Query 040420
Match_columns 169
No_of_seqs 188 out of 1037
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:15:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040420.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040420hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00730 rubredoxin Rubredoxin; 99.6 1.2E-16 2.6E-21 107.4 2.2 39 78-116 1-50 (50)
2 PF00301 Rubredoxin: Rubredoxi 99.6 2.7E-16 5.8E-21 104.6 2.5 36 78-113 1-47 (47)
3 COG1773 Rubredoxin [Energy pro 99.6 5.4E-16 1.2E-20 106.4 3.6 41 78-118 3-54 (55)
4 PRK05452 anaerobic nitric oxid 99.3 6.3E-13 1.4E-17 121.5 3.4 45 75-119 422-477 (479)
5 cd00350 rubredoxin_like Rubred 99.2 7.5E-12 1.6E-16 77.0 2.6 33 78-116 1-33 (33)
6 cd00729 rubredoxin_SM Rubredox 99.1 3.3E-11 7.2E-16 74.9 2.7 33 78-116 2-34 (34)
7 COG1592 Rubrerythrin [Energy p 98.6 2.2E-08 4.7E-13 81.9 2.1 33 77-116 133-165 (166)
8 PF09723 Zn-ribbon_8: Zinc rib 97.5 5E-05 1.1E-09 48.8 2.0 30 78-108 5-34 (42)
9 TIGR02605 CxxC_CxxC_SSSS putat 97.4 9.9E-05 2.1E-09 48.3 2.2 32 78-110 5-36 (52)
10 smart00834 CxxC_CXXC_SSSS Puta 97.3 0.00014 3.1E-09 45.0 2.2 31 78-109 5-35 (41)
11 PRK03824 hypA hydrogenase nick 96.3 0.0037 8.1E-08 49.1 3.2 35 76-110 68-117 (135)
12 PRK12496 hypothetical protein; 96.2 0.0027 5.8E-08 51.4 2.2 31 78-114 127-157 (164)
13 PRK00398 rpoP DNA-directed RNA 95.6 0.009 2E-07 38.6 2.2 31 77-111 2-32 (46)
14 PF05191 ADK_lid: Adenylate ki 95.5 0.016 3.4E-07 36.5 2.8 29 78-108 1-29 (36)
15 COG2260 Predicted Zn-ribbon RN 95.3 0.029 6.3E-07 39.3 3.9 53 78-145 5-57 (59)
16 COG3357 Predicted transcriptio 95.2 0.0091 2E-07 45.4 1.4 27 78-108 58-84 (97)
17 PF09845 DUF2072: Zn-ribbon co 95.2 0.0064 1.4E-07 48.5 0.5 38 79-120 2-39 (131)
18 smart00531 TFIIE Transcription 95.1 0.0088 1.9E-07 47.1 1.1 38 74-111 95-134 (147)
19 PRK12380 hydrogenase nickel in 95.1 0.018 3.9E-07 44.0 2.7 32 75-112 67-98 (113)
20 PRK06266 transcription initiat 95.1 0.0099 2.1E-07 48.8 1.3 36 75-113 114-149 (178)
21 PF01155 HypA: Hydrogenase exp 95.1 0.0077 1.7E-07 45.8 0.6 31 77-113 69-99 (113)
22 TIGR00373 conserved hypothetic 94.9 0.0093 2E-07 47.9 0.8 37 74-113 105-141 (158)
23 TIGR00100 hypA hydrogenase nic 94.8 0.026 5.7E-07 43.1 2.8 33 75-113 67-99 (115)
24 smart00659 RPOLCX RNA polymera 94.4 0.035 7.6E-07 36.3 2.4 27 78-109 2-28 (44)
25 PRK03681 hypA hydrogenase nick 94.4 0.033 7.2E-07 42.6 2.6 33 75-112 67-99 (114)
26 COG2331 Uncharacterized protei 94.2 0.012 2.5E-07 43.6 -0.2 36 74-110 8-43 (82)
27 COG3364 Zn-ribbon containing p 94.2 0.0087 1.9E-07 46.4 -0.9 37 78-118 2-38 (112)
28 PF07295 DUF1451: Protein of u 94.2 0.043 9.3E-07 44.1 2.9 36 73-114 107-142 (146)
29 PRK11823 DNA repair protein Ra 94.1 0.029 6.3E-07 51.5 2.1 29 76-112 5-33 (446)
30 COG4640 Predicted membrane pro 94.0 0.06 1.3E-06 50.2 3.9 30 80-117 3-32 (465)
31 TIGR00416 sms DNA repair prote 94.0 0.028 6.2E-07 51.8 1.8 30 76-113 5-34 (454)
32 COG1545 Predicted nucleic-acid 93.9 0.057 1.2E-06 42.7 3.1 32 78-117 29-61 (140)
33 PF14206 Cys_rich_CPCC: Cystei 93.7 0.11 2.4E-06 38.0 4.0 52 78-134 1-54 (78)
34 PRK00564 hypA hydrogenase nick 93.5 0.053 1.1E-06 41.6 2.2 34 75-113 68-101 (117)
35 COG1439 Predicted nucleic acid 92.7 0.073 1.6E-06 44.4 2.0 31 71-109 132-162 (177)
36 PF13248 zf-ribbon_3: zinc-rib 92.5 0.055 1.2E-06 31.4 0.8 23 79-109 3-25 (26)
37 COG1996 RPC10 DNA-directed RNA 92.1 0.091 2E-06 35.5 1.6 30 75-108 3-32 (49)
38 PF03604 DNA_RNApol_7kD: DNA d 91.9 0.11 2.4E-06 32.0 1.7 26 79-109 1-26 (32)
39 PRK05978 hypothetical protein; 91.6 0.41 8.8E-06 38.8 5.1 29 78-111 33-63 (148)
40 TIGR01384 TFS_arch transcripti 91.5 0.31 6.8E-06 35.8 4.0 41 77-117 15-79 (104)
41 PRK06260 threonine synthase; V 91.4 0.14 3E-06 45.9 2.4 26 78-109 3-28 (397)
42 cd01121 Sms Sms (bacterial rad 91.4 0.077 1.7E-06 47.9 0.8 26 79-112 1-26 (372)
43 PF13397 DUF4109: Domain of un 91.2 0.22 4.8E-06 38.5 3.1 37 78-115 28-65 (105)
44 PRK13130 H/ACA RNA-protein com 91.0 0.37 8.1E-06 33.3 3.7 23 77-109 4-26 (56)
45 PRK11788 tetratricopeptide rep 91.0 0.12 2.7E-06 43.7 1.6 30 74-111 350-379 (389)
46 PRK06450 threonine synthase; V 90.9 0.15 3.3E-06 45.2 2.1 25 78-109 3-27 (338)
47 TIGR00686 phnA alkylphosphonat 90.8 0.12 2.6E-06 40.2 1.3 24 80-110 4-29 (109)
48 COG2093 DNA-directed RNA polym 90.8 0.12 2.6E-06 36.8 1.1 23 80-110 6-28 (64)
49 PRK10220 hypothetical protein; 90.7 0.13 2.9E-06 40.1 1.4 24 80-110 5-30 (111)
50 PRK00762 hypA hydrogenase nick 90.7 0.21 4.6E-06 38.7 2.6 38 75-113 67-105 (124)
51 PF13240 zinc_ribbon_2: zinc-r 90.7 0.12 2.6E-06 29.5 0.9 22 80-109 1-22 (23)
52 PRK11032 hypothetical protein; 90.6 0.24 5.3E-06 40.5 3.0 36 74-115 120-155 (160)
53 PRK07591 threonine synthase; V 90.5 0.17 3.7E-06 45.9 2.2 26 78-110 18-43 (421)
54 PF14446 Prok-RING_1: Prokaryo 90.4 0.12 2.7E-06 35.5 0.9 29 78-112 5-33 (54)
55 PF09538 FYDLN_acid: Protein o 90.2 0.18 3.8E-06 38.7 1.7 28 77-110 8-36 (108)
56 PRK08579 anaerobic ribonucleos 90.1 0.16 3.4E-06 49.1 1.6 25 77-109 567-591 (625)
57 PF14311 DUF4379: Domain of un 90.0 0.16 3.5E-06 33.7 1.2 31 75-106 25-55 (55)
58 COG1066 Sms Predicted ATP-depe 90.0 0.19 4.1E-06 47.1 2.1 31 77-115 6-36 (456)
59 PRK08271 anaerobic ribonucleos 89.6 0.19 4.2E-06 48.6 1.8 25 77-109 565-589 (623)
60 TIGR01206 lysW lysine biosynth 89.4 0.25 5.5E-06 33.8 1.8 32 78-111 2-33 (54)
61 PF12172 DUF35_N: Rubredoxin-l 89.4 0.18 4E-06 31.0 1.0 24 78-109 11-34 (37)
62 PF14803 Nudix_N_2: Nudix N-te 89.2 0.088 1.9E-06 32.9 -0.5 12 77-88 21-32 (34)
63 PF08271 TF_Zn_Ribbon: TFIIB z 89.0 0.18 3.9E-06 32.0 0.8 24 79-108 1-27 (43)
64 PF07754 DUF1610: Domain of un 88.8 0.27 5.9E-06 28.8 1.4 23 81-107 1-23 (24)
65 PRK08270 anaerobic ribonucleos 88.6 0.28 6E-06 47.6 2.2 24 77-109 625-648 (656)
66 PRK12775 putative trifunctiona 88.4 0.27 5.8E-06 49.6 2.0 32 77-114 820-852 (1006)
67 PRK06393 rpoE DNA-directed RNA 88.4 0.24 5.2E-06 35.2 1.2 22 79-110 6-27 (64)
68 cd01675 RNR_III Class III ribo 87.9 0.3 6.4E-06 46.3 1.8 24 78-109 518-541 (555)
69 TIGR02098 MJ0042_CXXC MJ0042 f 87.4 0.22 4.8E-06 30.5 0.5 29 79-109 3-34 (38)
70 KOG2906 RNA polymerase III sub 87.4 0.6 1.3E-05 36.1 2.9 42 77-118 20-83 (105)
71 PRK08351 DNA-directed RNA poly 87.3 0.34 7.4E-06 34.1 1.4 21 80-110 5-25 (61)
72 PF13717 zinc_ribbon_4: zinc-r 87.1 0.34 7.4E-06 30.2 1.2 28 79-108 3-33 (36)
73 PF08274 PhnA_Zn_Ribbon: PhnA 87.0 0.21 4.6E-06 30.5 0.2 22 80-108 4-27 (30)
74 PF06676 DUF1178: Protein of u 86.6 0.27 5.8E-06 39.9 0.6 46 79-125 6-57 (148)
75 PHA00626 hypothetical protein 86.3 0.63 1.4E-05 32.6 2.3 32 76-119 21-52 (59)
76 COG1645 Uncharacterized Zn-fin 86.2 0.38 8.3E-06 38.4 1.3 26 74-108 24-52 (131)
77 COG1110 Reverse gyrase [DNA re 86.1 0.27 5.8E-06 50.5 0.5 25 78-110 694-718 (1187)
78 TIGR02300 FYDLN_acid conserved 86.1 0.51 1.1E-05 37.7 2.0 27 77-109 8-35 (129)
79 PRK14890 putative Zn-ribbon RN 85.7 0.47 1E-05 33.3 1.4 32 77-108 24-56 (59)
80 PF10263 SprT-like: SprT-like 85.7 0.46 1E-05 36.5 1.5 32 75-108 120-151 (157)
81 TIGR03844 cysteate_syn cysteat 85.5 0.58 1.3E-05 42.5 2.3 24 78-108 2-25 (398)
82 PF04641 Rtf2: Rtf2 RING-finge 85.3 0.32 7E-06 41.6 0.6 37 75-111 110-161 (260)
83 PF09986 DUF2225: Uncharacteri 85.3 0.59 1.3E-05 39.1 2.1 41 77-117 4-67 (214)
84 TIGR00375 conserved hypothetic 84.8 0.39 8.3E-06 43.9 0.9 26 80-109 242-267 (374)
85 PF13719 zinc_ribbon_5: zinc-r 84.8 0.44 9.6E-06 29.7 0.9 30 79-108 3-33 (37)
86 PF00641 zf-RanBP: Zn-finger i 84.4 1.2 2.5E-05 26.2 2.5 27 77-111 3-29 (30)
87 PF05605 zf-Di19: Drought indu 84.3 0.55 1.2E-05 31.0 1.2 30 77-108 1-39 (54)
88 PRK07111 anaerobic ribonucleos 83.8 0.61 1.3E-05 45.9 1.8 24 77-109 679-702 (735)
89 COG1867 TRM1 N2,N2-dimethylgua 83.7 2.1 4.5E-05 39.6 5.1 45 77-129 239-283 (380)
90 PRK09263 anaerobic ribonucleos 83.5 0.76 1.7E-05 45.1 2.3 30 76-109 639-668 (711)
91 PRK14704 anaerobic ribonucleos 83.5 0.71 1.5E-05 44.6 2.1 24 77-109 558-581 (618)
92 PRK08197 threonine synthase; V 83.4 0.67 1.5E-05 41.5 1.8 25 78-109 7-31 (394)
93 smart00661 RPOL9 RNA polymeras 83.4 0.66 1.4E-05 29.7 1.3 26 81-108 3-28 (52)
94 COG2956 Predicted N-acetylgluc 83.3 0.54 1.2E-05 43.3 1.1 26 75-108 351-376 (389)
95 PF13597 NRDD: Anaerobic ribon 83.0 0.35 7.6E-06 45.8 -0.2 30 77-115 490-520 (546)
96 PRK04351 hypothetical protein; 82.9 0.84 1.8E-05 36.7 2.0 30 77-108 111-140 (149)
97 PRK00481 NAD-dependent deacety 82.9 0.81 1.7E-05 38.4 1.9 33 77-111 121-153 (242)
98 COG2888 Predicted Zn-ribbon RN 82.9 0.95 2.1E-05 32.0 2.0 32 77-108 26-58 (61)
99 PF04810 zf-Sec23_Sec24: Sec23 82.7 0.31 6.6E-06 30.9 -0.5 30 79-108 3-32 (40)
100 COG0375 HybF Zn finger protein 82.6 0.79 1.7E-05 35.8 1.6 34 75-114 67-100 (115)
101 TIGR02827 RNR_anaer_Bdell anae 82.5 0.86 1.9E-05 44.0 2.2 25 77-109 531-555 (586)
102 COG0777 AccD Acetyl-CoA carbox 81.8 0.66 1.4E-05 41.5 1.1 59 76-139 25-104 (294)
103 PRK14892 putative transcriptio 81.6 1.5 3.2E-05 33.3 2.8 43 69-112 12-54 (99)
104 COG1594 RPB9 DNA-directed RNA 81.1 1.9 4.2E-05 33.1 3.3 42 75-116 19-88 (113)
105 PRK05654 acetyl-CoA carboxylas 80.9 0.49 1.1E-05 41.7 -0.0 30 77-110 25-56 (292)
106 TIGR00515 accD acetyl-CoA carb 80.8 0.51 1.1E-05 41.6 0.0 30 78-111 25-56 (285)
107 PF13894 zf-C2H2_4: C2H2-type 80.7 1.1 2.4E-05 23.5 1.3 12 79-90 1-12 (24)
108 PF14169 YdjO: Cold-inducible 80.7 2 4.3E-05 30.1 2.9 35 74-112 14-51 (59)
109 CHL00174 accD acetyl-CoA carbo 80.5 0.47 1E-05 42.3 -0.3 29 78-110 37-67 (296)
110 PF10571 UPF0547: Uncharacteri 80.2 1 2.2E-05 26.5 1.1 22 80-109 2-23 (26)
111 PRK12860 transcriptional activ 80.2 1.7 3.7E-05 36.6 3.0 35 75-111 131-165 (189)
112 PHA00626 hypothetical protein 79.7 1.3 2.8E-05 31.1 1.7 34 80-114 2-39 (59)
113 PRK12722 transcriptional activ 79.6 1.5 3.2E-05 36.8 2.4 34 76-111 132-165 (187)
114 COG1997 RPL43A Ribosomal prote 79.3 1.3 2.8E-05 33.4 1.8 28 77-108 34-61 (89)
115 PF00096 zf-C2H2: Zinc finger, 79.1 1.4 3E-05 23.7 1.4 12 79-90 1-12 (23)
116 COG1675 TFA1 Transcription ini 79.0 0.63 1.4E-05 38.6 0.0 38 74-114 109-146 (176)
117 TIGR02487 NrdD anaerobic ribon 79.0 1.1 2.5E-05 42.7 1.7 25 77-109 523-547 (579)
118 PF14319 Zn_Tnp_IS91: Transpos 78.6 1.9 4.2E-05 32.8 2.6 31 75-109 39-69 (111)
119 PF04161 Arv1: Arv1-like famil 78.1 1.2 2.7E-05 36.9 1.5 36 79-119 1-43 (208)
120 PF14205 Cys_rich_KTR: Cystein 77.8 2.5 5.5E-05 29.3 2.7 29 78-108 3-36 (55)
121 PRK00420 hypothetical protein; 77.8 1.3 2.9E-05 34.4 1.5 26 78-108 23-48 (112)
122 TIGR00627 tfb4 transcription f 77.4 1.9 4E-05 38.1 2.5 26 75-108 252-277 (279)
123 PF12773 DZR: Double zinc ribb 77.3 1.4 3.1E-05 28.1 1.3 9 101-109 30-38 (50)
124 COG0846 SIR2 NAD-dependent pro 77.1 1.5 3.1E-05 38.1 1.7 33 75-109 119-155 (250)
125 PRK05638 threonine synthase; V 77.1 1.5 3.2E-05 40.0 1.8 24 78-109 1-24 (442)
126 TIGR00595 priA primosomal prot 77.1 1.9 4.1E-05 40.3 2.6 10 101-110 254-263 (505)
127 PF07282 OrfB_Zn_ribbon: Putat 76.7 1.3 2.8E-05 30.1 1.0 29 77-109 27-55 (69)
128 COG2176 PolC DNA polymerase II 76.3 1.8 3.9E-05 45.4 2.4 32 77-109 913-948 (1444)
129 TIGR01405 polC_Gram_pos DNA po 75.9 1.6 3.4E-05 45.5 1.8 33 76-109 681-717 (1213)
130 PF13451 zf-trcl: Probable zin 75.4 1.2 2.6E-05 30.0 0.6 30 78-109 4-42 (49)
131 cd01412 SIRT5_Af1_CobB SIRT5_A 74.4 2.4 5.2E-05 34.9 2.3 34 76-110 107-140 (224)
132 PF01780 Ribosomal_L37ae: Ribo 74.0 2 4.3E-05 32.4 1.5 21 71-91 46-66 (90)
133 COG0675 Transposase and inacti 73.5 1.5 3.3E-05 36.2 0.8 24 76-108 307-330 (364)
134 PF14353 CpXC: CpXC protein 73.1 1.8 4E-05 32.7 1.2 8 101-108 39-46 (128)
135 PF11682 DUF3279: Protein of u 73.1 2.5 5.4E-05 33.6 1.9 26 75-109 94-119 (128)
136 PRK05580 primosome assembly pr 72.5 2.8 6E-05 40.6 2.5 11 100-110 421-431 (679)
137 cd01410 SIRT7 SIRT7: Eukaryoti 71.8 1.3 2.8E-05 36.7 0.1 34 76-109 93-129 (206)
138 PRK08329 threonine synthase; V 71.7 2.1 4.5E-05 37.8 1.3 23 79-109 2-24 (347)
139 smart00547 ZnF_RBZ Zinc finger 71.1 2.8 6E-05 23.6 1.4 24 78-109 2-25 (26)
140 COG2051 RPS27A Ribosomal prote 71.1 1.8 4E-05 31.1 0.7 27 79-108 20-46 (67)
141 TIGR00155 pqiA_fam integral me 70.9 4.3 9.3E-05 37.2 3.2 32 78-111 13-44 (403)
142 PTZ00255 60S ribosomal protein 70.9 2.8 6E-05 31.6 1.7 22 70-91 46-67 (90)
143 COG2824 PhnA Uncharacterized Z 70.7 2.3 5E-05 33.3 1.2 25 80-111 5-31 (112)
144 PLN02569 threonine synthase 70.4 3.3 7.2E-05 38.8 2.5 30 74-110 45-74 (484)
145 TIGR00280 L37a ribosomal prote 70.2 2.7 5.8E-05 31.7 1.5 22 70-91 45-66 (91)
146 PF04135 Nop10p: Nucleolar RNA 70.2 5 0.00011 27.5 2.6 20 80-109 7-26 (53)
147 PF02146 SIR2: Sir2 family; I 70.1 1.8 3.8E-05 34.4 0.5 30 78-109 105-138 (178)
148 PRK14138 NAD-dependent deacety 69.3 1.2 2.6E-05 37.8 -0.6 33 77-109 118-152 (244)
149 cd04718 BAH_plant_2 BAH, or Br 69.2 3.4 7.4E-05 33.6 2.0 21 92-112 9-30 (148)
150 PF06397 Desulfoferrod_N: Desu 69.0 3 6.5E-05 26.5 1.3 14 76-89 4-17 (36)
151 PRK15103 paraquat-inducible me 69.0 4.1 8.8E-05 37.6 2.7 27 76-110 219-245 (419)
152 cd01411 SIR2H SIR2H: Uncharact 68.2 3.6 7.7E-05 34.4 2.0 29 77-109 117-145 (225)
153 TIGR00354 polC DNA polymerase, 68.0 3.4 7.3E-05 42.6 2.0 26 75-110 622-647 (1095)
154 COG1997 RPL43A Ribosomal prote 67.8 2.3 5.1E-05 32.1 0.7 22 70-91 45-66 (89)
155 PF02891 zf-MIZ: MIZ/SP-RING z 67.6 2.1 4.6E-05 28.3 0.4 10 100-109 41-50 (50)
156 PF11672 DUF3268: Protein of u 67.3 8.4 0.00018 29.5 3.7 42 96-138 27-68 (102)
157 PF08792 A2L_zn_ribbon: A2L zi 67.2 4.6 0.0001 24.9 1.9 28 77-108 2-29 (33)
158 COG5257 GCD11 Translation init 67.2 4.7 0.0001 37.4 2.7 37 73-116 52-88 (415)
159 PTZ00408 NAD-dependent deacety 67.0 3.1 6.8E-05 35.5 1.4 40 77-118 116-158 (242)
160 COG1198 PriA Primosomal protei 67.0 7.5 0.00016 38.6 4.2 17 95-113 472-488 (730)
161 PRK14526 adenylate kinase; Pro 66.9 4.2 9.1E-05 33.7 2.1 30 77-108 121-150 (211)
162 TIGR01031 rpmF_bact ribosomal 66.4 4.2 9.1E-05 27.7 1.7 28 74-110 22-49 (55)
163 smart00731 SprT SprT homologue 66.4 3.9 8.5E-05 31.8 1.8 32 76-108 110-141 (146)
164 PRK14890 putative Zn-ribbon RN 66.4 4.5 9.7E-05 28.4 1.8 30 76-109 5-34 (59)
165 PF11931 DUF3449: Domain of un 66.2 1.9 4.2E-05 36.4 0.0 21 78-98 101-122 (196)
166 PRK04011 peptide chain release 65.7 4.7 0.0001 37.0 2.4 32 78-109 328-359 (411)
167 PF02132 RecR: RecR protein; 65.7 1.7 3.7E-05 27.6 -0.4 26 76-111 15-40 (41)
168 PRK03976 rpl37ae 50S ribosomal 65.2 3.8 8.2E-05 30.9 1.4 22 70-91 46-67 (90)
169 COG1328 NrdD Oxygen-sensitive 65.0 5.6 0.00012 39.4 2.9 36 73-116 636-672 (700)
170 PF09082 DUF1922: Domain of un 65.0 2.6 5.5E-05 30.4 0.4 24 78-108 3-27 (68)
171 TIGR03830 CxxCG_CxxCG_HTH puta 64.5 3 6.5E-05 30.8 0.8 8 101-108 32-39 (127)
172 cd01408 SIRT1 SIRT1: Eukaryoti 64.3 1.4 3.1E-05 37.1 -1.1 33 77-109 115-149 (235)
173 COG1503 eRF1 Peptide chain rel 64.3 3.9 8.5E-05 38.2 1.6 31 77-108 326-356 (411)
174 COG1379 PHP family phosphoeste 64.1 2.1 4.5E-05 39.5 -0.2 26 80-108 248-273 (403)
175 PF04438 zf-HIT: HIT zinc fing 63.9 2.3 4.9E-05 25.7 0.0 21 78-109 2-22 (30)
176 PRK14873 primosome assembly pr 63.2 6.4 0.00014 38.4 2.9 14 100-113 422-435 (665)
177 TIGR01384 TFS_arch transcripti 62.9 3.8 8.2E-05 30.0 1.0 24 80-109 2-25 (104)
178 PF08882 Acetone_carb_G: Aceto 62.8 3.2 6.9E-05 32.5 0.6 9 100-108 74-82 (112)
179 cd01413 SIR2_Af2 SIR2_Af2: Arc 62.5 4.9 0.00011 33.5 1.7 32 77-109 112-145 (222)
180 PRK00448 polC DNA polymerase I 62.4 4.9 0.00011 42.7 2.1 33 76-109 906-942 (1437)
181 TIGR00354 polC DNA polymerase, 62.4 5.2 0.00011 41.2 2.2 28 75-108 1009-1036(1095)
182 PRK12286 rpmF 50S ribosomal pr 61.6 6.3 0.00014 27.0 1.9 31 73-112 22-52 (57)
183 PF10058 DUF2296: Predicted in 61.5 4.1 8.9E-05 27.6 0.9 28 78-108 22-52 (54)
184 PRK15103 paraquat-inducible me 61.5 5.7 0.00012 36.6 2.1 31 79-111 11-41 (419)
185 PF05280 FlhC: Flagellar trans 61.4 4.6 0.0001 33.3 1.4 34 75-110 131-164 (175)
186 PF13465 zf-H2C2_2: Zinc-finge 61.3 7.4 0.00016 22.1 1.9 13 76-88 12-24 (26)
187 PF01783 Ribosomal_L32p: Ribos 61.2 13 0.00028 25.1 3.3 27 75-110 23-49 (56)
188 PRK04023 DNA polymerase II lar 61.1 5.8 0.00012 41.1 2.2 28 75-108 1034-1061(1121)
189 cd01407 SIR2-fam SIR2 family o 61.0 4.6 9.9E-05 33.3 1.3 32 77-109 108-142 (218)
190 COG1198 PriA Primosomal protei 60.9 4.5 9.8E-05 40.2 1.4 37 78-114 435-476 (730)
191 PF06170 DUF983: Protein of un 60.8 18 0.00039 26.6 4.3 18 95-114 5-22 (86)
192 KOG4477 RING1 interactor RYBP 60.6 4.7 0.0001 34.6 1.3 41 66-114 12-52 (228)
193 PHA02942 putative transposase; 60.6 4.4 9.5E-05 36.8 1.2 27 77-109 324-351 (383)
194 PRK12495 hypothetical protein; 60.3 4.8 0.0001 34.9 1.3 30 74-109 38-67 (226)
195 COG1655 Uncharacterized protei 60.1 3.1 6.7E-05 36.7 0.2 44 76-119 17-83 (267)
196 KOG2691 RNA polymerase II subu 60.1 9.8 0.00021 29.9 2.9 40 77-116 25-89 (113)
197 TIGR00319 desulf_FeS4 desulfof 59.6 6.7 0.00014 23.6 1.5 15 76-90 5-19 (34)
198 PF15616 TerY-C: TerY-C metal 59.6 6.3 0.00014 31.4 1.8 25 78-108 88-113 (131)
199 PRK14714 DNA polymerase II lar 59.3 6.3 0.00014 41.6 2.2 28 75-108 1250-1277(1337)
200 cd00924 Cyt_c_Oxidase_Vb Cytoc 58.9 6.7 0.00015 29.6 1.8 19 71-89 72-90 (97)
201 PTZ00409 Sir2 (Silent Informat 58.3 5.5 0.00012 34.6 1.4 14 77-90 136-149 (271)
202 TIGR00622 ssl1 transcription f 58.3 6.3 0.00014 30.7 1.6 22 79-108 2-23 (112)
203 cd00974 DSRD Desulforedoxin (D 57.9 8.4 0.00018 23.2 1.8 13 77-89 3-15 (34)
204 smart00504 Ubox Modified RING 57.8 1.7 3.6E-05 28.4 -1.5 31 80-110 15-45 (63)
205 PF11023 DUF2614: Protein of u 57.8 6.4 0.00014 30.9 1.5 39 73-117 64-102 (114)
206 PF03850 Tfb4: Transcription f 57.1 7 0.00015 34.2 1.8 28 74-107 249-276 (276)
207 PRK08402 replication factor A; 56.9 9 0.0002 34.8 2.6 32 79-114 213-246 (355)
208 PF05876 Terminase_GpA: Phage 56.7 5.7 0.00012 37.7 1.3 31 79-109 201-238 (557)
209 PF02150 RNA_POL_M_15KD: RNA p 56.7 9.2 0.0002 23.6 1.8 11 80-90 22-32 (35)
210 TIGR00155 pqiA_fam integral me 56.7 8.5 0.00018 35.3 2.4 26 78-110 215-240 (403)
211 PRK14715 DNA polymerase II lar 56.4 6.6 0.00014 41.9 1.8 25 75-109 671-695 (1627)
212 PF08772 NOB1_Zn_bind: Nin one 56.4 9.8 0.00021 27.5 2.2 30 78-114 9-38 (73)
213 KOG2462 C2H2-type Zn-finger pr 55.6 8.8 0.00019 34.2 2.2 13 78-90 161-173 (279)
214 TIGR00595 priA primosomal prot 55.2 7.4 0.00016 36.5 1.8 34 78-111 213-251 (505)
215 PF12760 Zn_Tnp_IS1595: Transp 54.8 7.9 0.00017 24.8 1.4 15 98-112 16-30 (46)
216 cd00296 SIR2 SIR2 superfamily 54.5 8.6 0.00019 31.1 1.9 33 76-109 111-143 (222)
217 PF11789 zf-Nse: Zinc-finger o 54.4 1.6 3.4E-05 29.7 -2.1 30 77-106 23-54 (57)
218 COG5188 PRP9 Splicing factor 3 54.3 3.6 7.8E-05 38.4 -0.4 19 78-96 374-393 (470)
219 PRK00432 30S ribosomal protein 54.2 9.2 0.0002 25.5 1.7 23 80-108 22-45 (50)
220 PF01927 Mut7-C: Mut7-C RNAse 53.9 8 0.00017 30.3 1.5 19 76-94 122-140 (147)
221 PRK14715 DNA polymerase II lar 53.8 8.7 0.00019 41.1 2.1 27 75-108 1539-1565(1627)
222 smart00350 MCM minichromosome 53.6 12 0.00025 35.0 2.8 33 76-110 35-71 (509)
223 PF10122 Mu-like_Com: Mu-like 53.5 3.7 8.1E-05 28.1 -0.3 30 77-108 3-32 (51)
224 PRK04338 N(2),N(2)-dimethylgua 53.5 13 0.00027 33.8 2.9 27 77-108 243-269 (382)
225 PTZ00088 adenylate kinase 1; P 53.4 25 0.00054 29.6 4.5 33 77-109 129-167 (229)
226 KOG2636 Splicing factor 3a, su 53.4 2 4.3E-05 40.8 -2.3 24 78-101 401-425 (497)
227 KOG4602 Nanos and related prot 53.2 6.2 0.00014 35.4 0.9 14 99-112 267-280 (318)
228 PRK14748 kdpF potassium-transp 52.8 19 0.00042 22.0 2.7 20 147-166 1-20 (29)
229 COG4031 Predicted metal-bindin 52.5 6.9 0.00015 33.7 1.0 20 80-109 2-21 (227)
230 COG1592 Rubrerythrin [Energy p 52.5 5.4 0.00012 32.9 0.4 13 100-112 134-146 (166)
231 PRK14750 kdpF potassium-transp 52.3 20 0.00044 21.9 2.8 20 147-166 1-20 (29)
232 KOG3134 Predicted membrane pro 52.0 3.5 7.5E-05 35.7 -0.8 36 79-119 1-43 (225)
233 TIGR00615 recR recombination p 51.7 9.1 0.0002 32.3 1.6 30 75-114 50-79 (195)
234 smart00778 Prim_Zn_Ribbon Zinc 51.6 11 0.00024 23.9 1.6 16 102-119 5-20 (37)
235 PRK05333 NAD-dependent deacety 51.5 14 0.0003 32.0 2.8 13 77-89 127-139 (285)
236 COG2401 ABC-type ATPase fused 51.5 7.3 0.00016 37.5 1.1 26 75-108 127-152 (593)
237 PLN00162 transport protein sec 51.4 7 0.00015 38.6 1.0 35 77-111 52-86 (761)
238 COG1571 Predicted DNA-binding 51.0 8.4 0.00018 36.1 1.4 32 80-116 352-385 (421)
239 PF15499 Peptidase_C98: Ubiqui 50.9 11 0.00023 33.7 2.0 34 78-111 134-181 (275)
240 PF03833 PolC_DP2: DNA polymer 50.7 5.2 0.00011 40.7 0.0 8 102-109 694-701 (900)
241 PF09332 Mcm10: Mcm10 replicat 50.6 8.1 0.00018 35.2 1.2 37 78-117 252-318 (344)
242 PRK00423 tfb transcription ini 50.3 9.2 0.0002 33.5 1.5 16 75-90 27-42 (310)
243 PRK00076 recR recombination pr 49.8 10 0.00022 32.0 1.6 30 75-114 50-79 (196)
244 PF13912 zf-C2H2_6: C2H2-type 49.7 11 0.00025 20.8 1.4 13 78-90 1-13 (27)
245 TIGR03831 YgiT_finger YgiT-typ 49.7 10 0.00022 23.2 1.3 17 73-89 27-43 (46)
246 PF06044 DRP: Dam-replacing fa 49.6 3.8 8.3E-05 36.1 -1.0 31 78-108 31-61 (254)
247 PRK13844 recombination protein 49.6 10 0.00022 32.2 1.6 29 75-113 54-82 (200)
248 KOG2462 C2H2-type Zn-finger pr 49.2 15 0.00031 32.9 2.6 33 75-108 127-169 (279)
249 PF04216 FdhE: Protein involve 49.2 11 0.00024 32.5 1.8 27 80-114 199-225 (290)
250 PF04423 Rad50_zn_hook: Rad50 48.9 5.4 0.00012 26.3 -0.1 8 102-109 22-29 (54)
251 smart00249 PHD PHD zinc finger 48.5 24 0.00051 20.8 2.8 32 75-106 11-47 (47)
252 PRK12366 replication factor A; 48.3 14 0.0003 35.8 2.5 26 78-109 532-557 (637)
253 PRK00464 nrdR transcriptional 48.2 12 0.00026 30.3 1.8 15 101-115 29-43 (154)
254 PF08273 Prim_Zn_Ribbon: Zinc- 48.1 12 0.00027 24.0 1.5 17 102-119 5-21 (40)
255 PRK07218 replication factor A; 48.0 12 0.00026 34.9 1.9 28 78-115 297-324 (423)
256 PF13909 zf-H2C2_5: C2H2-type 47.4 11 0.00025 20.4 1.1 10 79-88 1-10 (24)
257 PRK00415 rps27e 30S ribosomal 47.4 8.9 0.00019 26.9 0.8 27 79-108 12-38 (59)
258 PF09986 DUF2225: Uncharacteri 47.1 11 0.00024 31.6 1.4 22 77-99 47-68 (214)
259 TIGR00108 eRF peptide chain re 47.0 16 0.00034 33.6 2.5 31 78-109 324-355 (409)
260 PRK04023 DNA polymerase II lar 46.3 15 0.00032 38.3 2.4 15 17-31 592-606 (1121)
261 PRK14873 primosome assembly pr 46.1 9.6 0.00021 37.3 1.0 33 78-110 383-420 (665)
262 PHA00732 hypothetical protein 45.9 14 0.00031 26.6 1.7 30 79-110 2-37 (79)
263 PRK14559 putative protein seri 45.9 11 0.00024 36.9 1.4 27 80-114 29-55 (645)
264 COG5270 PUA domain (predicted 45.8 42 0.00092 28.7 4.7 49 75-133 11-59 (202)
265 PLN02294 cytochrome c oxidase 45.5 14 0.0003 30.9 1.8 9 98-108 141-149 (174)
266 KOG2593 Transcription initiati 45.5 7 0.00015 36.8 0.0 37 73-109 123-162 (436)
267 PTZ00410 NAD-dependent SIR2; P 45.5 10 0.00022 34.5 1.1 32 77-108 146-179 (349)
268 COG1096 Predicted RNA-binding 45.4 9.9 0.00021 32.2 0.9 37 67-109 136-174 (188)
269 PF01286 XPA_N: XPA protein N- 45.4 24 0.00053 22.1 2.4 26 79-108 4-29 (34)
270 PF01215 COX5B: Cytochrome c o 45.2 14 0.0003 29.7 1.6 20 71-90 105-124 (136)
271 PF04502 DUF572: Family of unk 44.9 8.7 0.00019 34.1 0.5 22 69-90 31-53 (324)
272 KOG2807 RNA polymerase II tran 44.3 16 0.00034 33.8 2.0 26 75-108 273-298 (378)
273 PLN02674 adenylate kinase 44.2 18 0.00039 31.1 2.3 30 77-108 157-186 (244)
274 smart00440 ZnF_C2C2 C2C2 Zinc 43.7 16 0.00036 23.0 1.5 14 76-89 26-39 (40)
275 PF14122 YokU: YokU-like prote 43.3 18 0.00039 27.2 1.9 21 71-91 28-48 (87)
276 COG3677 Transposase and inacti 43.3 11 0.00024 29.5 0.9 14 76-89 51-64 (129)
277 PF13878 zf-C2H2_3: zinc-finge 43.3 13 0.00028 23.7 1.0 14 79-92 14-27 (41)
278 PRK01110 rpmF 50S ribosomal pr 43.2 22 0.00048 24.6 2.2 28 75-112 24-51 (60)
279 PF03597 CcoS: Cytochrome oxid 42.9 30 0.00065 22.8 2.7 20 147-166 7-26 (45)
280 COG5349 Uncharacterized protei 42.9 7.3 0.00016 31.1 -0.2 29 78-111 21-51 (126)
281 smart00290 ZnF_UBP Ubiquitin C 42.9 15 0.00034 23.1 1.3 13 78-90 11-23 (50)
282 PRK06386 replication factor A; 42.9 19 0.00042 32.9 2.4 28 78-115 236-263 (358)
283 KOG0478 DNA replication licens 42.8 12 0.00025 37.7 1.1 33 77-109 263-295 (804)
284 PF07975 C1_4: TFIIH C1-like d 42.8 14 0.0003 25.0 1.2 13 76-88 19-31 (51)
285 PF13824 zf-Mss51: Zinc-finger 42.7 20 0.00044 24.8 1.9 12 98-109 12-23 (55)
286 PRK07225 DNA-directed RNA poly 42.6 15 0.00032 35.8 1.7 32 74-109 540-571 (605)
287 TIGR03670 rpoB_arch DNA-direct 42.5 16 0.00035 35.5 1.9 33 74-110 534-566 (599)
288 KOG3507 DNA-directed RNA polym 42.3 19 0.00041 25.5 1.8 30 74-108 16-45 (62)
289 COG5134 Uncharacterized conser 41.8 7.4 0.00016 34.1 -0.4 24 67-90 31-55 (272)
290 COG0333 RpmF Ribosomal protein 41.8 17 0.00037 25.2 1.5 29 75-112 24-52 (57)
291 PF07191 zinc-ribbons_6: zinc- 41.4 13 0.00028 26.9 0.8 30 77-115 16-45 (70)
292 COG5189 SFP1 Putative transcri 41.3 14 0.0003 34.3 1.2 36 55-90 373-410 (423)
293 PF15135 UPF0515: Uncharacteri 40.9 15 0.00032 32.8 1.3 38 76-115 130-170 (278)
294 PRK14714 DNA polymerase II lar 40.9 17 0.00038 38.5 2.0 9 78-86 667-675 (1337)
295 PF01096 TFIIS_C: Transcriptio 40.9 17 0.00037 22.7 1.3 14 75-88 25-38 (39)
296 PF02148 zf-UBP: Zn-finger in 40.7 21 0.00046 24.1 1.8 16 76-91 9-24 (63)
297 PRK05580 primosome assembly pr 40.5 16 0.00035 35.5 1.6 34 78-111 381-419 (679)
298 cd01409 SIRT4 SIRT4: Eukaryoti 40.3 9.7 0.00021 32.7 0.1 13 77-89 117-129 (260)
299 KOG1986 Vesicle coat complex C 40.1 12 0.00026 37.3 0.7 33 77-109 52-84 (745)
300 PF06221 zf-C2HC5: Putative zi 39.8 20 0.00043 24.8 1.5 27 78-109 18-44 (57)
301 COG1998 RPS31 Ribosomal protei 39.4 15 0.00033 25.1 0.9 24 80-108 21-45 (51)
302 PRK00279 adk adenylate kinase; 39.3 64 0.0014 26.0 4.7 30 77-108 126-155 (215)
303 PF04530 Viral_Beta_CD: Viral 39.2 68 0.0015 25.5 4.6 66 99-165 5-70 (122)
304 PRK14759 potassium-transportin 38.8 45 0.00096 20.4 2.8 20 147-166 1-20 (29)
305 smart00355 ZnF_C2H2 zinc finge 38.6 11 0.00023 19.5 0.0 10 79-88 1-10 (26)
306 KOG0320 Predicted E3 ubiquitin 38.5 15 0.00032 31.1 0.9 39 76-114 129-183 (187)
307 PF09796 QCR10: Ubiquinol-cyto 38.1 39 0.00084 23.9 2.9 21 148-168 15-35 (64)
308 COG0178 UvrA Excinuclease ATPa 38.1 22 0.00048 36.4 2.2 33 77-111 244-280 (935)
309 PF05129 Elf1: Transcription e 38.0 15 0.00033 26.6 0.8 23 96-118 18-40 (81)
310 PF12647 RNHCP: RNHCP domain; 37.9 23 0.0005 26.8 1.8 36 76-113 2-37 (92)
311 cd07973 Spt4 Transcription elo 37.8 20 0.00044 27.2 1.5 23 80-107 5-27 (98)
312 PTZ00043 cytochrome c oxidase 37.3 25 0.00055 31.0 2.2 29 102-130 183-214 (268)
313 PF01102 Glycophorin_A: Glycop 36.9 37 0.00079 26.7 2.8 16 150-165 72-87 (122)
314 PF03811 Zn_Tnp_IS1: InsA N-te 36.4 21 0.00045 22.4 1.1 17 68-84 19-35 (36)
315 PF03119 DNA_ligase_ZBD: NAD-d 36.3 15 0.00032 21.7 0.5 10 102-111 1-10 (28)
316 COG3809 Uncharacterized protei 36.0 19 0.00042 27.0 1.1 26 80-108 3-29 (88)
317 TIGR03826 YvyF flagellar opero 36.0 11 0.00024 30.1 -0.2 23 79-108 4-26 (137)
318 PRK01103 formamidopyrimidine/5 35.2 24 0.00052 30.3 1.7 26 80-107 247-272 (274)
319 PRK11088 rrmA 23S rRNA methylt 35.0 20 0.00043 30.1 1.2 25 78-108 2-26 (272)
320 PHA00733 hypothetical protein 35.0 9.8 0.00021 29.6 -0.6 33 77-109 72-108 (128)
321 TIGR00308 TRM1 tRNA(guanine-26 34.7 37 0.0008 30.9 2.9 29 77-108 232-260 (374)
322 KOG2324 Prolyl-tRNA synthetase 34.6 32 0.0007 32.5 2.5 33 75-109 224-256 (457)
323 COG4332 Uncharacterized protei 34.5 21 0.00045 30.5 1.2 32 77-115 48-79 (203)
324 TIGR00847 ccoS cytochrome oxid 34.4 48 0.001 22.5 2.7 19 147-165 8-26 (51)
325 COG5415 Predicted integral mem 34.3 21 0.00045 31.3 1.2 34 77-111 191-225 (251)
326 COG0266 Nei Formamidopyrimidin 34.3 26 0.00056 31.1 1.8 26 80-107 247-272 (273)
327 PF00628 PHD: PHD-finger; Int 34.2 7.2 0.00016 24.7 -1.3 34 74-107 10-49 (51)
328 TIGR03676 aRF1/eRF1 peptide ch 34.0 32 0.00069 31.7 2.4 31 78-109 320-351 (403)
329 KOG0477 DNA replication licens 33.8 19 0.00042 36.2 1.0 45 76-122 290-337 (854)
330 PF05290 Baculo_IE-1: Baculovi 33.8 33 0.00072 27.9 2.2 16 75-90 77-92 (140)
331 PHA00616 hypothetical protein 33.4 9.9 0.00021 25.1 -0.7 12 79-90 2-13 (44)
332 COG4888 Uncharacterized Zn rib 33.4 18 0.0004 28.0 0.6 8 78-85 22-29 (104)
333 PRK10996 thioredoxin 2; Provis 32.8 45 0.00097 25.4 2.7 29 79-109 3-31 (139)
334 PF02318 FYVE_2: FYVE-type zin 32.7 11 0.00024 28.5 -0.6 9 99-107 93-101 (118)
335 TIGR00630 uvra excinuclease AB 32.5 31 0.00066 35.2 2.2 30 77-108 249-282 (924)
336 PRK10445 endonuclease VIII; Pr 32.3 29 0.00063 29.8 1.8 9 99-107 254-262 (263)
337 COG0353 RecR Recombinational D 32.2 28 0.0006 29.7 1.6 33 74-116 50-82 (198)
338 cd03361 TOPRIM_TopoIA_RevGyr T 32.0 32 0.00068 27.7 1.8 22 79-108 78-99 (170)
339 KOG2857 Predicted MYND Zn-fing 32.0 24 0.00052 29.0 1.1 13 78-90 17-29 (157)
340 COG1656 Uncharacterized conser 32.0 22 0.00048 29.5 0.9 18 74-91 126-143 (165)
341 TIGR00570 cdk7 CDK-activating 32.0 20 0.00043 32.4 0.7 47 83-131 25-76 (309)
342 PRK14559 putative protein seri 31.9 25 0.00054 34.5 1.4 8 102-109 29-36 (645)
343 PF11238 DUF3039: Protein of u 31.9 33 0.00073 24.0 1.7 31 75-108 22-52 (58)
344 PF06353 DUF1062: Protein of u 31.9 23 0.00049 28.4 1.0 14 77-90 12-25 (142)
345 PRK09521 exosome complex RNA-b 31.7 24 0.00052 28.6 1.1 26 78-108 149-174 (189)
346 KOG1280 Uncharacterized conser 31.7 27 0.0006 32.4 1.6 11 98-108 77-87 (381)
347 PRK09401 reverse gyrase; Revie 31.5 22 0.00047 37.1 1.0 23 78-108 678-700 (1176)
348 PF08996 zf-DNA_Pol: DNA Polym 31.4 17 0.00037 29.7 0.2 40 69-108 9-53 (188)
349 KOG1859 Leucine-rich repeat pr 31.3 28 0.00061 35.8 1.7 32 77-108 672-704 (1096)
350 TIGR01562 FdhE formate dehydro 31.3 46 0.00099 29.8 2.9 11 102-112 226-236 (305)
351 PF03833 PolC_DP2: DNA polymer 31.2 16 0.00035 37.3 0.0 12 76-87 653-664 (900)
352 TIGR02159 PA_CoA_Oxy4 phenylac 31.1 15 0.00032 29.4 -0.2 38 79-116 106-146 (146)
353 PF06957 COPI_C: Coatomer (COP 31.0 28 0.0006 32.6 1.5 26 78-109 380-405 (422)
354 PF04564 U-box: U-box domain; 30.9 21 0.00045 24.7 0.5 12 97-108 1-12 (73)
355 PF05741 zf-nanos: Nanos RNA b 30.7 20 0.00044 24.6 0.4 10 100-109 33-42 (55)
356 KOG4317 Predicted Zn-finger pr 30.6 30 0.00065 31.9 1.6 27 78-114 7-33 (383)
357 PRK08665 ribonucleotide-diphos 30.6 36 0.00078 33.9 2.3 23 80-110 726-750 (752)
358 PRK14811 formamidopyrimidine-D 30.5 35 0.00075 29.5 1.9 28 80-109 237-264 (269)
359 PRK14810 formamidopyrimidine-D 30.0 27 0.00058 30.2 1.1 26 80-107 246-271 (272)
360 PF06093 Spt4: Spt4/RpoE2 zinc 29.9 27 0.00059 25.3 1.0 22 80-106 3-24 (77)
