Query psy13378
Match_columns 272
No_of_seqs 219 out of 333
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 17:56:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13378.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13378hhsearch_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 3.6E-35 7.7E-40 221.3 5.0 66 116-184 1-66 (66)
2 KOG3277|consensus 100.0 8.4E-34 1.8E-38 244.0 7.5 80 109-189 69-148 (165)
3 KOG3277|consensus 99.8 1.7E-21 3.7E-26 168.2 5.2 91 135-269 70-160 (165)
4 PF05180 zf-DNL: DNL zinc fing 99.8 5.3E-20 1.2E-24 139.1 3.0 65 142-252 2-66 (66)
5 PF13719 zinc_ribbon_5: zinc-r 94.4 0.032 7E-07 37.6 2.2 34 118-153 1-34 (37)
6 PF13717 zinc_ribbon_4: zinc-r 93.4 0.07 1.5E-06 35.9 2.4 33 118-152 1-33 (36)
7 PF01096 TFIIS_C: Transcriptio 91.8 0.1 2.2E-06 35.6 1.6 12 116-127 25-36 (39)
8 smart00440 ZnF_C2C2 C2C2 Zinc 91.4 0.17 3.6E-06 34.8 2.3 31 121-151 2-35 (40)
9 TIGR02098 MJ0042_CXXC MJ0042 f 91.2 0.17 3.6E-06 33.4 2.1 33 118-153 1-34 (38)
10 PF01096 TFIIS_C: Transcriptio 90.1 0.17 3.8E-06 34.4 1.5 34 120-153 1-37 (39)
11 smart00440 ZnF_C2C2 C2C2 Zinc 89.2 0.32 7E-06 33.4 2.2 37 87-128 1-37 (40)
12 PF05207 zf-CSL: CSL zinc fing 88.4 0.4 8.6E-06 35.0 2.3 33 118-153 17-49 (55)
13 PRK00398 rpoP DNA-directed RNA 88.0 0.4 8.7E-06 33.1 2.1 35 118-159 2-36 (46)
14 KOG2923|consensus 88.0 0.34 7.3E-06 37.6 1.9 32 119-152 20-52 (67)
15 PF03367 zf-ZPR1: ZPR1 zinc-fi 88.0 0.52 1.1E-05 40.8 3.3 53 88-144 3-56 (161)
16 TIGR00340 zpr1_rel ZPR1-relate 87.2 0.57 1.2E-05 41.1 3.0 46 89-140 1-49 (163)
17 TIGR01206 lysW lysine biosynth 85.9 0.59 1.3E-05 34.5 2.1 34 119-157 2-35 (54)
18 COG3478 Predicted nucleic-acid 85.7 0.71 1.5E-05 35.9 2.5 43 84-128 2-49 (68)
19 COG5216 Uncharacterized conser 83.6 1 2.2E-05 34.8 2.6 31 118-151 21-51 (67)
20 PRK03564 formate dehydrogenase 81.5 1.2 2.6E-05 42.7 2.8 51 88-163 189-241 (309)
21 TIGR01385 TFSII transcription 80.7 1.2 2.7E-05 42.2 2.6 33 120-152 259-294 (299)
22 PF09723 Zn-ribbon_8: Zinc rib 80.6 1.1 2.5E-05 30.7 1.7 14 86-99 5-18 (42)
23 PF05907 DUF866: Eukaryotic pr 80.6 1.7 3.6E-05 37.8 3.1 75 81-156 25-111 (161)
24 smart00709 Zpr1 Duplicated dom 77.4 3.3 7.2E-05 36.1 4.0 51 88-144 2-55 (160)
25 PF09855 DUF2082: Nucleic-acid 76.7 2.2 4.8E-05 32.4 2.4 42 87-128 1-45 (64)
26 PRK00398 rpoP DNA-directed RNA 76.7 2 4.4E-05 29.6 2.0 31 84-129 1-31 (46)
27 TIGR01562 FdhE formate dehydro 75.6 2.3 5E-05 40.7 2.7 52 88-164 186-240 (305)
28 TIGR01384 TFS_arch transcripti 75.1 2.4 5.1E-05 33.3 2.3 38 86-128 62-99 (104)
29 TIGR01385 TFSII transcription 73.4 2.6 5.6E-05 40.2 2.5 38 86-128 258-295 (299)
30 COG1594 RPB9 DNA-directed RNA 71.0 6.9 0.00015 32.3 4.2 35 119-153 72-109 (113)
31 PHA00626 hypothetical protein 71.0 2.8 6E-05 32.0 1.7 16 119-138 23-38 (59)
32 PF14353 CpXC: CpXC protein 69.8 2 4.3E-05 34.8 0.8 60 88-149 3-70 (128)
33 PF07282 OrfB_Zn_ribbon: Putat 69.0 3.7 8.1E-05 29.8 2.0 26 88-128 30-55 (69)
34 smart00834 CxxC_CXXC_SSSS Puta 67.6 3.6 7.8E-05 26.9 1.5 11 86-96 5-15 (41)
35 KOG2703|consensus 67.5 5.2 0.00011 40.5 3.2 54 88-147 41-96 (460)
36 COG1571 Predicted DNA-binding 67.2 2.2 4.8E-05 42.8 0.6 49 88-155 352-403 (421)
37 PF05129 Elf1: Transcription e 67.0 2.3 5.1E-05 33.3 0.6 14 140-153 42-55 (81)
38 PF05605 zf-Di19: Drought indu 66.5 2.1 4.6E-05 30.3 0.3 9 86-94 2-10 (54)
39 TIGR02605 CxxC_CxxC_SSSS putat 66.5 3.9 8.3E-05 28.4 1.6 39 86-136 5-44 (52)
40 PF09986 DUF2225: Uncharacteri 65.8 5.2 0.00011 35.9 2.6 44 86-129 5-58 (214)
41 PF13719 zinc_ribbon_5: zinc-r 65.3 3.6 7.8E-05 27.6 1.2 16 143-158 1-16 (37)
42 KOG2907|consensus 64.9 4.6 0.0001 34.3 2.0 34 88-128 76-111 (116)
43 TIGR00310 ZPR1_znf ZPR1 zinc f 64.4 5.6 0.00012 35.7 2.5 25 114-138 25-49 (192)
44 PRK03824 hypA hydrogenase nick 63.6 5.1 0.00011 33.8 2.0 51 84-134 68-122 (135)
45 KOG3507|consensus 62.5 8.6 0.00019 29.6 2.9 31 83-129 17-47 (62)
46 PRK00464 nrdR transcriptional 62.2 5 0.00011 35.0 1.8 36 88-128 2-37 (154)
47 PF07295 DUF1451: Protein of u 61.7 3.6 7.8E-05 35.6 0.8 28 119-153 112-139 (146)
48 KOG1074|consensus 61.4 3.6 7.8E-05 44.7 0.9 77 86-163 633-728 (958)
49 TIGR00100 hypA hydrogenase nic 61.3 5.1 0.00011 32.8 1.6 15 120-134 87-101 (115)
50 PF08271 TF_Zn_Ribbon: TFIIB z 61.0 8 0.00017 26.3 2.3 7 120-126 20-26 (43)
51 smart00659 RPOLCX RNA polymera 60.2 8.4 0.00018 27.2 2.3 11 86-96 2-12 (44)
52 PF13453 zf-TFIIB: Transcripti 59.8 8.7 0.00019 26.0 2.3 28 121-153 1-28 (41)
53 PRK12380 hydrogenase nickel in 59.4 6 0.00013 32.4 1.7 15 120-134 87-101 (113)
54 PHA02998 RNA polymerase subuni 59.3 7.3 0.00016 35.7 2.4 35 119-153 143-180 (195)
55 PF13717 zinc_ribbon_4: zinc-r 58.6 5.6 0.00012 26.7 1.2 17 143-159 1-17 (36)
56 PF03833 PolC_DP2: DNA polymer 57.7 3.4 7.4E-05 44.9 0.0 20 182-201 746-765 (900)
57 PRK00464 nrdR transcriptional 57.5 8.3 0.00018 33.7 2.3 35 121-155 2-39 (154)
58 TIGR00416 sms DNA repair prote 57.3 7 0.00015 38.8 2.1 29 119-158 7-35 (454)
59 PF04216 FdhE: Protein involve 56.4 4.6 0.0001 37.2 0.7 8 88-95 174-181 (290)
60 PF10122 Mu-like_Com: Mu-like 56.3 11 0.00023 28.1 2.4 32 119-156 4-36 (51)
61 PF05129 Elf1: Transcription e 56.2 5.8 0.00013 31.1 1.1 43 77-128 13-55 (81)
62 PRK00564 hypA hydrogenase nick 56.2 7.5 0.00016 32.0 1.8 15 120-134 89-103 (117)
63 COG1675 TFA1 Transcription ini 55.9 3.7 8.1E-05 36.7 -0.0 8 119-126 132-139 (176)
64 COG1594 RPB9 DNA-directed RNA 55.6 8.9 0.00019 31.7 2.1 38 86-128 72-109 (113)
65 PHA02998 RNA polymerase subuni 55.1 9.5 0.00021 34.9 2.4 37 87-128 144-180 (195)
66 PF09332 Mcm10: Mcm10 replicat 54.1 6.5 0.00014 38.4 1.3 82 85-183 251-338 (344)
67 COG2956 Predicted N-acetylgluc 53.7 9.2 0.0002 38.1 2.2 31 118-159 353-383 (389)
68 PRK11032 hypothetical protein; 53.5 6.2 0.00013 34.8 0.9 28 119-153 124-151 (160)
69 KOG2824|consensus 53.4 12 0.00025 36.1 2.8 7 87-93 230-236 (281)
70 PRK11823 DNA repair protein Ra 53.3 8.6 0.00019 37.9 2.0 29 119-158 7-35 (446)
71 PRK14892 putative transcriptio 53.1 12 0.00025 30.7 2.4 30 119-153 21-51 (99)
72 PF14354 Lar_restr_allev: Rest 53.0 12 0.00025 26.7 2.1 32 121-152 5-37 (61)
73 PF08996 zf-DNA_Pol: DNA Polym 52.4 7.7 0.00017 34.0 1.3 35 118-152 17-53 (188)
74 TIGR01384 TFS_arch transcripti 52.2 12 0.00025 29.4 2.2 36 118-153 61-99 (104)
75 TIGR00373 conserved hypothetic 51.9 5.1 0.00011 34.5 0.1 25 33-57 23-47 (158)
76 COG1779 C4-type Zn-finger prot 51.5 20 0.00043 33.1 3.8 60 86-149 14-73 (201)
77 COG1631 RPL42A Ribosomal prote 51.3 14 0.0003 30.6 2.5 21 108-128 57-77 (94)
78 PF01155 HypA: Hydrogenase exp 51.3 6.7 0.00015 31.9 0.8 9 118-126 69-77 (113)
79 PF01155 HypA: Hydrogenase exp 51.2 5.1 0.00011 32.6 0.0 36 82-134 66-101 (113)
80 COG4888 Uncharacterized Zn rib 51.1 11 0.00024 31.6 2.0 14 83-96 19-32 (104)
81 smart00653 eIF2B_5 domain pres 51.0 15 0.00033 30.4 2.8 30 120-153 81-110 (110)
82 COG0484 DnaJ DnaJ-class molecu 50.9 15 0.00032 36.5 3.1 14 115-128 179-192 (371)
83 KOG0416|consensus 50.7 6.5 0.00014 35.8 0.6 17 24-40 71-87 (189)
84 TIGR00100 hypA hydrogenase nic 49.3 11 0.00025 30.8 1.8 32 114-154 65-96 (115)
85 COG1198 PriA Primosomal protei 49.1 11 0.00025 40.1 2.2 58 83-160 432-491 (730)
86 PRK03681 hypA hydrogenase nick 48.2 13 0.00027 30.5 1.9 15 120-134 88-102 (114)
87 PF09538 FYDLN_acid: Protein o 47.1 9.6 0.00021 31.5 1.0 14 83-96 6-19 (108)
88 PRK03988 translation initiatio 46.7 20 0.00043 30.8 2.9 33 120-156 103-135 (138)
89 smart00531 TFIIE Transcription 46.2 9.7 0.00021 32.1 1.0 23 35-57 12-34 (147)
90 PF14205 Cys_rich_KTR: Cystein 45.9 15 0.00033 27.7 1.8 42 120-162 5-47 (55)
91 PF09082 DUF1922: Domain of un 45.7 14 0.0003 28.8 1.7 10 85-95 2-11 (68)
92 COG1645 Uncharacterized Zn-fin 45.4 8.3 0.00018 33.3 0.4 33 114-155 23-55 (131)
93 COG4888 Uncharacterized Zn rib 44.9 21 0.00045 30.0 2.7 45 116-161 19-63 (104)
94 PRK14714 DNA polymerase II lar 44.5 24 0.00052 40.2 3.8 10 87-96 668-677 (1337)
95 PRK04023 DNA polymerase II lar 44.1 14 0.00031 41.1 2.0 10 119-128 638-647 (1121)
96 PF12760 Zn_Tnp_IS1595: Transp 43.9 13 0.00029 25.6 1.2 9 87-95 19-27 (46)
97 PF01873 eIF-5_eIF-2B: Domain 43.8 14 0.00031 31.1 1.6 31 120-154 94-124 (125)
98 cd01121 Sms Sms (bacterial rad 43.4 12 0.00027 36.2 1.3 28 120-158 1-28 (372)
99 PF03226 Yippee-Mis18: Yippee 43.2 47 0.001 25.7 4.3 70 85-167 1-74 (96)
100 KOG2907|consensus 43.2 19 0.00041 30.7 2.2 38 117-154 72-112 (116)
101 TIGR00244 transcriptional regu 42.8 16 0.00035 32.1 1.8 35 121-155 2-39 (147)
102 PRK06266 transcription initiat 42.8 8.3 0.00018 33.9 0.1 26 32-57 30-55 (178)
103 PF10058 DUF2296: Predicted in 42.6 28 0.00061 25.5 2.8 33 85-128 21-53 (54)
104 PRK12336 translation initiatio 41.2 26 0.00057 31.3 3.0 37 119-159 98-134 (201)
105 PF05876 Terminase_GpA: Phage 40.7 25 0.00054 35.9 3.1 16 218-233 347-362 (557)
106 KOG3134|consensus 40.5 14 0.00029 34.6 1.1 31 120-152 1-32 (225)
107 COG5109 Uncharacterized conser 39.4 14 0.0003 36.7 1.0 30 131-160 359-392 (396)
108 COG1066 Sms Predicted ATP-depe 38.9 20 0.00043 36.6 2.0 30 118-158 6-35 (456)
109 PF04161 Arv1: Arv1-like famil 38.1 22 0.00048 31.7 2.0 35 120-158 1-35 (208)
110 COG1997 RPL43A Ribosomal prote 37.7 24 0.00053 28.9 2.0 41 80-139 29-69 (89)
111 TIGR00311 aIF-2beta translatio 37.5 33 0.00071 29.3 2.9 33 120-156 98-130 (133)
112 COG1592 Rubrerythrin [Energy p 37.5 27 0.00059 31.1 2.4 26 86-129 134-159 (166)
113 PF01780 Ribosomal_L37ae: Ribo 37.4 24 0.00053 28.7 2.0 17 119-139 53-69 (90)
114 KOG1105|consensus 37.3 24 0.00051 34.2 2.2 13 86-98 255-267 (296)
115 COG1933 Archaeal DNA polymeras 36.6 4 8.8E-05 38.6 -3.0 62 79-154 131-193 (253)
116 PRK14892 putative transcriptio 35.4 48 0.001 27.2 3.4 46 77-134 12-57 (99)
117 PRK09678 DNA-binding transcrip 35.3 27 0.00058 27.3 1.8 35 87-128 2-38 (72)
118 PF03119 DNA_ligase_ZBD: NAD-d 35.1 8.8 0.00019 24.7 -0.7 21 121-148 1-21 (28)
119 cd00730 rubredoxin Rubredoxin; 35.0 17 0.00036 26.4 0.6 40 87-128 2-43 (50)
120 KOG2879|consensus 34.8 22 0.00048 34.5 1.5 37 87-128 240-285 (298)
121 PF04216 FdhE: Protein involve 34.7 19 0.00041 33.3 1.1 57 85-161 196-254 (290)
122 PF12647 RNHCP: RNHCP domain; 34.7 54 0.0012 26.9 3.5 20 114-133 62-81 (92)
123 PF01927 Mut7-C: Mut7-C RNAse 34.5 28 0.00061 29.2 2.0 15 138-152 118-132 (147)
124 PRK14714 DNA polymerase II lar 34.4 30 0.00065 39.5 2.7 83 66-153 611-701 (1337)
125 COG2051 RPS27A Ribosomal prote 34.4 42 0.00091 26.3 2.7 33 115-153 15-47 (67)
126 COG1773 Rubredoxin [Energy pro 34.4 25 0.00054 26.4 1.5 40 86-127 3-44 (55)
127 cd00729 rubredoxin_SM Rubredox 34.2 30 0.00064 23.0 1.7 10 86-95 2-11 (34)
128 KOG4216|consensus 33.8 35 0.00076 34.8 2.8 61 49-126 10-70 (479)
129 PF04032 Rpr2: RNAse P Rpr2/Rp 33.3 39 0.00085 25.1 2.4 36 88-126 48-84 (85)
130 PF03811 Zn_Tnp_IS1: InsA N-te 32.9 51 0.0011 22.5 2.6 32 118-151 4-36 (36)
131 PHA02942 putative transposase; 32.7 36 0.00077 33.3 2.6 28 119-154 325-352 (383)
132 PRK11788 tetratricopeptide rep 32.6 37 0.00081 30.6 2.6 31 120-161 355-385 (389)
133 PRK00415 rps27e 30S ribosomal 32.5 47 0.001 25.3 2.6 34 114-153 6-39 (59)
134 smart00531 TFIIE Transcription 32.3 32 0.00069 29.0 1.9 11 145-155 124-134 (147)
135 PF03604 DNA_RNApol_7kD: DNA d 32.3 23 0.00049 23.7 0.8 8 121-128 19-26 (32)
136 PF02146 SIR2: Sir2 family; I 32.2 21 0.00046 30.3 0.9 46 119-167 105-150 (178)
137 PF11781 RRN7: RNA polymerase 30.9 29 0.00062 23.5 1.2 26 87-128 9-34 (36)
138 cd00350 rubredoxin_like Rubred 30.7 25 0.00054 22.9 0.8 27 86-129 1-27 (33)
139 PF07754 DUF1610: Domain of un 30.6 30 0.00064 22.1 1.1 10 117-126 14-23 (24)
140 COG1503 eRF1 Peptide chain rel 30.5 34 0.00073 34.5 2.1 42 114-159 322-363 (411)
141 COG1326 Uncharacterized archae 30.3 52 0.0011 30.5 3.1 35 117-154 4-40 (201)
142 COG0484 DnaJ DnaJ-class molecu 30.2 39 0.00084 33.6 2.4 37 119-156 159-195 (371)
143 PF05191 ADK_lid: Adenylate ki 30.0 42 0.00091 22.7 1.9 22 87-109 2-23 (36)
144 PRK04023 DNA polymerase II lar 29.9 26 0.00056 39.2 1.3 28 66-93 577-604 (1121)
145 PLN00209 ribosomal protein S27 29.9 63 0.0014 26.3 3.2 34 114-153 31-64 (86)
146 PRK00762 hypA hydrogenase nick 29.7 32 0.00069 28.6 1.5 10 120-129 93-102 (124)
147 KOG2691|consensus 29.4 47 0.001 28.3 2.4 36 88-128 75-110 (113)
148 COG2888 Predicted Zn-ribbon RN 29.4 36 0.00078 26.2 1.6 10 84-93 25-34 (61)
149 TIGR02159 PA_CoA_Oxy4 phenylac 29.2 13 0.00028 32.0 -0.9 34 120-153 106-139 (146)
150 PTZ00083 40S ribosomal protein 29.0 68 0.0015 26.1 3.2 34 114-153 30-63 (85)
151 PRK00420 hypothetical protein; 29.0 26 0.00057 29.4 0.9 35 116-158 20-54 (112)
152 PF09862 DUF2089: Protein of u 28.9 1.1E+02 0.0024 25.8 4.6 51 122-184 1-63 (113)
153 PF00301 Rubredoxin: Rubredoxi 28.3 25 0.00054 25.2 0.6 40 87-128 2-43 (47)
154 PRK12495 hypothetical protein; 28.3 30 0.00064 32.5 1.2 31 114-153 37-67 (226)
155 PLN02913 dihydrofolate synthet 28.1 28 0.00061 35.0 1.1 31 157-193 208-238 (510)
156 KOG2817|consensus 27.9 22 0.00048 35.7 0.3 84 53-158 297-388 (394)
157 COG0675 Transposase and inacti 27.7 40 0.00088 29.5 1.9 8 146-153 324-331 (364)
158 smart00350 MCM minichromosome 27.0 26 0.00056 35.0 0.6 34 118-154 36-71 (509)
159 COG2023 RPR2 RNase P subunit R 26.9 41 0.0009 28.2 1.7 44 77-128 48-91 (105)
160 TIGR00354 polC DNA polymerase, 26.9 39 0.00084 37.8 1.9 70 66-153 576-646 (1095)
161 PF01667 Ribosomal_S27e: Ribos 26.1 48 0.001 24.8 1.8 32 115-152 3-34 (55)
162 TIGR03655 anti_R_Lar restricti 26.0 76 0.0016 22.5 2.7 9 120-128 27-35 (53)
163 PTZ00157 60S ribosomal protein 26.0 62 0.0013 26.2 2.5 18 111-128 61-78 (84)
164 COG1655 Uncharacterized protei 25.7 49 0.0011 31.7 2.1 13 84-96 17-29 (267)
165 TIGR01562 FdhE formate dehydro 25.7 56 0.0012 31.5 2.6 57 84-161 208-269 (305)
166 PF14056 DUF4250: Domain of un 25.6 25 0.00055 26.2 0.2 31 30-60 12-42 (55)
167 TIGR02300 FYDLN_acid conserved 25.5 34 0.00073 29.7 1.0 15 82-96 5-19 (129)
168 PRK00241 nudC NADH pyrophospha 25.5 52 0.0011 30.4 2.2 32 88-134 101-132 (256)
169 PRK11788 tetratricopeptide rep 25.5 54 0.0012 29.6 2.3 23 87-128 355-377 (389)
170 PRK05452 anaerobic nitric oxid 25.3 38 0.00083 33.8 1.4 44 83-128 422-467 (479)
171 PF08792 A2L_zn_ribbon: A2L zi 25.3 60 0.0013 21.7 1.9 7 87-93 4-10 (33)
172 KOG2186|consensus 24.9 32 0.00068 33.1 0.7 47 84-141 1-47 (276)
173 PF10955 DUF2757: Protein of u 24.8 60 0.0013 25.7 2.2 14 83-96 1-14 (76)
174 PTZ00073 60S ribosomal protein 24.7 40 0.00088 27.7 1.2 31 84-132 14-44 (91)
175 PHA02942 putative transposase; 24.6 54 0.0012 32.0 2.3 10 119-128 342-351 (383)
176 TIGR00340 zpr1_rel ZPR1-relate 24.3 70 0.0015 28.2 2.7 34 122-155 1-39 (163)
177 cd01407 SIR2-fam SIR2 family o 24.3 44 0.00094 29.5 1.5 55 120-179 110-164 (218)
178 PRK14890 putative Zn-ribbon RN 24.3 41 0.00089 25.7 1.1 10 118-127 24-33 (59)
179 PF04981 NMD3: NMD3 family ; 24.1 80 0.0017 28.5 3.2 49 121-178 15-63 (236)
180 KOG2041|consensus 24.1 61 0.0013 35.8 2.7 49 88-152 1133-1182(1189)
181 COG5078 Ubiquitin-protein liga 23.7 50 0.0011 29.0 1.7 9 23-31 76-84 (153)
182 TIGR00280 L37a ribosomal prote 23.4 32 0.00069 28.1 0.4 11 83-93 32-42 (91)
183 smart00067 GHA Glycoprotein ho 23.2 42 0.00091 27.4 1.0 26 122-151 2-27 (87)
184 COG2816 NPY1 NTP pyrophosphohy 23.1 57 0.0012 31.3 2.1 63 119-189 129-204 (279)
185 PF04194 PDCD2_C: Programmed c 23.1 1.2E+02 0.0025 26.2 3.8 25 117-146 136-161 (164)
186 PF03107 C1_2: C1 domain; Int 23.0 59 0.0013 20.7 1.5 8 119-126 15-22 (30)
187 cd01735 LSm12_N LSm12 belongs 23.0 87 0.0019 23.7 2.7 29 196-225 25-53 (61)
188 PRK03976 rpl37ae 50S ribosomal 22.8 35 0.00075 27.8 0.5 10 142-151 52-61 (90)
189 PF00096 zf-C2H2: Zinc finger, 22.8 42 0.00091 19.2 0.7 8 120-127 1-8 (23)
190 PTZ00255 60S ribosomal protein 22.7 36 0.00078 27.7 0.6 13 81-93 31-43 (90)
191 PF04438 zf-HIT: HIT zinc fing 22.5 59 0.0013 21.3 1.4 9 120-128 14-22 (30)
192 PRK09521 exosome complex RNA-b 22.3 1E+02 0.0022 26.9 3.3 17 119-135 166-182 (189)
193 PRK14138 NAD-dependent deacety 22.2 49 0.0011 30.2 1.4 56 120-179 120-175 (244)
194 TIGR00686 phnA alkylphosphonat 21.8 1.7E+02 0.0038 24.8 4.4 31 179-209 73-104 (109)
195 PF06943 zf-LSD1: LSD1 zinc fi 21.8 50 0.0011 21.3 1.0 17 136-152 8-24 (25)
196 PF14196 ATC_hydrolase: L-2-am 21.5 55 0.0012 26.2 1.4 58 171-230 61-130 (149)
197 PHA00732 hypothetical protein 21.4 35 0.00075 26.6 0.3 12 87-98 2-13 (79)
198 COG1996 RPC10 DNA-directed RNA 21.0 1E+02 0.0022 22.7 2.5 33 116-155 3-35 (49)
199 PF13824 zf-Mss51: Zinc-finger 20.8 41 0.00089 25.2 0.5 11 118-128 13-23 (55)
200 KOG0417|consensus 20.6 37 0.00081 30.0 0.3 8 24-31 72-79 (148)
201 COG3058 FdhE Uncharacterized p 20.4 15 0.00032 35.8 -2.4 47 88-153 187-234 (308)
202 PF15446 zf-PHD-like: PHD/FYVE 20.3 62 0.0013 29.4 1.6 84 43-126 75-175 (175)
203 TIGR02642 phage_xxxx uncharact 20.3 97 0.0021 28.0 2.9 50 116-177 96-152 (186)
204 PF14446 Prok-RING_1: Prokaryo 20.2 60 0.0013 24.3 1.3 25 121-154 7-31 (54)
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=3.6e-35 Score=221.34 Aligned_cols=66 Identities=58% Similarity=1.065 Sum_probs=51.8
Q ss_pred eEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCee
Q psy13378 116 LKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQG 184 (272)
Q Consensus 116 ~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V 184 (272)
|+|.|||++|++||+|+|||+||++|+||||||||+|+||||||||||.|. +.||||||++|||+|
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 YQLTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIADNLGWFGEN---KRNIEDILKEKGEKV 66 (66)
T ss_dssp EEEEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES--SS-SGGGS------HHHHHHHH----
T ss_pred CeEEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeehhhhcccccC---CCCHHHHHHHcCCcC
Confidence 789999999999999999999999999999999999999999999999985 479999999999986
No 2
>KOG3277|consensus
Probab=100.00 E-value=8.4e-34 Score=244.02 Aligned_cols=80 Identities=63% Similarity=1.003 Sum_probs=76.3
Q ss_pred ccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCeeeece
Q psy13378 109 VIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGL 188 (272)
Q Consensus 109 v~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V~kg~ 188 (272)
+..++|+|+|.|||++|++|++|.|||+||++||||||||||+|+||||||||||.|.+ |++||||||++|||+|+++.
