Query psy2686
Match_columns 139
No_of_seqs 106 out of 174
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 22:37:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2686.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2686hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06957 COPI_C: Coatomer (COP 100.0 2.1E-68 4.6E-73 464.8 8.1 139 1-139 260-398 (422)
2 KOG0292|consensus 100.0 3.4E-53 7.4E-58 391.4 11.3 136 1-139 1047-1182(1202)
3 PF14853 Fis1_TPR_C: Fis1 C-te 95.0 0.052 1.1E-06 35.2 4.3 33 52-84 12-44 (53)
4 COG4391 Uncharacterized protei 93.3 0.037 7.9E-07 37.6 1.0 20 112-132 40-59 (62)
5 PF10276 zf-CHCC: Zinc-finger 91.4 0.085 1.8E-06 32.8 0.8 21 112-132 20-40 (40)
6 PRK00398 rpoP DNA-directed RNA 87.6 0.34 7.5E-06 29.9 1.5 12 121-132 21-32 (46)
7 TIGR02300 FYDLN_acid conserved 86.9 0.39 8.4E-06 36.9 1.6 31 106-136 10-41 (129)
8 PF09538 FYDLN_acid: Protein o 86.5 0.41 8.9E-06 35.3 1.5 28 107-134 11-39 (108)
9 PF14446 Prok-RING_1: Prokaryo 86.0 0.43 9.4E-06 31.5 1.3 26 106-134 9-34 (54)
10 smart00659 RPOLCX RNA polymera 82.5 0.68 1.5E-05 29.0 1.1 23 108-132 8-30 (44)
11 cd00729 rubredoxin_SM Rubredox 82.2 0.65 1.4E-05 27.5 0.8 16 115-130 11-27 (34)
12 COG1996 RPC10 DNA-directed RNA 81.6 0.77 1.7E-05 29.8 1.1 26 108-134 12-37 (49)
13 PF13432 TPR_16: Tetratricopep 81.4 6.6 0.00014 24.3 5.4 25 50-74 6-30 (65)
14 PF13913 zf-C2HC_2: zinc-finge 79.0 0.71 1.5E-05 25.5 0.2 15 120-134 1-15 (25)
15 COG1592 Rubrerythrin [Energy p 77.2 1.3 2.8E-05 35.2 1.3 21 107-131 139-159 (166)
16 PF07719 TPR_2: Tetratricopept 75.2 4.7 0.0001 21.7 3.0 25 49-73 9-33 (34)
17 PF13371 TPR_9: Tetratricopept 74.9 6.2 0.00013 24.8 3.9 48 36-84 25-72 (73)
18 cd00350 rubredoxin_like Rubred 73.3 1.9 4.1E-05 25.0 1.0 21 107-130 6-26 (33)
19 PF14369 zf-RING_3: zinc-finge 71.3 2.6 5.6E-05 25.2 1.3 27 108-134 8-34 (35)
20 COG1579 Zn-ribbon protein, pos 70.8 2.1 4.5E-05 35.8 1.1 24 107-130 199-230 (239)
21 KOG3364|consensus 70.6 9.7 0.00021 29.9 4.7 32 52-83 82-113 (149)
22 PF03604 DNA_RNApol_7kD: DNA d 70.1 2.9 6.4E-05 24.6 1.3 17 115-132 12-28 (32)
23 PF14255 Cys_rich_CPXG: Cystei 68.0 2.3 5.1E-05 27.6 0.7 10 122-131 1-10 (52)
24 PF13901 DUF4206: Domain of un 67.5 3.2 7E-05 33.2 1.5 28 106-134 156-185 (202)
25 PF14447 Prok-RING_4: Prokaryo 66.6 4.1 8.8E-05 27.1 1.6 23 107-133 29-51 (55)
26 TIGR02795 tol_pal_ybgF tol-pal 66.4 27 0.00058 23.1 5.7 30 52-81 87-116 (119)
27 PF05191 ADK_lid: Adenylate ki 65.3 2.8 6.1E-05 25.2 0.6 14 123-136 3-16 (36)
28 PF13465 zf-H2C2_2: Zinc-finge 63.9 3.4 7.3E-05 22.6 0.7 16 117-132 10-25 (26)
29 PF12660 zf-TFIIIC: Putative z 63.7 3.8 8.1E-05 29.5 1.1 33 101-134 36-68 (99)
30 PF02892 zf-BED: BED zinc fing 61.5 3.7 8.1E-05 24.6 0.7 23 112-134 7-29 (45)
31 PF06943 zf-LSD1: LSD1 zinc fi 61.4 4.9 0.00011 22.6 1.1 13 117-129 12-24 (25)
32 COG3931 Predicted N-formylglut 61.0 5 0.00011 34.0 1.5 20 102-121 143-162 (263)
33 TIGR02098 MJ0042_CXXC MJ0042 f 60.8 5 0.00011 23.4 1.1 16 117-132 21-36 (38)
34 smart00834 CxxC_CXXC_SSSS Puta 60.3 4.7 0.0001 23.5 0.9 24 108-131 11-36 (41)
35 PRK10246 exonuclease subunit S 60.2 3.8 8.2E-05 40.1 0.8 14 121-134 503-516 (1047)
36 PF14559 TPR_19: Tetratricopep 60.0 23 0.0005 21.7 4.2 22 52-73 36-57 (68)
37 PF05605 zf-Di19: Drought indu 59.4 4.6 0.0001 25.5 0.9 9 121-129 2-10 (54)
38 PF14354 Lar_restr_allev: Rest 59.2 4.2 9.1E-05 25.9 0.6 9 123-131 5-13 (61)
39 PF03811 Zn_Tnp_IS1: InsA N-te 56.9 5 0.00011 24.2 0.7 11 121-131 5-15 (36)
40 PF13894 zf-C2H2_4: C2H2-type 56.8 4.7 0.0001 20.1 0.5 10 123-132 2-11 (24)
41 TIGR02605 CxxC_CxxC_SSSS putat 56.8 5.6 0.00012 24.6 0.9 11 119-129 24-34 (52)
42 COG3919 Predicted ATP-grasp en 56.7 12 0.00026 33.3 3.2 52 52-103 212-276 (415)
