sum_probs=10.6
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
|+.|+.||...--
T Consensus 26 PivCP~CG~~~~~ 38 (108)
T PF09538_consen 26 PIVCPKCGTEFPP 38 (108)
T ss_pred CccCCCCCCccCc
Confidence 8889999987654
No 75
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=36.82 E-value=37 Score=26.42 Aligned_cols=30 Identities=27% Similarity=0.536 Sum_probs=17.7
Q ss_pred cccCCCccccchHHHHHHHHHccCChhhHHHhc
Q 035172 6 RCFTCGKVIGNKWDTYLDLLQADYPEGDALDAL 38 (71)
Q Consensus 6 RCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~L 38 (71)
.||+||. =|+. =.|...+ +|.+-.+|+..|
T Consensus 57 ~Cf~Cg~-~Gd~-i~fv~~~-~~~sf~eA~~~L 86 (415)
T TIGR01391 57 HCFGCGA-GGDA-IKFLMEI-EGISFVEAVEEL 86 (415)
T ss_pred EECCCCC-CCCH-HHHHHHH-hCCCHHHHHHHH
Confidence 6999997 2443 3444444 456666665544
No 76
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=36.61 E-value=16 Score=18.50 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=8.5
Q ss_pred cccCCCccccc
Q 035172 6 RCFTCGKVIGN 16 (71)
Q Consensus 6 RCfTCGkvi~~ 16 (71)
.|+.||+.|+.
T Consensus 2 ~CP~C~~~V~~ 12 (26)
T PF10571_consen 2 TCPECGAEVPE 12 (26)
T ss_pred cCCCCcCCchh
Confidence 58888888854
No 77
>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=36.12 E-value=21 Score=16.26 Aligned_cols=12 Identities=42% Similarity=0.988 Sum_probs=9.7
Q ss_pred cccCCCccccch
Q 035172 6 RCFTCGKVIGNK 17 (71)
Q Consensus 6 RCfTCGkvi~~~ 17 (71)
.|..||+.-+++
T Consensus 2 ~C~~C~~~f~~~ 13 (23)
T PF00096_consen 2 KCPICGKSFSSK 13 (23)
T ss_dssp EETTTTEEESSH
T ss_pred CCCCCCCccCCH
Confidence 588999988773
No 78
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 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 [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=36.11 E-value=13 Score=25.11 Aligned_cols=13 Identities=46% Similarity=1.117 Sum_probs=8.4
Q ss_pred ccccccCCCcccc
Q 035172 3 IPVRCFTCGKVIG 15 (71)
Q Consensus 3 iPvRCfTCGkvi~ 15 (71)
=||||..||+.+-
T Consensus 19 ~~V~C~nCgr~vP 31 (113)
T PF01283_consen 19 QPVRCDNCGRCVP 31 (113)
T ss_dssp -EEE-TTTB-EEE
T ss_pred cCEeeCcccccCc
Confidence 3899999998764
No 79
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=35.72 E-value=19 Score=19.52 Aligned_cols=12 Identities=33% Similarity=1.013 Sum_probs=9.0
Q ss_pred ccccCCCccccc
Q 035172 5 VRCFTCGKVIGN 16 (71)
Q Consensus 5 vRCfTCGkvi~~ 16 (71)
.+|..|++.|++
T Consensus 27 f~C~~C~~~l~~ 38 (58)
T PF00412_consen 27 FKCSKCGKPLND 38 (58)
T ss_dssp SBETTTTCBTTT
T ss_pred cccCCCCCccCC
Confidence 367788888876
No 80
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=35.48 E-value=17 Score=21.67 Aligned_cols=14 Identities=36% Similarity=0.973 Sum_probs=9.5
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
.+|+|-.||.+|+.
T Consensus 25 t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 25 TVVKCVVCGTVLAQ 38 (55)
T ss_dssp S-EE-SSSTSEEEE
T ss_pred eEEEcccCCCEecC
Confidence 46889999988864
No 81
>PRK07218 replication factor A; Provisional
Probab=34.45 E-value=17 Score=29.03 Aligned_cols=14 Identities=43% Similarity=0.918 Sum_probs=11.2
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
|--||+.|+|++.+
T Consensus 296 li~rCP~C~r~v~~ 309 (423)
T PRK07218 296 LIERCPECGRVIQK 309 (423)
T ss_pred ceecCcCccccccC
Confidence 34589999999965
No 82
>COG4709 Predicted membrane protein [Function unknown]
Probab=34.41 E-value=31 Score=25.43 Aligned_cols=23 Identities=17% Similarity=0.237 Sum_probs=17.8
Q ss_pred HHHHHHHHccCChhhHHHhcCCc
Q 035172 19 DTYLDLLQADYPEGDALDALGLV 41 (71)
Q Consensus 19 e~y~~~v~~~~~~~~vLd~Lg~~ 41 (71)
|-|.+-..+|.+++++.++||=.
T Consensus 31 ehF~~a~~~GksE~EI~~~LG~P 53 (195)
T COG4709 31 EHFREAQEAGKSEEEIAKDLGDP 53 (195)
T ss_pred HHHHhhhhcCCCHHHHHHHhCCH
Confidence 44555666899999999999953
No 83
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=33.90 E-value=21 Score=22.62 Aligned_cols=13 Identities=38% Similarity=0.904 Sum_probs=9.8
Q ss_pred cccCCCccccchH
Q 035172 6 RCFTCGKVIGNKW 18 (71)
Q Consensus 6 RCfTCGkvi~~~~ 18 (71)
||.+|++.|+-.|
T Consensus 60 rCr~C~~~I~~~y 72 (92)
T PF06750_consen 60 RCRYCGAPIPPRY 72 (92)
T ss_pred CCcccCCCCChHH
Confidence 7888888887644
No 84
>PF03489 SapB_2: Saposin-like type B, region 2; InterPro: IPR008138 Saposins are small lysosomal proteins that serve as activators of various lysosomal lipid-degrading enzymes []. They probably act by isolating the lipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammalian saposins are synthesized as a single precursor molecule (prosaposin) which contains four Saposin-B domains, yielding the active saposins after proteolytic cleavage, and two Saposin-A domains that are removed in the activation reaction. The Saposin-B domains also occur in other proteins, many of them active in the lysis of membranes [, ].; PDB: 3BQQ_A 2RB3_B 2R0R_A 3BQP_A 2R1Q_A 1NKL_A 1L9L_A 1QDM_C 3RFI_A 4DDJ_A ....
Probab=33.66 E-value=26 Score=17.80 Aligned_cols=31 Identities=16% Similarity=0.335 Sum_probs=21.8
Q ss_pred CCccccchHHHHHHHHHccCChhhHHHhcCC
Q 035172 10 CGKVIGNKWDTYLDLLQADYPEGDALDALGL 40 (71)
Q Consensus 10 CGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg~ 40 (71)
|-..+....+.-.+.+.++.+|.++=..+|+
T Consensus 4 C~~~V~~y~~~ii~~l~~~~~p~~iC~~i~~ 34 (35)
T PF03489_consen 4 CKNFVDQYGPQIIQLLEKQLDPQQICTKIGL 34 (35)
T ss_dssp HHHHHHHHHHHHHHHHHTTSTHHHHHHHTTS
T ss_pred HHHHHHHHHHHHHHHHHhcCChHHHHHHcCC
Confidence 4445555556677778888889888777764
No 85
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=33.63 E-value=16 Score=25.85 Aligned_cols=16 Identities=25% Similarity=0.818 Sum_probs=9.1
Q ss_pred cccCCCccccchHHHH
Q 035172 6 RCFTCGKVIGNKWDTY 21 (71)
Q Consensus 6 RCfTCGkvi~~~~e~y 21 (71)
||-.||.++.+.|.+|
T Consensus 2 iCIeCg~~v~~Ly~~Y 17 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQY 17 (208)
T ss_pred EeccCCCcchhhhhcc
Confidence 4555666655555555
No 86
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=33.49 E-value=20 Score=21.67 Aligned_cols=15 Identities=27% Similarity=0.570 Sum_probs=9.9
Q ss_pred cccCCCccccchHHH
Q 035172 6 RCFTCGKVIGNKWDT 20 (71)
Q Consensus 6 RCfTCGkvi~~~~e~ 20 (71)
.|++||+..+.+...