361 KOG1868 Ubiquitin C-terminal h 29.7 29 0.00063 34.3 1.5 20 93-112 508-529 (653)
362 PF06677 Auto_anti-p27: Sjogre 29.7 29 0.00064 22.4 1.0 23 80-107 19-41 (41)
363 cd04476 RPA1_DBD_C RPA1_DBD_C: 29.5 24 0.00053 27.6 0.8 25 79-109 35-60 (166)
364 KOG4784 Uncharacterized conser 29.4 39 0.00085 31.1 2.2 37 71-107 96-143 (348)
365 PRK13945 formamidopyrimidine-D 29.0 36 0.00077 29.5 1.8 9 99-107 273-281 (282)
366 KOG1100 Predicted E3 ubiquitin 29.0 40 0.00086 28.4 2.0 15 102-116 191-205 (207)
367 PF14577 SEO_C: Sieve element 28.2 41 0.00088 29.3 2.0 33 84-117 199-231 (235)
368 TIGR01351 adk adenylate kinase 28.0 48 0.001 26.6 2.2 30 77-108 123-152 (210)
369 PHA02768 hypothetical protein; 27.8 23 0.00051 24.4 0.3 31 78-108 5-39 (55)
370 TIGR00577 fpg formamidopyrimid 27.5 41 0.00089 29.0 1.9 7 100-106 265-271 (272)
371 PF13901 DUF4206: Domain of un 27.4 39 0.00084 28.0 1.6 29 78-108 152-180 (202)
372 COG4338 Uncharacterized protei 27.4 22 0.00049 24.4 0.2 17 96-113 9-25 (54)
373 PF04981 NMD3: NMD3 family ; 27.3 39 0.00084 28.4 1.6 10 101-110 36-45 (236)
374 PF10609 ParA: ParA/MinD ATPas 27.2 36 0.00079 24.9 1.3 17 73-89 60-76 (81)
375 PRK04179 rpl37e 50S ribosomal 27.0 53 0.0011 23.3 2.0 44 67-117 6-50 (62)
376 PF09855 DUF2082: Nucleic-acid 27.0 34 0.00073 24.1 1.0 10 101-110 1-10 (64)
377 COG4260 Membrane protease subu 26.8 32 0.00068 31.5 1.1 26 80-109 317-343 (345)
378 PRK00349 uvrA excinuclease ABC 26.8 45 0.00097 34.1 2.2 30 77-108 251-284 (943)
379 COG1241 MCM2 Predicted ATPase 26.8 43 0.00094 33.2 2.1 30 75-106 126-157 (682)
380 PHA02942 putative transposase; 26.5 42 0.00091 30.6 1.8 15 76-90 340-354 (383)
381 PF12874 zf-met: Zinc-finger o 26.5 50 0.0011 17.7 1.5 12 79-90 1-12 (25)
382 PLN02610 probable methionyl-tR 26.5 29 0.00063 34.7 0.9 27 79-110 171-197 (801)
383 PF03691 UPF0167: Uncharacteri 26.4 38 0.00083 28.2 1.4 32 78-110 24-59 (176)
384 COG2995 PqiA Uncharacterized p 26.3 65 0.0014 30.4 3.0 34 74-109 14-47 (418)
385 COG2126 RPL37A Ribosomal prote 26.2 45 0.00099 23.6 1.6 41 67-116 6-48 (61)
386 cd07153 Fur_like Ferric uptake 25.8 37 0.0008 24.6 1.1 14 77-90 72-85 (116)
387 PRK00635 excinuclease ABC subu 25.8 45 0.00098 36.7 2.1 30 77-108 243-276 (1809)
388 PF03966 Trm112p: Trm112p-like 25.7 53 0.0012 22.4 1.9 16 74-89 49-64 (68)
389 COG1326 Uncharacterized archae 25.7 36 0.00079 29.1 1.2 14 77-90 29-42 (201)
390 PRK00418 DNA gyrase inhibitor; 25.6 39 0.00084 23.9 1.1 9 101-109 7-15 (62)
391 PRK03564 formate dehydrogenase 25.6 65 0.0014 29.0 2.8 9 102-110 228-236 (309)
392 KOG0435 Leucyl-tRNA synthetase 25.6 41 0.00088 34.1 1.7 36 78-114 436-491 (876)
393 COG5533 UBP5 Ubiquitin C-termi 25.5 32 0.00068 32.0 0.8 14 98-111 282-295 (415)
394 smart00154 ZnF_AN1 AN1-like Zi 25.3 63 0.0014 20.3 2.0 24 78-104 12-35 (39)
395 PRK14740 kdbF potassium-transp 25.2 1E+02 0.0023 18.8 2.8 15 152-166 6-20 (29)
396 PRK14529 adenylate kinase; Pro 25.0 58 0.0012 27.5 2.3 31 77-108 125-156 (223)
397 PRK07217 replication factor A; 25.0 67 0.0015 29.1 2.8 31 75-115 185-217 (311)
398 KOG3623 Homeobox transcription 24.8 41 0.00089 34.4 1.5 25 77-108 280-317 (1007)
399 PF02005 TRM: N2,N2-dimethylgu 24.7 45 0.00097 30.4 1.7 32 77-111 239-270 (377)
400 KOG4080 Mitochondrial ribosoma 24.7 30 0.00065 29.1 0.5 24 74-106 89-112 (176)
401 COG5047 SEC23 Vesicle coat com 24.7 32 0.00069 34.2 0.7 33 78-110 53-86 (755)
402 TIGR00340 zpr1_rel ZPR1-relate 24.5 44 0.00096 27.3 1.4 13 78-90 28-40 (163)
403 COG1933 Archaeal DNA polymeras 24.5 33 0.00071 30.3 0.7 36 75-117 164-199 (253)
404 COG0068 HypF Hydrogenase matur 24.4 55 0.0012 33.0 2.3 32 80-114 153-186 (750)
405 PF01363 FYVE: FYVE zinc finge 24.3 47 0.001 22.2 1.3 15 76-90 23-37 (69)
406 smart00709 Zpr1 Duplicated dom 24.1 41 0.00089 27.3 1.2 13 78-90 29-41 (160)
407 PRK13208 valS valyl-tRNA synth 24.0 52 0.0011 32.4 2.0 32 77-108 411-448 (800)
408 PRK15033 tricarballylate utili 23.7 92 0.002 29.1 3.5 25 129-153 95-127 (389)
409 KOG0402 60S ribosomal protein 23.6 41 0.00089 25.5 1.0 29 76-108 34-62 (92)
410 TIGR00320 dfx_rbo desulfoferro 23.6 50 0.0011 25.7 1.6 14 76-89 5-18 (125)
411 PF09788 Tmemb_55A: Transmembr 23.5 2.1E+02 0.0046 25.4 5.5 15 76-90 63-77 (256)
412 PRK08565 DNA-directed RNA poly 23.4 49 0.0011 34.3 1.8 32 75-110 1039-1070(1103)
413 COG4068 Uncharacterized protei 23.3 2.3E+02 0.0051 20.2 4.7 8 102-109 10-17 (64)
414 PF00130 C1_1: Phorbol esters/ 23.3 63 0.0014 20.4 1.8 18 74-91 24-41 (53)
415 COG3183 Predicted restriction 23.1 22 0.00049 31.6 -0.5 12 79-90 196-207 (272)
416 PF07496 zf-CW: CW-type Zinc F 22.7 52 0.0011 21.5 1.3 26 80-105 5-34 (50)
417 PF04606 Ogr_Delta: Ogr/Delta- 22.6 55 0.0012 21.1 1.4 14 77-90 24-39 (47)
418 smart00442 FGF Acidic and basi 22.6 50 0.0011 25.5 1.3 24 68-91 45-69 (126)
419 PF02748 PyrI_C: Aspartate car 22.5 72 0.0016 21.4 1.9 28 63-90 20-47 (52)
420 PF05766 NinG: Bacteriophage L 22.4 27 0.00058 29.4 -0.2 26 78-107 6-31 (189)
421 COG2023 RPR2 RNase P subunit R 22.1 51 0.0011 25.5 1.3 12 77-88 81-92 (105)
422 PRK02935 hypothetical protein; 22.1 66 0.0014 25.2 1.9 38 74-117 66-103 (110)
423 COG3197 FixS Uncharacterized p 22.1 95 0.002 21.8 2.5 19 147-165 8-26 (58)
424 COG1571 Predicted DNA-binding 21.9 40 0.00086 31.8 0.8 60 29-90 314-379 (421)
425 TIGR01054 rgy reverse gyrase. 21.8 40 0.00087 35.2 0.9 21 79-107 679-699 (1171)
426 PF09862 DUF2089: Protein of u 21.8 42 0.00092 26.1 0.8 7 103-109 1-7 (113)
427 PF10013 DUF2256: Uncharacteri 21.7 62 0.0013 21.3 1.4 15 96-111 5-19 (42)
428 KOG2907 RNA polymerase I trans 21.5 39 0.00085 26.7 0.6 16 101-116 75-90 (116)
429 PF09567 RE_MamI: MamI restric 21.5 46 0.00099 30.0 1.0 25 77-109 81-105 (314)
430 TIGR00310 ZPR1_znf ZPR1 zinc f 21.5 53 0.0011 27.5 1.4 13 78-90 30-42 (192)
431 COG2995 PqiA Uncharacterized p 21.4 65 0.0014 30.4 2.0 32 76-114 218-249 (418)
432 TIGR03829 YokU_near_AblA uncha 21.4 53 0.0012 24.7 1.2 17 74-90 31-47 (89)
433 PF03854 zf-P11: P-11 zinc fin 21.1 8.9 0.00019 26.1 -2.7 24 78-109 21-44 (50)
434 PF03367 zf-ZPR1: ZPR1 zinc-fi 21.0 46 0.001 26.9 0.9 14 78-91 30-43 (161)
435 COG0498 ThrC Threonine synthas 20.9 39 0.00084 31.5 0.5 26 79-110 6-31 (411)
436 PF13005 zf-IS66: zinc-finger 20.9 59 0.0013 20.3 1.2 19 67-85 29-47 (47)
437 PF01485 IBR: IBR domain; Int 20.8 1E+02 0.0022 19.6 2.4 25 80-108 20-48 (64)
438 cd00058 FGF Acidic and basic f 20.8 59 0.0013 25.0 1.4 25 67-91 40-65 (123)
439 PRK00750 lysK lysyl-tRNA synth 20.6 34 0.00074 32.3 0.1 29 80-109 177-208 (510)
440 KOG3362 Predicted BBOX Zn-fing 20.5 43 0.00093 27.6 0.6 22 76-108 116-137 (156)
441 cd00029 C1 Protein kinase C co 20.5 55 0.0012 20.0 1.0 16 75-90 25-40 (50)
442 PF01667 Ribosomal_S27e: Ribos 20.4 44 0.00096 23.0 0.6 27 79-108 8-34 (55)
443 TIGR00467 lysS_arch lysyl-tRNA 20.4 32 0.00069 32.8 -0.2 29 80-109 170-199 (515)
444 PF09334 tRNA-synt_1g: tRNA sy 20.4 44 0.00096 30.3 0.7 26 79-109 150-175 (391)
445 PRK14894 glycyl-tRNA synthetas 20.4 58 0.0012 31.7 1.5 25 78-108 88-112 (539)
446 KOG0804 Cytoplasmic Zn-finger 20.4 41 0.00089 32.2 0.6 16 75-90 237-252 (493)
447 PF09297 zf-NADH-PPase: NADH p 20.2 57 0.0012 19.2 1.0 13 76-88 19-31 (32)
No 1
>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=99.62 E-value=1.2e-16 Score=107.38 Aligned_cols=39 Identities=56% Similarity=1.327 Sum_probs=36.2
Q ss_pred eEEcCCCCeeecC-----------CCCCCCCCCCCCCCCCCCCccCeeeC
Q 040420 78 AYICRDCGYIYNE-----------RKPFDQLPDNYFCPVCGAPKRRFRPY 116 (169)
Q Consensus 78 ~y~C~~CGyVYd~-----------~tpF~~lPd~~~CPvCgapK~~F~~~ 116 (169)
.|+|.+||||||+ +|+|++||++|+||+|+++|++|+++
T Consensus 1 ~y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~K~~F~~~ 50 (50)
T cd00730 1 KYECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAGKDDFEPL 50 (50)
T ss_pred CcCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCcHHHcEeC
Confidence 4999999999997 58999999999999999999999864
No 2
>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=99.61 E-value=2.7e-16 Score=104.55 Aligned_cols=36 Identities=56% Similarity=1.405 Sum_probs=29.4
Q ss_pred eEEcCCCCeeecC-----------CCCCCCCCCCCCCCCCCCCccCe
Q 040420 78 AYICRDCGYIYNE-----------RKPFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 78 ~y~C~~CGyVYd~-----------~tpF~~lPd~~~CPvCgapK~~F 113 (169)
.|+|.+||||||+ +|+|++||++|+||+|+++|++|
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~K~~F 47 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAPKSDF 47 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSBGGGE
T ss_pred CcCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCccccC
Confidence 4999999999998 58999999999999999999988
No 3
>COG1773 Rubredoxin [Energy production and conversion]
Probab=99.60 E-value=5.4e-16 Score=106.37 Aligned_cols=41 Identities=39% Similarity=1.065 Sum_probs=38.3
Q ss_pred eEEcCCCCeeecC-----------CCCCCCCCCCCCCCCCCCCccCeeeCCC
Q 040420 78 AYICRDCGYIYNE-----------RKPFDQLPDNYFCPVCGAPKRRFRPYTP 118 (169)
Q Consensus 78 ~y~C~~CGyVYd~-----------~tpF~~lPd~~~CPvCgapK~~F~~~~~ 118 (169)
.|+|++||||||+ +|+|+++|++|+||+||++|+.|+.+..
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg~~K~~F~~~~~ 54 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECGVGKKDFEMIDE 54 (55)
T ss_pred ceEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCCCCHhHeeeccC
Confidence 6999999999998 5999999999999999999999998753
No 4
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=99.33 E-value=6.3e-13 Score=121.50 Aligned_cols=45 Identities=29% Similarity=0.758 Sum_probs=40.7
Q ss_pred CCCeEEcCCCCeeecC-----------CCCCCCCCCCCCCCCCCCCccCeeeCCCc
Q 040420 75 SKQAYICRDCGYIYNE-----------RKPFDQLPDNYFCPVCGAPKRRFRPYTPA 119 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~-----------~tpF~~lPd~~~CPvCgapK~~F~~~~~~ 119 (169)
....|+|..|||+||+ +|+|++|||+|+||+||++|+.|+++..+
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~k~~f~~~~~~ 477 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGKDVFDELASE 477 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCcHHHhEecccc
Confidence 4468999999999998 58999999999999999999999988643
No 5
>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=99.21 E-value=7.5e-12 Score=76.97 Aligned_cols=33 Identities=48% Similarity=1.260 Sum_probs=28.8
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPY 116 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~ 116 (169)
.|+|.+|||+|++.. ++|+||+||+++++|+.+
T Consensus 1 ~~~C~~CGy~y~~~~------~~~~CP~Cg~~~~~F~~~ 33 (33)
T cd00350 1 KYVCPVCGYIYDGEE------APWVCPVCGAPKDKFEKL 33 (33)
T ss_pred CEECCCCCCEECCCc------CCCcCcCCCCcHHHcEEC
Confidence 499999999999863 567999999999999863
No 6
>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=99.13 E-value=3.3e-11 Score=74.94 Aligned_cols=33 Identities=42% Similarity=1.198 Sum_probs=29.0
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPY 116 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~ 116 (169)
.|+|.+|||+|++.. .|+ +||+||+++++|+++
T Consensus 2 ~~~C~~CG~i~~g~~----~p~--~CP~Cg~~~~~F~~~ 34 (34)
T cd00729 2 VWVCPVCGYIHEGEE----APE--KCPICGAPKEKFEEF 34 (34)
T ss_pred eEECCCCCCEeECCc----CCC--cCcCCCCchHHcEEC
Confidence 699999999999864 478 999999999999863
No 7
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=98.58 E-value=2.2e-08 Score=81.88 Aligned_cols=33 Identities=39% Similarity=1.188 Sum_probs=28.8
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPY 116 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~ 116 (169)
++|+|++|||+..+. .|+ +||+||++|.+|+..
T Consensus 133 ~~~vC~vCGy~~~ge-----~P~--~CPiCga~k~~F~~f 165 (166)
T COG1592 133 KVWVCPVCGYTHEGE-----APE--VCPICGAPKEKFEKF 165 (166)
T ss_pred CEEEcCCCCCcccCC-----CCC--cCCCCCChHHHhhcc
Confidence 389999999999873 377 999999999999854
No 8
>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=97.54 E-value=5e-05 Score=48.78 Aligned_cols=30 Identities=30% Similarity=0.831 Sum_probs=27.4
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.|+|..||++++...++.+ ++...||.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 5899999999999888888 77889999998
No 9
>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=97.42 E-value=9.9e-05 Score=48.33 Aligned_cols=32 Identities=28% Similarity=0.681 Sum_probs=25.9
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
.|+|.+||++|+...++++ .+...||.||+..
T Consensus 5 ey~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~ 36 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSD-DPLATCPECGGEK 36 (52)
T ss_pred EEEeCCCCCEeEEEEecCC-CCCCCCCCCCCCc
Confidence 5899999999998777776 4556899999843
No 10
>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=97.34 E-value=0.00014 Score=45.03 Aligned_cols=31 Identities=29% Similarity=0.740 Sum_probs=24.9
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.|+|..||.+|+...++.+ .+...||.||+.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD-DPLATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEecCC-CCCCCCCCCCCc
Confidence 5899999999987666655 455699999983
No 11
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=96.31 E-value=0.0037 Score=49.09 Aligned_cols=35 Identities=26% Similarity=0.729 Sum_probs=23.8
Q ss_pred CCeEEcCCCCeeecCC-----------CCCCCCC----CCCCCCCCCCCc
Q 040420 76 KQAYICRDCGYIYNER-----------KPFDQLP----DNYFCPVCGAPK 110 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~-----------tpF~~lP----d~~~CPvCgapK 110 (169)
...|+|.+||+++... +++.-+| ..+.||.||+..
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 3589999999998653 1222223 346899999754
No 12
>PRK12496 hypothetical protein; Provisional
Probab=96.25 E-value=0.0027 Score=51.37 Aligned_cols=31 Identities=29% Similarity=0.735 Sum_probs=23.3
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
.|+|..||.+|+.. ++.-.||+||++-.+..
T Consensus 127 ~~~C~gC~~~~~~~------~~~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 127 RKVCKGCKKKYPED------YPDDVCEICGSPVKRKM 157 (164)
T ss_pred eEECCCCCccccCC------CCCCcCCCCCChhhhcc
Confidence 57999999999764 22228999999865544
No 13
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.65 E-value=0.009 Score=38.56 Aligned_cols=31 Identities=26% Similarity=0.514 Sum_probs=21.5
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
..|+|.+||..++-... -..+.||.||.+-.
T Consensus 2 ~~y~C~~CG~~~~~~~~----~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEY----GTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCC----CCceECCCCCCeEE
Confidence 36999999977654311 12579999997554
No 14
>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=95.48 E-value=0.016 Score=36.52 Aligned_cols=29 Identities=31% Similarity=0.653 Sum_probs=21.3
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.|+|..||.+|.... .....+.+|..||.
T Consensus 1 Rr~C~~Cg~~Yh~~~--~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 1 RRICPKCGRIYHIEF--NPPKVEGVCDNCGG 29 (36)
T ss_dssp EEEETTTTEEEETTT--B--SSTTBCTTTTE
T ss_pred CcCcCCCCCcccccc--CCCCCCCccCCCCC
Confidence 489999999998753 22234459999998
No 15
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=95.27 E-value=0.029 Score=39.32 Aligned_cols=53 Identities=30% Similarity=0.548 Sum_probs=34.4
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCCCcccCCCChhHHHHHHHHHhhhccccCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYTPAVTRGANDTAVRKARKEQIQRDEAIGK 145 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~~~~~~~~n~~~v~~ar~~~~~~~~~~gn 145 (169)
..+|..|| +|. |-| .||+||.. ...+.-.++.-++.-.+=|.+..++.+.+.+
T Consensus 5 ~rkC~~cg-~YT-------Lke--~Cp~CG~~-----t~~~~PprFSPeD~y~kYR~~lkk~~~~~~~ 57 (59)
T COG2260 5 IRKCPKCG-RYT-------LKE--KCPVCGGD-----TKVPHPPRFSPEDKYGKYRRELKKRLGLLPN 57 (59)
T ss_pred hhcCcCCC-cee-------ecc--cCCCCCCc-----cccCCCCCCCccchHHHHHHHHHHHhccccC
Confidence 46899999 664 345 89999984 3333344555555566667777776665544
No 16
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=95.25 E-value=0.0091 Score=45.36 Aligned_cols=27 Identities=30% Similarity=0.880 Sum_probs=20.7
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-=+|..|||+++... -+.|. +||.|.+
T Consensus 58 Pa~CkkCGfef~~~~--ik~pS--RCP~CKS 84 (97)
T COG3357 58 PARCKKCGFEFRDDK--IKKPS--RCPKCKS 84 (97)
T ss_pred ChhhcccCccccccc--cCCcc--cCCcchh
Confidence 358999999998721 13478 9999987
No 17
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=95.20 E-value=0.0064 Score=48.47 Aligned_cols=38 Identities=24% Similarity=0.661 Sum_probs=28.9
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCCCcc
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYTPAV 120 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~~~~ 120 (169)
|+|..||.+|+.+.. ++=. =||.||..|-+|++-....
T Consensus 2 H~Ct~Cg~~f~dgs~--eil~--GCP~CGg~kF~yv~~~~~~ 39 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSK--EILS--GCPECGGNKFQYVPEEKDA 39 (131)
T ss_pred cccCcCCCCcCCCcH--HHHc--cCcccCCcceEEcCCCccc
Confidence 799999999998631 2334 6999999999998755443
No 18
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=95.13 E-value=0.0088 Score=47.11 Aligned_cols=38 Identities=21% Similarity=0.580 Sum_probs=25.3
Q ss_pred CCCCeEEcCCCCeeecCCCC--CCCCCCCCCCCCCCCCcc
Q 040420 74 ASKQAYICRDCGYIYNERKP--FDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tp--F~~lPd~~~CPvCgapK~ 111 (169)
.+...|+|+.||..|.-... ..+....+.||.||..-.
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEE
Confidence 35568999999988875211 112133399999998543
No 19
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=95.11 E-value=0.018 Score=43.98 Aligned_cols=32 Identities=22% Similarity=0.529 Sum_probs=22.9
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
.....+|.+||+.+... .-.+.||.||.....
T Consensus 67 vp~~~~C~~Cg~~~~~~------~~~~~CP~Cgs~~~~ 98 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIH------QHDAQCPHCHGERLR 98 (113)
T ss_pred eCcEEEcccCCCEEecC------CcCccCcCCCCCCcE
Confidence 33478999999888653 134579999976433
No 20
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=95.09 E-value=0.0099 Score=48.75 Aligned_cols=36 Identities=17% Similarity=0.612 Sum_probs=26.7
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCe
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F 113 (169)
+.+.|+|+.||..|.-.-. +-.+|.||.||..-..+
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA---~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEA---MEYGFRCPQCGEMLEEY 149 (178)
T ss_pred CCCEEECCCCCcEEeHHHH---hhcCCcCCCCCCCCeec
Confidence 5578999999977754322 24579999999976665
No 21
>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=95.08 E-value=0.0077 Score=45.81 Aligned_cols=31 Identities=32% Similarity=0.830 Sum_probs=20.6
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCe
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F 113 (169)
...+|.+||+.|+.. ..++.||.||...-..
T Consensus 69 ~~~~C~~Cg~~~~~~------~~~~~CP~Cgs~~~~i 99 (113)
T PF01155_consen 69 ARARCRDCGHEFEPD------EFDFSCPRCGSPDVEI 99 (113)
T ss_dssp -EEEETTTS-EEECH------HCCHH-SSSSSS-EEE
T ss_pred CcEECCCCCCEEecC------CCCCCCcCCcCCCcEE
Confidence 478999999999864 2235899999975433
No 22
>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=94.94 E-value=0.0093 Score=47.85 Aligned_cols=37 Identities=22% Similarity=0.505 Sum_probs=26.2
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCe
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F 113 (169)
.+.+.|+|+.|+..|.-.-. +-.+|.||.||..-..+
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA---~~~~F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEA---MELNFTCPRCGAMLDYL 141 (158)
T ss_pred cCCCeEECCCCCcEeeHHHH---HHcCCcCCCCCCEeeec
Confidence 35678999999977753222 24579999999974443
No 23
>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=94.77 E-value=0.026 Score=43.12 Aligned_cols=33 Identities=24% Similarity=0.458 Sum_probs=23.9
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCe
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F 113 (169)
.....+|.+||+.|.... ..+.||.||.+..+.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~------~~~~CP~Cgs~~~~i 99 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEI------DLYRCPKCHGIMLQV 99 (115)
T ss_pred eCcEEEcccCCCEEecCC------cCccCcCCcCCCcEE
Confidence 334789999998887531 246899999876443
No 24
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=94.42 E-value=0.035 Score=36.31 Aligned_cols=27 Identities=33% Similarity=0.698 Sum_probs=21.0
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.|+|..||...+.. ..+..+||.||+.
T Consensus 2 ~Y~C~~Cg~~~~~~-----~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK-----SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC-----CCCceECCCCCce
Confidence 59999999888754 1345699999984
No 25
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=94.39 E-value=0.033 Score=42.56 Aligned_cols=33 Identities=18% Similarity=0.348 Sum_probs=22.7
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
.....+|++||+.|.... ...+.||.||....+
T Consensus 67 ~p~~~~C~~Cg~~~~~~~-----~~~~~CP~Cgs~~~~ 99 (114)
T PRK03681 67 QEAECWCETCQQYVTLLT-----QRVRRCPQCHGDMLR 99 (114)
T ss_pred eCcEEEcccCCCeeecCC-----ccCCcCcCcCCCCcE
Confidence 334789999998886531 122679999976433
No 26
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.23 E-value=0.012 Score=43.55 Aligned_cols=36 Identities=25% Similarity=0.578 Sum_probs=28.9
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
+..-.|+|..||++||--..|.|-|. -.||.|+++-
T Consensus 8 MPtY~Y~c~~cg~~~dvvq~~~ddpl-t~ce~c~a~~ 43 (82)
T COG2331 8 MPTYSYECTECGNRFDVVQAMTDDPL-TTCEECGARL 43 (82)
T ss_pred ccceEEeecccchHHHHHHhcccCcc-ccChhhChHH
Confidence 44457999999999998777777776 4899999943
No 27
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=94.22 E-value=0.0087 Score=46.40 Aligned_cols=37 Identities=24% Similarity=0.678 Sum_probs=26.7
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYTP 118 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~~ 118 (169)
.|+|..||.+|+.+. +.+-. -||.||..|-.+.+-++
T Consensus 2 pH~CtrCG~vf~~g~--~~il~--GCp~CG~nkF~yv~~e~ 38 (112)
T COG3364 2 PHQCTRCGEVFDDGS--EEILS--GCPKCGCNKFLYVPEEK 38 (112)
T ss_pred Cceeccccccccccc--HHHHc--cCccccchheEeccccc
Confidence 389999999999862 12223 69999998777665444
No 28
>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=94.17 E-value=0.043 Score=44.11 Aligned_cols=36 Identities=33% Similarity=0.880 Sum_probs=26.1
Q ss_pred cCCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 73 VASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 73 ~~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
......|+|..||+...-.+| +.+|. ||.||+ ..|.
T Consensus 107 ~~g~G~l~C~~Cg~~~~~~~~-~~l~~---Cp~C~~--~~F~ 142 (146)
T PF07295_consen 107 VVGPGTLVCENCGHEVELTHP-ERLPP---CPKCGH--TEFT 142 (146)
T ss_pred EecCceEecccCCCEEEecCC-CcCCC---CCCCCC--Ceee
Confidence 345679999999987665554 45776 999987 3444
No 29
>PRK11823 DNA repair protein RadA; Provisional
Probab=94.15 E-value=0.029 Score=51.46 Aligned_cols=29 Identities=38% Similarity=0.684 Sum_probs=22.1
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
+..|+|..|||.+.. =-|+||.|++-...
T Consensus 5 ~~~y~C~~Cg~~~~~--------~~g~Cp~C~~w~t~ 33 (446)
T PRK11823 5 KTAYVCQECGAESPK--------WLGRCPECGAWNTL 33 (446)
T ss_pred CCeEECCcCCCCCcc--------cCeeCcCCCCccce
Confidence 567999999988742 35899999874443
No 30
>COG4640 Predicted membrane protein [Function unknown]
Probab=94.03 E-value=0.06 Score=50.16 Aligned_cols=30 Identities=23% Similarity=0.557 Sum_probs=22.2
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYT 117 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~ 117 (169)
-|..||-- .+.|++.||.||++-..+...+
T Consensus 3 fC~kcG~q--------k~Ed~~qC~qCG~~~t~~~sqa 32 (465)
T COG4640 3 FCPKCGSQ--------KAEDDVQCTQCGHKFTSRQSQA 32 (465)
T ss_pred cccccccc--------cccccccccccCCcCCchhhhh
Confidence 39999922 2356778999999888777544
No 31
>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=94.02 E-value=0.028 Score=51.76 Aligned_cols=30 Identities=27% Similarity=0.512 Sum_probs=22.4
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCe
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F 113 (169)
+..|+|..|||.... =-|+||.|++-...-
T Consensus 5 ~~~y~C~~Cg~~~~~--------~~g~Cp~C~~w~t~~ 34 (454)
T TIGR00416 5 KSKFVCQHCGADSPK--------WQGKCPACHAWNTIT 34 (454)
T ss_pred CCeEECCcCCCCCcc--------ccEECcCCCCccccc
Confidence 457999999988742 358999998754433
No 32
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=93.88 E-value=0.057 Score=42.67 Aligned_cols=32 Identities=25% Similarity=0.799 Sum_probs=23.5
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc-CeeeCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR-RFRPYT 117 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~-~F~~~~ 117 (169)
.-+|..||++|-+. .-.||.|+++-. .+.++.
T Consensus 29 g~kC~~CG~v~~PP--------r~~Cp~C~~~~~~E~vels 61 (140)
T COG1545 29 GTKCKKCGRVYFPP--------RAYCPKCGSETELEWVELS 61 (140)
T ss_pred EEEcCCCCeEEcCC--------cccCCCCCCCCceEEEEeC
Confidence 34999999999763 238999999843 555544
No 33
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=93.67 E-value=0.11 Score=37.99 Aligned_cols=52 Identities=31% Similarity=0.559 Sum_probs=37.6
Q ss_pred eEEcCCCCeeecCCCCCCCCCC--CCCCCCCCCCccCeeeCCCcccCCCChhHHHHHHH
Q 040420 78 AYICRDCGYIYNERKPFDQLPD--NYFCPVCGAPKRRFRPYTPAVTRGANDTAVRKARK 134 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd--~~~CPvCgapK~~F~~~~~~~~~~~n~~~v~~ar~ 134 (169)
.|.|+-|||.--+.. ++ -.+||||+=.-+-+..-.+....++|..+++-||.
T Consensus 1 K~~CPCCg~~Tl~~~-----~~~~ydIC~VC~WEdD~~q~~~pd~~~G~N~~SL~eAr~ 54 (78)
T PF14206_consen 1 KYPCPCCGYYTLEER-----GEGTYDICPVCFWEDDGVQLRDPDYYGGANHMSLNEARE 54 (78)
T ss_pred CccCCCCCcEEeccC-----CCcCceECCCCCcccCCccccCCcccCCCCHHHHHHHHH
Confidence 378999997654432 22 34999999877777655666667888888888765
No 34
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=93.50 E-value=0.053 Score=41.64 Aligned_cols=34 Identities=21% Similarity=0.497 Sum_probs=22.1
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCe
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F 113 (169)
.....+|.+||+.+.... ...++||.||.+....
T Consensus 68 vp~~~~C~~Cg~~~~~~~-----~~~~~CP~Cgs~~~~i 101 (117)
T PRK00564 68 EKVELECKDCSHVFKPNA-----LDYGVCEKCHSKNVII 101 (117)
T ss_pred cCCEEEhhhCCCccccCC-----ccCCcCcCCCCCceEE
Confidence 344789999997775421 1122599999875443
No 35
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=92.69 E-value=0.073 Score=44.37 Aligned_cols=31 Identities=39% Similarity=0.996 Sum_probs=22.9
Q ss_pred eecCCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 71 MRVASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 71 ~k~~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
++..-.-.|+|..|+.+|... -+ .||+||++
T Consensus 132 I~~v~~w~~rC~GC~~~f~~~------~~--~Cp~CG~~ 162 (177)
T COG1439 132 IKKVRKWRLRCHGCKRIFPEP------KD--FCPICGSP 162 (177)
T ss_pred cceEeeeeEEEecCceecCCC------CC--cCCCCCCc
Confidence 334444578999999999731 24 89999998
No 36
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=92.54 E-value=0.055 Score=31.43 Aligned_cols=23 Identities=43% Similarity=1.070 Sum_probs=17.4
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..|+.||...+. ++-.||.||++
T Consensus 3 ~~Cp~Cg~~~~~--------~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP--------DAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc--------ccccChhhCCC
Confidence 479999986543 44599999985
No 37
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=92.10 E-value=0.091 Score=35.53 Aligned_cols=30 Identities=27% Similarity=0.639 Sum_probs=21.7
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
....|+|..||-.++... .-+..+||-||+
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~----~~~~irCp~Cg~ 32 (49)
T COG1996 3 AMMEYKCARCGREVELDQ----ETRGIRCPYCGS 32 (49)
T ss_pred ceEEEEhhhcCCeeehhh----ccCceeCCCCCc
Confidence 345799999998886321 124469999997
No 38
>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=91.86 E-value=0.11 Score=32.03 Aligned_cols=26 Identities=38% Similarity=0.865 Sum_probs=17.9
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
|+|..||...+-. .-|..+||.||+.
T Consensus 1 Y~C~~Cg~~~~~~-----~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELK-----PGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BS-----TSSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcC-----CCCcEECCcCCCe
Confidence 8999999877632 1344699999973
No 39
>PRK05978 hypothetical protein; Provisional
Probab=91.60 E-value=0.41 Score=38.79 Aligned_cols=29 Identities=28% Similarity=0.674 Sum_probs=20.3
Q ss_pred eEEcCCCC--eeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 78 AYICRDCG--YIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 78 ~y~C~~CG--yVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
.-+|+.|| ..|+ .|-++.+ .||.||.+-+
T Consensus 33 ~grCP~CG~G~LF~---g~Lkv~~--~C~~CG~~~~ 63 (148)
T PRK05978 33 RGRCPACGEGKLFR---AFLKPVD--HCAACGEDFT 63 (148)
T ss_pred cCcCCCCCCCcccc---cccccCC--CccccCCccc
Confidence 35899999 3443 2456667 9999998533
No 40
>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=91.50 E-value=0.31 Score=35.78 Aligned_cols=41 Identities=27% Similarity=0.710 Sum_probs=28.5
Q ss_pred CeEEcCCCCeeecCC-----------------C------CCCCCCC-CCCCCCCCCCccCeeeCC
Q 040420 77 QAYICRDCGYIYNER-----------------K------PFDQLPD-NYFCPVCGAPKRRFRPYT 117 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~-----------------t------pF~~lPd-~~~CPvCgapK~~F~~~~ 117 (169)
..+.|+.|||++... + ....+|. ++.||.||+....|..+.
T Consensus 15 ~~~~C~~C~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~f~~~Q 79 (104)
T TIGR01384 15 GVYVCPSCGYEKEKKPEDDYKVTEKVKHKIKETIIIREEDSETLPTTRVECPKCGHKEAYYWLLQ 79 (104)
T ss_pred CeEECcCCCCccccccccccEEEEEeccccccceeeccccccCCCcccCCCCCCCCCeeEEEEec
Confidence 478999999776631 0 1112343 789999999999888653
No 41
>PRK06260 threonine synthase; Validated
Probab=91.42 E-value=0.14 Score=45.93 Aligned_cols=26 Identities=35% Similarity=0.777 Sum_probs=20.1
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.++|..||..|+.. .-.|.||.||.+
T Consensus 3 ~~~C~~cg~~~~~~------~~~~~Cp~cg~~ 28 (397)
T PRK06260 3 WLKCIECGKEYDPD------EIIYTCPECGGL 28 (397)
T ss_pred EEEECCCCCCCCCC------CccccCCCCCCe
Confidence 48999999999754 224799999754
No 42
>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=91.38 E-value=0.077 Score=47.89 Aligned_cols=26 Identities=35% Similarity=0.839 Sum_probs=19.5
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
|+|..|||.+-. =-|+||.|++-...