T Consensus 69 ~~~~kp~m~l~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~HliaDnL~~F~d~~-~~~nied~l~~kge~v~~~~ 147 (165)
T KOG3277|consen 69 FKVPKPRMQLAYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLIADNLGWFHDLK-GKRNIEDILAAKGEQVKRNL 147 (165)
T ss_pred ccCCCcceEEEEEeeccCCccccccChhhhhCceEEEECCCCccceeehhhhccccccc-ccccHHHHHHhccceeeeec
Confidence 36788999999999999999999999999999999999999999999999999999986 87899999999999999987
Q ss_pred e
Q psy13378 189 F 189 (272)
Q Consensus 189 ~ 189 (272)
.
T Consensus 148 g 148 (165)
T KOG3277|consen 148 G 148 (165)
T ss_pred c
Confidence 4
No 3
>KOG3277|consensus
Probab=99.84 E-value=1.7e-21 Score=168.17 Aligned_cols=91 Identities=42% Similarity=0.609 Sum_probs=78.5
Q ss_pred hhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCeeeeceeeeccceeccccceeEEEEeecchhh
Q psy13378 135 KHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLI 214 (272)
Q Consensus 135 K~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V~kg~~~~~~die~~~~~~~~vi~~C~~~~~ 214 (272)
+.---+..|..+|.-|+.|-. +||.+. .+.+|+ |||+|||
T Consensus 70 ~~~kp~m~l~yTCkvCntRs~---------------ktisk~------AY~~Gv----------------VivqC~g--- 109 (165)
T KOG3277|consen 70 KVPKPRMQLAYTCKVCNTRST---------------KTISKQ------AYEKGV----------------VIVQCPG--- 109 (165)
T ss_pred cCCCcceEEEEEeeccCCccc---------------cccChh------hhhCce----------------EEEECCC---
Confidence 445567889999999999865 588884 477777 8999997
Q ss_pred hcccccceeeecccCCccCCCCCcCCHHHHHHhcCCcEEEecCCCcEEEeccccc
Q psy13378 215 RETHGSHHLIADNLKWFSDLKPGVTNIEHILAEKGEQVRRIDSNGAIELIEDEKK 269 (272)
Q Consensus 215 ~~~C~n~HlIADnLGwF~d~~~g~~nIE~iL~~kGE~V~r~~~~~~lE~~~~~~~ 269 (272)
|.|+||||||||||.|.+ |++||||||++|||+|++..+|+..|.+.+.+|
T Consensus 110 ---C~~~HliaDnL~~F~d~~-~~~nied~l~~kge~v~~~~g~~~~e~i~~~~~ 160 (165)
T KOG3277|consen 110 ---CKNHHLIADNLGWFHDLK-GKRNIEDILAAKGEQVKRNLGDGEDEDIPEDSK 160 (165)
T ss_pred ---Cccceeehhhhccccccc-ccccHHHHHHhccceeeeecccccccccccccc
Confidence 999999999999999998 688999999999999999988888888766543
No 4
>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=99.78 E-value=5.3e-20 Score=139.13 Aligned_cols=65 Identities=38% Similarity=0.636 Sum_probs=41.2
Q ss_pred EEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCeeeeceeeeccceeccccceeEEEEeecchhhhcccccc
Q psy13378 142 VVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSH 221 (272)
Q Consensus 142 vViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V~kg~~~~~~die~~~~~~~~vi~~C~~~~~~~~C~n~ 221 (272)
.+.-+|..|..|-. ++|...+ +.+|+ |||+||+ |+|+
T Consensus 2 ~l~FTC~~C~~Rs~---------------~~~sk~a------Y~~Gv----------------Viv~C~g------C~~~ 38 (66)
T PF05180_consen 2 QLTFTCNKCGTRSA---------------KMFSKQA------YHKGV----------------VIVQCPG------CKNR 38 (66)
T ss_dssp EEEEEETTTTEEEE---------------EEEEHHH------HHTSE----------------EEEE-TT------S--E
T ss_pred eEEEEcCCCCCccc---------------eeeCHHH------HhCCe----------------EEEECCC------Ccce
Confidence 45678999987765 3444433 55555 8999997 9999
Q ss_pred eeeecccCCccCCCCCcCCHHHHHHhcCCcE
Q psy13378 222 HLIADNLKWFSDLKPGVTNIEHILAEKGEQV 252 (272)
Q Consensus 222 HlIADnLGwF~d~~~g~~nIE~iL~~kGE~V 252 (272)
||||||||||.|. ++||||||++|||+|
T Consensus 39 HlIaDnLg~f~e~---~~~iE~~l~~kge~v 66 (66)
T PF05180_consen 39 HLIADNLGWFGEN---KRNIEDILKEKGEKV 66 (66)
T ss_dssp EES--SS-SGGGS------HHHHHHHH----
T ss_pred eeehhhhcccccC---CCCHHHHHHHcCCcC
Confidence 9999999999984 689999999999987
No 5
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.40 E-value=0.032 Score=37.57 Aligned_cols=34 Identities=26% Similarity=0.565 Sum_probs=26.6
Q ss_pred EEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
|..+|+.|+++ ..|.+.....+-..++|+.|+..
T Consensus 1 M~i~CP~C~~~--f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 1 MIITCPNCQTR--FRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred CEEECCCCCce--EEcCHHHcccCCcEEECCCCCcE
Confidence 46789999976 88888776666668999999853
No 6
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=93.37 E-value=0.07 Score=35.94 Aligned_cols=33 Identities=21% Similarity=0.469 Sum_probs=24.4
Q ss_pred EEEEcCCCCcccccccchhcccceEEEEEcCCCCc
Q psy13378 118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSN 152 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n 152 (272)
|.++|+.|+++ ..|++...-..-+-+||+.|..
T Consensus 1 M~i~Cp~C~~~--y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 1 MIITCPNCQAK--YEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred CEEECCCCCCE--EeCCHHHCCCCCcEEECCCCCC
Confidence 35788888866 7777776666666888888874
No 7
>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=91.85 E-value=0.1 Score=35.55 Aligned_cols=12 Identities=42% Similarity=1.018 Sum_probs=6.0
Q ss_pred eEEEEEcCCCCc
Q psy13378 116 LKLAYTCKVCGT 127 (272)
Q Consensus 116 ~~L~FTCk~C~t 127 (272)
+.+-|+|..|++
T Consensus 25 ~T~fy~C~~C~~ 36 (39)
T PF01096_consen 25 MTLFYVCCNCGH 36 (39)
T ss_dssp SEEEEEESSSTE
T ss_pred CeEEEEeCCCCC
Confidence 344555555553
No 8
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=91.43 E-value=0.17 Score=34.78 Aligned_cols=31 Identities=26% Similarity=0.611 Sum_probs=14.5
Q ss_pred EcCCCCcccccccch---hcccceEEEEEcCCCC
Q psy13378 121 TCKVCGTRNSHLISK---HSYEKGVVIVKCEGCS 151 (272)
Q Consensus 121 TCk~C~tRS~h~ISK---~AY~kGvViVqC~gC~ 151 (272)
.|+.|+++.+..+.. .|-+-.+++..|..|.
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~ 35 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCG 35 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCC
Confidence 455555544444432 2334445555555554
No 9
>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=91.24 E-value=0.17 Score=33.39 Aligned_cols=33 Identities=21% Similarity=0.524 Sum_probs=20.2
Q ss_pred EEEEcCCCCcccccccchhcc-cceEEEEEcCCCCcc
Q psy13378 118 LAYTCKVCGTRNSHLISKHSY-EKGVVIVKCEGCSNN 153 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY-~kGvViVqC~gC~n~ 153 (272)
|.++|+.|++. -.|..... ..|. -++||.|+..
T Consensus 1 M~~~CP~C~~~--~~v~~~~~~~~~~-~v~C~~C~~~ 34 (38)
T TIGR02098 1 MRIQCPNCKTS--FRVVDSQLGANGG-KVRCGKCGHV 34 (38)
T ss_pred CEEECCCCCCE--EEeCHHHcCCCCC-EEECCCCCCE
Confidence 35788888865 44554333 3343 7788888753
No 10
>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=90.14 E-value=0.17 Score=34.43 Aligned_cols=34 Identities=18% Similarity=0.468 Sum_probs=25.9
Q ss_pred EEcCCCCcccccccch---hcccceEEEEEcCCCCcc
Q psy13378 120 YTCKVCGTRNSHLISK---HSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK---~AY~kGvViVqC~gC~n~ 153 (272)
|+|+.|+++.+..+.. .|-+..+++..|..|..+
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 4799999999888854 477888999999999854
No 11
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.22 E-value=0.32 Score=33.35 Aligned_cols=37 Identities=24% Similarity=0.665 Sum_probs=26.5
Q ss_pred eecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 87 YTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 87 fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
+.|+.|+.+.+.-+..| +......+.+-|+|..|+++
T Consensus 1 ~~Cp~C~~~~a~~~q~Q-----~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 1 APCPKCGNREATFFQLQ-----TRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred CcCCCCCCCeEEEEEEc-----ccCCCCCCeEEEEeCCCCCE
Confidence 47999997776644333 33445567799999999976
No 12
>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=88.35 E-value=0.4 Score=35.00 Aligned_cols=33 Identities=42% Similarity=0.856 Sum_probs=28.0
Q ss_pred EEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
..|.| .||.. -.|++...+.|.++|+|++|.-+
T Consensus 17 ~~y~C-RCG~~--f~i~e~~l~~~~~iv~C~sCSL~ 49 (55)
T PF05207_consen 17 YSYPC-RCGGE--FEISEEDLEEGEVIVQCDSCSLW 49 (55)
T ss_dssp EEEEE-TTSSE--EEEEHHHHHCT--EEEETTTTEE
T ss_pred EEEcC-CCCCE--EEEcchhccCcCEEEECCCCccE
Confidence 68999 99966 99999999999999999999864
No 13
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.01 E-value=0.4 Score=33.13 Aligned_cols=35 Identities=23% Similarity=0.510 Sum_probs=19.7
Q ss_pred EEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeecc
Q psy13378 118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADN 159 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADn 159 (272)
+.|.|+.|+.. -.+ ...+..++||.|.++=++.|+
T Consensus 2 ~~y~C~~CG~~--~~~-----~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 2 AEYKCARCGRE--VEL-----DEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred CEEECCCCCCE--EEE-----CCCCCceECCCCCCeEEEccC
Confidence 46777777754 222 122225677777776665444
No 14
>KOG2923|consensus
Probab=87.99 E-value=0.34 Score=37.59 Aligned_cols=32 Identities=31% Similarity=0.659 Sum_probs=28.6
Q ss_pred EEEcC-CCCcccccccchhcccceEEEEEcCCCCc
Q psy13378 119 AYTCK-VCGTRNSHLISKHSYEKGVVIVKCEGCSN 152 (272)
Q Consensus 119 ~FTCk-~C~tRS~h~ISK~AY~kGvViVqC~gC~n 152 (272)
+|+++ +||-| -.|++.-.+.|-.+++||+|.-
T Consensus 20 ~y~yPCpCGDr--f~It~edL~~ge~Va~CpsCSL 52 (67)
T KOG2923|consen 20 TYYYPCPCGDR--FQITLEDLENGEDVARCPSCSL 52 (67)
T ss_pred eEEcCCCCCCe--eeecHHHHhCCCeeecCCCceE
Confidence 57776 79988 9999999999999999999963
No 15
>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=87.96 E-value=0.52 Score=40.85 Aligned_cols=53 Identities=26% Similarity=0.546 Sum_probs=32.4
Q ss_pred ecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccchhcc-cceEEE
Q psy13378 88 TCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSY-EKGVVI 144 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY-~kGvVi 144 (272)
.|++|+......+ +...+--.+.-+.+.|.|+.|+.|+.-..+--+. .+|+.+
T Consensus 3 ~Cp~C~~~~~~~~----~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~~G~r~ 56 (161)
T PF03367_consen 3 LCPNCGENGTTRI----LLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQPKGVRI 56 (161)
T ss_dssp E-TTTSSCCEEEE----EEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-SSEEEE
T ss_pred cCCCCCCCcEEEE----EEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCCCceEE
Confidence 6999997643322 2222333456688999999999999888877777 455554
No 16
>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=87.17 E-value=0.57 Score=41.06 Aligned_cols=46 Identities=26% Similarity=0.526 Sum_probs=30.8
Q ss_pred cCCcCCccccc---ccCCcccccccccccceEEEEEcCCCCcccccccchhcccc
Q psy13378 89 CKVCGTRNSHL---ISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEK 140 (272)
Q Consensus 89 CkvC~TRSSh~---ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~k 140 (272)
|++|++..... .-+-+|- +.-+.+.|+|+.||.|++-..+--+.+.
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F------~evii~sf~C~~CGyr~~ev~~~~~~~p 49 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYF------GKIMLSTYICEKCGYRSTDVYQLEEKEP 49 (163)
T ss_pred CCCCCCcceEeeeEeccCCCc------ceEEEEEEECCCCCCchhheeEcCCcCC
Confidence 89999763222 1334443 3446789999999999887766665544
No 17
>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=85.91 E-value=0.59 Score=34.52 Aligned_cols=34 Identities=24% Similarity=0.612 Sum_probs=20.9
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcceeee
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIA 157 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIA 157 (272)
+|+|+.|+.. =.+. .-..|. ++.||.|....=+.
T Consensus 2 ~~~CP~CG~~--iev~--~~~~Ge-iV~Cp~CGaeleVv 35 (54)
T TIGR01206 2 QFECPDCGAE--IELE--NPELGE-LVICDECGAELEVV 35 (54)
T ss_pred ccCCCCCCCE--EecC--CCccCC-EEeCCCCCCEEEEE
Confidence 6888888853 2332 222255 55888888776553
No 18
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=85.69 E-value=0.71 Score=35.94 Aligned_cols=43 Identities=30% Similarity=0.604 Sum_probs=28.7
Q ss_pred eeeeecCCcCCcccccccCCcccc--ccc---ccccceEEEEEcCCCCcc
Q psy13378 84 KLAYTCKVCGTRNSHLISKHSYEK--GVI---KLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 84 ~i~fTCkvC~TRSSh~ISK~Sy~k--Gv~---~~~~~~~L~FTCk~C~tR 128 (272)
..+|.|+.|+-++-. .|+=..+ ++. .++..-.++.||+.|+-.
T Consensus 2 ~~~~kCpKCgn~~~~--ekei~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 2 KNAFKCPKCGNTNYE--EKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred CccccCCCcCCcchh--hceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence 356889999977643 2322222 222 566778889999999955
No 19
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=83.61 E-value=1 Score=34.76 Aligned_cols=31 Identities=39% Similarity=0.918 Sum_probs=26.8
Q ss_pred EEEEcCCCCcccccccchhcccceEEEEEcCCCC
Q psy13378 118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCS 151 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~ 151 (272)
..|-| +|+-| -.||-.-...|-|..+||+|.
T Consensus 21 ftyPC-PCGDR--FeIsLeDl~~GE~VArCPSCS 51 (67)
T COG5216 21 FTYPC-PCGDR--FEISLEDLRNGEVVARCPSCS 51 (67)
T ss_pred EEecC-CCCCE--eEEEHHHhhCCceEEEcCCce
Confidence 35556 59988 899999999999999999996
No 20
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=81.47 E-value=1.2 Score=42.73 Aligned_cols=51 Identities=29% Similarity=0.740 Sum_probs=30.6
Q ss_pred ecCCcCCccccccc--CCcccccccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeecccccc
Q psy13378 88 TCKVCGTRNSHLIS--KHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWF 163 (272)
Q Consensus 88 TCkvC~TRSSh~IS--K~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF 163 (272)
+|+|||..- .+| ..+...|.. -..|..|++. | .+|-++|+.|.+ .+.|..|
T Consensus 189 ~CPvCGs~P--~~s~v~~~~~~G~R--------yL~CslC~te---------W--~~~R~~C~~Cg~----~~~l~y~ 241 (309)
T PRK03564 189 FCPVCGSMP--VSSVVQIGTTQGLR--------YLHCNLCESE---------W--HVVRVKCSNCEQ----SGKLHYW 241 (309)
T ss_pred CCCCCCCcc--hhheeeccCCCCce--------EEEcCCCCCc---------c--cccCccCCCCCC----CCceeee
Confidence 899999543 222 111223442 4578889876 2 245678888887 3556655
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=80.70 E-value=1.2 Score=42.25 Aligned_cols=33 Identities=27% Similarity=0.663 Sum_probs=14.5
Q ss_pred EEcCCCCccccccc---chhcccceEEEEEcCCCCc
Q psy13378 120 YTCKVCGTRNSHLI---SKHSYEKGVVIVKCEGCSN 152 (272)
Q Consensus 120 FTCk~C~tRS~h~I---SK~AY~kGvViVqC~gC~n 152 (272)
|+|+.|+++..-.+ .+.|=+-.+++++|..|.+
T Consensus 259 ~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~ 294 (299)
T TIGR01385 259 FTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGN 294 (299)
T ss_pred ccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCC
Confidence 55555554433222 2223334455555555543
No 22
>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=80.59 E-value=1.1 Score=30.70 Aligned_cols=14 Identities=36% Similarity=0.850 Sum_probs=8.6
Q ss_pred eeecCCcCCccccc
Q psy13378 86 AYTCKVCGTRNSHL 99 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ 99 (272)
.|.|..||+.....