T Consensus 7 ~C~~Cg~r~~~~~k~ 21 (69)
T PF09706_consen 7 NCIFCGERPSKKKKG 21 (69)
T ss_pred cCcCCCCcccccccc
Confidence 699999655544333
No 87
>PRK00420 hypothetical protein; Validated
Probab=33.45 E-value=30 Score=23.17 Aligned_cols=13 Identities=38% Similarity=0.337 Sum_probs=9.2
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
.+.|+.||+++--
T Consensus 40 ~~~Cp~Cg~~~~v 52 (112)
T PRK00420 40 EVVCPVHGKVYIV 52 (112)
T ss_pred ceECCCCCCeeee
Confidence 3568888887653
No 88
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=33.42 E-value=14 Score=21.94 Aligned_cols=16 Identities=31% Similarity=0.818 Sum_probs=12.7
Q ss_pred CcccccccCCCccccc
Q 035172 1 MIIPVRCFTCGKVIGN 16 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~ 16 (71)
|+=-+||..|||.++.
T Consensus 1 m~~eiRC~~CnklLa~ 16 (51)
T PF10122_consen 1 MLKEIRCGHCNKLLAK 16 (51)
T ss_pred CCcceeccchhHHHhh
Confidence 5567899999998865
No 89
>smart00741 SapB Saposin (B) Domains. Present in multiple copies in prosaposin and in pulmonary surfactant-associated protein B. In plant aspartic proteinases, a saposin domain is circularly permuted. This causes the prediction algorithm to predict two such domains, where only one is truly present.
Probab=33.15 E-value=29 Score=19.00 Aligned_cols=30 Identities=23% Similarity=0.414 Sum_probs=21.6
Q ss_pred CCccccchHHHHHHHHHccCChhhHHHhcC
Q 035172 10 CGKVIGNKWDTYLDLLQADYPEGDALDALG 39 (71)
Q Consensus 10 CGkvi~~~~e~y~~~v~~~~~~~~vLd~Lg 39 (71)
|...+...++.....+.++.+|.++=..+|
T Consensus 45 C~~~v~~~~~~ii~~i~~~~~p~~iC~~l~ 74 (76)
T smart00741 45 CKEFVDQYGPEIIDLLEQGLDPKDVCQKLG 74 (76)
T ss_pred HHHHHHHHHHHHHHHHHhCCCHHHHHHHcC
Confidence 556666677777777777777877766665
No 90
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=33.08 E-value=9 Score=23.51 Aligned_cols=16 Identities=31% Similarity=0.899 Sum_probs=13.9
Q ss_pred CcccccccCCCccccc
Q 035172 1 MIIPVRCFTCGKVIGN 16 (71)
Q Consensus 1 MiiPvRCfTCGkvi~~ 16 (71)
||=-+||--|||+++.
T Consensus 1 ~~~tiRC~~CnKlLa~ 16 (60)
T COG4416 1 MMQTIRCAKCNKLLAE 16 (60)
T ss_pred CceeeehHHHhHHHHh
Confidence 6677999999999976
No 91
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=32.60 E-value=21 Score=19.58 Aligned_cols=12 Identities=33% Similarity=0.791 Sum_probs=9.0
Q ss_pred cccccCCCcccc
Q 035172 4 PVRCFTCGKVIG 15 (71)
Q Consensus 4 PvRCfTCGkvi~ 15 (71)
++.|.+||=+-.
T Consensus 13 ~~~C~~CgM~Y~ 24 (41)
T PF13878_consen 13 ATTCPTCGMLYS 24 (41)
T ss_pred CcCCCCCCCEEC
Confidence 578999996543
No 92
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=32.06 E-value=14 Score=20.13 Aligned_cols=15 Identities=27% Similarity=0.625 Sum_probs=7.6
Q ss_pred cccccCCCccccchH
Q 035172 4 PVRCFTCGKVIGNKW 18 (71)
Q Consensus 4 PvRCfTCGkvi~~~~ 18 (71)
+..|+-||++..+.|
T Consensus 3 ~~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 3 YPKCDECGKPFMDSY 17 (34)
T ss_dssp -EE-TTT--EES-SS
T ss_pred CchHhHhCCHHHHHH
Confidence 457999999987654
No 93
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=31.77 E-value=20 Score=19.47 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=10.1
Q ss_pred ccccCCCccccc
Q 035172 5 VRCFTCGKVIGN 16 (71)
Q Consensus 5 vRCfTCGkvi~~ 16 (71)
++|..||+.+..
T Consensus 6 l~C~~CG~~m~~ 17 (58)
T PF13408_consen 6 LRCGHCGSKMTR 17 (58)
T ss_pred EEcccCCcEeEE
Confidence 689999998766
No 94
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=31.56 E-value=74 Score=17.64 Aligned_cols=24 Identities=25% Similarity=0.462 Sum_probs=20.0
Q ss_pred hhHHHhcCCcchhhhhHHHHhHHH
Q 035172 32 GDALDALGLVRYCCRRMLMTHVDL 55 (71)
Q Consensus 32 ~~vLd~Lg~~ryCCRrmllthvdl 55 (71)
.+-|.++|++..--|+.+++.+.-
T Consensus 41 ~~~L~~lGI~~~~~r~kll~~i~~ 64 (66)
T PF07647_consen 41 EEDLKELGITNLGHRRKLLSAIQE 64 (66)
T ss_dssp HHHHHHTTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHH
Confidence 356679999999999999998764
No 95
>PRK13832 plasmid partitioning protein; Provisional
Probab=31.54 E-value=44 Score=27.84 Aligned_cols=35 Identities=23% Similarity=0.335 Sum_probs=29.0
Q ss_pred chHHHHHHHHHccCChhhHHHhcCCcchhhhh-HHH
Q 035172 16 NKWDTYLDLLQADYPEGDALDALGLVRYCCRR-MLM 50 (71)
Q Consensus 16 ~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRr-mll 50 (71)
+.|+.|..+++.|.+++++-..||+++-.=++ ++|
T Consensus 106 Eea~AfkrLie~G~T~EeIA~~lG~S~~~V~rlllL 141 (520)
T PRK13832 106 DQWRAIERLVALGWTEEAIAVALALPVRQIRKLRLL 141 (520)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 56899999999999999999999999755554 334
No 96
>PF12773 DZR: Double zinc ribbon
Probab=31.02 E-value=22 Score=19.27 Aligned_cols=14 Identities=21% Similarity=0.282 Sum_probs=9.5
Q ss_pred ccccCCCccccchH
Q 035172 5 VRCFTCGKVIGNKW 18 (71)
Q Consensus 5 vRCfTCGkvi~~~~ 18 (71)
+.|..||..+...|
T Consensus 30 ~~C~~Cg~~~~~~~ 43 (50)
T PF12773_consen 30 KICPNCGAENPPNA 43 (50)
T ss_pred CCCcCCcCCCcCCc
Confidence 45888888776543
No 97
>PLN00209 ribosomal protein S27; Provisional
Probab=30.92 E-value=22 Score=23.20 Aligned_cols=14 Identities=29% Similarity=0.532 Sum_probs=11.3
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
.+|.|-.||.+++.
T Consensus 54 t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 54 TVVVCGSCQTVLCQ 67 (86)
T ss_pred eEEEccccCCEeec
Confidence 47889999998864
No 98
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=30.27 E-value=23 Score=19.29 Aligned_cols=13 Identities=38% Similarity=1.111 Sum_probs=8.7
Q ss_pred cccccccCCCccc
Q 035172 2 IIPVRCFTCGKVI 14 (71)
Q Consensus 2 iiPvRCfTCGkvi 14 (71)
.+|++|..||+..
T Consensus 11 ~~~~~C~~C~~~F 23 (43)
T PF01428_consen 11 FLPFKCKHCGKSF 23 (43)
T ss_dssp TSHEE-TTTS-EE
T ss_pred CCCeECCCCCccc
Confidence 4789999999864
No 99
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.19 E-value=24 Score=18.82 Aligned_cols=9 Identities=67% Similarity=1.442 Sum_probs=6.2
Q ss_pred ccccCCCcc
Q 035172 5 VRCFTCGKV 13 (71)
Q Consensus 5 vRCfTCGkv 13 (71)
|+|..||.+
T Consensus 26 v~C~~C~~~ 34 (36)
T PF13717_consen 26 VRCSKCGHV 34 (36)
T ss_pred EECCCCCCE
Confidence 567777764
No 100
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=29.72 E-value=47 Score=18.89 Aligned_cols=23 Identities=26% Similarity=0.290 Sum_probs=14.4
Q ss_pred HHHHHHHHccCChhhHHHhcC-Cc
Q 035172 19 DTYLDLLQADYPEGDALDALG-LV 41 (71)
Q Consensus 19 e~y~~~v~~~~~~~~vLd~Lg-~~ 41 (71)
..-..++++|++++++++++. ++
T Consensus 22 ~~i~~~~~~G~s~eeI~~~yp~Lt 45 (56)
T PF04255_consen 22 RDILDLLAAGESPEEIAEDYPSLT 45 (56)
T ss_dssp HHHHHHHHTT--HHHHHHHSTT--
T ss_pred HHHHHHHHcCCCHHHHHHHCCCCC
Confidence 344556689999999999876 54
No 101
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=29.67 E-value=26 Score=17.27 Aligned_cols=12 Identities=33% Similarity=0.811 Sum_probs=9.0
Q ss_pred ccccCCCccccc
Q 035172 5 VRCFTCGKVIGN 16 (71)
Q Consensus 5 vRCfTCGkvi~~ 16 (71)
+.|.+||+--..