43 COG4530 Uncharacterized protei 54.8 6.5 0.00014 29.9 1.1 26 106-131 10-36 (129)
44 TIGR03655 anti_R_Lar restricti 54.5 5.6 0.00012 25.2 0.6 10 123-132 3-12 (53)
45 TIGR02552 LcrH_SycD type III s 54.4 69 0.0015 22.1 7.2 23 51-73 61-83 (135)
46 PF13878 zf-C2H2_3: zinc-finge 54.0 8.5 0.00018 23.5 1.4 15 121-135 13-27 (41)
47 COG2093 DNA-directed RNA polym 53.4 8.4 0.00018 26.3 1.3 19 119-137 16-35 (64)
48 PF04910 Tcf25: Transcriptiona 51.6 22 0.00047 30.8 4.0 37 37-73 99-135 (360)
49 PF13414 TPR_11: TPR repeat; P 51.0 35 0.00076 21.0 4.0 37 35-72 32-69 (69)
50 PF13371 TPR_9: Tetratricopept 50.7 18 0.00039 22.6 2.6 25 50-74 4-28 (73)
51 TIGR02552 LcrH_SycD type III s 49.5 84 0.0018 21.6 7.3 39 34-73 11-49 (135)
52 PF13248 zf-ribbon_3: zinc-rib 49.3 10 0.00022 20.8 1.0 10 121-130 16-25 (26)
53 PRK00564 hypA hydrogenase nick 48.3 10 0.00022 27.9 1.3 34 96-131 62-98 (117)
54 PHA00159 endonuclease I 48.2 18 0.00039 28.4 2.6 35 80-123 75-109 (148)
55 TIGR01053 LSD1 zinc finger dom 48.1 12 0.00025 21.9 1.2 15 116-130 14-28 (31)
56 TIGR02159 PA_CoA_Oxy4 phenylac 47.6 8.3 0.00018 29.7 0.7 12 121-132 105-116 (146)
57 PRK10866 outer membrane biogen 47.4 1.5E+02 0.0033 24.0 8.1 53 36-88 64-116 (243)
58 PF08274 PhnA_Zn_Ribbon: PhnA 47.0 7.5 0.00016 22.6 0.3 10 123-132 4-13 (30)
59 smart00028 TPR Tetratricopepti 46.9 33 0.00071 16.1 3.2 24 50-73 10-33 (34)
60 PF13174 TPR_6: Tetratricopept 46.9 43 0.00093 17.5 3.7 23 51-73 10-32 (33)
61 PF09723 Zn-ribbon_8: Zinc rib 46.7 9.7 0.00021 23.1 0.8 11 119-129 24-34 (42)
62 PRK06393 rpoE DNA-directed RNA 46.2 8.1 0.00018 26.3 0.4 16 123-138 19-35 (64)
63 PF13512 TPR_18: Tetratricopep 45.9 20 0.00043 27.7 2.6 35 51-85 57-91 (142)
64 PRK05452 anaerobic nitric oxid 45.8 35 0.00077 30.6 4.5 24 107-130 430-467 (479)
65 PF00096 zf-C2H2: Zinc finger, 44.8 8.6 0.00019 19.6 0.3 11 123-133 2-12 (23)
66 PF14353 CpXC: CpXC protein 44.7 11 0.00024 27.5 0.9 15 121-135 38-52 (128)
67 PF06676 DUF1178: Protein of u 44.7 9.7 0.00021 29.7 0.7 16 117-132 28-43 (148)
68 COG1281 Disulfide bond chapero 44.6 9 0.00019 32.9 0.5 17 117-133 262-278 (286)
69 TIGR03829 YokU_near_AblA uncha 44.5 9.1 0.0002 27.6 0.5 19 116-134 30-48 (89)
70 PF04423 Rad50_zn_hook: Rad50 43.9 11 0.00023 23.9 0.7 12 123-134 22-33 (54)
71 PRK03824 hypA hydrogenase nick 43.9 94 0.002 23.3 6.0 68 62-131 25-117 (135)
72 PF02591 DUF164: Putative zinc 43.6 8 0.00017 24.6 0.1 16 114-129 39-54 (56)
73 PF08271 TF_Zn_Ribbon: TFIIB z 43.4 11 0.00024 22.7 0.7 9 123-131 2-10 (43)
74 PF02151 UVR: UvrB/uvrC motif; 43.2 47 0.001 19.4 3.4 30 41-70 4-33 (36)
75 PF00515 TPR_1: Tetratricopept 42.7 41 0.00089 18.1 3.0 24 50-73 10-33 (34)
76 PRK15359 type III secretion sy 41.8 62 0.0013 23.7 4.6 39 31-73 18-56 (144)
77 PF04606 Ogr_Delta: Ogr/Delta- 41.5 12 0.00026 23.2 0.6 10 123-132 1-10 (47)
78 COG1675 TFA1 Transcription ini 40.8 31 0.00068 27.6 3.0 52 74-131 88-142 (176)
79 COG1656 Uncharacterized conser 40.3 24 0.00053 28.1 2.3 55 74-133 74-142 (165)
80 smart00238 BIR Baculoviral inh 39.9 22 0.00047 23.1 1.7 25 107-133 23-48 (71)
81 COG4357 Zinc finger domain con 39.4 15 0.00033 27.2 1.0 31 105-137 62-96 (105)
82 PF01430 HSP33: Hsp33 protein; 39.1 9.7 0.00021 31.7 -0.1 16 117-132 262-277 (280)
83 PF03704 BTAD: Bacterial trans 39.1 1.1E+02 0.0025 21.7 5.6 36 41-76 62-97 (146)
84 smart00614 ZnF_BED BED zinc fi 38.8 14 0.00029 23.0 0.6 17 117-133 14-30 (50)
85 PF13428 TPR_14: Tetratricopep 38.4 43 0.00093 19.6 2.7 26 51-76 11-36 (44)
86 PF11238 DUF3039: Protein of u 38.2 11 0.00024 25.3 0.1 26 106-131 29-54 (58)
87 PF13240 zinc_ribbon_2: zinc-r 37.9 19 0.00042 19.4 1.0 11 120-130 12-22 (23)
88 TIGR00100 hypA hydrogenase nic 37.7 16 0.00035 26.7 0.9 53 74-131 41-96 (115)