T Consensus 5 ey~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 5 EYRCEECGHEFEVL 18 (42)
T ss_pred EEEeCCCCCEEEEE
Confidence 46777777665443
No 23
>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=80.59 E-value=1.7 Score=37.82 Aligned_cols=75 Identities=16% Similarity=0.372 Sum_probs=40.7
Q ss_pred cceeeeeecCCcCCccccc--ccCCcccccccccccceEEEEEcCCCCcccccccch---hccc-------ceEEEEEcC
Q psy13378 81 HKLKLAYTCKVCGTRNSHL--ISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISK---HSYE-------KGVVIVKCE 148 (272)
Q Consensus 81 ~k~~i~fTCkvC~TRSSh~--ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK---~AY~-------kGvViVqC~ 148 (272)
..+.+...|..|++.+.+. |+..- ...+.--|+..-++++|+.|+..++-.|.+ .+|. .-++..-|.
T Consensus 25 ~~~~fkvkCt~CgE~~~k~V~i~~~e-~~e~~gsrG~aNfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~i~~fdCR 103 (161)
T PF05907_consen 25 FEWFFKVKCTSCGEVHPKWVYINRFE-KHEIPGSRGTANFVMKCKFCKRESSIDIIPGKGKPYTAEDSGKFVPILAFDCR 103 (161)
T ss_dssp --EEEEEEETTSS--EEEEEEE-TT--BEE-TTSS-EESEEE--SSSS--EEEEEE--TTTEEEGGGTTS-EEEEEEEEE
T ss_pred CEEEEEEEECCCCCccCcceEeecce-EEecCCCccceEeEecCcCcCCccEEEEEecCccccccccccCCceEEEEECC
Confidence 4588888999999877544 33321 112223456667899999999776655544 4565 446778899
Q ss_pred CCCcceee
Q psy13378 149 GCSNNHLI 156 (272)
Q Consensus 149 gC~n~HLI 156 (272)
||.----.
T Consensus 104 G~e~~~f~ 111 (161)
T PF05907_consen 104 GLEPVEFS 111 (161)
T ss_dssp SEEEEEE-
T ss_pred CcEeEEEe
Confidence 98654443
No 24
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=77.41 E-value=3.3 Score=36.08 Aligned_cols=51 Identities=27% Similarity=0.628 Sum_probs=30.4
Q ss_pred ecCCcCCcccc--cccCCcccccccccccceEEEEEcCCCCcccccccchhc-ccceEEE
Q psy13378 88 TCKVCGTRNSH--LISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHS-YEKGVVI 144 (272)
Q Consensus 88 TCkvC~TRSSh--~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~A-Y~kGvVi 144 (272)
.|++|+..... ..-+-+|- +.-+.+.|+|+.||.|++-..+--+ -.+|+.+
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F------~evii~sf~C~~CGyk~~ev~~~~~~~p~G~r~ 55 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYF------REVIIMSFECEHCGYRNNEVKSGGAIEPKGTRI 55 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCc------ceEEEEEEECCCCCCccceEEECcccCCCceEE
Confidence 48889854321 12223333 3446789999999999877644433 4456443
No 25
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=76.75 E-value=2.2 Score=32.44 Aligned_cols=42 Identities=21% Similarity=0.475 Sum_probs=23.3
Q ss_pred eecCCcCCcccccccCCccccccc---ccccceEEEEEcCCCCcc
Q psy13378 87 YTCKVCGTRNSHLISKHSYEKGVI---KLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 87 fTCkvC~TRSSh~ISK~Sy~kGv~---~~~~~~~L~FTCk~C~tR 128 (272)
|.|+.|+.+.-..-+-+..-.+++ .++.+-..+.+|+.|+..
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 689999966433222222222333 334555667788888754
No 26
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=76.72 E-value=2 Score=29.61 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=20.5
Q ss_pred eeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCccc
Q psy13378 84 KLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRN 129 (272)
Q Consensus 84 ~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS 129 (272)
++.|.|+.|+....- ..... .++|+.|+++-
T Consensus 1 ~~~y~C~~CG~~~~~-------~~~~~--------~~~Cp~CG~~~ 31 (46)
T PRK00398 1 MAEYKCARCGREVEL-------DEYGT--------GVRCPYCGYRI 31 (46)
T ss_pred CCEEECCCCCCEEEE-------CCCCC--------ceECCCCCCeE
Confidence 357899999976522 11110 48999999773
No 27
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=75.59 E-value=2.3 Score=40.72 Aligned_cols=52 Identities=29% Similarity=0.719 Sum_probs=29.2
Q ss_pred ecCCcCCccccccc---CCcccccccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccc
Q psy13378 88 TCKVCGTRNSHLIS---KHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFT 164 (272)
Q Consensus 88 TCkvC~TRSSh~IS---K~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~ 164 (272)
+|+|||.. +.+| ..+...|.. ...|..|++. | .+|-++|+.|.+. +.|+.|.
T Consensus 186 ~CPvCGs~--P~~s~~~~~~~~~G~R--------yL~CslC~te---------W--~~~R~~C~~Cg~~----~~l~y~~ 240 (305)
T TIGR01562 186 LCPACGSP--PVASMVRQGGKETGLR--------YLSCSLCATE---------W--HYVRVKCSHCEES----KHLAYLS 240 (305)
T ss_pred cCCCCCCh--hhhhhhcccCCCCCce--------EEEcCCCCCc---------c--cccCccCCCCCCC----CceeeEe
Confidence 89999944 3333 111233432 3568888765 2 2356778877773 5565553
No 28
>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=75.08 E-value=2.4 Score=33.33 Aligned_cols=38 Identities=18% Similarity=0.414 Sum_probs=23.4
Q ss_pred eeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
.+.|+.|+.+-+.-...| +......+.+-|+|..|+++
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q-----~RsadE~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQ-----TRRADEPETRFYKCTKCGYV 99 (104)
T ss_pred cCCCCCCCCCeeEEEEec-----cCCCCCCcEEEEEeCCCCCe
Confidence 468888887664432222 22233445688888888865
No 29
>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=73.42 E-value=2.6 Score=40.15 Aligned_cols=38 Identities=24% Similarity=0.586 Sum_probs=27.6
Q ss_pred eeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
.|+|+.|+.+-+.- |+..+......|.+-|+|..|++|
T Consensus 258 ~~~C~~C~~~~~~~-----~q~QtrsaDEpmT~f~~C~~Cg~~ 295 (299)
T TIGR01385 258 LFTCGKCKQKKCTY-----YQLQTRSADEPMTTFVTCEECGNR 295 (299)
T ss_pred cccCCCCCCccceE-----EEecccCCCCCCeEEEEcCCCCCe
Confidence 49999999876542 222344455667889999999987
No 30
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=71.03 E-value=6.9 Score=32.31 Aligned_cols=35 Identities=20% Similarity=0.454 Sum_probs=27.4
Q ss_pred EEEcCCCCcccccccchh---cccceEEEEEcCCCCcc
Q psy13378 119 AYTCKVCGTRNSHLISKH---SYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~---AY~kGvViVqC~gC~n~ 153 (272)
.++|+.|+++-....-.| |=+--+++.+|..|.++
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~ 109 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYR 109 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCE
Confidence 588999998866555444 55778899999999875
No 31
>PHA00626 hypothetical protein
Probab=71.03 E-value=2.8 Score=31.96 Aligned_cols=16 Identities=38% Similarity=0.717 Sum_probs=13.1
Q ss_pred EEEcCCCCcccccccchhcc
Q psy13378 119 AYTCKVCGTRNSHLISKHSY 138 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY 138 (272)
.|.|+.|+ +.|||.|+
T Consensus 23 rYkCkdCG----Y~ft~~~~ 38 (59)
T PHA00626 23 DYVCCDCG----YNDSKDAF 38 (59)
T ss_pred ceEcCCCC----Ceechhhh
Confidence 59999999 55888876
No 32
>PF14353 CpXC: CpXC protein
Probab=69.81 E-value=2 Score=34.85 Aligned_cols=60 Identities=22% Similarity=0.351 Sum_probs=30.1
Q ss_pred ecCCcCCcccccccCCccccc-----ccccccceEEEEEcCCCCcccccccchhccc---ceEEEEEcCC
Q psy13378 88 TCKVCGTRNSHLISKHSYEKG-----VIKLKHKLKLAYTCKVCGTRNSHLISKHSYE---KGVVIVKCEG 149 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~Sy~kG-----v~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~---kGvViVqC~g 149 (272)
||+.|++...-.+-.. .... ..++..-=...|||+.|++.. ..-.+-.|+ +..+|.--|.
T Consensus 3 tCP~C~~~~~~~v~~~-I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~-~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTS-INADEDPELKEKILDGSLFSFTCPSCGHKF-RLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred CCCCCCCeeEEEEEeE-EcCcCCHHHHHHHHcCCcCEEECCCCCCce-ecCCCEEEEcCCCCEEEEEcCC
Confidence 8999998754432211 1111 111222334589999999763 233333333 4455554444
No 33
>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=69.02 E-value=3.7 Score=29.82 Aligned_cols=26 Identities=42% Similarity=0.874 Sum_probs=16.9
Q ss_pred ecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 88 TCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
+|+.||.+.....+.. .|+|+.|+..
T Consensus 30 ~C~~CG~~~~~~~~~r---------------~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGR---------------VFTCPNCGFE 55 (69)
T ss_pred CccCcccccccccccc---------------eEEcCCCCCE
Confidence 7888887764411111 6899999854
No 34
>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=67.57 E-value=3.6 Score=26.89 Aligned_cols=11 Identities=36% Similarity=0.966 Sum_probs=5.7
Q ss_pred eeecCCcCCcc
Q psy13378 86 AYTCKVCGTRN 96 (272)
Q Consensus 86 ~fTCkvC~TRS 96 (272)
.|.|+.|++..
T Consensus 5 ~y~C~~Cg~~f 15 (41)
T smart00834 5 EYRCEDCGHTF 15 (41)
T ss_pred EEEcCCCCCEE
Confidence 35555555543
No 35
>KOG2703|consensus
Probab=67.48 E-value=5.2 Score=40.47 Aligned_cols=54 Identities=24% Similarity=0.596 Sum_probs=43.1
Q ss_pred ecCCcCCccc--ccccCCcccccccccccceEEEEEcCCCCcccccccchhcccceEEEEEc
Q psy13378 88 TCKVCGTRNS--HLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKC 147 (272)
Q Consensus 88 TCkvC~TRSS--h~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC 147 (272)
-|-.|++... -++.+.+|-+.+ +.+.|-|+.||.+|...+++-.-+.+-|-+.|
T Consensus 41 ~Cm~Cg~nG~TRlllT~IP~fREv------VimSF~CpHCG~kN~eiQ~a~~iQ~~Gvri~l 96 (460)
T KOG2703|consen 41 LCMNCGENGTTRLLLTSIPYFREV------VIMSFECPHCGHKNNEIQSAEEIQEGGVRIEL 96 (460)
T ss_pred hhhhcccCCceeEEEeecchhhee------eeEEeecCccCCccccccchhccccCceEEEE
Confidence 6888986532 235556665444 68999999999999999999999999888888
No 36
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=67.15 E-value=2.2 Score=42.77 Aligned_cols=49 Identities=33% Similarity=0.638 Sum_probs=33.5
Q ss_pred ecCCcCCcccccccCCcccccccccccceEEEEEcCCCCccccccc---chhcccceEEEEEcCCCCccee
Q psy13378 88 TCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLI---SKHSYEKGVVIVKCEGCSNNHL 155 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~I---SK~AY~kGvViVqC~gC~n~HL 155 (272)
.|+.||+|- .|+ -++ + |.|++|++|..+.. =+++.+.|+ .=|-|.-|||
T Consensus 352 ~Cp~Cg~~m---~S~---G~~-g---------~rC~kCg~~~~~~~~~~v~r~l~~g~---evp~~arRHL 403 (421)
T COG1571 352 VCPRCGGRM---KSA---GRN-G---------FRCKKCGTRARETLIKEVPRDLEPGV---EVPPVARRHL 403 (421)
T ss_pred CCCccCCch---hhc---CCC-C---------cccccccccCCcccccccccccCCCC---cCCchhhhhc
Confidence 699999764 222 222 3 89999999964433 234556676 5788999999
No 37
>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=67.03 E-value=2.3 Score=33.29 Aligned_cols=14 Identities=29% Similarity=0.852 Sum_probs=6.1
Q ss_pred ceEEEEEcCCCCcc
Q psy13378 140 KGVVIVKCEGCSNN 153 (272)
Q Consensus 140 kGvViVqC~gC~n~ 153 (272)
.|+-.+.|..|...
T Consensus 42 ~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 42 EGIGILSCRVCGES 55 (81)
T ss_dssp TTEEEEEESSS--E
T ss_pred CCEEEEEecCCCCe
Confidence 44555555555443
No 38
>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=66.49 E-value=2.1 Score=30.30 Aligned_cols=9 Identities=44% Similarity=1.357 Sum_probs=6.3
Q ss_pred eeecCCcCC
Q psy13378 86 AYTCKVCGT 94 (272)
Q Consensus 86 ~fTCkvC~T 94 (272)
.|+|++|+.
T Consensus 2 ~f~CP~C~~ 10 (54)
T PF05605_consen 2 SFTCPYCGK 10 (54)
T ss_pred CcCCCCCCC
Confidence 367777775
No 39
>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=66.47 E-value=3.9 Score=28.40 Aligned_cols=39 Identities=31% Similarity=0.572 Sum_probs=20.3
Q ss_pred eeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCccc-ccccchh
Q psy13378 86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRN-SHLISKH 136 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS-~h~ISK~ 136 (272)
.|.|+.|+++..-..+-. . .+ .-+|+.|+..+ .+.||.-
T Consensus 5 ey~C~~Cg~~fe~~~~~~-~-~~----------~~~CP~Cg~~~~~r~~s~~ 44 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMS-D-DP----------LATCPECGGEKLRRLLSAV 44 (52)
T ss_pred EEEeCCCCCEeEEEEecC-C-CC----------CCCCCCCCCCceeEEeccc
Confidence 467888887553322111 0 11 24588888643 3666643
No 40
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=65.78 E-value=5.2 Score=35.87 Aligned_cols=44 Identities=18% Similarity=0.334 Sum_probs=22.6
Q ss_pred eeecCCcCCcccccccCCccccc----------ccccccceEEEEEcCCCCccc
Q psy13378 86 AYTCKVCGTRNSHLISKHSYEKG----------VIKLKHKLKLAYTCKVCGTRN 129 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ISK~Sy~kG----------v~~~~~~~~L~FTCk~C~tRS 129 (272)
..+|++|++......=+.+..+. ...+.|-+..+.+||.|+--.
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~ 58 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAA 58 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcc
Confidence 36999999875443211111111 012345556666666666443
No 41
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=65.29 E-value=3.6 Score=27.63 Aligned_cols=16 Identities=25% Similarity=0.802 Sum_probs=13.8
Q ss_pred EEEEcCCCCcceeeec
Q psy13378 143 VIVKCEGCSNNHLIAD 158 (272)
Q Consensus 143 ViVqC~gC~n~HLIAD 158 (272)
++++||.|+....|.|
T Consensus 1 M~i~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPD 16 (37)
T ss_pred CEEECCCCCceEEcCH
Confidence 4799999999998766
No 42
>KOG2907|consensus
Probab=64.88 E-value=4.6 Score=34.34 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=17.7
Q ss_pred ecCCcCCc--ccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 88 TCKVCGTR--NSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 88 TCkvC~TR--SSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
.|+.||+. +-|+..-.|...|- -+-|||+.|+.|
T Consensus 76 kCpkCghe~m~Y~T~QlRSADEGQ-------TVFYTC~kC~~k 111 (116)
T KOG2907|consen 76 KCPKCGHEEMSYHTLQLRSADEGQ-------TVFYTCPKCKYK 111 (116)
T ss_pred cCcccCCchhhhhhhhcccccCCc-------eEEEEcCcccee
Confidence 67777755 22333333333332 256777777654
No 43
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=64.40 E-value=5.6 Score=35.75 Aligned_cols=25 Identities=20% Similarity=0.424 Sum_probs=17.8
Q ss_pred cceEEEEEcCCCCcccccccchhcc
Q psy13378 114 HKLKLAYTCKVCGTRNSHLISKHSY 138 (272)
Q Consensus 114 ~~~~L~FTCk~C~tRS~h~ISK~AY 138 (272)
.-+.+.|.|+.||.|++-..+--+.
T Consensus 25 evii~sf~C~~CGyr~~ev~~~g~~ 49 (192)
T TIGR00310 25 EVLETSTICEHCGYRSNDVKTLGAK 49 (192)
T ss_pred eEEEEEEECCCCCCccceeEECCCC
Confidence 4467889999999888766554433
No 44
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.59 E-value=5.1 Score=33.76 Aligned_cols=51 Identities=20% Similarity=0.433 Sum_probs=25.4
Q ss_pred eeeeecCCcCCcccccccCCc----ccccccccccceEEEEEcCCCCcccccccc
Q psy13378 84 KLAYTCKVCGTRNSHLISKHS----YEKGVIKLKHKLKLAYTCKVCGTRNSHLIS 134 (272)
Q Consensus 84 ~i~fTCkvC~TRSSh~ISK~S----y~kGv~~~~~~~~L~FTCk~C~tRS~h~IS 134 (272)
...|.|+.|+...+..--+++ ....+.-+..-+...+.||.|+.++.+.++
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVK 122 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEec
Confidence 356899999955433200111 111111111112234779999877666554
No 45
>KOG3507|consensus
Probab=62.51 E-value=8.6 Score=29.58 Aligned_cols=31 Identities=29% Similarity=0.689 Sum_probs=21.9
Q ss_pred eeeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCccc
Q psy13378 83 LKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRN 129 (272)
Q Consensus 83 ~~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS 129 (272)
-.+.|-|-.|+.+++- -++. .|.|..|+.|-
T Consensus 17 ~~miYiCgdC~~en~l-k~~D---------------~irCReCG~RI 47 (62)
T KOG3507|consen 17 ATMIYICGDCGQENTL-KRGD---------------VIRCRECGYRI 47 (62)
T ss_pred ccEEEEeccccccccc-cCCC---------------cEehhhcchHH
Confidence 4577899999988733 1111 58999999883
No 46
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=62.17 E-value=5 Score=34.97 Aligned_cols=36 Identities=28% Similarity=0.723 Sum_probs=20.3
Q ss_pred ecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 88 TCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
.|+.|++.-++.++...++.|.. ++ ..+.|+.|+.|
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~-~~----~~~~c~~c~~~ 37 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNA-IR----RRRECLACGKR 37 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCc-ee----eeeeccccCCc
Confidence 47777766666666665555531 11 12667777644
No 47
>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=61.71 E-value=3.6 Score=35.58 Aligned_cols=28 Identities=18% Similarity=0.553 Sum_probs=18.6
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
.|+|..|++. ..|.+-.+|..||.|...
T Consensus 112 ~l~C~~Cg~~-------~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 112 TLVCENCGHE-------VELTHPERLPPCPKCGHT 139 (146)
T ss_pred eEecccCCCE-------EEecCCCcCCCCCCCCCC
Confidence 5788888865 233344568888888754
No 48
>KOG1074|consensus
Probab=61.36 E-value=3.6 Score=44.72 Aligned_cols=77 Identities=17% Similarity=0.392 Sum_probs=52.7
Q ss_pred eeecCCcCCcccccccCCcccccccccccceEEEEEcC---CCCcccccccchh----------------cccceEEEEE
Q psy13378 86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCK---VCGTRNSHLISKH----------------SYEKGVVIVK 146 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk---~C~tRS~h~ISK~----------------AY~kGvViVq 146 (272)
-|.||+|++-.+. -=.-..+-++-+..+.+.+.|.|+ .|....++.|..+ |-+.+..--|
T Consensus 633 PFkCKiCgRAFtT-kGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lpQhIriH~~~~~s~g~~a~e~~~~adq 711 (958)
T KOG1074|consen 633 PFKCKICGRAFTT-KGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLPQHIRIHLGGQISNGGTAAEGILAADQ 711 (958)
T ss_pred ccccccccchhcc-ccchhhcccccccCccccccccCCchhhhcccccccccccceEEeecCCCCCCCcccccccchhcc
Confidence 4889999965422 111223336678888889999999 9998776666554 2244555679
Q ss_pred cCCCCcceeeecccccc
Q psy13378 147 CEGCSNNHLIADNLKWF 163 (272)
Q Consensus 147 C~gC~n~HLIADnLgwF 163 (272)
|+.|+..|.=|+++.=+
T Consensus 712 ~~~~qk~~~~a~~f~~~ 728 (958)
T KOG1074|consen 712 CSSCQKTFSDARSFSQQ 728 (958)
T ss_pred cchhhhcccccccchhh
Confidence 99999999766655543
No 49
>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=61.33 E-value=5.1 Score=32.81 Aligned_cols=15 Identities=20% Similarity=0.463 Sum_probs=9.4
Q ss_pred EEcCCCCcccccccc
Q psy13378 120 YTCKVCGTRNSHLIS 134 (272)
Q Consensus 120 FTCk~C~tRS~h~IS 134 (272)
|+||.|+.++.+.++
T Consensus 87 ~~CP~Cgs~~~~i~~ 101 (115)
T TIGR00100 87 YRCPKCHGIMLQVRA 101 (115)
T ss_pred ccCcCCcCCCcEEec
Confidence 667777766555444
No 50
>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=60.95 E-value=8 Score=26.33 Aligned_cols=7 Identities=43% Similarity=1.274 Sum_probs=3.1
Q ss_pred EEcCCCC
Q psy13378 120 YTCKVCG 126 (272)
Q Consensus 120 FTCk~C~ 126 (272)
+.|+.||
T Consensus 20 ~vC~~CG 26 (43)
T PF08271_consen 20 LVCPNCG 26 (43)
T ss_dssp EEETTT-
T ss_pred EECCCCC
Confidence 4555554
No 51
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=60.16 E-value=8.4 Score=27.15 Aligned_cols=11 Identities=45% Similarity=1.120 Sum_probs=6.1
Q ss_pred eeecCCcCCcc
Q psy13378 86 AYTCKVCGTRN 96 (272)
Q Consensus 86 ~fTCkvC~TRS 96 (272)
.|.|..||+..
T Consensus 2 ~Y~C~~Cg~~~ 12 (44)
T smart00659 2 IYICGECGREN 12 (44)
T ss_pred EEECCCCCCEe
Confidence 35666666543
No 52
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=59.75 E-value=8.7 Score=25.96 Aligned_cols=28 Identities=29% Similarity=0.608 Sum_probs=19.7
Q ss_pred EcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 121 TCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 121 TCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
.|+.|++. +.+..+ .++.+-.|++|.-.