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 469999987644
No 102
>PLN00214 putative protein; Provisional
Probab=29.44 E-value=62 Score=22.11 Aligned_cols=28 Identities=21% Similarity=0.450 Sum_probs=19.4
Q ss_pred hHHHhcCCcchhhhhHHHH----hHHHHHHHh
Q 035172 33 DALDALGLVRYCCRRMLMT----HVDLIEKLL 60 (71)
Q Consensus 33 ~vLd~Lg~~ryCCRrmllt----hvdlid~ll 60 (71)
.++.+=...++||+.++-+ |-.|+.-++
T Consensus 54 ~i~~N~t~s~~CC~~LVk~GK~CH~~LiK~i~ 85 (115)
T PLN00214 54 VVFENGTLIDPCCNDLVKEGKVCHDTLIKYIA 85 (115)
T ss_pred HHHcCCCCchHHHHHHHHHhhHHHHHHHHHHH
Confidence 3343334589999999987 667766665
No 103
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=28.96 E-value=18 Score=25.42 Aligned_cols=14 Identities=43% Similarity=0.895 Sum_probs=11.0
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
.|.|||+|+|-+|-
T Consensus 104 ~~~rC~~C~kk~gl 117 (167)
T KOG3173|consen 104 KKKRCFKCRKKVGL 117 (167)
T ss_pred cchhhhhhhhhhcc
Confidence 36789999987765
No 104
>smart00343 ZnF_C2HC zinc finger.
Probab=28.85 E-value=25 Score=16.92 Aligned_cols=8 Identities=50% Similarity=1.630 Sum_probs=6.2
Q ss_pred cccCCCcc
Q 035172 6 RCFTCGKV 13 (71)
Q Consensus 6 RCfTCGkv 13 (71)
+|+.||+.
T Consensus 1 ~C~~CG~~ 8 (26)
T smart00343 1 KCYNCGKE 8 (26)
T ss_pred CCccCCCC
Confidence 58889876
No 105
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=28.51 E-value=28 Score=18.51 Aligned_cols=11 Identities=45% Similarity=0.984 Sum_probs=8.9
Q ss_pred cccccCCCccc
Q 035172 4 PVRCFTCGKVI 14 (71)
Q Consensus 4 PvRCfTCGkvi 14 (71)
|.+|+-||..-
T Consensus 2 ~~~Cp~Cg~~~ 12 (47)
T PF14690_consen 2 PPRCPHCGSPS 12 (47)
T ss_pred CccCCCcCCCc
Confidence 77899999654
No 106
>PRK06386 replication factor A; Reviewed
Probab=28.23 E-value=25 Score=27.62 Aligned_cols=13 Identities=31% Similarity=0.800 Sum_probs=11.1
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
--||+.|+|++.+
T Consensus 236 i~rCP~C~R~l~~ 248 (358)
T PRK06386 236 FTKCSVCNKIIED 248 (358)
T ss_pred EecCcCCCeEccC
Confidence 4589999999985
No 107
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=27.19 E-value=29 Score=18.42 Aligned_cols=10 Identities=60% Similarity=1.245 Sum_probs=6.3
Q ss_pred cccccCCCcc
Q 035172 4 PVRCFTCGKV 13 (71)
Q Consensus 4 PvRCfTCGkv 13 (71)
.|||..||.+
T Consensus 25 ~vrC~~C~~~ 34 (37)
T PF13719_consen 25 KVRCPKCGHV 34 (37)
T ss_pred EEECCCCCcE
Confidence 3667777654
No 108
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.07 E-value=29 Score=19.92 Aligned_cols=10 Identities=30% Similarity=0.806 Sum_probs=8.6
Q ss_pred cccCCCcccc
Q 035172 6 RCFTCGKVIG 15 (71)
Q Consensus 6 RCfTCGkvi~ 15 (71)
-|.+||++.+
T Consensus 10 ~C~~C~rpf~ 19 (42)
T PF10013_consen 10 ICPVCGRPFT 19 (42)
T ss_pred cCcccCCcch
Confidence 3999999985
No 109
>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=26.71 E-value=26 Score=24.12 Aligned_cols=24 Identities=29% Similarity=0.773 Sum_probs=16.2
Q ss_pred ccccCCCccccc----------hHHHHHHHHHcc
Q 035172 5 VRCFTCGKVIGN----------KWDTYLDLLQAD 28 (71)
Q Consensus 5 vRCfTCGkvi~~----------~~e~y~~~v~~~ 28 (71)
-|||-||+..-+ .-.+.++.+.+|
T Consensus 63 ~~C~~CG~~l~~~~~C~~~~T~sq~d~~~~I~~G 96 (124)
T PF05515_consen 63 NRCFKCGRYLHNNGNCRRNTTRSQSDVLEVIREG 96 (124)
T ss_pred CccccccceeecCCcCCCccchhHHHHHHHHhcc
Confidence 489999997632 124566677666
No 110
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=26.35 E-value=52 Score=20.10 Aligned_cols=27 Identities=19% Similarity=0.359 Sum_probs=16.7
Q ss_pred hHHHHHHHHHc-cCChhhHHHhcCCcch
Q 035172 17 KWDTYLDLLQA-DYPEGDALDALGLVRY 43 (71)
Q Consensus 17 ~~e~y~~~v~~-~~~~~~vLd~Lg~~ry 43 (71)
.|-+|..-..+ +.--.+.|+|+|++|.
T Consensus 24 ~W~~~rr~r~eL~~lsd~~L~DiGisR~ 51 (63)
T COG5457 24 RWRRYRRTRRELLRLSDHLLSDIGISRA 51 (63)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHcCCCHH
Confidence 45555544421 2333589999999875
No 111
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=26.02 E-value=72 Score=13.81 Aligned_cols=27 Identities=22% Similarity=0.227 Sum_probs=18.7
Q ss_pred hHHHHHHHHHccCChhhHHHhcCCcch
Q 035172 17 KWDTYLDLLQADYPEGDALDALGLVRY 43 (71)
Q Consensus 17 ~~e~y~~~v~~~~~~~~vLd~Lg~~ry 43 (71)
.+........+|.+..++-..+|+.+-
T Consensus 10 ~~~~i~~~~~~~~s~~~ia~~~~is~~ 36 (42)
T cd00569 10 QIEEARRLLAAGESVAEIARRLGVSRS 36 (42)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHH
Confidence 344555556678888888888887643
No 112
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=25.91 E-value=38 Score=23.05 Aligned_cols=23 Identities=26% Similarity=0.289 Sum_probs=15.9
Q ss_pred cchHHHHHHHHHccCChhhHHHhc
Q 035172 15 GNKWDTYLDLLQADYPEGDALDAL 38 (71)
Q Consensus 15 ~~~~e~y~~~v~~~~~~~~vLd~L 38 (71)
...||-|++.. -|....||||+|
T Consensus 2 ~~yYElYRrs~-ig~~L~dalD~l 24 (113)
T COG5123 2 PGYYELYRRSM-IGKVLEDALDEL 24 (113)
T ss_pred ccHHHHHHHHH-HHHHHHHHHHHH
Confidence 34677776644 677788888865
No 113
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=25.49 E-value=32 Score=20.49 Aligned_cols=10 Identities=40% Similarity=0.806 Sum_probs=8.2
Q ss_pred ccccCCCccc
Q 035172 5 VRCFTCGKVI 14 (71)
Q Consensus 5 vRCfTCGkvi 14 (71)
|.|..||.+-
T Consensus 22 VvCp~Cgapy 31 (54)
T PF14446_consen 22 VVCPECGAPY 31 (54)
T ss_pred EECCCCCCcc
Confidence 6799999875
No 114
>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=25.44 E-value=28 Score=19.11 Aligned_cols=11 Identities=27% Similarity=0.972 Sum_probs=6.1
Q ss_pred cccCCCccccc
Q 035172 6 RCFTCGKVIGN 16 (71)
Q Consensus 6 RCfTCGkvi~~ 16 (71)
+|-.||+++.-
T Consensus 8 kC~~CGniVev 18 (36)
T PF06397_consen 8 KCEHCGNIVEV 18 (36)
T ss_dssp E-TTT--EEEE
T ss_pred EccCCCCEEEE
Confidence 69999998853
No 115
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=25.21 E-value=46 Score=20.70 Aligned_cols=28 Identities=25% Similarity=0.533 Sum_probs=20.4
Q ss_pred ccccchH--HHHHHHHHccCChhhHHHhcCCc
Q 035172 12 KVIGNKW--DTYLDLLQADYPEGDALDALGLV 41 (71)
Q Consensus 12 kvi~~~~--e~y~~~v~~~~~~~~vLd~Lg~~ 41 (71)
++|+.-| .+|+.++. .+|..||.++|++
T Consensus 8 ~ivarAw~Dp~Fr~~Ll--~DPraaL~e~G~~ 37 (77)
T TIGR03793 8 KIIAKAWEDEAFKQALL--TNPKEALEREGVQ 37 (77)
T ss_pred HHHHHHHcCHHHHHHHH--HCHHHHHHHhCCC
Confidence 3455556 68888773 4789999999975
No 116
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=25.16 E-value=32 Score=22.37 Aligned_cols=14 Identities=21% Similarity=0.382 Sum_probs=11.1
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
.+|.|-.||.+++.