89 cd00498 Hsp33 Heat shock prote 37.6 13 0.00029 30.9 0.5 15 118-132 259-273 (275)
90 PF08792 A2L_zn_ribbon: A2L zi 37.4 16 0.00034 21.5 0.7 15 117-131 17-31 (33)
91 PRK09783 copper/silver efflux 37.2 18 0.0004 31.5 1.3 26 113-138 50-75 (409)
92 PF14122 YokU: YokU-like prote 37.1 16 0.00034 26.4 0.7 18 117-134 31-48 (87)
93 PF01155 HypA: Hydrogenase exp 36.7 12 0.00027 27.2 0.2 53 74-131 41-96 (113)
94 PRK00114 hslO Hsp33-like chape 36.3 15 0.00032 31.0 0.6 15 118-132 265-279 (293)
95 PF13719 zinc_ribbon_5: zinc-r 36.3 21 0.00046 21.1 1.1 16 117-132 21-36 (37)
96 PF13805 Pil1: Eisosome compon 36.2 1.1E+02 0.0025 26.1 5.9 48 43-90 195-258 (271)
97 PRK14892 putative transcriptio 36.1 20 0.00043 26.2 1.1 20 114-133 35-54 (99)
98 PF13525 YfiO: Outer membrane 35.5 1.2E+02 0.0025 23.5 5.5 44 44-87 45-88 (203)
99 PF09889 DUF2116: Uncharacteri 35.4 21 0.00045 23.8 1.1 16 119-134 1-16 (59)
100 cd00189 TPR Tetratricopeptide 35.1 92 0.002 17.9 4.4 23 52-74 45-67 (100)
101 PF07754 DUF1610: Domain of un 34.5 24 0.00052 19.6 1.1 19 108-128 4-23 (24)
102 PRK01343 zinc-binding protein; 34.2 29 0.00062 23.1 1.6 18 118-135 6-23 (57)
103 TIGR02487 NrdD anaerobic ribon 33.8 46 0.001 30.8 3.4 45 78-130 501-547 (579)
104 PLN02294 cytochrome c oxidase 33.6 20 0.00043 28.9 0.9 26 111-137 128-157 (174)
105 PF14863 Alkyl_sulf_dimr: Alky 33.3 1.4E+02 0.003 22.8 5.4 31 46-76 75-105 (141)
106 COG4049 Uncharacterized protei 33.2 15 0.00032 24.9 0.1 16 117-132 13-28 (65)
107 PRK10803 tol-pal system protei 33.1 1.2E+02 0.0027 25.1 5.5 33 52-84 228-260 (263)
108 PF03119 DNA_ligase_ZBD: NAD-d 33.0 20 0.00043 20.3 0.6 10 123-132 1-10 (28)
109 PF13717 zinc_ribbon_4: zinc-r 32.7 20 0.00044 21.2 0.6 11 122-132 3-13 (36)
110 PF13597 NRDD: Anaerobic ribon 32.0 36 0.00078 31.2 2.4 48 76-130 465-513 (546)
111 COG3947 Response regulator con 31.8 88 0.0019 27.8 4.6 51 44-97 282-332 (361)
112 PRK11788 tetratricopeptide rep 31.7 1.8E+02 0.0039 23.7 6.3 59 36-94 244-316 (389)
113 TIGR02795 tol_pal_ybgF tol-pal 31.7 1.5E+02 0.0032 19.4 4.9 45 43-87 41-85 (119)
114 PF12760 Zn_Tnp_IS1595: Transp 31.7 22 0.00047 21.8 0.6 9 122-130 19-27 (46)
115 TIGR03504 FimV_Cterm FimV C-te 31.5 1.3E+02 0.0028 18.6 4.2 33 52-85 10-42 (44)
116 PF11475 VP_N-CPKC: Virion pro 31.5 8.5 0.00018 22.7 -1.1 18 105-129 7-24 (32)
117 cd00022 BIR Baculoviral inhibi 31.4 37 0.00079 21.8 1.8 15 119-133 32-46 (69)
118 PF14169 YdjO: Cold-inducible 30.8 30 0.00065 23.2 1.3 19 117-135 35-53 (59)
119 cd00924 Cyt_c_Oxidase_Vb Cytoc 30.4 20 0.00043 26.0 0.4 26 111-137 66-95 (97)
120 PF15616 TerY-C: TerY-C metal 30.4 38 0.00082 26.0 1.9 28 104-131 88-115 (131)
121 PRK09710 lar restriction allev 30.4 21 0.00046 24.4 0.5 10 121-130 6-15 (64)
122 PRK00762 hypA hydrogenase nick 30.0 28 0.0006 25.8 1.1 12 120-131 91-102 (124)
123 PF14690 zf-ISL3: zinc-finger 29.8 26 0.00056 20.9 0.8 11 121-131 2-12 (47)
124 PF14788 EF-hand_10: EF hand; 29.5 87 0.0019 20.3 3.2 32 65-96 8-39 (51)
125 KOG3352|consensus 29.0 26 0.00056 27.7 0.8 63 74-137 61-149 (153)
126 PRK03681 hypA hydrogenase nick 28.6 31 0.00068 25.2 1.2 55 74-131 41-97 (114)
127 COG1143 NuoI Formate hydrogenl 28.3 40 0.00086 26.7 1.8 41 86-130 62-103 (172)
128 TIGR01206 lysW lysine biosynth 27.8 27 0.00058 22.8 0.6 12 120-131 21-32 (54)
129 PF07743 HSCB_C: HSCB C-termin 27.6 1.5E+02 0.0032 19.5 4.3 31 38-68 37-67 (78)
130 PF05325 DUF730: Protein of un 27.2 41 0.0009 25.1 1.6 33 94-127 18-50 (122)
131 PF13812 PPR_3: Pentatricopept 27.0 1.1E+02 0.0023 16.1 3.8 29 43-71 3-31 (34)
132 COG3677 Transposase and inacti 26.6 40 0.00086 25.4 1.4 32 107-138 35-70 (129)
133 PLN03088 SGT1, suppressor of 26.6 2.6E+02 0.0056 23.8 6.6 44 34-78 64-107 (356)