T Consensus 1 ~CP~C~~~----l~~~~~-~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTE----LEPVRL-GDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcc----cceEEE-CCEEEEECCCCCeE
Confidence 38999752 334444 77889999999754
No 53
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=59.40 E-value=6 Score=32.40 Aligned_cols=15 Identities=13% Similarity=0.321 Sum_probs=9.7
Q ss_pred EEcCCCCcccccccc
Q psy13378 120 YTCKVCGTRNSHLIS 134 (272)
Q Consensus 120 FTCk~C~tRS~h~IS 134 (272)
|.||.|+.++.+.++
T Consensus 87 ~~CP~Cgs~~~~i~~ 101 (113)
T PRK12380 87 AQCPHCHGERLRVDT 101 (113)
T ss_pred ccCcCCCCCCcEEcc
Confidence 568888766555544
No 54
>PHA02998 RNA polymerase subunit; Provisional
Probab=59.33 E-value=7.3 Score=35.66 Aligned_cols=35 Identities=20% Similarity=0.475 Sum_probs=24.7
Q ss_pred EEEcCCCCcccccccchh---cccceEEEEEcCCCCcc
Q psy13378 119 AYTCKVCGTRNSHLISKH---SYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~---AY~kGvViVqC~gC~n~ 153 (272)
..+|+.|+++.+..+.-| |=|-.+++.+|..|..+
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~ 180 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKH 180 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCc
Confidence 467888888777665555 44666888888888765
No 55
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=58.56 E-value=5.6 Score=26.74 Aligned_cols=17 Identities=29% Similarity=0.720 Sum_probs=14.4
Q ss_pred EEEEcCCCCcceeeecc
Q psy13378 143 VIVKCEGCSNNHLIADN 159 (272)
Q Consensus 143 ViVqC~gC~n~HLIADn 159 (272)
++++||.|+....|.|.
T Consensus 1 M~i~Cp~C~~~y~i~d~ 17 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDE 17 (36)
T ss_pred CEEECCCCCCEEeCCHH
Confidence 36899999999998774
No 56
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=57.69 E-value=3.4 Score=44.88 Aligned_cols=20 Identities=20% Similarity=0.184 Sum_probs=0.0
Q ss_pred Ceeeeceeeeccceeccccc
Q psy13378 182 EQGCKGLFCLSHDIKLNTNI 201 (272)
Q Consensus 182 E~V~kg~~~~~~die~~~~~ 201 (272)
|-+-||.+-.-+|+-.+-+.
T Consensus 746 EPlEKGILRak~~v~vFKDG 765 (900)
T PF03833_consen 746 EPLEKGILRAKHGVYVFKDG 765 (900)
T ss_dssp --------------------
T ss_pred chHHHHHHhhhcCeeEecCc
Confidence 45566777666666555444
No 57
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=57.53 E-value=8.3 Score=33.65 Aligned_cols=35 Identities=26% Similarity=0.665 Sum_probs=29.4
Q ss_pred EcCCCCcccccccchhcccceEEE---EEcCCCCccee
Q psy13378 121 TCKVCGTRNSHLISKHSYEKGVVI---VKCEGCSNNHL 155 (272)
Q Consensus 121 TCk~C~tRS~h~ISK~AY~kGvVi---VqC~gC~n~HL 155 (272)
.||-|++.-++.++-..+..|-++ .||+.|.-+..
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence 699999988899999999998444 79999987754
No 58
>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=57.29 E-value=7 Score=38.75 Aligned_cols=29 Identities=24% Similarity=0.661 Sum_probs=21.7
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeec
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIAD 158 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIAD 158 (272)
.|.|..|+..+.+ -.-|||+|..|--+..
T Consensus 7 ~y~C~~Cg~~~~~-----------~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 7 KFVCQHCGADSPK-----------WQGKCPACHAWNTITE 35 (454)
T ss_pred eEECCcCCCCCcc-----------ccEECcCCCCccccch
Confidence 5899999866443 4578999998887655
No 59
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=56.38 E-value=4.6 Score=37.22 Aligned_cols=8 Identities=50% Similarity=1.294 Sum_probs=3.6
Q ss_pred ecCCcCCc
Q psy13378 88 TCKVCGTR 95 (272)
Q Consensus 88 TCkvC~TR 95 (272)
+|++||..
T Consensus 174 ~CPvCGs~ 181 (290)
T PF04216_consen 174 YCPVCGSP 181 (290)
T ss_dssp S-TTT---
T ss_pred cCCCCCCc
Confidence 89999944
No 60
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=56.33 E-value=11 Score=28.06 Aligned_cols=32 Identities=22% Similarity=0.535 Sum_probs=21.8
Q ss_pred EEEcCCCCcccccccch-hcccceEEEEEcCCCCcceee
Q psy13378 119 AYTCKVCGTRNSHLISK-HSYEKGVVIVKCEGCSNNHLI 156 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK-~AY~kGvViVqC~gC~n~HLI 156 (272)
.+.|+.|+ ++..+ ..|. .+-++||-|+....|
T Consensus 4 eiRC~~Cn----klLa~~g~~~--~leIKCpRC~tiN~~ 36 (51)
T PF10122_consen 4 EIRCGHCN----KLLAKAGEVI--ELEIKCPRCKTINHV 36 (51)
T ss_pred ceeccchh----HHHhhhcCcc--EEEEECCCCCccceE
Confidence 57899997 45555 2333 678899999876543
No 61
>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=56.20 E-value=5.8 Score=31.07 Aligned_cols=43 Identities=23% Similarity=0.560 Sum_probs=16.1
Q ss_pred cccccceeeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 77 IQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 77 ~q~~~k~~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
.+...++.-.|+|+.|++..+=.+.= .-..+++ ..+|..|+.+
T Consensus 13 kk~~~~l~~~F~CPfC~~~~sV~v~i-dkk~~~~--------~~~C~~Cg~~ 55 (81)
T PF05129_consen 13 KKKKPKLPKVFDCPFCNHEKSVSVKI-DKKEGIG--------ILSCRVCGES 55 (81)
T ss_dssp -------SS----TTT--SS-EEEEE-ETTTTEE--------EEEESSS--E
T ss_pred cCcCCCCCceEcCCcCCCCCeEEEEE-EccCCEE--------EEEecCCCCe
Confidence 34456777899999999665433221 1113343 6899999866
No 62
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.17 E-value=7.5 Score=32.01 Aligned_cols=15 Identities=20% Similarity=0.541 Sum_probs=9.9
Q ss_pred EEcCCCCcccccccc
Q psy13378 120 YTCKVCGTRNSHLIS 134 (272)
Q Consensus 120 FTCk~C~tRS~h~IS 134 (272)
++||.|+.++...++
T Consensus 89 ~~CP~Cgs~~~~i~~ 103 (117)
T PRK00564 89 GVCEKCHSKNVIITQ 103 (117)
T ss_pred CcCcCCCCCceEEec
Confidence 358888877655554
No 63
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=55.94 E-value=3.7 Score=36.69 Aligned_cols=8 Identities=50% Similarity=1.472 Sum_probs=4.1
Q ss_pred EEEcCCCC
Q psy13378 119 AYTCKVCG 126 (272)
Q Consensus 119 ~FTCk~C~ 126 (272)
.|||+.||
T Consensus 132 ~F~Cp~Cg 139 (176)
T COG1675 132 GFTCPKCG 139 (176)
T ss_pred CCCCCCCC
Confidence 35555554
No 64
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=55.56 E-value=8.9 Score=31.68 Aligned_cols=38 Identities=21% Similarity=0.464 Sum_probs=25.5
Q ss_pred eeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
-++|+.|+.+-..-.-.| +......+..-|+|..|++|
T Consensus 72 ~~~CpkCg~~ea~y~~~Q-----tRsaDEp~T~Fy~C~~Cg~~ 109 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQ-----TRSADEPETRFYKCTRCGYR 109 (113)
T ss_pred cccCCCCCCceeEEEeee-----hhccCCCceEEEEecccCCE
Confidence 579999998765432222 22233445678999999977
No 65
>PHA02998 RNA polymerase subunit; Provisional
Probab=55.14 E-value=9.5 Score=34.94 Aligned_cols=37 Identities=14% Similarity=0.327 Sum_probs=25.7
Q ss_pred eecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 87 YTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 87 fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
-+|+.|+.+.+.-+.- .+.....-+.+-|+|..|+++
T Consensus 144 v~CPkCg~~~A~f~ql-----QTRSADEPmT~FYkC~~CG~~ 180 (195)
T PHA02998 144 TPCPNCKSKNTTPMMI-----QTRAADEPPLVRHACRDCKKH 180 (195)
T ss_pred CCCCCCCCCceEEEEE-----eeccCCCCceEEEEcCCCCCc
Confidence 4799999887663333 233344455678999999976
No 66
>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=54.09 E-value=6.5 Score=38.44 Aligned_cols=82 Identities=24% Similarity=0.447 Sum_probs=25.9
Q ss_pred eeeecCCcCCcccccccC------CcccccccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeec
Q psy13378 85 LAYTCKVCGTRNSHLISK------HSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIAD 158 (272)
Q Consensus 85 i~fTCkvC~TRSSh~ISK------~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIAD 158 (272)
-+|+|+.|... ....+. |.+. ....+.=-|.|+.|+.|+. .+ .-|- ...|+.|...- =.
T Consensus 251 kav~C~~C~yt-~~~~~~~C~~~~H~l~-----~~~a~KRFFkC~~C~~Rt~-sl--~r~P----~~~C~~Cg~~~--we 315 (344)
T PF09332_consen 251 KAVTCKQCKYT-AFKPSDRCKEEGHPLK-----WHDAVKRFFKCKDCGNRTI-SL--ERLP----KKHCSNCGSSK--WE 315 (344)
T ss_dssp EEEEETTT--E-ESS--HHHHHTT--EE-----EEEEE-EEEE-T-TS-EEE-ES--SSS------S--TTT-S-----E
T ss_pred EEEEcCCCCCc-ccCcchhHHhcCCceE-----EeeeeeeeEECCCCCCeee-ec--ccCC----CCCCCcCCcCc--ee
Confidence 47899999733 333322 2221 1122223599999999854 22 2232 24899998642 23
Q ss_pred cccccccCCCCCCCHHHHHHHhCCe
Q psy13378 159 NLKWFTDLKPGVTNIEHILAEKGEQ 183 (272)
Q Consensus 159 nLgwF~d~~~g~~tIEdil~~kGE~ 183 (272)
.-+.+.+.+ | ..--|.|.-+|+.
T Consensus 316 r~~M~~ek~-~-~~~~e~L~~RG~E 338 (344)
T PF09332_consen 316 RTGMLKEKK-G-KLGGETLLPRGEE 338 (344)
T ss_dssp EE---SSS-----------------
T ss_pred ehhhhhhhc-c-cCCcccccccccc
Confidence 455566654 3 2334555566654
No 67
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=53.73 E-value=9.2 Score=38.10 Aligned_cols=31 Identities=23% Similarity=0.501 Sum_probs=24.0
Q ss_pred EEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeecc
Q psy13378 118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADN 159 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADn 159 (272)
..|+|..|+.+ .-+..-+||+|+.|-.|.=+
T Consensus 353 ~~YRC~~CGF~-----------a~~l~W~CPsC~~W~TikPi 383 (389)
T COG2956 353 PRYRCQNCGFT-----------AHTLYWHCPSCRAWETIKPI 383 (389)
T ss_pred CCceecccCCc-----------ceeeeeeCCCcccccccCCc
Confidence 47999999965 23567899999999876544
No 68
>PRK11032 hypothetical protein; Provisional
Probab=53.46 E-value=6.2 Score=34.83 Aligned_cols=28 Identities=18% Similarity=0.558 Sum_probs=21.0
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
.+.|..|++. ..+.+-.+|..||.|...
T Consensus 124 ~LvC~~Cg~~-------~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 124 NLVCEKCHHH-------LAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred eEEecCCCCE-------EEecCCCcCCCCCCCCCC
Confidence 5788888865 356677788888888764
No 69
>KOG2824|consensus
Probab=53.45 E-value=12 Score=36.11 Aligned_cols=7 Identities=43% Similarity=1.227 Sum_probs=4.3
Q ss_pred eecCCcC
Q psy13378 87 YTCKVCG 93 (272)
Q Consensus 87 fTCkvC~ 93 (272)
.+|.-||
T Consensus 230 ~~C~~CG 236 (281)
T KOG2824|consen 230 GVCESCG 236 (281)
T ss_pred CcCCCcC
Confidence 4666666
No 70
>PRK11823 DNA repair protein RadA; Provisional
Probab=53.33 E-value=8.6 Score=37.92 Aligned_cols=29 Identities=24% Similarity=0.754 Sum_probs=21.5
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeec
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIAD 158 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIAD 158 (272)
.|.|..|+..+.+ -.-|||.|..|--+..
T Consensus 7 ~y~C~~Cg~~~~~-----------~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 7 AYVCQECGAESPK-----------WLGRCPECGAWNTLVE 35 (446)
T ss_pred eEECCcCCCCCcc-----------cCeeCcCCCCccceee
Confidence 5889999866443 4568999988877654
No 71
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=53.07 E-value=12 Score=30.72 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=15.3
Q ss_pred EEEcCCCCcccc-cccchhcccceEEEEEcCCCCcc
Q psy13378 119 AYTCKVCGTRNS-HLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 119 ~FTCk~C~tRS~-h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
.|+|+.|+..+. -.|.+ |+..+.|+.|...
T Consensus 21 ~f~CP~Cge~~v~v~~~k-----~~~h~~C~~CG~y 51 (99)
T PRK14892 21 IFECPRCGKVSISVKIKK-----NIAIITCGNCGLY 51 (99)
T ss_pred EeECCCCCCeEeeeecCC-----CcceEECCCCCCc
Confidence 566666663211 01112 5666667776654
No 72
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=53.03 E-value=12 Score=26.68 Aligned_cols=32 Identities=22% Similarity=0.741 Sum_probs=19.4
Q ss_pred EcCCCCcccccccchhcccceE-EEEEcCCCCc
Q psy13378 121 TCKVCGTRNSHLISKHSYEKGV-VIVKCEGCSN 152 (272)
Q Consensus 121 TCk~C~tRS~h~ISK~AY~kGv-ViVqC~gC~n 152 (272)
-|+-||..............|. +.|.|..|..
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 3777765544444444433333 7788888877
No 73
>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=52.36 E-value=7.7 Score=34.01 Aligned_cols=35 Identities=26% Similarity=0.468 Sum_probs=13.9
Q ss_pred EEEEcCCCCccc-ccc-cchhcccceEEEEEcCCCCc
Q psy13378 118 LAYTCKVCGTRN-SHL-ISKHSYEKGVVIVKCEGCSN 152 (272)
Q Consensus 118 L~FTCk~C~tRS-~h~-ISK~AY~kGvViVqC~gC~n 152 (272)
+.|+|+.|++.+ ... +...+...-....+||.|+.
T Consensus 17 l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 17 LKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred eEeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 567777777654 111 22222222333567777776
No 74
>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=52.23 E-value=12 Score=29.42 Aligned_cols=36 Identities=19% Similarity=0.427 Sum_probs=28.1
Q ss_pred EEEEcCCCCcccccccc---hhcccceEEEEEcCCCCcc
Q psy13378 118 LAYTCKVCGTRNSHLIS---KHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 118 L~FTCk~C~tRS~h~IS---K~AY~kGvViVqC~gC~n~ 153 (272)
+...|+.|+++.+..+. +.|=+--+++..|..|..+
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYV 99 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCe
Confidence 46899999988766664 4466778999999999853
No 75
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=51.90 E-value=5.1 Score=34.47 Aligned_cols=25 Identities=24% Similarity=0.537 Sum_probs=18.0
Q ss_pred EEeecceeccccccccCCChhhhhh
Q psy13378 33 LIVENEFSVSKLCYDYGLSHSELKK 57 (272)
Q Consensus 33 ~~~~~~~~~~~~~~~~g~~~s~~~s 57 (272)
|+-..+.+...|+..-|++...|-.
T Consensus 23 L~~~~~~tdEeLa~~Lgi~~~~VRk 47 (158)
T TIGR00373 23 LGIKGEFTDEEISLELGIKLNEVRK 47 (158)
T ss_pred HhccCCCCHHHHHHHHCCCHHHHHH
Confidence 4445567788888888888877654
No 76
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=51.54 E-value=20 Score=33.10 Aligned_cols=60 Identities=23% Similarity=0.416 Sum_probs=38.8
Q ss_pred eeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCC
Q psy13378 86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEG 149 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~g 149 (272)
.-+|++|+. . .--+.|...+--..+-+..+.-|..|+.|++-.+.-.+-+---+.+++.+
T Consensus 14 ~~~CPvCg~-~---l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e~~eP~r~~lkve~ 73 (201)
T COG1779 14 RIDCPVCGG-T---LKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLEEREPRRYTLKVES 73 (201)
T ss_pred eecCCcccc-e---eeEEEeeecCCccceEEEEEEEccccCCcccceeecccCCCeEEEEEeCC
Confidence 348999995 2 11122222222223446677889999999988888777777777777754
No 77
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=51.34 E-value=14 Score=30.57 Aligned_cols=21 Identities=33% Similarity=0.662 Sum_probs=16.7
Q ss_pred cccccccceEEEEEcCCCCcc
Q psy13378 108 GVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 108 Gv~~~~~~~~L~FTCk~C~tR 128 (272)
|..++..++.|.|+|..|+..
T Consensus 57 g~~KptKKv~Lr~~Ct~Cgka 77 (94)
T COG1631 57 GKAKPTKKVDLRLRCTECGKA 77 (94)
T ss_pred ccCCccceEEEEEEehhhccc
Confidence 344666789999999999965
No 78
>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=51.33 E-value=6.7 Score=31.91 Aligned_cols=9 Identities=33% Similarity=0.933 Sum_probs=3.9
Q ss_pred EEEEcCCCC
Q psy13378 118 LAYTCKVCG 126 (272)
Q Consensus 118 L~FTCk~C~ 126 (272)
+.+.|+.|+
T Consensus 69 ~~~~C~~Cg 77 (113)
T PF01155_consen 69 ARARCRDCG 77 (113)
T ss_dssp -EEEETTTS
T ss_pred CcEECCCCC
Confidence 344444444
No 79
>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=51.18 E-value=5.1 Score=32.60 Aligned_cols=36 Identities=22% Similarity=0.647 Sum_probs=20.4
Q ss_pred ceeeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccc
Q psy13378 82 KLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLIS 134 (272)
Q Consensus 82 k~~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~IS 134 (272)
...+.+.|+.|++..+. +.. .|.||.|++++.+.++
T Consensus 66 ~~p~~~~C~~Cg~~~~~--~~~---------------~~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEP--DEF---------------DFSCPRCGSPDVEIIS 101 (113)
T ss_dssp EE--EEEETTTS-EEEC--HHC---------------CHH-SSSSSS-EEEEE
T ss_pred ecCCcEECCCCCCEEec--CCC---------------CCCCcCCcCCCcEEcc
Confidence 45677899999976532 111 1569999988666554
No 80
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=51.10 E-value=11 Score=31.55 Aligned_cols=14 Identities=36% Similarity=0.890 Sum_probs=7.3
Q ss_pred eeeeeecCCcCCcc
Q psy13378 83 LKLAYTCKVCGTRN 96 (272)
Q Consensus 83 ~~i~fTCkvC~TRS 96 (272)
|--.|||+.|++-+
T Consensus 19 L~k~FtCp~Cghe~ 32 (104)
T COG4888 19 LPKTFTCPRCGHEK 32 (104)
T ss_pred CCceEecCccCCee
Confidence 44455555555443
No 81
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=51.02 E-value=15 Score=30.36 Aligned_cols=30 Identities=30% Similarity=0.821 Sum_probs=24.8
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
..|+.|+...+.++-+ .++.+.+|..|.++
T Consensus 81 VlC~~C~spdT~l~k~----~r~~~l~C~aCGa~ 110 (110)
T smart00653 81 VLCPECGSPDTELIKE----NRLFFLKCEACGAR 110 (110)
T ss_pred EECCCCCCCCcEEEEe----CCeEEEEccccCCC
Confidence 6899999888887765 78899999999763
No 82
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=50.87 E-value=15 Score=36.45 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=7.8
Q ss_pred ceEEEEEcCCCCcc
Q psy13378 115 KLKLAYTCKVCGTR 128 (272)
Q Consensus 115 ~~~L~FTCk~C~tR 128 (272)
.+++.-||+.|+-+
T Consensus 179 ~~~~~~~C~~C~G~ 192 (371)
T COG0484 179 FFSFQQTCPTCNGT 192 (371)
T ss_pred EEEEEEECCCCccc
Confidence 35555566666543
No 83
>KOG0416|consensus
Probab=50.74 E-value=6.5 Score=35.79 Aligned_cols=17 Identities=24% Similarity=0.360 Sum_probs=11.2
Q ss_pred eeeeCCccEEEeeccee
Q psy13378 24 VIYHPNLNILIVENEFS 40 (272)
Q Consensus 24 ~~~~~~~~~~~~~~~~~ 40 (272)
-|||||+...--+-|+.
T Consensus 71 KIfHPNIDe~SGsVCLD 87 (189)
T KOG0416|consen 71 KIFHPNIDEASGSVCLD 87 (189)
T ss_pred eccCCCchhccCccHHH
Confidence 49999987654444443
No 84
>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=49.26 E-value=11 Score=30.80 Aligned_cols=32 Identities=16% Similarity=0.450 Sum_probs=22.1
Q ss_pred cceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcce
Q psy13378 114 HKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNH 154 (272)
Q Consensus 114 ~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~H 154 (272)
...-+.+.|+.|++. ++...+ ...||.|....
T Consensus 65 ~~~p~~~~C~~Cg~~----~~~~~~-----~~~CP~Cgs~~ 96 (115)
T TIGR00100 65 EDEPVECECEDCSEE----VSPEID-----LYRCPKCHGIM 96 (115)
T ss_pred EeeCcEEEcccCCCE----EecCCc-----CccCcCCcCCC
Confidence 445567999999943 433333 46799999865
No 85
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.08 E-value=11 Score=40.07 Aligned_cols=58 Identities=22% Similarity=0.402 Sum_probs=34.3
Q ss_pred eeeeeecCCcCCcccccc--cCCcccccccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccc
Q psy13378 83 LKLAYTCKVCGTRNSHLI--SKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNL 160 (272)
Q Consensus 83 ~~i~fTCkvC~TRSSh~I--SK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnL 160 (272)
|.-.-.|+.||+..-=.- ..-.|++..+ .-.|.-|++.. -+--+||.|...||.+==.