T Consensus 53 t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 53 TVVLCGGCSSQLCQ 66 (85)
T ss_pred eEEEccccCCEeec
Confidence 46889999988864
No 117
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=25.14 E-value=55 Score=22.70 Aligned_cols=13 Identities=23% Similarity=0.554 Sum_probs=11.2
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
+.+|-.||++.+.
T Consensus 114 ~~~C~~Cg~~f~~ 126 (181)
T PRK08222 114 LQRCSRCERPFAP 126 (181)
T ss_pred cCcCcccCCccCc
Confidence 5689999999984
No 118
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=25.02 E-value=17 Score=21.30 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=7.6
Q ss_pred ccccccCCCc
Q 035172 3 IPVRCFTCGK 12 (71)
Q Consensus 3 iPvRCfTCGk 12 (71)
-|.||.+|-+
T Consensus 32 ~p~RC~~CR~ 41 (49)
T PF13451_consen 32 EPKRCPSCRQ 41 (49)
T ss_pred CCccCHHHHH
Confidence 4899998843
No 119
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=24.91 E-value=30 Score=27.17 Aligned_cols=13 Identities=31% Similarity=0.843 Sum_probs=10.5
Q ss_pred ccccCCCccccch
Q 035172 5 VRCFTCGKVIGNK 17 (71)
Q Consensus 5 vRCfTCGkvi~~~ 17 (71)
.+|+.||-|+++.
T Consensus 22 tvC~~CGlVl~~r 34 (308)
T KOG1597|consen 22 TVCSECGLVLEDR 34 (308)
T ss_pred eecccCCeeeccc
Confidence 4799999998763
No 120
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=24.86 E-value=56 Score=23.44 Aligned_cols=20 Identities=35% Similarity=1.024 Sum_probs=15.2
Q ss_pred cccCCCcc--ccchHHHHHHHH
Q 035172 6 RCFTCGKV--IGNKWDTYLDLL 25 (71)
Q Consensus 6 RCfTCGkv--i~~~~e~y~~~v 25 (71)
||+.|||+ -|+.|+.-.+.+
T Consensus 132 ~C~~CgkiYW~GsHw~~m~~~~ 153 (165)
T COG1656 132 RCPKCGKIYWKGSHWRRMVERI 153 (165)
T ss_pred ECCCCcccccCchHHHHHHHHH
Confidence 59999998 477787777644
No 121
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.56 E-value=63 Score=19.81 Aligned_cols=23 Identities=22% Similarity=0.455 Sum_probs=17.3
Q ss_pred ccccccCCCccccchHHHHHHHH
Q 035172 3 IPVRCFTCGKVIGNKWDTYLDLL 25 (71)
Q Consensus 3 iPvRCfTCGkvi~~~~e~y~~~v 25 (71)
|-+.|-.||.+|--.-.+|...+
T Consensus 33 IkikC~nC~h~vm~pR~~Ferkl 55 (60)
T COG4481 33 IKIKCENCGHSVMMPRYDFERKL 55 (60)
T ss_pred EEEEecCCCcEEEecHHHHHHHH
Confidence 56789999999866556666655
No 122
>PHA02562 46 endonuclease subunit; Provisional
Probab=24.36 E-value=49 Score=25.62 Aligned_cols=13 Identities=31% Similarity=0.501 Sum_probs=11.7
Q ss_pred ccccCCCccccch
Q 035172 5 VRCFTCGKVIGNK 17 (71)
Q Consensus 5 vRCfTCGkvi~~~ 17 (71)
..|+|||+.+.+.
T Consensus 285 ~~Cp~C~~~~~~~ 297 (562)
T PHA02562 285 GVCPTCTQQISEG 297 (562)
T ss_pred CCCCCCCCcCCCc
Confidence 4799999999997
No 123
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=24.23 E-value=34 Score=22.85 Aligned_cols=16 Identities=44% Similarity=1.178 Sum_probs=10.9
Q ss_pred cccCCCccc--cchHHHH
Q 035172 6 RCFTCGKVI--GNKWDTY 21 (71)
Q Consensus 6 RCfTCGkvi--~~~~e~y 21 (71)
+|..|||+- |..|+.=
T Consensus 126 ~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 126 RCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred ECCCCCCEecccccHHHH
Confidence 699999984 4445443
No 124
>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=24.18 E-value=35 Score=17.38 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=5.2
Q ss_pred cccCCCcccc
Q 035172 6 RCFTCGKVIG 15 (71)
Q Consensus 6 RCfTCGkvi~ 15 (71)
.|++||..+-
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4889998774
No 125
>PRK05667 dnaG DNA primase; Validated
Probab=24.08 E-value=80 Score=26.01 Aligned_cols=30 Identities=27% Similarity=0.534 Sum_probs=16.4
Q ss_pred cccCCCccccchHHHHHHHHHccCChhhHHHhc
Q 035172 6 RCFTCGKVIGNKWDTYLDLLQADYPEGDALDAL 38 (71)
Q Consensus 6 RCfTCGkvi~~~~e~y~~~v~~~~~~~~vLd~L 38 (71)
.||+||+- |+.. .|.... +|.+-.+|+..|
T Consensus 59 ~CF~Cg~~-Gd~i-~fv~~~-~~~sf~eAv~~L 88 (580)
T PRK05667 59 HCFGCGAG-GDVI-KFLMEY-EGLSFVEAVEEL 88 (580)
T ss_pred EECCCCCC-CCHH-HHHHHH-hCCCHHHHHHHH
Confidence 69999973 3333 233333 455555555544
No 126
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=24.03 E-value=60 Score=20.26 Aligned_cols=21 Identities=33% Similarity=0.540 Sum_probs=12.9
Q ss_pred ccccCCCccccchHHHHHHHH
Q 035172 5 VRCFTCGKVIGNKWDTYLDLL 25 (71)
Q Consensus 5 vRCfTCGkvi~~~~e~y~~~v 25 (71)
..|-.||+++.-..++....+
T Consensus 81 ~iC~~Cg~v~~~~~~~~~~~~ 101 (120)
T PF01475_consen 81 FICTQCGKVIDLDDPELEEIL 101 (120)
T ss_dssp EEETTTS-EEEE-GHHHHHHH
T ss_pred EEECCCCCEEEecchhHHHHH
Confidence 569999999876655444433
No 127
>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=23.95 E-value=47 Score=15.97 Aligned_cols=11 Identities=27% Similarity=0.661 Sum_probs=9.7
Q ss_pred cccCCCccccc
Q 035172 6 RCFTCGKVIGN 16 (71)
Q Consensus 6 RCfTCGkvi~~ 16 (71)
.|..|++..++
T Consensus 3 ~C~~C~k~f~~ 13 (27)
T PF12171_consen 3 YCDACDKYFSS 13 (27)
T ss_dssp BBTTTTBBBSS
T ss_pred CcccCCCCcCC
Confidence 59999999988
No 128
>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=23.89 E-value=62 Score=21.15 Aligned_cols=56 Identities=23% Similarity=0.348 Sum_probs=33.1
Q ss_pred cccccCCCccccch----------------HHHHHHHHHccCC----------hhhHHHhcCCcchhhhhHHHHhHHHHH
Q 035172 4 PVRCFTCGKVIGNK----------------WDTYLDLLQADYP----------EGDALDALGLVRYCCRRMLMTHVDLIE 57 (71)
Q Consensus 4 PvRCfTCGkvi~~~----------------~e~y~~~v~~~~~----------~~~vLd~Lg~~ryCCRrmllthvdlid 57 (71)
-++|-+||+.+.-+ -++|.+.+.+|.. +-+.+..|.+... ...+-...+-++
T Consensus 43 ~l~C~~C~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~H~~~CpWr~~~cpl~~~~~l~l~~~--~~~l~~~~~r~~ 120 (133)
T PF07967_consen 43 MLKCESCGARLCVKLSDSPPDLDSEVYKKLVEKYSEQLVTGHKESCPWRNNSCPLDSLYRLPLTNP--SALLEQFKERLD 120 (133)
T ss_pred EEEeCCCCCEEEEeccccchHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCChhhhhcCCCCCH--HHHHHHHHHHHH
Confidence 36899999987666 2667777766532 2245555554444 444444555556
Q ss_pred HHhc
Q 035172 58 KLLN 61 (71)
Q Consensus 58 ~ll~ 61 (71)
.|.+
T Consensus 121 ~L~~ 124 (133)
T PF07967_consen 121 SLLQ 124 (133)
T ss_pred HHHh
Confidence 6554
No 129
>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=23.80 E-value=39 Score=17.80 Aligned_cols=12 Identities=33% Similarity=0.791 Sum_probs=8.9
Q ss_pred ccccccCCCccc
Q 035172 3 IPVRCFTCGKVI 14 (71)
Q Consensus 3 iPvRCfTCGkvi 14 (71)
.|-+|+.||..-
T Consensus 17 ~p~~CP~Cg~~~ 28 (34)
T cd00729 17 APEKCPICGAPK 28 (34)
T ss_pred CCCcCcCCCCch
Confidence 367899998753
No 130
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=23.75 E-value=47 Score=21.57 Aligned_cols=17 Identities=18% Similarity=0.479 Sum_probs=14.3
Q ss_pred ccCCCccccchHHHHHH
Q 035172 7 CFTCGKVIGNKWDTYLD 23 (71)
Q Consensus 7 CfTCGkvi~~~~e~y~~ 23 (71)
|++||..-+..|-+.+.