134 TIGR00373 conserved hypothetic 26.3 22 0.00047 27.4 -0.0 36 96-131 100-138 (158)
135 PRK06266 transcription initiat 26.2 27 0.00058 27.6 0.4 37 96-132 108-147 (178)
136 PF05367 Phage_endo_I: Phage e 25.9 90 0.002 24.6 3.3 37 77-122 72-108 (149)
137 PF11793 FANCL_C: FANCL C-term 25.7 23 0.00049 23.7 -0.0 12 122-133 56-67 (70)
138 PF13408 Zn_ribbon_recom: Reco 25.7 32 0.0007 21.0 0.7 15 120-134 4-18 (58)
139 smart00647 IBR In Between Ring 25.3 65 0.0014 19.8 2.1 18 117-134 36-53 (64)
140 cd03532 Rieske_RO_Alpha_VanA_D 24.9 52 0.0011 23.4 1.7 31 106-138 44-77 (116)
141 PF01215 COX5B: Cytochrome c o 24.7 15 0.00033 28.3 -1.2 27 110-137 98-128 (136)
142 PRK01402 hslO Hsp33-like chape 24.6 32 0.00069 29.8 0.7 15 118-132 305-319 (328)
143 cd03469 Rieske_RO_Alpha_N Ries 24.3 56 0.0012 22.7 1.8 31 106-138 41-75 (118)
144 COG5319 Uncharacterized protei 23.9 32 0.00069 26.8 0.5 14 118-131 29-42 (142)
145 PF05741 zf-nanos: Nanos RNA b 23.8 32 0.00069 22.7 0.4 9 122-130 34-42 (55)
146 TIGR02827 RNR_anaer_Bdell anae 23.6 1.1E+02 0.0023 28.8 3.9 46 78-130 509-555 (586)
147 TIGR03831 YgiT_finger YgiT-typ 23.6 45 0.00096 19.5 1.0 22 112-133 23-44 (46)
148 PF11290 DUF3090: Protein of u 23.4 47 0.001 26.7 1.3 12 123-134 156-167 (171)
149 PRK00420 hypothetical protein; 23.4 48 0.001 24.7 1.3 26 108-133 26-52 (112)
150 TIGR02378 nirD_assim_sml nitri 23.3 45 0.00098 23.1 1.2 28 107-134 42-77 (105)
151 PF04810 zf-Sec23_Sec24: Sec23 23.2 42 0.0009 20.1 0.8 19 112-130 15-33 (40)
152 PF02489 Herpes_glycop_H: Herp 23.0 34 0.00073 31.8 0.5 19 114-132 554-572 (657)
153 PF12475 Amdo_NSP: Amdovirus n 22.9 44 0.00095 21.6 0.9 17 25-41 25-43 (48)
154 PF01485 IBR: IBR domain; Int 22.7 74 0.0016 19.5 2.0 25 111-135 28-54 (64)
155 PF09866 DUF2093: Uncharacteri 22.6 46 0.001 21.0 0.9 15 102-116 4-18 (42)
156 TIGR03847 conserved hypothetic 22.1 51 0.0011 26.6 1.3 12 123-134 158-169 (177)
157 PF13041 PPR_2: PPR repeat fam 22.0 1.8E+02 0.0039 17.0 4.4 35 42-76 4-38 (50)
158 PF01475 FUR: Ferric uptake re 21.8 2.1E+02 0.0045 20.1 4.4 76 50-132 16-91 (120)
159 PF12773 DZR: Double zinc ribb 21.7 69 0.0015 19.4 1.6 18 118-135 26-43 (50)
160 PF09237 GAGA: GAGA factor; I 21.4 43 0.00093 22.2 0.7 14 118-131 21-34 (54)
161 smart00734 ZnF_Rad18 Rad18-lik 21.4 44 0.00095 18.5 0.6 10 122-131 2-11 (26)
162 smart00249 PHD PHD zinc finger 21.3 64 0.0014 18.1 1.4 21 117-137 10-30 (47)
163 PF03884 DUF329: Domain of unk 21.1 37 0.0008 22.5 0.3 13 121-133 2-14 (57)
164 PF07503 zf-HYPF: HypF finger; 21.1 48 0.001 19.7 0.8 14 118-131 18-31 (35)
165 PF00301 Rubredoxin: Rubredoxi 21.1 46 0.00099 21.1 0.7 13 123-135 3-15 (47)
166 PF01535 PPR: PPR repeat; Int 20.6 1.4E+02 0.003 15.1 3.1 28 44-71 3-30 (31)
167 PRK08579 anaerobic ribonucleos 20.5 1.1E+02 0.0023 28.9 3.3 91 29-130 500-591 (625)
168 PRK10747 putative protoheme IX 20.5 2.9E+02 0.0064 23.6 5.8 42 34-75 146-187 (398)
169 KOG0547|consensus 20.4 1.7E+02 0.0037 27.7 4.4 63 32-98 106-179 (606)
170 TIGR02710 CRISPR-associated pr 20.4 4E+02 0.0088 23.7 6.7 54 35-88 122-177 (380)
171 TIGR00618 sbcc exonuclease Sbc 20.1 46 0.001 32.5 0.9 17 119-135 499-515 (1042)
No 1
>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=100.00 E-value=2.1e-68 Score=464.80 Aligned_cols=139 Identities=63% Similarity=0.984 Sum_probs=118.1
Q ss_pred CccchhhhhhhhccCCchhhhHHHHHHHHhhhcCCchhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHHHHHH
Q psy2686 1 MGLQMETYRKEQLKSNESSQVRICELAAYFTHSKLQPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEVATQA 80 (139)
Q Consensus 1 ~gl~iEl~Rr~l~~~~~~~~kR~lELaAYFT~c~Lqp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~~~qA 80 (139)