T Consensus 1 ~~c~~cg~~~~~--------~~g~cp~c~~w~~~ 26 (372)
T cd01121 1 YVCSECGYVSPK--------WLGKCPECGEWNTL 26 (372)
T ss_pred CCCCCCCCCCCC--------ccEECcCCCCceee
Confidence 899999988742 24799999874443
No 43
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=91.23 E-value=0.22 Score=38.45 Aligned_cols=37 Identities=27% Similarity=0.561 Sum_probs=27.8
Q ss_pred eEEcCCCCeeecCCCCC-CCCCCCCCCCCCCCCccCeee
Q 040420 78 AYICRDCGYIYNERKPF-DQLPDNYFCPVCGAPKRRFRP 115 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF-~~lPd~~~CPvCgapK~~F~~ 115 (169)
.|.|.+ |+.++..-.- .++|+.|-||.||.+..+-..
T Consensus 28 ~Y~C~~-Gh~~~v~Fa~eAevP~~WeC~~cG~~A~~~~~ 65 (105)
T PF13397_consen 28 SYWCPN-GHETEVPFAAEAEVPATWECPRCGLPAGRDDG 65 (105)
T ss_pred EEECCC-CCEEeccccccCCCCCceeCCCCCCcccccCC
Confidence 699999 9888763111 257999999999998766543
No 44
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=90.97 E-value=0.37 Score=33.27 Aligned_cols=23 Identities=43% Similarity=1.230 Sum_probs=17.1
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..-.|..|| +|. |-+ +||.||.+
T Consensus 4 ~mr~C~~Cg-vYT-------Lk~--~CP~CG~~ 26 (56)
T PRK13130 4 KIRKCPKCG-VYT-------LKE--ICPVCGGK 26 (56)
T ss_pred cceECCCCC-CEE-------ccc--cCcCCCCC
Confidence 356899999 553 224 89999986
No 45
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=90.97 E-value=0.12 Score=43.70 Aligned_cols=30 Identities=33% Similarity=0.816 Sum_probs=22.3
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
.....|.|..||+++..= -|.||.|++-..
T Consensus 350 ~~~p~~~c~~cg~~~~~~--------~~~c~~c~~~~~ 379 (389)
T PRK11788 350 KRKPRYRCRNCGFTARTL--------YWHCPSCKAWET 379 (389)
T ss_pred hCCCCEECCCCCCCCccc--------eeECcCCCCccC
Confidence 344569999999998653 348999998443
No 46
>PRK06450 threonine synthase; Validated
Probab=90.89 E-value=0.15 Score=45.15 Aligned_cols=25 Identities=28% Similarity=0.666 Sum_probs=19.3
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.++|..||+.|+. ...|+||.||.+
T Consensus 3 ~~~C~~Cg~~~~~-------~~~~~C~~cg~~ 27 (338)
T PRK06450 3 KEVCMKCGKERES-------IYEIRCKKCGGP 27 (338)
T ss_pred eeEECCcCCcCCC-------cccccCCcCCCE
Confidence 4899999999953 224799999864
No 47
>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=90.84 E-value=0.12 Score=40.17 Aligned_cols=24 Identities=29% Similarity=0.819 Sum_probs=18.5
Q ss_pred EcCCCC--eeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 80 ICRDCG--YIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 80 ~C~~CG--yVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
.|+.|+ |+|+.+ +.|+||.|++.-
T Consensus 4 ~CP~C~seytY~dg-------~~~iCpeC~~EW 29 (109)
T TIGR00686 4 PCPKCNSEYTYHDG-------TQLICPSCLYEW 29 (109)
T ss_pred cCCcCCCcceEecC-------CeeECccccccc
Confidence 599998 777653 568999999843
No 48
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=90.81 E-value=0.12 Score=36.80 Aligned_cols=23 Identities=35% Similarity=1.065 Sum_probs=18.3
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
-|..|.++.++.+ + .||+||...
T Consensus 6 AC~~Ck~l~~~d~------e--~CP~Cgs~~ 28 (64)
T COG2093 6 ACKNCKRLTPEDT------E--ICPVCGSTD 28 (64)
T ss_pred HHhhccccCCCCC------c--cCCCCCCcc
Confidence 5999999987642 3 799999974
No 49
>PRK10220 hypothetical protein; Provisional
Probab=90.73 E-value=0.13 Score=40.06 Aligned_cols=24 Identities=33% Similarity=0.983 Sum_probs=18.5
Q ss_pred EcCCCC--eeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 80 ICRDCG--YIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 80 ~C~~CG--yVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
-|+.|+ |+|+.+ +.|+||.|++.-
T Consensus 5 ~CP~C~seytY~d~-------~~~vCpeC~hEW 30 (111)
T PRK10220 5 HCPKCNSEYTYEDN-------GMYICPECAHEW 30 (111)
T ss_pred cCCCCCCcceEcCC-------CeEECCcccCcC
Confidence 599998 777653 569999999843
No 50
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=90.73 E-value=0.21 Score=38.68 Aligned_cols=38 Identities=26% Similarity=0.579 Sum_probs=22.0
Q ss_pred CCCeEEcCCCCeeecCCC-CCCCCCCCCCCCCCCCCccCe
Q 040420 75 SKQAYICRDCGYIYNERK-PFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~t-pF~~lPd~~~CPvCgapK~~F 113 (169)
.....+| .||+.|.... +....--.+.||.||....+.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i 105 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHI 105 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEE
Confidence 3347899 9998875421 100000125799999765443
No 51
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=90.67 E-value=0.12 Score=29.50 Aligned_cols=22 Identities=41% Similarity=1.145 Sum_probs=16.5
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.|+.||...+++ .-.||.||++
T Consensus 1 ~Cp~CG~~~~~~--------~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD--------AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc--------CcchhhhCCc
Confidence 489999777643 3379999985
No 52
>PRK11032 hypothetical protein; Provisional
Probab=90.63 E-value=0.24 Score=40.52 Aligned_cols=36 Identities=28% Similarity=0.670 Sum_probs=24.9
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeee
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRP 115 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~ 115 (169)
......+|..||+...-.+| +.+|. ||.||+ ..|.+
T Consensus 120 vg~G~LvC~~Cg~~~~~~~p-~~i~p---Cp~C~~--~~F~R 155 (160)
T PRK11032 120 VGLGNLVCEKCHHHLAFYTP-EVLPL---CPKCGH--DQFQR 155 (160)
T ss_pred eecceEEecCCCCEEEecCC-CcCCC---CCCCCC--Ceeee
Confidence 34568999999987655443 34665 999987 45554
No 53
>PRK07591 threonine synthase; Validated
Probab=90.52 E-value=0.17 Score=45.93 Aligned_cols=26 Identities=38% Similarity=0.751 Sum_probs=20.3
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
.++|..||..|+.. .. |.||.||..-
T Consensus 18 ~l~C~~Cg~~~~~~------~~-~~C~~cg~~l 43 (421)
T PRK07591 18 ALKCRECGAEYPLG------PI-HVCEECFGPL 43 (421)
T ss_pred EEEeCCCCCcCCCC------CC-ccCCCCCCeE
Confidence 58999999999753 23 8999998543
No 54
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.42 E-value=0.12 Score=35.55 Aligned_cols=29 Identities=38% Similarity=0.871 Sum_probs=21.4
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
.-+|..||-.+..+ -|-.+||.||+|--|
T Consensus 5 ~~~C~~Cg~~~~~~------dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG------DDIVVCPECGAPYHR 33 (54)
T ss_pred CccChhhCCcccCC------CCEEECCCCCCcccH
Confidence 46899999766433 355799999998654
No 55
>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=90.22 E-value=0.18 Score=38.74 Aligned_cols=28 Identities=32% Similarity=0.753 Sum_probs=20.0
Q ss_pred CeEEcCCCCee-ecCCCCCCCCCCCCCCCCCCCCc
Q 040420 77 QAYICRDCGYI-YNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 77 ~~y~C~~CGyV-Yd~~tpF~~lPd~~~CPvCgapK 110 (169)
..++|..||.- |+-. +-|- +||.||+..
T Consensus 8 tKR~Cp~CG~kFYDLn----k~Pi--vCP~CG~~~ 36 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLN----KDPI--VCPKCGTEF 36 (108)
T ss_pred CcccCCCCcchhccCC----CCCc--cCCCCCCcc
Confidence 46899999965 4433 3366 999999843
No 56
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=90.06 E-value=0.16 Score=49.15 Aligned_cols=25 Identities=28% Similarity=0.692 Sum_probs=18.9
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..=+|..|||++.+. .+.||.||..
T Consensus 567 ~~~~C~~CG~~~~g~--------~~~CP~CGs~ 591 (625)
T PRK08579 567 AITVCNKCGRSTTGL--------YTRCPRCGSE 591 (625)
T ss_pred CCccCCCCCCccCCC--------CCcCcCCCCc
Confidence 355999999977432 3599999974
No 57
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=90.04 E-value=0.16 Score=33.71 Aligned_cols=31 Identities=26% Similarity=0.569 Sum_probs=20.3
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVC 106 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvC 106 (169)
.+.-|+|..||+.|..... +-.-..-.||.|
T Consensus 25 ~~v~W~C~~Cgh~w~~~v~-~R~~~~~~CP~C 55 (55)
T PF14311_consen 25 KKVWWKCPKCGHEWKASVN-DRTRRGKGCPYC 55 (55)
T ss_pred CEEEEECCCCCCeeEccHh-hhccCCCCCCCC
Confidence 3446899999999987421 111233489988
No 58
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=89.99 E-value=0.19 Score=47.14 Aligned_cols=31 Identities=32% Similarity=0.857 Sum_probs=22.0
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeee
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRP 115 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~ 115 (169)
..|+|..|||++..= -. +||.||+=...-+.
T Consensus 6 t~f~C~~CG~~s~KW------~G--kCp~Cg~Wns~vE~ 36 (456)
T COG1066 6 TAFVCQECGYVSPKW------LG--KCPACGAWNTLVEE 36 (456)
T ss_pred cEEEcccCCCCCccc------cc--cCCCCCCccceEEe
Confidence 679999999988531 12 89999975444433
No 59
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=89.57 E-value=0.19 Score=48.60 Aligned_cols=25 Identities=36% Similarity=0.874 Sum_probs=18.8
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..=+|.+|||+..+ +.+.||.||..
T Consensus 565 ~~~iC~~CG~~~~g--------~~~~CP~CGs~ 589 (623)
T PRK08271 565 KITICNDCHHIDKR--------TGKRCPICGSE 589 (623)
T ss_pred CCccCCCCCCcCCC--------CCcCCcCCCCc
Confidence 45599999998543 34699999974
No 60
>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=89.42 E-value=0.25 Score=33.76 Aligned_cols=32 Identities=31% Similarity=0.648 Sum_probs=21.9
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
.++|+.||...+-..+. .-+...||.||+.-.
T Consensus 2 ~~~CP~CG~~iev~~~~--~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIELENPE--LGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEecCCCc--cCCEEeCCCCCCEEE
Confidence 36899999877653322 245578999998543
No 61
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=89.36 E-value=0.18 Score=30.97 Aligned_cols=24 Identities=38% Similarity=0.883 Sum_probs=13.8
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.-+|..||.++-+ ....||.|++.
T Consensus 11 ~~rC~~Cg~~~~p--------Pr~~Cp~C~s~ 34 (37)
T PF12172_consen 11 GQRCRDCGRVQFP--------PRPVCPHCGSD 34 (37)
T ss_dssp EEE-TTT--EEES----------SEETTTT--
T ss_pred EEEcCCCCCEecC--------CCcCCCCcCcc
Confidence 4699999988754 33599999864
No 62
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=89.23 E-value=0.088 Score=32.88 Aligned_cols=12 Identities=33% Similarity=1.096 Sum_probs=6.7
Q ss_pred CeEEcCCCCeee
Q 040420 77 QAYICRDCGYIY 88 (169)
Q Consensus 77 ~~y~C~~CGyVY 88 (169)
..++|..||+|+
T Consensus 21 ~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 21 ERLVCPACGFIH 32 (34)
T ss_dssp -EEEETTTTEEE
T ss_pred cceECCCCCCEE
Confidence 356666666664
No 63
>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=88.98 E-value=0.18 Score=32.05 Aligned_cols=24 Identities=29% Similarity=0.913 Sum_probs=12.5
Q ss_pred EEcCCCCee---ecCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYI---YNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyV---Yd~~tpF~~lPd~~~CPvCga 108 (169)
|+|+.||.. +|.. -.+++|+.||.
T Consensus 1 m~Cp~Cg~~~~~~D~~------~g~~vC~~CG~ 27 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPE------RGELVCPNCGL 27 (43)
T ss_dssp ESBTTTSSSEEEEETT------TTEEEETTT-B
T ss_pred CCCcCCcCCceEEcCC------CCeEECCCCCC
Confidence 567777742 2322 23457777765
No 64
>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=88.76 E-value=0.27 Score=28.76 Aligned_cols=23 Identities=35% Similarity=0.892 Sum_probs=13.0
Q ss_pred cCCCCeeecCCCCCCCCCCCCCCCCCC
Q 040420 81 CRDCGYIYNERKPFDQLPDNYFCPVCG 107 (169)
Q Consensus 81 C~~CGyVYd~~tpF~~lPd~~~CPvCg 107 (169)
|..||..-.++ +.--.|.||.||
T Consensus 1 C~sC~~~i~~r----~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPR----EQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCc----ccCceEeCCCCC
Confidence 56676555543 123346777776
No 65
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=88.61 E-value=0.28 Score=47.64 Aligned_cols=24 Identities=38% Similarity=0.934 Sum_probs=17.9
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..=+|..|||+. + +.|.||.||.+
T Consensus 625 ~~~~C~~CG~~~-g--------~~~~CP~CG~~ 648 (656)
T PRK08270 625 TFSICPKHGYLS-G--------EHEFCPKCGEE 648 (656)
T ss_pred CCcccCCCCCcC-C--------CCCCCcCCcCc
Confidence 345999999853 2 24699999976
No 66
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=88.45 E-value=0.27 Score=49.61 Aligned_cols=32 Identities=28% Similarity=0.819 Sum_probs=25.2
Q ss_pred CeEEcCCCCeeecCCCCCCCCC-CCCCCCCCCCCccCee
Q 040420 77 QAYICRDCGYIYNERKPFDQLP-DNYFCPVCGAPKRRFR 114 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lP-d~~~CPvCgapK~~F~ 114 (169)
-.|+|.+||.+|.+- +.| + .||.||.......
T Consensus 820 ~~~~~~~~~~~~~~~----~~~~~--~~~~~~~~~~~~~ 852 (1006)
T PRK12775 820 LQWRCDDCGKVSEGF----AFPYG--MCPACGGKLQALD 852 (1006)
T ss_pred eeeehhhhccccccc----cCCcC--cCcccccchhhhh
Confidence 389999999999874 347 6 9999998754444
No 67
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=88.40 E-value=0.24 Score=35.20 Aligned_cols=22 Identities=36% Similarity=0.800 Sum_probs=17.7
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
--|+.|.|+-++ + .||+||...
T Consensus 6 ~AC~~C~~i~~~--------~--~Cp~Cgs~~ 27 (64)
T PRK06393 6 RACKKCKRLTPE--------K--TCPVHGDEK 27 (64)
T ss_pred hhHhhCCcccCC--------C--cCCCCCCCc
Confidence 369999999853 3 899999964
No 68
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=87.91 E-value=0.3 Score=46.30 Aligned_cols=24 Identities=46% Similarity=1.164 Sum_probs=18.2
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..+|..|||+..+ +.|.||.||..
T Consensus 518 ~~~C~~CG~~~~~--------~~~~CP~CGs~ 541 (555)
T cd01675 518 IDICNDCGYIGEG--------EGFKCPKCGSE 541 (555)
T ss_pred CccCCCCCCCCcC--------CCCCCcCCCCc
Confidence 4499999986643 23699999974
No 69
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=87.43 E-value=0.22 Score=30.51 Aligned_cols=29 Identities=24% Similarity=0.511 Sum_probs=19.2
Q ss_pred EEcCCCCeeecCCCCCCCCCC---CCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPD---NYFCPVCGAP 109 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd---~~~CPvCgap 109 (169)
..|+.||..|.-.. +.+++ ..+||.|++.
T Consensus 3 ~~CP~C~~~~~v~~--~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVD--SQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCH--HHcCCCCCEEECCCCCCE
Confidence 68999998765421 11222 3799999974
No 70
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=87.42 E-value=0.6 Score=36.06 Aligned_cols=42 Identities=21% Similarity=0.712 Sum_probs=29.8
Q ss_pred CeEEcCCCCeeecCC---------------------CCCCCC-CCCCCCCCCCCCccCeeeCCC
Q 040420 77 QAYICRDCGYIYNER---------------------KPFDQL-PDNYFCPVCGAPKRRFRPYTP 118 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~---------------------tpF~~l-Pd~~~CPvCgapK~~F~~~~~ 118 (169)
..+-|+-|+|+|.-. ..|+.+ .-+-.||.||+.+.+|..+.-
T Consensus 20 ~rf~C~tCpY~~~I~~ei~~r~~~~~Kevd~vlgg~~a~~nv~~t~~~Cp~Cgh~rayF~qlQt 83 (105)
T KOG2906|consen 20 NRFSCRTCPYVFPISREISSRKYPKLKEVDDVLGGDEAWENVDQTEATCPTCGHERAYFMQLQT 83 (105)
T ss_pred eeEEcCCCCceeeEeeeeeccccCchhhhhhhcCCcccccchhhccCcCCCCCCCceEEEEeee
Confidence 468999999998741 123332 123489999999999998743
No 71
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=87.35 E-value=0.34 Score=34.05 Aligned_cols=21 Identities=57% Similarity=1.311 Sum_probs=17.3
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
-|+.|.++-++ + +||+||...
T Consensus 5 AC~~C~~i~~~--------~--~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYITTE--------D--RCPVCGSRD 25 (61)
T ss_pred hhhhCCcccCC--------C--cCCCCcCCc
Confidence 69999999853 3 799999955
No 72
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=87.10 E-value=0.34 Score=30.18 Aligned_cols=28 Identities=25% Similarity=0.676 Sum_probs=19.7
Q ss_pred EEcCCCCeeecCCCCCCCCCC---CCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPD---NYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd---~~~CPvCga 108 (169)
-+|..|+..|+-. =+.+|+ ..+|+.|++
T Consensus 3 i~Cp~C~~~y~i~--d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEID--DEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCC--HHHCCCCCcEEECCCCCC
Confidence 4799999998752 122343 379999987
No 73
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=86.95 E-value=0.21 Score=30.47 Aligned_cols=22 Identities=41% Similarity=1.127 Sum_probs=11.1
Q ss_pred EcCCCC--eeecCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCG--YIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 80 ~C~~CG--yVYd~~tpF~~lPd~~~CPvCga 108 (169)
.|..|| |.|..+ .-++||.|++
T Consensus 4 ~Cp~C~se~~y~D~-------~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTYEDG-------ELLVCPECGH 27 (30)
T ss_dssp --TTT-----EE-S-------SSEEETTTTE
T ss_pred CCCCCCCcceeccC-------CEEeCCcccc
Confidence 588888 555433 3478888875
No 74
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=86.58 E-value=0.27 Score=39.87 Aligned_cols=46 Identities=26% Similarity=0.491 Sum_probs=31.6
Q ss_pred EEcCCCCeeecC----CCCCCCC--CCCCCCCCCCCCccCeeeCCCcccCCCC
Q 040420 79 YICRDCGYIYNE----RKPFDQL--PDNYFCPVCGAPKRRFRPYTPAVTRGAN 125 (169)
Q Consensus 79 y~C~~CGyVYd~----~tpF~~l--Pd~~~CPvCgapK~~F~~~~~~~~~~~n 125 (169)
.+|. |||+|++ ...|+++ -.-..||+||..+-.=...+|.+....+
T Consensus 6 L~C~-~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~~V~K~lmAP~v~~~~~ 57 (148)
T PF06676_consen 6 LRCE-NGHEFEGWFRSSAAFDRQQARGLVSCPVCGSTEVSKALMAPAVATSRS 57 (148)
T ss_pred EecC-CCCccceecCCHHHHHHHHHcCCccCCCCCCCeEeeecCCCeecCCCC
Confidence 4888 9999988 1233332 1225899999988887778887765433
No 75
>PHA00626 hypothetical protein
Probab=86.28 E-value=0.63 Score=32.62 Aligned_cols=32 Identities=28% Similarity=0.644 Sum_probs=18.8
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCCCc
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYTPA 119 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~~~ 119 (169)
.+.|+|.+|||.|... .|++ .+|..|..+..+
T Consensus 21 snrYkCkdCGY~ft~~-~~~~-----------~~~~~~~~~~~~ 52 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD-AFGE-----------RGKNEFVRINKE 52 (59)
T ss_pred CcceEcCCCCCeechh-hhhh-----------ccccceEEechh
Confidence 4567777777777542 2322 456677766544
No 76
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=86.17 E-value=0.38 Score=38.41 Aligned_cols=26 Identities=42% Similarity=0.948 Sum_probs=18.8
Q ss_pred CCCCeEEcCCCC---eeecCCCCCCCCCCCCCCCCCCC
Q 040420 74 ASKQAYICRDCG---YIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 74 ~~~~~y~C~~CG---yVYd~~tpF~~lPd~~~CPvCga 108 (169)
+.+-.+.|+.|| |-+|+ +..||+|+.
T Consensus 24 AkML~~hCp~Cg~PLF~KdG---------~v~CPvC~~ 52 (131)
T COG1645 24 AKMLAKHCPKCGTPLFRKDG---------EVFCPVCGY 52 (131)
T ss_pred hHHHHhhCcccCCcceeeCC---------eEECCCCCc
Confidence 444578999999 33443 349999997
No 77
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=86.07 E-value=0.27 Score=50.55 Aligned_cols=25 Identities=40% Similarity=0.954 Sum_probs=20.0
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
+++|++||+.|.+. .+ .||.||...
T Consensus 694 IKrC~dcg~q~~~~------~~--~cP~Cgs~~ 718 (1187)
T COG1110 694 IKRCRDCGEQFVDS------ED--KCPRCGSRN 718 (1187)
T ss_pred HHHHhhcCceeccc------cc--cCCCCCCcc
Confidence 67999999999753 23 899999843
No 78
>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=86.06 E-value=0.51 Score=37.70 Aligned_cols=27 Identities=26% Similarity=0.536 Sum_probs=19.9
Q ss_pred CeEEcCCCCee-ecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYI-YNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyV-Yd~~tpF~~lPd~~~CPvCgap 109 (169)
.+++|..||.- |+-. +-|- +||.||..
T Consensus 8 tKr~Cp~cg~kFYDLn----k~p~--vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKFYDLN----RRPA--VSPYTGEQ 35 (129)
T ss_pred ccccCCCcCccccccC----CCCc--cCCCcCCc
Confidence 46899999965 4433 2366 99999984
No 79
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.70 E-value=0.47 Score=33.28 Aligned_cols=32 Identities=28% Similarity=0.788 Sum_probs=15.5
Q ss_pred CeEEcCCCCeeecCC-CCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNER-KPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~-tpF~~lPd~~~CPvCga 108 (169)
..|.|++||.+--.+ ..=.++-..|+||.||-
T Consensus 24 ~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeechhHHhcCCceECCCCCC
Confidence 457777777441110 00012344567777763
No 80
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=85.69 E-value=0.46 Score=36.53 Aligned_cols=32 Identities=31% Similarity=0.759 Sum_probs=23.1
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
..-.|+|..||..+...... + ...|.|+.|+.
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~-~-~~~~~C~~C~~ 151 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRS-K-RKRYRCGRCGG 151 (157)
T ss_pred cceEEEcCCCCCEeeeeccc-c-hhhEECCCCCC
Confidence 44589999999888654332 2 35589999994
No 81
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=85.49 E-value=0.58 Score=42.53 Aligned_cols=24 Identities=21% Similarity=0.577 Sum_probs=18.3
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.++|..||..|+. + ..|.||.|+.
T Consensus 2 ~l~C~~Cg~~~~~-----~--~~~~C~~c~g 25 (398)
T TIGR03844 2 TLRCPGCGEVLPD-----H--YTLSCPLDCG 25 (398)
T ss_pred EEEeCCCCCccCC-----c--cccCCCCCCC
Confidence 4799999999952 1 2479999874
No 82
>PF04641 Rtf2: Rtf2 RING-finger
Probab=85.32 E-value=0.32 Score=41.55 Aligned_cols=37 Identities=35% Similarity=0.740 Sum_probs=24.2
Q ss_pred CCCeEEcCCCCeeecCC---------------CCCCCCCCCCCCCCCCCCcc
Q 040420 75 SKQAYICRDCGYIYNER---------------KPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~---------------tpF~~lPd~~~CPvCgapK~ 111 (169)
....|+|++++.+..+. ..++++..+|.||+|+.+-.
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCccc
Confidence 35577887666555441 24556655789999999744
No 83
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.29 E-value=0.59 Score=39.12 Aligned_cols=41 Identities=22% Similarity=0.714 Sum_probs=25.6
Q ss_pred CeEEcCCCCeeecCC-----------------CCCCCC-C---CCCCCCCCCCCc--cCeeeCC
Q 040420 77 QAYICRDCGYIYNER-----------------KPFDQL-P---DNYFCPVCGAPK--RRFRPYT 117 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~-----------------tpF~~l-P---d~~~CPvCgapK--~~F~~~~ 117 (169)
....|++||..+.-. .-++++ | +-|+||.||-.. ..|..+.
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~ 67 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLS 67 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccCC
Confidence 357999999777651 122222 3 458999999743 3566544
No 84
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=84.85 E-value=0.39 Score=43.93 Aligned_cols=26 Identities=27% Similarity=0.601 Sum_probs=19.7
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
-|+.|+..+++.- ...-.|+|| ||.+
T Consensus 242 ~c~~C~~~~~~~~---~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 242 ACEACGEPAVSED---AETACANCP-CGGR 267 (374)
T ss_pred hhcccCCcCCchh---hhhcCCCCC-CCCc
Confidence 7999999998642 123469999 9985
No 85
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.82 E-value=0.44 Score=29.70 Aligned_cols=30 Identities=20% Similarity=0.514 Sum_probs=19.3
Q ss_pred EEcCCCCeeecCCC-CCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERK-PFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~t-pF~~lPd~~~CPvCga 108 (169)
-+|+.|+..|+-.. ...+-....+||.|++
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 47999998887521 0111223579999987
No 86
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=84.37 E-value=1.2 Score=26.24 Aligned_cols=27 Identities=26% Similarity=0.779 Sum_probs=17.8
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
..|.|..|+++=. +.+..|-.|++++.
T Consensus 3 g~W~C~~C~~~N~--------~~~~~C~~C~~~rp 29 (30)
T PF00641_consen 3 GDWKCPSCTFMNP--------ASRSKCVACGAPRP 29 (30)
T ss_dssp SSEEETTTTEEEE--------SSSSB-TTT--BTT
T ss_pred cCccCCCCcCCch--------HHhhhhhCcCCCCc
Confidence 4699999996643 34459999999864
No 87
>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=84.33 E-value=0.55 Score=30.98 Aligned_cols=30 Identities=27% Similarity=0.825 Sum_probs=20.6
Q ss_pred CeEEcCCCCeeecC---------CCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNE---------RKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~---------~tpF~~lPd~~~CPvCga 108 (169)
+.|.|+.||..++. ..+.+ +.+++||+|..
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~--~~~v~CPiC~~ 39 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSE--SKNVVCPICSS 39 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCC--CCCccCCCchh
Confidence 35899999985554 23332 34689999975
No 88
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=83.82 E-value=0.61 Score=45.88 Aligned_cols=24 Identities=33% Similarity=0.733 Sum_probs=17.0
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..=+|.+|||+- + ..|.||.||..
T Consensus 679 ~~~~C~~CG~~~--~-------~~~~CP~CG~~ 702 (735)
T PRK07111 679 PVDRCPVCGYLG--V-------IEDKCPKCGST 702 (735)
T ss_pred CCeecCCCCCCC--C-------cCccCcCCCCc
Confidence 345999999533 2 12699999963
No 89
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=83.72 E-value=2.1 Score=39.59 Aligned_cols=45 Identities=24% Similarity=0.524 Sum_probs=29.7
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCCCcccCCCChhHH
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYTPAVTRGANDTAV 129 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~~~~~~~~n~~~v 129 (169)
-.|.|..||+++....+ .-+ .||.||. .|.-..|-=.+.-.|.++
T Consensus 239 ~~~~c~~cg~~~~~~~~---~~~--~c~~Cg~---~~~~~GPlW~GpL~d~~f 283 (380)
T COG1867 239 YIYHCSRCGEIVGSFRE---VDE--KCPHCGG---KVHLAGPLWLGPLHDEEF 283 (380)
T ss_pred cEEEcccccceeccccc---ccc--cCCcccc---cceeccCcccCcccCHHH
Confidence 47999999988876433 223 8999998 566555554444444443
No 90
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=83.48 E-value=0.76 Score=45.06 Aligned_cols=30 Identities=23% Similarity=0.690 Sum_probs=19.3
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
...=+|..||| .++.-.. -+.|.||.||..
T Consensus 639 ~~~~~C~~CG~--~Ge~~~~--~~~~~CP~CG~~ 668 (711)
T PRK09263 639 TPIDECYECGF--TGEFECT--EKGFTCPKCGNH 668 (711)
T ss_pred CCCcccCCCCC--CccccCC--CCCCcCcCCCCC
Confidence 34559999997 4432111 234799999964
No 91
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=83.46 E-value=0.71 Score=44.64 Aligned_cols=24 Identities=29% Similarity=0.701 Sum_probs=17.3
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..=+|..||| .++ ..|.||.||..
T Consensus 558 ~~~~C~~CGy--~g~-------~~~~CP~CG~~ 581 (618)
T PRK14704 558 PVDRCKCCSY--HGV-------IGNECPSCGNE 581 (618)
T ss_pred CCeecCCCCC--CCC-------cCccCcCCCCC
Confidence 3559999997 332 12699999964
No 92
>PRK08197 threonine synthase; Validated
Probab=83.44 E-value=0.67 Score=41.51 Aligned_cols=25 Identities=32% Similarity=0.887 Sum_probs=19.1
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.++|..||+.|+.. .-.|.| .||.+
T Consensus 7 ~~~C~~Cg~~~~~~------~~~~~C-~cg~~ 31 (394)
T PRK08197 7 HLECSKCGETYDAD------QVHNLC-KCGKP 31 (394)
T ss_pred EEEECCCCCCCCCC------Ccceec-CCCCe
Confidence 58999999999753 224789 79865
No 93
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.39 E-value=0.66 Score=29.75 Aligned_cols=26 Identities=23% Similarity=0.735 Sum_probs=12.3
Q ss_pred cCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 81 CRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 81 C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
|+.||.+..... .++ -..|+||.||.
T Consensus 3 Cp~Cg~~l~~~~-~~~-~~~~vC~~Cg~ 28 (52)
T smart00661 3 CPKCGNMLIPKE-GKE-KRRFVCRKCGY 28 (52)
T ss_pred CCCCCCcccccc-CCC-CCEEECCcCCC
Confidence 666775443220 000 12466777765
No 94
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=83.33 E-value=0.54 Score=43.26 Aligned_cols=26 Identities=35% Similarity=0.949 Sum_probs=20.3
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.+..|+|..|||.-. -=-|.||.|++
T Consensus 351 ~~~~YRC~~CGF~a~--------~l~W~CPsC~~ 376 (389)
T COG2956 351 RKPRYRCQNCGFTAH--------TLYWHCPSCRA 376 (389)
T ss_pred hcCCceecccCCcce--------eeeeeCCCccc
Confidence 456899999997643 23699999976
No 95
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=83.04 E-value=0.35 Score=45.76 Aligned_cols=30 Identities=40% Similarity=0.845 Sum_probs=13.4
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC-ccCeee
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP-KRRFRP 115 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap-K~~F~~ 115 (169)
..=+|.+|||+..+ .+.||.||.. -+...+
T Consensus 490 ~~~~C~~CG~~~~~---------~~~CP~CGs~~~~~~~R 520 (546)
T PF13597_consen 490 PIDICPDCGYIGGE---------GDKCPKCGSENIEVYSR 520 (546)
T ss_dssp -EEEETTT---S-----------EEE-CCC----EEEEB-
T ss_pred CcccccCCCcCCCC---------CCCCCCCCCcccceEEE
Confidence 35599999987643 3489999998 333333
No 96
>PRK04351 hypothetical protein; Provisional
Probab=82.90 E-value=0.84 Score=36.65 Aligned_cols=30 Identities=27% Similarity=0.753 Sum_probs=22.9
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-.|+|..||.+|--...++ +..|+|-.|+.
T Consensus 111 y~Y~C~~Cg~~~~r~Rr~n--~~~yrCg~C~g 140 (149)
T PRK04351 111 YLYECQSCGQQYLRKRRIN--TKRYRCGKCRG 140 (149)
T ss_pred EEEECCCCCCEeeeeeecC--CCcEEeCCCCc
Confidence 4799999999886533332 57899999985
No 97
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=82.88 E-value=0.81 Score=38.41 Aligned_cols=33 Identities=30% Similarity=0.681 Sum_probs=21.3
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
..++|..||++|+...... .+.-.||.||..-.
T Consensus 121 ~~~~C~~C~~~~~~~~~~~--~~~p~C~~Cgg~lr 153 (242)
T PRK00481 121 LRARCTKCGQTYDLDEYLK--PEPPRCPKCGGILR 153 (242)
T ss_pred CceeeCCCCCCcChhhhcc--CCCCCCCCCCCccC
Confidence 3679999999987532211 12225999987533
No 98
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.85 E-value=0.95 Score=31.98 Aligned_cols=32 Identities=31% Similarity=0.722 Sum_probs=17.3
Q ss_pred CeEEcCCCCeeecCC-CCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNER-KPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~-tpF~~lPd~~~CPvCga 108 (169)
..|.|++||.+--.+ ..=.++-..|+||.||-
T Consensus 26 v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 467888888443321 00112345578888873
No 99
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=82.68 E-value=0.31 Score=30.87 Aligned_cols=30 Identities=30% Similarity=0.658 Sum_probs=15.1
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-+|..|+-...+=..|++--..|+|+.|+.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 468888855555444444445788998876
No 100
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=82.58 E-value=0.79 Score=35.85 Aligned_cols=34 Identities=29% Similarity=0.609 Sum_probs=23.4
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
......|.+|+..+.... -++.||.||+..-+-+
T Consensus 67 ~p~~~~C~~C~~~~~~e~------~~~~CP~C~s~~~~i~ 100 (115)
T COG0375 67 EPAECWCLDCGQEVELEE------LDYRCPKCGSINLRII 100 (115)
T ss_pred eccEEEeccCCCeecchh------heeECCCCCCCceEEe
Confidence 334679999987776542 3467999998654443
No 101
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=82.50 E-value=0.86 Score=43.95 Aligned_cols=25 Identities=44% Similarity=0.905 Sum_probs=17.6
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..=+|.+|||+. ++ ..+.||.||..
T Consensus 531 ~~siC~~CGy~~-g~-------~~~~CP~CGs~ 555 (586)
T TIGR02827 531 KITICNDCHHID-KR-------TLHRCPVCGSA 555 (586)
T ss_pred CCeecCCCCCcC-CC-------cCCcCcCCCCc
Confidence 455999999853 22 12599999964
No 102
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=81.76 E-value=0.66 Score=41.47 Aligned_cols=59 Identities=24% Similarity=0.532 Sum_probs=34.9
Q ss_pred CCeE-EcCCCCee-ecCCCCCCCCC-CCCCCCCCCCC--------------ccCeeeCCCcccC----CCChhHHHHHHH
Q 040420 76 KQAY-ICRDCGYI-YNERKPFDQLP-DNYFCPVCGAP--------------KRRFRPYTPAVTR----GANDTAVRKARK 134 (169)
Q Consensus 76 ~~~y-~C~~CGyV-Yd~~tpF~~lP-d~~~CPvCgap--------------K~~F~~~~~~~~~----~~n~~~v~~ar~ 134 (169)
...| +|+.||.+ |.. ||- +-|+||.|++- .+.|+++...... ...|.++.+.|-
T Consensus 25 e~lw~KCp~c~~~~y~~-----eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~gsf~el~~~l~~~dPL~F~d~k~Y~~rL 99 (294)
T COG0777 25 EGLWTKCPSCGEMLYRK-----ELESNLKVCPKCGHHMRISARERLEALLDEGSFEELDSPLEPKDPLKFPDSKKYKDRL 99 (294)
T ss_pred CCceeECCCccceeeHH-----HHHhhhhcccccCcccccCHHHHHHHhhCCCcceecccCCCcCCcccCCcchhhHHHH
Confidence 4567 99999966 543 343 45899999974 4456666554222 344544555444
Q ss_pred HHhhh
Q 040420 135 EQIQR 139 (169)
Q Consensus 135 ~~~~~ 139 (169)
+..|+
T Consensus 100 ~~a~~ 104 (294)
T COG0777 100 EAARK 104 (294)
T ss_pred HHHHh
Confidence 44433
No 103
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=81.65 E-value=1.5 Score=33.32 Aligned_cols=43 Identities=14% Similarity=0.270 Sum_probs=25.7
Q ss_pred cceecCCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 69 FSMRVASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 69 ~~~k~~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
.+++......+.|+.||.. .-..+++.---...||+||.-..+
T Consensus 12 ~k~k~klpt~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 12 IRPKPKLPKIFECPRCGKV-SISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cccccCCCcEeECCCCCCe-EeeeecCCCcceEECCCCCCccCE
Confidence 4444555678999999942 211122221123599999997665
No 104
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=81.08 E-value=1.9 Score=33.09 Aligned_cols=42 Identities=24% Similarity=0.597 Sum_probs=28.2
Q ss_pred CCCeEEcCCCCeeecCC--------------------CCC--CCC-----CC-CCCCCCCCCCccCeeeC
Q 040420 75 SKQAYICRDCGYIYNER--------------------KPF--DQL-----PD-NYFCPVCGAPKRRFRPY 116 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~--------------------tpF--~~l-----Pd-~~~CPvCgapK~~F~~~ 116 (169)
....++|+.|||.++-. .-. +.. |. +..||.||+.+..|...
T Consensus 19 ~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~ea~y~~~ 88 (113)
T COG1594 19 EGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPKCGNKEAYYWQL 88 (113)
T ss_pred CCcEEECCCCCcchhccccceeEEEEeeccCCcceeeeeecccccCccccccccccCCCCCCceeEEEee
Confidence 44489999999988752 000 111 12 35799999999998754
No 105
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=80.90 E-value=0.49 Score=41.75 Aligned_cols=30 Identities=27% Similarity=0.721 Sum_probs=20.4
Q ss_pred CeE-EcCCCCeeecCCCCCCCCCC-CCCCCCCCCCc
Q 040420 77 QAY-ICRDCGYIYNERKPFDQLPD-NYFCPVCGAPK 110 (169)
Q Consensus 77 ~~y-~C~~CGyVYd~~tpF~~lPd-~~~CPvCgapK 110 (169)
..| +|+.|+.+.... ++-+ .++||.|++.-
T Consensus 25 ~~~~~c~~c~~~~~~~----~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 25 GLWTKCPSCGQVLYRK----ELEANLNVCPKCGHHM 56 (292)
T ss_pred CCeeECCCccchhhHH----HHHhcCCCCCCCCCCe
Confidence 346 999999765432 2333 36999999853
No 106
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=80.83 E-value=0.51 Score=41.59 Aligned_cols=30 Identities=27% Similarity=0.734 Sum_probs=20.7
Q ss_pred eE-EcCCCCeeecCCCCCCCCC-CCCCCCCCCCCcc
Q 040420 78 AY-ICRDCGYIYNERKPFDQLP-DNYFCPVCGAPKR 111 (169)
Q Consensus 78 ~y-~C~~CGyVYd~~tpF~~lP-d~~~CPvCgapK~ 111 (169)
.| +|..||.+.... ++- +-++||.|++.-.
T Consensus 25 ~~~~c~~c~~~~~~~----~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 25 VWTKCPKCGQVLYTK----ELERNLEVCPKCDHHMR 56 (285)
T ss_pred CeeECCCCcchhhHH----HHHhhCCCCCCCCCcCc
Confidence 46 999999765432 232 3479999999644
No 107
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=80.71 E-value=1.1 Score=23.51 Aligned_cols=12 Identities=25% Similarity=0.827 Sum_probs=7.2
Q ss_pred EEcCCCCeeecC
Q 040420 79 YICRDCGYIYNE 90 (169)
Q Consensus 79 y~C~~CGyVYd~ 90 (169)
|+|..||..|..
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 678888877753
No 108
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=80.66 E-value=2 Score=30.08 Aligned_cols=35 Identities=23% Similarity=0.801 Sum_probs=22.8
Q ss_pred CCCCeEEcCC--CC-eeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 74 ASKQAYICRD--CG-YIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 74 ~~~~~y~C~~--CG-yVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
.+..+|.|.. |. +.=+ ...|++.| .||.|+++=.+
T Consensus 14 e~t~VW~Ct~e~C~gWmR~-nFs~~~~p---~CPlC~s~M~~ 51 (59)
T PF14169_consen 14 EETKVWECTSEDCNGWMRD-NFSFEEEP---VCPLCKSPMVS 51 (59)
T ss_pred eeeeeEEeCCCCCCccccc-ccccCCCc---cCCCcCCcccc
Confidence 4577999998 75 3332 33455544 69999986443
No 109
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=80.52 E-value=0.47 Score=42.26 Aligned_cols=29 Identities=21% Similarity=0.500 Sum_probs=20.1
Q ss_pred eE-EcCCCCeeecCCCCCCCCC-CCCCCCCCCCCc
Q 040420 78 AY-ICRDCGYIYNERKPFDQLP-DNYFCPVCGAPK 110 (169)
Q Consensus 78 ~y-~C~~CGyVYd~~tpF~~lP-d~~~CPvCgapK 110 (169)
.| +|..|+.+.... ++. ..++||.|++.-
T Consensus 37 lw~kc~~C~~~~~~~----~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 37 LWVQCENCYGLNYKK----FLKSKMNICEQCGYHL 67 (296)
T ss_pred CeeECCCccchhhHH----HHHHcCCCCCCCCCCc
Confidence 46 999999765432 233 347999999853
No 110
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=80.18 E-value=1 Score=26.52 Aligned_cols=22 Identities=41% Similarity=0.972 Sum_probs=13.9
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.|+.||.+.... .-.||.||+.