T Consensus 63 CP~C~~~~~~~W~~~~~ 79 (111)
T PF14319_consen 63 CPSCQAKATEQWIEKQR 79 (111)
T ss_pred CCCCCChHHHHHHHHHH
Confidence 89999999998977654
No 131
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.75 E-value=37 Score=18.34 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=7.7
Q ss_pred cccCCCccccc
Q 035172 6 RCFTCGKVIGN 16 (71)
Q Consensus 6 RCfTCGkvi~~ 16 (71)
-|..||..+-.
T Consensus 2 FCp~Cg~~l~~ 12 (52)
T smart00661 2 FCPKCGNMLIP 12 (52)
T ss_pred CCCCCCCcccc
Confidence 38888887633
No 132
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=23.72 E-value=60 Score=26.04 Aligned_cols=20 Identities=25% Similarity=0.428 Sum_probs=14.2
Q ss_pred cccccCCCccccchHHHHHH
Q 035172 4 PVRCFTCGKVIGNKWDTYLD 23 (71)
Q Consensus 4 PvRCfTCGkvi~~~~e~y~~ 23 (71)
-+-|+|||+.-.+....-.+
T Consensus 261 ~iaCP~CGR~~~dv~~~~~~ 280 (361)
T COG0821 261 VIACPTCGRTEFDVIQTLNE 280 (361)
T ss_pred EEECCCCCceeehHHHHHHH
Confidence 35699999998876544333
No 133
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=23.70 E-value=38 Score=19.28 Aligned_cols=16 Identities=25% Similarity=0.609 Sum_probs=13.7
Q ss_pred ccccccCCCccccchH
Q 035172 3 IPVRCFTCGKVIGNKW 18 (71)
Q Consensus 3 iPvRCfTCGkvi~~~~ 18 (71)
.+.+|+.||..-+..|
T Consensus 2 ~~~~C~~C~~~~T~~W 17 (52)
T smart00401 2 SGRSCSNCGTTETPLW 17 (52)
T ss_pred CCCCcCCCCCCCCCcc
Confidence 3678999999888888
No 134
>PF07541 EIF_2_alpha: Eukaryotic translation initiation factor 2 alpha subunit; InterPro: IPR011488 In Eukaryota and Archaea, translation initiation factor 2 (eIF2/aIF2), which contains three subunits (alpha, beta and gamma), is pivotal for binding of charged initiator tRNA to the small ribosomal subunit. This entry represents the alpha subunit of both eukaryota and archaeal translation initiator factor 2.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0005850 eukaryotic translation initiation factor 2 complex; PDB: 2QN6_B 3CW2_C 2AHO_B 3QSY_B 3V11_B 2QMU_B 1YZ7_A 1YZ6_A 3AEV_A 1KL9_A ....
Probab=23.50 E-value=61 Score=21.10 Aligned_cols=24 Identities=21% Similarity=0.468 Sum_probs=17.5
Q ss_pred cchHHHHH-HHHHccCChhhHHHhcCCc
Q 035172 15 GNKWDTYL-DLLQADYPEGDALDALGLV 41 (71)
Q Consensus 15 ~~~~e~y~-~~v~~~~~~~~vLd~Lg~~ 41 (71)
|+.|+.|. ....+| .++|++||+.
T Consensus 15 g~~y~aFe~~~~~~~---~~vl~~l~i~ 39 (114)
T PF07541_consen 15 GSLYDAFELSAADNG---EEVLKKLGIP 39 (114)
T ss_dssp SSHHHHHHHHHHHHG---GGGGBTTTBS
T ss_pred CcHHHHHHHHHcCCC---cceeccCCCC
Confidence 68889998 555443 4788888876
No 135
>PF00482 T2SF: Type II secretion system (T2SS), protein F; InterPro: IPR018076 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) [], have been found to be evolutionary related. These are proteins of about 400 amino acids that are highly hydrophobic and which are thought to be integral protein of the inner membrane. Proteins with this domain form a platform for the type II secretion machinery, as well as the type IV pili and the archaeal flagellae [].; PDB: 2VMA_A 3C1Q_A 2VMB_B 2WHN_B.
Probab=23.24 E-value=55 Score=19.05 Aligned_cols=28 Identities=14% Similarity=0.127 Sum_probs=20.2
Q ss_pred ccccchHHHHHHHHHccCChhhHHHhcC
Q 035172 12 KVIGNKWDTYLDLLQADYPEGDALDALG 39 (71)
Q Consensus 12 kvi~~~~e~y~~~v~~~~~~~~vLd~Lg 39 (71)
..+++.+++-...++.|.+++++|...|
T Consensus 29 ~~l~~~~~~~~~~l~~G~~~~~al~~~~ 56 (124)
T PF00482_consen 29 GPLREELQKIRRRLRNGGSLEEALERTG 56 (124)
T ss_dssp HHHHHHHHHHHHHHHTT--HHHHHCTST
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHhc
Confidence 3455667777888889999999999765
No 136
>cd01775 CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase. CYR1 is a fungal adenylate cyclase with at least four domains, an N-terminal RA (Ras association) domain, a middle leucine-rich repeat domain, a catalytic domain. The N-terminal RA domain of CYR1 post-translationally modifies a small GTPase called Ras. The Ras-CYR1 pathway has been implicated in the transduction of a glucose-triggered signal to an intracellular environment where a protein phosphorylation cascade is initiated by cyclic AMP.
Probab=23.08 E-value=56 Score=21.60 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=22.9
Q ss_pred ccccCCCccccch---HHHHHHH-HHccCChhhHHHhcCCc
Q 035172 5 VRCFTCGKVIGNK---WDTYLDL-LQADYPEGDALDALGLV 41 (71)
Q Consensus 5 vRCfTCGkvi~~~---~e~y~~~-v~~~~~~~~vLd~Lg~~ 41 (71)
+++.-+-|+++.. ---.+.+ .+.|+++.|=|+++|.+
T Consensus 48 l~~~~l~RvL~p~ErPl~IqkrlL~q~GY~~~D~l~~lGre 88 (97)
T cd01775 48 LKKHDLSRVLRPTEKPLLIQKRLLLQVGYEERDRIEDIGRE 88 (97)
T ss_pred EEECCeeeecCCcCCcHHHHHHHHHHcCCCCCCcHHHhCcc
Confidence 4445555555431 1112333 36899999999999986
No 137
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=23.04 E-value=62 Score=19.27 Aligned_cols=23 Identities=26% Similarity=0.521 Sum_probs=16.8
Q ss_pred ccccCCCcccc----------chHHHHHHHHHc
Q 035172 5 VRCFTCGKVIG----------NKWDTYLDLLQA 27 (71)
Q Consensus 5 vRCfTCGkvi~----------~~~e~y~~~v~~ 27 (71)
-.|..||.+.. ++|-+|+..++.
