Query 029824
Match_columns 187
No_of_seqs 118 out of 220
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 04:14:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029824hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05180 zf-DNL: DNL zinc fing 100.0 1.4E-38 3.1E-43 228.8 4.3 65 100-164 1-66 (66)
2 KOG3277 Uncharacterized conser 100.0 5.6E-36 1.2E-40 245.9 7.8 76 95-170 71-149 (165)
3 PF05207 zf-CSL: CSL zinc fing 93.5 0.068 1.5E-06 37.0 2.5 34 101-137 16-49 (55)
4 PRK00398 rpoP DNA-directed RNA 90.1 0.25 5.4E-06 32.3 2.1 36 101-143 1-36 (46)
5 PF13719 zinc_ribbon_5: zinc-r 89.2 0.41 8.9E-06 30.5 2.6 34 102-137 1-34 (37)
6 PF01096 TFIIS_C: Transcriptio 88.4 0.38 8.2E-06 31.1 2.0 34 104-137 1-37 (39)
7 PF13717 zinc_ribbon_4: zinc-r 88.3 0.55 1.2E-05 29.9 2.7 34 102-137 1-34 (36)
8 TIGR02098 MJ0042_CXXC MJ0042 f 87.9 0.55 1.2E-05 29.2 2.5 33 102-137 1-34 (38)
9 KOG2923 Uncharacterized conser 87.8 0.43 9.4E-06 35.2 2.2 31 103-136 22-52 (67)
10 smart00440 ZnF_C2C2 C2C2 Zinc 87.8 0.54 1.2E-05 30.6 2.5 34 104-137 1-37 (40)
11 TIGR01206 lysW lysine biosynth 87.6 0.47 1E-05 33.2 2.2 35 102-141 1-35 (54)
12 COG5216 Uncharacterized conser 86.3 0.78 1.7E-05 33.7 2.9 37 97-136 16-52 (67)
13 TIGR00416 sms DNA repair prote 81.6 1.1 2.3E-05 42.0 2.4 29 102-141 6-34 (454)
14 PRK11823 DNA repair protein Ra 78.8 1.5 3.2E-05 40.9 2.4 30 102-142 6-35 (446)
15 PF07295 DUF1451: Protein of u 77.3 1.1 2.3E-05 36.8 0.8 29 103-138 112-140 (146)
16 PRK11788 tetratricopeptide rep 76.4 2.4 5.2E-05 36.0 2.8 33 104-147 355-387 (389)
17 COG1066 Sms Predicted ATP-depe 76.0 1.6 3.6E-05 41.9 1.9 28 102-140 6-33 (456)
18 PF13453 zf-TFIIB: Transcripti 75.7 2.1 4.5E-05 27.4 1.8 27 106-137 2-28 (41)
19 PF13719 zinc_ribbon_5: zinc-r 73.4 2 4.2E-05 27.4 1.2 17 127-143 1-17 (37)
20 smart00834 CxxC_CXXC_SSSS Puta 73.2 1.8 3.8E-05 26.8 0.9 32 101-136 3-34 (41)
21 TIGR01385 TFSII transcription 72.5 3.1 6.7E-05 37.6 2.6 35 103-137 258-295 (299)
22 cd01121 Sms Sms (bacterial rad 72.4 2 4.4E-05 39.3 1.5 28 104-142 1-28 (372)
23 COG2956 Predicted N-acetylgluc 70.5 3 6.4E-05 39.4 2.1 32 103-145 354-385 (389)
24 PRK11032 hypothetical protein; 69.9 2 4.3E-05 35.9 0.8 28 103-137 124-151 (160)
25 PF13717 zinc_ribbon_4: zinc-r 68.6 2.9 6.2E-05 26.6 1.1 18 127-144 1-18 (36)
26 TIGR02605 CxxC_CxxC_SSSS putat 67.5 2.8 6.1E-05 27.5 1.0 33 101-137 3-35 (52)
27 PF03367 zf-ZPR1: ZPR1 zinc-fi 64.6 5.1 0.00011 32.9 2.2 32 97-128 24-56 (161)
28 PF09723 Zn-ribbon_8: Zinc rib 63.9 3.6 7.8E-05 26.7 0.9 32 102-137 4-35 (42)
29 PRK14892 putative transcriptio 63.8 6.8 0.00015 30.4 2.6 37 99-140 17-54 (99)
30 PF05129 Elf1: Transcription e 61.2 4.7 0.0001 29.9 1.3 41 97-140 16-58 (81)
31 KOG2703 C4-type Zn-finger prot 60.1 8.7 0.00019 37.0 3.1 36 96-131 61-96 (460)
32 smart00659 RPOLCX RNA polymera 59.7 9.1 0.0002 25.5 2.3 31 102-140 1-31 (44)
33 PF02146 SIR2: Sir2 family; I 58.3 7.1 0.00015 31.3 1.9 49 101-152 103-151 (178)
34 PRK12495 hypothetical protein; 56.2 6.3 0.00014 35.0 1.4 30 99-137 38-67 (226)
35 PRK00564 hypA hydrogenase nick 56.1 5.5 0.00012 31.0 0.9 29 101-137 69-97 (117)
36 TIGR00100 hypA hydrogenase nic 55.9 6.1 0.00013 30.6 1.2 30 100-138 67-96 (115)
37 COG1645 Uncharacterized Zn-fin 54.0 5.1 0.00011 32.8 0.5 30 99-137 24-53 (131)
38 COG0602 NrdG Organic radical a 53.1 16 0.00034 31.0 3.3 29 131-159 36-64 (212)
39 PF14354 Lar_restr_allev: Rest 53.1 14 0.0003 24.8 2.4 31 106-136 6-37 (61)
40 COG2023 RPR2 RNase P subunit R 51.4 8.5 0.00018 30.5 1.3 39 103-141 56-95 (105)
41 smart00249 PHD PHD zinc finger 50.4 13 0.00028 22.2 1.8 23 105-137 1-23 (47)
42 PF01927 Mut7-C: Mut7-C RNAse 49.8 13 0.00029 29.5 2.2 32 105-137 93-133 (147)
43 KOG2186 Cell growth-regulating 49.2 7.8 0.00017 35.3 0.9 36 101-136 1-37 (276)
44 COG4888 Uncharacterized Zn rib 48.9 19 0.00042 28.6 2.9 61 100-161 19-82 (104)
45 PRK00464 nrdR transcriptional 48.8 13 0.00027 30.8 2.0 34 105-138 2-38 (154)
46 PF04161 Arv1: Arv1-like famil 48.1 13 0.00028 31.3 2.0 32 104-136 1-32 (208)
47 PF04032 Rpr2: RNAse P Rpr2/Rp 46.3 17 0.00036 25.6 2.1 15 121-135 70-84 (85)
48 PF08996 zf-DNA_Pol: DNA Polym 45.6 9.7 0.00021 31.6 0.9 38 100-137 15-54 (188)
49 smart00653 eIF2B_5 domain pres 45.5 20 0.00042 28.1 2.5 29 105-137 82-110 (110)
50 COG0272 Lig NAD-dependent DNA 45.3 8 0.00017 38.9 0.4 72 102-184 403-486 (667)
51 KOG3134 Predicted membrane pro 45.0 10 0.00023 33.6 1.0 32 104-137 1-33 (225)
52 PRK03824 hypA hydrogenase nick 44.4 16 0.00035 29.1 1.9 12 101-112 68-79 (135)
53 TIGR00340 zpr1_rel ZPR1-relate 44.0 16 0.00035 30.4 1.9 26 97-122 22-47 (163)
54 smart00709 Zpr1 Duplicated dom 43.8 17 0.00037 30.0 2.0 32 97-128 23-55 (160)
55 PF01155 HypA: Hydrogenase exp 43.2 15 0.00033 28.2 1.5 30 100-138 67-96 (113)
56 TIGR00310 ZPR1_znf ZPR1 zinc f 42.1 19 0.0004 30.7 2.1 44 97-140 24-69 (192)
57 COG2051 RPS27A Ribosomal prote 41.3 23 0.0005 26.2 2.2 18 126-143 17-34 (67)
58 PRK03681 hypA hydrogenase nick 41.2 16 0.00034 28.3 1.4 31 100-138 67-97 (114)
59 PF08271 TF_Zn_Ribbon: TFIIB z 40.9 32 0.00069 22.0 2.6 32 104-143 1-32 (43)
60 PF05876 Terminase_GpA: Phage 39.9 22 0.00049 34.2 2.5 37 101-137 198-238 (557)
61 PRK14138 NAD-dependent deacety 39.6 15 0.00032 31.7 1.1 45 103-150 119-163 (244)
62 smart00350 MCM minichromosome 39.5 20 0.00043 33.8 2.0 36 100-138 34-71 (509)
63 PF01873 eIF-5_eIF-2B: Domain 39.4 22 0.00047 28.4 1.9 30 105-138 95-124 (125)
64 PRK03988 translation initiatio 39.3 29 0.00062 28.2 2.6 32 105-140 104-135 (138)
65 PF03604 DNA_RNApol_7kD: DNA d 38.5 17 0.00036 23.0 0.9 29 104-140 1-29 (32)
66 COG1326 Uncharacterized archae 38.4 29 0.00063 30.4 2.7 36 100-138 3-40 (201)
67 PF01667 Ribosomal_S27e: Ribos 38.1 29 0.00062 24.6 2.2 18 126-143 5-22 (55)
68 KOG4216 Steroid hormone nuclea 38.1 16 0.00034 35.4 1.1 25 103-135 46-70 (479)
69 PRK12380 hydrogenase nickel in 37.9 16 0.00035 28.3 1.0 29 100-137 67-95 (113)
70 PRK12336 translation initiatio 37.3 31 0.00068 29.2 2.7 36 104-143 99-134 (201)
71 PF11023 DUF2614: Protein of u 37.2 16 0.00035 29.5 0.9 15 127-141 68-82 (114)
72 PF00628 PHD: PHD-finger; Int 36.5 30 0.00065 22.1 1.9 23 105-137 1-23 (51)
73 COG1996 RPC10 DNA-directed RNA 36.3 41 0.00088 23.4 2.6 34 100-140 3-36 (49)
74 PF04502 DUF572: Family of unk 35.8 27 0.00059 31.4 2.2 40 100-140 35-89 (324)
75 PRK00241 nudC NADH pyrophospha 35.3 32 0.00069 30.0 2.5 26 106-138 102-127 (256)
76 PF04690 YABBY: YABBY protein; 35.3 20 0.00043 30.4 1.2 33 104-137 13-45 (170)
77 TIGR00340 zpr1_rel ZPR1-relate 34.6 35 0.00076 28.4 2.5 34 106-139 1-39 (163)
78 PRK00420 hypothetical protein; 34.6 27 0.00057 27.8 1.7 34 101-142 21-54 (112)
79 PF00096 zf-C2H2: Zinc finger, 33.6 19 0.00041 19.5 0.6 9 104-112 1-9 (23)
80 PF10058 DUF2296: Predicted in 33.6 56 0.0012 22.6 3.0 36 97-137 18-53 (54)
81 PRK00415 rps27e 30S ribosomal 33.5 37 0.00081 24.4 2.2 17 127-143 10-26 (59)
82 PF05907 DUF866: Eukaryotic pr 33.1 20 0.00043 29.5 0.9 45 96-140 57-111 (161)
83 PHA02942 putative transposase; 32.7 34 0.00074 31.6 2.4 27 104-138 326-352 (383)
84 PF03330 DPBB_1: Rare lipoprot 32.6 38 0.00082 23.8 2.1 14 126-139 43-56 (78)
85 COG0846 SIR2 NAD-dependent pro 32.1 26 0.00057 30.9 1.5 58 101-160 120-180 (250)
86 PF13894 zf-C2H2_4: C2H2-type 32.1 24 0.00052 18.4 0.8 9 104-112 1-9 (24)
87 PRK00762 hypA hydrogenase nick 31.8 27 0.00058 27.5 1.3 35 100-138 67-102 (124)
88 KOG1105 Transcription elongati 31.7 36 0.00077 31.2 2.3 37 101-137 253-292 (296)
89 PF12874 zf-met: Zinc-finger o 31.5 25 0.00055 19.4 0.9 9 104-112 1-9 (25)
90 cd01407 SIR2-fam SIR2 family o 31.4 25 0.00055 29.2 1.2 53 103-158 109-163 (218)
91 PF00935 Ribosomal_L44: Riboso 31.3 46 0.001 24.9 2.5 19 99-117 49-67 (77)
92 TIGR01384 TFS_arch transcripti 31.2 42 0.00092 24.8 2.3 35 103-137 62-99 (104)
93 TIGR00311 aIF-2beta translatio 30.6 47 0.001 26.8 2.6 33 104-140 98-130 (133)
94 PHA02998 RNA polymerase subuni 30.3 41 0.00089 29.4 2.3 36 102-137 142-180 (195)
95 cd01408 SIRT1 SIRT1: Eukaryoti 30.0 20 0.00043 30.6 0.4 45 103-150 116-160 (235)
96 PF05605 zf-Di19: Drought indu 29.9 15 0.00032 24.5 -0.3 31 103-136 2-39 (54)
97 smart00661 RPOL9 RNA polymeras 29.5 59 0.0013 20.9 2.5 14 128-141 20-33 (52)
98 PF14446 Prok-RING_1: Prokaryo 29.3 36 0.00079 24.1 1.5 25 105-138 7-31 (54)
99 PF07282 OrfB_Zn_ribbon: Putat 29.0 49 0.0011 22.6 2.1 26 105-137 30-55 (69)
100 PF05907 DUF866: Eukaryotic pr 28.9 70 0.0015 26.4 3.4 45 96-140 23-76 (161)
101 PF09332 Mcm10: Mcm10 replicat 28.1 53 0.0012 30.6 2.8 43 102-144 251-301 (344)
102 PLN02913 dihydrofolate synthet 27.7 26 0.00056 33.3 0.7 26 141-168 208-233 (510)
103 PF06943 zf-LSD1: LSD1 zinc fi 27.5 36 0.00078 20.7 1.1 17 120-136 8-24 (25)
104 COG2816 NPY1 NTP pyrophosphohy 27.1 49 0.0011 30.2 2.3 56 106-168 114-203 (279)
105 COG3364 Zn-ribbon containing p 27.1 20 0.00043 28.8 -0.1 68 103-182 2-82 (112)
106 PF09986 DUF2225: Uncharacteri 27.0 45 0.00097 28.3 2.0 40 103-142 5-62 (214)
107 PF14311 DUF4379: Domain of un 27.0 38 0.00083 22.6 1.3 36 95-134 20-55 (55)
108 COG1503 eRF1 Peptide chain rel 26.7 35 0.00076 32.6 1.4 66 97-169 321-386 (411)
109 COG1571 Predicted DNA-binding 26.6 21 0.00046 34.2 -0.0 7 106-112 353-359 (421)
110 COG4049 Uncharacterized protei 26.5 30 0.00064 25.4 0.7 42 124-165 13-63 (65)
111 TIGR01053 LSD1 zinc finger dom 26.2 49 0.0011 20.7 1.5 26 105-137 3-28 (31)
112 COG0675 Transposase and inacti 26.0 51 0.0011 27.2 2.1 21 105-137 311-331 (364)
113 COG1631 RPL42A Ribosomal prote 25.9 47 0.001 26.1 1.7 18 98-115 63-80 (94)
114 COG1655 Uncharacterized protei 25.5 44 0.00094 30.4 1.7 10 103-112 19-28 (267)
115 PF12760 Zn_Tnp_IS1595: Transp 25.2 46 0.001 21.6 1.4 27 104-136 19-45 (46)
116 KOG4846 Nuclear receptor [Sign 25.0 71 0.0015 31.4 3.1 26 102-135 131-156 (538)
117 COG5254 ARV1 Predicted membran 24.8 24 0.00052 31.5 -0.1 32 105-137 2-33 (239)
118 PRK14106 murD UDP-N-acetylmura 24.8 25 0.00054 31.5 0.1 24 141-167 187-210 (450)
119 PF13912 zf-C2H2_6: C2H2-type 24.7 39 0.00085 18.9 0.9 9 104-112 2-10 (27)
120 PF14205 Cys_rich_KTR: Cystein 24.6 56 0.0012 23.4 1.8 43 103-146 4-47 (55)
121 PTZ00083 40S ribosomal protein 24.5 63 0.0014 24.9 2.2 18 94-112 27-44 (85)
122 cd01410 SIRT7 SIRT7: Eukaryoti 24.4 54 0.0012 27.5 2.0 46 103-150 95-140 (206)
123 PRK04860 hypothetical protein; 24.3 95 0.002 25.7 3.3 40 100-141 116-156 (160)
124 COG0484 DnaJ DnaJ-class molecu 24.0 45 0.00099 31.4 1.6 31 105-136 161-191 (371)
125 PRK02935 hypothetical protein; 23.9 45 0.00097 26.8 1.3 15 126-140 68-82 (110)
126 PRK14714 DNA polymerase II lar 23.4 57 0.0012 35.5 2.3 34 103-137 667-701 (1337)
127 PHA03112 IL-18 binding protein 23.2 44 0.00095 27.7 1.2 33 123-156 37-70 (141)
128 PF13465 zf-H2C2_2: Zinc-finge 23.1 38 0.00083 19.6 0.6 9 104-112 15-23 (26)
129 PF07754 DUF1610: Domain of un 23.1 60 0.0013 19.6 1.4 16 95-111 9-24 (24)
130 PRK06260 threonine synthase; V 22.8 46 0.00099 30.2 1.3 25 102-135 2-26 (397)
131 TIGR03655 anti_R_Lar restricti 22.7 1E+02 0.0022 20.6 2.7 32 106-137 4-35 (53)
132 PRK02705 murD UDP-N-acetylmura 22.7 28 0.00062 31.3 -0.0 23 141-166 192-214 (459)
133 COG1198 PriA Primosomal protei 22.6 47 0.001 33.8 1.5 21 125-145 472-492 (730)
134 PRK00481 NAD-dependent deacety 22.6 83 0.0018 26.7 2.8 41 103-150 122-162 (242)
135 PF12898 Stc1: Stc1 domain; I 22.4 32 0.00069 25.4 0.2 36 101-137 48-84 (84)
136 PF10955 DUF2757: Protein of u 22.3 48 0.001 24.9 1.1 14 100-113 1-14 (76)
137 PRK03976 rpl37ae 50S ribosomal 22.3 80 0.0017 24.4 2.4 31 100-137 33-63 (90)
138 PLN00209 ribosomal protein S27 22.2 1.2E+02 0.0027 23.3 3.4 39 92-137 26-64 (86)
139 cd01411 SIR2H SIR2H: Uncharact 22.0 1E+02 0.0022 26.1 3.2 39 103-150 118-156 (225)
140 PF09788 Tmemb_55A: Transmembr 22.0 63 0.0014 29.3 2.0 37 100-141 154-190 (256)
141 COG3809 Uncharacterized protei 21.8 89 0.0019 24.2 2.5 42 106-161 4-45 (88)
142 TIGR01499 folC folylpolyglutam 21.7 34 0.00073 30.5 0.3 25 141-167 142-166 (397)
143 PTZ00408 NAD-dependent deacety 21.5 92 0.002 27.0 2.9 42 103-149 117-158 (242)
144 PRK14350 ligA NAD-dependent DN 21.2 34 0.00074 34.2 0.2 66 103-182 398-475 (669)