T Consensus 432 ys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~--------~L~CH~Cg~~~------------~~p~~Cp~Cgs~~L~~~G~ 491 (730)
T COG1198 432 YAPLLLCRDCGYIAECPNCDSPLTLHKATG--------QLRCHYCGYQE------------PIPQSCPECGSEHLRAVGP 491 (730)
T ss_pred ccceeecccCCCcccCCCCCcceEEecCCC--------eeEeCCCCCCC------------CCCCCCCCCCCCeeEEecc
Confidence 343457888887632111 1123444443 46788888552 2345799999999976433
No 86
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=48.24 E-value=13 Score=30.54 Aligned_cols=15 Identities=13% Similarity=0.432 Sum_probs=9.8
Q ss_pred EEcCCCCcccccccc
Q psy13378 120 YTCKVCGTRNSHLIS 134 (272)
Q Consensus 120 FTCk~C~tRS~h~IS 134 (272)
|.||.|+..+...++
T Consensus 88 ~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 88 RRCPQCHGDMLRIVA 102 (114)
T ss_pred CcCcCcCCCCcEEcc
Confidence 568888876555544
No 87
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=47.12 E-value=9.6 Score=31.51 Aligned_cols=14 Identities=36% Similarity=0.717 Sum_probs=8.9
Q ss_pred eeeeeecCCcCCcc
Q psy13378 83 LKLAYTCKVCGTRN 96 (272)
Q Consensus 83 ~~i~fTCkvC~TRS 96 (272)
++.-.+|+.||+|.
T Consensus 6 lGtKR~Cp~CG~kF 19 (108)
T PF09538_consen 6 LGTKRTCPSCGAKF 19 (108)
T ss_pred cCCcccCCCCcchh
Confidence 44445777777776
No 88
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=46.71 E-value=20 Score=30.80 Aligned_cols=33 Identities=30% Similarity=0.779 Sum_probs=27.2
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcceee
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLI 156 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLI 156 (272)
..|+.|+...++++- +..+.+.+|..|.++.-+
T Consensus 103 VlC~~C~spdT~l~k----~~r~~~l~C~ACGa~~~V 135 (138)
T PRK03988 103 VICPECGSPDTKLIK----EGRIWVLKCEACGAETPV 135 (138)
T ss_pred EECCCCCCCCcEEEE----cCCeEEEEcccCCCCCcC
Confidence 689999999888874 367889999999987654
No 89
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=46.20 E-value=9.7 Score=32.06 Aligned_cols=23 Identities=17% Similarity=0.247 Sum_probs=14.4
Q ss_pred eecceeccccccccCCChhhhhh
Q psy13378 35 VENEFSVSKLCYDYGLSHSELKK 57 (272)
Q Consensus 35 ~~~~~~~~~~~~~~g~~~s~~~s 57 (272)
-..+.+-..|+..-|+...+|-+
T Consensus 12 ~~~~~~dedLa~~l~i~~n~vRk 34 (147)
T smart00531 12 RNGCVTEEDLAELLGIKQKQLRK 34 (147)
T ss_pred hcCCcCHHHHHHHhCCCHHHHHH
Confidence 34456666677777777666543
No 90
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=45.88 E-value=15 Score=27.67 Aligned_cols=42 Identities=26% Similarity=0.563 Sum_probs=24.3
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcceee-eccccc
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLI-ADNLKW 162 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLI-ADnLgw 162 (272)
.-|+.|+++..-.|-+..--+. ...-||.|+.-.|| +.+|.+
T Consensus 5 i~CP~CgnKTR~kir~DT~LkN-fPlyCpKCK~EtlI~v~~~~i 47 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKN-FPLYCPKCKQETLIDVKQLKI 47 (55)
T ss_pred EECCCCCCccceeeecCceecc-ccccCCCCCceEEEEeeccEE
Confidence 5688888665333322221111 23469999998887 555543
No 91
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=45.73 E-value=14 Score=28.83 Aligned_cols=10 Identities=40% Similarity=1.092 Sum_probs=4.0
Q ss_pred eeeecCCcCCc
Q psy13378 85 LAYTCKVCGTR 95 (272)
Q Consensus 85 i~fTCkvC~TR 95 (272)
+.|.| .||..
T Consensus 2 lifrC-~Cgr~ 11 (68)
T PF09082_consen 2 LIFRC-DCGRY 11 (68)
T ss_dssp EEEEE-TTS--
T ss_pred EEEEe-cCCCE
Confidence 34555 35533
No 92
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=45.42 E-value=8.3 Score=33.31 Aligned_cols=33 Identities=33% Similarity=0.646 Sum_probs=19.5
Q ss_pred cceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCccee
Q psy13378 114 HKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHL 155 (272)
Q Consensus 114 ~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HL 155 (272)
+.-+|..+|+.|++. +|= ..|.|+ ||.|..+-.
T Consensus 23 GAkML~~hCp~Cg~P---LF~----KdG~v~--CPvC~~~~~ 55 (131)
T COG1645 23 GAKMLAKHCPKCGTP---LFR----KDGEVF--CPVCGYREV 55 (131)
T ss_pred hhHHHHhhCcccCCc---cee----eCCeEE--CCCCCceEE
Confidence 445666777777765 332 455554 777775433
No 93
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=44.92 E-value=21 Score=29.97 Aligned_cols=45 Identities=16% Similarity=0.260 Sum_probs=27.8
Q ss_pred eEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeecccc
Q psy13378 116 LKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLK 161 (272)
Q Consensus 116 ~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLg 161 (272)
|-=.|||+.|++-+.-.-+ .--..++=.+.|..|..+|-.-=+-+
T Consensus 19 L~k~FtCp~Cghe~vs~ct-vkk~~~~g~~~Cg~CGls~e~ev~~l 63 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCT-VKKTVNIGTAVCGNCGLSFECEVPEL 63 (104)
T ss_pred CCceEecCccCCeeeeEEE-EEecCceeEEEcccCcceEEEecccc
Confidence 5568999999976322111 11223444678999999997533433
No 94
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=44.51 E-value=24 Score=40.22 Aligned_cols=10 Identities=40% Similarity=0.979 Sum_probs=7.6
Q ss_pred eecCCcCCcc
Q psy13378 87 YTCKVCGTRN 96 (272)
Q Consensus 87 fTCkvC~TRS 96 (272)
+.|+.||+.+
T Consensus 668 rkCPkCG~~t 677 (1337)
T PRK14714 668 RRCPSCGTET 677 (1337)
T ss_pred EECCCCCCcc
Confidence 7888888754
No 95
>PRK04023 DNA polymerase II large subunit; Validated
Probab=44.06 E-value=14 Score=41.13 Aligned_cols=10 Identities=40% Similarity=0.933 Sum_probs=7.1
Q ss_pred EEEcCCCCcc
Q psy13378 119 AYTCKVCGTR 128 (272)
Q Consensus 119 ~FTCk~C~tR 128 (272)
.|.|+.|+++
T Consensus 638 ~frCP~CG~~ 647 (1121)
T PRK04023 638 YRRCPFCGTH 647 (1121)
T ss_pred cccCCCCCCC
Confidence 4777777765
No 96
>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=43.86 E-value=13 Score=25.63 Aligned_cols=9 Identities=33% Similarity=1.235 Sum_probs=5.8
Q ss_pred eecCCcCCc
Q psy13378 87 YTCKVCGTR 95 (272)
Q Consensus 87 fTCkvC~TR 95 (272)
|.|+.|+..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 567777744
No 97
>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=43.76 E-value=14 Score=31.10 Aligned_cols=31 Identities=26% Similarity=0.793 Sum_probs=24.2
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcce
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNH 154 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~H 154 (272)
..|+.|+...+.++-+ .++.+.+|..|.+.+
T Consensus 94 VlC~~C~spdT~l~k~----~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE----GRLIFLKCKACGASR 124 (125)
T ss_dssp SSCTSTSSSSEEEEEE----TTCCEEEETTTSCEE
T ss_pred EEcCCCCCCccEEEEc----CCEEEEEecccCCcC
Confidence 4688888887777766 778888888888754
No 98
>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=43.39 E-value=12 Score=36.23 Aligned_cols=28 Identities=25% Similarity=0.698 Sum_probs=20.2
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcceeeec
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIAD 158 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIAD 158 (272)
|.|..|+..+.+ -.-|||.|..|.-+..
T Consensus 1 ~~c~~cg~~~~~-----------~~g~cp~c~~w~~~~e 28 (372)
T cd01121 1 YVCSECGYVSPK-----------WLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCC-----------ccEECcCCCCceeeee
Confidence 678888865443 4568888888887654
No 99
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=43.24 E-value=47 Score=25.67 Aligned_cols=70 Identities=23% Similarity=0.326 Sum_probs=40.1
Q ss_pred eeeecCCcCCc---ccccccCCcccccccccccceEE-EEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccc
Q psy13378 85 LAYTCKVCGTR---NSHLISKHSYEKGVIKLKHKLKL-AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNL 160 (272)
Q Consensus 85 i~fTCkvC~TR---SSh~ISK~Sy~kGv~~~~~~~~L-~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnL 160 (272)
+.|.|+.|.+- +...+|.++.. .+.+.+ ..+..+...|...+- ....++-+-.+.|.+|+. .|
T Consensus 1 ~vf~C~~C~t~l~ds~~lvs~~g~~------~~a~l~~~v~~~~~~~~~~~t~-~~~~~~~~~~l~C~~C~~------~l 67 (96)
T PF03226_consen 1 SVFQCKNCKTILADSNELVSFHGRE------GKAYLFNNVSNGVPVDRELMTG-ETGGDHTVRDLFCSGCNT------IL 67 (96)
T ss_pred CEEECCCCCCCcCCHHHheecCCCC------ccEEEEeeeeecccccceEEEe-eCCCCEEEEEeEcccCCh------hH
Confidence 47999999986 44456622111 122222 233444444432222 223447788999999975 58
Q ss_pred cccccCC
Q psy13378 161 KWFTDLK 167 (272)
Q Consensus 161 gwF~d~~ 167 (272)
||.-..+
T Consensus 68 GwkY~~a 74 (96)
T PF03226_consen 68 GWKYESA 74 (96)
T ss_pred CcEEEEc
Confidence 9998754
No 100
>KOG2907|consensus
Probab=43.17 E-value=19 Score=30.72 Aligned_cols=38 Identities=21% Similarity=0.500 Sum_probs=26.3
Q ss_pred EEEEEcCCCCccc--cccc-chhcccceEEEEEcCCCCcce
Q psy13378 117 KLAYTCKVCGTRN--SHLI-SKHSYEKGVVIVKCEGCSNNH 154 (272)
Q Consensus 117 ~L~FTCk~C~tRS--~h~I-SK~AY~kGvViVqC~gC~n~H 154 (272)
.|--.|++|++-- -|+. -+.|=|--+|+.+|+.|+-+-
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~ 112 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKF 112 (116)
T ss_pred chhccCcccCCchhhhhhhhcccccCCceEEEEcCccceee
Confidence 4677899999762 1221 234556679999999998653
No 101
>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=42.83 E-value=16 Score=32.12 Aligned_cols=35 Identities=23% Similarity=0.576 Sum_probs=27.7
Q ss_pred EcCCCCcccccccchhcccceEEE---EEcCCCCccee
Q psy13378 121 TCKVCGTRNSHLISKHSYEKGVVI---VKCEGCSNNHL 155 (272)
Q Consensus 121 TCk~C~tRS~h~ISK~AY~kGvVi---VqC~gC~n~HL 155 (272)
.||-|++-.++.+--...+.|..| -.|+.|..+..
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 488888888888888888888887 45888887765
No 102
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=42.79 E-value=8.3 Score=33.95 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=18.6
Q ss_pred EEEeecceeccccccccCCChhhhhh
Q psy13378 32 ILIVENEFSVSKLCYDYGLSHSELKK 57 (272)
Q Consensus 32 ~~~~~~~~~~~~~~~~~g~~~s~~~s 57 (272)
.|+-..+.+...|+...|++..++-.
T Consensus 30 ~L~~~g~~tdeeLA~~Lgi~~~~VRk 55 (178)
T PRK06266 30 ALIKKGEVTDEEIAEQTGIKLNTVRK 55 (178)
T ss_pred HHHHcCCcCHHHHHHHHCCCHHHHHH
Confidence 34444577888888888998887744
No 103
>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=42.60 E-value=28 Score=25.53 Aligned_cols=33 Identities=30% Similarity=0.706 Sum_probs=19.2
Q ss_pred eeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 85 LAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 85 i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
.+--|+.|.+-+ .+.+++.+ -.+.|.|..|+.-
T Consensus 21 ~aLIC~~C~~hN-Gla~~~~~----------~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 21 YALICSKCFSHN-GLAPKEEF----------EEIQYRCPYCGAL 53 (54)
T ss_pred eeEECcccchhh-cccccccC----------CceEEEcCCCCCc
Confidence 344588888433 33332222 2358999999864
No 104
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=41.16 E-value=26 Score=31.35 Aligned_cols=37 Identities=19% Similarity=0.680 Sum_probs=30.4
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeecc
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADN 159 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADn 159 (272)
-..|+.|+...+.++-+ ..+.+.+|..|.+..-++=+
T Consensus 98 yV~C~~C~~pdT~l~k~----~~~~~l~C~aCGa~~~v~~~ 134 (201)
T PRK12336 98 YVICSECGLPDTRLVKE----DRVLMLRCDACGAHRPVKKR 134 (201)
T ss_pred eEECCCCCCCCcEEEEc----CCeEEEEcccCCCCcccccc
Confidence 36899999998888743 57889999999999887643
No 105
>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=40.69 E-value=25 Score=35.86 Aligned_cols=16 Identities=13% Similarity=0.223 Sum_probs=8.9
Q ss_pred cccceeeecccCCccC
Q psy13378 218 HGSHHLIADNLKWFSD 233 (272)
Q Consensus 218 C~n~HlIADnLGwF~d 233 (272)
++-.+|---=.||-.+
T Consensus 347 vQ~~rle~~v~gwg~~ 362 (557)
T PF05876_consen 347 VQDDRLEVEVVGWGPG 362 (557)
T ss_pred ecCCEEEEEEEEECCC
Confidence 4555665555566544
No 106
>KOG3134|consensus
Probab=40.52 E-value=14 Score=34.65 Aligned_cols=31 Identities=32% Similarity=0.909 Sum_probs=25.4
Q ss_pred EEcCCCCcccccccchhcccce-EEEEEcCCCCc
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKG-VVIVKCEGCSN 152 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kG-vViVqC~gC~n 152 (272)
|+|-.|+.+-.+.+.+ |-+| +=+.+||+|+.
T Consensus 1 ~~CVeCg~~vksLy~~--Ys~g~irlt~C~nC~e 32 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQ--YSPGNIRLTKCPNCQE 32 (225)
T ss_pred CcccccCchHHHHHHh--cCCCcEEEeeCCchhh
Confidence 5799999997777765 6677 77899999985
No 107
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=39.39 E-value=14 Score=36.71 Aligned_cols=30 Identities=33% Similarity=0.584 Sum_probs=20.9
Q ss_pred cccchhcc----cceEEEEEcCCCCcceeeeccc
Q psy13378 131 HLISKHSY----EKGVVIVKCEGCSNNHLIADNL 160 (272)
Q Consensus 131 h~ISK~AY----~kGvViVqC~gC~n~HLIADnL 160 (272)
|.|||.|. .+|+.--+||-|-+....+|-+
T Consensus 359 HVIskeal~~LS~nG~~~FKCPYCP~~~~~~~~~ 392 (396)
T COG5109 359 HVISKEALSVLSQNGVLSFKCPYCPEMSKYENIL 392 (396)
T ss_pred ceeeHHHHHHHhhcCcEEeeCCCCCcchhhhhhh
Confidence 66666654 5788888888888776655543
No 108
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=38.94 E-value=20 Score=36.57 Aligned_cols=30 Identities=23% Similarity=0.671 Sum_probs=22.7
Q ss_pred EEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeec
Q psy13378 118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIAD 158 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIAD 158 (272)
-.|.|..|+..+.|- +-|||+|..|.-+..
T Consensus 6 t~f~C~~CG~~s~KW-----------~GkCp~Cg~Wns~vE 35 (456)
T COG1066 6 TAFVCQECGYVSPKW-----------LGKCPACGAWNTLVE 35 (456)
T ss_pred cEEEcccCCCCCccc-----------cccCCCCCCccceEE
Confidence 369999998776654 468999998887644
No 109
>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=38.12 E-value=22 Score=31.66 Aligned_cols=35 Identities=29% Similarity=0.602 Sum_probs=25.1
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcceeeec
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIAD 158 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIAD 158 (272)
|.|-.|+++....+.+-+ ...+-+.+|+.|+ -+||
T Consensus 1 miCIeCg~~v~~Ly~~Ys-~~~irLt~C~~C~---~vaD 35 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYS-PGNIRLTKCPNCG---KVAD 35 (208)
T ss_pred CEeccCCCcchhhhhccC-CCcEEEeeccccC---Cccc
Confidence 468889988766666543 2348899999996 5676
No 110
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=37.72 E-value=24 Score=28.86 Aligned_cols=41 Identities=24% Similarity=0.647 Sum_probs=22.1
Q ss_pred ccceeeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccchhccc
Q psy13378 80 EHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYE 139 (272)
Q Consensus 80 ~~k~~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~ 139 (272)
+....--+.|++|+...-..++. | +..|..|+ +.|..-||.
T Consensus 29 e~~~~~~~~Cp~C~~~~VkR~a~-----G----------IW~C~kCg----~~fAGgay~ 69 (89)
T COG1997 29 EAQQRAKHVCPFCGRTTVKRIAT-----G----------IWKCRKCG----AKFAGGAYT 69 (89)
T ss_pred HHHHhcCCcCCCCCCcceeeecc-----C----------eEEcCCCC----Ceecccccc
Confidence 33444456777777553221211 2 47777777 456666664
No 111
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=37.53 E-value=33 Score=29.30 Aligned_cols=33 Identities=27% Similarity=0.727 Sum_probs=25.1
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcceee
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLI 156 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLI 156 (272)
..|+.|+...+.++- +..+.+.+|..|.+..-+
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 679999988888774 245667899999887654
No 112
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=37.46 E-value=27 Score=31.08 Aligned_cols=26 Identities=31% Similarity=0.870 Sum_probs=17.3
Q ss_pred eeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCccc
Q psy13378 86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRN 129 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS 129 (272)
.|.|++||.-.-. .. --.||.|+++-
T Consensus 134 ~~vC~vCGy~~~g-------e~-----------P~~CPiCga~k 159 (166)
T COG1592 134 VWVCPVCGYTHEG-------EA-----------PEVCPICGAPK 159 (166)
T ss_pred EEEcCCCCCcccC-------CC-----------CCcCCCCCChH
Confidence 7999999844322 11 13599999774
No 113
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=37.39 E-value=24 Score=28.72 Aligned_cols=17 Identities=29% Similarity=0.811 Sum_probs=9.6
Q ss_pred EEEcCCCCcccccccchhccc
Q psy13378 119 AYTCKVCGTRNSHLISKHSYE 139 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~ 139 (272)
+..|..|+ +.|+--||.
T Consensus 53 IW~C~~C~----~~~AGGAy~ 69 (90)
T PF01780_consen 53 IWKCKKCG----KKFAGGAYT 69 (90)
T ss_dssp EEEETTTT----EEEE-BSSS
T ss_pred EeecCCCC----CEEeCCCcc
Confidence 37777776 455555553
No 114
>KOG1105|consensus
Probab=37.25 E-value=24 Score=34.15 Aligned_cols=13 Identities=23% Similarity=0.756 Sum_probs=7.6
Q ss_pred eeecCCcCCcccc
Q psy13378 86 AYTCKVCGTRNSH 98 (272)
Q Consensus 86 ~fTCkvC~TRSSh 98 (272)
.|+|.+|..+...
T Consensus 255 ~fkcgkckk~~ct 267 (296)
T KOG1105|consen 255 LFKCGKCKKKNCT 267 (296)
T ss_pred ceeecccccccee
Confidence 4666666665544
No 115
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=36.56 E-value=4 Score=38.59 Aligned_cols=62 Identities=21% Similarity=0.396 Sum_probs=44.6
Q ss_pred cccceeeeeecCCcCCc-ccccccCCcccccccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcce
Q psy13378 79 LEHKLKLAYTCKVCGTR-NSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNH 154 (272)
Q Consensus 79 ~~~k~~i~fTCkvC~TR-SSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~H 154 (272)
+..++...|.|.||.+. ++|-+++- .+-.+......|.|..|++. |..-=+.++|+.|.+.-
T Consensus 131 La~~iRavd~~dva~~v~~~hfLpd~-----~gn~r~f~rq~~rc~~c~~k---------~rr~pl~g~c~kcg~~~ 193 (253)
T COG1933 131 LARRIRAVDEHDVAERVLNSHFIPDL-----RGNLRSFTRQEFRCVKCNTK---------FRRPPLDGKCPICGGKI 193 (253)
T ss_pred HHHHHHHHHhHHHHHHhhccCCCcch-----hhhhhhhhhheeehHhhhhh---------hcCCCccccccccCCeE
Confidence 46788888999999976 55544442 33445555678999999865 55566788999999843
No 116
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=35.45 E-value=48 Score=27.20 Aligned_cols=46 Identities=24% Similarity=0.482 Sum_probs=26.4
Q ss_pred cccccceeeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccc
Q psy13378 77 IQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLIS 134 (272)
Q Consensus 77 ~q~~~k~~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~IS 134 (272)
++-..++--.|+|+.|+.-+ -++... ++. ...+|+.|+......|+
T Consensus 12 ~k~k~klpt~f~CP~Cge~~-v~v~~~---k~~--------~h~~C~~CG~y~~~~V~ 57 (99)
T PRK14892 12 IRPKPKLPKIFECPRCGKVS-ISVKIK---KNI--------AIITCGNCGLYTEFEVP 57 (99)
T ss_pred cccccCCCcEeECCCCCCeE-eeeecC---CCc--------ceEECCCCCCccCEECC
Confidence 33334455679999999422 111111 133 36899999977444443
No 117
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=35.32 E-value=27 Score=27.25 Aligned_cols=35 Identities=14% Similarity=0.417 Sum_probs=21.4
Q ss_pred eecCCcCCcccccccCCcccccccccccceEEEEEcC--CCCcc
Q psy13378 87 YTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCK--VCGTR 128 (272)
Q Consensus 87 fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk--~C~tR 128 (272)
+.|+.|+... +..+......++. .+-++|. .|++|
T Consensus 2 m~CP~Cg~~a-~irtSr~~s~~~~------~~Y~qC~N~eCg~t 38 (72)
T PRK09678 2 FHCPLCQHAA-HARTSRYITDTTK------ERYHQCQNVNCSAT 38 (72)
T ss_pred ccCCCCCCcc-EEEEChhcChhhh------eeeeecCCCCCCCE
Confidence 6789998765 4433333333332 3568888 88876
No 118
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=35.12 E-value=8.8 Score=24.69 Aligned_cols=21 Identities=43% Similarity=0.956 Sum_probs=9.2
Q ss_pred EcCCCCcccccccchhcccceEEEEEcC
Q psy13378 121 TCKVCGTRNSHLISKHSYEKGVVIVKCE 148 (272)
Q Consensus 121 TCk~C~tRS~h~ISK~AY~kGvViVqC~ 148 (272)
+|+.|++. .-+..|-|.++|+
T Consensus 1 ~CP~C~s~-------l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSK-------LVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--B-------EEE-CCTTCEEE-
T ss_pred CcCCCCCE-------eEcCCCCEeEECC
Confidence 57788744 2244555666665
No 119
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=34.99 E-value=17 Score=26.38 Aligned_cols=40 Identities=25% Similarity=0.581 Sum_probs=20.7
Q ss_pred eecCCcCCcccccc--cCCcccccccccccceEEEEEcCCCCcc
Q psy13378 87 YTCKVCGTRNSHLI--SKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 87 fTCkvC~TRSSh~I--SK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
|.|++|+..-.... +.++...|+. -..+--.|+|+.|+..