T Consensus 18 ~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~kk 50 (56)
T PRK13130 18 EICPVCGGKTKNPHPPRFSPEDKYGKYRRALKK 50 (56)
T ss_pred ccCcCCCCCCCCCCCCCCCCCCccHHHHHHHHH
Confidence 46888998764 578888877753
No 138
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=22.73 E-value=1.4e+02 Score=15.97 Aligned_cols=40 Identities=18% Similarity=0.473 Sum_probs=25.9
Q ss_pred chHHHHHHHHH---c-cCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhcc
Q 035172 16 NKWDTYLDLLQ---A-DYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLNY 62 (71)
Q Consensus 16 ~~~e~y~~~v~---~-~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~y 62 (71)
+.|++|++.++ + ..+..++.. .....|-.|-||+++.-.|
T Consensus 2 ~~Y~~FL~il~~y~~~~~~~~~v~~-------~v~~Ll~~hpdLl~~F~~F 45 (47)
T PF02671_consen 2 EVYNEFLKILNDYKKGRISRSEVIE-------EVSELLRGHPDLLEEFNRF 45 (47)
T ss_dssp HHHHHHHHHHHHHHCTCSCHHHHHH-------HHHHHTTT-HHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHH-------HHHHHHccCHHHHHHHHhh
Confidence 46788888775 2 345666665 3456666799999887655
No 139
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=22.68 E-value=41 Score=28.23 Aligned_cols=13 Identities=31% Similarity=1.040 Sum_probs=11.2
Q ss_pred cccccccCCCccc
Q 035172 2 IIPVRCFTCGKVI 14 (71)
Q Consensus 2 iiPvRCfTCGkvi 14 (71)
.+|-.|++||..+
T Consensus 402 ~~P~~CP~Cgs~l 414 (665)
T PRK07956 402 VMPTHCPVCGSEL 414 (665)
T ss_pred cCCCCCCCCCCEe
Confidence 4789999999876
No 140
>TIGR02289 M3_not_pepF oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family.
Probab=22.57 E-value=89 Score=24.93 Aligned_cols=26 Identities=19% Similarity=0.158 Sum_probs=22.0
Q ss_pred hHHHHHHHHHcc--CChhhHHHhcCCcc
Q 035172 17 KWDTYLDLLQAD--YPEGDALDALGLVR 42 (71)
Q Consensus 17 ~~e~y~~~v~~~--~~~~~vLd~Lg~~r 42 (71)
-|+.|++.++.| .++.+++...|++.
T Consensus 500 ~~~~Y~~~L~~Ggs~~~~ell~~aGid~ 527 (549)
T TIGR02289 500 ALKDYKKLCSAGGSQSFLELYETAGLTF 527 (549)
T ss_pred HHHHHHHHHhccCCcCHHHHHHHhCCCC
Confidence 478999999877 68899999999874
No 141
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=22.53 E-value=71 Score=23.75 Aligned_cols=24 Identities=29% Similarity=0.559 Sum_probs=17.5
Q ss_pred cchHHHHHHHHHccCChhhHHHhcCCc
Q 035172 15 GNKWDTYLDLLQADYPEGDALDALGLV 41 (71)
Q Consensus 15 ~~~~e~y~~~v~~~~~~~~vLd~Lg~~ 41 (71)
|+.|+.|...+.+| .++|++||+.
T Consensus 131 g~~y~af~~~~~~~---~~~l~~~~~~ 154 (262)
T PRK03987 131 GDLYDAFEEAAIEG---EEALDDLGVP 154 (262)
T ss_pred CcHHHHHHHHHhcC---hhhhccCCCC
Confidence 46677777767544 4899999987
No 142
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=22.40 E-value=64 Score=22.75 Aligned_cols=23 Identities=13% Similarity=0.437 Sum_probs=16.4
Q ss_pred HHHccCChhhHHHhcCCcchhhhh
Q 035172 24 LLQADYPEGDALDALGLVRYCCRR 47 (71)
Q Consensus 24 ~v~~~~~~~~vLd~Lg~~ryCCRr 47 (71)
.+++--.-.++|..+|+. +||.-
T Consensus 4 iv~~~p~~~~vf~~~gid-~cc~g 26 (216)
T TIGR03652 4 IVTEIPRAARIFRKYGID-FCCGG 26 (216)
T ss_pred HHHhCccHHHHHHHcCCC-ccCCC
Confidence 344433446799999999 99963
No 143
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=22.29 E-value=1.6e+02 Score=17.46 Aligned_cols=24 Identities=21% Similarity=0.374 Sum_probs=17.7
Q ss_pred ChhhHHHhcCCcchhhhhHHHHhHH
Q 035172 30 PEGDALDALGLVRYCCRRMLMTHVD 54 (71)
Q Consensus 30 ~~~~vLd~Lg~~ryCCRrmllthvd 54 (71)
..+..|.++|+ --==||.+|.+++
T Consensus 29 ~~s~~LK~~GI-p~r~RryiL~~~e 52 (57)
T PF09597_consen 29 TSSKQLKELGI-PVRQRRYILRWRE 52 (57)
T ss_pred cCHHHHHHCCC-CHHHHHHHHHHHH
Confidence 45788999999 3335778887776
No 144
>PF06336 Corona_5a: Coronavirus 5a protein; InterPro: IPR009404 This family consists of several Coronavirus 5a proteins. The function of this family is unknown [].
Probab=22.21 E-value=84 Score=19.45 Aligned_cols=32 Identities=38% Similarity=0.644 Sum_probs=22.4
Q ss_pred hhHHHhc----CCc--chhhhhHHHHhHHHHHHHhccCc
Q 035172 32 GDALDAL----GLV--RYCCRRMLMTHVDLIEKLLNYNT 64 (71)
Q Consensus 32 ~~vLd~L----g~~--ryCCRrmllthvdlid~ll~y~~ 64 (71)
-.+||.| |.+ --|-||.+|-|.|++-.|. |.|
T Consensus 23 lrvldrlil~hgp~r~ltc~rrvll~qldlvyrla-ytp 60 (65)
T PF06336_consen 23 LRVLDRLILDHGPKRTLTCARRVLLVQLDLVYRLA-YTP 60 (65)
T ss_pred HHHHHHHHHhcCCcceehhhHHHHHHHHHHHHHHh-cCC
Confidence 3455554 333 3699999999999998764 443
No 145
>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=22.19 E-value=31 Score=28.98 Aligned_cols=54 Identities=28% Similarity=0.466 Sum_probs=37.2
Q ss_pred cCCCccccchHHH----------HHHHHH---ccCChhhHHHh-----------------cCCcchhhhhHHHHhHHHHH
Q 035172 8 FTCGKVIGNKWDT----------YLDLLQ---ADYPEGDALDA-----------------LGLVRYCCRRMLMTHVDLIE 57 (71)
Q Consensus 8 fTCGkvi~~~~e~----------y~~~v~---~~~~~~~vLd~-----------------Lg~~ryCCRrmllthvdlid 57 (71)
|-|||.|.|-|++ |.+..+ +|-++..+.|+ +|+.|.| ||||--.-|.
T Consensus 470 Fi~~kEicNAYtElNdP~~Qr~rFe~Q~~~k~~GDDEa~~~De~Fc~ALEYGlPPtgGwGmGIDRL~---MllTds~~I~ 546 (560)
T KOG1885|consen 470 FIAGKEICNAYTELNDPVDQRQRFEQQARDKDAGDDEAQMVDEDFCTALEYGLPPTGGWGMGIDRLV---MLLTDSNNIR 546 (560)
T ss_pred hhhhHHHhhhhhhhcCHHHHHHHHHHHHHHhhcCCcccccccHHHHHHHHcCCCCCCccccchhhhh---hhhcCCcchh
Confidence 6688888887743 333332 44454444443 6788887 9999999999
Q ss_pred HHhccCc
Q 035172 58 KLLNYNT 64 (71)
Q Consensus 58 ~ll~y~~ 64 (71)
++|.|-.