145 cd01412 SIRT5_Af1_CobB SIRT5_A 21.2 48 0.001 27.6 1.1 42 103-150 109-150 (224)
146 PF01606 Arteri_env: Arterivir 21.2 56 0.0012 28.7 1.5 25 99-126 46-71 (214)
147 TIGR00280 L37a ribosomal prote 20.8 90 0.0019 24.2 2.4 31 100-137 32-62 (91)
148 TIGR00244 transcriptional regu 20.5 74 0.0016 26.6 2.0 35 105-139 2-39 (147)
149 CHL00136 rpl31 ribosomal prote 20.4 1.7E+02 0.0037 21.3 3.6 61 94-161 6-66 (68)
150 KOG2907 RNA polymerase I trans 20.4 81 0.0018 25.6 2.2 37 101-137 72-111 (116)
151 PF09862 DUF2089: Protein of u 20.3 2.1E+02 0.0045 22.8 4.4 23 126-148 10-32 (113)
152 PF03119 DNA_ligase_ZBD: NAD-d 20.2 29 0.00062 21.1 -0.4 22 105-133 1-22 (28)
No 1
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=100.00 E-value=1.4e-38 Score=228.77 Aligned_cols=65 Identities=54% Similarity=1.056 Sum_probs=51.2
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCC-CCCHHHHHHHcCCce
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGE-PGSIEDFLAARGEEV 164 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e-~~nIEdil~~kGe~V 164 (187)
|+|+|||++|++||+|+|||+||++||||||||||+|+||||||||||+| +.||||||++|||+|
T Consensus 1 ~~l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlIaDnLg~f~e~~~~iE~~l~~kge~v 66 (66)
T PF05180_consen 1 YQLTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIADNLGWFGENKRNIEDILKEKGEKV 66 (66)
T ss_dssp EEEEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES--SS-SGGGS---HHHHHHHH----
T ss_pred CeEEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeehhhhcccccCCCCHHHHHHHcCCcC
Confidence 68999999999999999999999999999999999999999999999998 789999999999987
No 2
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.6e-36 Score=245.92 Aligned_cols=76 Identities=53% Similarity=0.995 Sum_probs=71.6
Q ss_pred CCCCceEEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCC---CCCHHHHHHHcCCceeeeccc
Q 029824 95 SARHDLAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGE---PGSIEDFLAARGEEVKKGSVD 170 (187)
Q Consensus 95 ~pR~~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e---~~nIEdil~~kGe~V~kg~~~ 170 (187)
.|+++|+|.|||++|+||+.|+|||+||++|||||||+||+|+||||||||||.| ++||||||++|||.|+++..+
T Consensus 71 ~~kp~m~l~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~HliaDnL~~F~d~~~~~nied~l~~kge~v~~~~g~ 149 (165)
T KOG3277|consen 71 VPKPRMQLAYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLIADNLGWFHDLKGKRNIEDILAAKGEQVKRNLGD 149 (165)
T ss_pred CCCcceEEEEEeeccCCccccccChhhhhCceEEEECCCCccceeehhhhcccccccccccHHHHHHhccceeeeeccc
Confidence 5788899999999999999999999999999999999999999999999999987 457999999999999997644
No 3
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=93.47 E-value=0.068 Score=36.98 Aligned_cols=34 Identities=24% Similarity=0.603 Sum_probs=29.0
Q ss_pred EEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 101 AMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 101 ~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
...|.| -||.. -.|++.-.+.|.++|+|++|.-+
T Consensus 16 ~~~y~C-RCG~~--f~i~e~~l~~~~~iv~C~sCSL~ 49 (55)
T PF05207_consen 16 VYSYPC-RCGGE--FEISEEDLEEGEVIVQCDSCSLW 49 (55)
T ss_dssp EEEEEE-TTSSE--EEEEHHHHHCT--EEEETTTTEE
T ss_pred EEEEcC-CCCCE--EEEcchhccCcCEEEECCCCccE
Confidence 578999 99998 78999999999999999999865
No 4
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.07 E-value=0.25 Score=32.34 Aligned_cols=36 Identities=17% Similarity=0.337 Sum_probs=25.8
Q ss_pred EEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeecc
Q 029824 101 AMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADH 143 (187)
Q Consensus 101 ~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADn 143 (187)
++.|.|..||.... +...+..++||.|.+.=++.|+
T Consensus 1 ~~~y~C~~CG~~~~-------~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 1 MAEYKCARCGREVE-------LDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred CCEEECCCCCCEEE-------ECCCCCceECCCCCCeEEEccC
Confidence 36899999998732 2333337899999988666654
No 5
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.24 E-value=0.41 Score=30.50 Aligned_cols=34 Identities=32% Similarity=0.634 Sum_probs=23.3
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
|..+|..|+++- .|.....-.+-..|+|+.|+..
T Consensus 1 M~i~CP~C~~~f--~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 1 MIITCPNCQTRF--RVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred CEEECCCCCceE--EcCHHHcccCCcEEECCCCCcE
Confidence 467888898773 4444444455568899999764
No 6
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=88.41 E-value=0.38 Score=31.08 Aligned_cols=34 Identities=18% Similarity=0.352 Sum_probs=24.0
Q ss_pred EecCCCCCcccccc---ChhhccCceEEEEcCCCCcc
Q 029824 104 FTCKVCETRSVKTA---CRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 104 FTC~~C~tRs~k~i---Sk~AY~~GvViVqC~gC~n~ 137 (187)
++|..|+.+.+..+ .|.|-+.-+++..|-.|..+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 46888988887777 55677777889999888754
No 7
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=88.28 E-value=0.55 Score=29.93 Aligned_cols=34 Identities=26% Similarity=0.540 Sum_probs=21.9
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
|..+|..|+++- .|.-...-.+-+-|||+.|...
T Consensus 1 M~i~Cp~C~~~y--~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 1 MIITCPNCQAKY--EIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred CEEECCCCCCEE--eCCHHHCCCCCcEEECCCCCCE
Confidence 467888888764 3444334455568888888753
No 8
>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=87.89 E-value=0.55 Score=29.24 Aligned_cols=33 Identities=27% Similarity=0.636 Sum_probs=22.6
Q ss_pred EEEecCCCCCccccccChhhc-cCceEEEEcCCCCcc
Q 029824 102 MIFTCKVCETRSVKTACRESY-EKGVVVARCGGCNNL 137 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY-~~GvViVqC~gC~n~ 137 (187)
|.++|..|++.. .|..... ..|. .|+||.|...
T Consensus 1 M~~~CP~C~~~~--~v~~~~~~~~~~-~v~C~~C~~~ 34 (38)
T TIGR02098 1 MRIQCPNCKTSF--RVVDSQLGANGG-KVRCGKCGHV 34 (38)
T ss_pred CEEECCCCCCEE--EeCHHHcCCCCC-EEECCCCCCE
Confidence 568999999874 3443333 3443 8999999864
No 9
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.84 E-value=0.43 Score=35.19 Aligned_cols=31 Identities=35% Similarity=0.681 Sum_probs=26.9
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCc
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNN 136 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n 136 (187)
.|-| .||-| -.|++.-.+.|-.+++||+|.-
T Consensus 22 ~yPC-pCGDr--f~It~edL~~ge~Va~CpsCSL 52 (67)
T KOG2923|consen 22 YYPC-PCGDR--FQITLEDLENGEDVARCPSCSL 52 (67)
T ss_pred EcCC-CCCCe--eeecHHHHhCCCeeecCCCceE
Confidence 4444 79999 7899999999999999999974
No 10
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=87.82 E-value=0.54 Score=30.56 Aligned_cols=34 Identities=24% Similarity=0.398 Sum_probs=26.1
Q ss_pred EecCCCCCcccccc---ChhhccCceEEEEcCCCCcc
Q 029824 104 FTCKVCETRSVKTA---CRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 104 FTC~~C~tRs~k~i---Sk~AY~~GvViVqC~gC~n~ 137 (187)
|.|..|+.+.+..+ .|.|-+-=+++..|..|..+
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 47889998877666 45666777899999999754
No 11
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=87.60 E-value=0.47 Score=33.22 Aligned_cols=35 Identities=20% Similarity=0.392 Sum_probs=24.4
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCCcceeee
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIA 141 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIA 141 (187)
|+|+|..|+..- .+. ..+. |- ||.||.|...+=|.
T Consensus 1 ~~~~CP~CG~~i--ev~-~~~~-Ge-iV~Cp~CGaeleVv 35 (54)
T TIGR01206 1 MQFECPDCGAEI--ELE-NPEL-GE-LVICDECGAELEVV 35 (54)
T ss_pred CccCCCCCCCEE--ecC-CCcc-CC-EEeCCCCCCEEEEE
Confidence 479999999853 232 2233 66 66999999887654
No 12
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=86.32 E-value=0.78 Score=33.67 Aligned_cols=37 Identities=32% Similarity=0.679 Sum_probs=30.0
Q ss_pred CCceEEEEecCCCCCccccccChhhccCceEEEEcCCCCc
Q 029824 97 RHDLAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNN 136 (187)
Q Consensus 97 R~~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n 136 (187)
|...+.+|.| .||-|- .||-.-...|-|+.+||+|.-
T Consensus 16 ~e~~~ftyPC-PCGDRF--eIsLeDl~~GE~VArCPSCSL 52 (67)
T COG5216 16 REEKTFTYPC-PCGDRF--EISLEDLRNGEVVARCPSCSL 52 (67)
T ss_pred CCCceEEecC-CCCCEe--EEEHHHhhCCceEEEcCCceE
Confidence 3445678888 699884 688889999999999999973
No 13
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=81.60 E-value=1.1 Score=42.03 Aligned_cols=29 Identities=28% Similarity=0.620 Sum_probs=23.3
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCCcceeee
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIA 141 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIA 141 (187)
..|.|..||..+.+- .-|||+|..|--+.
T Consensus 6 ~~y~C~~Cg~~~~~~-----------~g~Cp~C~~w~t~~ 34 (454)
T TIGR00416 6 SKFVCQHCGADSPKW-----------QGKCPACHAWNTIT 34 (454)
T ss_pred CeEECCcCCCCCccc-----------cEECcCCCCccccc
Confidence 369999999887664 47999999995554
No 14
>PRK11823 DNA repair protein RadA; Provisional
Probab=78.75 E-value=1.5 Score=40.85 Aligned_cols=30 Identities=23% Similarity=0.657 Sum_probs=24.0
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeec
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIAD 142 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIAD 142 (187)
..|.|..||..+.+- .-|||.|..|--+.-
T Consensus 6 ~~y~C~~Cg~~~~~~-----------~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 6 TAYVCQECGAESPKW-----------LGRCPECGAWNTLVE 35 (446)
T ss_pred CeEECCcCCCCCccc-----------CeeCcCCCCccceee
Confidence 369999999987664 479999999966544
No 15
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=77.30 E-value=1.1 Score=36.79 Aligned_cols=29 Identities=14% Similarity=0.440 Sum_probs=23.4
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcce
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~H 138 (187)
.|.|..||.. ..|.+-.+|..||.|....
T Consensus 112 ~l~C~~Cg~~-------~~~~~~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 112 TLVCENCGHE-------VELTHPERLPPCPKCGHTE 140 (146)
T ss_pred eEecccCCCE-------EEecCCCcCCCCCCCCCCe
Confidence 7999999987 3455567899999998753
No 16
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=76.42 E-value=2.4 Score=36.02 Aligned_cols=33 Identities=18% Similarity=0.390 Sum_probs=26.2
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCc
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWF 147 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF 147 (187)
|.|..||+.+.+.. -.||+|..+|-|-=.+|.=
T Consensus 355 ~~c~~cg~~~~~~~-----------~~c~~c~~~~~~~~~~~~~ 387 (389)
T PRK11788 355 YRCRNCGFTARTLY-----------WHCPSCKAWETIKPIRGLD 387 (389)
T ss_pred EECCCCCCCCccce-----------eECcCCCCccCcCCcccCC
Confidence 78999999876543 5799999999887666653
No 17
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=76.04 E-value=1.6 Score=41.90 Aligned_cols=28 Identities=25% Similarity=0.591 Sum_probs=23.3
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCCcceee
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLI 140 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLI 140 (187)
-.|.|+.||..+.|-+ -|||+|..|--+
T Consensus 6 t~f~C~~CG~~s~KW~-----------GkCp~Cg~Wns~ 33 (456)
T COG1066 6 TAFVCQECGYVSPKWL-----------GKCPACGAWNTL 33 (456)
T ss_pred cEEEcccCCCCCcccc-----------ccCCCCCCccce
Confidence 4799999999988864 689999998444
No 18
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=75.69 E-value=2.1 Score=27.43 Aligned_cols=27 Identities=22% Similarity=0.605 Sum_probs=19.3
Q ss_pred cCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 106 CKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 106 C~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
|..|++ ... ...+ .++.+-.|++|.-.
T Consensus 2 CP~C~~-~l~---~~~~-~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 2 CPRCGT-ELE---PVRL-GDVEIDVCPSCGGI 28 (41)
T ss_pred cCCCCc-ccc---eEEE-CCEEEEECCCCCeE
Confidence 788877 322 3333 77999999999865
No 19
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=73.37 E-value=2 Score=27.38 Aligned_cols=17 Identities=18% Similarity=0.602 Sum_probs=14.8
Q ss_pred EEEEcCCCCcceeeecc
Q 029824 127 VVARCGGCNNLHLIADH 143 (187)
Q Consensus 127 ViVqC~gC~n~HLIADn 143 (187)
.+++||.|+...-|.|.