T Consensus 2 ~CP~C~~~V~~~--------~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPES--------AKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhh--------cCcCCCCCCC
Confidence 488888655322 1278888873
No 111
>PRK12860 transcriptional activator FlhC; Provisional
Probab=80.15 E-value=1.7 Score=36.56 Aligned_cols=35 Identities=29% Similarity=0.596 Sum_probs=24.4
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
.-+.+.|..||--|.. ...++-.+++||.|.-|.+
T Consensus 131 ~L~l~~C~~Cgg~fv~--~~~e~~~~f~CplC~~psR 165 (189)
T PRK12860 131 MLQLARCCRCGGKFVT--HAHDLRHNFVCGLCQPPSR 165 (189)
T ss_pred CeeeccCCCCCCCeec--cccccCCCCcCCCCCCccc
Confidence 4468899999966542 2335567799999984443
No 112
>PHA00626 hypothetical protein
Probab=79.66 E-value=1.3 Score=31.13 Aligned_cols=34 Identities=35% Similarity=0.778 Sum_probs=21.3
Q ss_pred EcCCCCe--eecCCCCCCCCCCCCCCCCCCC--CccCee
Q 040420 80 ICRDCGY--IYNERKPFDQLPDNYFCPVCGA--PKRRFR 114 (169)
Q Consensus 80 ~C~~CGy--VYd~~tpF~~lPd~~~CPvCga--pK~~F~ 114 (169)
.|+.||. |+.-++ -.+....|+||.||. .|+.|-
T Consensus 2 ~CP~CGS~~Ivrcg~-cr~~snrYkCkdCGY~ft~~~~~ 39 (59)
T PHA00626 2 SCPKCGSGNIAKEKT-MRGWSDDYVCCDCGYNDSKDAFG 39 (59)
T ss_pred CCCCCCCceeeeece-ecccCcceEcCCCCCeechhhhh
Confidence 5899996 454322 112357899999998 344443
No 113
>PRK12722 transcriptional activator FlhC; Provisional
Probab=79.63 E-value=1.5 Score=36.84 Aligned_cols=34 Identities=24% Similarity=0.529 Sum_probs=23.9
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
-+.+.|..||--|.. ...++-.+++||.|.-|.+
T Consensus 132 L~l~~C~~Cgg~fv~--~~~e~~~~f~CplC~~psR 165 (187)
T PRK12722 132 LQLSSCNCCGGHFVT--HAHDPVGSFVCGLCQPPSR 165 (187)
T ss_pred EeeccCCCCCCCeec--cccccCCCCcCCCCCCccc
Confidence 357899999966542 2235567799999987544
No 114
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=79.27 E-value=1.3 Score=33.38 Aligned_cols=28 Identities=29% Similarity=0.592 Sum_probs=14.8
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
+.|+|+.||..-..+.. -.-|.|..||.
T Consensus 34 ~~~~Cp~C~~~~VkR~a----~GIW~C~kCg~ 61 (89)
T COG1997 34 AKHVCPFCGRTTVKRIA----TGIWKCRKCGA 61 (89)
T ss_pred cCCcCCCCCCcceeeec----cCeEEcCCCCC
Confidence 35666666655333321 34466666665
No 115
>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=79.06 E-value=1.4 Score=23.73 Aligned_cols=12 Identities=33% Similarity=0.913 Sum_probs=9.7
Q ss_pred EEcCCCCeeecC
Q 040420 79 YICRDCGYIYNE 90 (169)
Q Consensus 79 y~C~~CGyVYd~ 90 (169)
|+|..||..|..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 789999988854
No 116
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=79.00 E-value=0.63 Score=38.65 Aligned_cols=38 Identities=21% Similarity=0.662 Sum_probs=24.6
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
.+...|+|+.|..-|.-...| --.+.||.||+.-..+.
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~---~~~F~Cp~Cg~~L~~~d 146 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAM---ELGFTCPKCGEDLEEYD 146 (176)
T ss_pred ccCCceeCCCCCCcccHHHHH---HhCCCCCCCCchhhhcc
Confidence 355689998888444322222 23489999999766555
No 117
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=78.98 E-value=1.1 Score=42.68 Aligned_cols=25 Identities=44% Similarity=1.036 Sum_probs=16.8
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..=+|.+|||+ ++. . .+.||.||..
T Consensus 523 ~~~~C~~CG~~--g~~----~--~~~CP~Cgs~ 547 (579)
T TIGR02487 523 PVDVCEDCGYT--GEG----L--NDKCPKCGSH 547 (579)
T ss_pred CCccCCCCCCC--CCC----C--CCcCcCCCCc
Confidence 34599999983 221 1 2599999964
No 118
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=78.62 E-value=1.9 Score=32.76 Aligned_cols=31 Identities=32% Similarity=0.547 Sum_probs=20.7
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
....|+|.+||++..- +++= .+-.||.|++.
T Consensus 39 G~~~~~C~~Cg~~~~~--~~SC--k~R~CP~C~~~ 69 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKIV--YNSC--KNRHCPSCQAK 69 (111)
T ss_pred CcceeecCCCCceEEe--cCcc--cCcCCCCCCCh
Confidence 4458999999987643 2222 12289999983
No 119
>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=78.08 E-value=1.2 Score=36.95 Aligned_cols=36 Identities=28% Similarity=0.651 Sum_probs=25.6
Q ss_pred EEcCCCCeeec-------CCCCCCCCCCCCCCCCCCCCccCeeeCCCc
Q 040420 79 YICRDCGYIYN-------ERKPFDQLPDNYFCPVCGAPKRRFRPYTPA 119 (169)
Q Consensus 79 y~C~~CGyVYd-------~~tpF~~lPd~~~CPvCgapK~~F~~~~~~ 119 (169)
++|..||+.-+ ++. -.+ . .||.|+...+.+++++.-
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~--irL-t--~C~~C~~vaDkYiE~d~v 43 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGN--IRL-T--KCPNCGKVADKYIEYDNV 43 (208)
T ss_pred CEeccCCCcchhhhhccCCCc--EEE-e--eccccCCcccceeccccH
Confidence 58999996532 221 111 2 799999999999998754
No 120
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=77.79 E-value=2.5 Score=29.30 Aligned_cols=29 Identities=28% Similarity=0.816 Sum_probs=20.6
Q ss_pred eE-EcCCCCee----ecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AY-ICRDCGYI----YNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y-~C~~CGyV----Yd~~tpF~~lPd~~~CPvCga 108 (169)
.| .|++||.- .-+.|-....|- .||.|..
T Consensus 3 ~Wi~CP~CgnKTR~kir~DT~LkNfPl--yCpKCK~ 36 (55)
T PF14205_consen 3 EWILCPICGNKTRLKIREDTVLKNFPL--YCPKCKQ 36 (55)
T ss_pred eEEECCCCCCccceeeecCceeccccc--cCCCCCc
Confidence 45 89999933 233455666787 9999976
No 121
>PRK00420 hypothetical protein; Validated
Probab=77.78 E-value=1.3 Score=34.35 Aligned_cols=26 Identities=31% Similarity=0.551 Sum_probs=17.6
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.-.|+.||+..-.- --....||.||.
T Consensus 23 ~~~CP~Cg~pLf~l-----k~g~~~Cp~Cg~ 48 (112)
T PRK00420 23 SKHCPVCGLPLFEL-----KDGEVVCPVHGK 48 (112)
T ss_pred cCCCCCCCCcceec-----CCCceECCCCCC
Confidence 36899999665331 123359999998
No 122
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.38 E-value=1.9 Score=38.06 Aligned_cols=26 Identities=15% Similarity=0.575 Sum_probs=21.1
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
....|+|..|.-+|-+ +|. .||+||+
T Consensus 252 v~~GyvCs~Clsi~C~------~p~--~C~~Cgt 277 (279)
T TIGR00627 252 VSIGFVCSVCLSVLCQ------YTP--ICKTCKT 277 (279)
T ss_pred ccceEECCCccCCcCC------CCC--CCCCCCC
Confidence 3446999999999875 466 8999997
No 123
>PF12773 DZR: Double zinc ribbon
Probab=77.30 E-value=1.4 Score=28.14 Aligned_cols=9 Identities=56% Similarity=1.324 Sum_probs=4.9
Q ss_pred CCCCCCCCC
Q 040420 101 YFCPVCGAP 109 (169)
Q Consensus 101 ~~CPvCgap 109 (169)
+.||.||+.
T Consensus 30 ~~C~~Cg~~ 38 (50)
T PF12773_consen 30 KICPNCGAE 38 (50)
T ss_pred CCCcCCcCC
Confidence 456666553
No 124
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=77.14 E-value=1.5 Score=38.10 Aligned_cols=33 Identities=33% Similarity=0.746 Sum_probs=21.9
Q ss_pred CCCeEEcCCCCeeecCCCCCC----CCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFD----QLPDNYFCPVCGAP 109 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~----~lPd~~~CPvCgap 109 (169)
+-..++|..||+.|+...-.. .++. +||.||.+
T Consensus 119 sl~~~~C~~C~~~~~~~~~~~~~~~~~~p--~C~~Cg~~ 155 (250)
T COG0846 119 SLKRVRCSKCGNQYYDEDVIKFIEDGLIP--RCPKCGGP 155 (250)
T ss_pred ceeeeEeCCCcCccchhhhhhhcccCCCC--cCccCCCc
Confidence 344789999998887432111 1233 79999995
No 125
>PRK05638 threonine synthase; Validated
Probab=77.10 E-value=1.5 Score=40.04 Aligned_cols=24 Identities=38% Similarity=0.855 Sum_probs=17.2
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.++|..||..|+.. ..|.| .|+.+
T Consensus 1 ~l~C~~Cg~~~~~~-------~~~~C-~c~~~ 24 (442)
T PRK05638 1 KMKCPKCGREYNSY-------IPPFC-ICGEL 24 (442)
T ss_pred CeEeCCCCCCCCCC-------Cceec-CCCCc
Confidence 37899999998632 12789 79754
No 126
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.08 E-value=1.9 Score=40.34 Aligned_cols=10 Identities=40% Similarity=1.082 Sum_probs=8.3
Q ss_pred CCCCCCCCCc
Q 040420 101 YFCPVCGAPK 110 (169)
Q Consensus 101 ~~CPvCgapK 110 (169)
|.||.||...
T Consensus 254 ~~Cp~C~s~~ 263 (505)
T TIGR00595 254 KTCPQCGSED 263 (505)
T ss_pred CCCCCCCCCe
Confidence 4999999864
No 127
>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=76.71 E-value=1.3 Score=30.09 Aligned_cols=29 Identities=28% Similarity=0.670 Sum_probs=20.5
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..-.|..||++.... .-...|.||.||..
T Consensus 27 TSq~C~~CG~~~~~~----~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKR----RSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccc----cccceEEcCCCCCE
Confidence 345799999887651 12456899999873
No 128
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=76.30 E-value=1.8 Score=45.42 Aligned_cols=32 Identities=38% Similarity=0.901 Sum_probs=21.5
Q ss_pred CeEEcCCCCee--ec-CC-CCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYI--YN-ER-KPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyV--Yd-~~-tpF~~lPd~~~CPvCgap 109 (169)
.-|+|+.|-|- ++ ++ ..-=|||+. .||.||++
T Consensus 913 PHY~Cp~Cky~Ef~~d~svgsGfDLpdK-~CPkCg~p 948 (1444)
T COG2176 913 PHYLCPECKYSEFIDDGSVGSGFDLPDK-DCPKCGTP 948 (1444)
T ss_pred ccccCCCCceeeeecCCCcCCCCCCCCC-CCCcCCCc
Confidence 46999999964 33 21 122356764 89999997
No 129
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=75.91 E-value=1.6 Score=45.48 Aligned_cols=33 Identities=39% Similarity=0.751 Sum_probs=21.8
Q ss_pred CCeEEcCCCCeeecC--C--CCCCCCCCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNE--R--KPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~--~--tpF~~lPd~~~CPvCgap 109 (169)
..-|+|+.|.|.--. + ..-=|||| ..||.||.+
T Consensus 681 ~phy~c~~c~~~ef~~~~~~~sg~dlp~-k~cp~c~~~ 717 (1213)
T TIGR01405 681 PPHYLCPNCKYSEFITDGSVGSGFDLPD-KDCPKCGAP 717 (1213)
T ss_pred cccccCcccccccccccccccccccCcc-ccCcccccc
Confidence 346999999974211 0 12236777 499999985
No 130
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=75.37 E-value=1.2 Score=30.04 Aligned_cols=30 Identities=37% Similarity=1.065 Sum_probs=21.0
Q ss_pred eEEcCCCC--eeecC-------CCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCG--YIYNE-------RKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CG--yVYd~-------~tpF~~lPd~~~CPvCgap 109 (169)
..+|.+|| +|+.. +.-|+..|. +||.|...
T Consensus 4 ~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~--RC~~CR~~ 42 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAGEQKFYAEKGFDNEPK--RCPSCRQA 42 (49)
T ss_pred eEEcccCCCeEEEehhHHHHHHhcCCcCCCc--cCHHHHHH
Confidence 57999999 33332 234766788 99999753
No 131
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=74.40 E-value=2.4 Score=34.95 Aligned_cols=34 Identities=24% Similarity=0.562 Sum_probs=21.8
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
....+|..|+++|+......+ .....||.||..-
T Consensus 107 ~~~~~C~~C~~~~~~~~~~~~-~~~p~C~~Cgg~l 140 (224)
T cd01412 107 LFRVRCSSCGYVGENNEEIPE-EELPRCPKCGGLL 140 (224)
T ss_pred cCccccCCCCCCCCcchhhhc-cCCCCCCCCCCcc
Confidence 346799999998876421111 1224799999743
No 132
>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=74.05 E-value=2 Score=32.38 Aligned_cols=21 Identities=14% Similarity=0.562 Sum_probs=11.5
Q ss_pred eecCCCCeEEcCCCCeeecCC
Q 040420 71 MRVASKQAYICRDCGYIYNER 91 (169)
Q Consensus 71 ~k~~~~~~y~C~~CGyVYd~~ 91 (169)
++.....+|+|..||+++.++
T Consensus 46 vkR~a~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 46 VKRVATGIWKCKKCGKKFAGG 66 (90)
T ss_dssp EEEEETTEEEETTTTEEEE-B
T ss_pred eEEeeeEEeecCCCCCEEeCC
Confidence 444555566666666666554
No 133
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.45 E-value=1.5 Score=36.16 Aligned_cols=24 Identities=29% Similarity=0.618 Sum_probs=17.2
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
...=.|..||+ . -...|.||.||.
T Consensus 307 ~tS~~C~~cg~---~------~~r~~~C~~cg~ 330 (364)
T COG0675 307 YTSKTCPCCGH---L------SGRLFKCPRCGF 330 (364)
T ss_pred CCcccccccCC---c------cceeEECCCCCC
Confidence 33458999998 1 034589999997
No 134
>PF14353 CpXC: CpXC protein
Probab=73.11 E-value=1.8 Score=32.74 Aligned_cols=8 Identities=50% Similarity=1.593 Sum_probs=4.1
Q ss_pred CCCCCCCC
Q 040420 101 YFCPVCGA 108 (169)
Q Consensus 101 ~~CPvCga 108 (169)
++||.||+
T Consensus 39 ~~CP~Cg~ 46 (128)
T PF14353_consen 39 FTCPSCGH 46 (128)
T ss_pred EECCCCCC
Confidence 45555554
No 135
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=73.08 E-value=2.5 Score=33.63 Aligned_cols=26 Identities=35% Similarity=0.952 Sum_probs=21.9
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.+..|.|.-||.-|.++ . .||.|+.+
T Consensus 94 ~~~~W~Cv~C~~~Y~Ge-------K--~C~~C~tG 119 (128)
T PF11682_consen 94 RKTDWHCVMCGNHYHGE-------K--YCPKCGTG 119 (128)
T ss_pred cCceEEEecCCCccCcC-------E--ecCCCCCc
Confidence 55689999999999885 2 89999874
No 136
>PRK05580 primosome assembly protein PriA; Validated
Probab=72.54 E-value=2.8 Score=40.60 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=8.6
Q ss_pred CCCCCCCCCCc
Q 040420 100 NYFCPVCGAPK 110 (169)
Q Consensus 100 ~~~CPvCgapK 110 (169)
.|.||.||...
T Consensus 421 ~~~Cp~Cg~~~ 431 (679)
T PRK05580 421 PKACPECGSTD 431 (679)
T ss_pred CCCCCCCcCCe
Confidence 34999998864
No 137
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=71.82 E-value=1.3 Score=36.70 Aligned_cols=34 Identities=21% Similarity=0.481 Sum_probs=20.9
Q ss_pred CCeEEcCCCCeeecCCCCCCCC---CCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNERKPFDQL---PDNYFCPVCGAP 109 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~l---Pd~~~CPvCgap 109 (169)
....+|..|+++|+-....+.+ .....||.||..
T Consensus 93 ~~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 93 MFIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGI 129 (206)
T ss_pred cCcccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCc
Confidence 3467999999888643211111 112469999875
No 138
>PRK08329 threonine synthase; Validated
Probab=71.66 E-value=2.1 Score=37.82 Aligned_cols=23 Identities=35% Similarity=0.876 Sum_probs=16.7
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
++|..||..|+.. ..|.| .|+.+
T Consensus 2 l~C~~Cg~~~~~~-------~~~~C-~c~~~ 24 (347)
T PRK08329 2 LRCTKCGRTYEEK-------FKLRC-DCGGT 24 (347)
T ss_pred cCcCCCCCCcCCC-------Cceec-CCCCc
Confidence 6899999988642 12689 69765
No 139
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=71.15 E-value=2.8 Score=23.55 Aligned_cols=24 Identities=29% Similarity=0.791 Sum_probs=16.9
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.|+|..|++.=. ++...|-.|+.+
T Consensus 2 ~W~C~~C~~~N~--------~~~~~C~~C~~p 25 (26)
T smart00547 2 DWECPACTFLNF--------ASRSKCFACGAP 25 (26)
T ss_pred cccCCCCCCcCh--------hhhccccccCCc
Confidence 589999985532 344588888875
No 140
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=71.12 E-value=1.8 Score=31.07 Aligned_cols=27 Identities=30% Similarity=0.664 Sum_probs=19.6
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-+|++||++-. =|+.......|++||.
T Consensus 20 VkCpdC~N~q~---vFshast~V~C~~CG~ 46 (67)
T COG2051 20 VKCPDCGNEQV---VFSHASTVVTCLICGT 46 (67)
T ss_pred EECCCCCCEEE---EeccCceEEEeccccc
Confidence 48999997642 2444455679999998
No 141
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=70.91 E-value=4.3 Score=37.23 Aligned_cols=32 Identities=19% Similarity=0.537 Sum_probs=21.3
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
.=.|..||.+++.. +. +..+...||.||+.-.
T Consensus 13 ~~~C~~Cd~l~~~~-~l-~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 13 HILCSQCDMLVALP-RI-ESGQKAACPRCGTTLT 44 (403)
T ss_pred eeeCCCCCCccccc-CC-CCCCeeECCCCCCCCc
Confidence 34699999998653 11 1134458999999653
No 142
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=70.88 E-value=2.8 Score=31.58 Aligned_cols=22 Identities=9% Similarity=0.324 Sum_probs=12.3
Q ss_pred ceecCCCCeEEcCCCCeeecCC
Q 040420 70 SMRVASKQAYICRDCGYIYNER 91 (169)
Q Consensus 70 ~~k~~~~~~y~C~~CGyVYd~~ 91 (169)
.++.....+|.|..||+++.++
T Consensus 46 ~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 46 AVKRQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred ceeeeeeEEEEcCCCCCEEeCC
Confidence 3444455566666666666554
No 143
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=70.70 E-value=2.3 Score=33.26 Aligned_cols=25 Identities=28% Similarity=0.844 Sum_probs=19.4
Q ss_pred EcCCCC--eeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 80 ICRDCG--YIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 80 ~C~~CG--yVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
.|+.|+ |+|+.++ -+.||.|.+.-.
T Consensus 5 ~cp~c~sEytYed~~-------~~~cpec~~ew~ 31 (112)
T COG2824 5 PCPKCNSEYTYEDGG-------QLICPECAHEWN 31 (112)
T ss_pred CCCccCCceEEecCc-------eEeCchhccccc
Confidence 589997 8887753 469999998654
No 144
>PLN02569 threonine synthase
Probab=70.37 E-value=3.3 Score=38.80 Aligned_cols=30 Identities=17% Similarity=0.052 Sum_probs=21.1
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
.....++|..||..|+.. +-.|+| .||.+-
T Consensus 45 ~~~~~l~C~~Cg~~y~~~------~~~~~C-~cgg~l 74 (484)
T PLN02569 45 KYVPFLECPLTGEKYSLD------EVVYRS-KSGGLL 74 (484)
T ss_pred ccccccEeCCCCCcCCCc------cccccC-CCCCeE
Confidence 334468999999999764 335799 697543
No 145
>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=70.20 E-value=2.7 Score=31.74 Aligned_cols=22 Identities=23% Similarity=0.634 Sum_probs=12.9
Q ss_pred ceecCCCCeEEcCCCCeeecCC
Q 040420 70 SMRVASKQAYICRDCGYIYNER 91 (169)
Q Consensus 70 ~~k~~~~~~y~C~~CGyVYd~~ 91 (169)
.++.....+|+|..||+++.++
T Consensus 45 ~vkR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 45 TVKRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred ceEEEeeEEEEcCCCCCEEeCC
Confidence 3444555566666666666554
No 146
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=70.16 E-value=5 Score=27.47 Aligned_cols=20 Identities=50% Similarity=1.311 Sum_probs=15.8
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.|..|+ +|. |-| .||.||.+
T Consensus 7 ~c~~~~-~YT-------Lk~--~cp~cG~~ 26 (53)
T PF04135_consen 7 KCPGCR-VYT-------LKD--KCPPCGGP 26 (53)
T ss_dssp ECTTTC-EEE-------SSS--BBTTTSSB
T ss_pred cCCCCC-cEe-------CCC--ccCCCCCC
Confidence 599999 885 345 89999984
No 147
>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=70.06 E-value=1.8 Score=34.42 Aligned_cols=30 Identities=30% Similarity=0.726 Sum_probs=20.2
Q ss_pred eEEcCCCCeeecCCCC----CCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKP----FDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tp----F~~lPd~~~CPvCgap 109 (169)
..+|..||+.|+...- ..+.+. .||.|+..
T Consensus 105 ~~~C~~C~~~~~~~~~~~~~~~~~~~--~C~~C~~~ 138 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVDSIDEEEPP--RCPKCGGL 138 (178)
T ss_dssp EEEETTTSBEEEGHHHHHHHHTTSSC--BCTTTSCB
T ss_pred eeeecCCCccccchhhcccccccccc--cccccCcc
Confidence 6799999999976310 011123 89999983
No 148
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=69.29 E-value=1.2 Score=37.80 Aligned_cols=33 Identities=27% Similarity=0.615 Sum_probs=20.3
Q ss_pred CeEEcCCCCeeecCCCCCCCC--CCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQL--PDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~l--Pd~~~CPvCgap 109 (169)
..++|..|++.|+-......+ .+-..||.||..
T Consensus 118 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 118 EEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGL 152 (244)
T ss_pred CeeEECCCCCcccHHHHHHHHhcCCCCCCCCCCCe
Confidence 467999999998752111100 112369999974
No 149
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=69.24 E-value=3.4 Score=33.60 Aligned_cols=21 Identities=29% Similarity=0.985 Sum_probs=15.7
Q ss_pred CCCCCCCC-CCCCCCCCCCccC
Q 040420 92 KPFDQLPD-NYFCPVCGAPKRR 112 (169)
Q Consensus 92 tpF~~lPd-~~~CPvCgapK~~ 112 (169)
-|...+|+ +|.||.|...+..
T Consensus 9 Ppl~~~P~g~W~Cp~C~~~~~~ 30 (148)
T cd04718 9 PPLKEVPEGDWICPFCEVEKSG 30 (148)
T ss_pred CCCCCCCCCCcCCCCCcCCCCC
Confidence 46667776 7999999875543
No 150
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=68.98 E-value=3 Score=26.48 Aligned_cols=14 Identities=36% Similarity=0.876 Sum_probs=8.8
Q ss_pred CCeEEcCCCCeeec
Q 040420 76 KQAYICRDCGYIYN 89 (169)
Q Consensus 76 ~~~y~C~~CGyVYd 89 (169)
.+.|+|..||.|..
T Consensus 4 ~~~YkC~~CGniVe 17 (36)
T PF06397_consen 4 GEFYKCEHCGNIVE 17 (36)
T ss_dssp TEEEE-TTT--EEE
T ss_pred ccEEEccCCCCEEE
Confidence 46899999998874
No 151
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=68.97 E-value=4.1 Score=37.61 Aligned_cols=27 Identities=22% Similarity=0.477 Sum_probs=19.4
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
...-.|..||.++.++ .-.||.||+.-
T Consensus 219 ~~l~~C~~Cd~l~~~~--------~a~CpRC~~~L 245 (419)
T PRK15103 219 QGLRSCSCCTAILPAD--------QPVCPRCHTKG 245 (419)
T ss_pred cCCCcCCCCCCCCCCC--------CCCCCCCCCcC
Confidence 3444699999987542 22899999954
No 152
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=68.21 E-value=3.6 Score=34.42 Aligned_cols=29 Identities=17% Similarity=0.394 Sum_probs=20.0
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
...+|..|+..|+-. +.-+...||.||..
T Consensus 117 ~~~~C~~C~~~~~~~----~~~~~p~C~~Cgg~ 145 (225)
T cd01411 117 YRIYCTVCGKTVDWE----EYLKSPYHAKCGGV 145 (225)
T ss_pred CeeEeCCCCCccchh----hcCCCCCCCCCCCE
Confidence 367999999888643 22122479999975
No 153
>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=67.95 E-value=3.4 Score=42.57 Aligned_cols=26 Identities=31% Similarity=0.672 Sum_probs=18.2
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
+....+|+.||.. . + .++||.||...
T Consensus 622 ev~~RKCPkCG~y-T-------l--k~rCP~CG~~T 647 (1095)
T TIGR00354 622 EIAIRKCPQCGKE-S-------F--WLKCPVCGELT 647 (1095)
T ss_pred EEEEEECCCCCcc-c-------c--cccCCCCCCcc
Confidence 4457899999932 1 1 23899999873
No 154
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=67.77 E-value=2.3 Score=32.06 Aligned_cols=22 Identities=18% Similarity=0.575 Sum_probs=18.3
Q ss_pred ceecCCCCeEEcCCCCeeecCC
Q 040420 70 SMRVASKQAYICRDCGYIYNER 91 (169)
Q Consensus 70 ~~k~~~~~~y~C~~CGyVYd~~ 91 (169)
.-+.....+|+|..|||++-++
T Consensus 45 ~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 45 TVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred ceeeeccCeEEcCCCCCeeccc
Confidence 4456678899999999999885
No 155
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=67.57 E-value=2.1 Score=28.28 Aligned_cols=10 Identities=40% Similarity=1.427 Sum_probs=3.4
Q ss_pred CCCCCCCCCC
Q 040420 100 NYFCPVCGAP 109 (169)
Q Consensus 100 ~~~CPvCgap 109 (169)
.|.||+|+.+
T Consensus 41 ~W~CPiC~~~ 50 (50)
T PF02891_consen 41 KWKCPICNKP 50 (50)
T ss_dssp --B-TTT---
T ss_pred CeECcCCcCc
Confidence 3888888753
No 156
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=67.25 E-value=8.4 Score=29.48 Aligned_cols=42 Identities=24% Similarity=0.297 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCCCCccCeeeCCCcccCCCChhHHHHHHHHHhh
Q 040420 96 QLPDNYFCPVCGAPKRRFRPYTPAVTRGANDTAVRKARKEQIQ 138 (169)
Q Consensus 96 ~lPd~~~CPvCgapK~~F~~~~~~~~~~~n~~~v~~ar~~~~~ 138 (169)
+-|--|+|..|++--+-+..-....+ .-.+..+|.+|++..+
T Consensus 27 ~~~~~y~C~~C~AyVG~H~~t~~PlG-tLAd~~lR~~R~~ah~ 68 (102)
T PF11672_consen 27 DGPYLYVCTPCDAYVGCHPGTDIPLG-TLADAELRRARKAAHR 68 (102)
T ss_pred CCceeEECCCCCceeeeeCCCCCcCc-ccCCHHHHHHHHHHHH
Confidence 33444788888776555553322222 3456778888874433
No 157
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=67.24 E-value=4.6 Score=24.87 Aligned_cols=28 Identities=25% Similarity=0.440 Sum_probs=16.0
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
+.|+|..||.--.-- +-.+.++|+-||.
T Consensus 2 ~~~~C~~C~~~~i~~----~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVN----KEDDYEVCIFCGS 29 (33)
T ss_pred CceEcCCCCCCeEEE----ecCCeEEcccCCc
Confidence 457888888432110 1135568888876
No 158
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=67.17 E-value=4.7 Score=37.45 Aligned_cols=37 Identities=27% Similarity=0.493 Sum_probs=24.7
Q ss_pred cCCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeC
Q 040420 73 VASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPY 116 (169)
Q Consensus 73 ~~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~ 116 (169)
-++...|+|.+|++- +. -...-.||.||+....-+.+
T Consensus 52 YAd~~i~kC~~c~~~-~~------y~~~~~C~~cg~~~~l~R~V 88 (415)
T COG5257 52 YADAKIYKCPECYRP-EC------YTTEPKCPNCGAETELVRRV 88 (415)
T ss_pred cccCceEeCCCCCCC-cc------cccCCCCCCCCCCccEEEEE
Confidence 457789999999953 11 12223899999988554443
No 159
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=67.02 E-value=3.1 Score=35.46 Aligned_cols=40 Identities=13% Similarity=0.312 Sum_probs=23.0
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCC---CCccCeeeCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCG---APKRRFRPYTP 118 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCg---apK~~F~~~~~ 118 (169)
..++|..|++.|+-...... +...||.|| .-|-...-+.+
T Consensus 116 ~~~~C~~C~~~~~~~~~~~~--~~p~C~~Cg~~g~lrP~vV~FGE 158 (242)
T PTZ00408 116 LKVRCTATGHVFDWTEDVVH--GSSRCKCCGCVGTLRPHIVWFGE 158 (242)
T ss_pred ceEEECCCCcccCchhhhhc--CCCccccCCCCCCCCCCEEEcCC
Confidence 36899999988864211111 124799997 23444444443
No 160
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=66.97 E-value=7.5 Score=38.64 Aligned_cols=17 Identities=35% Similarity=0.935 Sum_probs=12.5
Q ss_pred CCCCCCCCCCCCCCCccCe
Q 040420 95 DQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 95 ~~lPd~~~CPvCgapK~~F 113 (169)
+..|. .||.||...-++
T Consensus 472 ~~~p~--~Cp~Cgs~~L~~ 488 (730)
T COG1198 472 EPIPQ--SCPECGSEHLRA 488 (730)
T ss_pred CCCCC--CCCCCCCCeeEE
Confidence 45688 999999984333
No 161
>PRK14526 adenylate kinase; Provisional
Probab=66.86 E-value=4.2 Score=33.72 Aligned_cols=30 Identities=27% Similarity=0.573 Sum_probs=21.0
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
..+.|+.||.+|+-. |...+..-.|.+|+.
T Consensus 121 ~R~~~~~~g~~y~~~--~~pp~~~~~~~~~~~ 150 (211)
T PRK14526 121 GRRICKSCNNIFNIY--TLPTKEKGICDVCKG 150 (211)
T ss_pred CCCcccccCCccccc--cCCCCccCcCCCCCC
Confidence 478899999999864 222233348999975
No 162
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=66.42 E-value=4.2 Score=27.65 Aligned_cols=28 Identities=32% Similarity=0.790 Sum_probs=19.0
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
.....-.|..||...- |- .+||.||.=+
T Consensus 22 ~~p~l~~C~~cG~~~~--------~H-~vc~~cG~Y~ 49 (55)
T TIGR01031 22 TAPTLVVCPNCGEFKL--------PH-RVCPSCGYYK 49 (55)
T ss_pred cCCcceECCCCCCccc--------Ce-eECCccCeEC
Confidence 3455678999995443 32 4999999633
No 163
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=66.42 E-value=3.9 Score=31.83 Aligned_cols=32 Identities=31% Similarity=0.709 Sum_probs=23.0
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
+-.|+|..||..|--.....+ +..|+|-.|+.
T Consensus 110 ~~~y~C~~C~~~~~~~rr~~~-~~~y~C~~C~g 141 (146)
T smart00731 110 KYPYRCTGCGQRYLRVRRSNN-VSRYRCGKCGG 141 (146)
T ss_pred eEEEECCCCCCCCceEccccC-cceEEcCCCCC
Confidence 448999999987754333333 36799999986
No 164
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=66.40 E-value=4.5 Score=28.41 Aligned_cols=30 Identities=27% Similarity=0.753 Sum_probs=20.4
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
....+|..||..-.+. +. -..|.||.||..
T Consensus 5 ~~~~~CtSCg~~i~~~---~~-~~~F~CPnCG~~ 34 (59)
T PRK14890 5 MEPPKCTSCGIEIAPR---EK-AVKFLCPNCGEV 34 (59)
T ss_pred ccCccccCCCCcccCC---Cc-cCEeeCCCCCCe
Confidence 4457899999766543 11 235799999873
No 165
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=66.22 E-value=1.9 Score=36.42 Aligned_cols=21 Identities=38% Similarity=0.792 Sum_probs=0.0
Q ss_pred eEEcCCCC-eeecCCCCCCCCC
Q 040420 78 AYICRDCG-YIYNERKPFDQLP 98 (169)
Q Consensus 78 ~y~C~~CG-yVYd~~tpF~~lP 98 (169)
.|.|.+|| ++|-++..|++--
T Consensus 101 ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 101 EYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ----------------------
T ss_pred eeeeEeCCCcceecHHHHHHhc
Confidence 59999999 6798877666643
No 166
>PRK04011 peptide chain release factor 1; Provisional
Probab=65.68 E-value=4.7 Score=36.99 Aligned_cols=32 Identities=28% Similarity=0.670 Sum_probs=20.4
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.|+|.+||+.-..-..-.+..+...||.||..
T Consensus 328 ~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~ 359 (411)
T PRK04011 328 TYKCPNCGYEEEKTVKRREELPEKTCPKCGSE 359 (411)
T ss_pred EEEcCCCCcceeeecccccccccccCcccCcc
Confidence 68999999765431111122455699999974
No 167
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=65.66 E-value=1.7 Score=27.59 Aligned_cols=26 Identities=38% Similarity=0.919 Sum_probs=14.7
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
..+..|..||++-+. + .|++|..+++
T Consensus 15 ~~i~~C~~C~nlse~--------~--~C~IC~d~~R 40 (41)
T PF02132_consen 15 ENIKFCSICGNLSEE--------D--PCEICSDPKR 40 (41)
T ss_dssp HH-EE-SSS--EESS--------S--S-HHHH-TTS
T ss_pred HcCCccCCCCCcCCC--------C--cCcCCCCCCC
Confidence 346899999987764 2 8999987664
No 168
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=65.25 E-value=3.8 Score=30.86 Aligned_cols=22 Identities=18% Similarity=0.548 Sum_probs=12.9
Q ss_pred ceecCCCCeEEcCCCCeeecCC
Q 040420 70 SMRVASKQAYICRDCGYIYNER 91 (169)
Q Consensus 70 ~~k~~~~~~y~C~~CGyVYd~~ 91 (169)
.++.....+|.|..||+++.++
T Consensus 46 ~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 46 KVKRVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred ceEEEEEEEEEcCCCCCEEeCC
Confidence 3444555566666666666554
No 169
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=65.00 E-value=5.6 Score=39.42 Aligned_cols=36 Identities=25% Similarity=0.553 Sum_probs=24.7
Q ss_pred cCCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC-ccCeeeC
Q 040420 73 VASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP-KRRFRPY 116 (169)
Q Consensus 73 ~~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap-K~~F~~~ 116 (169)
-.....=+|..|||.++.. .+ .||.||.. .+-+.++
T Consensus 636 ~~n~~i~~C~~cg~~~~~~------~~--~Cp~CG~~dve~~~Ri 672 (700)
T COG1328 636 GYTTPISVCNRCGYSGEGL------RT--RCPKCGSEDVEVFSRI 672 (700)
T ss_pred ecCCCceeeccCCcccccc------cc--cCCCCCCccceeeeee
Confidence 3345567999999999753 45 49999976 4444443
No 170
>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=65.00 E-value=2.6 Score=30.38 Aligned_cols=24 Identities=42% Similarity=1.155 Sum_probs=13.4
Q ss_pred eEEcCCCC-eeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCG-YIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CG-yVYd~~tpF~~lPd~~~CPvCga 108 (169)
+|+| +|| +.|..+. -..-.| +||.
T Consensus 3 ifrC-~Cgr~lya~e~-----~kTkkC-~CG~ 27 (68)
T PF09082_consen 3 IFRC-DCGRYLYAKEG-----AKTKKC-VCGK 27 (68)
T ss_dssp EEEE-TTS--EEEETT------SEEEE-TTTE
T ss_pred EEEe-cCCCEEEecCC-----cceeEe-cCCC
Confidence 5788 788 4554431 122378 8875
No 171
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=64.45 E-value=3 Score=30.78 Aligned_cols=8 Identities=50% Similarity=1.933 Sum_probs=5.8
Q ss_pred CCCCCCCC
Q 040420 101 YFCPVCGA 108 (169)
Q Consensus 101 ~~CPvCga 108 (169)
|+||.||.
T Consensus 32 ~~C~~CGe 39 (127)
T TIGR03830 32 WYCPACGE 39 (127)
T ss_pred eECCCCCC
Confidence 67777766
No 172
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=64.32 E-value=1.4 Score=37.08 Aligned_cols=33 Identities=21% Similarity=0.426 Sum_probs=19.8
Q ss_pred CeEEcCCCCeeecCCCCCCCC--CCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQL--PDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~l--Pd~~~CPvCgap 109 (169)
...+|..|+++|+-......+ .+...||.||..
T Consensus 115 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 149 (235)
T cd01408 115 ATAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGL 149 (235)
T ss_pred CccccccCCCcCCHHHHHHHHhCCCCccCCCCCCC
Confidence 467999999988742100000 012379999864
No 173
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=64.31 E-value=3.9 Score=38.15 Aligned_cols=31 Identities=32% Similarity=0.723 Sum_probs=22.7
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
..|.|..|||.++-.....+.+ .+.||.||.
T Consensus 326 ~~~~c~~~~~e~~~t~~~~~~~-~~~~~~~~~ 356 (411)
T COG1503 326 VTYKCPTCGYENLKSKREFEQK-RFRCPECGS 356 (411)
T ss_pred eeecCCCcchhhhhcccccccc-cccCccccc
Confidence 3799999999987643333334 449999998
No 174
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=64.07 E-value=2.1 Score=39.52 Aligned_cols=26 Identities=27% Similarity=0.669 Sum_probs=19.4
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-|..|...|..+- ...-+|+||.||.
T Consensus 248 AC~rC~t~y~le~---A~~~~wrCpkCGg 273 (403)
T COG1379 248 ACSRCYTRYSLEE---AKSLRWRCPKCGG 273 (403)
T ss_pred HHHHhhhccCcch---hhhhcccCccccc
Confidence 6999998887541 2245799999997
No 175
>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=63.92 E-value=2.3 Score=25.69 Aligned_cols=21 Identities=48% Similarity=1.183 Sum_probs=12.1
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
...|.+||. +..|.||.|+.+
T Consensus 2 ~~~C~vC~~-----------~~kY~Cp~C~~~ 22 (30)
T PF04438_consen 2 RKLCSVCGN-----------PAKYRCPRCGAR 22 (30)
T ss_dssp -EEETSSSS-----------EESEE-TTT--E
T ss_pred cCCCccCcC-----------CCEEECCCcCCc
Confidence 357888884 235789999864
No 176
>PRK14873 primosome assembly protein PriA; Provisional
Probab=63.18 E-value=6.4 Score=38.45 Aligned_cols=14 Identities=36% Similarity=0.990 Sum_probs=10.0
Q ss_pred CCCCCCCCCCccCe
Q 040420 100 NYFCPVCGAPKRRF 113 (169)
Q Consensus 100 ~~~CPvCgapK~~F 113 (169)
.|.||.||...-+.
T Consensus 422 p~~Cp~Cgs~~l~~ 435 (665)
T PRK14873 422 DWRCPRCGSDRLRA 435 (665)
T ss_pred CccCCCCcCCccee
Confidence 45999999865333
No 177
>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=62.94 E-value=3.8 Score=30.01 Aligned_cols=24 Identities=33% Similarity=0.999 Sum_probs=18.3
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
-|+.||.+.... .+.+.||.|+..
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCCc
Confidence 499999887543 246899999974
No 178
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=62.79 E-value=3.2 Score=32.50 Aligned_cols=9 Identities=56% Similarity=1.785 Sum_probs=7.5
Q ss_pred CCCCCCCCC
Q 040420 100 NYFCPVCGA 108 (169)
Q Consensus 100 ~~~CPvCga 108 (169)
.|.||.||.
T Consensus 74 EyyCP~Cgt 82 (112)
T PF08882_consen 74 EYYCPGCGT 82 (112)
T ss_pred EEECCCCcc
Confidence 368999997
No 179
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=62.47 E-value=4.9 Score=33.46 Aligned_cols=32 Identities=28% Similarity=0.606 Sum_probs=19.9
Q ss_pred CeEEcCCCCeeecCCC--CCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERK--PFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~t--pF~~lPd~~~CPvCgap 109 (169)
..++|..||..|+-.. .+.. .....||.||..
T Consensus 112 ~~~~C~~C~~~~~~~~~~~~~~-~~~p~C~~Cgg~ 145 (222)
T cd01413 112 QTAYCVNCGSKYDLEEVKYAKK-HEVPRCPKCGGI 145 (222)
T ss_pred CcceECCCCCCcchhHHHHhcc-CCCCcCCCCCCc
Confidence 4679999998886431 0110 112379999874
No 180
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=62.44 E-value=4.9 Score=42.69 Aligned_cols=33 Identities=33% Similarity=0.671 Sum_probs=22.2
Q ss_pred CCeEEcCCCCeeecC--C--CCCCCCCCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNE--R--KPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~--~--tpF~~lPd~~~CPvCgap 109 (169)
..-|+|+.|.|.--. + ..-=||||. .||.||.+
T Consensus 906 ~phy~C~~C~~~ef~~~~~~~sG~Dlpdk-~Cp~Cg~~ 942 (1437)
T PRK00448 906 PPHYVCPNCKYSEFFTDGSVGSGFDLPDK-DCPKCGTK 942 (1437)
T ss_pred CccccCcccccccccccccccccccCccc-cCcccccc
Confidence 346999999965221 1 122367874 99999985
No 181
>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=62.43 E-value=5.2 Score=41.24 Aligned_cols=28 Identities=32% Similarity=0.649 Sum_probs=23.1
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
+.|.++|..||-.|.. .|=.-.||.||.