T Consensus 547 EVL~Fp~ 553 (560)
T KOG1885|consen 547 EVLLFPA 553 (560)
T ss_pred heeeccc
Confidence 9999863
No 146
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=22.18 E-value=41 Score=19.67 Aligned_cols=11 Identities=45% Similarity=0.975 Sum_probs=7.9
Q ss_pred cccccCCCccc
Q 035172 4 PVRCFTCGKVI 14 (71)
Q Consensus 4 PvRCfTCGkvi 14 (71)
.+||.-||.-|
T Consensus 24 ~irCp~Cg~rI 34 (49)
T COG1996 24 GIRCPYCGSRI 34 (49)
T ss_pred ceeCCCCCcEE
Confidence 57888888654
No 147
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=22.18 E-value=41 Score=20.22 Aligned_cols=12 Identities=42% Similarity=0.827 Sum_probs=9.7
Q ss_pred cccCCCccccch
Q 035172 6 RCFTCGKVIGNK 17 (71)
Q Consensus 6 RCfTCGkvi~~~ 17 (71)
.|.-||++|-..
T Consensus 5 HC~~CG~~Ip~~ 16 (59)
T PF09889_consen 5 HCPVCGKPIPPD 16 (59)
T ss_pred cCCcCCCcCCcc
Confidence 399999999753
No 148
>PF13342 Toprim_Crpt: C-terminal repeat of topoisomerase
Probab=22.17 E-value=78 Score=18.81 Aligned_cols=20 Identities=20% Similarity=0.355 Sum_probs=16.5
Q ss_pred CCccccchHHHHHHHHHccCCh
Q 035172 10 CGKVIGNKWDTYLDLLQADYPE 31 (71)
Q Consensus 10 CGkvi~~~~e~y~~~v~~~~~~ 31 (71)
+||.|+. ++-.+++++|.++
T Consensus 12 ~gk~lt~--~~~~~Ll~~gkT~ 31 (62)
T PF13342_consen 12 AGKKLTD--EEVKELLEKGKTG 31 (62)
T ss_pred cCCCCCH--HHHHHHHHcCCcc
Confidence 6888887 8888999888765
No 149
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=22.14 E-value=1e+02 Score=19.51 Aligned_cols=26 Identities=12% Similarity=-0.009 Sum_probs=21.1
Q ss_pred HHHHHHHHccCChhhHHHhcCCcchh
Q 035172 19 DTYLDLLQADYPEGDALDALGLVRYC 44 (71)
Q Consensus 19 e~y~~~v~~~~~~~~vLd~Lg~~ryC 44 (71)
++....+.+|.+..++-+.||+.+-=
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsT 66 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTAT 66 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHH
Confidence 55666788999999999999997643
No 150
>PF15629 Perm-CXXC: Permuted single zf-CXXC unit
Probab=22.02 E-value=32 Score=18.73 Aligned_cols=8 Identities=38% Similarity=1.452 Sum_probs=6.2
Q ss_pred cccCCCcc
Q 035172 6 RCFTCGKV 13 (71)
Q Consensus 6 RCfTCGkv 13 (71)
.||+|..+
T Consensus 18 tCfsCNsi 25 (32)
T PF15629_consen 18 TCFSCNSI 25 (32)
T ss_pred cccccccH
Confidence 49999864
No 151
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=21.83 E-value=28 Score=21.74 Aligned_cols=16 Identities=25% Similarity=0.698 Sum_probs=12.3
Q ss_pred ccccCCCccccchHHH
Q 035172 5 VRCFTCGKVIGNKWDT 20 (71)
Q Consensus 5 vRCfTCGkvi~~~~e~ 20 (71)
-||+||.-+|.-.|++
T Consensus 45 ArCPSCSLiv~vvyd~ 60 (67)
T COG5216 45 ARCPSCSLIVCVVYDA 60 (67)
T ss_pred EEcCCceEEEEEEecH
Confidence 4899999888776643
No 152
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=21.72 E-value=33 Score=20.63 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=9.2
Q ss_pred cccccCCCccc
Q 035172 4 PVRCFTCGKVI 14 (71)
Q Consensus 4 PvRCfTCGkvi 14 (71)
-|+|..|||+.
T Consensus 2 ~vkC~lCdk~~ 12 (56)
T PF09963_consen 2 RVKCILCDKKE 12 (56)
T ss_pred eeEEEecCCEE
Confidence 37899999975
No 153
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=21.51 E-value=43 Score=17.27 Aligned_cols=11 Identities=36% Similarity=0.742 Sum_probs=8.3
Q ss_pred cccccCCCccc
Q 035172 4 PVRCFTCGKVI 14 (71)
Q Consensus 4 PvRCfTCGkvi 14 (71)
|-+|+.||..=
T Consensus 17 ~~~CP~Cg~~~ 27 (33)
T cd00350 17 PWVCPVCGAPK 27 (33)
T ss_pred CCcCcCCCCcH
Confidence 56899998743
No 154
>PF14353 CpXC: CpXC protein
Probab=21.45 E-value=44 Score=21.42 Aligned_cols=20 Identities=25% Similarity=0.393 Sum_probs=16.0
Q ss_pred hhhhHHHHhHHHHHHHhccC
Q 035172 44 CCRRMLMTHVDLIEKLLNYN 63 (71)
Q Consensus 44 CCRrmllthvdlid~ll~y~ 63 (71)
.=.|...+.-+|+||++-|.
T Consensus 97 ~~~R~v~~~~~l~EKI~i~e 116 (128)
T PF14353_consen 97 YRVRIVIDYNELREKILIFE 116 (128)
T ss_pred ceeEEeCCHHHHHHHHHHHH
Confidence 34567788999999999886
No 155
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.44 E-value=59 Score=23.28 Aligned_cols=24 Identities=33% Similarity=0.865 Sum_probs=18.0
Q ss_pred ccccccCCCccccchH-----HHHHHHHHcc
Q 035172 3 IPVRCFTCGKVIGNKW-----DTYLDLLQAD 28 (71)
Q Consensus 3 iPvRCfTCGkvi~~~~-----e~y~~~v~~~ 28 (71)
.|-.|..||++- .| +.+.+++++.
T Consensus 67 ~PsYC~~CGkpy--PWt~~~L~aa~el~ee~ 95 (158)
T PF10083_consen 67 APSYCHNCGKPY--PWTENALEAANELIEED 95 (158)
T ss_pred CChhHHhCCCCC--chHHHHHHHHHHHHHHh
Confidence 477899999997 66 6677777633
No 156
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=21.43 E-value=44 Score=15.89 Aligned_cols=9 Identities=44% Similarity=1.357 Sum_probs=6.4
Q ss_pred ccccCCCcc
Q 035172 5 VRCFTCGKV 13 (71)
Q Consensus 5 vRCfTCGkv 13 (71)
..|+.||.+
T Consensus 17 ~~C~~C~~p 25 (26)
T smart00547 17 SKCFACGAP 25 (26)
T ss_pred ccccccCCc
Confidence 358888864
No 157
>cd00435 ACBP Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.
Probab=21.25 E-value=1.6e+02 Score=18.26 Aligned_cols=29 Identities=28% Similarity=0.604 Sum_probs=19.4
Q ss_pred hHHHHHHHHHccCChhhHHHhcCCcchhhhhHHHHhHHHHHHHhc
Q 035172 17 KWDTYLDLLQADYPEGDALDALGLVRYCCRRMLMTHVDLIEKLLN 61 (71)
Q Consensus 17 ~~e~y~~~v~~~~~~~~vLd~Lg~~ryCCRrmllthvdlid~ll~ 61 (71)
||++...+ .|.++.+|.. ..|++++++++
T Consensus 54 K~~AW~~l--~~ms~~eA~~--------------~YV~~~~~l~~ 82 (85)
T cd00435 54 KWDAWNSL--KGMSKEDAMK--------------AYIAKVEELIA 82 (85)
T ss_pred HHHHHHHc--CCCCHHHHHH--------------HHHHHHHHHhh
Confidence 56666654 5677777765 45777777765
No 158
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=21.24 E-value=56 Score=17.70 Aligned_cols=14 Identities=43% Similarity=0.643 Sum_probs=10.8
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
..+.|.+||++|..
T Consensus 3 ~~~~C~~C~~~i~g 16 (44)
T smart00291 3 HSYSCDTCGKPIVG 16 (44)
T ss_pred CCcCCCCCCCCCcC
Confidence 35679999998765
No 159
>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=21.13 E-value=42 Score=17.47 Aligned_cols=11 Identities=36% Similarity=0.788 Sum_probs=8.6
Q ss_pred cccCCCccccc
Q 035172 6 RCFTCGKVIGN 16 (71)
Q Consensus 6 RCfTCGkvi~~ 16 (71)
.|-.||..|..