T Consensus 1 M~i~CP~C~~~f~v~~~ 17 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDD 17 (37)
T ss_pred CEEECCCCCceEEcCHH
Confidence 37999999999999874
No 20
>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=73.22 E-value=1.8 Score=26.83 Aligned_cols=32 Identities=16% Similarity=0.309 Sum_probs=21.5
Q ss_pred EEEEecCCCCCccccccChhhccCceEEEEcCCCCc
Q 029824 101 AMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNN 136 (187)
Q Consensus 101 ~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n 136 (187)
...|.|..||+.-....+-.. --.+.||.|..
T Consensus 3 ~Y~y~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~ 34 (41)
T smart00834 3 IYEYRCEDCGHTFEVLQKISD----DPLATCPECGG 34 (41)
T ss_pred CEEEEcCCCCCEEEEEEecCC----CCCCCCCCCCC
Confidence 357999999996543332211 35678999987
No 21
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=72.46 E-value=3.1 Score=37.55 Aligned_cols=35 Identities=26% Similarity=0.554 Sum_probs=27.9
Q ss_pred EEecCCCCCcccccc---ChhhccCceEEEEcCCCCcc
Q 029824 103 IFTCKVCETRSVKTA---CRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 103 ~FTC~~C~tRs~k~i---Sk~AY~~GvViVqC~gC~n~ 137 (187)
.|+|..|+.+..-.+ .|.|=+-=++|+.|..|.++
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~ 295 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNR 295 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCe
Confidence 599999998876444 55566666999999999875
No 22
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=72.35 E-value=2 Score=39.28 Aligned_cols=28 Identities=21% Similarity=0.636 Sum_probs=22.8
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCcceeeec
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIAD 142 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIAD 142 (187)
|.|..||..+.|- .-|||+|..|--+.-
T Consensus 1 ~~c~~cg~~~~~~-----------~g~cp~c~~w~~~~e 28 (372)
T cd01121 1 YVCSECGYVSPKW-----------LGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCCc-----------cEECcCCCCceeeee
Confidence 7899999887664 579999999976653
No 23
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=70.47 E-value=3 Score=39.40 Aligned_cols=32 Identities=19% Similarity=0.456 Sum_probs=24.8
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeecccc
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLG 145 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLg 145 (187)
.|+|..||.++. +..-+||+|+.|--|.=+.|
T Consensus 354 ~YRC~~CGF~a~-----------~l~W~CPsC~~W~TikPir~ 385 (389)
T COG2956 354 RYRCQNCGFTAH-----------TLYWHCPSCRAWETIKPIRG 385 (389)
T ss_pred CceecccCCcce-----------eeeeeCCCcccccccCCccc
Confidence 699999997743 45789999999977765544
No 24
>PRK11032 hypothetical protein; Provisional
Probab=69.91 E-value=2 Score=35.88 Aligned_cols=28 Identities=18% Similarity=0.488 Sum_probs=24.0
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
++.|..||+. ..|.+-.+|..||+|...
T Consensus 124 ~LvC~~Cg~~-------~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 124 NLVCEKCHHH-------LAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred eEEecCCCCE-------EEecCCCcCCCCCCCCCC
Confidence 6899999997 367788899999999875
No 25
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=68.55 E-value=2.9 Score=26.63 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=15.5
Q ss_pred EEEEcCCCCcceeeeccc
Q 029824 127 VVARCGGCNNLHLIADHL 144 (187)
Q Consensus 127 ViVqC~gC~n~HLIADnL 144 (187)
.+|+||.|+...-|.|..
T Consensus 1 M~i~Cp~C~~~y~i~d~~ 18 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEK 18 (36)
T ss_pred CEEECCCCCCEEeCCHHH
Confidence 378999999999999863
No 26
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=67.51 E-value=2.8 Score=27.48 Aligned_cols=33 Identities=18% Similarity=0.347 Sum_probs=21.2
Q ss_pred EEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 101 AMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 101 ~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
...|.|+.|+++-....+-.. --.+.||.|...
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~~ 35 (52)
T TIGR02605 3 IYEYRCTACGHRFEVLQKMSD----DPLATCPECGGE 35 (52)
T ss_pred CEEEEeCCCCCEeEEEEecCC----CCCCCCCCCCCC
Confidence 357999999986544322111 234679999974
No 27
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=64.62 E-value=5.1 Score=32.92 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=21.8
Q ss_pred CCceEEEEecCCCCCccccccChhhc-cCceEE
Q 029824 97 RHDLAMIFTCKVCETRSVKTACRESY-EKGVVV 128 (187)
Q Consensus 97 R~~l~l~FTC~~C~tRs~k~iSk~AY-~~GvVi 128 (187)
+.-+.|.|.|..||.|+....+-.++ .+|+.+
T Consensus 24 ~evii~sf~C~~CGyk~~ev~~~~~~~~~G~r~ 56 (161)
T PF03367_consen 24 KEVIIMSFECEHCGYKNNEVKSGGQIQPKGVRI 56 (161)
T ss_dssp EEEEEEEEE-TTT--EEEEEEEECSS-SSEEEE
T ss_pred ceEEEEEeECCCCCCEeeeEEECccCCCCceEE
Confidence 45688999999999999888777777 455544
No 28
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry 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=63.92 E-value=3.6 Score=26.71 Aligned_cols=32 Identities=13% Similarity=0.272 Sum_probs=22.9
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
..|.|..||+.-....+-.. --.+.||.|...
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISE----DDPVPCPECGST 35 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCC----CCCCcCCCCCCC
Confidence 47999999987655554333 445789999873
No 29
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=63.83 E-value=6.8 Score=30.42 Aligned_cols=37 Identities=24% Similarity=0.593 Sum_probs=25.8
Q ss_pred ceEEEEecCCCCCccc-cccChhhccCceEEEEcCCCCcceee
Q 029824 99 DLAMIFTCKVCETRSV-KTACRESYEKGVVVARCGGCNNLHLI 140 (187)
Q Consensus 99 ~l~l~FTC~~C~tRs~-k~iSk~AY~~GvViVqC~gC~n~HLI 140 (187)
.+-=.|+|..|+..+. -.+.| |+..+.|+.|....--
T Consensus 17 klpt~f~CP~Cge~~v~v~~~k-----~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 17 KLPKIFECPRCGKVSISVKIKK-----NIAIITCGNCGLYTEF 54 (99)
T ss_pred CCCcEeECCCCCCeEeeeecCC-----CcceEECCCCCCccCE
Confidence 3445899999995322 12333 8999999999887433
No 30
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=61.17 E-value=4.7 Score=29.90 Aligned_cols=41 Identities=17% Similarity=0.496 Sum_probs=20.5
Q ss_pred CCceEEEEecCCCCCccc--cccChhhccCceEEEEcCCCCcceee
Q 029824 97 RHDLAMIFTCKVCETRSV--KTACRESYEKGVVVARCGGCNNLHLI 140 (187)
Q Consensus 97 R~~l~l~FTC~~C~tRs~--k~iSk~AY~~GvViVqC~gC~n~HLI 140 (187)
+..+.-.|+|-.|++..+ -.|.|. .|+-.+.|.-|...+-.
T Consensus 16 ~~~l~~~F~CPfC~~~~sV~v~idkk---~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 16 KPKLPKVFDCPFCNHEKSVSVKIDKK---EGIGILSCRVCGESFQT 58 (81)
T ss_dssp ----SS----TTT--SS-EEEEEETT---TTEEEEEESSS--EEEE
T ss_pred CCCCCceEcCCcCCCCCeEEEEEEcc---CCEEEEEecCCCCeEEE
Confidence 345667999999995542 234444 89999999999876654
No 31
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=60.10 E-value=8.7 Score=37.04 Aligned_cols=36 Identities=22% Similarity=0.369 Sum_probs=31.6
Q ss_pred CCCceEEEEecCCCCCccccccChhhccCceEEEEc
Q 029824 96 ARHDLAMIFTCKVCETRSVKTACRESYEKGVVVARC 131 (187)
Q Consensus 96 pR~~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC 131 (187)
=|.-+.|.|-|.+||.+|...+++..-..|-|-+.|
T Consensus 61 fREvVimSF~CpHCG~kN~eiQ~a~~iQ~~Gvri~l 96 (460)
T KOG2703|consen 61 FREVVIMSFECPHCGHKNNEIQSAEEIQEGGVRIEL 96 (460)
T ss_pred hheeeeEEeecCccCCccccccchhccccCceEEEE
Confidence 377799999999999999999999998888776655
No 32
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=59.71 E-value=9.1 Score=25.53 Aligned_cols=31 Identities=32% Similarity=0.613 Sum_probs=21.8
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCCcceee
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLI 140 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLI 140 (187)
|.|.|..||....-. .. =-|+||.|..+=|.
T Consensus 1 ~~Y~C~~Cg~~~~~~------~~--~~irC~~CG~rIly 31 (44)
T smart00659 1 MIYICGECGRENEIK------SK--DVVRCRECGYRILY 31 (44)
T ss_pred CEEECCCCCCEeecC------CC--CceECCCCCceEEE
Confidence 579999999975432 11 23899999987553
No 33
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=58.32 E-value=7.1 Score=31.29 Aligned_cols=49 Identities=20% Similarity=0.425 Sum_probs=30.2
Q ss_pred EEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCCCC
Q 029824 101 AMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEPGS 152 (187)
Q Consensus 101 ~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~~n 152 (187)
+-.+.|..|+......--...+..+.+ .+|+.|.. +|-++.=||+|.-.
T Consensus 103 l~~~~C~~C~~~~~~~~~~~~~~~~~~-~~C~~C~~--~lrp~vv~fgE~~~ 151 (178)
T PF02146_consen 103 LFRLRCSKCGKEYDREDIVDSIDEEEP-PRCPKCGG--LLRPDVVLFGESLP 151 (178)
T ss_dssp EEEEEETTTSBEEEGHHHHHHHHTTSS-CBCTTTSC--BEEEEE--BTSB-S
T ss_pred hceeeecCCCccccchhhccccccccc-ccccccCc--cCCCCeeecCCCCH
Confidence 446799999987543322222222222 19999998 69999999999544
No 34
>PRK12495 hypothetical protein; Provisional
Probab=56.15 E-value=6.3 Score=34.96 Aligned_cols=30 Identities=17% Similarity=0.306 Sum_probs=23.8
Q ss_pred ceEEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 99 DLAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 99 ~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
.-++.|.|.+||..-. +| .|+| .|+.|+..
T Consensus 38 atmsa~hC~~CG~PIp------a~-pG~~--~Cp~CQ~~ 67 (226)
T PRK12495 38 ATMTNAHCDECGDPIF------RH-DGQE--FCPTCQQP 67 (226)
T ss_pred cccchhhcccccCccc------CC-CCee--ECCCCCCc
Confidence 3578899999999955 56 7876 59999943
No 35
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.12 E-value=5.5 Score=31.01 Aligned_cols=29 Identities=17% Similarity=0.383 Sum_probs=19.5
Q ss_pred EEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 101 AMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 101 ~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
-+.+.|+.|+.. ++...| .+.+||.|...
T Consensus 69 p~~~~C~~Cg~~----~~~~~~----~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHV----FKPNAL----DYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCc----cccCCc----cCCcCcCCCCC
Confidence 458999999944 333222 23579999976
No 36
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=55.86 E-value=6.1 Score=30.60 Aligned_cols=30 Identities=20% Similarity=0.482 Sum_probs=20.2
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcce
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~H 138 (187)
.-+.+.|+.|+.. ++...| ...||.|....
T Consensus 67 ~p~~~~C~~Cg~~----~~~~~~-----~~~CP~Cgs~~ 96 (115)
T TIGR00100 67 EPVECECEDCSEE----VSPEID-----LYRCPKCHGIM 96 (115)
T ss_pred eCcEEEcccCCCE----EecCCc-----CccCcCCcCCC
Confidence 3457999999954 333222 46799999863
No 37
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=54.01 E-value=5.1 Score=32.79 Aligned_cols=30 Identities=23% Similarity=0.471 Sum_probs=23.6
Q ss_pred ceEEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 99 DLAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 99 ~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
--++..+|..||+.=++ ..|.|+ ||-|..+
T Consensus 24 AkML~~hCp~Cg~PLF~-------KdG~v~--CPvC~~~ 53 (131)
T COG1645 24 AKMLAKHCPKCGTPLFR-------KDGEVF--CPVCGYR 53 (131)
T ss_pred hHHHHhhCcccCCccee-------eCCeEE--CCCCCce
Confidence 35788999999999443 578775 9999964
No 38
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=53.08 E-value=16 Score=30.99 Aligned_cols=29 Identities=31% Similarity=0.501 Sum_probs=17.1
Q ss_pred cCCCCcceeeeccccCcCCCCCHHHHHHH
Q 029824 131 CGGCNNLHLIADHLGWFGEPGSIEDFLAA 159 (187)
Q Consensus 131 C~gC~n~HLIADnLgwF~e~~nIEdil~~ 159 (187)
|++|.+.|-...+-+-=...-++++|++.
T Consensus 36 C~~Cdt~~t~~~~~~~~~~~~~~~~I~~~ 64 (212)
T COG0602 36 CPGCDTKYTWDFNYGKPGTPMSADEILAD 64 (212)
T ss_pred CCCCCChhhhcccccCCCCccCHHHHHHH
Confidence 88999887655443222234566666543
No 39
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=53.07 E-value=14 Score=24.82 Aligned_cols=31 Identities=23% Similarity=0.633 Sum_probs=21.8
Q ss_pred cCCCCCccccccChhhccCce-EEEEcCCCCc
Q 029824 106 CKVCETRSVKTACRESYEKGV-VVARCGGCNN 136 (187)
Q Consensus 106 C~~C~tRs~k~iSk~AY~~Gv-ViVqC~gC~n 136 (187)
|..||..............|. +.|.|..|..
T Consensus 6 CPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 6 CPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 888977665555544444443 8899999988
No 40
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=51.43 E-value=8.5 Score=30.53 Aligned_cols=39 Identities=31% Similarity=0.451 Sum_probs=22.9
Q ss_pred EEecCCCCCccccccC-hhhccCceEEEEcCCCCcceeee
Q 029824 103 IFTCKVCETRSVKTAC-RESYEKGVVVARCGGCNNLHLIA 141 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iS-k~AY~~GvViVqC~gC~n~HLIA 141 (187)
..+|+.|.+-=..-.+ +.-..+|.|+|+|.+|.-..=+.
T Consensus 56 R~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 56 RTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYP 95 (105)
T ss_pred HHhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEec
Confidence 3579999983111110 12234455999999998665443
No 41
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the 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=49.80 E-value=13 Score=29.45 Aligned_cols=32 Identities=28% Similarity=0.641 Sum_probs=22.5
Q ss_pred ecCCCCCccccccChh---------hccCceEEEEcCCCCcc
Q 029824 105 TCKVCETRSVKTACRE---------SYEKGVVVARCGGCNNL 137 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~---------AY~~GvViVqC~gC~n~ 137 (187)
-|-.|+.+- ..++|. .|...-.+-+|++|...
T Consensus 93 RC~~CN~~L-~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 93 RCPKCNGPL-RPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred ccCCCCcEe-eechhhccccccCccccccCCeEEECCCCCCE
Confidence 399999853 334554 45555669999999864
No 43
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=49.21 E-value=7.8 Score=35.27 Aligned_cols=36 Identities=19% Similarity=0.388 Sum_probs=20.7
Q ss_pred EEEEecCCCCCccc-cccChhhccCceEEEEcCCCCc
Q 029824 101 AMIFTCKVCETRSV-KTACRESYEKGVVVARCGGCNN 136 (187)
Q Consensus 101 ~l~FTC~~C~tRs~-k~iSk~AY~~GvViVqC~gC~n 136 (187)
|+.|||++||.--. ..+-||.|-=----..|-.|.+
T Consensus 1 MV~FtCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k 37 (276)
T KOG2186|consen 1 MVFFTCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGK 37 (276)
T ss_pred CeEEehhhhhhhccccchHHHHHhccCCeeEEeeccc
Confidence 57899999997543 3455555421113345555544
No 44
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=48.92 E-value=19 Score=28.61 Aligned_cols=61 Identities=21% Similarity=0.301 Sum_probs=40.9
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCC---CCCHHHHHHHcC
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGE---PGSIEDFLAARG 161 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e---~~nIEdil~~kG 161 (187)
|-=.|||-.|++-+.-.-+ .--..++=.+.|..|...|-.-=+-+|-.- .--|...++-+|
T Consensus 19 L~k~FtCp~Cghe~vs~ct-vkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvDay~eg~~ 82 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCT-VKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWVDAYLEGRG 82 (104)
T ss_pred CCceEecCccCCeeeeEEE-EEecCceeEEEcccCcceEEEeccccccchhHHHHHHHHHHhccc
Confidence 6679999999987533111 112334556789999999988777777542 345666777666
No 45
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=48.76 E-value=13 Score=30.78 Aligned_cols=34 Identities=18% Similarity=0.466 Sum_probs=27.2
Q ss_pred ecCCCCCccccccChhhccCceEE---EEcCCCCcce
Q 029824 105 TCKVCETRSVKTACRESYEKGVVV---ARCGGCNNLH 138 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvVi---VqC~gC~n~H 138 (187)
.|..|++.-++-++-..+..|-++ -||+.|.-..