T Consensus 1009 srQ~fRC~kC~~kYRR------~PL~G~C~kCGg 1036 (1095)
T TIGR00354 1009 SRQEVRCTKCNTKYRR------IPLVGKCLKCGN 1036 (1095)
T ss_pred hccceeecccCCcccc------CCCCCcccccCC
Confidence 6789999999988864 355559999998
No 182
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=61.59 E-value=6.3 Score=27.04 Aligned_cols=31 Identities=32% Similarity=0.659 Sum_probs=20.8
Q ss_pred cCCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 73 VASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 73 ~~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
........|..||..-- | -.+||.||.-+++
T Consensus 22 l~~~~l~~C~~CG~~~~--------~-H~vC~~CG~Y~gr 52 (57)
T PRK12286 22 LKAPGLVECPNCGEPKL--------P-HRVCPSCGYYKGR 52 (57)
T ss_pred ccCCcceECCCCCCccC--------C-eEECCCCCcCCCE
Confidence 34556789999995442 2 2499999975443
No 183
>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=61.49 E-value=4.1 Score=27.64 Aligned_cols=28 Identities=43% Similarity=0.952 Sum_probs=18.0
Q ss_pred eEEcCCCCeeecCC---CCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNER---KPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~---tpF~~lPd~~~CPvCga 108 (169)
.-+|..|. .+.+- ..|+.+ .|+||.||+
T Consensus 22 aLIC~~C~-~hNGla~~~~~~~i--~y~C~~Cg~ 52 (54)
T PF10058_consen 22 ALICSKCF-SHNGLAPKEEFEEI--QYRCPYCGA 52 (54)
T ss_pred eEECcccc-hhhcccccccCCce--EEEcCCCCC
Confidence 45999998 33332 223333 699999986
No 184
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=61.46 E-value=5.7 Score=36.64 Aligned_cols=31 Identities=19% Similarity=0.607 Sum_probs=20.5
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
-.|..||.+++... . +..+...||.||+.-.
T Consensus 11 ~~C~~Cd~l~~~~~-l-~~g~~a~CpRCg~~L~ 41 (419)
T PRK15103 11 ILCPQCDMLVALPR-L-EHGQKAACPRCGTTLT 41 (419)
T ss_pred ccCCCCCceeecCC-C-CCCCeeECCCCCCCCc
Confidence 56999999986421 0 0123358999999653
No 185
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=61.40 E-value=4.6 Score=33.29 Aligned_cols=34 Identities=26% Similarity=0.632 Sum_probs=12.1
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
.-+...|..||-.|.-. ..++-.++.||.|.-+.
T Consensus 131 ~l~l~~C~~C~~~fv~~--~~~~~~~~~Cp~C~~ps 164 (175)
T PF05280_consen 131 MLQLAPCRRCGGHFVTH--AHDPRHSFVCPFCQPPS 164 (175)
T ss_dssp SEEEEE-TTT--EEEEE--SS--SS----TT-----
T ss_pred CccccCCCCCCCCeECc--CCCCCcCcCCCCCCCcc
Confidence 34578999999544421 12334578999998543
No 186
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=61.30 E-value=7.4 Score=22.15 Aligned_cols=13 Identities=31% Similarity=0.917 Sum_probs=10.3
Q ss_pred CCeEEcCCCCeee
Q 040420 76 KQAYICRDCGYIY 88 (169)
Q Consensus 76 ~~~y~C~~CGyVY 88 (169)
...|.|..||+.|
T Consensus 12 ~k~~~C~~C~k~F 24 (26)
T PF13465_consen 12 EKPYKCPYCGKSF 24 (26)
T ss_dssp SSSEEESSSSEEE
T ss_pred CCCCCCCCCcCee
Confidence 3459999999876
No 187
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=61.17 E-value=13 Score=25.10 Aligned_cols=27 Identities=33% Similarity=0.712 Sum_probs=18.9
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
..+.-.|..||..-- |- .+||.||.-+
T Consensus 23 ~~~l~~c~~cg~~~~--------~H-~vc~~cG~y~ 49 (56)
T PF01783_consen 23 APNLVKCPNCGEPKL--------PH-RVCPSCGYYK 49 (56)
T ss_dssp TTSEEESSSSSSEES--------TT-SBCTTTBBSS
T ss_pred ccceeeeccCCCEec--------cc-EeeCCCCeEC
Confidence 337789999995543 32 4999998533
No 188
>PRK04023 DNA polymerase II large subunit; Validated
Probab=61.08 E-value=5.8 Score=41.12 Aligned_cols=28 Identities=39% Similarity=0.896 Sum_probs=22.8
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
+.|.++|..||-.|.. .|=.-.||.||.
T Consensus 1034 srQ~fRC~kC~~kYRR------~PL~G~C~kCGg 1061 (1121)
T PRK04023 1034 SRQEFRCTKCGAKYRR------PPLSGKCPKCGG 1061 (1121)
T ss_pred cccceeecccCccccc------CCCCCcCccCCC
Confidence 6789999999998864 355559999976
No 189
>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=61.03 E-value=4.6 Score=33.29 Aligned_cols=32 Identities=28% Similarity=0.614 Sum_probs=19.8
Q ss_pred CeEEcCCCCeeecCCCC---CCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKP---FDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tp---F~~lPd~~~CPvCgap 109 (169)
...+|..|++.|..... +.+ ...-.||.||..
T Consensus 108 ~~~~C~~C~~~~~~~~~~~~~~~-~~~p~C~~Cg~~ 142 (218)
T cd01407 108 FRVRCTKCGKEYPRDELQADIDR-EEVPRCPKCGGL 142 (218)
T ss_pred CcceeCCCcCCCcHHHHhHhhcc-CCCCcCCCCCCc
Confidence 46799999988764310 001 112369999975
No 190
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=60.85 E-value=4.5 Score=40.16 Aligned_cols=37 Identities=27% Similarity=0.597 Sum_probs=20.4
Q ss_pred eEEcCCCCeeecCC-----CCCCCCCCCCCCCCCCCCccCee
Q 040420 78 AYICRDCGYIYNER-----KPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 78 ~y~C~~CGyVYd~~-----tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
.-.|.+|||+..=. .-+-.--...+|.-||+....-.
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~ 476 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQ 476 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCC
Confidence 45788888876431 00111113348999998744433
No 191
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=60.75 E-value=18 Score=26.60 Aligned_cols=18 Identities=28% Similarity=0.551 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCCCCccCee
Q 040420 95 DQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 95 ~~lPd~~~CPvCgapK~~F~ 114 (169)
=++.| .|+.||.+-++.+
T Consensus 5 Lk~~~--~C~~CG~d~~~~~ 22 (86)
T PF06170_consen 5 LKVAP--RCPHCGLDYSHAR 22 (86)
T ss_pred ccCCC--cccccCCccccCC
Confidence 34566 8999998554443
No 192
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=60.64 E-value=4.7 Score=34.59 Aligned_cols=41 Identities=15% Similarity=0.336 Sum_probs=32.0
Q ss_pred CCccceecCCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 66 APKFSMRVASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 66 ~p~~~~k~~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
|-+.++..++...|-|.+|-|.-. -+.|.|-+|+..|+--.
T Consensus 12 pkr~akp~~Deg~WdCsvCTFrNs--------AeAfkC~vCdvRKGTST 52 (228)
T KOG4477|consen 12 PKRDAKPNDDEGKWDCSVCTFRNS--------AEAFKCFVCDVRKGTST 52 (228)
T ss_pred ccccCCCccccCceeeeeeeecch--------hhhhheeeecccccccc
Confidence 566777788889999999986543 46689999999876543
No 193
>PHA02942 putative transposase; Provisional
Probab=60.62 E-value=4.4 Score=36.82 Aligned_cols=27 Identities=30% Similarity=0.795 Sum_probs=18.8
Q ss_pred CeEEcCCCCeeecCCCCCCCCC-CCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLP-DNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lP-d~~~CPvCgap 109 (169)
..=.|..||++... +. ..|.||.||..
T Consensus 324 TSq~Cs~CG~~~~~------l~~r~f~C~~CG~~ 351 (383)
T PHA02942 324 SSVSCPKCGHKMVE------IAHRYFHCPSCGYE 351 (383)
T ss_pred CCccCCCCCCccCc------CCCCEEECCCCCCE
Confidence 34579999987632 22 34899999983
No 194
>PRK12495 hypothetical protein; Provisional
Probab=60.34 E-value=4.8 Score=34.94 Aligned_cols=30 Identities=30% Similarity=0.685 Sum_probs=21.5
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..+..+.|.+||.--. .+|...+||+|+..
T Consensus 38 atmsa~hC~~CG~PIp------a~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 38 ATMTNAHCDECGDPIF------RHDGQEFCPTCQQP 67 (226)
T ss_pred cccchhhcccccCccc------CCCCeeECCCCCCc
Confidence 3556789999993321 45777799999863
No 195
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.13 E-value=3.1 Score=36.67 Aligned_cols=44 Identities=23% Similarity=0.538 Sum_probs=28.7
Q ss_pred CCeEEcCCCCeeecCC-----------------CCCCCC-C---CCCCCCCCCC--CccCeeeCCCc
Q 040420 76 KQAYICRDCGYIYNER-----------------KPFDQL-P---DNYFCPVCGA--PKRRFRPYTPA 119 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~-----------------tpF~~l-P---d~~~CPvCga--pK~~F~~~~~~ 119 (169)
+....|++|+.++..+ .-|+++ | +-|+||.|.- =++.|+.+...
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yAaf~sDFe~I~~~ 83 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYAAFKSDFEKIKSY 83 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHHHhhHHHHhhhhc
Confidence 3467999999888752 123332 2 5689999985 45667765433
No 196
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=60.09 E-value=9.8 Score=29.85 Aligned_cols=40 Identities=25% Similarity=0.576 Sum_probs=28.1
Q ss_pred CeEEcCCCCeeecCC-------------------------CCCCCCCCCCCCCCCCCCccCeeeC
Q 040420 77 QAYICRDCGYIYNER-------------------------KPFDQLPDNYFCPVCGAPKRRFRPY 116 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~-------------------------tpF~~lPd~~~CPvCgapK~~F~~~ 116 (169)
-.|-|++|.|+.... -|+=..-.+-.||.||+.+.-|-..
T Consensus 25 L~laCrnCd~ve~A~s~~vY~~~~~~e~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~eavffQ~ 89 (113)
T KOG2691|consen 25 LLLACRNCDYVEEADSSRVYVNELSHEHDELTQIIMDLASDPTLPRTSDKHCPKCGHREAVFFQA 89 (113)
T ss_pred EEEEecCCcceEecCCcceEcCCcccchhhHHHHHHhhccCCCcCccccccCCccCCcceEEEec
Confidence 378999999988761 1321111456899999999888753
No 197
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=59.58 E-value=6.7 Score=23.62 Aligned_cols=15 Identities=40% Similarity=0.778 Sum_probs=12.4
Q ss_pred CCeEEcCCCCeeecC
Q 040420 76 KQAYICRDCGYIYNE 90 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~ 90 (169)
.+.|+|..||.+..-
T Consensus 5 ~~~ykC~~Cgniv~v 19 (34)
T TIGR00319 5 GQVYKCEVCGNIVEV 19 (34)
T ss_pred CcEEEcCCCCcEEEE
Confidence 458999999988853
No 198
>PF15616 TerY-C: TerY-C metal binding domain
Probab=59.56 E-value=6.3 Score=31.44 Aligned_cols=25 Identities=32% Similarity=0.957 Sum_probs=16.8
Q ss_pred eE-EcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AY-ICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y-~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.+ +| .||.++--. . +++..||.||.
T Consensus 88 ~fa~C-~CGkl~Ci~----g-~~~~~CPwCg~ 113 (131)
T PF15616_consen 88 AFAVC-GCGKLFCID----G-EGEVTCPWCGN 113 (131)
T ss_pred cEEEe-cCCCEEEeC----C-CCCEECCCCCC
Confidence 44 45 788775421 1 56789999987
No 199
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=59.30 E-value=6.3 Score=41.61 Aligned_cols=28 Identities=36% Similarity=0.821 Sum_probs=23.1
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
+.|.++|..||-.|.. .|=.-.||.||.
T Consensus 1250 srQ~~RC~kC~~kyRR------~PL~G~C~kCGg 1277 (1337)
T PRK14714 1250 SRQEFRCLKCGTKYRR------MPLAGKCRKCGG 1277 (1337)
T ss_pred hccceeecccCccccc------CCCCCcccccCC
Confidence 6789999999988864 355559999998
No 200
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=58.91 E-value=6.7 Score=29.64 Aligned_cols=19 Identities=21% Similarity=0.684 Sum_probs=13.4
Q ss_pred eecCCCCeEEcCCCCeeec
Q 040420 71 MRVASKQAYICRDCGYIYN 89 (169)
Q Consensus 71 ~k~~~~~~y~C~~CGyVYd 89 (169)
+.......++|..||++|.
T Consensus 72 ~~l~~g~~~rC~eCG~~fk 90 (97)
T cd00924 72 MWLEKGKPKRCPECGHVFK 90 (97)
T ss_pred EEEeCCCceeCCCCCcEEE
Confidence 3444556788888888875
No 201
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=58.33 E-value=5.5 Score=34.64 Aligned_cols=14 Identities=14% Similarity=0.171 Sum_probs=11.3
Q ss_pred CeEEcCCCCeeecC
Q 040420 77 QAYICRDCGYIYNE 90 (169)
Q Consensus 77 ~~y~C~~CGyVYd~ 90 (169)
...+|..||+.|+.
T Consensus 136 ~~~~C~~C~~~~~~ 149 (271)
T PTZ00409 136 FEARCCTCRKTIQL 149 (271)
T ss_pred CcceeCCCCCCccc
Confidence 36799999988764
No 202
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=58.31 E-value=6.3 Score=30.72 Aligned_cols=22 Identities=41% Similarity=1.047 Sum_probs=16.0
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
|.|+.|+-.|- +||- .||+||-
T Consensus 2 Y~CPrC~skvC------~LP~--~CpiCgL 23 (112)
T TIGR00622 2 YFCPQCRAKVC------ELPV--ECPICGL 23 (112)
T ss_pred ccCCCCCCCcc------CCCC--cCCcCCC
Confidence 78888886664 3577 7888875
No 203
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=57.92 E-value=8.4 Score=23.23 Aligned_cols=13 Identities=38% Similarity=0.925 Sum_probs=11.3
Q ss_pred CeEEcCCCCeeec
Q 040420 77 QAYICRDCGYIYN 89 (169)
Q Consensus 77 ~~y~C~~CGyVYd 89 (169)
+.|+|..||.+..
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 5799999998885
No 204
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=57.79 E-value=1.7 Score=28.41 Aligned_cols=31 Identities=26% Similarity=0.266 Sum_probs=17.4
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
+...||++|+...=.+-+-....||+|+.+-
T Consensus 15 v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~ 45 (63)
T smart00504 15 VILPSGQTYERRAIEKWLLSHGTDPVTGQPL 45 (63)
T ss_pred EECCCCCEEeHHHHHHHHHHCCCCCCCcCCC
Confidence 4457899998631000001134899998753
No 205
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=57.77 E-value=6.4 Score=30.94 Aligned_cols=39 Identities=18% Similarity=0.284 Sum_probs=25.7
Q ss_pred cCCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCC
Q 040420 73 VASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYT 117 (169)
Q Consensus 73 ~~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~ 117 (169)
.......+|++||....-. +. -| .|+-|++|-.-....+
T Consensus 64 Stkav~V~CP~C~K~TKmL---Gr-~D--~CM~C~~pLTLd~~le 102 (114)
T PF11023_consen 64 STKAVQVECPNCGKQTKML---GR-VD--ACMHCKEPLTLDPSLE 102 (114)
T ss_pred cccceeeECCCCCChHhhh---ch-hh--ccCcCCCcCccCchhh
Confidence 3344567899999765321 11 25 9999999877666543
No 206
>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p34 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0000439 core TFIIH complex
Probab=57.09 E-value=7 Score=34.23 Aligned_cols=28 Identities=39% Similarity=0.920 Sum_probs=21.9
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCC
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCG 107 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCg 107 (169)
.....|+|.+|--||-.. |++-.||+||
T Consensus 249 ~vd~g~vCsvCLsIfc~~------p~~~~C~tC~ 276 (276)
T PF03850_consen 249 VVDIGYVCSVCLSIFCEF------PDGGICPTCG 276 (276)
T ss_pred cccceeEchhhhhhhhCC------CCCCCCCCCC
Confidence 344589999999999763 6555899997
No 207
>PRK08402 replication factor A; Reviewed
Probab=56.88 E-value=9 Score=34.81 Aligned_cols=32 Identities=22% Similarity=0.491 Sum_probs=22.4
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCC--CCccCee
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCG--APKRRFR 114 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCg--apK~~F~ 114 (169)
..|+.|....... +-...|+|+.|+ .|..+++
T Consensus 213 ~aCp~CnKkv~~~----~~~~~~~Ce~~~~v~p~~ryi 246 (355)
T PRK08402 213 DACPECRRKVDYD----PATDTWICPEHGEVEPIKITI 246 (355)
T ss_pred ecCCCCCeEEEEe----cCCCCEeCCCCCCcCcceeEE
Confidence 4899999877421 124679999999 5665543
No 208
>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=56.71 E-value=5.7 Score=37.73 Aligned_cols=31 Identities=32% Similarity=0.790 Sum_probs=19.8
Q ss_pred EEcCCCCeeecCC---CCCC--CCCC--CCCCCCCCCC
Q 040420 79 YICRDCGYIYNER---KPFD--QLPD--NYFCPVCGAP 109 (169)
Q Consensus 79 y~C~~CGyVYd~~---tpF~--~lPd--~~~CPvCgap 109 (169)
+.|+.||+-+... .-|+ +.|+ .|+||-||..
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~ 238 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCE 238 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCC
Confidence 3999999666542 1111 1233 3899999985
No 209
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=56.70 E-value=9.2 Score=23.64 Aligned_cols=11 Identities=45% Similarity=0.978 Sum_probs=8.1
Q ss_pred EcCCCCeeecC
Q 040420 80 ICRDCGYIYNE 90 (169)
Q Consensus 80 ~C~~CGyVYd~ 90 (169)
.|+.|||+++.
T Consensus 22 ~C~~C~Y~~~~ 32 (35)
T PF02150_consen 22 ACRTCGYEEPI 32 (35)
T ss_dssp EESSSS-EEE-
T ss_pred CCCCCCCccCC
Confidence 89999999864
No 210
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=56.67 E-value=8.5 Score=35.31 Aligned_cols=26 Identities=23% Similarity=0.551 Sum_probs=19.0
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
.-.|..||.+...+ +...||.||+.-
T Consensus 215 ~~~C~~Cd~~~~~~-------~~a~CpRC~~~L 240 (403)
T TIGR00155 215 LRSCSACHTTILPA-------QEPVCPRCSTPL 240 (403)
T ss_pred CCcCCCCCCccCCC-------CCcCCcCCCCcc
Confidence 44699999976442 334899999954
No 211
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=56.45 E-value=6.6 Score=41.91 Aligned_cols=25 Identities=28% Similarity=0.737 Sum_probs=18.6
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
+...++|+.||.+-- ..+||.||..
T Consensus 671 ei~~~~Cp~Cg~~~~----------~~~Cp~CG~~ 695 (1627)
T PRK14715 671 EIAFFKCPKCGKVGL----------YHVCPFCGTR 695 (1627)
T ss_pred EEEeeeCCCCCCccc----------cccCcccCCc
Confidence 344689999996532 1389999987
No 212
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=56.37 E-value=9.8 Score=27.46 Aligned_cols=30 Identities=27% Similarity=0.607 Sum_probs=14.2
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
+.+|-.|-.++.+. +...||.||...-.=+
T Consensus 9 vlrC~aCf~~t~~~-------~k~FCp~CGn~TL~rv 38 (73)
T PF08772_consen 9 VLRCHACFKITKDM-------TKQFCPKCGNATLKRV 38 (73)
T ss_dssp EEE-SSS--EES-S-------S--S-SSS--S--EEE
T ss_pred eEEccccccCcCCC-------CceeCcccCCCcceEE
Confidence 56999999999753 3349999999744333
No 213
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=55.64 E-value=8.8 Score=34.25 Aligned_cols=13 Identities=38% Similarity=1.076 Sum_probs=6.1
Q ss_pred eEEcCCCCeeecC
Q 040420 78 AYICRDCGYIYNE 90 (169)
Q Consensus 78 ~y~C~~CGyVYd~ 90 (169)
.++|..||.+|..
T Consensus 161 a~~C~~C~K~YvS 173 (279)
T KOG2462|consen 161 AFSCKYCGKVYVS 173 (279)
T ss_pred cccCCCCCceeee
Confidence 4445555544443
No 214
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.18 E-value=7.4 Score=36.46 Aligned_cols=34 Identities=26% Similarity=0.675 Sum_probs=17.5
Q ss_pred eEEcCCCCeeecCC-----CCCCCCCCCCCCCCCCCCcc
Q 040420 78 AYICRDCGYIYNER-----KPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 78 ~y~C~~CGyVYd~~-----tpF~~lPd~~~CPvCgapK~ 111 (169)
...|..||++..=. .-+.+-.....|..||....
T Consensus 213 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred eeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCC
Confidence 45888888775320 00111122346777776544
No 215
>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=54.81 E-value=7.9 Score=24.79 Aligned_cols=15 Identities=47% Similarity=1.249 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCCccC
Q 040420 98 PDNYFCPVCGAPKRR 112 (169)
Q Consensus 98 Pd~~~CPvCgapK~~ 112 (169)
|+.++||-||+.+..
T Consensus 16 ~~g~~CP~Cg~~~~~ 30 (46)
T PF12760_consen 16 PDGFVCPHCGSTKHY 30 (46)
T ss_pred CCCCCCCCCCCeeeE
Confidence 555678888776333
No 216
>cd00296 SIR2 SIR2 superfamily 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. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=54.47 E-value=8.6 Score=31.06 Aligned_cols=33 Identities=24% Similarity=0.595 Sum_probs=21.2
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
-...+|..|+.+|+...-... .....||.|+..
T Consensus 111 ~~~~~C~~C~~~~~~~~~~~~-~~~p~C~~C~~~ 143 (222)
T cd00296 111 LDRVRCTSCGKEYPRDEVLER-EKPPRCPKCGGL 143 (222)
T ss_pred CCccEECCCCCCcchhhhhhc-cCCCCCCCCCCc
Confidence 346799999988765422211 223479999864
No 217
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=54.41 E-value=1.6 Score=29.74 Aligned_cols=30 Identities=20% Similarity=0.481 Sum_probs=15.0
Q ss_pred CeEEcCCCCeeecCCC--CCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERK--PFDQLPDNYFCPVC 106 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~t--pF~~lPd~~~CPvC 106 (169)
+-++...|||+|+..- .+-.--....||+-
T Consensus 23 ~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv~ 54 (57)
T PF11789_consen 23 DPVKSKKCGHTFEKEAILQYIQRNGSKRCPVA 54 (57)
T ss_dssp SEEEESSS--EEEHHHHHHHCTTTS-EE-SCC
T ss_pred CCcCcCCCCCeecHHHHHHHHHhcCCCCCCCC
Confidence 4578889999999731 00011234589983
No 218
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=54.31 E-value=3.6 Score=38.40 Aligned_cols=19 Identities=42% Similarity=1.097 Sum_probs=15.9
Q ss_pred eEEcCCCC-eeecCCCCCCC
Q 040420 78 AYICRDCG-YIYNERKPFDQ 96 (169)
Q Consensus 78 ~y~C~~CG-yVYd~~tpF~~ 96 (169)
.|.|.+|| |||.++..|+.
T Consensus 374 ef~CEICgNyvy~GR~~Fdr 393 (470)
T COG5188 374 EFECEICGNYVYYGRDRFDR 393 (470)
T ss_pred ceeeeecccccccchHHHHh
Confidence 59999999 99999766554
No 219
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=54.22 E-value=9.2 Score=25.48 Aligned_cols=23 Identities=35% Similarity=0.912 Sum_probs=11.2
Q ss_pred EcCCCCe-eecCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGY-IYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 80 ~C~~CGy-VYd~~tpF~~lPd~~~CPvCga 108 (169)
.|+.||. ..... -+.|.|+.||-
T Consensus 22 fCP~Cg~~~m~~~------~~r~~C~~Cgy 45 (50)
T PRK00432 22 FCPRCGSGFMAEH------LDRWHCGKCGY 45 (50)
T ss_pred cCcCCCcchhecc------CCcEECCCcCC
Confidence 4555555 43332 14455555553
No 220
>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=53.85 E-value=8 Score=30.30 Aligned_cols=19 Identities=32% Similarity=0.732 Sum_probs=15.2
Q ss_pred CCeEEcCCCCeeecCCCCC
Q 040420 76 KQAYICRDCGYIYNERKPF 94 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF 94 (169)
...|+|..||.+|=+|+=|
T Consensus 122 ~~f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHW 140 (147)
T ss_pred CeEEECCCCCCEecccccH
Confidence 3489999999999887543
No 221
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=53.83 E-value=8.7 Score=41.09 Aligned_cols=27 Identities=41% Similarity=0.988 Sum_probs=21.9
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
+.|.++| .||-.|.. .|-.-.||.||.
T Consensus 1539 srQ~~RC-kC~~kyRR------~PL~G~C~kCGg 1565 (1627)
T PRK14715 1539 SRQEFRC-KCGAKYRR------VPLKGKCPKCGS 1565 (1627)
T ss_pred hccceee-cCCCcccc------CCCCCcCcccCC
Confidence 6689999 99988864 355559999998
No 222
>smart00350 MCM minichromosome maintenance proteins.
Probab=53.61 E-value=12 Score=34.95 Aligned_cols=33 Identities=24% Similarity=0.741 Sum_probs=21.1
Q ss_pred CCeEEcCCCCeeecCCC-CC-CCCCCCCCCCC--CCCCc
Q 040420 76 KQAYICRDCGYIYNERK-PF-DQLPDNYFCPV--CGAPK 110 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~t-pF-~~lPd~~~CPv--CgapK 110 (169)
...|+|..||+.+.... .+ -..|. .||. |+..+
T Consensus 35 ~~~f~C~~C~~~~~~~~~~~~~~~p~--~C~~~~C~~~~ 71 (509)
T smart00350 35 RASFTCEKCGATLGPEIQSGRETEPT--VCPPRECQSPT 71 (509)
T ss_pred EEEEEecCCCCEEeEEecCCcccCCC--cCCCCcCCCCC
Confidence 45799999997653211 11 12355 8998 98764
No 223
>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=53.48 E-value=3.7 Score=28.06 Aligned_cols=30 Identities=20% Similarity=0.480 Sum_probs=19.4
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
+.++|..|+..--....+.++.- .||-|+.
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leI--KCpRC~t 32 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEI--KCPRCKT 32 (51)
T ss_pred cceeccchhHHHhhhcCccEEEE--ECCCCCc
Confidence 35799999955433223444434 8999987
No 224
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=53.47 E-value=13 Score=33.84 Aligned_cols=27 Identities=37% Similarity=0.843 Sum_probs=18.9
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-.|.|..||+...... ..+. .||.|+.
T Consensus 243 ~~~~C~~c~~~~~~~~---~~~~--~C~~c~~ 269 (382)
T PRK04338 243 YVYYCPKCLYREEVEG---LPPE--ECPVCGG 269 (382)
T ss_pred eEEECCCCCcEEEecC---CCCC--CCCCCCC
Confidence 3789999997654321 2344 8999976
No 225
>PTZ00088 adenylate kinase 1; Provisional
Probab=53.45 E-value=25 Score=29.61 Aligned_cols=33 Identities=27% Similarity=0.576 Sum_probs=21.1
Q ss_pred CeEEcCCCCeeecCCC----CCCCCC--CCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERK----PFDQLP--DNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~t----pF~~lP--d~~~CPvCgap 109 (169)
..++|+.||.+|+... +++..| ....|..|+..
T Consensus 129 ~Rr~~~~~g~~y~~~~~~~~~~~~pp~~~~~~c~~~~~~ 167 (229)
T PTZ00088 129 GRRICNTCNRNFNIAHIRSDPYDMPPILPPADCEGCKGN 167 (229)
T ss_pred cCcCCCccCCcceecccccccccCCCCCCCCcccccCCc
Confidence 3689999999997631 121111 13489999863
No 226
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=53.40 E-value=2 Score=40.79 Aligned_cols=24 Identities=42% Similarity=1.010 Sum_probs=17.9
Q ss_pred eEEcCCCC-eeecCCCCCCCCCCCC
Q 040420 78 AYICRDCG-YIYNERKPFDQLPDNY 101 (169)
Q Consensus 78 ~y~C~~CG-yVYd~~tpF~~lPd~~ 101 (169)
.|.|.+|| |+|.++..|+.--..|
T Consensus 401 ey~CEICGNy~Y~GrkaF~RHF~Ew 425 (497)
T KOG2636|consen 401 EYNCEICGNYVYKGRKAFDRHFNEW 425 (497)
T ss_pred ccceeeccCccccCcHHHHHHhHHH
Confidence 79999999 9999976665543333
No 227
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=53.21 E-value=6.2 Score=35.37 Aligned_cols=14 Identities=43% Similarity=1.194 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCccC
Q 040420 99 DNYFCPVCGAPKRR 112 (169)
Q Consensus 99 d~~~CPvCgapK~~ 112 (169)
.+|+||+||+..++
T Consensus 267 R~YVCPiCGATgDn 280 (318)
T KOG4602|consen 267 RSYVCPICGATGDN 280 (318)
T ss_pred hhhcCccccccCCc
Confidence 46999999996654
No 228
>PRK14748 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=52.82 E-value=19 Score=22.02 Aligned_cols=20 Identities=15% Similarity=0.167 Sum_probs=14.7
Q ss_pred chHHHHHHHHHHHHHHHHhh
Q 040420 147 LPIAIAVAAVALAGLYFYLN 166 (169)
Q Consensus 147 lpi~~~~G~~al~~l~fyl~ 166 (169)
|.+++|+|++....|+-||.
T Consensus 1 Ms~~vi~G~ilv~lLlgYLv 20 (29)
T PRK14748 1 MSAGVITGVLLVFLLLGYLV 20 (29)
T ss_pred CcHHHHHHHHHHHHHHHHHH
Confidence 56788888887777777763
No 229
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=52.54 E-value=6.9 Score=33.69 Aligned_cols=20 Identities=45% Similarity=1.084 Sum_probs=15.8
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
+| -||+..+ .|+ .|+.||.+
T Consensus 2 ~C-rCG~~l~-------~p~--~Cl~Cg~~ 21 (227)
T COG4031 2 IC-RCGAELS-------SPA--FCLNCGRR 21 (227)
T ss_pred cc-ccCCccc-------ccc--hhcccCCc
Confidence 68 8997664 376 99999986
No 230
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=52.49 E-value=5.4 Score=32.94 Aligned_cols=13 Identities=38% Similarity=1.037 Sum_probs=10.4
Q ss_pred CCCCCCCCCCccC
Q 040420 100 NYFCPVCGAPKRR 112 (169)
Q Consensus 100 ~~~CPvCgapK~~ 112 (169)
-|+||+||..-..
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 6999999985444
No 231
>PRK14750 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=52.31 E-value=20 Score=21.91 Aligned_cols=20 Identities=25% Similarity=0.271 Sum_probs=14.9
Q ss_pred chHHHHHHHHHHHHHHHHhh
Q 040420 147 LPIAIAVAAVALAGLYFYLN 166 (169)
Q Consensus 147 lpi~~~~G~~al~~l~fyl~ 166 (169)
|-+++|.|++....|+-||-
T Consensus 1 Ms~~vi~g~llv~lLl~YLv 20 (29)
T PRK14750 1 MNFSIVCGALLVLLLLGYLV 20 (29)
T ss_pred CcHHHHHHHHHHHHHHHHHH
Confidence 45788888888777777763
No 232
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=51.98 E-value=3.5 Score=35.74 Aligned_cols=36 Identities=22% Similarity=0.495 Sum_probs=25.4
Q ss_pred EEcCCCCeeec-------CCCCCCCCCCCCCCCCCCCCccCeeeCCCc
Q 040420 79 YICRDCGYIYN-------ERKPFDQLPDNYFCPVCGAPKRRFRPYTPA 119 (169)
Q Consensus 79 y~C~~CGyVYd-------~~tpF~~lPd~~~CPvCgapK~~F~~~~~~ 119 (169)
|+|..||..-+ ++. -.+ -.||-|+...+++++++.-
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~--irl---t~C~nC~e~vDkYiE~d~v 43 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGN--IRL---TKCPNCQEVVDKYIELDVV 43 (225)
T ss_pred CcccccCchHHHHHHhcCCCc--EEE---eeCCchhhHHHhHeehhhH
Confidence 68999994333 231 011 2799999999999998765
No 233
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=51.71 E-value=9.1 Score=32.34 Aligned_cols=30 Identities=23% Similarity=0.668 Sum_probs=22.4
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
...+..|..||+.-+. + .|++|..+++.-.
T Consensus 50 ~~~i~~C~~C~~lse~--------~--~C~IC~d~~Rd~~ 79 (195)
T TIGR00615 50 KENLRTCSVCGAISDQ--------E--VCNICSDERRDNS 79 (195)
T ss_pred HHcCCcCCCCCCCCCC--------C--cCCCCCCCCCCCC
Confidence 4457899999966543 2 8999999887653
No 234
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=51.62 E-value=11 Score=23.88 Aligned_cols=16 Identities=44% Similarity=1.080 Sum_probs=12.4
Q ss_pred CCCCCCCCccCeeeCCCc
Q 040420 102 FCPVCGAPKRRFRPYTPA 119 (169)
Q Consensus 102 ~CPvCgapK~~F~~~~~~ 119 (169)
-||.||. +++|. +...
T Consensus 5 pCP~CGG-~DrFr-~~d~ 20 (37)
T smart00778 5 PCPNCGG-SDRFR-FDDK 20 (37)
T ss_pred CCCCCCC-ccccc-cccC
Confidence 6999975 88998 6553
No 235
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=51.48 E-value=14 Score=31.99 Aligned_cols=13 Identities=23% Similarity=0.468 Sum_probs=10.6
Q ss_pred CeEEcCCCCeeec
Q 040420 77 QAYICRDCGYIYN 89 (169)
Q Consensus 77 ~~y~C~~CGyVYd 89 (169)
..++|..|++.|+
T Consensus 127 ~~~~C~~C~~~~~ 139 (285)
T PRK05333 127 DGVRCMGCGARHP 139 (285)
T ss_pred CEEEECCCCCcCC
Confidence 4689999998765
No 236
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=51.47 E-value=7.3 Score=37.54 Aligned_cols=26 Identities=31% Similarity=0.820 Sum_probs=19.0
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
....|+|..||.+-+..+. | .| .||.
T Consensus 127 ~va~w~c~~cg~~iean~k----p---~c-~cg~ 152 (593)
T COG2401 127 KVALWRCEKCGTIIEANTK----P---EC-KCGS 152 (593)
T ss_pred eEEEEecchhchhhhhcCC----c---cc-CCCC
Confidence 3448999999977766542 5 48 8886
No 237
>PLN00162 transport protein sec23; Provisional
Probab=51.39 E-value=7 Score=38.65 Aligned_cols=35 Identities=23% Similarity=0.512 Sum_probs=24.3
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
..-+|+.|+-+-++=..|+.--..|+||.|+..-.
T Consensus 52 ~pvRC~~CraylNPf~~~d~~~~~W~C~~C~~~N~ 86 (761)
T PLN00162 52 DPLRCRTCRAVLNPYCRVDFQAKIWICPFCFQRNH 86 (761)
T ss_pred CCCccCCCcCEECCceEEecCCCEEEccCCCCCCC
Confidence 45789999966665444444446799999987543
No 238
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=50.98 E-value=8.4 Score=36.13 Aligned_cols=32 Identities=19% Similarity=0.581 Sum_probs=18.5
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCC--CccCeeeC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGA--PKRRFRPY 116 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCga--pK~~F~~~ 116 (169)
+|+.||-.....- -..|+||.||. +...+..+
T Consensus 352 ~Cp~Cg~~m~S~G-----~~g~rC~kCg~~~~~~~~~~v 385 (421)
T COG1571 352 VCPRCGGRMKSAG-----RNGFRCKKCGTRARETLIKEV 385 (421)
T ss_pred CCCccCCchhhcC-----CCCcccccccccCCccccccc
Confidence 7888885554321 12688888876 33444433
No 239
>PF15499 Peptidase_C98: Ubiquitin-specific peptidase-like, SUMO isopeptidase
Probab=50.85 E-value=11 Score=33.68 Aligned_cols=34 Identities=24% Similarity=0.718 Sum_probs=25.0
Q ss_pred eEEcCCCCeeecCC-----CCCCCCCCCC---------CCCCCCCCcc
Q 040420 78 AYICRDCGYIYNER-----KPFDQLPDNY---------FCPVCGAPKR 111 (169)
Q Consensus 78 ~y~C~~CGyVYd~~-----tpF~~lPd~~---------~CPvCgapK~ 111 (169)
.+.|..|||.|..+ +-|.++..|| -|+.|+++.-
T Consensus 134 eFeC~~Cg~~~~~R~~K~L~TFtnv~pdwhPLnA~h~~pCn~C~~ksQ 181 (275)
T PF15499_consen 134 EFECSQCGHKYQNRCTKTLVTFTNVIPDWHPLNAVHFGPCNSCNSKSQ 181 (275)
T ss_pred EEEccccCChhhhhheeeecccCCCCCCCCcccccccCCCcccCChHH
Confidence 56999999999984 3566655556 5999987543
No 240
>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=50.71 E-value=5.2 Score=40.66 Aligned_cols=8 Identities=50% Similarity=1.269 Sum_probs=0.0
Q ss_pred CCCCCCCC
Q 040420 102 FCPVCGAP 109 (169)
Q Consensus 102 ~CPvCgap 109 (169)
.||.|+..
T Consensus 694 ~C~~C~~~ 701 (900)
T PF03833_consen 694 ECPKCGRE 701 (900)
T ss_dssp --------
T ss_pred cccccccc
Confidence 45555443
No 241
>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=50.56 E-value=8.1 Score=35.23 Aligned_cols=37 Identities=24% Similarity=0.681 Sum_probs=18.2
Q ss_pred eEEcCCCCeeecC------------------------------CCCCCCCCCCCCCCCCCCCccCeeeCC
Q 040420 78 AYICRDCGYIYNE------------------------------RKPFDQLPDNYFCPVCGAPKRRFRPYT 117 (169)
Q Consensus 78 ~y~C~~CGyVYd~------------------------------~tpF~~lPd~~~CPvCgapK~~F~~~~ 117 (169)
+|.|..|.|+|.- .+.|+.+|. -.|+.||.. .|++..
T Consensus 252 av~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~sl~r~P~-~~C~~Cg~~--~wer~~ 318 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTISLERLPK-KHCSNCGSS--KWERTG 318 (344)
T ss_dssp EEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEESSSS---S--TTT-S-----EEE-
T ss_pred EEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeeecccCCC-CCCCcCCcC--ceeehh
Confidence 7888888888875 135667775 289889864 466543
No 242
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=50.26 E-value=9.2 Score=33.53 Aligned_cols=16 Identities=31% Similarity=0.935 Sum_probs=10.5
Q ss_pred CCCeEEcCCCCeeecC
Q 040420 75 SKQAYICRDCGYIYNE 90 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~ 90 (169)
....++|.+||+|.++
T Consensus 27 ~~Ge~vC~~CG~Vl~e 42 (310)
T PRK00423 27 ERGEIVCADCGLVIEE 42 (310)
T ss_pred CCCeEeecccCCcccc
Confidence 4456777777776655
No 243
>PRK00076 recR recombination protein RecR; Reviewed
Probab=49.76 E-value=10 Score=31.98 Aligned_cols=30 Identities=27% Similarity=0.720 Sum_probs=22.3
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
...+..|..||..-+. + .|++|..+++.-.
T Consensus 50 ~~~i~~C~~C~~lse~--------~--~C~IC~d~~Rd~~ 79 (196)
T PRK00076 50 KEKIKHCSVCGNLTEQ--------D--PCEICSDPRRDQS 79 (196)
T ss_pred HHcCCcCCCCCCcCCC--------C--cCCCCCCCCCCCC
Confidence 4457899999965542 2 8999998877554
No 244
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=49.67 E-value=11 Score=20.77 Aligned_cols=13 Identities=23% Similarity=0.979 Sum_probs=10.4
Q ss_pred eEEcCCCCeeecC
Q 040420 78 AYICRDCGYIYNE 90 (169)
Q Consensus 78 ~y~C~~CGyVYd~ 90 (169)
.|+|..|+-.|..
T Consensus 1 ~~~C~~C~~~F~~ 13 (27)
T PF13912_consen 1 PFECDECGKTFSS 13 (27)
T ss_dssp SEEETTTTEEESS
T ss_pred CCCCCccCCccCC
Confidence 3889999988864
No 245
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=49.66 E-value=10 Score=23.19 Aligned_cols=17 Identities=29% Similarity=0.718 Sum_probs=11.9
Q ss_pred cCCCCeEEcCCCCeeec
Q 040420 73 VASKQAYICRDCGYIYN 89 (169)
Q Consensus 73 ~~~~~~y~C~~CGyVYd 89 (169)
......|+|..||-.|-
T Consensus 27 i~~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 27 IENVPALVCPQCGEEYL 43 (46)
T ss_pred EeCCCccccccCCCEee
Confidence 34556788999986653
No 246
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=49.61 E-value=3.8 Score=36.06 Aligned_cols=31 Identities=19% Similarity=0.604 Sum_probs=10.5
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-.-|+.||..+-...+=...-.|+.||.|+.
T Consensus 31 n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~e 61 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRPVADFYCPNCNE 61 (254)
T ss_dssp H---TTT--SS-EE--------EEE-TTT--
T ss_pred CCcCCCCCChhHhhccCCCccceeECCCCch
Confidence 3569999976433211111136789999986
No 247
>PRK13844 recombination protein RecR; Provisional
Probab=49.56 E-value=10 Score=32.22 Aligned_cols=29 Identities=21% Similarity=0.543 Sum_probs=21.7
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCe
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F 113 (169)
......|..||..-+. + .|++|..+++.-
T Consensus 54 ~~~i~~C~~C~~lte~--------~--~C~IC~d~~Rd~ 82 (200)
T PRK13844 54 TANIKKCVYCQALTED--------D--VCNICSNTNRDD 82 (200)
T ss_pred HHhCCcCCCCCCCCCC--------C--CCCCCCCCCCCC
Confidence 4457899999966543 2 799999877644
No 248
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=49.22 E-value=15 Score=32.91 Aligned_cols=33 Identities=27% Similarity=0.791 Sum_probs=23.6
Q ss_pred CCCeEEcCCCCeeecCCC----------CCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERK----------PFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~t----------pF~~lPd~~~CPvCga 108 (169)
....|+|..||..|-.-. +-++ +..+.|+.|+-
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s-~ka~~C~~C~K 169 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDS-KKAFSCKYCGK 169 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccc-cccccCCCCCc
Confidence 446899999999997621 3333 45578999975
No 249
>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=49.15 E-value=11 Score=32.53 Aligned_cols=27 Identities=26% Similarity=0.549 Sum_probs=11.9
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
.|..||+.+.- ....||.||..+..=.