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~--f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTP--FEDLPDDWVCPVCGAG 43 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCC--HhHCCCCCCCCCCCCc
Confidence 67888886643221 2233333331 1223346788888754
No 120
>KOG2879|consensus
Probab=34.80 E-value=22 Score=34.48 Aligned_cols=37 Identities=27% Similarity=0.611 Sum_probs=21.2
Q ss_pred eecCCcCCcccccccCCccccc---------ccccccceEEEEEcCCCCcc
Q psy13378 87 YTCKVCGTRNSHLISKHSYEKG---------VIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 87 fTCkvC~TRSSh~ISK~Sy~kG---------v~~~~~~~~L~FTCk~C~tR 128 (272)
=+|++|+.+.+- ++.-| =.....--...|||+.|++-
T Consensus 240 ~~C~~Cg~~Pti-----P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~ 285 (298)
T KOG2879|consen 240 TECPVCGEPPTI-----PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGEN 285 (298)
T ss_pred ceeeccCCCCCC-----CeeeccccceeehhhhhhhhcchhhcccCccCCC
Confidence 389999987643 22222 00112223356999999954
No 121
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=34.74 E-value=19 Score=33.28 Aligned_cols=57 Identities=21% Similarity=0.487 Sum_probs=32.8
Q ss_pred eeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccchh--cccceEEEEEcCCCCcceeeecccc
Q psy13378 85 LAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKH--SYEKGVVIVKCEGCSNNHLIADNLK 161 (272)
Q Consensus 85 i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~--AY~kGvViVqC~gC~n~HLIADnLg 161 (272)
...+|..|+|.=- | .-.+|+-|++.....+.-. .-+.++-+-.|..|+..-.+.| ..
T Consensus 196 R~L~Cs~C~t~W~-------~------------~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd-~~ 254 (290)
T PF04216_consen 196 RYLHCSLCGTEWR-------F------------VRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD-RE 254 (290)
T ss_dssp EEEEETTT--EEE---------------------TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE-TT
T ss_pred EEEEcCCCCCeee-------e------------cCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh-hh
Confidence 5669999997641 1 1357999997754433332 2344788999999999999999 44
No 122
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=34.65 E-value=54 Score=26.92 Aligned_cols=20 Identities=25% Similarity=0.471 Sum_probs=13.0
Q ss_pred cceEEEEEcCCCCccccccc
Q psy13378 114 HKLKLAYTCKVCGTRNSHLI 133 (272)
Q Consensus 114 ~~~~L~FTCk~C~tRS~h~I 133 (272)
...+|+..|..|++.+...+
T Consensus 62 g~w~iiHrC~~Cg~l~~Nr~ 81 (92)
T PF12647_consen 62 GEWMIIHRCTRCGELRSNRI 81 (92)
T ss_pred CCEEEEEecCCCCCcccCCC
Confidence 56777777777776654433
No 123
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=34.50 E-value=28 Score=29.24 Aligned_cols=15 Identities=33% Similarity=0.758 Sum_probs=7.5
Q ss_pred ccceEEEEEcCCCCc
Q psy13378 138 YEKGVVIVKCEGCSN 152 (272)
Q Consensus 138 Y~kGvViVqC~gC~n 152 (272)
|...-.+.+||+|..
T Consensus 118 ~~~~~~f~~C~~C~k 132 (147)
T PF01927_consen 118 YETYDEFWRCPGCGK 132 (147)
T ss_pred cccCCeEEECCCCCC
Confidence 333334666666653
No 124
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.44 E-value=30 Score=39.49 Aligned_cols=83 Identities=18% Similarity=0.345 Sum_probs=40.8
Q ss_pred eccCCCCCCCccccccceeeeeecCCcCCcccccccCCc-------ccccccccccceEEEEEcCCCCcccccccchh-c
Q psy13378 66 TRNSTPGNPEPIQLEHKLKLAYTCKVCGTRNSHLISKHS-------YEKGVIKLKHKLKLAYTCKVCGTRNSHLISKH-S 137 (272)
Q Consensus 66 ~~~~~pgn~~~~q~~~k~~i~fTCkvC~TRSSh~ISK~S-------y~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~-A 137 (272)
.|-|-|+-+.+++.+|.....|-=..-| .+...+.+-. -..|...++ .-.|.|+.|++.+...+-+. .
T Consensus 611 ~RmGRPeKs~~R~mkP~~h~LFPig~aG-G~qR~I~kAa~~a~~~~d~~G~ieVE---V~~rkCPkCG~~t~~~fCP~CG 686 (1337)
T PRK14714 611 NRMGRPEKSKPRKMKPPVHTLFPIGEAG-GAQRDVAKAAKHAPDMSDEGGVIEVE---VGRRRCPSCGTETYENRCPDCG 686 (1337)
T ss_pred cccCCcccccccccCCCCcccccccccC-cccccHHHHHHhhhhccccCCeEEEE---EEEEECCCCCCccccccCcccC
Confidence 3445577777788777777777555544 2222233321 122222111 12588888887644333332 1
Q ss_pred ccceEEEEEcCCCCcc
Q psy13378 138 YEKGVVIVKCEGCSNN 153 (272)
Q Consensus 138 Y~kGvViVqC~gC~n~ 153 (272)
.+. .....||.|...
T Consensus 687 s~t-e~vy~CPsCGae 701 (1337)
T PRK14714 687 THT-EPVYVCPDCGAE 701 (1337)
T ss_pred CcC-CCceeCccCCCc
Confidence 111 112366666653
No 125
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=34.42 E-value=42 Score=26.26 Aligned_cols=33 Identities=21% Similarity=0.524 Sum_probs=20.0
Q ss_pred ceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 115 KLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 115 ~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
...|-.+|+.|++... -|-+-.-.|+|..|..-
T Consensus 15 s~Fl~VkCpdC~N~q~------vFshast~V~C~~CG~~ 47 (67)
T COG2051 15 SRFLRVKCPDCGNEQV------VFSHASTVVTCLICGTT 47 (67)
T ss_pred ceEEEEECCCCCCEEE------EeccCceEEEecccccE
Confidence 3456778888876521 23344556788888654
No 126
>COG1773 Rubredoxin [Energy production and conversion]
Probab=34.41 E-value=25 Score=26.40 Aligned_cols=40 Identities=23% Similarity=0.473 Sum_probs=22.3
Q ss_pred eeecCCcCCccccc--ccCCcccccccccccceEEEEEcCCCCc
Q psy13378 86 AYTCKVCGTRNSHL--ISKHSYEKGVIKLKHKLKLAYTCKVCGT 127 (272)
Q Consensus 86 ~fTCkvC~TRSSh~--ISK~Sy~kGv~~~~~~~~L~FTCk~C~t 127 (272)
.|.|++||.---.- -..++-..|+. =..+-..+.|+.|+.
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~pgT~--fedlPd~w~CP~Cg~ 44 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIAPGTP--FEDLPDDWVCPECGV 44 (55)
T ss_pred ceEecCCceEeccccCCccCCCCCCCc--hhhCCCccCCCCCCC
Confidence 68888888653221 22233333331 134556788888884
No 127
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=34.18 E-value=30 Score=23.00 Aligned_cols=10 Identities=40% Similarity=1.075 Sum_probs=7.6
Q ss_pred eeecCCcCCc
Q psy13378 86 AYTCKVCGTR 95 (272)
Q Consensus 86 ~fTCkvC~TR 95 (272)
.|.|++||.-
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 5889999843
No 128
>KOG4216|consensus
Probab=33.78 E-value=35 Score=34.80 Aligned_cols=61 Identities=25% Similarity=0.439 Sum_probs=33.3
Q ss_pred CCChhhhhhccccceeeeccCCCCCCCccccccceeeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCC
Q psy13378 49 GLSHSELKKRANLLKFYTRNSTPGNPEPIQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCG 126 (272)
Q Consensus 49 g~~~s~~~sr~n~~~~~~~~~~pgn~~~~q~~~k~~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~ 126 (272)
++..+++-.-++....-..+.--++.+..-....+.+. -||+||-.||. .+-|| .||..|+
T Consensus 10 ~~~~~el~~~~~~~~q~~~~~~g~~~~~g~~~aQIEvI-PCKiCGDKSSG------iHYGV----------ITCEGCK 70 (479)
T KOG4216|consen 10 TPRSSELDESGCRLSQCMFHIGGGDLQMGNMKAQIEII-PCKICGDKSSG------IHYGV----------ITCEGCK 70 (479)
T ss_pred ccccccchhhhhhccccccccccchhhcccccceeEEE-eeeeccCCCCc------ceeee----------Eeeccch
Confidence 44444444444444332233222233222234455555 89999988854 44455 8999997
No 129
>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=33.26 E-value=39 Score=25.12 Aligned_cols=36 Identities=39% Similarity=0.632 Sum_probs=14.2
Q ss_pred ecCCcCCcccccccCCccccccc-ccccceEEEEEcCCCC
Q psy13378 88 TCKVCGTRNSHLISKHSYEKGVI-KLKHKLKLAYTCKVCG 126 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~Sy~kGv~-~~~~~~~L~FTCk~C~ 126 (272)
-|+.|++-- |+......-+. +-...-.|.+||..|+
T Consensus 48 ~Ck~C~~~l---iPG~~~~vri~~~~~~~~~l~~~C~~C~ 84 (85)
T PF04032_consen 48 ICKKCGSLL---IPGVNCSVRIRKKKKKKNFLVYTCLNCG 84 (85)
T ss_dssp B-TTT--B-----CTTTEEEEEE---SSS-EEEEEETTTT
T ss_pred cccCCCCEE---eCCCccEEEEEecCCCCCEEEEEccccC
Confidence 799998543 44433221111 0113445667777765
No 130
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=32.92 E-value=51 Score=22.48 Aligned_cols=32 Identities=19% Similarity=0.537 Sum_probs=18.0
Q ss_pred EEEEcCCCCcccccccchhccc-ceEEEEEcCCCC
Q psy13378 118 LAYTCKVCGTRNSHLISKHSYE-KGVVIVKCEGCS 151 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY~-kGvViVqC~gC~ 151 (272)
|...|+-|+ +++.|=|++.. +|---.+|..|+
T Consensus 4 i~v~CP~C~--s~~~v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 4 IDVHCPRCQ--STEGVKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred EeeeCCCCC--CCCcceeCCCCCCCCEeEecCcCC
Confidence 456666666 33445555553 455566666663
No 131
>PHA02942 putative transposase; Provisional
Probab=32.74 E-value=36 Score=33.26 Aligned_cols=28 Identities=21% Similarity=0.661 Sum_probs=15.5
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcce
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNH 154 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~H 154 (272)
.=||+.|++... ..+.. ...|+.|...|
T Consensus 325 Sq~Cs~CG~~~~-~l~~r-------~f~C~~CG~~~ 352 (383)
T PHA02942 325 SVSCPKCGHKMV-EIAHR-------YFHCPSCGYEN 352 (383)
T ss_pred CccCCCCCCccC-cCCCC-------EEECCCCCCEe
Confidence 356777776542 11111 56777777654
No 132
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=32.55 E-value=37 Score=30.58 Aligned_cols=31 Identities=26% Similarity=0.547 Sum_probs=20.3
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcceeeecccc
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLK 161 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLg 161 (272)
|.|..|++.+.+. .-.||+|+.+|-|-=-+|
T Consensus 355 ~~c~~cg~~~~~~-----------~~~c~~c~~~~~~~~~~~ 385 (389)
T PRK11788 355 YRCRNCGFTARTL-----------YWHCPSCKAWETIKPIRG 385 (389)
T ss_pred EECCCCCCCCccc-----------eeECcCCCCccCcCCccc
Confidence 6688888664432 357888888887543333
No 133
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=32.48 E-value=47 Score=25.29 Aligned_cols=34 Identities=21% Similarity=0.584 Sum_probs=20.4
Q ss_pred cceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 114 HKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 114 ~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
+++.|-..|+.|++-+ . -|.|-.-.|+|..|...
T Consensus 6 ~S~F~~VkCp~C~n~q--~----vFsha~t~V~C~~Cg~~ 39 (59)
T PRK00415 6 RSRFLKVKCPDCGNEQ--V----VFSHASTVVRCLVCGKT 39 (59)
T ss_pred CCeEEEEECCCCCCeE--E----EEecCCcEEECcccCCC
Confidence 3456677788887442 1 23344556778777653
No 134
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=32.29 E-value=32 Score=28.99 Aligned_cols=11 Identities=18% Similarity=0.582 Sum_probs=5.9
Q ss_pred EEcCCCCccee
Q psy13378 145 VKCEGCSNNHL 155 (272)
Q Consensus 145 VqC~gC~n~HL 155 (272)
.+||.|...=.
T Consensus 124 f~Cp~Cg~~l~ 134 (147)
T smart00531 124 FTCPRCGEELE 134 (147)
T ss_pred EECCCCCCEEE
Confidence 55666655444
No 135
>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=32.26 E-value=23 Score=23.68 Aligned_cols=8 Identities=50% Similarity=1.302 Sum_probs=4.0
Q ss_pred EcCCCCcc
Q psy13378 121 TCKVCGTR 128 (272)
Q Consensus 121 TCk~C~tR 128 (272)
.|+.|++|
T Consensus 19 rC~~CG~R 26 (32)
T PF03604_consen 19 RCPECGHR 26 (32)
T ss_dssp SBSSSS-S
T ss_pred ECCcCCCe
Confidence 55555555
No 136
>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=32.19 E-value=21 Score=30.26 Aligned_cols=46 Identities=17% Similarity=0.381 Sum_probs=24.4
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCC
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLK 167 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~ 167 (272)
.+.|..|+......-......... .-+||.|.. ++-++.=||+|.-
T Consensus 105 ~~~C~~C~~~~~~~~~~~~~~~~~-~~~C~~C~~--~lrp~vv~fgE~~ 150 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVDSIDEEE-PPRCPKCGG--LLRPDVVLFGESL 150 (178)
T ss_dssp EEEETTTSBEEEGHHHHHHHHTTS-SCBCTTTSC--BEEEEE--BTSB-
T ss_pred eeeecCCCccccchhhcccccccc-cccccccCc--cCCCCeeecCCCC
Confidence 357888876532211111111111 118999988 5789999999864
No 137
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=30.90 E-value=29 Score=23.55 Aligned_cols=26 Identities=42% Similarity=1.044 Sum_probs=16.5
Q ss_pred eecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 87 YTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 87 fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
+.|.+|+.+ .-.+.. |. |.|..|+|.
T Consensus 9 ~~C~~C~~~--~~~~~d----G~----------~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR--WFYSDD----GF----------YYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCe--EeEccC----CE----------EEhhhCceE
Confidence 458899866 223333 32 888888864
No 138
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=30.66 E-value=25 Score=22.94 Aligned_cols=27 Identities=33% Similarity=0.875 Sum_probs=17.2
Q ss_pred eeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCccc
Q psy13378 86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRN 129 (272)
Q Consensus 86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS 129 (272)
.|.|++||..-.. +. --++|+.|+..-
T Consensus 1 ~~~C~~CGy~y~~---~~--------------~~~~CP~Cg~~~ 27 (33)
T cd00350 1 KYVCPVCGYIYDG---EE--------------APWVCPVCGAPK 27 (33)
T ss_pred CEECCCCCCEECC---Cc--------------CCCcCcCCCCcH
Confidence 3789999955311 11 137899998753
No 139
>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=30.63 E-value=30 Score=22.08 Aligned_cols=10 Identities=30% Similarity=1.122 Sum_probs=7.7
Q ss_pred EEEEEcCCCC
Q psy13378 117 KLAYTCKVCG 126 (272)
Q Consensus 117 ~L~FTCk~C~ 126 (272)
.+.|.|+.|+
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 3478888887
No 140
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=30.51 E-value=34 Score=34.52 Aligned_cols=42 Identities=19% Similarity=0.472 Sum_probs=30.5
Q ss_pred cceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeecc
Q psy13378 114 HKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADN 159 (272)
Q Consensus 114 ~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADn 159 (272)
+...+.|.|+.|+..+.|+....... =+ +||.|..-|...+-
T Consensus 322 ~~~r~~~~c~~~~~e~~~t~~~~~~~---~~-~~~~~~~e~~~v~~ 363 (411)
T COG1503 322 EKERVTYKCPTCGYENLKSKREFEQK---RF-RCPECGSEMEEVEV 363 (411)
T ss_pred cccceeecCCCcchhhhhcccccccc---cc-cCccccccccchhh
Confidence 34456899999998887766555555 34 99999998886543
No 141
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=30.29 E-value=52 Score=30.48 Aligned_cols=35 Identities=34% Similarity=0.780 Sum_probs=20.5
Q ss_pred EEEEEcCCCCccc-ccccchh-cccceEEEEEcCCCCcce
Q psy13378 117 KLAYTCKVCGTRN-SHLISKH-SYEKGVVIVKCEGCSNNH 154 (272)
Q Consensus 117 ~L~FTCk~C~tRS-~h~ISK~-AY~kGvViVqC~gC~n~H 154 (272)
.+-+.|+.|+.-. .|.+=|. .++ ++++|..|..-|
T Consensus 4 ~iy~~Cp~Cg~eev~hEVik~~g~~---~lvrC~eCG~V~ 40 (201)
T COG1326 4 EIYIECPSCGSEEVSHEVIKERGRE---PLVRCEECGTVH 40 (201)
T ss_pred eEEEECCCCCcchhhHHHHHhcCCc---eEEEccCCCcEe
Confidence 3456777777222 3333333 444 777888887766
No 142
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=30.17 E-value=39 Score=33.60 Aligned_cols=37 Identities=16% Similarity=0.279 Sum_probs=26.5
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcceee
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLI 156 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLI 156 (272)
.-||+.|+.+-.....++. -.-.+-..||.|.=.=.|
T Consensus 159 ~~tC~tC~G~G~v~~~~~~-g~~~~~~~C~~C~G~G~~ 195 (371)
T COG0484 159 PKTCPTCNGSGQVRTVQRT-GFFSFQQTCPTCNGTGKI 195 (371)
T ss_pred CCcCCCCCCcCeEEEEEee-eEEEEEEECCCCccceeE
Confidence 3699999988777777766 444556779999765443
No 143
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=29.96 E-value=42 Score=22.74 Aligned_cols=22 Identities=27% Similarity=0.465 Sum_probs=11.4
Q ss_pred eecCCcCCcccccccCCcccccc
Q psy13378 87 YTCKVCGTRNSHLISKHSYEKGV 109 (272)
Q Consensus 87 fTCkvC~TRSSh~ISK~Sy~kGv 109 (272)
++|+.|++ .-|...+.+-..|+
T Consensus 2 r~C~~Cg~-~Yh~~~~pP~~~~~ 23 (36)
T PF05191_consen 2 RICPKCGR-IYHIEFNPPKVEGV 23 (36)
T ss_dssp EEETTTTE-EEETTTB--SSTTB
T ss_pred cCcCCCCC-ccccccCCCCCCCc
Confidence 67888883 44544444444444
No 144
>PRK04023 DNA polymerase II large subunit; Validated
Probab=29.94 E-value=26 Score=39.21 Aligned_cols=28 Identities=11% Similarity=0.290 Sum_probs=15.3
Q ss_pred eccCCCCCCCccccccceeeeeecCCcC
Q psy13378 66 TRNSTPGNPEPIQLEHKLKLAYTCKVCG 93 (272)
Q Consensus 66 ~~~~~pgn~~~~q~~~k~~i~fTCkvC~ 93 (272)
.+-|-|+-+.+++..|.-...|-=...|
T Consensus 577 ~RmGRPEKa~~RkMkP~~h~LFPiG~~G 604 (1121)
T PRK04023 577 ARMGRPEKAKERKMKPPVHVLFPIGNAG 604 (1121)
T ss_pred cccCCCcccccccCCCCCcccccccccC
Confidence 3445566666666666555555444443
No 145
>PLN00209 ribosomal protein S27; Provisional
Probab=29.86 E-value=63 Score=26.33 Aligned_cols=34 Identities=15% Similarity=0.437 Sum_probs=20.4
Q ss_pred cceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 114 HKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 114 ~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
+++.|-..|+.|.+-+ . -|-+-...|.|.+|...
T Consensus 31 nS~Fm~VkCp~C~n~q--~----VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 31 NSFFMDVKCQGCFNIT--T----VFSHSQTVVVCGSCQTV 64 (86)
T ss_pred CCEEEEEECCCCCCee--E----EEecCceEEEccccCCE
Confidence 4556677777777442 1 23445566777777653
No 146
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.68 E-value=32 Score=28.59 Aligned_cols=10 Identities=40% Similarity=1.168 Sum_probs=4.9
Q ss_pred EEcCCCCccc
Q psy13378 120 YTCKVCGTRN 129 (272)
Q Consensus 120 FTCk~C~tRS 129 (272)
|.||.|+..+
T Consensus 93 ~~CP~Cgs~~ 102 (124)
T PRK00762 93 IECPVCGNKR 102 (124)
T ss_pred CcCcCCCCCC
Confidence 4455555443
No 147
>KOG2691|consensus
Probab=29.38 E-value=47 Score=28.31 Aligned_cols=36 Identities=28% Similarity=0.742 Sum_probs=26.3
Q ss_pred ecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 88 TCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
.|+.|+.|-+--...| ..+-+..|.|-|-|--|++|
T Consensus 75 ~C~~C~~~eavffQ~~-----~~r~d~~m~l~yvC~~C~h~ 110 (113)
T KOG2691|consen 75 HCPKCGHREAVFFQAQ-----TRRADEAMRLFYVCCSCGHR 110 (113)
T ss_pred cCCccCCcceEEEecc-----cccccceEEEEEEecccccc
Confidence 7999998865533333 44455678899999999977
No 148
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=29.36 E-value=36 Score=26.20 Aligned_cols=10 Identities=30% Similarity=1.099 Sum_probs=5.2
Q ss_pred eeeeecCCcC
Q psy13378 84 KLAYTCKVCG 93 (272)
Q Consensus 84 ~i~fTCkvC~ 93 (272)
...|-|+-||
T Consensus 25 ~v~F~CPnCG 34 (61)
T COG2888 25 AVKFPCPNCG 34 (61)
T ss_pred eeEeeCCCCC
Confidence 4445555555
No 149
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=29.21 E-value=13 Score=31.97 Aligned_cols=34 Identities=18% Similarity=0.530 Sum_probs=22.7
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
..|+.|+.++++++|.-+-.-=-=+.+|..|...