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 589999988888888888888444 6899998764
No 46
>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=48.13 E-value=13 Score=31.29 Aligned_cols=32 Identities=16% Similarity=0.404 Sum_probs=23.6
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCc
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNN 136 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n 136 (187)
|-|-.||.+....+.+-+ ...+-+.+|+.|+.
T Consensus 1 miCIeCg~~v~~Ly~~Ys-~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYS-PGNIRLTKCPNCGK 32 (208)
T ss_pred CEeccCCCcchhhhhccC-CCcEEEeeccccCC
Confidence 469999999655555432 34589999999985
No 47
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=46.35 E-value=17 Score=25.61 Aligned_cols=15 Identities=27% Similarity=0.558 Sum_probs=8.3
Q ss_pred hccCceEEEEcCCCC
Q 029824 121 SYEKGVVVARCGGCN 135 (187)
Q Consensus 121 AY~~GvViVqC~gC~ 135 (187)
.-..+.|+++|-.|.
T Consensus 70 ~~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 70 KKKKNFLVYTCLNCG 84 (85)
T ss_dssp -SSS-EEEEEETTTT
T ss_pred CCCCCEEEEEccccC
Confidence 444566777776664
No 48
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=45.59 E-value=9.7 Score=31.56 Aligned_cols=38 Identities=16% Similarity=0.337 Sum_probs=19.5
Q ss_pred eEEEEecCCCCCcc-ccccCh-hhccCceEEEEcCCCCcc
Q 029824 100 LAMIFTCKVCETRS-VKTACR-ESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 100 l~l~FTC~~C~tRs-~k~iSk-~AY~~GvViVqC~gC~n~ 137 (187)
--+.|+|..|++.. ...+.+ .+...-....+|+.|...
T Consensus 15 ~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~ 54 (188)
T PF08996_consen 15 EPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTP 54 (188)
T ss_dssp --EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B
T ss_pred CceEeECCCCCCCccccccccCCccccccCcCcCCCCCCc
Confidence 45799999999986 333333 333333447899999983
No 49
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=45.47 E-value=20 Score=28.09 Aligned_cols=29 Identities=14% Similarity=0.462 Sum_probs=24.2
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
.|..|+...++.+-. .++.+.+|..|.++
T Consensus 82 lC~~C~spdT~l~k~----~r~~~l~C~aCGa~ 110 (110)
T smart00653 82 LCPECGSPDTELIKE----NRLFFLKCEACGAR 110 (110)
T ss_pred ECCCCCCCCcEEEEe----CCeEEEEccccCCC
Confidence 699999998877654 78999999999763
No 50
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=45.25 E-value=8 Score=38.92 Aligned_cols=72 Identities=33% Similarity=0.486 Sum_probs=47.7
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCC---CCcceeeeccccCcCCC---------CCHHHHHHHcCCceeeecc
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGG---CNNLHLIADHLGWFGEP---------GSIEDFLAARGEEVKKGSV 169 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~g---C~n~HLIADnLgwF~e~---------~nIEdil~~kGe~V~kg~~ 169 (187)
+--.|..|++.-.+ ..|-|.++|++ |... +.-.|-||-.+ .-+.+.|-++| ..+.-.
T Consensus 403 ~P~~CP~C~s~l~r-------~~~e~~~rC~n~~~C~aq--~~e~l~hfvSr~AmdI~GLG~k~i~~L~e~~--lI~~~~ 471 (667)
T COG0272 403 FPTHCPVCGSELVR-------EEGEVVIRCTNGLNCPAQ--LKERLIHFVSRNALDIDGLGEKIIEQLFEKG--LIKDIA 471 (667)
T ss_pred CCCCCCCCCCeeEe-------ccCceeEecCCCCCChHH--HhhheeeEecCCccCCCCcCHHHHHHHHHcC--ccCCHH
Confidence 44569999987554 67888999998 8764 34466777542 12333344444 444456
Q ss_pred cccCcccccccCccc
Q 029824 170 DTLNLTLEDLAGREV 184 (187)
Q Consensus 170 ~~~~lt~eDl~g~~~ 184 (187)
|=+.|+.|||..-+-
T Consensus 472 Dly~Lt~~~l~~l~~ 486 (667)
T COG0272 472 DLYTLTEEDLLSLEG 486 (667)
T ss_pred HHHhCCHHHHhhccc
Confidence 777899999876553
No 51
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=45.00 E-value=10 Score=33.60 Aligned_cols=32 Identities=19% Similarity=0.685 Sum_probs=26.5
Q ss_pred EecCCCCCccccccChhhccCc-eEEEEcCCCCcc
Q 029824 104 FTCKVCETRSVKTACRESYEKG-VVVARCGGCNNL 137 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~G-vViVqC~gC~n~ 137 (187)
|+|-.||.+-...+.+ |-+| +=+.+||+|+..
T Consensus 1 ~~CVeCg~~vksLy~~--Ys~g~irlt~C~nC~e~ 33 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQ--YSPGNIRLTKCPNCQEV 33 (225)
T ss_pred CcccccCchHHHHHHh--cCCCcEEEeeCCchhhH
Confidence 5799999998777765 7788 778999999863
No 52
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.45 E-value=16 Score=29.08 Aligned_cols=12 Identities=17% Similarity=0.780 Sum_probs=9.5
Q ss_pred EEEEecCCCCCc
Q 029824 101 AMIFTCKVCETR 112 (187)
Q Consensus 101 ~l~FTC~~C~tR 112 (187)
-..+.|..||..
T Consensus 68 p~~~~C~~CG~~ 79 (135)
T PRK03824 68 EAVLKCRNCGNE 79 (135)
T ss_pred ceEEECCCCCCE
Confidence 357999999954
No 53
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=43.99 E-value=16 Score=30.41 Aligned_cols=26 Identities=19% Similarity=0.284 Sum_probs=20.1
Q ss_pred CCceEEEEecCCCCCccccccChhhc
Q 029824 97 RHDLAMIFTCKVCETRSVKTACRESY 122 (187)
Q Consensus 97 R~~l~l~FTC~~C~tRs~k~iSk~AY 122 (187)
|.-+.|.|.|..||.|+....+=.++
T Consensus 22 ~evii~sf~C~~CGyr~~ev~~~~~~ 47 (163)
T TIGR00340 22 GKIMLSTYICEKCGYRSTDVYQLEEK 47 (163)
T ss_pred ceEEEEEEECCCCCCchhheeEcCCc
Confidence 55688999999999998766554444
No 54
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=43.80 E-value=17 Score=30.03 Aligned_cols=32 Identities=25% Similarity=0.463 Sum_probs=22.0
Q ss_pred CCceEEEEecCCCCCccccccChhh-ccCceEE
Q 029824 97 RHDLAMIFTCKVCETRSVKTACRES-YEKGVVV 128 (187)
Q Consensus 97 R~~l~l~FTC~~C~tRs~k~iSk~A-Y~~GvVi 128 (187)
|.=+.|.|.|..||.|+....+=.+ =.+|+.+
T Consensus 23 ~evii~sf~C~~CGyk~~ev~~~~~~~p~G~r~ 55 (160)
T smart00709 23 REVIIMSFECEHCGYRNNEVKSGGAIEPKGTRI 55 (160)
T ss_pred ceEEEEEEECCCCCCccceEEECcccCCCceEE
Confidence 5568889999999999876644333 3345444
No 55
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=43.19 E-value=15 Score=28.23 Aligned_cols=30 Identities=13% Similarity=0.456 Sum_probs=16.8
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcce
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~H 138 (187)
.-+.+.|+.|+.... ...|. ..||.|....
T Consensus 67 ~p~~~~C~~Cg~~~~----~~~~~-----~~CP~Cgs~~ 96 (113)
T PF01155_consen 67 VPARARCRDCGHEFE----PDEFD-----FSCPRCGSPD 96 (113)
T ss_dssp E--EEEETTTS-EEE----CHHCC-----HH-SSSSSS-
T ss_pred cCCcEECCCCCCEEe----cCCCC-----CCCcCCcCCC
Confidence 456899999998642 22222 2399999875
No 56
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=42.07 E-value=19 Score=30.71 Aligned_cols=44 Identities=16% Similarity=0.130 Sum_probs=26.0
Q ss_pred CCceEEEEecCCCCCccccccChhhcc--CceEEEEcCCCCcceee
Q 029824 97 RHDLAMIFTCKVCETRSVKTACRESYE--KGVVVARCGGCNNLHLI 140 (187)
Q Consensus 97 R~~l~l~FTC~~C~tRs~k~iSk~AY~--~GvViVqC~gC~n~HLI 140 (187)
+.-+.|.|.|..||.|+....+=.+.. +=++-|+.+.=-++-+|
T Consensus 24 ~evii~sf~C~~CGyr~~ev~~~g~~~p~r~~l~V~~~~DL~r~Vv 69 (192)
T TIGR00310 24 GEVLETSTICEHCGYRSNDVKTLGAKEPKRYILKIDDEADLNRRVV 69 (192)
T ss_pred ceEEEEEEECCCCCCccceeEECCCCCCEEEEEEECChhcccceEE
Confidence 556889999999999986554322222 33444444443444333
No 57
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=41.31 E-value=23 Score=26.20 Aligned_cols=18 Identities=22% Similarity=0.665 Sum_probs=9.9
Q ss_pred eEEEEcCCCCcceeeecc
Q 029824 126 VVVARCGGCNNLHLIADH 143 (187)
Q Consensus 126 vViVqC~gC~n~HLIADn 143 (187)
-+-|+||+|.|.-.+=+|
T Consensus 17 Fl~VkCpdC~N~q~vFsh 34 (67)
T COG2051 17 FLRVKCPDCGNEQVVFSH 34 (67)
T ss_pred EEEEECCCCCCEEEEecc
Confidence 455666666665555333
No 58
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=41.23 E-value=16 Score=28.33 Aligned_cols=31 Identities=19% Similarity=0.339 Sum_probs=19.7
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcce
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~H 138 (187)
.-+.+.|+.|+.. |....+ -+.+||.|....
T Consensus 67 ~p~~~~C~~Cg~~----~~~~~~----~~~~CP~Cgs~~ 97 (114)
T PRK03681 67 QEAECWCETCQQY----VTLLTQ----RVRRCPQCHGDM 97 (114)
T ss_pred eCcEEEcccCCCe----eecCCc----cCCcCcCcCCCC
Confidence 3458999999952 222211 125799999764
No 59
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=40.92 E-value=32 Score=22.04 Aligned_cols=32 Identities=19% Similarity=0.621 Sum_probs=19.1
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCcceeeecc
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADH 143 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADn 143 (187)
|+|..|+.+.. .+. +.+|-+ -|+.|. .+|.|+
T Consensus 1 m~Cp~Cg~~~~-~~D---~~~g~~--vC~~CG--~Vl~e~ 32 (43)
T PF08271_consen 1 MKCPNCGSKEI-VFD---PERGEL--VCPNCG--LVLEEN 32 (43)
T ss_dssp ESBTTTSSSEE-EEE---TTTTEE--EETTT---BBEE-T
T ss_pred CCCcCCcCCce-EEc---CCCCeE--ECCCCC--CEeecc
Confidence 68999998752 112 566765 688885 334444
No 60
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=39.89 E-value=22 Score=34.24 Aligned_cols=37 Identities=19% Similarity=0.337 Sum_probs=30.8
Q ss_pred EEEEecCCCCCccccccChhhccCc----eEEEEcCCCCcc
Q 029824 101 AMIFTCKVCETRSVKTACRESYEKG----VVVARCGGCNNL 137 (187)
Q Consensus 101 ~l~FTC~~C~tRs~k~iSk~AY~~G----vViVqC~gC~n~ 137 (187)
...-.|..|++...-.+...-|.+| .|..+|+.|.-.
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~ 238 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCE 238 (557)
T ss_pred EEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCC
Confidence 4456799999999888888888866 899999999754
No 61
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=39.65 E-value=15 Score=31.67 Aligned_cols=45 Identities=33% Similarity=0.643 Sum_probs=29.2
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCC
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEP 150 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~ 150 (187)
...|..|+.+-...--...+..+. +-+||.|.. ++-.+.=||+|.
T Consensus 119 ~~~C~~C~~~~~~~~~~~~~~~~~-~p~Cp~Cgg--~lrP~Vv~FgE~ 163 (244)
T PRK14138 119 EYYCVRCGKRYTVEDVIEKLEKSD-VPRCDDCSG--LIRPNIVFFGEA 163 (244)
T ss_pred eeEECCCCCcccHHHHHHHHhcCC-CCCCCCCCC--eECCCEEECCCc
Confidence 456999997643211111222332 478999975 689999999994
No 62
>smart00350 MCM minichromosome maintenance proteins.
Probab=39.46 E-value=20 Score=33.85 Aligned_cols=36 Identities=17% Similarity=0.250 Sum_probs=25.2
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCC--CCcce
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGG--CNNLH 138 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~g--C~n~H 138 (187)
..+.|.|..|++.....+..-.|. .-..|++ |.+.+
T Consensus 34 ~~~~f~C~~C~~~~~~~~~~~~~~---~p~~C~~~~C~~~~ 71 (509)
T smart00350 34 KRASFTCEKCGATLGPEIQSGRET---EPTVCPPRECQSPT 71 (509)
T ss_pred EEEEEEecCCCCEEeEEecCCccc---CCCcCCCCcCCCCC
Confidence 468999999999865555433332 3467999 99864
No 63
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=39.40 E-value=22 Score=28.37 Aligned_cols=30 Identities=13% Similarity=0.463 Sum_probs=25.3
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCcce
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~H 138 (187)
.|..|+...+..+-+ .++.+.+|..|...+
T Consensus 95 lC~~C~spdT~l~k~----~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 95 LCPECGSPDTELIKE----GRLIFLKCKACGASR 124 (125)
T ss_dssp SCTSTSSSSEEEEEE----TTCCEEEETTTSCEE
T ss_pred EcCCCCCCccEEEEc----CCEEEEEecccCCcC
Confidence 599999988777655 899999999998764
No 64
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=39.32 E-value=29 Score=28.24 Aligned_cols=32 Identities=22% Similarity=0.479 Sum_probs=26.7
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCcceee
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLI 140 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLI 140 (187)
.|..|+...++.+- +..+.+.+|..|.+..-+
T Consensus 104 lC~~C~spdT~l~k----~~r~~~l~C~ACGa~~~V 135 (138)
T PRK03988 104 ICPECGSPDTKLIK----EGRIWVLKCEACGAETPV 135 (138)
T ss_pred ECCCCCCCCcEEEE----cCCeEEEEcccCCCCCcC
Confidence 69999999988874 377999999999987654
No 65
>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=38.47 E-value=17 Score=23.01 Aligned_cols=29 Identities=21% Similarity=0.424 Sum_probs=17.4
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCcceee
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLI 140 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLI 140 (187)
|.|..|+.... +.. . .. |+|+.|..+.|.