+||+||++||++++++.+++||+||||||||||+|||+|++||||+||+++||+|||+||++|||||||++|++++++||
T Consensus 260 lgl~iEl~Rr~l~~~~~~~~kR~lELAAYFThc~LQp~H~~LaLr~AM~~~~K~KNf~tAa~FArRLLel~p~~~~a~qA 339 (422)
T PF06957_consen 260 LGLSIELERRELPKDPVEDQKRNLELAAYFTHCKLQPSHLILALRSAMSQAFKLKNFITAASFARRLLELNPSPEVAEQA 339 (422)
T ss_dssp HHHHHHHHHCTS-TTTHHHHHHHHHHHHHHCCS---HHHHHHHHHHHHHHCCCTTBHHHHHHHHHHHHCT--SCHHHHHH
T ss_pred HHHHHHHHHHhccccchhhHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 58999999999999988899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCceeecCCCCCCeeeeccccccccCCCccccccCCCccccCCCCCCC
Q psy2686 81 RKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGEL 139 (139)
Q Consensus 81 rkil~~~e~~~~da~~i~yD~~~~F~iC~~s~tPIy~g~~~v~Cp~cga~y~p~~kG~l 139 (139)
|||+++||++|+|+|+||||++|||+||++||||||+|+|+|+||||||+|+|+|||+|
T Consensus 340 rKil~~~e~~~tDa~~i~yD~~npF~ICa~s~tPIY~G~~~v~CP~cgA~y~~~~kG~l 398 (422)
T PF06957_consen 340 RKILQACERNPTDAHEIDYDERNPFDICAASYTPIYRGSPSVKCPYCGAKYHPEYKGQL 398 (422)
T ss_dssp HHHHHHHCCS--BSS--S--TTS-EEEBTTT--EEETTS-EEE-TTT--EEEGGGTTSB
T ss_pred HHHHHHHhcCCCCceecCCCCCCCceeeecccccccCCCCCeeCCCCCCccChhhCCCC
Confidence 99999999999999999999999999999999999999999999999999999999986
No 2
>KOG0292|consensus
Probab=100.00 E-value=3.4e-53 Score=391.36 Aligned_cols=136 Identities=56% Similarity=0.931 Sum_probs=133.4
Q ss_pred CccchhhhhhhhccCCchhhhHHHHHHHHhhhcCCchhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHHHHHH
Q psy2686 1 MGLQMETYRKEQLKSNESSQVRICELAAYFTHSKLQPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEVATQA 80 (139)
Q Consensus 1 ~gl~iEl~Rr~l~~~~~~~~kR~lELaAYFT~c~Lqp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~~~qA 80 (139)
+||+||++||+|++++ .+|+||||||||||+|||.|++||||+||+++||+|||+||++||+|||++.|.+++++||
T Consensus 1047 ~gL~~E~~Rr~l~~~~---~~~~~ElAaYFt~~~Lqp~H~ilalrtA~n~ffK~kN~ktAs~fa~rLlel~~~~~~A~q~ 1123 (1202)
T KOG0292|consen 1047 VGLSVELERRKLKKPN---LEQQLELAAYFTHCKLQPMHRILALRTAMNVFFKLKNLKTAAEFARRLLELAPSPPVAEQA 1123 (1202)
T ss_pred hhheeeeeecccCCch---HHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhCCCChHHHHH
Confidence 5899999999999988 7888999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCceeecCCCCCCeeeeccccccccCCCccccccCCCccccCCCCCCC
Q psy2686 81 RKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGEL 139 (139)
Q Consensus 81 rkil~~~e~~~~da~~i~yD~~~~F~iC~~s~tPIy~g~~~v~Cp~cga~y~p~~kG~l 139 (139)
|||+++||+||+|+++|+||+||||+||+.||+|||+|+|.|+||||||+|.|.++|+|
T Consensus 1124 rki~~a~eknp~Da~~l~yd~~n~f~iC~~t~~Piy~g~p~~~cp~cga~y~~~~~g~i 1182 (1202)
T KOG0292|consen 1124 RKIKQAAEKNPTDAYELNYDPHNPFVICGATYVPIYRGRPDVSCPYCGACFVPSSKGNI 1182 (1202)
T ss_pred HHHHHHhhcCcccccccCcccCCCeeEecccceeeecCCCCcCCCcccceeccccCCce
Confidence 99999999999999999999999999999999999999999999999999999999985
No 3
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=95.04 E-value=0.052 Score=35.23 Aligned_cols=33 Identities=27% Similarity=0.575 Sum_probs=26.8
Q ss_pred HhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHH
Q psy2686 52 FKLKNYKTTASFAHRLLELGPSMEVATQARKLL 84 (139)
Q Consensus 52 ~K~kN~~tAa~fArRLLel~p~~~~~~qArkil 84 (139)
||.|||.+|-.++.+||++.|....+.+=++++
T Consensus 12 ykl~~Y~~A~~~~~~lL~~eP~N~Qa~~L~~~i 44 (53)
T PF14853_consen 12 YKLGEYEKARRYCDALLEIEPDNRQAQSLKELI 44 (53)
T ss_dssp HHTT-HHHHHHHHHHHHHHTTS-HHHHHHHHHH
T ss_pred HHhhhHHHHHHHHHHHHhhCCCcHHHHHHHHHH
Confidence 999999999999999999999887766655554
No 4
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=93.34 E-value=0.037 Score=37.58 Aligned_cols=20 Identities=20% Similarity=0.629 Sum_probs=15.8
Q ss_pred cccccCCCccccccCCCcccc
Q psy2686 112 YTPIYHGRESEACVYCGASYL 132 (139)
Q Consensus 112 ~tPIy~g~~~v~Cp~cga~y~ 132 (139)
|-+| ..+..|.|||||+.|.