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEP 139 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCc
Confidence 6778888777777776655544455667666643
No 150
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=29.02 E-value=68 Score=26.12 Aligned_cols=34 Identities=21% Similarity=0.556 Sum_probs=20.2
Q ss_pred cceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 114 HKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 114 ~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
+++.|...|+.|.+-+ . -|-+-.-.|.|.+|.+.
T Consensus 30 nS~Fm~VkCp~C~n~q--~----VFShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 30 NSYFMDVKCPGCSQIT--T----VFSHAQTVVLCGGCSSQ 63 (85)
T ss_pred CCeEEEEECCCCCCee--E----EEecCceEEEccccCCE
Confidence 4556777777777442 1 23344556777777653
No 151
>PRK00420 hypothetical protein; Validated
Probab=28.98 E-value=26 Score=29.36 Aligned_cols=35 Identities=26% Similarity=0.425 Sum_probs=23.1
Q ss_pred eEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeec
Q psy13378 116 LKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIAD 158 (272)
Q Consensus 116 ~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIAD 158 (272)
-++.-+|+.|++.-.+. ..| -+.||.|...-.+.|
T Consensus 20 ~ml~~~CP~Cg~pLf~l------k~g--~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 20 KMLSKHCPVCGLPLFEL------KDG--EVVCPVHGKVYIVKS 54 (112)
T ss_pred HHccCCCCCCCCcceec------CCC--ceECCCCCCeeeecc
Confidence 34678899998653222 334 357999999766655
No 152
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=28.87 E-value=1.1e+02 Score=25.76 Aligned_cols=51 Identities=31% Similarity=0.708 Sum_probs=30.2
Q ss_pred cCCCCcccccccchhcccceEEEEEcCCCCcceeeec-cccccccCCCC-----------CCCHHHHHHHhCCee
Q psy13378 122 CKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIAD-NLKWFTDLKPG-----------VTNIEHILAEKGEQG 184 (272)
Q Consensus 122 Ck~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIAD-nLgwF~d~~~g-----------~~tIEdil~~kGE~V 184 (272)
||+|+.. =. |.-.+|+.|... +-++ -|.||....+. .-||.++.++-|=++
T Consensus 1 CPvCg~~--l~---------vt~l~C~~C~t~-i~G~F~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe~e~~lgiSY 63 (113)
T PF09862_consen 1 CPVCGGE--LV---------VTRLKCPSCGTE-IEGEFELPWFARLSPEQLEFIKLFIKNRGNLKEMEKELGISY 63 (113)
T ss_pred CCCCCCc--eE---------EEEEEcCCCCCE-EEeeeccchhhcCCHHHHHHHHHHHHhcCCHHHHHHHHCCCc
Confidence 8888854 11 334678888874 3344 78899765321 125666665555444
No 153
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=28.35 E-value=25 Score=25.23 Aligned_cols=40 Identities=28% Similarity=0.565 Sum_probs=17.1
Q ss_pred eecCCcCCcccccc--cCCcccccccccccceEEEEEcCCCCcc
Q psy13378 87 YTCKVCGTRNSHLI--SKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 87 fTCkvC~TRSSh~I--SK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
|.|++|+..-.... +.++...|+. -..+-=.|+|+.|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~--F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTP--FEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT----GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCC--HHHCCCCCcCcCCCCc
Confidence 67888886532211 1122233321 1222234888888854
No 154
>PRK12495 hypothetical protein; Provisional
Probab=28.28 E-value=30 Score=32.50 Aligned_cols=31 Identities=19% Similarity=0.351 Sum_probs=19.8
Q ss_pred cceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 114 HKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 114 ~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
+.-++.|.|..|+..-. +| .|++ .|+.|+..
T Consensus 37 gatmsa~hC~~CG~PIp------a~-pG~~--~Cp~CQ~~ 67 (226)
T PRK12495 37 GATMTNAHCDECGDPIF------RH-DGQE--FCPTCQQP 67 (226)
T ss_pred hcccchhhcccccCccc------CC-CCee--ECCCCCCc
Confidence 34456788888876632 45 6664 58888743
No 155
>PLN02913 dihydrofolate synthetase
Probab=28.11 E-value=28 Score=34.96 Aligned_cols=31 Identities=16% Similarity=0.084 Sum_probs=25.6
Q ss_pred eccccccccCCCCCCCHHHHHHHhCCeeeeceeeecc
Q psy13378 157 ADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSH 193 (272)
Q Consensus 157 ADnLgwF~d~~~g~~tIEdil~~kGE~V~kg~~~~~~ 193 (272)
-||++|+++ |+|+|+++|.+-++.|.....+
T Consensus 208 ~DH~~~LG~------Tle~IA~eKagIik~g~pvV~~ 238 (510)
T PLN02913 208 EEHLAALGG------SLESIALAKSGIIKQGRPVVLG 238 (510)
T ss_pred HHHHhhhcc------cHHHHHHHHhhhccCCCCEEEC
Confidence 589999985 8999999999999888654333
No 156
>KOG2817|consensus
Probab=27.85 E-value=22 Score=35.66 Aligned_cols=84 Identities=27% Similarity=0.506 Sum_probs=44.1
Q ss_pred hhhhhcccccee--eeccCCCCCCCcccccc--ceeeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 53 SELKKRANLLKF--YTRNSTPGNPEPIQLEH--KLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 53 s~~~sr~n~~~~--~~~~~~pgn~~~~q~~~--k~~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
++|..=++++.. -.-..+-..|.++++.. .|--.|+|++-.+-++ -+ -|-|+| .||
T Consensus 297 p~Llk~~~v~~~~~~~W~~~deLPveIeL~~~~~fHSvF~CPVlKeqts-------de------NPPm~L-----~CG-- 356 (394)
T KOG2817|consen 297 PQLLKYKSVMELKHGEWNTKDELPVEIELGKEYHFHSVFICPVLKEQTS-------DE------NPPMML-----ICG-- 356 (394)
T ss_pred HHHHHHHHHHHHhccCccccccCccceeccccccccceeecccchhhcc-------CC------CCCeee-----ecc--
Confidence 444555555521 11122334566777643 4678899998222110 00 011222 266
Q ss_pred cccccchhcccc----eEEEEEcCCCCcceeeec
Q psy13378 129 NSHLISKHSYEK----GVVIVKCEGCSNNHLIAD 158 (272)
Q Consensus 129 S~h~ISK~AY~k----GvViVqC~gC~n~HLIAD 158 (272)
|.|||+|..+ |..--+||=|=+--+.+|
T Consensus 357 --HVISkdAlnrLS~ng~~sfKCPYCP~e~~~~~ 388 (394)
T KOG2817|consen 357 --HVISKDALNRLSKNGSQSFKCPYCPVEQLASD 388 (394)
T ss_pred --ceecHHHHHHHhhCCCeeeeCCCCCcccCHHh
Confidence 6777777653 555567888776666555
No 157
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.67 E-value=40 Score=29.50 Aligned_cols=8 Identities=38% Similarity=0.825 Sum_probs=4.2
Q ss_pred EcCCCCcc
Q psy13378 146 KCEGCSNN 153 (272)
Q Consensus 146 qC~gC~n~ 153 (272)
.||.|...
T Consensus 324 ~C~~cg~~ 331 (364)
T COG0675 324 KCPRCGFV 331 (364)
T ss_pred ECCCCCCe
Confidence 45555543
No 158
>smart00350 MCM minichromosome maintenance proteins.
Probab=27.00 E-value=26 Score=35.01 Aligned_cols=34 Identities=21% Similarity=0.443 Sum_probs=16.9
Q ss_pred EEEEcCCCCcccccccchhcccceEEEEEcCC--CCcce
Q psy13378 118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEG--CSNNH 154 (272)
Q Consensus 118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~g--C~n~H 154 (272)
..|+|..|++.....+..-.| ..-..|++ |++.+
T Consensus 36 ~~f~C~~C~~~~~~~~~~~~~---~~p~~C~~~~C~~~~ 71 (509)
T smart00350 36 ASFTCEKCGATLGPEIQSGRE---TEPTVCPPRECQSPT 71 (509)
T ss_pred EEEEecCCCCEEeEEecCCcc---cCCCcCCCCcCCCCC
Confidence 457777776553333322111 12345766 77654
No 159
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=26.91 E-value=41 Score=28.19 Aligned_cols=44 Identities=27% Similarity=0.561 Sum_probs=23.2
Q ss_pred cccccceeeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 77 IQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 77 ~q~~~k~~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
+.+++++... +|+.|.+-- ++.-. .-..++... |++||..||+-
T Consensus 48 v~lp~~iKR~-~CkkC~t~L---vpg~n---~rvR~~~~~-v~vtC~~CG~~ 91 (105)
T COG2023 48 VRLPREIKRT-ICKKCYTPL---VPGKN---ARVRLRKGR-VVVTCLECGTI 91 (105)
T ss_pred cccCHHHHHH-hccccCccc---ccCcc---eEEEEcCCe-EEEEecCCCcE
Confidence 3455566655 799987521 22111 111222222 78888888864
No 160
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=26.85 E-value=39 Score=37.80 Aligned_cols=70 Identities=17% Similarity=0.314 Sum_probs=40.0
Q ss_pred eccCCCCCCCccccccceeeeeecCCcCCcccccccCCccccc-ccccccceEEEEEcCCCCcccccccchhcccceEEE
Q psy13378 66 TRNSTPGNPEPIQLEHKLKLAYTCKVCGTRNSHLISKHSYEKG-VIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVI 144 (272)
Q Consensus 66 ~~~~~pgn~~~~q~~~k~~i~fTCkvC~TRSSh~ISK~Sy~kG-v~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvVi 144 (272)
.+-|-|+-+.+++.+|.....|-=...| .+...|.+-+ .+| ... --.-.+.|+.|++-+.+
T Consensus 576 ~RmGRPEKa~~RkMkPp~h~LFPiG~aG-G~~R~i~~A~-~~g~~i~---vev~~RKCPkCG~yTlk------------- 637 (1095)
T TIGR00354 576 ARMGRPEKAKERKMSPPPHILFPIGMAG-GNTRDIKNAI-NYTKEIE---VEIAIRKCPQCGKESFW------------- 637 (1095)
T ss_pred cccCCCcccccccCCCCCcccccccccC-cchhhHHHHh-ccCCeeE---EEEEEEECCCCCccccc-------------
Confidence 4455588777888877777777666555 2333333322 333 211 11235788888866543
Q ss_pred EEcCCCCcc
Q psy13378 145 VKCEGCSNN 153 (272)
Q Consensus 145 VqC~gC~n~ 153 (272)
.+||.|..+
T Consensus 638 ~rCP~CG~~ 646 (1095)
T TIGR00354 638 LKCPVCGEL 646 (1095)
T ss_pred ccCCCCCCc
Confidence 357777766
No 161
>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=26.09 E-value=48 Score=24.78 Aligned_cols=32 Identities=19% Similarity=0.494 Sum_probs=14.7
Q ss_pred ceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCc
Q psy13378 115 KLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSN 152 (272)
Q Consensus 115 ~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n 152 (272)
++.|...|+.|.+-+ .| |-|-...|.|.+|..
T Consensus 3 S~Fm~VkCp~C~~~q--~v----FSha~t~V~C~~Cg~ 34 (55)
T PF01667_consen 3 SYFMDVKCPGCYNIQ--TV----FSHAQTVVKCVVCGT 34 (55)
T ss_dssp --EEEEE-TTT-SEE--EE----ETT-SS-EE-SSSTS
T ss_pred ccEEEEECCCCCCee--EE----EecCCeEEEcccCCC
Confidence 455677788887542 22 333445677777765
No 162
>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=26.05 E-value=76 Score=22.50 Aligned_cols=9 Identities=33% Similarity=1.298 Sum_probs=4.7
Q ss_pred EEcCCCCcc
Q psy13378 120 YTCKVCGTR 128 (272)
Q Consensus 120 FTCk~C~tR 128 (272)
|.|..|+.+
T Consensus 27 ~~C~~Cga~ 35 (53)
T TIGR03655 27 FECSTCGAS 35 (53)
T ss_pred EECCCCCCC
Confidence 355555544
No 163
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=25.95 E-value=62 Score=26.23 Aligned_cols=18 Identities=28% Similarity=0.647 Sum_probs=11.7
Q ss_pred ccccceEEEEEcCCCCcc
Q psy13378 111 KLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 111 ~~~~~~~L~FTCk~C~tR 128 (272)
++..+..|.|+|..|+..
T Consensus 61 K~TKKi~Lrl~C~~C~~~ 78 (84)
T PTZ00157 61 KTTKKIVLKLECTKCKSK 78 (84)
T ss_pred cccceeEEEEEecccCce
Confidence 444566777777777754
No 164
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.72 E-value=49 Score=31.68 Aligned_cols=13 Identities=38% Similarity=0.749 Sum_probs=10.1
Q ss_pred eeeeecCCcCCcc
Q psy13378 84 KLAYTCKVCGTRN 96 (272)
Q Consensus 84 ~i~fTCkvC~TRS 96 (272)
.=.++|+||+|..
T Consensus 17 kk~ieCPvC~tkF 29 (267)
T COG1655 17 KKTIECPVCNTKF 29 (267)
T ss_pred hceeccCcccchh
Confidence 3467999999874
No 165
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=25.70 E-value=56 Score=31.49 Aligned_cols=57 Identities=21% Similarity=0.399 Sum_probs=40.5
Q ss_pred eeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccchhccc-----ceEEEEEcCCCCcceeeec
Q psy13378 84 KLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYE-----KGVVIVKCEGCSNNHLIAD 158 (272)
Q Consensus 84 ~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~-----kGvViVqC~gC~n~HLIAD 158 (272)
.....|..|+|.=. | ...+|+-|++. +.+.-...+ .++-+-.|..|+..-.+-|
T Consensus 208 ~RyL~CslC~teW~-------~------------~R~~C~~Cg~~--~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~ 266 (305)
T TIGR01562 208 LRYLSCSLCATEWH-------Y------------VRVKCSHCEES--KHLAYLSLEHDAEKAVLKAETCDSCQGYLKILY 266 (305)
T ss_pred ceEEEcCCCCCccc-------c------------cCccCCCCCCC--CceeeEeecCCCCCcceEEeeccccccchhhhc
Confidence 34559999997641 1 24789999964 555545443 3678889999999999887
Q ss_pred ccc
Q psy13378 159 NLK 161 (272)
Q Consensus 159 nLg 161 (272)
.-.
T Consensus 267 ~~~ 269 (305)
T TIGR01562 267 QEK 269 (305)
T ss_pred ccc
Confidence 543
No 166
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=25.61 E-value=25 Score=26.21 Aligned_cols=31 Identities=29% Similarity=0.665 Sum_probs=25.7
Q ss_pred ccEEEeecceeccccccccCCChhhhhhccc
Q psy13378 30 LNILIVENEFSVSKLCYDYGLSHSELKKRAN 60 (272)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~~g~~~s~~~sr~n 60 (272)
+|-.+-+.+.|+..||++++++..++.+|=.
T Consensus 12 VN~kLRD~~~sLd~Lc~~~~id~~~l~~kL~ 42 (55)
T PF14056_consen 12 VNMKLRDEYSSLDELCYDYDIDKEELEEKLA 42 (55)
T ss_pred HHHHHHhccCCHHHHHHHhCCCHHHHHHHHH
Confidence 3444567889999999999999999998853
No 167
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=25.50 E-value=34 Score=29.70 Aligned_cols=15 Identities=20% Similarity=0.339 Sum_probs=10.4
Q ss_pred ceeeeeecCCcCCcc
Q psy13378 82 KLKLAYTCKVCGTRN 96 (272)
Q Consensus 82 k~~i~fTCkvC~TRS 96 (272)
.++.-.+|+.||+|.
T Consensus 5 elGtKr~Cp~cg~kF 19 (129)
T TIGR02300 5 DLGTKRICPNTGSKF 19 (129)
T ss_pred hhCccccCCCcCccc
Confidence 344456888888886
No 168
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.48 E-value=52 Score=30.37 Aligned_cols=32 Identities=25% Similarity=0.438 Sum_probs=19.0
Q ss_pred ecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccc
Q psy13378 88 TCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLIS 134 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~IS 134 (272)
-|+.||++... . ..+. ...|+.|+.+..-.++
T Consensus 101 fC~~CG~~~~~---~---~~~~---------~~~C~~c~~~~yp~~~ 132 (256)
T PRK00241 101 FCGYCGHPMHP---S---KTEW---------AMLCPHCRERYYPRIA 132 (256)
T ss_pred cccccCCCCee---c---CCce---------eEECCCCCCEECCCCC
Confidence 48888866522 1 1222 5789999977444333
No 169
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=25.45 E-value=54 Score=29.55 Aligned_cols=23 Identities=30% Similarity=0.860 Sum_probs=18.4
Q ss_pred eecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 87 YTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 87 fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
|.|+.||+.+.. ..+-|+.|++-
T Consensus 355 ~~c~~cg~~~~~-------------------~~~~c~~c~~~ 377 (389)
T PRK11788 355 YRCRNCGFTART-------------------LYWHCPSCKAW 377 (389)
T ss_pred EECCCCCCCCcc-------------------ceeECcCCCCc
Confidence 789999987743 36999999954
No 170
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=25.35 E-value=38 Score=33.81 Aligned_cols=44 Identities=16% Similarity=0.254 Sum_probs=27.4
Q ss_pred eeeeeecCCcCCccccc--ccCCcccccccccccceEEEEEcCCCCcc
Q psy13378 83 LKLAYTCKVCGTRNSHL--ISKHSYEKGVIKLKHKLKLAYTCKVCGTR 128 (272)
Q Consensus 83 ~~i~fTCkvC~TRSSh~--ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR 128 (272)
-.-.|.|++|+..-... -+.++.+.|+. -..+--.++|+.|+.+
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~--~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTP--WSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCC--hhhCCCCCcCcCCCCc
Confidence 34568999999875443 23455555552 1223335799999966
No 171
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=25.30 E-value=60 Score=21.69 Aligned_cols=7 Identities=43% Similarity=1.236 Sum_probs=3.6
Q ss_pred eecCCcC
Q psy13378 87 YTCKVCG 93 (272)
Q Consensus 87 fTCkvC~ 93 (272)
+.|++|+
T Consensus 4 ~~C~~C~ 10 (33)
T PF08792_consen 4 KKCSKCG 10 (33)
T ss_pred eEcCCCC
Confidence 3555555
No 172
>KOG2186|consensus
Probab=24.86 E-value=32 Score=33.13 Aligned_cols=47 Identities=28% Similarity=0.663 Sum_probs=27.4
Q ss_pred eeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccchhcccce
Q psy13378 84 KLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKG 141 (272)
Q Consensus 84 ~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kG 141 (272)
|+.|||.+||.. +.|...++=..+=+. --|||=-|+ ++|-+..|+.-
T Consensus 1 MV~FtCnvCgEs----vKKp~vekH~srCrn---~~fSCIDC~----k~F~~~sYknH 47 (276)
T KOG2186|consen 1 MVFFTCNVCGES----VKKPQVEKHMSRCRN---AYFSCIDCG----KTFERVSYKNH 47 (276)
T ss_pred CeEEehhhhhhh----ccccchHHHHHhccC---CeeEEeecc----cccccchhhhh
Confidence 568999999943 223222221111111 259999998 66777777653
No 173
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=24.80 E-value=60 Score=25.74 Aligned_cols=14 Identities=36% Similarity=1.023 Sum_probs=11.8
Q ss_pred eeeeeecCCcCCcc
Q psy13378 83 LKLAYTCKVCGTRN 96 (272)
Q Consensus 83 ~~i~fTCkvC~TRS 96 (272)
+++.|.|+-|++.=
T Consensus 1 Mai~Y~CRHCg~~I 14 (76)
T PF10955_consen 1 MAIHYYCRHCGTKI 14 (76)
T ss_pred CceEEEecCCCCEE
Confidence 57899999999873
No 174
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=24.71 E-value=40 Score=27.72 Aligned_cols=31 Identities=32% Similarity=0.775 Sum_probs=22.0
Q ss_pred eeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccc
Q psy13378 84 KLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHL 132 (272)
Q Consensus 84 ~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ 132 (272)
..+..|+-||.+|-| +.| =+|-.|+.+++++
T Consensus 14 ktHtlCrRCG~~syH-~qK-----------------~~CasCGypsak~ 44 (91)
T PTZ00073 14 KTHTLCRRCGKRSFH-VQK-----------------KRCASCGYPSAKM 44 (91)
T ss_pred cCcchhcccCccccc-ccc-----------------ccchhcCCchhhc
Confidence 567789999988866 222 2588898876544
No 175
>PHA02942 putative transposase; Provisional
Probab=24.57 E-value=54 Score=32.01 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=7.0
Q ss_pred EEEcCCCCcc
Q psy13378 119 AYTCKVCGTR 128 (272)
Q Consensus 119 ~FTCk~C~tR 128 (272)
.|+|+.||..