T Consensus 1 Y~C~~Cg~~~~--~~~--~-~~---irC~~CG~RIly 29 (32)
T PF03604_consen 1 YICGECGAEVE--LKP--G-DP---IRCPECGHRILY 29 (32)
T ss_dssp EBESSSSSSE---BST--S-ST---SSBSSSS-SEEB
T ss_pred CCCCcCCCeeE--cCC--C-Cc---EECCcCCCeEEE
Confidence 67888888765 221 1 11 589999887664
No 66
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=38.42 E-value=29 Score=30.41 Aligned_cols=36 Identities=22% Similarity=0.587 Sum_probs=26.3
Q ss_pred eEEEEecCCCCCc-cccccChh-hccCceEEEEcCCCCcce
Q 029824 100 LAMIFTCKVCETR-SVKTACRE-SYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 100 l~l~FTC~~C~tR-s~k~iSk~-AY~~GvViVqC~gC~n~H 138 (187)
..+.+-|.-|+.- ..|.+=|. .++ ++++|..|..-|
T Consensus 3 ~~iy~~Cp~Cg~eev~hEVik~~g~~---~lvrC~eCG~V~ 40 (201)
T COG1326 3 EEIYIECPSCGSEEVSHEVIKERGRE---PLVRCEECGTVH 40 (201)
T ss_pred ceEEEECCCCCcchhhHHHHHhcCCc---eEEEccCCCcEe
Confidence 3577889999933 34445554 555 999999999887
No 67
>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=38.13 E-value=29 Score=24.57 Aligned_cols=18 Identities=28% Similarity=0.778 Sum_probs=11.6
Q ss_pred eEEEEcCCCCcceeeecc
Q 029824 126 VVVARCGGCNNLHLIADH 143 (187)
Q Consensus 126 vViVqC~gC~n~HLIADn 143 (187)
-+-|+||+|.|.-.|=+|
T Consensus 5 Fm~VkCp~C~~~q~vFSh 22 (55)
T PF01667_consen 5 FMDVKCPGCYNIQTVFSH 22 (55)
T ss_dssp EEEEE-TTT-SEEEEETT
T ss_pred EEEEECCCCCCeeEEEec
Confidence 356889999888777554
No 68
>KOG4216 consensus Steroid hormone nuclear receptor [Transcription]
Probab=38.07 E-value=16 Score=35.38 Aligned_cols=25 Identities=40% Similarity=0.987 Sum_probs=19.0
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCC
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCN 135 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~ 135 (187)
+--||+||-.|. ..|-|| |+|.||+
T Consensus 46 vIPCKiCGDKSS------GiHYGV--ITCEGCK 70 (479)
T KOG4216|consen 46 IIPCKICGDKSS------GIHYGV--ITCEGCK 70 (479)
T ss_pred EEeeeeccCCCC------cceeee--Eeeccch
Confidence 457999998864 456665 6899997
No 69
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=37.91 E-value=16 Score=28.28 Aligned_cols=29 Identities=17% Similarity=0.205 Sum_probs=18.7
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
.-+.+.|+.|+.. +.... ....||.|...
T Consensus 67 vp~~~~C~~Cg~~----~~~~~-----~~~~CP~Cgs~ 95 (113)
T PRK12380 67 KPAQAWCWDCSQV----VEIHQ-----HDAQCPHCHGE 95 (113)
T ss_pred eCcEEEcccCCCE----EecCC-----cCccCcCCCCC
Confidence 3458999999944 22221 22359999965
No 70
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=37.30 E-value=31 Score=29.21 Aligned_cols=36 Identities=17% Similarity=0.473 Sum_probs=29.7
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCcceeeecc
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADH 143 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADn 143 (187)
=.|..|+..-++.+-. .++.+.+|..|.+..-|.=+
T Consensus 99 V~C~~C~~pdT~l~k~----~~~~~l~C~aCGa~~~v~~~ 134 (201)
T PRK12336 99 VICSECGLPDTRLVKE----DRVLMLRCDACGAHRPVKKR 134 (201)
T ss_pred EECCCCCCCCcEEEEc----CCeEEEEcccCCCCcccccc
Confidence 3699999998888743 58999999999999888644
No 71
>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=37.23 E-value=16 Score=29.46 Aligned_cols=15 Identities=20% Similarity=0.505 Sum_probs=12.9
Q ss_pred EEEEcCCCCcceeee
Q 029824 127 VVARCGGCNNLHLIA 141 (187)
Q Consensus 127 ViVqC~gC~n~HLIA 141 (187)
|.|+||+|...+++-
T Consensus 68 v~V~CP~C~K~TKmL 82 (114)
T PF11023_consen 68 VQVECPNCGKQTKML 82 (114)
T ss_pred eeeECCCCCChHhhh
Confidence 889999999998763
No 72
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=36.50 E-value=30 Score=22.12 Aligned_cols=23 Identities=26% Similarity=0.689 Sum_probs=16.3
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
+|.+|+. ...+--+|+|.+|..+
T Consensus 1 ~C~vC~~----------~~~~~~~i~C~~C~~~ 23 (51)
T PF00628_consen 1 YCPVCGQ----------SDDDGDMIQCDSCNRW 23 (51)
T ss_dssp EBTTTTS----------SCTTSSEEEBSTTSCE
T ss_pred eCcCCCC----------cCCCCCeEEcCCCChh
Confidence 4777877 3344557899999875
No 73
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=36.29 E-value=41 Score=23.39 Aligned_cols=34 Identities=21% Similarity=0.435 Sum_probs=24.4
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcceee
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLI 140 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLI 140 (187)
.++.|-|-.|+..- . -....--++||-|..+=|+
T Consensus 3 ~~~~Y~C~~Cg~~~----~---~~~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 3 AMMEYKCARCGREV----E---LDQETRGIRCPYCGSRILV 36 (49)
T ss_pred ceEEEEhhhcCCee----e---hhhccCceeCCCCCcEEEE
Confidence 57899999999875 1 1223345899999987554
No 74
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=35.77 E-value=27 Score=31.44 Aligned_cols=40 Identities=25% Similarity=0.509 Sum_probs=27.3
Q ss_pred eEEEEe--cCCCCCcccc---------ccChhhccCceEE----EEcCCCCcceee
Q 029824 100 LAMIFT--CKVCETRSVK---------TACRESYEKGVVV----ARCGGCNNLHLI 140 (187)
Q Consensus 100 l~l~FT--C~~C~tRs~k---------~iSk~AY~~GvVi----VqC~gC~n~HLI 140 (187)
++|-|+ |+.|+..-.+ .+-..-|. |+-| ++|+.|.++..|
T Consensus 35 f~~Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yl-s~~I~rF~~kC~~C~~~i~~ 89 (324)
T PF04502_consen 35 FMMPFNIWCNTCGEYIYKGVRFNARKEKVGNEKYL-STPIYRFYIKCPRCSNEIEF 89 (324)
T ss_pred EcCCccCcCCCCccccccceeeeeeeEecCCCccc-cceEEEEEEEcCCCCCEEee
Confidence 455555 9999977422 24455588 6655 689999997665
No 75
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=35.35 E-value=32 Score=30.00 Aligned_cols=26 Identities=15% Similarity=0.363 Sum_probs=14.2
Q ss_pred cCCCCCccccccChhhccCceEEEEcCCCCcce
Q 029824 106 CKVCETRSVKTACRESYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 106 C~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~H 138 (187)
|..||++.... ..| ..-.|+.|...|
T Consensus 102 C~~CG~~~~~~------~~~-~~~~C~~c~~~~ 127 (256)
T PRK00241 102 CGYCGHPMHPS------KTE-WAMLCPHCRERY 127 (256)
T ss_pred ccccCCCCeec------CCc-eeEECCCCCCEE
Confidence 66777664321 233 335577777655
No 76
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=35.33 E-value=20 Score=30.40 Aligned_cols=33 Identities=33% Similarity=0.590 Sum_probs=24.1
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
--|+-|+|-=+-.+--.+ ---+|-|||+.|.|.
T Consensus 13 VhCnFC~TiLaVsVP~ss-L~~~VTVRCGHCtNL 45 (170)
T PF04690_consen 13 VHCNFCNTILAVSVPCSS-LLKTVTVRCGHCTNL 45 (170)
T ss_pred EEcCCcCeEEEEecchhh-hhhhhceeccCccce
Confidence 369999998655443333 236899999999986
No 77
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=34.65 E-value=35 Score=28.39 Aligned_cols=34 Identities=24% Similarity=0.539 Sum_probs=25.0
Q ss_pred cCCCCCccccc---cChhhccCceEE--EEcCCCCccee
Q 029824 106 CKVCETRSVKT---ACRESYEKGVVV--ARCGGCNNLHL 139 (187)
Q Consensus 106 C~~C~tRs~k~---iSk~AY~~GvVi--VqC~gC~n~HL 139 (187)
|.+|++...+. ...--|.+=|+| ..|+.|.-++-
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchh
Confidence 89999874433 366777777777 47999988754
No 78
>PRK00420 hypothetical protein; Validated
Probab=34.62 E-value=27 Score=27.78 Aligned_cols=34 Identities=15% Similarity=0.335 Sum_probs=24.8
Q ss_pred EEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeec
Q 029824 101 AMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIAD 142 (187)
Q Consensus 101 ~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIAD 142 (187)
++.-+|.+||+.-.+. ..| -+.||.|...-.+.|
T Consensus 21 ml~~~CP~Cg~pLf~l------k~g--~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 21 MLSKHCPVCGLPLFEL------KDG--EVVCPVHGKVYIVKS 54 (112)
T ss_pred HccCCCCCCCCcceec------CCC--ceECCCCCCeeeecc
Confidence 4778999999875442 344 357999999766655
No 79
>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=33.62 E-value=19 Score=19.53 Aligned_cols=9 Identities=22% Similarity=1.102 Sum_probs=7.0
Q ss_pred EecCCCCCc
Q 029824 104 FTCKVCETR 112 (187)
Q Consensus 104 FTC~~C~tR 112 (187)
|+|..|+..
T Consensus 1 y~C~~C~~~ 9 (23)
T PF00096_consen 1 YKCPICGKS 9 (23)
T ss_dssp EEETTTTEE
T ss_pred CCCCCCCCc
Confidence 788888865
No 80
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=33.60 E-value=56 Score=22.62 Aligned_cols=36 Identities=28% Similarity=0.629 Sum_probs=22.6
Q ss_pred CCceEEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 97 RHDLAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 97 R~~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
..++.|+ |..|...+--.. ++.|.. |.-+|+.|..+
T Consensus 18 ~~r~aLI--C~~C~~hNGla~-~~~~~~--i~y~C~~Cg~~ 53 (54)
T PF10058_consen 18 SNRYALI--CSKCFSHNGLAP-KEEFEE--IQYRCPYCGAL 53 (54)
T ss_pred cCceeEE--Ccccchhhcccc-cccCCc--eEEEcCCCCCc
Confidence 3334444 999988764332 555543 47789999754
No 81
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=33.51 E-value=37 Score=24.44 Aligned_cols=17 Identities=24% Similarity=0.708 Sum_probs=10.3
Q ss_pred EEEEcCCCCcceeeecc
Q 029824 127 VVARCGGCNNLHLIADH 143 (187)
Q Consensus 127 ViVqC~gC~n~HLIADn 143 (187)
+-|+||+|.|.-.|=+|
T Consensus 10 ~~VkCp~C~n~q~vFsh 26 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSH 26 (59)
T ss_pred EEEECCCCCCeEEEEec
Confidence 45666666666655444
No 82
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=33.14 E-value=20 Score=29.54 Aligned_cols=45 Identities=18% Similarity=0.443 Sum_probs=25.4
Q ss_pred CCCceEEEEecCCCCCccccccCh---hhcc-------CceEEEEcCCCCcceee
Q 029824 96 ARHDLAMIFTCKVCETRSVKTACR---ESYE-------KGVVVARCGGCNNLHLI 140 (187)
Q Consensus 96 pR~~l~l~FTC~~C~tRs~k~iSk---~AY~-------~GvViVqC~gC~n~HLI 140 (187)
.|+..-+.++|+.|+..+.-.|.+ .+|. .-+|..-|.||.-.=.+
T Consensus 57 srG~aNfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~i~~fdCRG~e~~~f~ 111 (161)
T PF05907_consen 57 SRGTANFVMKCKFCKRESSIDIIPGKGKPYTAEDSGKFVPILAFDCRGLEPVEFS 111 (161)
T ss_dssp SS-EESEEE--SSSS--EEEEEE--TTTEEEGGGTTS-EEEEEEEEESEEEEEE-
T ss_pred CccceEeEecCcCcCCccEEEEEecCccccccccccCCceEEEEECCCcEeEEEe
Confidence 366778888899998776655543 4565 33667788888654433
No 83
>PHA02942 putative transposase; Provisional
Probab=32.72 E-value=34 Score=31.56 Aligned_cols=27 Identities=19% Similarity=0.501 Sum_probs=18.1
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCcce
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~H 138 (187)
=||..||.... ..+. =+-.|+.|...|
T Consensus 326 q~Cs~CG~~~~-~l~~-------r~f~C~~CG~~~ 352 (383)
T PHA02942 326 VSCPKCGHKMV-EIAH-------RYFHCPSCGYEN 352 (383)
T ss_pred ccCCCCCCccC-cCCC-------CEEECCCCCCEe
Confidence 46999998753 2221 157899998753
No 84
>PF03330 DPBB_1: Rare lipoprotein A (RlpA)-like double-psi beta-barrel; InterPro: IPR009009 Beta barrels are commonly observed in protein structures. They are classified in terms of two integral parameters: the number of strands in the sheet, n, and the shear number, S, a measure of the stagger of the strands in the beta-sheet. These two parameters have been shown to determine the major geometrical features of beta-barrels. Six-stranded beta-barrels with a pseudo-twofold axis are found in several proteins. One involving parallel strands forming two psi structures is known as the double-psi barrel. The first psi structure consists of the loop connecting strands beta1 and beta2 (a 'psi loop') and the strand beta5, whereas the second psi structure consists of the loop connecting strands beta4 and beta5 and the strand beta2. All the psi structures in double-psi barrels have a unique handedness, in that beta1 (beta4), beta2 (beta5) and the loop following beta5 (beta2) form a right-handed helix. The unique handedness may be related to the fact that the twisting angle between the parallel pair of strands is always larger than that between the antiparallel pair [].; PDB: 1N10_B 3D30_A 2BH0_A 2HCZ_X.
Probab=32.56 E-value=38 Score=23.75 Aligned_cols=14 Identities=57% Similarity=1.056 Sum_probs=10.6
Q ss_pred eEEEEcCCCCccee
Q 029824 126 VVVARCGGCNNLHL 139 (187)
Q Consensus 126 vViVqC~gC~n~HL 139 (187)
+|.=+||+|...||
T Consensus 43 ~V~D~Cp~~~~~~l 56 (78)
T PF03330_consen 43 TVVDRCPGCPPNHL 56 (78)
T ss_dssp EEEEE-TTSSSSEE
T ss_pred EEEccCCCCcCCEE
Confidence 45568999999987
No 85
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=32.13 E-value=26 Score=30.92 Aligned_cols=58 Identities=21% Similarity=0.479 Sum_probs=37.0
Q ss_pred EEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCCC---CHHHHHHHc
Q 029824 101 AMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEPG---SIEDFLAAR 160 (187)
Q Consensus 101 ~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~~---nIEdil~~k 160 (187)
+..+.|..|+..-...- ...+....-+-+|+.|... +|-=+.=||+|.- .++.++++.
T Consensus 120 l~~~~C~~C~~~~~~~~-~~~~~~~~~~p~C~~Cg~~-~lrP~VV~fGE~lp~~~~~~~~~~~ 180 (250)
T COG0846 120 LKRVRCSKCGNQYYDED-VIKFIEDGLIPRCPKCGGP-VLRPDVVWFGEPLPASFLDEALEAL 180 (250)
T ss_pred eeeeEeCCCcCccchhh-hhhhcccCCCCcCccCCCc-cccCCEEEeCCCCCHHHHHHHHHHh
Confidence 45788999986643111 1222333378899999997 6666777999942 245555554
No 86
>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=32.07 E-value=24 Score=18.43 Aligned_cols=9 Identities=33% Similarity=1.169 Sum_probs=5.7
Q ss_pred EecCCCCCc
Q 029824 104 FTCKVCETR 112 (187)
Q Consensus 104 FTC~~C~tR 112 (187)
|.|..|+..
T Consensus 1 ~~C~~C~~~ 9 (24)
T PF13894_consen 1 FQCPICGKS 9 (24)
T ss_dssp EE-SSTS-E
T ss_pred CCCcCCCCc
Confidence 788899865
No 87
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.85 E-value=27 Score=27.46 Aligned_cols=35 Identities=23% Similarity=0.500 Sum_probs=19.1
Q ss_pred eEEEEecCCCCCccccc-cChhhccCceEEEEcCCCCcce
Q 029824 100 LAMIFTCKVCETRSVKT-ACRESYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~-iSk~AY~~GvViVqC~gC~n~H 138 (187)
.-+.+.| .|+....-. +....| .....||.|....