T Consensus 40 ~L~m-g~~gev~CPYC~t~y~ 59 (62)
T COG4391 40 FLDM-GDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEEc-CCCCcEecCccccEEE
Confidence 4455 5578899999999985
No 5
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=91.45 E-value=0.085 Score=32.76 Aligned_cols=21 Identities=29% Similarity=0.757 Sum_probs=13.8
Q ss_pred cccccCCCccccccCCCcccc
Q psy2686 112 YTPIYHGRESEACVYCGASYL 132 (139)
Q Consensus 112 ~tPIy~g~~~v~Cp~cga~y~ 132 (139)
|-+|-+....+.|||||..|.
T Consensus 20 yl~l~~~~~~~~CpYCg~~yv 40 (40)
T PF10276_consen 20 YLNLDDEPGPVVCPYCGTRYV 40 (40)
T ss_dssp EEE-TTTTCEEEETTTTEEEE
T ss_pred EEecCCCCCeEECCCCCCEEC
Confidence 334433335799999999873
No 6
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.64 E-value=0.34 Score=29.93 Aligned_cols=12 Identities=42% Similarity=0.955 Sum_probs=10.7
Q ss_pred cccccCCCcccc
Q psy2686 121 SEACVYCGASYL 132 (139)
Q Consensus 121 ~v~Cp~cga~y~ 132 (139)
.++||+||+...
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 799999999775
No 7
>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=86.86 E-value=0.39 Score=36.86 Aligned_cols=31 Identities=23% Similarity=0.561 Sum_probs=24.7
Q ss_pred eeeccccccccC-CCccccccCCCccccCCCC
Q psy2686 106 QICARSYTPIYH-GRESEACVYCGASYLPKYK 136 (139)
Q Consensus 106 ~iC~~s~tPIy~-g~~~v~Cp~cga~y~p~~k 136 (139)
-+|..+=+.-|- ++..+.||+||+.|.+.+.
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCccCcchh
Confidence 367776677774 7889999999999998854
No 8
>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=86.49 E-value=0.41 Score=35.34 Aligned_cols=28 Identities=21% Similarity=0.691 Sum_probs=20.6
Q ss_pred eeccccccccC-CCccccccCCCccccCC
Q psy2686 107 ICARSYTPIYH-GRESEACVYCGASYLPK 134 (139)
Q Consensus 107 iC~~s~tPIy~-g~~~v~Cp~cga~y~p~ 134 (139)
+|...=+.-|- ++..+.||+||+.|.|+
T Consensus 11 ~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 55555555563 55668899999999987
No 9
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.03 E-value=0.43 Score=31.52 Aligned_cols=26 Identities=27% Similarity=0.768 Sum_probs=19.9
Q ss_pred eeeccccccccCCCccccccCCCccccCC
Q psy2686 106 QICARSYTPIYHGRESEACVYCGASYLPK 134 (139)
Q Consensus 106 ~iC~~s~tPIy~g~~~v~Cp~cga~y~p~ 134 (139)
.+|...| -.|.+.|.||-|||.||-+
T Consensus 9 ~~Cg~~~---~~~dDiVvCp~CgapyHR~ 34 (54)
T PF14446_consen 9 PVCGKKF---KDGDDIVVCPECGAPYHRD 34 (54)
T ss_pred hhhCCcc---cCCCCEEECCCCCCcccHH
Confidence 3555555 4489999999999999854
No 10
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.52 E-value=0.68 Score=29.01 Aligned_cols=23 Identities=26% Similarity=0.602 Sum_probs=16.2
Q ss_pred eccccccccCCCccccccCCCcccc
Q psy2686 108 CARSYTPIYHGRESEACVYCGASYL 132 (139)
Q Consensus 108 C~~s~tPIy~g~~~v~Cp~cga~y~ 132 (139)
|...++. .....++||+||...+
T Consensus 8 Cg~~~~~--~~~~~irC~~CG~rIl 30 (44)
T smart00659 8 CGRENEI--KSKDVVRCRECGYRIL 30 (44)
T ss_pred CCCEeec--CCCCceECCCCCceEE
Confidence 4444444 2567899999999865
No 11
>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=82.23 E-value=0.65 Score=27.47 Aligned_cols=16 Identities=44% Similarity=0.889 Sum_probs=12.0
Q ss_pred ccCCC-ccccccCCCcc
Q psy2686 115 IYHGR-ESEACVYCGAS 130 (139)
Q Consensus 115 Iy~g~-~~v~Cp~cga~ 130 (139)
||.|. +...||.||+.
T Consensus 11 i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 11 IHEGEEAPEKCPICGAP 27 (34)
T ss_pred EeECCcCCCcCcCCCCc
Confidence 34554 77899999984
No 12
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=81.65 E-value=0.77 Score=29.77 Aligned_cols=26 Identities=31% Similarity=0.622 Sum_probs=18.1
Q ss_pred eccccccccCCCccccccCCCccccCC
Q psy2686 108 CARSYTPIYHGRESEACVYCGASYLPK 134 (139)
Q Consensus 108 C~~s~tPIy~g~~~v~Cp~cga~y~p~ 134 (139)
|+..+.-+ ...+.++||+||++.+-+
T Consensus 12 Cg~~~~~~-~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 12 CGREVELD-QETRGIRCPYCGSRILVK 37 (49)
T ss_pred cCCeeehh-hccCceeCCCCCcEEEEe
Confidence 55555433 367889999999987643
No 13
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=81.37 E-value=6.6 Score=24.30 Aligned_cols=25 Identities=12% Similarity=0.291 Sum_probs=21.2
Q ss_pred HHHhhhcHHHHHHHHHHHHhcCCCh
Q psy2686 50 LFFKLKNYKTTASFAHRLLELGPSM 74 (139)
Q Consensus 50 ~~~K~kN~~tAa~fArRLLel~p~~ 74 (139)
..++.|+|..|...-+++|+..|..