T Consensus 199 ~Cs~C~t~W~~--------~R~~Cp~Cg~~~~~~l 225 (290)
T PF04216_consen 199 HCSLCGTEWRF--------VRIKCPYCGNTDHEKL 225 (290)
T ss_dssp EETTT--EEE----------TTS-TTT---SS-EE
T ss_pred EcCCCCCeeee--------cCCCCcCCCCCCCcce
Confidence 77777766532 1238999998665533
No 250
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=48.90 E-value=5.4 Score=26.27 Aligned_cols=8 Identities=63% Similarity=1.879 Sum_probs=4.2
Q ss_pred CCCCCCCC
Q 040420 102 FCPVCGAP 109 (169)
Q Consensus 102 ~CPvCgap 109 (169)
.||+|+.+
T Consensus 22 ~CPlC~r~ 29 (54)
T PF04423_consen 22 CCPLCGRP 29 (54)
T ss_dssp E-TTT--E
T ss_pred cCCCCCCC
Confidence 89999874
No 251
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PRK12366 replication factor A; Reviewed
Probab=48.32 E-value=14 Score=35.85 Aligned_cols=26 Identities=31% Similarity=0.847 Sum_probs=20.3
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
...|+.|....... ...|.||.|+..
T Consensus 532 y~aCp~CnkKv~~~------~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKRVEEV------DGEYICEFCGEV 557 (637)
T ss_pred EecccccCeEeEcC------CCcEECCCCCCC
Confidence 44999999776532 577999999984
No 253
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=48.19 E-value=12 Score=30.31 Aligned_cols=15 Identities=27% Similarity=0.516 Sum_probs=8.0
Q ss_pred CCCCCCCCCccCeee
Q 040420 101 YFCPVCGAPKRRFRP 115 (169)
Q Consensus 101 ~~CPvCgapK~~F~~ 115 (169)
+.||.||-.-..++.
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 566666654444433
No 254
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=48.05 E-value=12 Score=24.02 Aligned_cols=17 Identities=47% Similarity=1.130 Sum_probs=10.6
Q ss_pred CCCCCCCCccCeeeCCCc
Q 040420 102 FCPVCGAPKRRFRPYTPA 119 (169)
Q Consensus 102 ~CPvCgapK~~F~~~~~~ 119 (169)
-||+|+. +++|..+...
T Consensus 5 pCP~CGG-~DrFri~~d~ 21 (40)
T PF08273_consen 5 PCPICGG-KDRFRIFDDK 21 (40)
T ss_dssp --TTTT--TTTEEEETT-
T ss_pred CCCCCcC-ccccccCcCc
Confidence 5999976 8999966543
No 255
>PRK07218 replication factor A; Provisional
Probab=48.01 E-value=12 Score=34.89 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=21.7
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeee
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRP 115 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~ 115 (169)
+.+|+.|+-+-+ .|.||.||.....+.-
T Consensus 297 i~rCP~C~r~v~----------~~~C~~hG~ve~~~dl 324 (423)
T PRK07218 297 IERCPECGRVIQ----------KGQCRSHGAVEGEDDL 324 (423)
T ss_pred eecCcCcccccc----------CCcCCCCCCcCCeeee
Confidence 679999996663 3799999987666543
No 256
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=47.39 E-value=11 Score=20.43 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=6.1
Q ss_pred EEcCCCCeee
Q 040420 79 YICRDCGYIY 88 (169)
Q Consensus 79 y~C~~CGyVY 88 (169)
|+|..|.|..
T Consensus 1 y~C~~C~y~t 10 (24)
T PF13909_consen 1 YKCPHCSYST 10 (24)
T ss_dssp EE-SSSS-EE
T ss_pred CCCCCCCCcC
Confidence 6788888765
No 257
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=47.36 E-value=8.9 Score=26.88 Aligned_cols=27 Identities=33% Similarity=0.650 Sum_probs=18.6
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-+|++|+.+- +=|+..-....|++||.
T Consensus 12 VkCp~C~n~q---~vFsha~t~V~C~~Cg~ 38 (59)
T PRK00415 12 VKCPDCGNEQ---VVFSHASTVVRCLVCGK 38 (59)
T ss_pred EECCCCCCeE---EEEecCCcEEECcccCC
Confidence 4899999553 22444445569999998
No 258
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=47.11 E-value=11 Score=31.57 Aligned_cols=22 Identities=32% Similarity=0.878 Sum_probs=16.6
Q ss_pred CeEEcCCCCeeecCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPD 99 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd 99 (169)
.+|+|+.|||...++ -|+.+++
T Consensus 47 ~V~vCP~CgyA~~~~-~F~~l~~ 68 (214)
T PF09986_consen 47 EVWVCPHCGYAAFEE-DFEKLSP 68 (214)
T ss_pred eEEECCCCCCccccc-ccccCCH
Confidence 489999999998764 3666654
No 259
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=47.03 E-value=16 Score=33.64 Aligned_cols=31 Identities=29% Similarity=0.733 Sum_probs=19.6
Q ss_pred eEEcCCCCeeecCCCCCCCC-CCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQL-PDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~l-Pd~~~CPvCgap 109 (169)
.|+|..||++ +..++-+.- .....||.||..
T Consensus 324 ~~r~~~~~~~-~~~~~~~~~~~~~~~c~~~~~~ 355 (409)
T TIGR00108 324 TYKCAECGEV-IEKTVRELKDKKFAICPACGQE 355 (409)
T ss_pred EEEcCCCCce-eecccccccccccccCcccCcc
Confidence 4999999986 433322111 123589999985
No 260
>PRK04023 DNA polymerase II large subunit; Validated
Probab=46.32 E-value=15 Score=38.27 Aligned_cols=15 Identities=40% Similarity=0.676 Sum_probs=6.8
Q ss_pred CCCCCCCCccCCCCC
Q 040420 17 TPPPLLAPTGNNAGL 31 (169)
Q Consensus 17 ~~~~~~~~~~~~~~l 31 (169)
|+|-.|-|.++..|-
T Consensus 592 P~~h~LFPiG~~GG~ 606 (1121)
T PRK04023 592 PPVHVLFPIGNAGGS 606 (1121)
T ss_pred CCCcccccccccCcc
Confidence 334455555544433
No 261
>PRK14873 primosome assembly protein PriA; Provisional
Probab=46.11 E-value=9.6 Score=37.27 Aligned_cols=33 Identities=18% Similarity=0.319 Sum_probs=17.7
Q ss_pred eEEcCCCCeeecCC-----CCCCCCCCCCCCCCCCCCc
Q 040420 78 AYICRDCGYIYNER-----KPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 78 ~y~C~~CGyVYd~~-----tpF~~lPd~~~CPvCgapK 110 (169)
.-.|..||++..=. .-+.+-.....|..||...
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAA 420 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCC
Confidence 44777777665421 1111112234799999854
No 262
>PHA00732 hypothetical protein
Probab=45.88 E-value=14 Score=26.64 Aligned_cols=30 Identities=23% Similarity=0.506 Sum_probs=18.6
Q ss_pred EEcCCCCeeecCCC------CCCCCCCCCCCCCCCCCc
Q 040420 79 YICRDCGYIYNERK------PFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 79 y~C~~CGyVYd~~t------pF~~lPd~~~CPvCgapK 110 (169)
|+|..||..+.... .....+ +.|+.|+..-
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~--~~C~~CgKsF 37 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL--TKCPVCNKSY 37 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC--CccCCCCCEe
Confidence 78999998886510 001113 3899998743
No 263
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=45.87 E-value=11 Score=36.94 Aligned_cols=27 Identities=33% Similarity=0.704 Sum_probs=18.7
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
.|..||+...+ +.-.||.||++-..+-
T Consensus 29 ~Cp~CG~~~~~--------~~~fC~~CG~~~~~~~ 55 (645)
T PRK14559 29 PCPQCGTEVPV--------DEAHCPNCGAETGTIW 55 (645)
T ss_pred cCCCCCCCCCc--------ccccccccCCcccchh
Confidence 58888866543 3338999999777663
No 264
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=45.79 E-value=42 Score=28.72 Aligned_cols=49 Identities=27% Similarity=0.437 Sum_probs=28.5
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCCCcccCCCChhHHHHHH
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYTPAVTRGANDTAVRKAR 133 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~~~~~~~~n~~~v~~ar 133 (169)
...+|-|+.|.-.--+ + +|++||..-...+-..|...+.+..-|...-|
T Consensus 11 k~~iyWCe~cNlPl~~--------~--~c~~cg~~~~~l~LTpPaD~R~~fp~die~Ir 59 (202)
T COG5270 11 KFPIYWCEKCNLPLLG--------R--RCSVCGSKVEELRLTPPADVRPAFPYDIEVIR 59 (202)
T ss_pred ccceeehhhCCCcccc--------c--cccccCCcceEEEeCCCCCccccCchHHHHHH
Confidence 3458999999944322 3 89999954444444444444444444444433
No 265
>PLN02294 cytochrome c oxidase subunit Vb
Probab=45.54 E-value=14 Score=30.95 Aligned_cols=9 Identities=44% Similarity=0.914 Sum_probs=7.2
Q ss_pred CCCCCCCCCCC
Q 040420 98 PDNYFCPVCGA 108 (169)
Q Consensus 98 Pd~~~CPvCga 108 (169)
|. +||.||+
T Consensus 141 p~--RCpeCG~ 149 (174)
T PLN02294 141 SF--ECPVCTQ 149 (174)
T ss_pred ce--eCCCCCC
Confidence 55 7999987
No 266
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=45.52 E-value=7 Score=36.83 Aligned_cols=37 Identities=22% Similarity=0.634 Sum_probs=26.0
Q ss_pred cCCCCeEEcCCCCeeecCC---CCCCCCCCCCCCCCCCCC
Q 040420 73 VASKQAYICRDCGYIYNER---KPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 73 ~~~~~~y~C~~CGyVYd~~---tpF~~lPd~~~CPvCgap 109 (169)
....+.|+|++|+..|+.- .-|+-.-..|.|-.|+.+
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccccCCccccchhhhHHHHhhcccCceEEEecCCCc
Confidence 4566789999999999862 112222357899999984
No 267
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=45.46 E-value=10 Score=34.55 Aligned_cols=32 Identities=22% Similarity=0.533 Sum_probs=19.4
Q ss_pred CeEEcCCCCeeecCCCCCCCC--CCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQL--PDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~l--Pd~~~CPvCga 108 (169)
...+|..|+..|+-....... .+-..||.||.
T Consensus 146 ~~~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG 179 (349)
T PTZ00410 146 SAASCIECHTPYDIEQAYLEARSGKVPHCSTCGG 179 (349)
T ss_pred CeeEeCCCCCCcchhHHHHHhhcCCCCCCCCCCC
Confidence 367999999888743211110 11236999986
No 268
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=45.39 E-value=9.9 Score=32.16 Aligned_cols=37 Identities=22% Similarity=0.468 Sum_probs=22.2
Q ss_pred CccceecCCCC-eE-EcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 67 PKFSMRVASKQ-AY-ICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 67 p~~~~k~~~~~-~y-~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
...+.+..+-. +| +|..||+..... -..-.||.||.-
T Consensus 136 ~~Lst~~~dlGVI~A~CsrC~~~L~~~------~~~l~Cp~Cg~t 174 (188)
T COG1096 136 IQLSTKGNDLGVIYARCSRCRAPLVKK------GNMLKCPNCGNT 174 (188)
T ss_pred eEEEecCCcceEEEEEccCCCcceEEc------CcEEECCCCCCE
Confidence 33443333333 44 999999765432 123499999984
No 269
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=45.37 E-value=24 Score=22.08 Aligned_cols=26 Identities=31% Similarity=0.697 Sum_probs=13.2
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
=+|..||..+.... |-+.|-++||..
T Consensus 4 ~~C~eC~~~f~dSy----L~~~F~~~VCD~ 29 (34)
T PF01286_consen 4 PKCDECGKPFMDSY----LLNNFDLPVCDK 29 (34)
T ss_dssp EE-TTT--EES-SS----CCCCTS-S--TT
T ss_pred chHhHhCCHHHHHH----HHHhCCcccccc
Confidence 48999998887652 456677888865
No 270
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=45.17 E-value=14 Score=29.70 Aligned_cols=20 Identities=15% Similarity=0.561 Sum_probs=13.6
Q ss_pred eecCCCCeEEcCCCCeeecC
Q 040420 71 MRVASKQAYICRDCGYIYNE 90 (169)
Q Consensus 71 ~k~~~~~~y~C~~CGyVYd~ 90 (169)
|........+|..||++|.-
T Consensus 105 ~~l~~g~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 105 FWLHKGKPQRCPECGQVFKL 124 (136)
T ss_dssp EEEETTSEEEETTTEEEEEE
T ss_pred EEEeCCCccCCCCCCeEEEE
Confidence 34445557788889888753
No 271
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=44.94 E-value=8.7 Score=34.09 Aligned_cols=22 Identities=32% Similarity=0.777 Sum_probs=14.6
Q ss_pred cceecCCCCeEEcCCCC-eeecC
Q 040420 69 FSMRVASKQAYICRDCG-YIYNE 90 (169)
Q Consensus 69 ~~~k~~~~~~y~C~~CG-yVYd~ 90 (169)
...+.+..-.-+|..|| |||.+
T Consensus 31 ~~VRf~~Pf~i~C~~C~~~I~kG 53 (324)
T PF04502_consen 31 LTVRFMMPFNIWCNTCGEYIYKG 53 (324)
T ss_pred eEEEEcCCccCcCCCCccccccc
Confidence 33444444456899999 88876
No 272
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=44.32 E-value=16 Score=33.82 Aligned_cols=26 Identities=35% Similarity=0.783 Sum_probs=20.6
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
...-|.|+.|+-.+- +||- .||+|+-
T Consensus 273 ~~~Gy~CP~CkakvC------sLP~--eCpiC~l 298 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVC------SLPI--ECPICSL 298 (378)
T ss_pred ccCceeCCcccCeee------cCCc--cCCccce
Confidence 335799999997776 4688 8999985
No 273
>PLN02674 adenylate kinase
Probab=44.16 E-value=18 Score=31.12 Aligned_cols=30 Identities=20% Similarity=0.248 Sum_probs=21.0
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
..++|+.||.+|+.. |...+....|..||.
T Consensus 157 gR~~~~~~g~~yn~~--~~pp~~~~~~~~~g~ 186 (244)
T PLN02674 157 GRWIHPSSGRTYHTK--FAPPKVPGVDDVTGE 186 (244)
T ss_pred ccccccccCCccccc--cCCCcccCcccccCC
Confidence 478999999999864 333233347888875
No 274
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=43.74 E-value=16 Score=23.02 Aligned_cols=14 Identities=29% Similarity=0.878 Sum_probs=10.7
Q ss_pred CCeEEcCCCCeeec
Q 040420 76 KQAYICRDCGYIYN 89 (169)
Q Consensus 76 ~~~y~C~~CGyVYd 89 (169)
...|+|.+||+.+.
T Consensus 26 T~fy~C~~C~~~w~ 39 (40)
T smart00440 26 TVFYVCTKCGHRWR 39 (40)
T ss_pred eEEEEeCCCCCEeC
Confidence 34789999998763
No 275
>PF14122 YokU: YokU-like protein
Probab=43.35 E-value=18 Score=27.22 Aligned_cols=21 Identities=29% Similarity=0.922 Sum_probs=17.1
Q ss_pred eecCCCCeEEcCCCCeeecCC
Q 040420 71 MRVASKQAYICRDCGYIYNER 91 (169)
Q Consensus 71 ~k~~~~~~y~C~~CGyVYd~~ 91 (169)
+...+.....|..||-+|.+.
T Consensus 28 IeI~~tP~i~C~~CgmvYq~d 48 (87)
T PF14122_consen 28 IEITDTPAIICSNCGMVYQDD 48 (87)
T ss_pred EEecCCceeeecCCCcEEehh
Confidence 445677789999999999874
No 276
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.29 E-value=11 Score=29.46 Aligned_cols=14 Identities=36% Similarity=1.054 Sum_probs=7.2
Q ss_pred CCeEEcCCCCeeec
Q 040420 76 KQAYICRDCGYIYN 89 (169)
Q Consensus 76 ~~~y~C~~CGyVYd 89 (169)
.+.|+|..||+.+.
T Consensus 51 ~qRyrC~~C~~tf~ 64 (129)
T COG3677 51 HQRYKCKSCGSTFT 64 (129)
T ss_pred ccccccCCcCccee
Confidence 44555555554443
No 277
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=43.25 E-value=13 Score=23.68 Aligned_cols=14 Identities=29% Similarity=0.859 Sum_probs=11.9
Q ss_pred EEcCCCCeeecCCC
Q 040420 79 YICRDCGYIYNERK 92 (169)
Q Consensus 79 y~C~~CGyVYd~~t 92 (169)
-+|..||-+|..+.
T Consensus 14 ~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 14 TTCPTCGMLYSPGS 27 (41)
T ss_pred cCCCCCCCEECCCC
Confidence 48999999998763
No 278
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=43.24 E-value=22 Score=24.55 Aligned_cols=28 Identities=21% Similarity=0.198 Sum_probs=18.3
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
....-+|..||..-- |- -+|| ||.-+++
T Consensus 24 ~~~~~~c~~cg~~~~--------pH-~vc~-cG~Y~gr 51 (60)
T PRK01110 24 APTLSVDKTTGEYHL--------PH-HVSP-KGYYKGR 51 (60)
T ss_pred CCceeEcCCCCceec--------cc-eecC-CcccCCe
Confidence 344679999995543 32 2899 9964443
No 279
>PF03597 CcoS: Cytochrome oxidase maturation protein cbb3-type; InterPro: IPR004714 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation []. Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Probab=42.92 E-value=30 Score=22.76 Aligned_cols=20 Identities=20% Similarity=0.602 Sum_probs=14.7
Q ss_pred chHHHHHHHHHHHHHHHHhh
Q 040420 147 LPIAIAVAAVALAGLYFYLN 166 (169)
Q Consensus 147 lpi~~~~G~~al~~l~fyl~ 166 (169)
+|+++++|++++++++.-+.
T Consensus 7 ip~sl~l~~~~l~~f~Wavk 26 (45)
T PF03597_consen 7 IPVSLILGLIALAAFLWAVK 26 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHc
Confidence 47888888888877665543
No 280
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.90 E-value=7.3 Score=31.08 Aligned_cols=29 Identities=24% Similarity=0.606 Sum_probs=19.4
Q ss_pred eEEcCCCC--eeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 78 AYICRDCG--YIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 78 ~y~C~~CG--yVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
.-+|+.|| +-|++ |-+.-+ .|-.||..-+
T Consensus 21 ~grCP~CGeGrLF~g---FLK~~p--~C~aCG~dyg 51 (126)
T COG5349 21 RGRCPRCGEGRLFRG---FLKVVP--ACEACGLDYG 51 (126)
T ss_pred cCCCCCCCCchhhhh---hcccCc--hhhhcccccc
Confidence 46899998 34443 445555 8999997443
No 281
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=42.87 E-value=15 Score=23.12 Aligned_cols=13 Identities=23% Similarity=0.715 Sum_probs=8.3
Q ss_pred eEEcCCCCeeecC
Q 040420 78 AYICRDCGYIYNE 90 (169)
Q Consensus 78 ~y~C~~CGyVYd~ 90 (169)
.|+|..||+++-.
T Consensus 11 l~~CL~C~~~~c~ 23 (50)
T smart00290 11 LWLCLTCGQVGCG 23 (50)
T ss_pred eEEecCCCCcccC
Confidence 6677777666643
No 282
>PRK06386 replication factor A; Reviewed
Probab=42.87 E-value=19 Score=32.89 Aligned_cols=28 Identities=14% Similarity=0.171 Sum_probs=21.8
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeee
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRP 115 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~ 115 (169)
+.+|+.|+-+-+ +|.||.||.....+.-
T Consensus 236 i~rCP~C~R~l~----------~g~C~~HG~v~~~~dl 263 (358)
T PRK06386 236 FTKCSVCNKIIE----------DGVCKDHPDAPVYLDI 263 (358)
T ss_pred EecCcCCCeEcc----------CCcCCCCCCCCCeeEE
Confidence 679999997764 3699999986666543
No 283
>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]
Probab=42.83 E-value=12 Score=37.70 Aligned_cols=33 Identities=18% Similarity=0.513 Sum_probs=23.0
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
..|+|..|||.-..+..=+..++-+.|+.|++.
T Consensus 263 afFrC~vC~~~~~ve~drg~i~eP~~C~~C~~~ 295 (804)
T KOG0478|consen 263 AFFRCSVCGHEIAVESDRGRIKEPMLCKECGTT 295 (804)
T ss_pred HhhhhhhcCceEEEEeecCccCCCcccccccCc
Confidence 478999999875543222345666799999764
No 284
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=42.82 E-value=14 Score=25.03 Aligned_cols=13 Identities=23% Similarity=0.721 Sum_probs=6.8
Q ss_pred CCeEEcCCCCeee
Q 040420 76 KQAYICRDCGYIY 88 (169)
Q Consensus 76 ~~~y~C~~CGyVY 88 (169)
...|+|..|+.+|
T Consensus 19 ~~~y~C~~C~~~F 31 (51)
T PF07975_consen 19 SSRYRCPKCKNHF 31 (51)
T ss_dssp -EEE--TTTT--B
T ss_pred CCeEECCCCCCcc
Confidence 5689999999544
No 285
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=42.71 E-value=20 Score=24.75 Aligned_cols=12 Identities=50% Similarity=1.168 Sum_probs=7.9
Q ss_pred CCCCCCCCCCCC
Q 040420 98 PDNYFCPVCGAP 109 (169)
Q Consensus 98 Pd~~~CPvCgap 109 (169)
..+|.||.||-|
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 455677777764
No 286
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=42.60 E-value=15 Score=35.81 Aligned_cols=32 Identities=28% Similarity=0.823 Sum_probs=21.0
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
+..+.|+|..||.+-... .....+.|+.|+..
T Consensus 540 D~~~~~vC~~CG~~~~~~----~~~~~~~C~~C~~~ 571 (605)
T PRK07225 540 DKVEIYVCAKCGMIAIYD----KKRNRKYCPICGEE 571 (605)
T ss_pred cceeEEeecCcCcceehh----cccCceeecccCCC
Confidence 345689999999654221 11235689999864
No 287
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=42.52 E-value=16 Score=35.51 Aligned_cols=33 Identities=36% Similarity=0.830 Sum_probs=22.1
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
+....|+|..||-+-.... ..+.|.|..|+...
T Consensus 534 D~~~~~vC~~CG~~~~~~~----~~~~~~C~~c~~~~ 566 (599)
T TIGR03670 534 DKYVVYVCENCGHIAWEDK----RKGTAYCPVCGETG 566 (599)
T ss_pred cceeEEeecccCceeehhc----ccCceeccccCCCC
Confidence 3446899999997643221 13457899998754
No 288
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=42.27 E-value=19 Score=25.53 Aligned_cols=30 Identities=33% Similarity=0.657 Sum_probs=20.7
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
...-+|+|-+||-.-.-. --|-.+|-.||+
T Consensus 16 ~~~miYiCgdC~~en~lk-----~~D~irCReCG~ 45 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTLK-----RGDVIRCRECGY 45 (62)
T ss_pred cccEEEEecccccccccc-----CCCcEehhhcch
Confidence 455589999999443221 135579999997
No 289
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=41.81 E-value=7.4 Score=34.12 Aligned_cols=24 Identities=25% Similarity=0.537 Sum_probs=19.0
Q ss_pred CccceecCCCCeEEcCCCC-eeecC
Q 040420 67 PKFSMRVASKQAYICRDCG-YIYNE 90 (169)
Q Consensus 67 p~~~~k~~~~~~y~C~~CG-yVYd~ 90 (169)
--.+++++..-..+|..|| |||..
T Consensus 31 rglSiRL~TPF~~RCL~C~~YI~K~ 55 (272)
T COG5134 31 RGLSIRLETPFPVRCLNCENYIQKG 55 (272)
T ss_pred ccceEEeccCcceeecchhhhhhcc
Confidence 3356777787788999999 88876
No 290
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=41.79 E-value=17 Score=25.20 Aligned_cols=29 Identities=34% Similarity=0.729 Sum_probs=19.0
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRR 112 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~ 112 (169)
....-+|.+||... +|- -+|+.||.-+++
T Consensus 24 ~~~~~~c~~cG~~~--------l~H-rvc~~cg~Y~g~ 52 (57)
T COG0333 24 APTLSVCPNCGEYK--------LPH-RVCLKCGYYKGR 52 (57)
T ss_pred CccceeccCCCCcc--------cCc-eEcCCCCCccCe
Confidence 34467999999433 233 289999975543
No 291
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=41.43 E-value=13 Score=26.88 Aligned_cols=30 Identities=33% Similarity=0.887 Sum_probs=19.1
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeee
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRP 115 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~ 115 (169)
..|.|..|+-.|... . .||.|+.+-...+.
T Consensus 16 ~~~~C~~C~~~~~~~-------a--~CPdC~~~Le~LkA 45 (70)
T PF07191_consen 16 GHYHCEACQKDYKKE-------A--FCPDCGQPLEVLKA 45 (70)
T ss_dssp TEEEETTT--EEEEE-------E--E-TTT-SB-EEEEE
T ss_pred CEEECccccccceec-------c--cCCCcccHHHHHHH
Confidence 689999999888642 2 79999998776664
No 292
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=41.26 E-value=14 Score=34.25 Aligned_cols=36 Identities=28% Similarity=0.428 Sum_probs=19.7
Q ss_pred CccchhhhhccCCcccee--cCCCCeEEcCCCCeeecC
Q 040420 55 PPHQQQLLASAAPKFSMR--VASKQAYICRDCGYIYNE 90 (169)
Q Consensus 55 ~~~~~~~~~~a~p~~~~k--~~~~~~y~C~~CGyVYd~ 90 (169)
++.+.+...+-|..+++. ..+..-|+|.+|+.-|.-
T Consensus 373 hGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKN 410 (423)
T COG5189 373 HGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKN 410 (423)
T ss_pred ccccCcccCCCCCccccccccccCCceeccccchhhcc
Confidence 444444344444334433 344457888888877753
No 293
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=40.92 E-value=15 Score=32.76 Aligned_cols=38 Identities=29% Similarity=0.631 Sum_probs=22.2
Q ss_pred CCeEEcCCCCeeecCC---CCCCCCCCCCCCCCCCCCccCeee
Q 040420 76 KQAYICRDCGYIYNER---KPFDQLPDNYFCPVCGAPKRRFRP 115 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~---tpF~~lPd~~~CPvCgapK~~F~~ 115 (169)
+++-+|+.|..-||+- ..|+- ..|.||.|++.-.-|..
T Consensus 130 KeVSRCr~C~~rYDPVP~dkmwG~--aef~C~~C~h~F~G~~q 170 (278)
T PF15135_consen 130 KEVSRCRKCRKRYDPVPCDKMWGI--AEFHCPKCRHNFRGFAQ 170 (278)
T ss_pred cccccccccccccCCCccccccce--eeeecccccccchhhhh
Confidence 3456777777777762 11111 24788888886555543
No 294
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=40.91 E-value=17 Score=38.49 Aligned_cols=9 Identities=33% Similarity=0.833 Sum_probs=6.7
Q ss_pred eEEcCCCCe
Q 040420 78 AYICRDCGY 86 (169)
Q Consensus 78 ~y~C~~CGy 86 (169)
..+|+.||.
T Consensus 667 ~rkCPkCG~ 675 (1337)
T PRK14714 667 RRRCPSCGT 675 (1337)
T ss_pred EEECCCCCC
Confidence 578888884
No 295
>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=40.91 E-value=17 Score=22.74 Aligned_cols=14 Identities=29% Similarity=0.828 Sum_probs=11.1
Q ss_pred CCCeEEcCCCCeee
Q 040420 75 SKQAYICRDCGYIY 88 (169)
Q Consensus 75 ~~~~y~C~~CGyVY 88 (169)
....|+|..||+.+
T Consensus 25 ~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 25 MTLFYVCCNCGHRW 38 (39)
T ss_dssp SEEEEEESSSTEEE
T ss_pred CeEEEEeCCCCCee
Confidence 34478999999876
No 296
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=40.73 E-value=21 Score=24.06 Aligned_cols=16 Identities=31% Similarity=0.893 Sum_probs=12.7
Q ss_pred CCeEEcCCCCeeecCC
Q 040420 76 KQAYICRDCGYIYNER 91 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~ 91 (169)
...|+|..||++.-++
T Consensus 9 ~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 9 SNLWLCLTCGYVGCGR 24 (63)
T ss_dssp SSEEEETTTS-EEETT
T ss_pred CceEEeCCCCcccccC
Confidence 5689999999998764
No 297
>PRK05580 primosome assembly protein PriA; Validated
Probab=40.52 E-value=16 Score=35.46 Aligned_cols=34 Identities=24% Similarity=0.671 Sum_probs=17.3
Q ss_pred eEEcCCCCeeecCC---CC--CCCCCCCCCCCCCCCCcc
Q 040420 78 AYICRDCGYIYNER---KP--FDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 78 ~y~C~~CGyVYd~~---tp--F~~lPd~~~CPvCgapK~ 111 (169)
...|..||++..=. .+ +.+--..-.|..||....
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCC
Confidence 45788888764210 01 001122236888887544
No 298
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=40.26 E-value=9.7 Score=32.66 Aligned_cols=13 Identities=23% Similarity=0.779 Sum_probs=10.9
Q ss_pred CeEEcCCCCeeec
Q 040420 77 QAYICRDCGYIYN 89 (169)
Q Consensus 77 ~~y~C~~CGyVYd 89 (169)
...+|..||+.|+
T Consensus 117 ~~~~C~~C~~~~~ 129 (260)
T cd01409 117 HRVVCLSCGFRTP 129 (260)
T ss_pred CEEEeCCCcCccC
Confidence 3679999999885
No 299
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.06 E-value=12 Score=37.32 Aligned_cols=33 Identities=24% Similarity=0.662 Sum_probs=23.8
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
+-.+|..||-++++--.-+---..|.||.|...
T Consensus 52 ~P~~C~~C~AvlNPyc~vd~~a~~W~CpfC~qr 84 (745)
T KOG1986|consen 52 DPLRCSKCGAVLNPYCSVDFRAKSWICPFCNQR 84 (745)
T ss_pred CCchhccchhhcCcceeecccCceEeccccccC
Confidence 457999999999873322233467999999763
No 300
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=39.83 E-value=20 Score=24.84 Aligned_cols=27 Identities=44% Similarity=0.866 Sum_probs=19.4
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
+-.|..||.|+-.. +-| .-.||-||.+
T Consensus 18 ~~NCl~CGkIiC~~----Eg~-~~pC~fCg~~ 44 (57)
T PF06221_consen 18 APNCLNCGKIICEQ----EGP-LGPCPFCGTP 44 (57)
T ss_pred cccccccChhhccc----ccC-cCcCCCCCCc
Confidence 34799999998763 223 3489999964
No 301
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=39.41 E-value=15 Score=25.11 Aligned_cols=24 Identities=29% Similarity=0.855 Sum_probs=14.1
Q ss_pred EcCCCCe-eecCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGY-IYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 80 ~C~~CGy-VYd~~tpF~~lPd~~~CPvCga 108 (169)
.|+.||- ++-. +--|.|.|-.||.
T Consensus 21 ~CPrCG~gvfmA-----~H~dR~~CGkCgy 45 (51)
T COG1998 21 FCPRCGPGVFMA-----DHKDRWACGKCGY 45 (51)
T ss_pred cCCCCCCcchhh-----hcCceeEeccccc
Confidence 5777873 2221 2246777877775
No 302
>PRK00279 adk adenylate kinase; Reviewed
Probab=39.29 E-value=64 Score=25.98 Aligned_cols=30 Identities=30% Similarity=0.614 Sum_probs=19.9
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
....|+.||.+|.... ...+..-.|..||.
T Consensus 126 ~R~~~~~~g~~~~~~~--~~p~~~~~~~~~~~ 155 (215)
T PRK00279 126 GRRICPACGRTYHVKF--NPPKVEGKCDVCGE 155 (215)
T ss_pred CCcccCccCCcccccC--CCCCCcCcCcCCCC
Confidence 3579999999997642 22223337888874
No 303
>PF04530 Viral_Beta_CD: Viral Beta C/D like family; InterPro: IPR007617 This is a family of ssRNA positive-strand viral proteins. Conserved region is found in the Beta C and Beta D transcripts.
Probab=39.17 E-value=68 Score=25.53 Aligned_cols=66 Identities=14% Similarity=0.109 Sum_probs=31.3
Q ss_pred CCCCCCCCCCCccCeeeCCCcccCCCChhHHHHHHHHHhhhccccCCCchHHHHHHHHHHHHHHHHh
Q 040420 99 DNYFCPVCGAPKRRFRPYTPAVTRGANDTAVRKARKEQIQRDEAIGKALPIAIAVAAVALAGLYFYL 165 (169)
Q Consensus 99 d~~~CPvCgapK~~F~~~~~~~~~~~n~~~v~~ar~~~~~~~~~~gn~lpi~~~~G~~al~~l~fyl 165 (169)
-+..|+.|.-+..-|....... .+++...-++++.+...-..+-.|-+-+.+++++|....+|||+
T Consensus 5 ~~C~CsdC~ws~~~~~~t~~~~-~~~~~~ve~t~~~~~~~~sv~~~~y~l~~~~v~~L~~~~~y~~~ 70 (122)
T PF04530_consen 5 SGCCCSDCQWSGSPTVDTGSQS-QDSGSPVEMTARRETTFLSVLNDNYVLFVCAVCMLFSILVYLYS 70 (122)
T ss_pred CCCcCCcccCCCCCcccccccc-ccCCccHhHhhhhhcchhhhhhhhHHHHHHHHHHHHHHHHHhee
Confidence 3467888888888777655442 22222222233333222223333444444444555333455554
No 304
>PRK14759 potassium-transporting ATPase subunit F; Provisional
Probab=38.84 E-value=45 Score=20.42 Aligned_cols=20 Identities=25% Similarity=0.478 Sum_probs=13.6
Q ss_pred chHHHHHHHHHHHHHHHHhh
Q 040420 147 LPIAIAVAAVALAGLYFYLN 166 (169)
Q Consensus 147 lpi~~~~G~~al~~l~fyl~ 166 (169)
|++-.++|++..++++.||.
T Consensus 1 m~~~~~l~~~va~~L~vYL~ 20 (29)
T PRK14759 1 MILDYSLAGAVSLGLLIYLT 20 (29)
T ss_pred CcHHHHHHHHHHHHHHHHHH
Confidence 34455677777777888874
No 305
>smart00355 ZnF_C2H2 zinc finger.
Probab=38.61 E-value=11 Score=19.54 Aligned_cols=10 Identities=40% Similarity=1.428 Sum_probs=5.0
Q ss_pred EEcCCCCeee
Q 040420 79 YICRDCGYIY 88 (169)
Q Consensus 79 y~C~~CGyVY 88 (169)
|+|..|++.+
T Consensus 1 ~~C~~C~~~f 10 (26)
T smart00355 1 YRCPECGKVF 10 (26)
T ss_pred CCCCCCcchh
Confidence 3455555444
No 306
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.54 E-value=15 Score=31.13 Aligned_cols=39 Identities=28% Similarity=0.642 Sum_probs=22.5
Q ss_pred CCeEEcCCCCeeecCCCCC--------------CCCCCCCCCCCCC--CCccCee
Q 040420 76 KQAYICRDCGYIYNERKPF--------------DQLPDNYFCPVCG--APKRRFR 114 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF--------------~~lPd~~~CPvCg--apK~~F~ 114 (169)
...|.|.+|---|.+..|| +.+-..-.||+|+ -.+.+|.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~~ 183 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQFH 183 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhhe
Confidence 3469998887666654333 1122234899998 3444444
No 307
>PF09796 QCR10: Ubiquinol-cytochrome-c reductase complex subunit (QCR10); InterPro: IPR019182 This entry represents subunit 10 of the cytochrome b-c1 complex (also known as the ubiquinol-cytochrome c reductase complex or complex III). This complex is located on the inner mitochondrial membrane and it couples electron transfer from ubiquinol to cytochrome. Subunit 10 is required for stable association of the iron-sulphur protein with the complex [].
Probab=38.14 E-value=39 Score=23.88 Aligned_cols=21 Identities=19% Similarity=0.240 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHHHHHHHhhcC
Q 040420 148 PIAIAVAAVALAGLYFYLNSA 168 (169)
Q Consensus 148 pi~~~~G~~al~~l~fyl~~~ 168 (169)
|....+|+.++++++||...+
T Consensus 15 p~~a~wG~aa~~~v~~f~~~v 35 (64)
T PF09796_consen 15 PNLALWGGAAGAAVLFFTSGV 35 (64)
T ss_pred HHHHHHHHHHHHHHHHHhcCC
Confidence 677889999999999998753
No 308
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=38.13 E-value=22 Score=36.41 Aligned_cols=33 Identities=24% Similarity=0.638 Sum_probs=23.8
Q ss_pred CeEEcCCCCeeecCCC----CCCCCCCCCCCCCCCCCcc
Q 040420 77 QAYICRDCGYIYNERK----PFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~t----pF~~lPd~~~CPvCgapK~ 111 (169)
+.+-|+.||+.|.+.. .|...-. .||.|..--.
T Consensus 244 ~~~acp~~g~~~~eleprlFSFNsP~G--aCp~C~GlG~ 280 (935)
T COG0178 244 ENFACPVCGFSIPELEPRLFSFNSPFG--ACPTCDGLGV 280 (935)
T ss_pred cccCCCccCcccCCCCcccccCCCCCC--CCCcCCCcce
Confidence 3579999999999852 4555334 8999965333
No 309
>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=37.95 E-value=15 Score=26.65 Aligned_cols=23 Identities=26% Similarity=0.524 Sum_probs=8.3
Q ss_pred CCCCCCCCCCCCCCccCeeeCCC
Q 040420 96 QLPDNYFCPVCGAPKRRFRPYTP 118 (169)
Q Consensus 96 ~lPd~~~CPvCgapK~~F~~~~~ 118 (169)
.+|..|.||.|++.+.-=..++.
T Consensus 18 ~l~~~F~CPfC~~~~sV~v~idk 40 (81)
T PF05129_consen 18 KLPKVFDCPFCNHEKSVSVKIDK 40 (81)
T ss_dssp --SS----TTT--SS-EEEEEET
T ss_pred CCCceEcCCcCCCCCeEEEEEEc
Confidence 35666777777776665555543
No 310
>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=37.88 E-value=23 Score=26.83 Aligned_cols=36 Identities=17% Similarity=0.423 Sum_probs=22.4
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCe
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F 113 (169)
...|.|..||....+..+-..--. -||.|=+..---
T Consensus 2 ~~~F~C~~CG~~V~p~~~g~~~RN--HCP~CL~S~Hvd 37 (92)
T PF12647_consen 2 NESFTCVHCGLTVSPLAAGSAHRN--HCPSCLSSLHVD 37 (92)
T ss_pred CcccCccccCCCcccCCCCCCccC--cCcccccccccC
Confidence 356899999976644322222233 799997755433
No 311
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=37.78 E-value=20 Score=27.16 Aligned_cols=23 Identities=39% Similarity=0.872 Sum_probs=16.5
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCG 107 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCg 107 (169)
-|+.|++|-... .|.+ + .||.|+
T Consensus 5 AC~~C~~I~~~~-qf~~--~--gCpnC~ 27 (98)
T cd07973 5 ACLLCSLIKTED-QFER--D--GCPNCE 27 (98)
T ss_pred hhccCCcccccc-cccC--C--CCCCCc
Confidence 599999988543 2332 3 899996
No 312
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=37.34 E-value=25 Score=31.03 Aligned_cols=29 Identities=17% Similarity=0.124 Sum_probs=15.1
Q ss_pred CCCCCCCCccC---eeeCCCcccCCCChhHHH
Q 040420 102 FCPVCGAPKRR---FRPYTPAVTRGANDTAVR 130 (169)
Q Consensus 102 ~CPvCgapK~~---F~~~~~~~~~~~n~~~v~ 130 (169)
+||.||.--.- +..+.+.....-+|+||.
T Consensus 183 RCpECGqVFKLVr~~~s~~dg~dp~~~dpdv~ 214 (268)
T PTZ00043 183 RCGECDQIFMLVRVLYSLPDGEDPFPNDPDVD 214 (268)
T ss_pred cCCCCCcEEEEEEEEeecCCCCCCCCCCCchh
Confidence 78888762211 112444444566666664
No 313
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=36.87 E-value=37 Score=26.71 Aligned_cols=16 Identities=13% Similarity=0.243 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHh
Q 040420 150 AIAVAAVALAGLYFYL 165 (169)
Q Consensus 150 ~~~~G~~al~~l~fyl 165 (169)
|++.|++++.+|.+|+
T Consensus 72 gv~aGvIg~Illi~y~ 87 (122)
T PF01102_consen 72 GVMAGVIGIILLISYC 87 (122)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4566777776666665
No 314
>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=36.45 E-value=21 Score=22.40 Aligned_cols=17 Identities=35% Similarity=0.727 Sum_probs=12.6
Q ss_pred ccceecCCCCeEEcCCC
Q 040420 68 KFSMRVASKQAYICRDC 84 (169)
Q Consensus 68 ~~~~k~~~~~~y~C~~C 84 (169)
+.+......+.|+|.+|
T Consensus 19 k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 19 KNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eCCCCCCCCEeEecCcC
Confidence 34555567789999998
No 315
>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=36.32 E-value=15 Score=21.71 Aligned_cols=10 Identities=50% Similarity=1.158 Sum_probs=5.1
Q ss_pred CCCCCCCCcc
Q 040420 102 FCPVCGAPKR 111 (169)
Q Consensus 102 ~CPvCgapK~ 111 (169)
.||+||++-.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4999998654
No 316
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.05 E-value=19 Score=26.99 Aligned_cols=26 Identities=27% Similarity=0.686 Sum_probs=13.7
Q ss_pred EcCCCCeeecCCCCCCCC-CCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQL-PDNYFCPVCGA 108 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~l-Pd~~~CPvCga 108 (169)
.|++||-....... ..+ -| .||.|+.