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~---~~~~~CP~Cgs~~ 102 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHY---AAVIECPVCGNKR 102 (124)
T ss_pred cCeeEEe-eCcCcccccccchhcc---ccCCcCcCCCCCC
Confidence 4568999 999542110 111111 1146799999654
No 88
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=31.67 E-value=36 Score=31.24 Aligned_cols=37 Identities=22% Similarity=0.536 Sum_probs=29.5
Q ss_pred EEEEecCCCCCccc---cccChhhccCceEEEEcCCCCcc
Q 029824 101 AMIFTCKVCETRSV---KTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 101 ~l~FTC~~C~tRs~---k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
--.|+|.+|+.++- .+=+|.+=+-=+-||.|-.|.|+
T Consensus 253 td~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ecgnr 292 (296)
T KOG1105|consen 253 TDLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNECGNR 292 (296)
T ss_pred ccceeeccccccceeEEeeccCCCCCCcceeeeecccCCc
Confidence 33799999998763 34566777777889999999997
No 89
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=31.49 E-value=25 Score=19.40 Aligned_cols=9 Identities=33% Similarity=1.202 Sum_probs=7.4
Q ss_pred EecCCCCCc
Q 029824 104 FTCKVCETR 112 (187)
Q Consensus 104 FTC~~C~tR 112 (187)
|+|++|+..
T Consensus 1 ~~C~~C~~~ 9 (25)
T PF12874_consen 1 FYCDICNKS 9 (25)
T ss_dssp EEETTTTEE
T ss_pred CCCCCCCCC
Confidence 789999765
No 90
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=31.42 E-value=25 Score=29.23 Aligned_cols=53 Identities=19% Similarity=0.467 Sum_probs=31.6
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCCCC--HHHHHH
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEPGS--IEDFLA 158 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~~n--IEdil~ 158 (187)
...|..|+.+....--...+.... +-+||.|. ..+-.+.=||+|.-. +++.++
T Consensus 109 ~~~C~~C~~~~~~~~~~~~~~~~~-~p~C~~Cg--~~lrP~Vv~fgE~~p~~~~~a~~ 163 (218)
T cd01407 109 RVRCTKCGKEYPRDELQADIDREE-VPRCPKCG--GLLRPDVVFFGESLPEELDEAAE 163 (218)
T ss_pred cceeCCCcCCCcHHHHhHhhccCC-CCcCCCCC--CccCCCeEECCCCCcHHHHHHHH
Confidence 456999987643221001122332 56899997 458888889998421 554443
No 91
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 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 consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=31.31 E-value=46 Score=24.95 Aligned_cols=19 Identities=11% Similarity=0.532 Sum_probs=14.3
Q ss_pred ceEEEEecCCCCCcccccc
Q 029824 99 DLAMIFTCKVCETRSVKTA 117 (187)
Q Consensus 99 ~l~l~FTC~~C~tRs~k~i 117 (187)
.+.|.|+|..|+....+.+
T Consensus 49 Ki~Lrl~C~~C~~~~~~~~ 67 (77)
T PF00935_consen 49 KIVLRLECTECGKAHMRPG 67 (77)
T ss_dssp BBEEEEEETTTS-EEEEE-
T ss_pred cEEEEEEeCCCCccccccc
Confidence 5889999999998876654
No 92
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=31.17 E-value=42 Score=24.76 Aligned_cols=35 Identities=17% Similarity=0.362 Sum_probs=25.3
Q ss_pred EEecCCCCCcccccc---ChhhccCceEEEEcCCCCcc
Q 029824 103 IFTCKVCETRSVKTA---CRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 103 ~FTC~~C~tRs~k~i---Sk~AY~~GvViVqC~gC~n~ 137 (187)
...|.+||.+-+.-+ .|.|=+-=+++-.|..|..+
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYV 99 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCe
Confidence 468999988775444 45566677888899888753
No 93
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=30.62 E-value=47 Score=26.84 Aligned_cols=33 Identities=18% Similarity=0.503 Sum_probs=25.9
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCcceee
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLI 140 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLI 140 (187)
=.|..|+..-++.+- +..+.+.+|..|....-|
T Consensus 98 VlC~~C~sPdT~l~k----~~r~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 98 VICRECNRPDTRIIK----EGRVSLLKCEACGAKAPL 130 (133)
T ss_pred EECCCCCCCCcEEEE----eCCeEEEecccCCCCCcc
Confidence 369999999888773 256678899999987654
No 94
>PHA02998 RNA polymerase subunit; Provisional
Probab=30.31 E-value=41 Score=29.38 Aligned_cols=36 Identities=19% Similarity=0.445 Sum_probs=28.3
Q ss_pred EEEecCCCCCccccccC---hhhccCceEEEEcCCCCcc
Q 029824 102 MIFTCKVCETRSVKTAC---RESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iS---k~AY~~GvViVqC~gC~n~ 137 (187)
..-+|..|+.+.+.-+. |.|=|--+++.+|..|.++
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~ 180 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKH 180 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCc
Confidence 34679999999876544 4566777999999999876
No 95
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=30.05 E-value=20 Score=30.60 Aligned_cols=45 Identities=24% Similarity=0.484 Sum_probs=28.1
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCC
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEP 150 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~ 150 (187)
...|..|+.+-....-+.....+ .+-+|+.|. .++-++.=||+|.
T Consensus 116 ~~~C~~C~~~~~~~~~~~~~~~~-~~p~C~~Cg--g~lrP~Vv~FGE~ 160 (235)
T cd01408 116 TAHCIKCKHKYPGDWMREDIFNQ-EVPKCPRCG--GLVKPDIVFFGES 160 (235)
T ss_pred ccccccCCCcCCHHHHHHHHhCC-CCccCCCCC--CCccCcEEECCCC
Confidence 35698999864321111111122 147899997 5699999999994
No 96
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=29.87 E-value=15 Score=24.53 Aligned_cols=31 Identities=23% Similarity=0.448 Sum_probs=20.3
Q ss_pred EEecCCCCCccc-------cccChhhccCceEEEEcCCCCc
Q 029824 103 IFTCKVCETRSV-------KTACRESYEKGVVVARCGGCNN 136 (187)
Q Consensus 103 ~FTC~~C~tRs~-------k~iSk~AY~~GvViVqC~gC~n 136 (187)
.|+|..|+. .. +-...+.++.. -|.||=|..
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~--~v~CPiC~~ 39 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESK--NVVCPICSS 39 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCC--CccCCCchh
Confidence 589999998 42 12334455444 478999986
No 97
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=29.49 E-value=59 Score=20.85 Aligned_cols=14 Identities=21% Similarity=0.309 Sum_probs=9.1
Q ss_pred EEEcCCCCcceeee
Q 029824 128 VARCGGCNNLHLIA 141 (187)
Q Consensus 128 iVqC~gC~n~HLIA 141 (187)
...|+.|...|-|.
T Consensus 20 ~~vC~~Cg~~~~~~ 33 (52)
T smart00661 20 RFVCRKCGYEEPIE 33 (52)
T ss_pred EEECCcCCCeEECC
Confidence 45688888665543
No 98
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=29.30 E-value=36 Score=24.06 Aligned_cols=25 Identities=24% Similarity=0.705 Sum_probs=18.1
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCcce
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNNLH 138 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~H 138 (187)
-|.+|+.+ ...|-=||.||-|...|
T Consensus 7 ~C~~Cg~~---------~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 7 KCPVCGKK---------FKDGDDIVVCPECGAPY 31 (54)
T ss_pred cChhhCCc---------ccCCCCEEECCCCCCcc
Confidence 47888876 33455688999998865
No 99
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=29.05 E-value=49 Score=22.58 Aligned_cols=26 Identities=31% Similarity=0.544 Sum_probs=14.4
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
||..||.+..+..+. =...|+.|...
T Consensus 30 ~C~~CG~~~~~~~~~-------r~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSG-------RVFTCPNCGFE 55 (69)
T ss_pred CccCccccccccccc-------ceEEcCCCCCE
Confidence 577777776552221 13457777543
No 100
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=28.92 E-value=70 Score=26.36 Aligned_cols=45 Identities=18% Similarity=0.268 Sum_probs=23.9
Q ss_pred CCCceEEEEecCCCCCccccc--cChhhc-----cC--ceEEEEcCCCCcceee
Q 029824 96 ARHDLAMIFTCKVCETRSVKT--ACRESY-----EK--GVVVARCGGCNNLHLI 140 (187)
Q Consensus 96 pR~~l~l~FTC~~C~tRs~k~--iSk~AY-----~~--GvViVqC~gC~n~HLI 140 (187)
+...+.+...|.-|++.+.+. |++.-= -+ .-...+|..|+..+-|
T Consensus 23 ~~~~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si 76 (161)
T PF05907_consen 23 PDFEWFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSI 76 (161)
T ss_dssp TT--EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEE
T ss_pred CCCEEEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEE
Confidence 556789999999999877555 443211 11 2357799999987765
No 101
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=28.12 E-value=53 Score=30.57 Aligned_cols=43 Identities=23% Similarity=0.476 Sum_probs=19.1
Q ss_pred EEEecCCCCCccccccC-----hhhcc--Cce-EEEEcCCCCcceeeeccc
Q 029824 102 MIFTCKVCETRSVKTAC-----RESYE--KGV-VVARCGGCNNLHLIADHL 144 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iS-----k~AY~--~Gv-ViVqC~gC~n~HLIADnL 144 (187)
=.|+|..|.....+.-. +|.|+ +++ =|.+|++|.++=.--|.|
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~sl~r~ 301 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTISLERL 301 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEESSSS
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeeecccC
Confidence 36899999755333221 22222 111 157899999985544543
No 102
>PLN02913 dihydrofolate synthetase
Probab=27.66 E-value=26 Score=33.30 Aligned_cols=26 Identities=35% Similarity=0.625 Sum_probs=22.0
Q ss_pred eccccCcCCCCCHHHHHHHcCCceeeec
Q 029824 141 ADHLGWFGEPGSIEDFLAARGEEVKKGS 168 (187)
Q Consensus 141 ADnLgwF~e~~nIEdil~~kGe~V~kg~ 168 (187)
-||++|++ .|+|+|.++|..-++.|.
T Consensus 208 ~DH~~~LG--~Tle~IA~eKagIik~g~ 233 (510)
T PLN02913 208 EEHLAALG--GSLESIALAKSGIIKQGR 233 (510)
T ss_pred HHHHhhhc--ccHHHHHHHHhhhccCCC
Confidence 59999997 499999999988777654
No 103
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=27.49 E-value=36 Score=20.70 Aligned_cols=17 Identities=29% Similarity=0.739 Sum_probs=14.8
Q ss_pred hhccCceEEEEcCCCCc
Q 029824 120 ESYEKGVVVARCGGCNN 136 (187)
Q Consensus 120 ~AY~~GvViVqC~gC~n 136 (187)
.+|-.|..-|+|..|+.
T Consensus 8 L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 8 LMYPRGAPSVRCACCHT 24 (25)
T ss_pred EEcCCCCCCeECCccCc
Confidence 57999999999999974
No 104
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=27.10 E-value=49 Score=30.15 Aligned_cols=56 Identities=29% Similarity=0.497 Sum_probs=38.1
Q ss_pred cCCCCCccccccChhhccCceEEEEcCCCCcce------------------eeeccccCcCC-----------CCCHHH-
Q 029824 106 CKVCETRSVKTACRESYEKGVVVARCGGCNNLH------------------LIADHLGWFGE-----------PGSIED- 155 (187)
Q Consensus 106 C~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~H------------------LIADnLgwF~e-----------~~nIEd- 155 (187)
|..||+++. .++.| .-.+|++|.+.| |+|-+--+|.. ..|||+
T Consensus 114 Cg~CG~~~~------~~~~g-~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ilLa~~~~h~~g~yS~LAGFVE~GETlE~A 186 (279)
T COG2816 114 CGRCGTKTY------PREGG-WARVCPKCGHEHFPRIDPCVIVAVIRGDEILLARHPRHFPGMYSLLAGFVEPGETLEQA 186 (279)
T ss_pred CCCCCCcCc------cccCc-eeeeCCCCCCccCCCCCCeEEEEEecCCceeecCCCCCCCcceeeeeecccCCccHHHH
Confidence 888998842 23344 446899999987 66777777632 248885
Q ss_pred ----HHHHcCCceeeec
Q 029824 156 ----FLAARGEEVKKGS 168 (187)
Q Consensus 156 ----il~~kGe~V~kg~ 168 (187)
++.|-|=.|++.+
T Consensus 187 V~REv~EE~Gi~V~~vr 203 (279)
T COG2816 187 VAREVFEEVGIKVKNVR 203 (279)
T ss_pred HHHHHHHhhCeEEeeee
Confidence 5777787777643
No 105
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=27.05 E-value=20 Score=28.83 Aligned_cols=68 Identities=19% Similarity=0.345 Sum_probs=36.8
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCc-CCC---------CCHHHHHHHcC---Cceeeecc
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWF-GEP---------GSIEDFLAARG---EEVKKGSV 169 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF-~e~---------~nIEdil~~kG---e~V~kg~~ 169 (187)
...|..||++-..- | -.++--||.|..+-.. .. +++ .-+-|=.-++| |+|+--.-
T Consensus 2 pH~CtrCG~vf~~g-~------~~il~GCp~CG~nkF~-----yv~~e~rpa~~e~~d~~vrde~~a~ge~ietIrI~~p 69 (112)
T COG3364 2 PHQCTRCGEVFDDG-S------EEILSGCPKCGCNKFL-----YVPEEKRPAVAEAADPEVRDEDGAQGEPIETIRILRP 69 (112)
T ss_pred Cceecccccccccc-c------HHHHccCccccchheE-----ecccccccchhhhcCCcccchhhcccCcceEEEEecC
Confidence 45799999883322 1 1345569999765211 11 122 11223334556 55555556
Q ss_pred cccCcccccccCc
Q 029824 170 DTLNLTLEDLAGR 182 (187)
Q Consensus 170 ~~~~lt~eDl~g~ 182 (187)
+.+++.+|.|.-.
T Consensus 70 G~YeiNl~~Lld~ 82 (112)
T COG3364 70 GVYEINLESLLDR 82 (112)
T ss_pred ceEEEehhhhccC
Confidence 6777777776653
No 106
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=27.03 E-value=45 Score=28.32 Aligned_cols=40 Identities=30% Similarity=0.410 Sum_probs=22.8
Q ss_pred EEecCCCCCcc--ccccChhh-----------ccCce-----EEEEcCCCCcceeeec
Q 029824 103 IFTCKVCETRS--VKTACRES-----------YEKGV-----VVARCGGCNNLHLIAD 142 (187)
Q Consensus 103 ~FTC~~C~tRs--~k~iSk~A-----------Y~~Gv-----ViVqC~gC~n~HLIAD 142 (187)
.+||.+|++.- .+..|... +.+|| +++-||.|.---.-.|
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~ 62 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEED 62 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccc
Confidence 57899999753 22222211 12332 6788999986544333
No 107
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=26.97 E-value=38 Score=22.61 Aligned_cols=36 Identities=11% Similarity=0.265 Sum_probs=22.2
Q ss_pred CCCCceEEEEecCCCCCccccccChhhccCceEEEEcCCC
Q 029824 95 SARHDLAMIFTCKVCETRSVKTACRESYEKGVVVARCGGC 134 (187)
Q Consensus 95 ~pR~~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC 134 (187)
.|.....+.+.|..|++.=...|+... .--..||-|
T Consensus 20 ~~~s~~~v~W~C~~Cgh~w~~~v~~R~----~~~~~CP~C 55 (55)
T PF14311_consen 20 TPGSNKKVWWKCPKCGHEWKASVNDRT----RRGKGCPYC 55 (55)
T ss_pred CcCCCCEEEEECCCCCCeeEccHhhhc----cCCCCCCCC
Confidence 344456889999999886555555443 112346665
No 108
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=26.73 E-value=35 Score=32.64 Aligned_cols=66 Identities=14% Similarity=0.241 Sum_probs=42.8
Q ss_pred CCceEEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCCCCHHHHHHHcCCceeeecc
Q 029824 97 RHDLAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEPGSIEDFLAARGEEVKKGSV 169 (187)
Q Consensus 97 R~~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~~nIEdil~~kGe~V~kg~~ 169 (187)
++.....|.|..|+..+.++....... =+ +||.|..-|...+.-..-+ -+-+...+.|.+|--.+.