T Consensus 6 ~~~~~g~~~~A~~~~~~~l~~~P~~ 30 (65)
T PF13432_consen 6 ALYQQGDYDEAIAAFEQALKQDPDN 30 (65)
T ss_dssp HHHHCTHHHHHHHHHHHHHCCSTTH
T ss_pred HHHHcCCHHHHHHHHHHHHHHCCCC
Confidence 4578899999999999999998863
No 14
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=78.96 E-value=0.71 Score=25.50 Aligned_cols=15 Identities=33% Similarity=0.815 Sum_probs=12.4
Q ss_pred ccccccCCCccccCC
Q psy2686 120 ESEACVYCGASYLPK 134 (139)
Q Consensus 120 ~~v~Cp~cga~y~p~ 134 (139)
+.+.||.||-+|.|+
T Consensus 1 ~l~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 1 ELVPCPICGRKFNPD 15 (25)
T ss_pred CCCcCCCCCCEECHH
Confidence 457899999999765
No 15
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=77.20 E-value=1.3 Score=35.17 Aligned_cols=21 Identities=33% Similarity=0.823 Sum_probs=16.0
Q ss_pred eeccccccccCCCccccccCCCccc
Q psy2686 107 ICARSYTPIYHGRESEACVYCGASY 131 (139)
Q Consensus 107 iC~~s~tPIy~g~~~v~Cp~cga~y 131 (139)
+|+.++ .|.|...||.||+..
T Consensus 139 vCGy~~----~ge~P~~CPiCga~k 159 (166)
T COG1592 139 VCGYTH----EGEAPEVCPICGAPK 159 (166)
T ss_pred CCCCcc----cCCCCCcCCCCCChH
Confidence 555444 579999999999863
No 16
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=75.20 E-value=4.7 Score=21.71 Aligned_cols=25 Identities=28% Similarity=0.689 Sum_probs=21.2
Q ss_pred HHHHhhhcHHHHHHHHHHHHhcCCC
Q psy2686 49 NLFFKLKNYKTTASFAHRLLELGPS 73 (139)
Q Consensus 49 ~~~~K~kN~~tAa~fArRLLel~p~ 73 (139)
...++.|+|..|...-++.|++.|+
T Consensus 9 ~~~~~~~~~~~A~~~~~~al~l~p~ 33 (34)
T PF07719_consen 9 QAYYQLGNYEEAIEYFEKALELDPN 33 (34)
T ss_dssp HHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHhCCHHHHHHHHHHHHHHCcC
Confidence 4568999999999999999999875
No 17
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=74.85 E-value=6.2 Score=24.79 Aligned_cols=48 Identities=31% Similarity=0.387 Sum_probs=33.2
Q ss_pred chhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHH
Q psy2686 36 QPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEVATQARKLL 84 (139)
Q Consensus 36 qp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~~~qArkil 84 (139)
.|.+-.+-+..|+ .-++.|+|..|...-.+.|+++|....+.+++..+
T Consensus 25 ~p~~~~~~~~~a~-~~~~~g~~~~A~~~l~~~l~~~p~~~~~~~~~a~l 72 (73)
T PF13371_consen 25 DPDDPELWLQRAR-CLFQLGRYEEALEDLERALELSPDDPDARALRAML 72 (73)
T ss_pred CcccchhhHHHHH-HHHHhccHHHHHHHHHHHHHHCCCcHHHHHHHHhc
Confidence 3444333333333 45788899999999999999999887777766543
No 18
>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=73.28 E-value=1.9 Score=25.04 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=14.3
Q ss_pred eeccccccccCCCccccccCCCcc
Q psy2686 107 ICARSYTPIYHGRESEACVYCGAS 130 (139)
Q Consensus 107 iC~~s~tPIy~g~~~v~Cp~cga~ 130 (139)
+|...|.| ..+.-.||.||+.
T Consensus 6 ~CGy~y~~---~~~~~~CP~Cg~~ 26 (33)
T cd00350 6 VCGYIYDG---EEAPWVCPVCGAP 26 (33)
T ss_pred CCCCEECC---CcCCCcCcCCCCc
Confidence 56555443 2378899999984
No 19
>PF14369 zf-RING_3: zinc-finger
Probab=71.35 E-value=2.6 Score=25.15 Aligned_cols=27 Identities=19% Similarity=0.383 Sum_probs=17.1
Q ss_pred eccccccccCCCccccccCCCccccCC
Q psy2686 108 CARSYTPIYHGRESEACVYCGASYLPK 134 (139)
Q Consensus 108 C~~s~tPIy~g~~~v~Cp~cga~y~p~ 134 (139)
|..+..+--.+.+.+.||.|+.-++-+
T Consensus 8 C~~~V~~~~~~~~~~~CP~C~~gFvEe 34 (35)
T PF14369_consen 8 CNRFVRIAPSPDSDVACPRCHGGFVEE 34 (35)
T ss_pred CCCEeEeCcCCCCCcCCcCCCCcEeEe
Confidence 444444433466677899999877643
No 20
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=70.79 E-value=2.1 Score=35.78 Aligned_cols=24 Identities=25% Similarity=0.563 Sum_probs=19.1
Q ss_pred eecccccccc--------CCCccccccCCCcc
Q psy2686 107 ICARSYTPIY--------HGRESEACVYCGAS 130 (139)
Q Consensus 107 iC~~s~tPIy--------~g~~~v~Cp~cga~ 130 (139)
+|++=+--|+ .+.+.|.||+||.-
T Consensus 199 ~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred cccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 7887666554 57899999999975
No 21
>KOG3364|consensus
Probab=70.57 E-value=9.7 Score=29.92 Aligned_cols=32 Identities=25% Similarity=0.500 Sum_probs=26.5
Q ss_pred HhhhcHHHHHHHHHHHHhcCCChHHHHHHHHH
Q psy2686 52 FKLKNYKTTASFAHRLLELGPSMEVATQARKL 83 (139)
Q Consensus 52 ~K~kN~~tAa~fArRLLel~p~~~~~~qArki 83 (139)
||.|||..+....+.||+..|+...+-.-++.