T Consensus 3 lCP~C~v~l~~~~r-s~vEiD--~CPrCrG 29 (88)
T COG3809 3 LCPICGVELVMSVR-SGVEID--YCPRCRG 29 (88)
T ss_pred ccCcCCceeeeeee-cCceee--eCCcccc
Confidence 58888843332110 011 13 7888875
No 317
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=35.98 E-value=11 Score=30.10 Aligned_cols=23 Identities=30% Similarity=0.785 Sum_probs=16.7
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-.|+.||-.|... ..+ +||.|..
T Consensus 4 ~nC~~CgklF~~~-----~~~--iCp~C~~ 26 (137)
T TIGR03826 4 ANCPKCGRLFVKT-----GRD--VCPSCYE 26 (137)
T ss_pred ccccccchhhhhc-----CCc--cCHHHhH
Confidence 3699999766542 245 8999976
No 318
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=35.25 E-value=24 Score=30.35 Aligned_cols=26 Identities=35% Similarity=0.838 Sum_probs=13.3
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCG 107 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCg 107 (169)
.|+.||..-...+ ... -..|.||.|.
T Consensus 247 pC~~Cg~~I~~~~-~~g-R~t~~CP~CQ 272 (274)
T PRK01103 247 PCRRCGTPIEKIK-QGG-RSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCeeEEEE-ECC-CCcEECcCCC
Confidence 3888874432210 001 3457788875
No 319
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=34.98 E-value=20 Score=30.14 Aligned_cols=25 Identities=20% Similarity=0.499 Sum_probs=17.0
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.|+|++|+--.. .-...|+|+.+..
T Consensus 2 ~~~CP~C~~~l~------~~~~~~~C~~~h~ 26 (272)
T PRK11088 2 SYQCPLCHQPLT------LEENSWICPQNHQ 26 (272)
T ss_pred cccCCCCCcchh------cCCCEEEcCCCCC
Confidence 389999994432 2246799998654
No 320
>PHA00733 hypothetical protein
Probab=34.97 E-value=9.8 Score=29.56 Aligned_cols=33 Identities=24% Similarity=0.702 Sum_probs=20.5
Q ss_pred CeEEcCCCCeeecCCCCCC---CC-CCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFD---QL-PDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~---~l-Pd~~~CPvCgap 109 (169)
..|+|..||..|.....+. .. ...+.|++|+..
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~ 108 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKE 108 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCc
Confidence 4599999998877521000 00 123699999863
No 321
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=34.73 E-value=37 Score=30.89 Aligned_cols=29 Identities=24% Similarity=0.435 Sum_probs=18.6
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-.|.|..||+....+. +...++ .||.|+.
T Consensus 232 ~v~~C~~c~~~~~~~~-~~~~~~--~C~~c~~ 260 (374)
T TIGR00308 232 YTYHCSRCLHNKPVNG-ISQRKG--RCKECGG 260 (374)
T ss_pred eEEECCCccccccccc-ccCCCC--CCCCCCC
Confidence 3788999997643221 122234 7999997
No 322
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=34.61 E-value=32 Score=32.45 Aligned_cols=33 Identities=27% Similarity=0.578 Sum_probs=23.3
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
+...+.|+.|||.-+.++ -++|.--.||.|...
T Consensus 224 ED~l~~C~~C~~s~n~e~--~~~sk~~~Cp~C~~~ 256 (457)
T KOG2324|consen 224 EDTLMSCPSCGYSKNSED--LDLSKIASCPKCNEG 256 (457)
T ss_pred ccceeecCcCCccCchhh--hcCCccccCCcccCC
Confidence 445899999998776653 134533489999884
No 323
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.50 E-value=21 Score=30.52 Aligned_cols=32 Identities=19% Similarity=0.384 Sum_probs=22.7
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeee
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRP 115 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~ 115 (169)
-+|+|.+|.|..+-+ +-+ +|++|.-...-...
T Consensus 48 lIYkC~~Cd~tWN~~-----Ife--R~~~~~Iep~llea 79 (203)
T COG4332 48 LIYKCTHCDYTWNIS-----IFE--RLNVSDIEPDLLEA 79 (203)
T ss_pred EEEEeeccCCccchh-----hhh--ccCcccCCHHHHHH
Confidence 489999999999863 234 78888765544443
No 324
>TIGR00847 ccoS cytochrome oxidase maturation protein, cbb3-type. CcoS from Rhodobacter capsulatus has been shown essential for incorporation of redox-active prosthetic groups (heme, Cu) into cytochrome cbb(3) oxidase. FixS of Bradyrhizobium japonicum appears to have the same function. Members of this family are found so far in organisms with a cbb3-type cytochrome oxidase, including Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Caulobacter crescentus, Bradyrhizobium japonicum, and Rhodobacter capsulatus.
Probab=34.39 E-value=48 Score=22.47 Aligned_cols=19 Identities=26% Similarity=0.634 Sum_probs=14.2
Q ss_pred chHHHHHHHHHHHHHHHHh
Q 040420 147 LPIAIAVAAVALAGLYFYL 165 (169)
Q Consensus 147 lpi~~~~G~~al~~l~fyl 165 (169)
+|+++++|++++++++.-+
T Consensus 8 IpiSl~l~~~~l~~f~Wav 26 (51)
T TIGR00847 8 IPISLLLGGVGLVAFLWSL 26 (51)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4778888888888766554
No 325
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=34.31 E-value=21 Score=31.27 Aligned_cols=34 Identities=26% Similarity=0.619 Sum_probs=20.8
Q ss_pred CeEEcCCCCeeecCCCCCCCCC-CCCCCCCCCCCcc
Q 040420 77 QAYICRDCGYIYNERKPFDQLP-DNYFCPVCGAPKR 111 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lP-d~~~CPvCgapK~ 111 (169)
..-+|..|-+- ++-....+-| +.|+||-|.+--+
T Consensus 191 ~alIC~~C~hh-ngl~~~~ek~~~efiC~~Cn~~n~ 225 (251)
T COG5415 191 KALICPQCHHH-NGLYRLAEKPIIEFICPHCNHKND 225 (251)
T ss_pred hhhcccccccc-ccccccccccchheecccchhhcC
Confidence 35699999843 2211112223 4599999998554
No 326
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.31 E-value=26 Score=31.10 Aligned_cols=26 Identities=31% Similarity=0.893 Sum_probs=16.2
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCG 107 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCg 107 (169)
-|+.||-+-... -++. -..|.||.|.
T Consensus 247 pC~~CGt~I~k~-~~~g-R~t~~CP~CQ 272 (273)
T COG0266 247 PCRRCGTPIEKI-KLGG-RSTFYCPVCQ 272 (273)
T ss_pred CCCccCCEeEEE-EEcC-CcCEeCCCCC
Confidence 599999655431 1112 3568899995
No 327
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=34.16 E-value=7.2 Score=24.66 Aligned_cols=34 Identities=21% Similarity=0.674 Sum_probs=21.3
Q ss_pred CCCCeEEcCCCCeeecCC---CC---CCCCCCCCCCCCCC
Q 040420 74 ASKQAYICRDCGYIYNER---KP---FDQLPDNYFCPVCG 107 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~---tp---F~~lPd~~~CPvCg 107 (169)
.....-+|..|+..|-.. .+ .+.....|.||.|.
T Consensus 10 ~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 10 DDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp TTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred CCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 345567899999777662 11 11223489999884
No 328
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=33.96 E-value=32 Score=31.66 Aligned_cols=31 Identities=32% Similarity=0.851 Sum_probs=18.4
Q ss_pred eEEcCCCCeeecCC-CCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNER-KPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~-tpF~~lPd~~~CPvCgap 109 (169)
.|+|..||+.-... .+..+ .+...||.||..
T Consensus 320 ~~rc~~c~~~~~~~~~~~~~-~~~~~~~~~~~~ 351 (403)
T TIGR03676 320 TFKCPNCGYEEEKTVKPEEG-DKSEACPKCGSE 351 (403)
T ss_pred EEEcCCCCcceeeecccccc-cccccCcccCcc
Confidence 49999999754321 11111 122479999985
No 329
>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]
Probab=33.83 E-value=19 Score=36.17 Aligned_cols=45 Identities=22% Similarity=0.408 Sum_probs=29.9
Q ss_pred CCeEEcCCCCeeecCC---CCCCCCCCCCCCCCCCCCccCeeeCCCcccC
Q 040420 76 KQAYICRDCGYIYNER---KPFDQLPDNYFCPVCGAPKRRFRPYTPAVTR 122 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~---tpF~~lPd~~~CPvCgapK~~F~~~~~~~~~ 122 (169)
...|.|..||++.-+- .-++--|. .||-|....-.+...+..+.+
T Consensus 290 ~vky~C~KC~~vlgPF~qs~n~evkp~--~C~~cqSkGpf~vn~e~Tvyr 337 (854)
T KOG0477|consen 290 VVKYDCLKCGFVLGPFVQSSNSEVKPG--SCPECQSKGPFEVNVEETVYR 337 (854)
T ss_pred HHhhhHHhhCCccCceeeccCceeCCC--CCccccCCCCCccchhhhhhc
Confidence 3479999999876541 11112266 899999887666666655544
No 330
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=33.77 E-value=33 Score=27.85 Aligned_cols=16 Identities=25% Similarity=0.455 Sum_probs=12.7
Q ss_pred CCCeEEcCCCCeeecC
Q 040420 75 SKQAYICRDCGYIYNE 90 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~ 90 (169)
+...|+|.+|..+-.+
T Consensus 77 d~~lYeCnIC~etS~e 92 (140)
T PF05290_consen 77 DPKLYECNICKETSAE 92 (140)
T ss_pred CCCceeccCcccccch
Confidence 3479999999977665
No 331
>PHA00616 hypothetical protein
Probab=33.39 E-value=9.9 Score=25.12 Aligned_cols=12 Identities=42% Similarity=1.099 Sum_probs=8.7
Q ss_pred EEcCCCCeeecC
Q 040420 79 YICRDCGYIYNE 90 (169)
Q Consensus 79 y~C~~CGyVYd~ 90 (169)
|+|.-||.++.-
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 778888876654
No 332
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=33.39 E-value=18 Score=27.98 Aligned_cols=8 Identities=38% Similarity=1.394 Sum_probs=5.1
Q ss_pred eEEcCCCC
Q 040420 78 AYICRDCG 85 (169)
Q Consensus 78 ~y~C~~CG 85 (169)
.|-|+.||
T Consensus 22 ~FtCp~Cg 29 (104)
T COG4888 22 TFTCPRCG 29 (104)
T ss_pred eEecCccC
Confidence 46666666
No 333
>PRK10996 thioredoxin 2; Provisional
Probab=32.79 E-value=45 Score=25.43 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=19.0
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
-+|..|.-+|... -+..-+.-.||.|++.
T Consensus 3 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~ 31 (139)
T PRK10996 3 TVCTSCQAINRLP--DERIEDAAKCGRCGHD 31 (139)
T ss_pred EECCCCCCcCCCC--CccccCCCcCCCCCCc
Confidence 3799999888542 2223344589999873
No 334
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=32.73 E-value=11 Score=28.54 Aligned_cols=9 Identities=33% Similarity=1.014 Sum_probs=5.4
Q ss_pred CCCCCCCCC
Q 040420 99 DNYFCPVCG 107 (169)
Q Consensus 99 d~~~CPvCg 107 (169)
..|.|-+|.
T Consensus 93 ~~WlC~vC~ 101 (118)
T PF02318_consen 93 PIWLCKVCQ 101 (118)
T ss_dssp CCEEEHHHH
T ss_pred CCEEChhhH
Confidence 346776663
No 335
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.48 E-value=31 Score=35.22 Aligned_cols=30 Identities=30% Similarity=0.800 Sum_probs=21.6
Q ss_pred CeEEcCCCCeeecCCC----CCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERK----PFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~t----pF~~lPd~~~CPvCga 108 (169)
..+.|..||+.|.+-+ .|.. |. -.||.|+.
T Consensus 249 ~~~~c~~~g~~~~~~~~~~FSfNs-p~-G~Cp~C~G 282 (924)
T TIGR00630 249 KHAACPECGFSLPELEPRLFSFNS-PY-GACPECSG 282 (924)
T ss_pred hcccCcccCcccCcCChhhcCCCC-Cc-CCCCCCcc
Confidence 3578999999998643 4555 32 38999965
No 336
>PRK10445 endonuclease VIII; Provisional
Probab=32.27 E-value=29 Score=29.80 Aligned_cols=9 Identities=44% Similarity=1.254 Sum_probs=4.7
Q ss_pred CCCCCCCCC
Q 040420 99 DNYFCPVCG 107 (169)
Q Consensus 99 d~~~CPvCg 107 (169)
..|.||.|.
T Consensus 254 ~t~~CP~CQ 262 (263)
T PRK10445 254 PFYWCPGCQ 262 (263)
T ss_pred CcEECCCCc
Confidence 345566553
No 337
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=32.25 E-value=28 Score=29.74 Aligned_cols=33 Identities=24% Similarity=0.537 Sum_probs=24.4
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeC
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPY 116 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~ 116 (169)
.......|..||..-+. | .|.+|..+.+....+
T Consensus 50 a~~~i~~C~~C~~~te~--------d--~C~ICsd~~Rd~~~i 82 (198)
T COG0353 50 AKENIKHCSVCGNLTES--------D--PCDICSDESRDKSQL 82 (198)
T ss_pred HHhcCccccccCCcCCC--------C--cCcCcCCcccCCceE
Confidence 45567899999965543 3 899999887776644
No 338
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=32.03 E-value=32 Score=27.73 Aligned_cols=22 Identities=55% Similarity=1.322 Sum_probs=16.5
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
+.|..|++.|+.. .+ .||+|+.
T Consensus 78 ~~c~pc~~lF~~~------~~--~cp~c~~ 99 (170)
T cd03361 78 KRCRDCGYQFTED------SD--KCPRCGS 99 (170)
T ss_pred eccCCcccccccc------cc--cCCcCCC
Confidence 4899999998632 23 7999984
No 339
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=32.02 E-value=24 Score=29.04 Aligned_cols=13 Identities=31% Similarity=0.790 Sum_probs=6.7
Q ss_pred eEEcCCCCeeecC
Q 040420 78 AYICRDCGYIYNE 90 (169)
Q Consensus 78 ~y~C~~CGyVYd~ 90 (169)
.|+|+.|-.-|-.
T Consensus 17 KYKCpkC~vPYCS 29 (157)
T KOG2857|consen 17 KYKCPKCSVPYCS 29 (157)
T ss_pred hccCCCCCCcccc
Confidence 4555555544443
No 340
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=31.97 E-value=22 Score=29.50 Aligned_cols=18 Identities=33% Similarity=0.728 Sum_probs=14.3
Q ss_pred CCCCeEEcCCCCeeecCC
Q 040420 74 ASKQAYICRDCGYIYNER 91 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~ 91 (169)
....-|+|..||-+|=.|
T Consensus 126 ~~~~f~~C~~CgkiYW~G 143 (165)
T COG1656 126 NYEEFYRCPKCGKIYWKG 143 (165)
T ss_pred cccceeECCCCcccccCc
Confidence 344579999999999765
No 341
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.96 E-value=20 Score=32.38 Aligned_cols=47 Identities=28% Similarity=0.429 Sum_probs=24.3
Q ss_pred CCCeeecCC---CCCCCCCCCCCCCCCCCC--ccCeeeCCCcccCCCChhHHHH
Q 040420 83 DCGYIYNER---KPFDQLPDNYFCPVCGAP--KRRFRPYTPAVTRGANDTAVRK 131 (169)
Q Consensus 83 ~CGyVYd~~---tpF~~lPd~~~CPvCgap--K~~F~~~~~~~~~~~n~~~v~~ 131 (169)
.|||.+-.. .-|..-+. .||+|+.+ +..|.+..-....-..+.++|+
T Consensus 25 ~CGH~~C~sCv~~l~~~~~~--~CP~C~~~lrk~~fr~q~F~D~~vekEV~iRk 76 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVRGSG--SCPECDTPLRKNNFRVQLFEDPTVEKEVDIRK 76 (309)
T ss_pred CCCCcccHHHHHHHhcCCCC--CCCCCCCccchhhccccccccHHHHHHHHHHH
Confidence 467666552 12333333 89999884 4446544333322334455555
No 342
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=31.92 E-value=25 Score=34.48 Aligned_cols=8 Identities=50% Similarity=1.331 Sum_probs=6.0
Q ss_pred CCCCCCCC
Q 040420 102 FCPVCGAP 109 (169)
Q Consensus 102 ~CPvCgap 109 (169)
.||.||+.
T Consensus 29 ~Cp~CG~~ 36 (645)
T PRK14559 29 PCPQCGTE 36 (645)
T ss_pred cCCCCCCC
Confidence 68888875
No 343
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=31.88 E-value=33 Score=24.02 Aligned_cols=31 Identities=16% Similarity=0.410 Sum_probs=19.6
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.....+=-.||.++.+...-+.. -+||.|..
T Consensus 22 v~G~pVvALCGk~wvp~rdp~~~---PVCP~Ck~ 52 (58)
T PF11238_consen 22 VMGTPVVALCGKVWVPTRDPKPF---PVCPECKE 52 (58)
T ss_pred hcCceeEeeeCceeCCCCCCCCC---CCCcCHHH
Confidence 33455666799999886432232 36999853
No 344
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=31.87 E-value=23 Score=28.45 Aligned_cols=14 Identities=36% Similarity=0.954 Sum_probs=12.0
Q ss_pred CeEEcCCCCeeecC
Q 040420 77 QAYICRDCGYIYNE 90 (169)
Q Consensus 77 ~~y~C~~CGyVYd~ 90 (169)
-+|+|..|+++++-
T Consensus 12 LIYrC~~C~~TwN~ 25 (142)
T PF06353_consen 12 LIYRCEKCDYTWNM 25 (142)
T ss_pred EEEEcccCcCcccc
Confidence 38999999988875
No 345
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=31.71 E-value=24 Score=28.62 Aligned_cols=26 Identities=23% Similarity=0.598 Sum_probs=18.5
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
..+|..||-...+. .|.+ ..||.||.
T Consensus 149 ~a~~~~~g~~~~~~-~~~~----~~c~~~~~ 174 (189)
T PRK09521 149 YAMCSRCRTPLVKK-GENE----LKCPNCGN 174 (189)
T ss_pred EEEccccCCceEEC-CCCE----EECCCCCC
Confidence 45899999777653 2333 48999996
No 346
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=31.65 E-value=27 Score=32.37 Aligned_cols=11 Identities=45% Similarity=1.440 Sum_probs=8.0
Q ss_pred CCCCCCCCCCC
Q 040420 98 PDNYFCPVCGA 108 (169)
Q Consensus 98 Pd~~~CPvCga 108 (169)
|..|.||.|+-
T Consensus 77 ~qSftCPyC~~ 87 (381)
T KOG1280|consen 77 PQSFTCPYCGI 87 (381)
T ss_pred cccccCCcccc
Confidence 56788888865
No 347
>PRK09401 reverse gyrase; Reviewed
Probab=31.51 E-value=22 Score=37.14 Aligned_cols=23 Identities=48% Similarity=1.250 Sum_probs=17.1
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
..+|..||+.++.. .+ .||.|+.
T Consensus 678 ~k~c~~~g~~f~~~------~~--~~~~c~~ 700 (1176)
T PRK09401 678 IKRCRDCGYQFTDE------SD--KCPRCGS 700 (1176)
T ss_pred eccccccccccccc------cc--ccccccc
Confidence 44799999888653 23 8999974
No 348
>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=31.35 E-value=17 Score=29.67 Aligned_cols=40 Identities=20% Similarity=0.520 Sum_probs=19.1
Q ss_pred cceecCCCCeEEcCCCCeeecCCCCCCC-----CCCCCCCCCCCC
Q 040420 69 FSMRVASKQAYICRDCGYIYNERKPFDQ-----LPDNYFCPVCGA 108 (169)
Q Consensus 69 ~~~k~~~~~~y~C~~CGyVYd~~tpF~~-----lPd~~~CPvCga 108 (169)
+.++.-+.-...|+.||..+.=..-|++ .+..+.||.|+.
T Consensus 9 erf~~c~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 9 ERFKDCEPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp TTTTT---EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred HHhcCCCceEeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 4445555557899999966543222221 255789999998
No 349
>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]
Probab=31.34 E-value=28 Score=35.85 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=20.1
Q ss_pred CeEEcCCCCeeecCCCCCC-CCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFD-QLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~-~lPd~~~CPvCga 108 (169)
.+|+|..||+.+.++.|=. .--+.|+||.|..
T Consensus 672 ~i~~C~~cgt~F~~eqp~kg~~~kelr~pd~~k 704 (1096)
T KOG1859|consen 672 SIYRCVNCGTQFLIEQPEKGSKIKELRCPDSRK 704 (1096)
T ss_pred ceeeeccccccccccCcccccchhhhcCcchhh
Confidence 3899999998887753311 1234466666643
No 350
>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=31.33 E-value=46 Score=29.85 Aligned_cols=11 Identities=27% Similarity=0.585 Sum_probs=8.8
Q ss_pred CCCCCCCCccC
Q 040420 102 FCPVCGAPKRR 112 (169)
Q Consensus 102 ~CPvCgapK~~ 112 (169)
.||.||..+.-
T Consensus 226 ~C~~Cg~~~~l 236 (305)
T TIGR01562 226 KCSHCEESKHL 236 (305)
T ss_pred cCCCCCCCCce
Confidence 89999997643
No 351
>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=31.25 E-value=16 Score=37.29 Aligned_cols=12 Identities=25% Similarity=0.459 Sum_probs=0.0
Q ss_pred CCeEEcCCCCee
Q 040420 76 KQAYICRDCGYI 87 (169)
Q Consensus 76 ~~~y~C~~CGyV 87 (169)
....+|+.||..
T Consensus 653 i~~r~Cp~Cg~~ 664 (900)
T PF03833_consen 653 IGRRRCPKCGKE 664 (900)
T ss_dssp ------------
T ss_pred eecccCcccCCc
Confidence 345677777743
No 352
>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=31.07 E-value=15 Score=29.43 Aligned_cols=38 Identities=26% Similarity=0.555 Sum_probs=28.3
Q ss_pred EEcCCCCeeecCC-CCCCCCC--CCCCCCCCCCCccCeeeC
Q 040420 79 YICRDCGYIYNER-KPFDQLP--DNYFCPVCGAPKRRFRPY 116 (169)
Q Consensus 79 y~C~~CGyVYd~~-tpF~~lP--d~~~CPvCgapK~~F~~~ 116 (169)
-.|+.||-.+... ..|+.-. .-|+|-.|..|-++|+.+
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf~~fk~~ 146 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEPFEYFKPI 146 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcHhhcccC
Confidence 5899999766552 3566542 448999999999999853
No 353
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=31.04 E-value=28 Score=32.62 Aligned_cols=26 Identities=31% Similarity=0.768 Sum_probs=13.0
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.-+|+-||-.|.+.. ..-.|++|+..
T Consensus 380 ~v~CP~cgA~y~~~~------kG~lC~vC~l~ 405 (422)
T PF06957_consen 380 SVKCPYCGAKYHPEY------KGQLCPVCELS 405 (422)
T ss_dssp EEE-TTT--EEEGGG------TTSB-TTTTTB
T ss_pred CeeCCCCCCccChhh------CCCCCCCCcce
Confidence 346888887777631 11278888763
No 354
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=30.94 E-value=21 Score=24.74 Aligned_cols=12 Identities=42% Similarity=1.425 Sum_probs=9.0
Q ss_pred CCCCCCCCCCCC
Q 040420 97 LPDNYFCPVCGA 108 (169)
Q Consensus 97 lPd~~~CPvCga 108 (169)
+|+.+.||+|+.
T Consensus 1 iP~~f~CpIt~~ 12 (73)
T PF04564_consen 1 IPDEFLCPITGE 12 (73)
T ss_dssp SSGGGB-TTTSS
T ss_pred CCcccCCcCcCc
Confidence 478889999987
No 355
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=30.66 E-value=20 Score=24.65 Aligned_cols=10 Identities=60% Similarity=1.713 Sum_probs=2.8
Q ss_pred CCCCCCCCCC
Q 040420 100 NYFCPVCGAP 109 (169)
Q Consensus 100 ~~~CPvCgap 109 (169)
.|+||+||+-
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 3678888774
No 356
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=30.57 E-value=30 Score=31.93 Aligned_cols=27 Identities=26% Similarity=0.621 Sum_probs=17.4
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
.-.|.+||- .+..|.||.|+.+-=-.+
T Consensus 7 ~~~C~ic~v----------q~~~YtCPRCn~~YCsl~ 33 (383)
T KOG4317|consen 7 FLACGICGV----------QKREYTCPRCNLLYCSLK 33 (383)
T ss_pred eeecccccc----------ccccccCCCCCccceeee
Confidence 347888881 245589999987644333
No 357
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=30.56 E-value=36 Score=33.86 Aligned_cols=23 Identities=39% Similarity=0.871 Sum_probs=15.7
Q ss_pred EcCCCCee--ecCCCCCCCCCCCCCCCCCCCCc
Q 040420 80 ICRDCGYI--YNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 80 ~C~~CGyV--Yd~~tpF~~lPd~~~CPvCgapK 110 (169)
.|+.||.. |.++ =..|..||..|
T Consensus 726 ~Cp~Cg~~l~~~~G--------C~~C~~CG~sk 750 (752)
T PRK08665 726 ACPECGSILEHEEG--------CVVCHSCGYSK 750 (752)
T ss_pred CCCCCCcccEECCC--------CCcCCCCCCCC
Confidence 59999943 3343 23899998765
No 358
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.53 E-value=35 Score=29.49 Aligned_cols=28 Identities=25% Similarity=0.577 Sum_probs=15.9
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.|+.||..-.-.. ... -..|.||.|...
T Consensus 237 pC~~Cg~~I~~~~-~~g-R~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTPIEKIV-VGG-RGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCeeEEEE-ECC-CCcEECCCCcCC
Confidence 5888885433210 001 356888888653
No 359
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.01 E-value=27 Score=30.20 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=11.7
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCG 107 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCg 107 (169)
.|+.||..-.... ... -..|.||.|.
T Consensus 246 pCprCG~~I~~~~-~~g-R~t~~CP~CQ 271 (272)
T PRK14810 246 PCLNCKTPIRRVV-VAG-RSSHYCPHCQ 271 (272)
T ss_pred cCCCCCCeeEEEE-ECC-CccEECcCCc
Confidence 5666664332210 001 3446666664
No 360
>PF06093 Spt4: Spt4/RpoE2 zinc finger; InterPro: IPR022800 This entry consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 []. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles []. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in []. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. ; PDB: 2EXU_A 3H7H_A 3LPE_F 3P8B_A 1RYQ_A 3QQC_E.
Probab=29.87 E-value=27 Score=25.26 Aligned_cols=22 Identities=36% Similarity=0.899 Sum_probs=12.9
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVC 106 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvC 106 (169)
-|..|+.|..... |.+ + .||.|
T Consensus 3 AC~~C~~i~t~~q-F~~--~--gCpnC 24 (77)
T PF06093_consen 3 ACLRCRLIKTEDQ-FRD--E--GCPNC 24 (77)
T ss_dssp EETTT-BEECCCH-HHH--H----TTT
T ss_pred ccccCCcccCHhH-ccC--C--CCCCC
Confidence 4999999987541 222 2 69999
No 361
>KOG1868 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=29.74 E-value=29 Score=34.26 Aligned_cols=20 Identities=20% Similarity=0.640 Sum_probs=13.0
Q ss_pred CCCCC--CCCCCCCCCCCCccC
Q 040420 93 PFDQL--PDNYFCPVCGAPKRR 112 (169)
Q Consensus 93 pF~~l--Pd~~~CPvCgapK~~ 112 (169)
..+++ -+.|.||.|++..+-
T Consensus 508 ~~ekle~~~~w~Cp~c~~~~~~ 529 (653)
T KOG1868|consen 508 KEEKLEGDEAWLCPRCKHKESS 529 (653)
T ss_pred chhhcccccccCCccccCcccc
Confidence 33444 345999999985443
No 362
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=29.74 E-value=29 Score=22.36 Aligned_cols=23 Identities=30% Similarity=0.781 Sum_probs=11.3
Q ss_pred EcCCCCeeecCCCCCCCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQLPDNYFCPVCG 107 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~lPd~~~CPvCg 107 (169)
.|..||..--.. --....||.|+
T Consensus 19 ~Cp~C~~PL~~~-----k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLMRD-----KDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeEEe-----cCCCEECCCCC
Confidence 577776443221 11224677774
No 363
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=29.52 E-value=24 Score=27.57 Aligned_cols=25 Identities=24% Similarity=0.534 Sum_probs=17.4
Q ss_pred EEcCCCCeeecCCCCCCCCC-CCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLP-DNYFCPVCGAP 109 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lP-d~~~CPvCgap 109 (169)
+-|+.|....... + +.|.|+.|+..
T Consensus 35 ~aC~~C~kkv~~~------~~~~~~C~~C~~~ 60 (166)
T cd04476 35 PACPGCNKKVVEE------GNGTYRCEKCNKS 60 (166)
T ss_pred ccccccCcccEeC------CCCcEECCCCCCc
Confidence 3799998654432 3 56899999874
No 364
>KOG4784 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.42 E-value=39 Score=31.11 Aligned_cols=37 Identities=19% Similarity=0.414 Sum_probs=26.6
Q ss_pred eecCCCCeEEcCCCCeeecCC-----------CCCCCCCCCCCCCCCC
Q 040420 71 MRVASKQAYICRDCGYIYNER-----------KPFDQLPDNYFCPVCG 107 (169)
Q Consensus 71 ~k~~~~~~y~C~~CGyVYd~~-----------tpF~~lPd~~~CPvCg 107 (169)
.+..+...+.|.+|+.+-... .=|.++||.|.|+.|+
T Consensus 96 ~~~~~~~s~~C~~C~e~ii~~r~~~~l~~lPSe~W~el~d~w~CH~~~ 143 (348)
T KOG4784|consen 96 LREDEPCSFHCLNCKEEIIGQRSYRSLNELPSENWTELPDCWSCHNDE 143 (348)
T ss_pred hccCCCceeEeccCcceEeccchhhhhhhcChhhhhhcCceecccCCc
Confidence 334445689999999765531 2367889999999964
No 365
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.99 E-value=36 Score=29.52 Aligned_cols=9 Identities=33% Similarity=1.102 Sum_probs=5.4
Q ss_pred CCCCCCCCC
Q 040420 99 DNYFCPVCG 107 (169)
Q Consensus 99 d~~~CPvCg 107 (169)
..|.||.|.
T Consensus 273 ~t~~CP~CQ 281 (282)
T PRK13945 273 STHWCPNCQ 281 (282)
T ss_pred ccEECCCCc
Confidence 446666664
No 366
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.96 E-value=40 Score=28.43 Aligned_cols=15 Identities=33% Similarity=0.862 Sum_probs=12.4
Q ss_pred CCCCCCCCccCeeeC
Q 040420 102 FCPVCGAPKRRFRPY 116 (169)
Q Consensus 102 ~CPvCgapK~~F~~~ 116 (169)
.||+|..++..+..+
T Consensus 191 ~CPiC~~~~~s~~~v 205 (207)
T KOG1100|consen 191 ICPICRSPKTSSVEV 205 (207)
T ss_pred cCCCCcChhhceeec
Confidence 599999999887753
No 367
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=28.24 E-value=41 Score=29.34 Aligned_cols=33 Identities=27% Similarity=0.771 Sum_probs=23.6
Q ss_pred CCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCC
Q 040420 84 CGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYT 117 (169)
Q Consensus 84 CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~ 117 (169)
|.+..-+.+. +++|+...||.|+.+=..|+.|.
T Consensus 199 C~~~~~p~~~-g~ipe~i~CpeC~R~MEk~v~Yk 231 (235)
T PF14577_consen 199 CNRLEFPNSA-GRIPETIVCPECGRPMEKFVMYK 231 (235)
T ss_pred CeeEeccCcc-cCCCceeECCCCCCchhhceeee
Confidence 4444334332 56799999999999988888763
No 368
>TIGR01351 adk adenylate kinases. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
Probab=28.01 E-value=48 Score=26.60 Aligned_cols=30 Identities=23% Similarity=0.442 Sum_probs=19.5
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
..+.|..||.+|+.. |...++...|..|+.
T Consensus 123 ~R~~~~~~g~~y~~~--~~~p~~~~~~~~~~~ 152 (210)
T TIGR01351 123 GRRICPSCGRVYHLK--FNPPKVPGCDDCTGE 152 (210)
T ss_pred CCCccCCcCCccccc--cCCCccCCcCcccCC
Confidence 368999999999864 222223346777753
No 369
>PHA02768 hypothetical protein; Provisional
Probab=27.78 E-value=23 Score=24.35 Aligned_cols=31 Identities=32% Similarity=0.574 Sum_probs=18.7
Q ss_pred eEEcCCCCeeecCCCCC----CCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPF----DQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF----~~lPd~~~CPvCga 108 (169)
.|+|..||..|.-...+ ..-...+.|..|+-
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCcccCCcccc
Confidence 48999999988762000 00012348888876
No 370
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.50 E-value=41 Score=28.97 Aligned_cols=7 Identities=57% Similarity=1.635 Sum_probs=3.7
Q ss_pred CCCCCCC
Q 040420 100 NYFCPVC 106 (169)
Q Consensus 100 ~~~CPvC 106 (169)
.|.||.|
T Consensus 265 t~~CP~C 271 (272)
T TIGR00577 265 THFCPQC 271 (272)
T ss_pred CEECCCC
Confidence 3555555
No 371
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=27.36 E-value=39 Score=28.01 Aligned_cols=29 Identities=28% Similarity=0.640 Sum_probs=18.3
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.|+|..|... +.--||+. -...+|+.|++
T Consensus 152 GfiCe~C~~~-~~IfPF~~-~~~~~C~~C~~ 180 (202)
T PF13901_consen 152 GFICEICNSD-DIIFPFQI-DTTVRCPKCKS 180 (202)
T ss_pred CCCCccCCCC-CCCCCCCC-CCeeeCCcCcc
Confidence 5777777644 44457766 24457777776
No 372
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.36 E-value=22 Score=24.40 Aligned_cols=17 Identities=47% Similarity=0.976 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCCCccCe
Q 040420 96 QLPDNYFCPVCGAPKRRF 113 (169)
Q Consensus 96 ~lPd~~~CPvCgapK~~F 113 (169)
.+|+. .||+|+.|-..-
T Consensus 9 ~lp~K-ICpvCqRPFsWR 25 (54)
T COG4338 9 TLPDK-ICPVCQRPFSWR 25 (54)
T ss_pred ccchh-hhhhhcCchHHH
Confidence 46663 899999875543
No 373
>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=27.30 E-value=39 Score=28.44 Aligned_cols=10 Identities=40% Similarity=1.119 Sum_probs=7.3
Q ss_pred CCCCCCCCCc
Q 040420 101 YFCPVCGAPK 110 (169)
Q Consensus 101 ~~CPvCgapK 110 (169)
..||.||+-+
T Consensus 36 ~~C~~Cg~~~ 45 (236)
T PF04981_consen 36 TICPKCGRYR 45 (236)
T ss_pred eECCCCCCEE
Confidence 5788888833
No 374
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=27.21 E-value=36 Score=24.92 Aligned_cols=17 Identities=24% Similarity=0.608 Sum_probs=10.2
Q ss_pred cCCCCeEEcCCCCeeec
Q 040420 73 VASKQAYICRDCGYIYN 89 (169)
Q Consensus 73 ~~~~~~y~C~~CGyVYd 89 (169)
.+.+..|+|..||..++
T Consensus 60 VENMs~~~Cp~Cg~~~~ 76 (81)
T PF10609_consen 60 VENMSYFVCPHCGERIY 76 (81)
T ss_dssp EECT-EEE-TTT--EEE
T ss_pred EECCCccCCCCCCCeec
Confidence 45777899999998775
No 375
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=27.01 E-value=53 Score=23.32 Aligned_cols=44 Identities=30% Similarity=0.739 Sum_probs=26.5
Q ss_pred CccceecCCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC-CccCeeeCC
Q 040420 67 PKFSMRVASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA-PKRRFRPYT 117 (169)
Q Consensus 67 p~~~~k~~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga-pK~~F~~~~ 117 (169)
+.++.+.....--.|+-||.. .|...-. .|-.||- |..+.+.|.
T Consensus 6 ~SfGKr~~k~tHt~CrRCG~~-----syh~qK~--~CasCGygps~k~R~Yn 50 (62)
T PRK04179 6 PSMGKRNKGKTHIRCRRCGRH-----SYNVRKK--YCAACGFGRSKRIRRYS 50 (62)
T ss_pred cccccccCCcccchhcccCcc-----ccccccc--chhhcCCCccccccccc
Confidence 345544333234489999933 2222234 8999999 676666654
No 376
>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=26.95 E-value=34 Score=24.07 Aligned_cols=10 Identities=50% Similarity=1.344 Sum_probs=6.3
Q ss_pred CCCCCCCCCc
Q 040420 101 YFCPVCGAPK 110 (169)
Q Consensus 101 ~~CPvCgapK 110 (169)
|.||.||...
T Consensus 1 y~C~KCg~~~ 10 (64)
T PF09855_consen 1 YKCPKCGNEE 10 (64)
T ss_pred CCCCCCCCcc
Confidence 5677777643
No 377
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=26.83 E-value=32 Score=31.46 Aligned_cols=26 Identities=38% Similarity=0.967 Sum_probs=15.5
Q ss_pred EcCCCCeeecCCCCCCC-CCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQ-LPDNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~-lPd~~~CPvCgap 109 (169)
.|.+||-+.... |+. .+. .||.||.+
T Consensus 317 fc~ncG~~~t~~--~~ng~a~--fcp~cgq~ 343 (345)
T COG4260 317 FCLNCGCGTTAD--FDNGKAK--FCPECGQG 343 (345)
T ss_pred cccccCcccccC--Cccchhh--hChhhcCC
Confidence 788888444332 111 145 89999865
No 378
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=26.77 E-value=45 Score=34.15 Aligned_cols=30 Identities=30% Similarity=0.835 Sum_probs=21.6
Q ss_pred CeEEcCCCCeeecCCC----CCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERK----PFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~t----pF~~lPd~~~CPvCga 108 (169)
..+.|..||..|.+-+ .|.. |. -.||.|+.
T Consensus 251 ~~~~c~~~g~~~~~~~p~~FSfN~-p~-G~Cp~C~G 284 (943)
T PRK00349 251 EKFACPVCGFSIPELEPRLFSFNS-PY-GACPTCDG 284 (943)
T ss_pred ccccCcccCCCcCcCChhhcCCCC-cc-CCCCcCCC
Confidence 4679999999998643 4555 33 28999965
No 379
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=26.76 E-value=43 Score=33.25 Aligned_cols=30 Identities=27% Similarity=0.660 Sum_probs=18.9
Q ss_pred CCCeEEcCCCCeeecCCC-CCC-CCCCCCCCCCC
Q 040420 75 SKQAYICRDCGYIYNERK-PFD-QLPDNYFCPVC 106 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~t-pF~-~lPd~~~CPvC 106 (169)
.+..|+|..||++..... .+. ..|. .||.|
T Consensus 126 ~~~~~~C~~Cg~~~~~~~~~~~~~~~~--~C~~~ 157 (682)
T COG1241 126 KKAVFECPKCGREVEVEQSEFRVEPPR--ECENC 157 (682)
T ss_pred EEEEEEcCCCCCEEEEEeccccccCCc--cCCCc
Confidence 345799999997765422 111 1233 79999
No 380
>PHA02942 putative transposase; Provisional
Probab=26.54 E-value=42 Score=30.55 Aligned_cols=15 Identities=27% Similarity=0.851 Sum_probs=12.8
Q ss_pred CCeEEcCCCCeeecC
Q 040420 76 KQAYICRDCGYIYNE 90 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~ 90 (169)
...|+|..|||+.|.
T Consensus 340 ~r~f~C~~CG~~~dr 354 (383)
T PHA02942 340 HRYFHCPSCGYENDR 354 (383)
T ss_pred CCEEECCCCCCEeCc
Confidence 357999999999886
No 381
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=26.53 E-value=50 Score=17.72 Aligned_cols=12 Identities=17% Similarity=0.722 Sum_probs=8.2
Q ss_pred EEcCCCCeeecC
Q 040420 79 YICRDCGYIYNE 90 (169)
Q Consensus 79 y~C~~CGyVYd~ 90 (169)
|.|.+|+..+..
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 677888766643
No 382
>PLN02610 probable methionyl-tRNA synthetase
Probab=26.53 E-value=29 Score=34.70 Aligned_cols=27 Identities=30% Similarity=0.632 Sum_probs=16.7
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
.+|..||..|++. ++ .+-+|..||.+-
T Consensus 171 d~Ce~Cg~~~~p~----eL-i~p~c~~~g~~~ 197 (801)
T PLN02610 171 DQCEKCGKLLNPT----EL-IDPKCKVCKNTP 197 (801)
T ss_pred chhhhccccCChh----hh-cCCcccCCCCcc
Confidence 4666777777653 23 123788888754
No 383
>PF03691 UPF0167: Uncharacterised protein family (UPF0167); InterPro: IPR005363 The proteins in this family are about 200 amino acids long and each contain 3 CXXC motifs.
Probab=26.39 E-value=38 Score=28.16 Aligned_cols=32 Identities=31% Similarity=0.767 Sum_probs=19.9
Q ss_pred eEEcCCCC----eeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 78 AYICRDCG----YIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 78 ~y~C~~CG----yVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
.=.|..|| |+|.+. .+..-.-+..||.|=+..
T Consensus 24 ~~~C~cCgk~~~~~Y~~~-~Y~~~dv~~lCPwCIAdG 59 (176)
T PF03691_consen 24 EVVCDCCGKARGYYYTGP-FYSEEDVEYLCPWCIADG 59 (176)
T ss_pred CCCcCCCCCCceeEecCC-ceecCCccccCHhHhcCc
Confidence 34799999 778763 122222347999996543
No 384
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=26.34 E-value=65 Score=30.39 Aligned_cols=34 Identities=21% Similarity=0.711 Sum_probs=21.8
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
...+.-.|..||-..+-.+ .+. -+.=.||-||+.