T Consensus 321 l~~~r~~~~c~~~~~e~~~t~~~~~~~---~~-~~~~~~~e~~~v~~~d~vd---~l~e~a~~~Ga~ve~is~ 386 (411)
T COG1503 321 LEKERVTYKCPTCGYENLKSKREFEQK---RF-RCPECGSEMEEVEVSDLVD---ELAELAEESGAKVEIISD 386 (411)
T ss_pred ccccceeecCCCcchhhhhcccccccc---cc-cCccccccccchhhhhHHH---HHHHHHHhcCCeEEEecC
Confidence 444567999999999988776665555 34 9999999887765432211 123445556766654443
No 109
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=26.65 E-value=21 Score=34.17 Aligned_cols=7 Identities=43% Similarity=1.103 Sum_probs=3.8
Q ss_pred cCCCCCc
Q 029824 106 CKVCETR 112 (187)
Q Consensus 106 C~~C~tR 112 (187)
|..||+|
T Consensus 353 Cp~Cg~~ 359 (421)
T COG1571 353 CPRCGGR 359 (421)
T ss_pred CCccCCc
Confidence 5555554
No 110
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=26.50 E-value=30 Score=25.38 Aligned_cols=42 Identities=21% Similarity=0.288 Sum_probs=29.5
Q ss_pred CceEEEEcCCCCc---------ceeeeccccCcCCCCCHHHHHHHcCCcee
Q 029824 124 KGVVVARCGGCNN---------LHLIADHLGWFGEPGSIEDFLAARGEEVK 165 (187)
Q Consensus 124 ~GvViVqC~gC~n---------~HLIADnLgwF~e~~nIEdil~~kGe~V~ 165 (187)
.|-.+.+||.|.. +|+=--|+-.|+-+.-|-.-|+.+|+.+.
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~~~~~r~k~~~k~~Kk~~d~l~ 63 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHGWLFGRGKPKGKRLKKKYDKLL 63 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhhhhhcCCchhHHHHHHhhhhhh
Confidence 4666777777764 56666666667777788888888887653
No 111
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=26.19 E-value=49 Score=20.74 Aligned_cols=26 Identities=31% Similarity=0.727 Sum_probs=19.8
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
.|.-|++- .+|-.|.--|||.-|...
T Consensus 3 ~C~~C~t~-------L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 3 VCGGCRTL-------LMYPRGASSVRCALCQTV 28 (31)
T ss_pred CcCCCCcE-------eecCCCCCeEECCCCCeE
Confidence 36666654 678899999999999753
No 112
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.03 E-value=51 Score=27.22 Aligned_cols=21 Identities=24% Similarity=0.621 Sum_probs=14.2
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
||..||. ++ .=...||.|...
T Consensus 311 ~C~~cg~-----~~-------~r~~~C~~cg~~ 331 (364)
T COG0675 311 TCPCCGH-----LS-------GRLFKCPRCGFV 331 (364)
T ss_pred cccccCC-----cc-------ceeEECCCCCCe
Confidence 6999998 22 113579999865
No 113
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=25.88 E-value=47 Score=26.07 Aligned_cols=18 Identities=11% Similarity=0.477 Sum_probs=14.8
Q ss_pred CceEEEEecCCCCCcccc
Q 029824 98 HDLAMIFTCKVCETRSVK 115 (187)
Q Consensus 98 ~~l~l~FTC~~C~tRs~k 115 (187)
..+.|.|+|.+|+..-.+
T Consensus 63 KKv~Lr~~Ct~Cgkah~~ 80 (94)
T COG1631 63 KKVDLRLRCTECGKAHQR 80 (94)
T ss_pred ceEEEEEEehhhcccccc
Confidence 468999999999987554
No 114
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.52 E-value=44 Score=30.40 Aligned_cols=10 Identities=40% Similarity=1.072 Sum_probs=8.9
Q ss_pred EEecCCCCCc
Q 029824 103 IFTCKVCETR 112 (187)
Q Consensus 103 ~FTC~~C~tR 112 (187)
.++|.+|+|.
T Consensus 19 ~ieCPvC~tk 28 (267)
T COG1655 19 TIECPVCNTK 28 (267)
T ss_pred eeccCcccch
Confidence 6899999986
No 115
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.16 E-value=46 Score=21.64 Aligned_cols=27 Identities=22% Similarity=0.473 Sum_probs=16.1
Q ss_pred EecCCCCCccccccChhhccCceEEEEcCCCCc
Q 029824 104 FTCKVCETRSVKTACRESYEKGVVVARCGGCNN 136 (187)
Q Consensus 104 FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n 136 (187)
|+|..|+......+.. .-.-+|.+|..
T Consensus 19 ~~CP~Cg~~~~~~~~~------~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT------RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCC------CCeEECCCCCC
Confidence 6788888764444444 33456777753
No 116
>KOG4846 consensus Nuclear receptor [Signal transduction mechanisms]
Probab=25.04 E-value=71 Score=31.42 Aligned_cols=26 Identities=38% Similarity=0.958 Sum_probs=20.3
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCC
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCN 135 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~ 135 (187)
++--|+|||-.- .+||-||- -|.||+
T Consensus 131 ~~~lCkVCgDkA------SGfHYGV~--aCEGCK 156 (538)
T KOG4846|consen 131 AISLCKVCGDKA------SGFHYGVT--ACEGCK 156 (538)
T ss_pred eeEeehhhcccc------ccceecee--ecccch
Confidence 455699999873 47899974 699997
No 117
>COG5254 ARV1 Predicted membrane protein [Function unknown]
Probab=24.84 E-value=24 Score=31.50 Aligned_cols=32 Identities=28% Similarity=0.566 Sum_probs=28.0
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
-|-.||.|-.+.+.+-+ +..+=+.|||.|+..
T Consensus 2 vCIeCg~~vdsLyt~ys-ts~iqls~Cp~C~~~ 33 (239)
T COG5254 2 VCIECGSRVDSLYTRYS-TSAIQLSRCPSCNRK 33 (239)
T ss_pred eeeEcCCccceeeeecc-CcceehhcCchHHHH
Confidence 58899999999998888 788999999999863
No 118
>PRK14106 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=24.82 E-value=25 Score=31.52 Aligned_cols=24 Identities=21% Similarity=0.473 Sum_probs=19.8
Q ss_pred eccccCcCCCCCHHHHHHHcCCceeee
Q 029824 141 ADHLGWFGEPGSIEDFLAARGEEVKKG 167 (187)
Q Consensus 141 ADnLgwF~e~~nIEdil~~kGe~V~kg 167 (187)
.||++||+ |+|+|.++|.+-++.+
T Consensus 187 ~dHl~~~g---t~e~ia~~K~~i~~~~ 210 (450)
T PRK14106 187 PDHLDRHK---TMENYIKAKARIFENQ 210 (450)
T ss_pred cchhcccC---CHHHHHHHHHHHHhCC
Confidence 59999996 9999999987776543
No 119
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=24.66 E-value=39 Score=18.95 Aligned_cols=9 Identities=33% Similarity=1.021 Sum_probs=7.2
Q ss_pred EecCCCCCc
Q 029824 104 FTCKVCETR 112 (187)
Q Consensus 104 FTC~~C~tR 112 (187)
|+|+.|+..
T Consensus 2 ~~C~~C~~~ 10 (27)
T PF13912_consen 2 FECDECGKT 10 (27)
T ss_dssp EEETTTTEE
T ss_pred CCCCccCCc
Confidence 789999864
No 120
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=24.56 E-value=56 Score=23.40 Aligned_cols=43 Identities=19% Similarity=0.385 Sum_probs=26.4
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceee-eccccC
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLI-ADHLGW 146 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLI-ADnLgw 146 (187)
..-|.+||.+.--.+-+..--+. ...-||.|+.-.|| +.+|..
T Consensus 4 Wi~CP~CgnKTR~kir~DT~LkN-fPlyCpKCK~EtlI~v~~~~i 47 (55)
T PF14205_consen 4 WILCPICGNKTRLKIREDTVLKN-FPLYCPKCKQETLIDVKQLKI 47 (55)
T ss_pred EEECCCCCCccceeeecCceecc-ccccCCCCCceEEEEeeccEE
Confidence 34699999775333333222221 13579999999998 666654
No 121
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=24.50 E-value=63 Score=24.90 Aligned_cols=18 Identities=17% Similarity=0.313 Sum_probs=10.1
Q ss_pred cCCCCceEEEEecCCCCCc
Q 029824 94 TSARHDLAMIFTCKVCETR 112 (187)
Q Consensus 94 ~~pR~~l~l~FTC~~C~tR 112 (187)
.+|+ ++.|.-.|..|+.-
T Consensus 27 ~~Pn-S~Fm~VkCp~C~n~ 44 (85)
T PTZ00083 27 QGPN-SYFMDVKCPGCSQI 44 (85)
T ss_pred cCCC-CeEEEEECCCCCCe
Confidence 3454 45566666666543
No 122
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=24.40 E-value=54 Score=27.49 Aligned_cols=46 Identities=28% Similarity=0.501 Sum_probs=27.5
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCC
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEP 150 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~ 150 (187)
...|..|+.+....--.......-.+.+|+.|. .++-.+.=||+|.
T Consensus 95 ~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cg--g~lrP~VV~FgE~ 140 (206)
T cd01410 95 IEVCKSCGPEYVRDDVVETRGDKETGRRCHACG--GILKDTIVDFGER 140 (206)
T ss_pred cccCCCCCCccchHHHHHHhhcCCCCCcCCCCc--CccCCcEEECCCC
Confidence 445999996632111000111111246799997 4689999999994
No 123
>PRK04860 hypothetical protein; Provisional
Probab=24.25 E-value=95 Score=25.70 Aligned_cols=40 Identities=25% Similarity=0.537 Sum_probs=27.3
Q ss_pred eEEEEecCCCCCccccccChh-hccCceEEEEcCCCCcceeee
Q 029824 100 LAMIFTCKVCETRSVKTACRE-SYEKGVVVARCGGCNNLHLIA 141 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~-AY~~GvViVqC~gC~n~HLIA 141 (187)
....|.|. |+.. ...+.++ --++|..--+|..|.-.-...
T Consensus 116 ~~~~Y~C~-C~~~-~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 116 KTFPYRCK-CQEH-QLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred CEEEEEcC-CCCe-eCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 34689998 9983 3333444 356788889999998764433
No 124
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=23.98 E-value=45 Score=31.39 Aligned_cols=31 Identities=19% Similarity=0.409 Sum_probs=13.7
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCCCCc
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGGCNN 136 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n 136 (187)
||..|+.+-.....++. -.=.+-+.|+.|.=
T Consensus 161 tC~tC~G~G~v~~~~~~-g~~~~~~~C~~C~G 191 (371)
T COG0484 161 TCPTCNGSGQVRTVQRT-GFFSFQQTCPTCNG 191 (371)
T ss_pred cCCCCCCcCeEEEEEee-eEEEEEEECCCCcc
Confidence 45555555544444444 11112334555543
No 125
>PRK02935 hypothetical protein; Provisional
Probab=23.90 E-value=45 Score=26.83 Aligned_cols=15 Identities=20% Similarity=0.468 Sum_probs=11.4
Q ss_pred eEEEEcCCCCcceee
Q 029824 126 VVVARCGGCNNLHLI 140 (187)
Q Consensus 126 vViVqC~gC~n~HLI 140 (187)
.|.|+||+|+..-.+
T Consensus 68 avqV~CP~C~K~TKm 82 (110)
T PRK02935 68 AVQVICPSCEKPTKM 82 (110)
T ss_pred ceeeECCCCCchhhh
Confidence 478999999876443
No 126
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.40 E-value=57 Score=35.53 Aligned_cols=34 Identities=21% Similarity=0.461 Sum_probs=19.1
Q ss_pred EEecCCCCCccccccChh-hccCceEEEEcCCCCcc
Q 029824 103 IFTCKVCETRSVKTACRE-SYEKGVVVARCGGCNNL 137 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~-AY~~GvViVqC~gC~n~ 137 (187)
.|.|..||+.+...+.+. ..+.-.+ ..||.|...
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~te~v-y~CPsCGae 701 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHTEPV-YVCPDCGAE 701 (1337)
T ss_pred EEECCCCCCccccccCcccCCcCCCc-eeCccCCCc
Confidence 477888887765555552 2222222 367777664
No 127
>PHA03112 IL-18 binding protein; Provisional
Probab=23.16 E-value=44 Score=27.74 Aligned_cols=33 Identities=30% Similarity=0.469 Sum_probs=19.2
Q ss_pred cCceEEEEcCCCCcceeeeccccCc-CCCCCHHHH
Q 029824 123 EKGVVVARCGGCNNLHLIADHLGWF-GEPGSIEDF 156 (187)
Q Consensus 123 ~~GvViVqC~gC~n~HLIADnLgwF-~e~~nIEdi 156 (187)
+.|.|+.+|-||. +|--=--|=|- ++.++++|.
T Consensus 37 ~~~~vvL~C~gcs-~fp~fS~lYWl~gn~~s~~d~ 70 (141)
T PHA03112 37 ETEKVVLECRGCS-YFPKFSYVYWLIGNNKSDVDQ 70 (141)
T ss_pred CCCEEEEEEECcc-CCCCceEEEEEcCCCccchhc
Confidence 3889999999993 32221234555 343455544
No 128
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=23.11 E-value=38 Score=19.64 Aligned_cols=9 Identities=22% Similarity=0.947 Sum_probs=7.8
Q ss_pred EecCCCCCc
Q 029824 104 FTCKVCETR 112 (187)
Q Consensus 104 FTC~~C~tR 112 (187)
|.|..|+.+
T Consensus 15 ~~C~~C~k~ 23 (26)
T PF13465_consen 15 YKCPYCGKS 23 (26)
T ss_dssp EEESSSSEE
T ss_pred CCCCCCcCe
Confidence 999999865
No 129
>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=23.07 E-value=60 Score=19.56 Aligned_cols=16 Identities=31% Similarity=0.686 Sum_probs=11.4
Q ss_pred CCCCceEEEEecCCCCC
Q 029824 95 SARHDLAMIFTCKVCET 111 (187)
Q Consensus 95 ~pR~~l~l~FTC~~C~t 111 (187)
.|| ...+.|.|..||.
T Consensus 9 ~~r-~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 9 APR-EQAVPFPCPNCGF 24 (24)
T ss_pred cCc-ccCceEeCCCCCC
Confidence 455 3477899999874
No 130
>PRK06260 threonine synthase; Validated
Probab=22.77 E-value=46 Score=30.25 Aligned_cols=25 Identities=20% Similarity=0.689 Sum_probs=18.5
Q ss_pred EEEecCCCCCccccccChhhccCceEEEEcCCCC
Q 029824 102 MIFTCKVCETRSVKTACRESYEKGVVVARCGGCN 135 (187)
Q Consensus 102 l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~ 135 (187)
..|.|..|+++ |.-..+..+||.|.
T Consensus 2 ~~~~C~~cg~~---------~~~~~~~~~Cp~cg 26 (397)
T PRK06260 2 YWLKCIECGKE---------YDPDEIIYTCPECG 26 (397)
T ss_pred CEEEECCCCCC---------CCCCCccccCCCCC
Confidence 46899999987 44444567899995
No 131
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=22.70 E-value=1e+02 Score=20.60 Aligned_cols=32 Identities=16% Similarity=0.187 Sum_probs=14.0
Q ss_pred cCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 106 CKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 106 C~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
|..||.......+...-..+.-++.|.+|...
T Consensus 4 CPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 4 CPFCGGADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence 56666644322211222222223367766654
No 132
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=22.65 E-value=28 Score=31.34 Aligned_cols=23 Identities=26% Similarity=0.641 Sum_probs=18.8
Q ss_pred eccccCcCCCCCHHHHHHHcCCceee
Q 029824 141 ADHLGWFGEPGSIEDFLAARGEEVKK 166 (187)
Q Consensus 141 ADnLgwF~e~~nIEdil~~kGe~V~k 166 (187)
.|||.||+ |+|+|.++|.+-++.
T Consensus 192 ~DHld~~g---t~e~~~~~K~~i~~~ 214 (459)
T PRK02705 192 PDHLERHG---TLENYFAIKASLLER 214 (459)
T ss_pred hhhhcccC---CHHHHHHHHHHHhcc
Confidence 49999996 899999998776654
No 133
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.59 E-value=47 Score=33.78 Aligned_cols=21 Identities=29% Similarity=0.436 Sum_probs=15.9
Q ss_pred ceEEEEcCCCCcceeeecccc
Q 029824 125 GVVVARCGGCNNLHLIADHLG 145 (187)
Q Consensus 125 GvViVqC~gC~n~HLIADnLg 145 (187)
.-+--+||.|...||.+==.|
T Consensus 472 ~~~p~~Cp~Cgs~~L~~~G~G 492 (730)
T COG1198 472 EPIPQSCPECGSEHLRAVGPG 492 (730)
T ss_pred CCCCCCCCCCCCCeeEEeccc
Confidence 456678999999998875555
No 134
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=22.59 E-value=83 Score=26.68 Aligned_cols=41 Identities=24% Similarity=0.455 Sum_probs=26.0
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCC
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEP 150 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~ 150 (187)
...|..|+.+-. ...+... -+..||.|. ..+-.|.=||+|.