T Consensus 5 ~C~~CGe~I~~ 15 (36)
T PF01258_consen 5 ICEDCGEPIPE 15 (36)
T ss_dssp B-TTTSSBEEH
T ss_pred CccccCChHHH
Confidence 39999999976
No 160
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=21.04 E-value=76 Score=23.60 Aligned_cols=32 Identities=19% Similarity=0.211 Sum_probs=26.3
Q ss_pred ccchHHHHHHHHHccCChhhHHHhcCCcchhh
Q 035172 14 IGNKWDTYLDLLQADYPEGDALDALGLVRYCC 45 (71)
Q Consensus 14 i~~~~e~y~~~v~~~~~~~~vLd~Lg~~ryCC 45 (71)
|-+..++=.++-.+|.+-+++-|+|++.|-==
T Consensus 4 IeeLi~kA~eLk~~Glt~gEIAdELNvSreTa 35 (203)
T COG0856 4 IEELIKKARELKSKGLTTGEIADELNVSRETA 35 (203)
T ss_pred HHHHHHHHHHHHHCCCcHHHhhhhhhhhHHHH
Confidence 44667777888889999999999999987643
No 161
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=20.99 E-value=18 Score=22.53 Aligned_cols=33 Identities=24% Similarity=0.597 Sum_probs=22.4
Q ss_pred ccCCCcc-ccchHHHHHHHHHccCChhhHHHhcCCc
Q 035172 7 CFTCGKV-IGNKWDTYLDLLQADYPEGDALDALGLV 41 (71)
Q Consensus 7 CfTCGkv-i~~~~e~y~~~v~~~~~~~~vLd~Lg~~ 41 (71)
|+-||.. .+..|.-|.-.+ .-+.+++-+.||++
T Consensus 21 CP~Cgs~~~te~W~G~~iIi--dpe~SeIAkrlgi~ 54 (64)
T COG2093 21 CPVCGSTDLTEEWFGLLIII--DPEKSEIAKRLGIK 54 (64)
T ss_pred CCCCCCcccchhhccEEEEE--cCcHHHHHHHhCCC
Confidence 9999988 888886665444 12234777777775
No 162
>PF01450 IlvC: Acetohydroxy acid isomeroreductase, catalytic domain; InterPro: IPR000506 Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine []. The enzyme forms a tetramer of similar but non-identical chains, and requires magnesium as a cofactor.; GO: 0004455 ketol-acid reductoisomerase activity, 0009082 branched chain family amino acid biosynthetic process, 0055114 oxidation-reduction process; PDB: 1QMG_A 1YVE_J 1NP3_C 1YRL_C 3FR8_B 3FR7_A.
Probab=20.88 E-value=47 Score=22.61 Aligned_cols=30 Identities=23% Similarity=0.234 Sum_probs=21.1
Q ss_pred ccCCCccccchHHHHHHHHHccCChhhHHH
Q 035172 7 CFTCGKVIGNKWDTYLDLLQADYPEGDALD 36 (71)
Q Consensus 7 CfTCGkvi~~~~e~y~~~v~~~~~~~~vLd 36 (71)
..=||-+.+-.=..|..++++|++|+.|.-
T Consensus 14 ~vL~Ggv~~lv~~~Fe~lve~G~~pE~Ay~ 43 (145)
T PF01450_consen 14 AVLCGGVHALVEAGFETLVEAGYSPEIAYF 43 (145)
T ss_dssp TTTTHHHHHHHHHHHHHHHHTT--HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 344677666666789999999999987765
No 163
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=20.76 E-value=40 Score=24.32 Aligned_cols=11 Identities=55% Similarity=1.422 Sum_probs=9.1
Q ss_pred cccccccCCCcc
Q 035172 2 IIPVRCFTCGKV 13 (71)
Q Consensus 2 iiPvRCfTCGkv 13 (71)
-+||+| .||+.
T Consensus 182 ~v~vkC-~cg~~ 192 (205)
T PF12322_consen 182 AVPVKC-KCGKE 192 (205)
T ss_pred EEEEee-cCCcc
Confidence 379999 99975
No 164
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=20.75 E-value=42 Score=23.52 Aligned_cols=16 Identities=25% Similarity=0.353 Sum_probs=12.5
Q ss_pred ccccccCCCccccchH
Q 035172 3 IPVRCFTCGKVIGNKW 18 (71)
Q Consensus 3 iPvRCfTCGkvi~~~~ 18 (71)
..|+|.+||++.-+.-
T Consensus 104 ~yv~C~~c~s~dt~l~ 119 (151)
T COG1601 104 EYVKCKECGSPDTELI 119 (151)
T ss_pred heeEeccCCCCchhhh
Confidence 3689999999986643
No 165
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=20.74 E-value=44 Score=18.60 Aligned_cols=10 Identities=50% Similarity=0.919 Sum_probs=5.7
Q ss_pred cccccCCCcc
Q 035172 4 PVRCFTCGKV 13 (71)
Q Consensus 4 PvRCfTCGkv 13 (71)
|-.||-|||-
T Consensus 2 ~~~CprC~kg 11 (36)
T PF14787_consen 2 PGLCPRCGKG 11 (36)
T ss_dssp --C-TTTSSS
T ss_pred CccCcccCCC
Confidence 5679999984
No 166
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.71 E-value=84 Score=21.58 Aligned_cols=37 Identities=11% Similarity=0.300 Sum_probs=28.0
Q ss_pred ccccCCCccccchHHHHHHHHHc--c--CChhhHHHhcCCc
Q 035172 5 VRCFTCGKVIGNKWDTYLDLLQA--D--YPEGDALDALGLV 41 (71)
Q Consensus 5 vRCfTCGkvi~~~~e~y~~~v~~--~--~~~~~vLd~Lg~~ 41 (71)
-.|.+|.+..-..|++=.+.|.+ + -+..+|-+++|+.
T Consensus 19 ~iCp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs 59 (137)
T TIGR03826 19 DVCPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVS 59 (137)
T ss_pred ccCHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcC
Confidence 35888888888888877777762 2 4667888988886
No 167
>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=20.69 E-value=72 Score=19.22 Aligned_cols=13 Identities=46% Similarity=1.009 Sum_probs=8.0
Q ss_pred cccccCCCccccc
Q 035172 4 PVRCFTCGKVIGN 16 (71)
Q Consensus 4 PvRCfTCGkvi~~ 16 (71)
|-.|+-||.+++.
T Consensus 24 PatCP~C~a~~~~ 36 (54)
T PF09237_consen 24 PATCPICGAVIRQ 36 (54)
T ss_dssp -EE-TTT--EESS
T ss_pred CCCCCcchhhccc
Confidence 6679999999987
No 168
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.67 E-value=46 Score=21.92 Aligned_cols=11 Identities=36% Similarity=0.863 Sum_probs=8.2
Q ss_pred cccccCCCccc
Q 035172 4 PVRCFTCGKVI 14 (71)
Q Consensus 4 PvRCfTCGkvi 14 (71)
|++|.-||..+
T Consensus 2 p~~CpYCg~~~ 12 (102)
T PF11672_consen 2 PIICPYCGGPA 12 (102)
T ss_pred CcccCCCCCee
Confidence 77888888754
No 169
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.52 E-value=85 Score=16.51 Aligned_cols=26 Identities=19% Similarity=0.318 Sum_probs=16.5
Q ss_pred HHHHHHccCChhhHHHhcCCcchhhh
Q 035172 21 YLDLLQADYPEGDALDALGLVRYCCR 46 (71)
Q Consensus 21 y~~~v~~~~~~~~vLd~Lg~~ryCCR 46 (71)
...++.+|.+..++-..||+.+--=+
T Consensus 10 ii~l~~~G~s~~~ia~~lgvs~~Tv~ 35 (50)
T PF13384_consen 10 IIRLLREGWSIREIAKRLGVSRSTVY 35 (50)
T ss_dssp HHHHHHHT--HHHHHHHHTS-HHHHH
T ss_pred HHHHHHCCCCHHHHHHHHCcCHHHHH
Confidence 34455569999999999998765433
No 170
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=20.00 E-value=43 Score=22.69 Aligned_cols=14 Identities=43% Similarity=0.811 Sum_probs=11.7
Q ss_pred ccccccCCCccccc
Q 035172 3 IPVRCFTCGKVIGN 16 (71)
Q Consensus 3 iPvRCfTCGkvi~~ 16 (71)
=+|+|-.||+.+-.
T Consensus 19 ~~v~CdnCg~~vPk 32 (108)
T COG4830 19 KYVRCDNCGKAVPK 32 (108)
T ss_pred cceeeccccccCCc
Confidence 37899999998865
Done!