T Consensus 14 ~~~~~~~C~eCd~~~~~P~-l~~-~q~A~CPRC~~~ 47 (418)
T COG2995 14 PPGHLILCPECDMLVSLPR-LDS-GQSAYCPRCGHT 47 (418)
T ss_pred CccceecCCCCCceecccc-CCC-CCcccCCCCCCc
Confidence 3445668999998776531 111 123489999984
No 385
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=26.23 E-value=45 Score=23.58 Aligned_cols=41 Identities=39% Similarity=0.865 Sum_probs=25.3
Q ss_pred CccceecCCCCeEEcCCCCee-ecCCCCCCCCCCCCCCCCCCCC-ccCeeeC
Q 040420 67 PKFSMRVASKQAYICRDCGYI-YNERKPFDQLPDNYFCPVCGAP-KRRFRPY 116 (169)
Q Consensus 67 p~~~~k~~~~~~y~C~~CGyV-Yd~~tpF~~lPd~~~CPvCgap-K~~F~~~ 116 (169)
|.++++.. ..--+|+-||.. |.-. -. .|-.||-+ ..+...|
T Consensus 6 ~S~GKrnk-~tH~~CRRCGr~syhv~------k~--~CaaCGfgrs~r~R~y 48 (61)
T COG2126 6 PSFGKRNK-KTHIRCRRCGRRSYHVR------KK--YCAACGFGRSARMRSY 48 (61)
T ss_pred ccccccCC-cceehhhhccchheeec------cc--eecccCCCCccccccc
Confidence 44555544 344499999933 4332 33 89999998 4455544
No 386
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=25.79 E-value=37 Score=24.57 Aligned_cols=14 Identities=29% Similarity=0.783 Sum_probs=11.3
Q ss_pred CeEEcCCCCeeecC
Q 040420 77 QAYICRDCGYIYNE 90 (169)
Q Consensus 77 ~~y~C~~CGyVYd~ 90 (169)
.-.+|..||.+++-
T Consensus 72 ~H~~C~~Cg~i~~~ 85 (116)
T cd07153 72 HHLICTKCGKVIDF 85 (116)
T ss_pred CceEeCCCCCEEEe
Confidence 34799999999874
No 387
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=25.76 E-value=45 Score=36.65 Aligned_cols=30 Identities=13% Similarity=0.222 Sum_probs=21.5
Q ss_pred CeEEcCCCCeeecCCC----CCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERK----PFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~t----pF~~lPd~~~CPvCga 108 (169)
..|.|+.||+.|.+-+ .|.. |. -.||.|+.
T Consensus 243 ~~~~cp~~~~~~~~~~p~~FSfNs-p~-GaCp~C~G 276 (1809)
T PRK00635 243 TQATIPETQQTYTPLTPQLFSPHS-LE-DRCPQCQG 276 (1809)
T ss_pred ccccCCccCcccCcCChhhcCCCC-cc-ccCCCCCC
Confidence 4689999999998633 4444 32 38999965
No 388
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=25.73 E-value=53 Score=22.44 Aligned_cols=16 Identities=31% Similarity=0.754 Sum_probs=12.6
Q ss_pred CCCCeEEcCCCCeeec
Q 040420 74 ASKQAYICRDCGYIYN 89 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd 89 (169)
...+.-+|+.||.+|-
T Consensus 49 i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 49 IVEGELICPECGREYP 64 (68)
T ss_dssp TTTTEEEETTTTEEEE
T ss_pred ccCCEEEcCCCCCEEe
Confidence 3456789999999883
No 389
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=25.71 E-value=36 Score=29.13 Aligned_cols=14 Identities=21% Similarity=0.617 Sum_probs=11.8
Q ss_pred CeEEcCCCCeeecC
Q 040420 77 QAYICRDCGYIYNE 90 (169)
Q Consensus 77 ~~y~C~~CGyVYd~ 90 (169)
..++|..||++|..
T Consensus 29 ~lvrC~eCG~V~~~ 42 (201)
T COG1326 29 PLVRCEECGTVHPA 42 (201)
T ss_pred eEEEccCCCcEeec
Confidence 47899999999944
No 390
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=25.63 E-value=39 Score=23.87 Aligned_cols=9 Identities=56% Similarity=1.486 Sum_probs=5.5
Q ss_pred CCCCCCCCC
Q 040420 101 YFCPVCGAP 109 (169)
Q Consensus 101 ~~CPvCgap 109 (169)
..||+|+.+
T Consensus 7 v~CP~C~k~ 15 (62)
T PRK00418 7 VNCPTCGKP 15 (62)
T ss_pred ccCCCCCCc
Confidence 356666665
No 391
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=25.62 E-value=65 Score=28.99 Aligned_cols=9 Identities=22% Similarity=0.600 Sum_probs=7.4
Q ss_pred CCCCCCCCc
Q 040420 102 FCPVCGAPK 110 (169)
Q Consensus 102 ~CPvCgapK 110 (169)
.||.||..+
T Consensus 228 ~C~~Cg~~~ 236 (309)
T PRK03564 228 KCSNCEQSG 236 (309)
T ss_pred cCCCCCCCC
Confidence 899999854
No 392
>KOG0435 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=25.55 E-value=41 Score=34.11 Aligned_cols=36 Identities=33% Similarity=0.797 Sum_probs=23.4
Q ss_pred eEEcCCCCeeecCC--C---------------CCCCCCCCC---CCCCCCCCccCee
Q 040420 78 AYICRDCGYIYNER--K---------------PFDQLPDNY---FCPVCGAPKRRFR 114 (169)
Q Consensus 78 ~y~C~~CGyVYd~~--t---------------pF~~lPd~~---~CPvCgapK~~F~ 114 (169)
+-+|.+||-|-.++ . |.+. ++.| .||.||.+..|-.
T Consensus 436 ivhc~~cG~vpVpes~LPV~LP~l~~~~~kG~Pls~-~~e~vn~~cP~cg~pAkRET 491 (876)
T KOG0435|consen 436 IVHCDDCGAVPVPESELPVTLPELNDFTPKGPPLSK-ADEWVNVDCPRCGEPAKRET 491 (876)
T ss_pred eEEcCCCCcccCcHHHCCcccccccccCCCCCcccc-hhhheeccCccCCCcccccc
Confidence 56899999776652 1 2211 2444 6999999877643
No 393
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=25.52 E-value=32 Score=31.99 Aligned_cols=14 Identities=36% Similarity=0.952 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCCcc
Q 040420 98 PDNYFCPVCGAPKR 111 (169)
Q Consensus 98 Pd~~~CPvCgapK~ 111 (169)
-|.|.||+|+....
T Consensus 282 ~d~W~CpkC~~k~s 295 (415)
T COG5533 282 KDAWRCPKCGRKES 295 (415)
T ss_pred cccccCchhccccc
Confidence 46799999997544
No 394
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=25.31 E-value=63 Score=20.27 Aligned_cols=24 Identities=33% Similarity=0.987 Sum_probs=18.7
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCP 104 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CP 104 (169)
.++|..|+.+|=..+. +|++-.|+
T Consensus 12 ~f~C~~C~~~FC~~HR---~~e~H~C~ 35 (39)
T smart00154 12 GFKCRHCGNLFCGEHR---LPEDHDCP 35 (39)
T ss_pred CeECCccCCccccccC---CccccCCc
Confidence 5899999999988653 57777775
No 395
>PRK14740 kdbF potassium-transporting ATPase subunit F; Provisional
Probab=25.24 E-value=1e+02 Score=18.84 Aligned_cols=15 Identities=27% Similarity=0.467 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHhh
Q 040420 152 AVAAVALAGLYFYLN 166 (169)
Q Consensus 152 ~~G~~al~~l~fyl~ 166 (169)
-++++..++|++||-
T Consensus 6 wls~a~a~~Lf~YLv 20 (29)
T PRK14740 6 WLSLALATGLFVYLL 20 (29)
T ss_pred HHHHHHHHHHHHHHH
Confidence 345566667888873
No 396
>PRK14529 adenylate kinase; Provisional
Probab=24.99 E-value=58 Score=27.55 Aligned_cols=31 Identities=29% Similarity=0.534 Sum_probs=18.0
Q ss_pred CeEEcCCCCeeecCCCCCC-CCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFD-QLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~-~lPd~~~CPvCga 108 (169)
..+.|..||.+|.-.. |. ..++.-.|..||.
T Consensus 125 ~R~~c~~~~~~~~~~~-~~~p~~~~~~cd~~~~ 156 (223)
T PRK14529 125 GRRLCKNDNNHPNNIF-IDAIKPDGDVCRVCGG 156 (223)
T ss_pred CCccccccCCcccccc-cCCCcccCCcCcCcCC
Confidence 3789999886554321 11 0112237999986
No 397
>PRK07217 replication factor A; Reviewed
Probab=24.98 E-value=67 Score=29.11 Aligned_cols=31 Identities=19% Similarity=0.342 Sum_probs=23.5
Q ss_pred CCCeEEcCC--CCeeecCCCCCCCCCCCCCCCCCCCCccCeee
Q 040420 75 SKQAYICRD--CGYIYNERKPFDQLPDNYFCPVCGAPKRRFRP 115 (169)
Q Consensus 75 ~~~~y~C~~--CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~ 115 (169)
+.-+++|+. |+-+-.- ..||.||.....|.-
T Consensus 185 sglI~rCP~~~C~Rvl~~----------g~C~~HG~ve~~~DL 217 (311)
T PRK07217 185 SGLIKRCPEEDCTRVLQN----------GRCSEHGKVEGEFDL 217 (311)
T ss_pred CCCeecCCccccCccccC----------CCCCCCCCcCCceee
Confidence 445899999 9977632 489999987776643
No 398
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=24.82 E-value=41 Score=34.37 Aligned_cols=25 Identities=32% Similarity=0.939 Sum_probs=17.4
Q ss_pred CeEEcCCCCee-------------ecCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYI-------------YNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyV-------------Yd~~tpF~~lPd~~~CPvCga 108 (169)
-.|+|..||.- +.++.| |-||.|+-
T Consensus 280 RKFKCtECgKAFKfKHHLKEHlRIHSGEKP-------feCpnCkK 317 (1007)
T KOG3623|consen 280 RKFKCTECGKAFKFKHHLKEHLRIHSGEKP-------FECPNCKK 317 (1007)
T ss_pred ccccccccchhhhhHHHHHhhheeecCCCC-------cCCccccc
Confidence 37999999943 333433 47999975
No 399
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=24.72 E-value=45 Score=30.38 Aligned_cols=32 Identities=31% Similarity=0.800 Sum_probs=16.1
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCcc
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKR 111 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~ 111 (169)
-.|.|..|++.-... -..+.+. .||.||....
T Consensus 239 ~v~~C~~C~~~~~~~-~~~~~~~--~c~~cg~~~~ 270 (377)
T PF02005_consen 239 YVYYCPSCGYREEVK-GLQKLKS--KCPECGSKLH 270 (377)
T ss_dssp EEEEETTT--EECCT--GCC--C--EETTT-SCCC
T ss_pred EEEECCCcccccccc-CccccCC--cCCCCCCccc
Confidence 378999998642221 1111223 8999988544
No 400
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=24.70 E-value=30 Score=29.06 Aligned_cols=24 Identities=25% Similarity=0.668 Sum_probs=16.2
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCC
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVC 106 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvC 106 (169)
+....=.|+.||++... +..|+-|
T Consensus 89 ~k~nl~~CP~CGh~k~a---------~~LC~~C 112 (176)
T KOG4080|consen 89 PKDNLNTCPACGHIKPA---------HTLCDYC 112 (176)
T ss_pred chhccccCcccCccccc---------cccHHHH
Confidence 34446789999987744 3367777
No 401
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=24.66 E-value=32 Score=34.23 Aligned_cols=33 Identities=21% Similarity=0.596 Sum_probs=23.5
Q ss_pred eEEcCC-CCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 78 AYICRD-CGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 78 ~y~C~~-CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
--.|.. |+-++++---.+.--..|.||.|....
T Consensus 53 pv~C~~pC~avlnpyC~id~r~~~W~CpfCnqrn 86 (755)
T COG5047 53 PVKCTAPCKAVLNPYCHIDERNQSWICPFCNQRN 86 (755)
T ss_pred CceecccchhhcCcceeeccCCceEecceecCCC
Confidence 457999 999998843333334579999998744
No 402
>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=24.53 E-value=44 Score=27.29 Aligned_cols=13 Identities=46% Similarity=1.270 Sum_probs=9.5
Q ss_pred eEEcCCCCeeecC
Q 040420 78 AYICRDCGYIYNE 90 (169)
Q Consensus 78 ~y~C~~CGyVYd~ 90 (169)
.+.|..|||-+.+
T Consensus 28 sf~C~~CGyr~~e 40 (163)
T TIGR00340 28 TYICEKCGYRSTD 40 (163)
T ss_pred EEECCCCCCchhh
Confidence 5777777777766
No 403
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=24.53 E-value=33 Score=30.32 Aligned_cols=36 Identities=25% Similarity=0.623 Sum_probs=25.8
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCC
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYT 117 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~ 117 (169)
..|.++|..|+.-|-- .|-.-.||.||. .....-..
T Consensus 164 ~rq~~rc~~c~~k~rr------~pl~g~c~kcg~-~~~ltv~~ 199 (253)
T COG1933 164 TRQEFRCVKCNTKFRR------PPLDGKCPICGG-KIVLTVSK 199 (253)
T ss_pred hhheeehHhhhhhhcC------CCccccccccCC-eEEEEEec
Confidence 5578999999976632 366669999998 55555333
No 404
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=24.39 E-value=55 Score=32.98 Aligned_cols=32 Identities=28% Similarity=0.688 Sum_probs=20.4
Q ss_pred EcCCCCeeecCC--CCCCCCCCCCCCCCCCCCccCee
Q 040420 80 ICRDCGYIYNER--KPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 80 ~C~~CGyVYd~~--tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
.|..|-..|... ..|-..|- .||.||= +-++.
T Consensus 153 lC~~C~~EY~dP~nRRfHAQp~--aCp~CGP-~~~l~ 186 (750)
T COG0068 153 LCPFCDKEYKDPLNRRFHAQPI--ACPKCGP-HLFLV 186 (750)
T ss_pred CCHHHHHHhcCccccccccccc--cCcccCC-CeEEE
Confidence 677776666552 35666677 9999974 44444
No 405
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=24.28 E-value=47 Score=22.22 Aligned_cols=15 Identities=27% Similarity=0.762 Sum_probs=8.5
Q ss_pred CCeEEcCCCCeeecC
Q 040420 76 KQAYICRDCGYIYNE 90 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~ 90 (169)
...|.|+.||.++-.
T Consensus 23 ~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 23 RRRHHCRNCGRVVCS 37 (69)
T ss_dssp S-EEE-TTT--EEEC
T ss_pred eeeEccCCCCCEECC
Confidence 557999999977643
No 406
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=24.09 E-value=41 Score=27.28 Aligned_cols=13 Identities=46% Similarity=1.160 Sum_probs=8.4
Q ss_pred eEEcCCCCeeecC
Q 040420 78 AYICRDCGYIYNE 90 (169)
Q Consensus 78 ~y~C~~CGyVYd~ 90 (169)
.+.|..|||-+.+
T Consensus 29 sf~C~~CGyk~~e 41 (160)
T smart00709 29 SFECEHCGYRNNE 41 (160)
T ss_pred EEECCCCCCccce
Confidence 4667777766665
No 407
>PRK13208 valS valyl-tRNA synthetase; Reviewed
Probab=23.95 E-value=52 Score=32.45 Aligned_cols=32 Identities=34% Similarity=0.858 Sum_probs=22.7
Q ss_pred CeEEcCCCCeeecC------CCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNE------RKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 77 ~~y~C~~CGyVYd~------~tpF~~lPd~~~CPvCga 108 (169)
..|.|..||.++.+ -.+..+.+..+.|+.||.
T Consensus 411 P~~~~~~~g~~~~~~~~~l~~~~~~d~~~~~~~~~~g~ 448 (800)
T PRK13208 411 PVWYCKDCGHPILPDEEDLPVDPTKDEPPGYKCPQCGS 448 (800)
T ss_pred eEEEeCCCCCeecCchhhhccCchhhccccccccccCC
Confidence 48999999988643 124445566689999974
No 408
>PRK15033 tricarballylate utilization protein B; Provisional
Probab=23.74 E-value=92 Score=29.08 Aligned_cols=25 Identities=28% Similarity=0.488 Sum_probs=13.8
Q ss_pred HHHHHHHHhhhc---cccC-----CCchHHHHH
Q 040420 129 VRKARKEQIQRD---EAIG-----KALPIAIAV 153 (169)
Q Consensus 129 v~~ar~~~~~~~---~~~g-----n~lpi~~~~ 153 (169)
...+|.+.++.| ++.| |.+++.+++
T Consensus 95 l~~~r~~sy~~yawP~~lgkl~~~~~l~i~~ai 127 (389)
T PRK15033 95 MAQVRLETYQEYAWPAALGALYRRNGLTLSLAL 127 (389)
T ss_pred HHHHHHHHHHHccCcHHHHHhhccCccHHHHHH
Confidence 334555666666 3233 567776555
No 409
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=23.62 E-value=41 Score=25.48 Aligned_cols=29 Identities=28% Similarity=0.540 Sum_probs=18.5
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
...|.|..||..-..+. .-.-|.|-.|+-
T Consensus 34 haky~CsfCGK~~vKR~----AvGiW~C~~C~k 62 (92)
T KOG0402|consen 34 HAKYTCSFCGKKTVKRK----AVGIWKCGSCKK 62 (92)
T ss_pred hhhhhhhhcchhhhhhh----ceeEEecCCccc
Confidence 34688888886544432 345688888864
No 410
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=23.59 E-value=50 Score=25.75 Aligned_cols=14 Identities=43% Similarity=0.854 Sum_probs=11.8
Q ss_pred CCeEEcCCCCeeec
Q 040420 76 KQAYICRDCGYIYN 89 (169)
Q Consensus 76 ~~~y~C~~CGyVYd 89 (169)
...|+|..||.+..
T Consensus 5 ~~fYkC~~CGniv~ 18 (125)
T TIGR00320 5 LQVYKCEVCGNIVE 18 (125)
T ss_pred CcEEECCCCCcEEE
Confidence 45899999999884
No 411
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=23.48 E-value=2.1e+02 Score=25.39 Aligned_cols=15 Identities=20% Similarity=0.474 Sum_probs=10.6
Q ss_pred CCeEEcCCCCeeecC
Q 040420 76 KQAYICRDCGYIYNE 90 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~ 90 (169)
...-.|++|++.-|-
T Consensus 63 ~p~v~CrVCq~~I~i 77 (256)
T PF09788_consen 63 APVVTCRVCQSLIDI 77 (256)
T ss_pred CceEEeecCCceecc
Confidence 346688888877664
No 412
>PRK08565 DNA-directed RNA polymerase subunit B; Provisional
Probab=23.43 E-value=49 Score=34.33 Aligned_cols=32 Identities=28% Similarity=0.683 Sum_probs=21.3
Q ss_pred CCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 75 SKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
....|+|..||.+-.... -...|.|.+|+...
T Consensus 1039 ~~~~~vC~~Cg~~~~~~~----~~~~~~C~~c~~~~ 1070 (1103)
T PRK08565 1039 KTTIYVCELCGHIAWYDR----RKNKYVCPIHGDKG 1070 (1103)
T ss_pred ceeeeeeccccccccccc----ccCceeccccCCCC
Confidence 445899999997643221 13457899998743
No 413
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=23.34 E-value=2.3e+02 Score=20.16 Aligned_cols=8 Identities=50% Similarity=1.290 Sum_probs=5.8
Q ss_pred CCCCCCCC
Q 040420 102 FCPVCGAP 109 (169)
Q Consensus 102 ~CPvCgap 109 (169)
-|++||.+
T Consensus 10 HC~VCg~a 17 (64)
T COG4068 10 HCVVCGKA 17 (64)
T ss_pred cccccCCc
Confidence 68888763
No 414
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.27 E-value=63 Score=20.42 Aligned_cols=18 Identities=33% Similarity=0.794 Sum_probs=13.3
Q ss_pred CCCCeEEcCCCCeeecCC
Q 040420 74 ASKQAYICRDCGYIYNER 91 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~ 91 (169)
...+.|+|..|+++.-.+
T Consensus 24 ~~~~g~~C~~C~~~~H~~ 41 (53)
T PF00130_consen 24 LGKQGYRCSWCGLVCHKK 41 (53)
T ss_dssp SSSCEEEETTTT-EEETT
T ss_pred CCCCeEEECCCCChHhhh
Confidence 456789999999887653
No 415
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=23.14 E-value=22 Score=31.64 Aligned_cols=12 Identities=17% Similarity=0.791 Sum_probs=9.3
Q ss_pred EEcCCCCeeecC
Q 040420 79 YICRDCGYIYNE 90 (169)
Q Consensus 79 y~C~~CGyVYd~ 90 (169)
+.|.+|++.+..
T Consensus 196 ~vC~vC~fdF~k 207 (272)
T COG3183 196 TVCDVCEFDFQK 207 (272)
T ss_pred ceeeecCccHHH
Confidence 899999965543
No 416
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=22.65 E-value=52 Score=21.50 Aligned_cols=26 Identities=27% Similarity=0.672 Sum_probs=11.8
Q ss_pred EcCCCCe--eecCCCC--CCCCCCCCCCCC
Q 040420 80 ICRDCGY--IYNERKP--FDQLPDNYFCPV 105 (169)
Q Consensus 80 ~C~~CGy--VYd~~tp--F~~lPd~~~CPv 105 (169)
+|..|+. +-..+.. .+.+|+.|.|-.
T Consensus 5 QCd~C~KWR~lp~~~~~~~~~~~d~W~C~~ 34 (50)
T PF07496_consen 5 QCDSCLKWRRLPEEVDPIREELPDPWYCSM 34 (50)
T ss_dssp E-TTT--EEEE-CCHHCTSCCSSTT--GGG
T ss_pred ECCCCCceeeCChhhCcccccCCCeEEcCC
Confidence 7888881 1112222 256788999976
No 417
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=22.64 E-value=55 Score=21.06 Aligned_cols=14 Identities=21% Similarity=0.607 Sum_probs=11.5
Q ss_pred CeEEcCC--CCeeecC
Q 040420 77 QAYICRD--CGYIYNE 90 (169)
Q Consensus 77 ~~y~C~~--CGyVYd~ 90 (169)
..|+|.+ ||+.|..
T Consensus 24 ~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 24 LYCQCTNPECGHTFVA 39 (47)
T ss_pred EEEEECCCcCCCEEEE
Confidence 4779999 9998864
No 418
>smart00442 FGF Acidic and basic fibroblast growth factor family. Mitogens that stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family play essential roles in patterning and differentiation during vertebrate embryogenesis, and have neurotrophic activities.
Probab=22.58 E-value=50 Score=25.46 Aligned_cols=24 Identities=21% Similarity=0.725 Sum_probs=19.8
Q ss_pred ccceecCCCCeEEcCC-CCeeecCC
Q 040420 68 KFSMRVASKQAYICRD-CGYIYNER 91 (169)
Q Consensus 68 ~~~~k~~~~~~y~C~~-CGyVYd~~ 91 (169)
.+.++......|.|.+ ||+.|-..
T Consensus 45 ~V~ik~~~s~~YLCmn~~G~ly~s~ 69 (126)
T smart00442 45 VVAIKGVASCRYLCMNKCGKLYGSK 69 (126)
T ss_pred EEEEEEcccceEEEECCCCCEEEcc
Confidence 4677788889999997 99999754
No 419
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=22.52 E-value=72 Score=21.42 Aligned_cols=28 Identities=18% Similarity=0.300 Sum_probs=18.2
Q ss_pred hccCCccceecCCCCeEEcCCCCeeecC
Q 040420 63 ASAAPKFSMRVASKQAYICRDCGYIYNE 90 (169)
Q Consensus 63 ~~a~p~~~~k~~~~~~y~C~~CGyVYd~ 90 (169)
.+..++|.....+...|+|.=|+.+++.
T Consensus 20 E~v~~~F~v~~~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 20 EPVESRFYVIDKEPIKLRCHYCERIITE 47 (52)
T ss_dssp SSS--EEEEEETTTCEEEETTT--EEEH
T ss_pred CCCCceEEEEeCCCCEEEeeCCCCEecc
Confidence 3555667666678889999999988763
No 420
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=22.40 E-value=27 Score=29.45 Aligned_cols=26 Identities=19% Similarity=0.512 Sum_probs=19.6
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCG 107 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCg 107 (169)
.-.|.+||-.|.+... . ..|.||.|+
T Consensus 6 ~rKCKvCg~~F~P~~s---~-q~vCSpeCa 31 (189)
T PF05766_consen 6 RRKCKVCGEWFVPARS---N-QKVCSPECA 31 (189)
T ss_pred CCcCcccCCccccCCC---c-eeeeCHHHH
Confidence 3589999988876432 2 358999998
No 421
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=22.13 E-value=51 Score=25.53 Aligned_cols=12 Identities=33% Similarity=0.758 Sum_probs=10.7
Q ss_pred CeEEcCCCCeee
Q 040420 77 QAYICRDCGYIY 88 (169)
Q Consensus 77 ~~y~C~~CGyVY 88 (169)
-.+.|..||+++
T Consensus 81 v~vtC~~CG~~~ 92 (105)
T COG2023 81 VVVTCLECGTIR 92 (105)
T ss_pred EEEEecCCCcEE
Confidence 689999999886
No 422
>PRK02935 hypothetical protein; Provisional
Probab=22.12 E-value=66 Score=25.21 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=24.1
Q ss_pred CCCCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCeeeCC
Q 040420 74 ASKQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFRPYT 117 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~~~~ 117 (169)
.....-+|++|+..-.-. .--| .|.-|+.|-.-....+
T Consensus 66 tkavqV~CP~C~K~TKmL----GrvD--~CM~C~~PLTLd~~le 103 (110)
T PRK02935 66 TKAVQVICPSCEKPTKML----GRVD--ACMHCNQPLTLDRSLE 103 (110)
T ss_pred ccceeeECCCCCchhhhc----ccee--ecCcCCCcCCcCcccc
Confidence 333445999999654321 1134 9999999876655443
No 423
>COG3197 FixS Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]
Probab=22.10 E-value=95 Score=21.79 Aligned_cols=19 Identities=26% Similarity=0.635 Sum_probs=13.5
Q ss_pred chHHHHHHHHHHHHHHHHh
Q 040420 147 LPIAIAVAAVALAGLYFYL 165 (169)
Q Consensus 147 lpi~~~~G~~al~~l~fyl 165 (169)
+|++++.|.+++.+++.-+
T Consensus 8 ipvsi~l~~v~l~~flWav 26 (58)
T COG3197 8 IPVSILLGAVGLGAFLWAV 26 (58)
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 3777888888887766544
No 424
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.87 E-value=40 Score=31.76 Aligned_cols=60 Identities=18% Similarity=0.358 Sum_probs=32.6
Q ss_pred CCCCCCCCccceeccccccccc---cccCCcc-chhhhhccCCccc--eecCCCCeEEcCCCCeeecC
Q 040420 29 AGLRRPADRFALKSSFSAPSLH---LLLSPPH-QQQLLASAAPKFS--MRVASKQAYICRDCGYIYNE 90 (169)
Q Consensus 29 ~~l~~~~d~~al~ssf~~~~l~---~~~~~~~-~~~~~~~a~p~~~--~k~~~~~~y~C~~CGyVYd~ 90 (169)
.-|.++ |.+..+-++=...++ +.+.... .. ...|-=|+=+ |+......|+|+.||+.+..
T Consensus 314 ~~L~pG-D~i~~~G~~~~~~~n~ek~~v~~l~~~~-~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 314 RKLIPG-DEITVYGSVKPGTLNLEKFQVLKLARYE-RVNPVCPRCGGRMKSAGRNGFRCKKCGTRARE 379 (421)
T ss_pred HhcCCC-CEEEEecCccccceeEEEEEEEEeeeeE-EcCCCCCccCCchhhcCCCCcccccccccCCc
Confidence 345665 888777777766655 1110100 11 1222223333 33333347999999999976
No 425
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=21.84 E-value=40 Score=35.18 Aligned_cols=21 Identities=52% Similarity=1.328 Sum_probs=15.3
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCG 107 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCg 107 (169)
.+|..||+.++.. .+ .||.|+
T Consensus 679 k~~~~~~~~f~~~------~~--~~p~~~ 699 (1171)
T TIGR01054 679 KRCRDCGYQFTED------RE--SCPKCG 699 (1171)
T ss_pred ccCCchhhhcccc------cc--cccccc
Confidence 3688888877653 23 899996
No 426
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.78 E-value=42 Score=26.12 Aligned_cols=7 Identities=71% Similarity=1.929 Sum_probs=5.2
Q ss_pred CCCCCCC
Q 040420 103 CPVCGAP 109 (169)
Q Consensus 103 CPvCgap 109 (169)
||+||.+
T Consensus 1 CPvCg~~ 7 (113)
T PF09862_consen 1 CPVCGGE 7 (113)
T ss_pred CCCCCCc
Confidence 8888764
No 427
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.70 E-value=62 Score=21.34 Aligned_cols=15 Identities=53% Similarity=1.302 Sum_probs=10.4
Q ss_pred CCCCCCCCCCCCCCcc
Q 040420 96 QLPDNYFCPVCGAPKR 111 (169)
Q Consensus 96 ~lPd~~~CPvCgapK~ 111 (169)
+||.. .||+||-|-.
T Consensus 5 ~lp~K-~C~~C~rpf~ 19 (42)
T PF10013_consen 5 NLPSK-ICPVCGRPFT 19 (42)
T ss_pred cCCCC-cCcccCCcch
Confidence 45653 8999987643
No 428
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=21.55 E-value=39 Score=26.66 Aligned_cols=16 Identities=25% Similarity=0.704 Sum_probs=12.9
Q ss_pred CCCCCCCCCccCeeeC
Q 040420 101 YFCPVCGAPKRRFRPY 116 (169)
Q Consensus 101 ~~CPvCgapK~~F~~~ 116 (169)
-+||.||+++..|...
T Consensus 75 ~kCpkCghe~m~Y~T~ 90 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTL 90 (116)
T ss_pred ccCcccCCchhhhhhh
Confidence 4899999999877643
No 429
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=21.53 E-value=46 Score=29.99 Aligned_cols=25 Identities=36% Similarity=0.830 Sum_probs=17.7
Q ss_pred CeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 77 QAYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 77 ~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
|.=.|.+||-.... +.. .||.|++.
T Consensus 81 Ql~~C~~CGa~V~~------~e~--~Cp~C~St 105 (314)
T PF09567_consen 81 QLGKCNNCGANVSR------LEE--SCPNCGST 105 (314)
T ss_pred hhhhhccccceeee------hhh--cCCCCCcc
Confidence 45689999966532 233 79999983
No 430
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=21.49 E-value=53 Score=27.50 Aligned_cols=13 Identities=46% Similarity=1.117 Sum_probs=8.5
Q ss_pred eEEcCCCCeeecC
Q 040420 78 AYICRDCGYIYNE 90 (169)
Q Consensus 78 ~y~C~~CGyVYd~ 90 (169)
.+.|..|||-+.+
T Consensus 30 sf~C~~CGyr~~e 42 (192)
T TIGR00310 30 STICEHCGYRSND 42 (192)
T ss_pred EEECCCCCCccce
Confidence 4667777766665
No 431
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=21.41 E-value=65 Score=30.42 Aligned_cols=32 Identities=28% Similarity=0.503 Sum_probs=23.0
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCCCccCee
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGAPKRRFR 114 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK~~F~ 114 (169)
+..--|..|-|+.+.+ +.-+||.||++-.+-+
T Consensus 218 ~~~~~C~~C~~~~~~~-------~~~~CpRC~~~Ly~rr 249 (418)
T COG2995 218 EGLRSCLCCHYILPHD-------AEPRCPRCGSKLYVRR 249 (418)
T ss_pred ccceecccccccCCHh-------hCCCCCCCCChhhccC
Confidence 3345899999998763 2348999999765544
No 432
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=21.36 E-value=53 Score=24.66 Aligned_cols=17 Identities=24% Similarity=0.714 Sum_probs=13.0
Q ss_pred CCCCeEEcCCCCeeecC
Q 040420 74 ASKQAYICRDCGYIYNE 90 (169)
Q Consensus 74 ~~~~~y~C~~CGyVYd~ 90 (169)
.......|..||.+|-.
T Consensus 31 knVPa~~C~~CGe~y~~ 47 (89)
T TIGR03829 31 KETPSISCSHCGMEYQD 47 (89)
T ss_pred ecCCcccccCCCcEeec
Confidence 45567889999988765
No 433
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=21.08 E-value=8.9 Score=26.14 Aligned_cols=24 Identities=42% Similarity=1.115 Sum_probs=14.7
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
-|.|..|-.+.-.. .| .||+|+.+
T Consensus 21 HYLCl~CLt~ml~~------s~--~C~iC~~~ 44 (50)
T PF03854_consen 21 HYLCLNCLTLMLSR------SD--RCPICGKP 44 (50)
T ss_dssp -EEEHHHHHHT-SS------SS--EETTTTEE
T ss_pred hhHHHHHHHHHhcc------cc--CCCcccCc
Confidence 46777776554332 45 89999874
No 434
>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=21.03 E-value=46 Score=26.86 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=9.2
Q ss_pred eEEcCCCCeeecCC
Q 040420 78 AYICRDCGYIYNER 91 (169)
Q Consensus 78 ~y~C~~CGyVYd~~ 91 (169)
.+.|..|||-+.+-
T Consensus 30 sf~C~~CGyk~~ev 43 (161)
T PF03367_consen 30 SFECEHCGYKNNEV 43 (161)
T ss_dssp EEE-TTT--EEEEE
T ss_pred EeECCCCCCEeeeE
Confidence 68999999998873
No 435
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=20.93 E-value=39 Score=31.46 Aligned_cols=26 Identities=27% Similarity=0.612 Sum_probs=16.3
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCCc
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAPK 110 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgapK 110 (169)
-+|..||..|.+. -..+.||.||..-
T Consensus 6 ~rc~~cg~~f~~a------~~~~~c~~cGl~l 31 (411)
T COG0498 6 LRCLKCGREFSQA------LLQGLCPDCGLFL 31 (411)
T ss_pred eecCCCCcchhhH------HhhCcCCcCCccc
Confidence 4788888666532 1235788888743
No 436
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=20.87 E-value=59 Score=20.26 Aligned_cols=19 Identities=26% Similarity=0.590 Sum_probs=12.0
Q ss_pred CccceecCCCCeEEcCCCC
Q 040420 67 PKFSMRVASKQAYICRDCG 85 (169)
Q Consensus 67 p~~~~k~~~~~~y~C~~CG 85 (169)
+++....-....|.|+.||
T Consensus 29 ~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 29 AKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred cceEEEEEEeceEECCCCC
Confidence 3344334445689999997
No 437
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=20.83 E-value=1e+02 Score=19.63 Aligned_cols=25 Identities=32% Similarity=0.893 Sum_probs=11.9
Q ss_pred EcCC--CCeeecCCCCCCCCCCC--CCCCCCCC
Q 040420 80 ICRD--CGYIYNERKPFDQLPDN--YFCPVCGA 108 (169)
Q Consensus 80 ~C~~--CGyVYd~~tpF~~lPd~--~~CPvCga 108 (169)
.|+. |++++..... ... ..|+.|+.
T Consensus 20 ~Cp~~~C~~~~~~~~~----~~~~~~~C~~C~~ 48 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDG----CNSPIVTCPSCGT 48 (64)
T ss_dssp --TTSST---ECS-SS----TTS--CCTTSCCS
T ss_pred CCCCCCCcccEEecCC----CCCCeeECCCCCC
Confidence 7876 9988765421 222 58998875
No 438
>cd00058 FGF Acidic and basic fibroblast growth factor family; FGFs are mitogens, which stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family plays essential roles in patterning and differentiation during vertebrate embryogenesis, and has neurotrophic activities. FGFs have a high affinity for heparan sulfate proteoglycans and require heparan sulfate to activate one of four cell surface FGF receptors. Upon binding to FGF, the receptors dimerize and their intracellular tyrosine kinase domains become active. FGFs have internal pseudo-threefold symmetry (beta-trefoil topology).
Probab=20.77 E-value=59 Score=24.95 Aligned_cols=25 Identities=24% Similarity=0.690 Sum_probs=20.1
Q ss_pred CccceecCCCCeEEcCC-CCeeecCC
Q 040420 67 PKFSMRVASKQAYICRD-CGYIYNER 91 (169)
Q Consensus 67 p~~~~k~~~~~~y~C~~-CGyVYd~~ 91 (169)
-.+.++......|.|.+ ||++|-..
T Consensus 40 g~v~i~~v~s~~YLCmn~~G~ly~s~ 65 (123)
T cd00058 40 GVVSIKGVASCRYLCMNKCGKLYGSK 65 (123)
T ss_pred CEEEEEEcccceEEEECCCCCEEECC
Confidence 34667778888999998 99999753
No 439
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=20.56 E-value=34 Score=32.27 Aligned_cols=29 Identities=31% Similarity=0.784 Sum_probs=16.5
Q ss_pred EcCCCCeeecCCC-CCCCCC--CCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERK-PFDQLP--DNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~t-pF~~lP--d~~~CPvCgap 109 (169)
+|..||.+..-.+ .++.-. -.|.|. ||+.
T Consensus 177 ic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~ 208 (510)
T PRK00750 177 ICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHE 208 (510)
T ss_pred eCCCCCccceEEEEEEeCCCCEEEEEcC-CCCE
Confidence 8999997764321 222111 257775 8773
No 440
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=20.53 E-value=43 Score=27.61 Aligned_cols=22 Identities=36% Similarity=0.979 Sum_probs=15.3
Q ss_pred CCeEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 76 KQAYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 76 ~~~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
....-|.+|| |+ .-|.|-.||+
T Consensus 116 P~r~fCaVCG--~~---------S~ysC~~CG~ 137 (156)
T KOG3362|consen 116 PLRKFCAVCG--YD---------SKYSCVNCGT 137 (156)
T ss_pred CcchhhhhcC--CC---------chhHHHhcCC
Confidence 3456799999 43 2358888887
No 441
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=20.51 E-value=55 Score=20.00 Aligned_cols=16 Identities=25% Similarity=0.343 Sum_probs=12.8
Q ss_pred CCCeEEcCCCCeeecC
Q 040420 75 SKQAYICRDCGYIYNE 90 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~ 90 (169)
..+.|+|.+|+++...
T Consensus 25 ~~~~~~C~~C~~~~H~ 40 (50)
T cd00029 25 FKQGLRCSWCKVKCHK 40 (50)
T ss_pred ccceeEcCCCCCchhh
Confidence 3578999999988665
No 442
>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=20.44 E-value=44 Score=22.99 Aligned_cols=27 Identities=30% Similarity=0.582 Sum_probs=14.2
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
-+|++|+.+-. =|+..--...|.+|+.
T Consensus 8 VkCp~C~~~q~---vFSha~t~V~C~~Cg~ 34 (55)
T PF01667_consen 8 VKCPGCYNIQT---VFSHAQTVVKCVVCGT 34 (55)
T ss_dssp EE-TTT-SEEE---EETT-SS-EE-SSSTS
T ss_pred EECCCCCCeeE---EEecCCeEEEcccCCC
Confidence 48999996532 2344444568999987
No 443
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=20.39 E-value=32 Score=32.80 Aligned_cols=29 Identities=28% Similarity=0.754 Sum_probs=18.2
Q ss_pred EcCCCCeeecCCCCCCC-CCCCCCCCCCCCC
Q 040420 80 ICRDCGYIYNERKPFDQ-LPDNYFCPVCGAP 109 (169)
Q Consensus 80 ~C~~CGyVYd~~tpF~~-lPd~~~CPvCgap 109 (169)
+|..||.+....+.++. -.-.|.|. ||+.
T Consensus 170 ic~~cGrv~~~~~~~~~~~~v~Y~c~-cG~~ 199 (515)
T TIGR00467 170 FCENCGRDTTTVNNYDNEYSIEYSCE-CGNQ 199 (515)
T ss_pred ecCCcCccCceEEEecCCceEEEEcC-CCCE
Confidence 89999988554332321 14568885 8874
No 444
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=20.38 E-value=44 Score=30.31 Aligned_cols=26 Identities=35% Similarity=0.864 Sum_probs=12.2
Q ss_pred EEcCCCCeeecCCCCCCCCCCCCCCCCCCCC
Q 040420 79 YICRDCGYIYNERKPFDQLPDNYFCPVCGAP 109 (169)
Q Consensus 79 y~C~~CGyVYd~~tpF~~lPd~~~CPvCgap 109 (169)
.+|..||..+++. ++ .+.+|.+||.+
T Consensus 150 ~~Ce~cG~~~~~~----~l-~~p~~~~~g~~ 175 (391)
T PF09334_consen 150 DQCENCGRPLEPE----EL-INPVCKICGSP 175 (391)
T ss_dssp TEETTTSSBEECC----CS-ECEEETTTS-B
T ss_pred CcccCCCCCcccc----cc-cCCcccccccc
Confidence 3455555555432 22 22466666664
No 445
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=20.38 E-value=58 Score=31.68 Aligned_cols=25 Identities=32% Similarity=0.828 Sum_probs=18.3
Q ss_pred eEEcCCCCeeecCCCCCCCCCCCCCCCCCCC
Q 040420 78 AYICRDCGYIYNERKPFDQLPDNYFCPVCGA 108 (169)
Q Consensus 78 ~y~C~~CGyVYd~~tpF~~lPd~~~CPvCga 108 (169)
.=.|+.|+..|-..+ +- .+||.||.
T Consensus 88 mV~CkkCk~ryRaD~----Li--ikCP~CGs 112 (539)
T PRK14894 88 LVDCRDCKMRWRADH----IQ--GVCPNCGS 112 (539)
T ss_pred eeECCCCCccccCcc----ce--eeCCCCCC
Confidence 348999999986532 22 38999995
No 446
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=20.36 E-value=41 Score=32.22 Aligned_cols=16 Identities=25% Similarity=0.609 Sum_probs=12.7
Q ss_pred CCCeEEcCCCCeeecC
Q 040420 75 SKQAYICRDCGYIYNE 90 (169)
Q Consensus 75 ~~~~y~C~~CGyVYd~ 90 (169)
....|+|.+||||--+
T Consensus 237 ~~~LwicliCg~vgcg 252 (493)
T KOG0804|consen 237 TEDLWICLICGNVGCG 252 (493)
T ss_pred cccEEEEEEccceecc
Confidence 5679999999988544
No 447
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=20.16 E-value=57 Score=19.24 Aligned_cols=13 Identities=31% Similarity=0.424 Sum_probs=8.5
Q ss_pred CCeEEcCCCCeee
Q 040420 76 KQAYICRDCGYIY 88 (169)
Q Consensus 76 ~~~y~C~~CGyVY 88 (169)
.-.-+|..||+++
T Consensus 19 g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 19 GWARRCPSCGHEH 31 (32)
T ss_dssp SS-EEESSSS-EE
T ss_pred cCEeECCCCcCEe
Confidence 3456999999775
Done!