T Consensus 122 ~~~C~~C~~~~~----~~~~~~~-~~p~C~~Cg--g~lrP~Vv~fge~ 162 (242)
T PRK00481 122 RARCTKCGQTYD----LDEYLKP-EPPRCPKCG--GILRPDVVLFGEM 162 (242)
T ss_pred ceeeCCCCCCcC----hhhhccC-CCCCCCCCC--CccCCCeEECCCC
Confidence 466999976532 1111111 145699996 6688888899984
No 135
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=22.44 E-value=32 Score=25.45 Aligned_cols=36 Identities=22% Similarity=0.496 Sum_probs=27.6
Q ss_pred EEEEecCCCC-CccccccChhhccCceEEEEcCCCCcc
Q 029824 101 AMIFTCKVCE-TRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 101 ~l~FTC~~C~-tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
....||.+|+ ++..-.|||.--.++.-- +|-.|..|
T Consensus 48 ~~El~C~~C~~~k~ld~FSK~QR~~~~~a-~C~~Cv~~ 84 (84)
T PF12898_consen 48 VVELTCSPCGKTKPLDEFSKNQRRKPDPA-RCKDCVQW 84 (84)
T ss_pred cCcCEeccCCCCcCHHHHhHHhhcCCCcc-cchhhhcC
Confidence 4466999999 567889999888886543 88888654
No 136
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=22.33 E-value=48 Score=24.88 Aligned_cols=14 Identities=29% Similarity=0.833 Sum_probs=11.6
Q ss_pred eEEEEecCCCCCcc
Q 029824 100 LAMIFTCKVCETRS 113 (187)
Q Consensus 100 l~l~FTC~~C~tRs 113 (187)
|.+.|+|..|+++-
T Consensus 1 Mai~Y~CRHCg~~I 14 (76)
T PF10955_consen 1 MAIHYYCRHCGTKI 14 (76)
T ss_pred CceEEEecCCCCEE
Confidence 46889999999873
No 137
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=22.29 E-value=80 Score=24.40 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=24.3
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
+.-.|+|..|+....+.. ++=|-+|..|...
T Consensus 33 q~a~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~ 63 (90)
T PRK03976 33 MRAKHVCPVCGRPKVKRV-------GTGIWECRKCGAK 63 (90)
T ss_pred HhcCccCCCCCCCceEEE-------EEEEEEcCCCCCE
Confidence 345799999988866653 6778999999865
No 138
>PLN00209 ribosomal protein S27; Provisional
Probab=22.16 E-value=1.2e+02 Score=23.35 Aligned_cols=39 Identities=23% Similarity=0.524 Sum_probs=28.7
Q ss_pred CccCCCCceEEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 92 LKTSARHDLAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 92 ~k~~pR~~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
+-.+|+ ++.|.-.|..|+.-+. -|-+....|.|.+|...
T Consensus 26 Lv~~Pn-S~Fm~VkCp~C~n~q~------VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 26 LVQSPN-SFFMDVKCQGCFNITT------VFSHSQTVVVCGSCQTV 64 (86)
T ss_pred eecCCC-CEEEEEECCCCCCeeE------EEecCceEEEccccCCE
Confidence 334565 5788889999998743 35566778999999864
No 139
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=21.97 E-value=1e+02 Score=26.07 Aligned_cols=39 Identities=23% Similarity=0.376 Sum_probs=27.0
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCC
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEP 150 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~ 150 (187)
...|..|+.+- ....|.+ +-+|+.|. .++-.|.=||+|.
T Consensus 118 ~~~C~~C~~~~----~~~~~~~---~p~C~~Cg--g~lrP~vv~fge~ 156 (225)
T cd01411 118 RIYCTVCGKTV----DWEEYLK---SPYHAKCG--GVIRPDIVLYEEM 156 (225)
T ss_pred eeEeCCCCCcc----chhhcCC---CCCCCCCC--CEeCCCEEEcCCC
Confidence 45799997543 2233332 36899997 5788888899984
No 140
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=21.97 E-value=63 Score=29.26 Aligned_cols=37 Identities=16% Similarity=0.381 Sum_probs=25.7
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeee
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIA 141 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIA 141 (187)
....|+|..|...-... .+. .-=+++||.|++.+-|.
T Consensus 154 ~~~rv~CghC~~~Fl~~----~~~-~~tlARCPHCrKvSSVG 190 (256)
T PF09788_consen 154 GSCRVICGHCSNTFLFN----TLT-SNTLARCPHCRKVSSVG 190 (256)
T ss_pred CceeEECCCCCCcEecc----CCC-CCccccCCCCceecccc
Confidence 36789999998764222 122 11269999999998885
No 141
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.76 E-value=89 Score=24.22 Aligned_cols=42 Identities=17% Similarity=0.558 Sum_probs=29.4
Q ss_pred cCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCCCCHHHHHHHcC
Q 029824 106 CKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEPGSIEDFLAARG 161 (187)
Q Consensus 106 C~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~~nIEdil~~kG 161 (187)
|..|+-- +++.+ -.||=|-.||.|.-- +-+.+-++.||+..+
T Consensus 4 CP~C~v~---l~~~~--rs~vEiD~CPrCrGV---------WLDrGELdKli~r~r 45 (88)
T COG3809 4 CPICGVE---LVMSV--RSGVEIDYCPRCRGV---------WLDRGELDKLIERSR 45 (88)
T ss_pred cCcCCce---eeeee--ecCceeeeCCccccE---------eecchhHHHHHHHhc
Confidence 7777743 33322 458999999999743 447788888887765
No 142
>TIGR01499 folC folylpolyglutamate synthase/dihydrofolate synthase. A mutation study of the FolC gene of E. coli suggests that both activitities belong to the same active site. Because some examples are monofunctional (and these cannot be separated phylogenetically), the model is treated as subfamily, not equivalog.
Probab=21.68 E-value=34 Score=30.54 Aligned_cols=25 Identities=24% Similarity=0.466 Sum_probs=20.7
Q ss_pred eccccCcCCCCCHHHHHHHcCCceeee
Q 029824 141 ADHLGWFGEPGSIEDFLAARGEEVKKG 167 (187)
Q Consensus 141 ADnLgwF~e~~nIEdil~~kGe~V~kg 167 (187)
-|||.|++ .|+|+|.++|..-++.+
T Consensus 142 ~DHl~~lG--~t~e~ia~~Ka~I~k~~ 166 (397)
T TIGR01499 142 LDHTEILG--DTLEEIAWEKAGIIKEG 166 (397)
T ss_pred HHHHHHhC--ccHHHHHHHHhCccCCC
Confidence 58999995 58999999998887755
No 143
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=21.47 E-value=92 Score=26.97 Aligned_cols=42 Identities=24% Similarity=0.510 Sum_probs=28.4
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCC
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGE 149 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e 149 (187)
...|..|+.+-. +... +..+ +-+|+.|....++-.+.=||+|
T Consensus 117 ~~~C~~C~~~~~--~~~~-~~~~--~p~C~~Cg~~g~lrP~vV~FGE 158 (242)
T PTZ00408 117 KVRCTATGHVFD--WTED-VVHG--SSRCKCCGCVGTLRPHIVWFGE 158 (242)
T ss_pred eEEECCCCcccC--chhh-hhcC--CCccccCCCCCCCCCCEEEcCC
Confidence 356999987532 1111 1122 3679999866789999999999
No 144
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=21.25 E-value=34 Score=34.22 Aligned_cols=66 Identities=18% Similarity=0.406 Sum_probs=39.8
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcC--CCCcceeeeccccCcCCC----------CCHHHHHHHcCCceeeeccc
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCG--GCNNLHLIADHLGWFGEP----------GSIEDFLAARGEEVKKGSVD 170 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~--gC~n~HLIADnLgwF~e~----------~nIEdil~~kGe~V~kg~~~ 170 (187)
--+|..|++.-.+ .| |..+|+ .|....+ -.|-||-.+ .+|+.++ ++| ..+--.|
T Consensus 398 P~~CP~C~s~l~~--------~~-~~~~C~n~~C~aq~~--~~i~hf~sr~aldI~GlG~~~i~~L~-~~G--~i~~~~D 463 (669)
T PRK14350 398 PDNCPSCKTALIK--------EG-AHLFCVNNHCPSVIV--ERIKYFCSKKCMNIVGLSDKTIEFLF-EKK--FISSEID 463 (669)
T ss_pred CCCCCCCCCEeee--------CC-EEEEECCCCCHHHHH--hhhheeccCCcccccCcCHHHHHHHH-HcC--CcCCHHH
Confidence 3479999987543 24 788997 4966532 155677432 2455544 455 2233456
Q ss_pred ccCcccccccCc
Q 029824 171 TLNLTLEDLAGR 182 (187)
Q Consensus 171 ~~~lt~eDl~g~ 182 (187)
=+.|+.|||...
T Consensus 464 ly~L~~~~l~~l 475 (669)
T PRK14350 464 LYTFNFDRLINL 475 (669)
T ss_pred HhhCCHHHHhhc
Confidence 667888887643
No 145
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=21.20 E-value=48 Score=27.59 Aligned_cols=42 Identities=26% Similarity=0.606 Sum_probs=27.5
Q ss_pred EEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCC
Q 029824 103 IFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEP 150 (187)
Q Consensus 103 ~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~ 150 (187)
...|..|+.+.... ..+... -+-+||.|. ..+-.+.=||+|.
T Consensus 109 ~~~C~~C~~~~~~~---~~~~~~-~~p~C~~Cg--g~lrp~Vv~fge~ 150 (224)
T cd01412 109 RVRCSSCGYVGENN---EEIPEE-ELPRCPKCG--GLLRPGVVWFGES 150 (224)
T ss_pred ccccCCCCCCCCcc---hhhhcc-CCCCCCCCC--CccCCceEECCCC
Confidence 35699998875332 111111 257899996 5677888899984
No 146
>PF01606 Arteri_env: Arterivirus envelope protein; InterPro: IPR002556 This family consists of viral envelope proteins from the Arteriviridae; this includes Porcine reproductive and respiratory syndrome virus (PRRSV) envelope protein GP3 and Lactate dehydrogenase-elevating virus (LDV) structural glycoprotein. Arteriviruses consists of positive ssRNA and do not have a DNA stage.
Probab=21.19 E-value=56 Score=28.70 Aligned_cols=25 Identities=40% Similarity=0.751 Sum_probs=19.8
Q ss_pred ceEEEEe-cCCCCCccccccChhhccCce
Q 029824 99 DLAMIFT-CKVCETRSVKTACRESYEKGV 126 (187)
Q Consensus 99 ~l~l~FT-C~~C~tRs~k~iSk~AY~~Gv 126 (187)
.|.+-|| |+.|.|| .-..+.|+-|-
T Consensus 46 EL~vNyTvC~pClt~---qaa~q~~epgr 71 (214)
T PF01606_consen 46 ELTVNYTVCPPCLTR---QAAAQIYEPGR 71 (214)
T ss_pred EEEEeeEecCCccch---HHHHHhcCCCC
Confidence 4788888 9999999 55677888774
No 147
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=20.76 E-value=90 Score=24.20 Aligned_cols=31 Identities=19% Similarity=0.522 Sum_probs=24.0
Q ss_pred eEEEEecCCCCCccccccChhhccCceEEEEcCCCCcc
Q 029824 100 LAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 100 l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~ 137 (187)
+.-.|+|..|+....+.. ++=|-+|..|...
T Consensus 32 q~a~y~CpfCgk~~vkR~-------a~GIW~C~~C~~~ 62 (91)
T TIGR00280 32 QKAKYVCPFCGKKTVKRG-------STGIWTCRKCGAK 62 (91)
T ss_pred HhcCccCCCCCCCceEEE-------eeEEEEcCCCCCE
Confidence 345799999997766543 5778999999865
No 148
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=20.48 E-value=74 Score=26.57 Aligned_cols=35 Identities=17% Similarity=0.456 Sum_probs=29.7
Q ss_pred ecCCCCCccccccChhhccCceEEE---EcCCCCccee
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVA---RCGGCNNLHL 139 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViV---qC~gC~n~HL 139 (187)
.|..|+.-.++-+.-...+.|..|- .|++|..+.-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 4899999999999888889999884 5999998753
No 149
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=20.42 E-value=1.7e+02 Score=21.30 Aligned_cols=61 Identities=11% Similarity=0.123 Sum_probs=33.0
Q ss_pred cCCCCceEEEEecCCCCCccccccChhhccCceEEEEcCCCCcceeeeccccCcCCCCCHHHHHHHcC
Q 029824 94 TSARHDLAMIFTCKVCETRSVKTACRESYEKGVVVARCGGCNNLHLIADHLGWFGEPGSIEDFLAARG 161 (187)
Q Consensus 94 ~~pR~~l~l~FTC~~C~tRs~k~iSk~AY~~GvViVqC~gC~n~HLIADnLgwF~e~~nIEdil~~kG 161 (187)
+.|.....+.++|+ |+..-. .+.-+.. +.+--|++|.---- .. ....+..+-||.|.+.-|
T Consensus 6 IHP~y~~~~~v~c~-~~~~~~---~~ST~~~-i~vdv~s~~HPfyT-G~-~~~~~~~Grv~kF~kr~~ 66 (68)
T CHL00136 6 IHPQWFPETKVYCD-GQLVMT---VGSTKPE-LNVDIWSGNHPFYT-GS-QKIIDTEGRVERFMKKYG 66 (68)
T ss_pred CCCCceeeEEEEEc-CCCEEE---EeecCCC-EEEEeCCCCCccCc-CC-eeEecccccHHHHHHHhC
Confidence 46754446688895 887522 1222233 88888999864311 11 112223456777766544
No 150
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=20.41 E-value=81 Score=25.59 Aligned_cols=37 Identities=19% Similarity=0.391 Sum_probs=26.9
Q ss_pred EEEEecCCCCCccc--c-ccChhhccCceEEEEcCCCCcc
Q 029824 101 AMIFTCKVCETRSV--K-TACRESYEKGVVVARCGGCNNL 137 (187)
Q Consensus 101 ~l~FTC~~C~tRs~--k-~iSk~AY~~GvViVqC~gC~n~ 137 (187)
.|.-.|.+||+--+ + +=.|.|=+--+|+-.|++|+-+
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k 111 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYK 111 (116)
T ss_pred chhccCcccCCchhhhhhhhcccccCCceEEEEcCcccee
Confidence 45667999997631 1 2246677778999999999865
No 151
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.32 E-value=2.1e+02 Score=22.82 Aligned_cols=23 Identities=26% Similarity=0.483 Sum_probs=13.0
Q ss_pred eEEEEcCCCCcceeeeccccCcC
Q 029824 126 VVVARCGGCNNLHLIADHLGWFG 148 (187)
Q Consensus 126 vViVqC~gC~n~HLIADnLgwF~ 148 (187)
|.=.+|+.|...=-=-=-|+||.
T Consensus 10 vt~l~C~~C~t~i~G~F~l~~~~ 32 (113)
T PF09862_consen 10 VTRLKCPSCGTEIEGEFELPWFA 32 (113)
T ss_pred EEEEEcCCCCCEEEeeeccchhh
Confidence 34467888876411122467885
No 152
>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=20.18 E-value=29 Score=21.10 Aligned_cols=22 Identities=45% Similarity=0.839 Sum_probs=9.5
Q ss_pred ecCCCCCccccccChhhccCceEEEEcCC
Q 029824 105 TCKVCETRSVKTACRESYEKGVVVARCGG 133 (187)
Q Consensus 105 TC~~C~tRs~k~iSk~AY~~GvViVqC~g 133 (187)
+|-+|++.-. +..|-|.++|++
T Consensus 1 ~CP~C~s~l~-------~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGSKLV-------REEGEVDIRCPN 22 (28)
T ss_dssp B-TTT--BEE-------E-CCTTCEEE--
T ss_pred CcCCCCCEeE-------cCCCCEeEECCC
Confidence 5777876633 344556667764
Done!