T Consensus 342 ~f~C~~CG~~ 351 (383)
T PHA02942 342 YFHCPSCGYE 351 (383)
T ss_pred EEECCCCCCE
Confidence 5777777754
No 176
>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=24.32 E-value=70 Score=28.18 Aligned_cols=34 Identities=26% Similarity=0.576 Sum_probs=22.0
Q ss_pred cCCCCcccccc---cchhcccceEEE--EEcCCCCccee
Q psy13378 122 CKVCGTRNSHL---ISKHSYEKGVVI--VKCEGCSNNHL 155 (272)
Q Consensus 122 Ck~C~tRS~h~---ISK~AY~kGvVi--VqC~gC~n~HL 155 (272)
|+.|++...+. ..+--|-+=+++ ..|+.|.-++-
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchh
Confidence 99999763333 244445554544 47999998875
No 177
>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=24.30 E-value=44 Score=29.50 Aligned_cols=55 Identities=15% Similarity=0.427 Sum_probs=30.9
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHH
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAE 179 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~ 179 (272)
..|..|+.+....--...+... .+-+||.|. ..+-.|.=||+|.-+.. +++.+++
T Consensus 110 ~~C~~C~~~~~~~~~~~~~~~~-~~p~C~~Cg--~~lrP~Vv~fgE~~p~~--~~~a~~~ 164 (218)
T cd01407 110 VRCTKCGKEYPRDELQADIDRE-EVPRCPKCG--GLLRPDVVFFGESLPEE--LDEAAEA 164 (218)
T ss_pred ceeCCCcCCCcHHHHhHhhccC-CCCcCCCCC--CccCCCeEECCCCCcHH--HHHHHHH
Confidence 5587887542211000011222 256799997 45778999999975432 5555543
No 178
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=24.30 E-value=41 Score=25.67 Aligned_cols=10 Identities=30% Similarity=1.062 Sum_probs=7.5
Q ss_pred EEEEcCCCCc
Q psy13378 118 LAYTCKVCGT 127 (272)
Q Consensus 118 L~FTCk~C~t 127 (272)
+.|-|+.|+.
T Consensus 24 ~~F~CPnCG~ 33 (59)
T PRK14890 24 VKFLCPNCGE 33 (59)
T ss_pred CEeeCCCCCC
Confidence 3688888874
No 179
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=24.15 E-value=80 Score=28.49 Aligned_cols=49 Identities=14% Similarity=0.362 Sum_probs=32.1
Q ss_pred EcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHH
Q psy13378 121 TCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILA 178 (272)
Q Consensus 121 TCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~ 178 (272)
.|..|=... +.+.. ...-+-+..||.|.....= -.|..- +...+++++.
T Consensus 15 lC~~C~~~~-~~i~e--i~~~i~v~~C~~Cg~~~~~---~~W~~~---~~~el~~~~l 63 (236)
T PF04981_consen 15 LCPDCYLKR-FDIIE--IPDRIEVTICPKCGRYRIG---GRWVDP---ESRELEELCL 63 (236)
T ss_pred cChHHhccc-CCeee--cCCccCceECCCCCCEECC---CEeeec---CcccHHHHHH
Confidence 488886443 33433 4555789999999987762 456654 1357888844
No 180
>KOG2041|consensus
Probab=24.14 E-value=61 Score=35.78 Aligned_cols=49 Identities=27% Similarity=0.462 Sum_probs=32.1
Q ss_pred ecCCcCCcccccccCCcccccccccccceEEEEEcCCCCccc-ccccchhcccceEEEEEcCCCCc
Q psy13378 88 TCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRN-SHLISKHSYEKGVVIVKCEGCSN 152 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS-~h~ISK~AY~kGvViVqC~gC~n 152 (272)
+|+.|.++..--|+.- ++--.++ ..-|+.|.+|- .|.||++. .||-|..
T Consensus 1133 ~c~ec~~kfP~CiasG-------~pIt~~~-fWlC~~CkH~a~~~EIs~y~--------~CPLCHs 1182 (1189)
T KOG2041|consen 1133 QCSECQTKFPVCIASG-------RPITDNI-FWLCPRCKHRAHQHEISKYN--------CCPLCHS 1182 (1189)
T ss_pred CChhhcCcCceeeccC-------Cccccce-EEEccccccccccccccccc--------cCccccC
Confidence 6888888865444322 2221222 57799999886 78999875 5888854
No 181
>COG5078 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.75 E-value=50 Score=28.97 Aligned_cols=9 Identities=44% Similarity=1.121 Sum_probs=7.4
Q ss_pred ceeeeCCcc
Q psy13378 23 SVIYHPNLN 31 (272)
Q Consensus 23 ~~~~~~~~~ 31 (272)
+-|||||++
T Consensus 76 t~i~HPNV~ 84 (153)
T COG5078 76 TKIFHPNVD 84 (153)
T ss_pred cCCcCCCcC
Confidence 459999987
No 182
>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=23.41 E-value=32 Score=28.14 Aligned_cols=11 Identities=45% Similarity=1.117 Sum_probs=5.2
Q ss_pred eeeeeecCCcC
Q psy13378 83 LKLAYTCKVCG 93 (272)
Q Consensus 83 ~~i~fTCkvC~ 93 (272)
....|+|+.|+
T Consensus 32 q~a~y~CpfCg 42 (91)
T TIGR00280 32 QKAKYVCPFCG 42 (91)
T ss_pred HhcCccCCCCC
Confidence 33444555554
No 183
>smart00067 GHA Glycoprotein hormone alpha chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.
Probab=23.20 E-value=42 Score=27.37 Aligned_cols=26 Identities=35% Similarity=0.875 Sum_probs=19.8
Q ss_pred cCCCCcccccccchhcccceEEEEEcCCCC
Q psy13378 122 CKVCGTRNSHLISKHSYEKGVVIVKCEGCS 151 (272)
Q Consensus 122 Ck~C~tRS~h~ISK~AY~kGvViVqC~gC~ 151 (272)
|+.|.-|-.+.||+. |.-|.||-||=
T Consensus 2 C~EC~L~~N~~FS~~----~~PiyQC~GCC 27 (87)
T smart00067 2 CPECTLKENKIFSKP----GAPIYQCMGCC 27 (87)
T ss_pred CccceeccccccCCC----CCceeEeccee
Confidence 777887778888873 66788888884
No 184
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=23.15 E-value=57 Score=31.34 Aligned_cols=63 Identities=22% Similarity=0.424 Sum_probs=34.2
Q ss_pred EEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccC--------CCCCCCHHHH-----HHHhCCeee
Q psy13378 119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDL--------KPGVTNIEHI-----LAEKGEQGC 185 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~--------~~g~~tIEdi-----l~~kGE~V~ 185 (272)
...|+.|+++-.-.+++-.- |++++-.. =|+|-+-.+|.+. .+| -|||+. +.|-|=+|+
T Consensus 129 ~~~C~~cg~~~fPR~dP~vI---v~v~~~~~----ilLa~~~~h~~g~yS~LAGFVE~G-ETlE~AV~REv~EE~Gi~V~ 200 (279)
T COG2816 129 ARVCPKCGHEHFPRIDPCVI---VAVIRGDE----ILLARHPRHFPGMYSLLAGFVEPG-ETLEQAVAREVFEEVGIKVK 200 (279)
T ss_pred eeeCCCCCCccCCCCCCeEE---EEEecCCc----eeecCCCCCCCcceeeeeecccCC-ccHHHHHHHHHHHhhCeEEe
Confidence 36677777665555555321 22222222 2556666666442 234 689864 556677777
Q ss_pred ecee
Q psy13378 186 KGLF 189 (272)
Q Consensus 186 kg~~ 189 (272)
+-++
T Consensus 201 ~vrY 204 (279)
T COG2816 201 NVRY 204 (279)
T ss_pred eeeE
Confidence 6665
No 185
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=23.14 E-value=1.2e+02 Score=26.17 Aligned_cols=25 Identities=32% Similarity=0.549 Sum_probs=17.4
Q ss_pred EEEEEcCC-CCcccccccchhcccceEEEEE
Q psy13378 117 KLAYTCKV-CGTRNSHLISKHSYEKGVVIVK 146 (272)
Q Consensus 117 ~L~FTCk~-C~tRS~h~ISK~AY~kGvViVq 146 (272)
.++|||.. |.. ....+|-.-.|+||
T Consensus 136 v~VyTCs~sC~~-----~~~~~y~eE~v~vQ 161 (164)
T PF04194_consen 136 VLVYTCSASCWP-----NDSVGYVEEFVWVQ 161 (164)
T ss_pred EEEEEehHHcCC-----CCCCceEEEEEEEE
Confidence 58999974 743 34567777777776
No 186
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=23.05 E-value=59 Score=20.74 Aligned_cols=8 Identities=38% Similarity=1.016 Sum_probs=6.5
Q ss_pred EEEcCCCC
Q psy13378 119 AYTCKVCG 126 (272)
Q Consensus 119 ~FTCk~C~ 126 (272)
.|+|+.|.
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 58898887
No 187
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=23.03 E-value=87 Score=23.72 Aligned_cols=29 Identities=14% Similarity=0.283 Sum_probs=21.1
Q ss_pred eccccceeEEEEeecchhhhcccccceeee
Q psy13378 196 KLNTNIVRLMIETCLCHLIRETHGSHHLIA 225 (272)
Q Consensus 196 e~~~~~~~~vi~~C~~~~~~~~C~n~HlIA 225 (272)
.|..+ +.++|+.||+..-+.++.+.|+|-
T Consensus 25 afD~~-tk~lIlk~~s~~~~~~~~dv~ivn 53 (61)
T cd01735 25 AFDYP-SKMLILKCPSSSGKPNHADILLVN 53 (61)
T ss_pred EecCC-CcEEEEECccccCCCCcceEEEEE
Confidence 34444 778999999866666788888873
No 188
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=22.79 E-value=35 Score=27.85 Aligned_cols=10 Identities=30% Similarity=0.733 Sum_probs=4.7
Q ss_pred EEEEEcCCCC
Q psy13378 142 VVIVKCEGCS 151 (272)
Q Consensus 142 vViVqC~gC~ 151 (272)
+=|-+|..|.
T Consensus 52 ~GIW~C~~C~ 61 (90)
T PRK03976 52 TGIWECRKCG 61 (90)
T ss_pred EEEEEcCCCC
Confidence 3444555554
No 189
>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=22.78 E-value=42 Score=19.22 Aligned_cols=8 Identities=50% Similarity=1.667 Sum_probs=5.9
Q ss_pred EEcCCCCc
Q psy13378 120 YTCKVCGT 127 (272)
Q Consensus 120 FTCk~C~t 127 (272)
|+|+.|+.
T Consensus 1 y~C~~C~~ 8 (23)
T PF00096_consen 1 YKCPICGK 8 (23)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 67888873
No 190
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=22.73 E-value=36 Score=27.75 Aligned_cols=13 Identities=31% Similarity=0.769 Sum_probs=6.2
Q ss_pred cceeeeeecCCcC
Q psy13378 81 HKLKLAYTCKVCG 93 (272)
Q Consensus 81 ~k~~i~fTCkvC~ 93 (272)
-...-.|+|+.|+
T Consensus 31 ~~q~a~y~CpfCg 43 (90)
T PTZ00255 31 ISQHAKYFCPFCG 43 (90)
T ss_pred HHHhCCccCCCCC
Confidence 3334445555555
No 191
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=22.47 E-value=59 Score=21.25 Aligned_cols=9 Identities=56% Similarity=1.475 Sum_probs=4.7
Q ss_pred EEcCCCCcc
Q psy13378 120 YTCKVCGTR 128 (272)
Q Consensus 120 FTCk~C~tR 128 (272)
|+|+.|+.+
T Consensus 14 Y~Cp~C~~~ 22 (30)
T PF04438_consen 14 YRCPRCGAR 22 (30)
T ss_dssp EE-TTT--E
T ss_pred EECCCcCCc
Confidence 888888765
No 192
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=22.26 E-value=1e+02 Score=26.86 Aligned_cols=17 Identities=24% Similarity=0.608 Sum_probs=13.2
Q ss_pred EEEcCCCCcccccccch
Q psy13378 119 AYTCKVCGTRNSHLISK 135 (272)
Q Consensus 119 ~FTCk~C~tRS~h~ISK 135 (272)
.+.|+.|+++-.+.+|+
T Consensus 166 ~~~c~~~~~~e~rkva~ 182 (189)
T PRK09521 166 ELKCPNCGNIETRKLSS 182 (189)
T ss_pred EEECCCCCCEEeeccch
Confidence 47788888888777774
No 193
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=22.19 E-value=49 Score=30.15 Aligned_cols=56 Identities=27% Similarity=0.544 Sum_probs=32.5
Q ss_pred EEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHH
Q psy13378 120 YTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAE 179 (272)
Q Consensus 120 FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~ 179 (272)
..|..|+.+-...-.....+.+. +-+||.|.. .+-.+.=||+|.-|. ..++++.++
T Consensus 120 ~~C~~C~~~~~~~~~~~~~~~~~-~p~Cp~Cgg--~lrP~Vv~FgE~~p~-~~~~~~~~~ 175 (244)
T PRK14138 120 YYCVRCGKRYTVEDVIEKLEKSD-VPRCDDCSG--LIRPNIVFFGEALPQ-DALREAIRL 175 (244)
T ss_pred eEECCCCCcccHHHHHHHHhcCC-CCCCCCCCC--eECCCEEECCCcCCH-HHHHHHHHH
Confidence 56888886532111111222222 467999975 688999999996432 245554443
No 194
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=21.81 E-value=1.7e+02 Score=24.79 Aligned_cols=31 Identities=13% Similarity=0.065 Sum_probs=16.6
Q ss_pred HhCCeeeeceee-eccceeccccceeEEEEee
Q psy13378 179 EKGEQGCKGLFC-LSHDIKLNTNIVRLMIETC 209 (272)
Q Consensus 179 ~kGE~V~kg~~~-~~~die~~~~~~~~vi~~C 209 (272)
.+|-.|+.=++. .+++|+=.-++..+||.++
T Consensus 73 K~GTkVknIrL~d~~h~Idckv~~g~m~Lks~ 104 (109)
T TIGR00686 73 KKGTKIKNIRLVNGDHNVDCKIEGGSLSLKSE 104 (109)
T ss_pred eCccEEEEEEecCCCceEeeEeCceeEEEEEE
Confidence 334444443433 3356665556667777765
No 195
>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=21.77 E-value=50 Score=21.26 Aligned_cols=17 Identities=29% Similarity=0.730 Sum_probs=13.9
Q ss_pred hcccceEEEEEcCCCCc
Q psy13378 136 HSYEKGVVIVKCEGCSN 152 (272)
Q Consensus 136 ~AY~kGvViVqC~gC~n 152 (272)
.+|-.|-.-|+|+.|+.
T Consensus 8 L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 8 LMYPRGAPSVRCACCHT 24 (25)
T ss_pred EEcCCCCCCeECCccCc
Confidence 57888888899988864
No 196
>PF14196 ATC_hydrolase: L-2-amino-thiazoline-4-carboxylic acid hydrolase
Probab=21.49 E-value=55 Score=26.22 Aligned_cols=58 Identities=9% Similarity=0.116 Sum_probs=37.3
Q ss_pred CCHHHHHHHhCCeeeeceeeeccceeccccceeEEEEeec-chhhhc---------ccccceeeeccc--CC
Q psy13378 171 TNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCL-CHLIRE---------THGSHHLIADNL--KW 230 (272)
Q Consensus 171 ~tIEdil~~kGE~V~kg~~~~~~die~~~~~~~~vi~~C~-~~~~~~---------~C~n~HlIADnL--Gw 230 (272)
.+++.+++..-..-..+.+. ..++-+++...+.+..|| ....++ -|..+|.+++.+ |+
T Consensus 61 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~Cp~~~~~k~~G~~e~~~~~C~~D~~~~~~~~~~~ 130 (149)
T PF14196_consen 61 DDFEKFAEMMKDYPSDWVFE--EVVEDDEDEFEFDFTRCPYAEFWKEYGLPELGPIYCDIDYAMAEGFNPGI 130 (149)
T ss_pred hhHHHHHHHHhcCCccccce--eeecCCCCeEEEEEEeChHHHHHHHcCCchHHhHhhhhhHHHHHhCCCCc
Confidence 45665555222222223322 667788889999999999 444444 688888888877 65
No 197
>PHA00732 hypothetical protein
Probab=21.39 E-value=35 Score=26.59 Aligned_cols=12 Identities=25% Similarity=0.946 Sum_probs=9.1
Q ss_pred eecCCcCCcccc
Q psy13378 87 YTCKVCGTRNSH 98 (272)
Q Consensus 87 fTCkvC~TRSSh 98 (272)
|.|+.|+...+.
T Consensus 2 y~C~~Cgk~F~s 13 (79)
T PHA00732 2 FKCPICGFTTVT 13 (79)
T ss_pred ccCCCCCCccCC
Confidence 689999977543
No 198
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.03 E-value=1e+02 Score=22.72 Aligned_cols=33 Identities=21% Similarity=0.641 Sum_probs=19.8
Q ss_pred eEEEEEcCCCCcccccccchhcccceEEEEEcCCCCccee
Q psy13378 116 LKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHL 155 (272)
Q Consensus 116 ~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HL 155 (272)
.++.|.|-.|+.. |+ -....--++||-|..+=|
T Consensus 3 ~~~~Y~C~~Cg~~----~~---~~~~~~~irCp~Cg~rIl 35 (49)
T COG1996 3 AMMEYKCARCGRE----VE---LDQETRGIRCPYCGSRIL 35 (49)
T ss_pred ceEEEEhhhcCCe----ee---hhhccCceeCCCCCcEEE
Confidence 3567888888744 32 112223468888877766
No 199
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=20.81 E-value=41 Score=25.23 Aligned_cols=11 Identities=27% Similarity=0.942 Sum_probs=7.6
Q ss_pred EEEEcCCCCcc
Q psy13378 118 LAYTCKVCGTR 128 (272)
Q Consensus 118 L~FTCk~C~tR 128 (272)
+.|+|+.||-.
T Consensus 13 v~~~Cp~cGip 23 (55)
T PF13824_consen 13 VNFECPDCGIP 23 (55)
T ss_pred cCCcCCCCCCc
Confidence 46888888744
No 200
>KOG0417|consensus
Probab=20.62 E-value=37 Score=29.98 Aligned_cols=8 Identities=63% Similarity=1.352 Sum_probs=6.9
Q ss_pred eeeeCCcc
Q psy13378 24 VIYHPNLN 31 (272)
Q Consensus 24 ~~~~~~~~ 31 (272)
-|||||++
T Consensus 72 kIyHPNI~ 79 (148)
T KOG0417|consen 72 KIYHPNID 79 (148)
T ss_pred ccccCCcC
Confidence 39999987
No 201
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=20.36 E-value=15 Score=35.79 Aligned_cols=47 Identities=30% Similarity=0.620 Sum_probs=26.6
Q ss_pred ecCCcCCcccccccCCc-ccccccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378 88 TCKVCGTRNSHLISKHS-YEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN 153 (272)
Q Consensus 88 TCkvC~TRSSh~ISK~S-y~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~ 153 (272)
-|++||.+-.-++=..+ ..+|.. --.|+.|.|- =-+|-++|..|.+.
T Consensus 187 ~CPvCGS~PvaSmV~~g~~~~GlR--------YL~CslC~te-----------W~~VR~KC~nC~~t 234 (308)
T COG3058 187 YCPVCGSMPVASMVQIGETEQGLR--------YLHCSLCETE-----------WHYVRVKCSNCEQS 234 (308)
T ss_pred cCCCcCCCCcceeeeecCccccch--------hhhhhhHHHH-----------HHHHHHHhcccccc
Confidence 79999966333322233 566663 2357777643 12456677777653
No 202
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=20.35 E-value=62 Score=29.42 Aligned_cols=84 Identities=15% Similarity=0.305 Sum_probs=49.7
Q ss_pred ccccccCCChhhhhhccccc-----eeeeccCCCCCCCcc-ccccceeeeeecCCcCCc--ccccccCCccc--------
Q psy13378 43 KLCYDYGLSHSELKKRANLL-----KFYTRNSTPGNPEPI-QLEHKLKLAYTCKVCGTR--NSHLISKHSYE-------- 106 (272)
Q Consensus 43 ~~~~~~g~~~s~~~sr~n~~-----~~~~~~~~pgn~~~~-q~~~k~~i~fTCkvC~TR--SSh~ISK~Sy~-------- 106 (272)
.-|..-|++..|+..|...- +---.+.-|-++... .+-..=-+.|.|..|-+. --|+.+...+.
T Consensus 75 ~~C~~~G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~RawH~~HLP~~~~~~~~~~~~~~ 154 (175)
T PF15446_consen 75 QQCKKPGPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRAWHFEHLPPPSGTTSDDDDDDD 154 (175)
T ss_pred cccCCCCCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecCCccceeehhhCCCCcCCCCCcccccc
Confidence 46788899999997777322 122233345566553 345555689999999733 22332322111
Q ss_pred ccccccc-cceEEEEEcCCCC
Q psy13378 107 KGVIKLK-HKLKLAYTCKVCG 126 (272)
Q Consensus 107 kGv~~~~-~~~~L~FTCk~C~ 126 (272)
..+.+.+ ..|.+.++|+.|.
T Consensus 155 ~~~~~~R~~EYs~~W~C~dC~ 175 (175)
T PF15446_consen 155 TDLRSQRLKEYSIDWQCKDCA 175 (175)
T ss_pred hhHHHHHHHHhCCccccCCCC
Confidence 1223333 6799999999994
No 203
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=20.32 E-value=97 Score=28.01 Aligned_cols=50 Identities=18% Similarity=0.335 Sum_probs=29.1
Q ss_pred eEEEEEcCCCCcccccccchhcccceEEEE---EcCCCCcceee----eccccccccCCCCCCCHHHHH
Q psy13378 116 LKLAYTCKVCGTRNSHLISKHSYEKGVVIV---KCEGCSNNHLI----ADNLKWFTDLKPGVTNIEHIL 177 (272)
Q Consensus 116 ~~L~FTCk~C~tRS~h~ISK~AY~kGvViV---qC~gC~n~HLI----ADnLgwF~d~~~g~~tIEdil 177 (272)
|...-+|+.|+.+ |.++. .|+.|...=.+ .+.+..|......++++++.-
T Consensus 96 y~~~~~C~~C~G~------------G~~i~~~~~C~~C~G~G~v~~~~~~~~k~~g~~~g~~it~~~~~ 152 (186)
T TIGR02642 96 VLNSCKCPRCRGT------------GLIQRRQRECDTCAGTGRFRPTVEDLLKSFGVDSGAAIVLKDNW 152 (186)
T ss_pred HHcCCcCCCCCCe------------eEEecCCCCCCCCCCccEEeeeEEEEEEeeeccCCceeeHHHhH
Confidence 3347899999855 77775 69999874333 233344443222345666543
No 204
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=20.19 E-value=60 Score=24.28 Aligned_cols=25 Identities=36% Similarity=0.897 Sum_probs=16.1
Q ss_pred EcCCCCcccccccchhcccceEEEEEcCCCCcce
Q psy13378 121 TCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNH 154 (272)
Q Consensus 121 TCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~H 154 (272)
.|+.|+.+ ...+-=||.||-|.+.|
T Consensus 7 ~C~~Cg~~---------~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 7 KCPVCGKK---------FKDGDDIVVCPECGAPY 31 (54)
T ss_pred cChhhCCc---------ccCCCCEEECCCCCCcc
Confidence 47777744 22344477888888766
Done!