T Consensus 82 yRlkeY~~s~~yvd~ll~~e~~n~Qa~~Lk~~ 113 (149)
T KOG3364|consen 82 YRLKEYSKSLRYVDALLETEPNNRQALELKET 113 (149)
T ss_pred HHHhhHHHHHHHHHHHHhhCCCcHHHHHHHHH
Confidence 89999999999999999999887665444433
No 22
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=70.10 E-value=2.9 Score=24.62 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=11.7
Q ss_pred ccCCCccccccCCCcccc
Q psy2686 115 IYHGRESEACVYCGASYL 132 (139)
Q Consensus 115 Iy~g~~~v~Cp~cga~y~ 132 (139)
|. ..+.|+||+||...+
T Consensus 12 ~~-~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 12 LK-PGDPIRCPECGHRIL 28 (32)
T ss_dssp BS-TSSTSSBSSSS-SEE
T ss_pred cC-CCCcEECCcCCCeEE
Confidence 43 356799999998754
No 23
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=67.95 E-value=2.3 Score=27.64 Aligned_cols=10 Identities=40% Similarity=1.079 Sum_probs=8.3
Q ss_pred ccccCCCccc
Q psy2686 122 EACVYCGASY 131 (139)
Q Consensus 122 v~Cp~cga~y 131 (139)
+.|||||...
T Consensus 1 i~CPyCge~~ 10 (52)
T PF14255_consen 1 IQCPYCGEPI 10 (52)
T ss_pred CCCCCCCCee
Confidence 5799999865
No 24
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=67.53 E-value=3.2 Score=33.17 Aligned_cols=28 Identities=18% Similarity=0.489 Sum_probs=23.5
Q ss_pred eeeccccccccC-C-CccccccCCCccccCC
Q psy2686 106 QICARSYTPIYH-G-RESEACVYCGASYLPK 134 (139)
Q Consensus 106 ~iC~~s~tPIy~-g-~~~v~Cp~cga~y~p~ 134 (139)
+||..+ .+||+ . +..++|+-|+|.||.+
T Consensus 156 e~C~~~-~~IfPF~~~~~~~C~~C~~v~H~~ 185 (202)
T PF13901_consen 156 EICNSD-DIIFPFQIDTTVRCPKCKSVFHKS 185 (202)
T ss_pred ccCCCC-CCCCCCCCCCeeeCCcCccccchh
Confidence 588878 99997 3 4899999999999865
No 25
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=66.65 E-value=4.1 Score=27.05 Aligned_cols=23 Identities=26% Similarity=0.853 Sum_probs=18.6
Q ss_pred eeccccccccCCCccccccCCCccccC
Q psy2686 107 ICARSYTPIYHGRESEACVYCGASYLP 133 (139)
Q Consensus 107 iC~~s~tPIy~g~~~v~Cp~cga~y~p 133 (139)
||-.+| .|+..--|||||..+.+
T Consensus 29 I~~~~f----~~~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 29 ICDNCF----PGERYNGCPFCGTPFEF 51 (55)
T ss_pred eecccc----ChhhccCCCCCCCcccC
Confidence 666666 78899999999998765
No 26
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=66.38 E-value=27 Score=23.08 Aligned_cols=30 Identities=13% Similarity=0.167 Sum_probs=15.8
Q ss_pred HhhhcHHHHHHHHHHHHhcCCChHHHHHHH
Q psy2686 52 FKLKNYKTTASFAHRLLELGPSMEVATQAR 81 (139)
Q Consensus 52 ~K~kN~~tAa~fArRLLel~p~~~~~~qAr 81 (139)
.+.+++..|...-+++++..|+...+.+|+
T Consensus 87 ~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~ 116 (119)
T TIGR02795 87 QELGDKEKAKATLQQVIKRYPGSSAAKLAQ 116 (119)
T ss_pred HHhCChHHHHHHHHHHHHHCcCChhHHHHH
Confidence 445555555555555555555555444443
No 27
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=65.30 E-value=2.8 Score=25.15 Aligned_cols=14 Identities=29% Similarity=0.783 Sum_probs=12.3
Q ss_pred cccCCCccccCCCC
Q psy2686 123 ACVYCGASYLPKYK 136 (139)
Q Consensus 123 ~Cp~cga~y~p~~k 136 (139)
.||-||+.|+-.|.
T Consensus 3 ~C~~Cg~~Yh~~~~ 16 (36)
T PF05191_consen 3 ICPKCGRIYHIEFN 16 (36)
T ss_dssp EETTTTEEEETTTB
T ss_pred CcCCCCCccccccC
Confidence 69999999998775
No 28
>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=63.86 E-value=3.4 Score=22.62 Aligned_cols=16 Identities=38% Similarity=0.949 Sum_probs=13.3
Q ss_pred CCCccccccCCCcccc
Q psy2686 117 HGRESEACVYCGASYL 132 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~ 132 (139)
.|+....||+|+.+|.
T Consensus 10 ~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSSEEESSSSEEES
T ss_pred CCCCCCCCCCCcCeeC
Confidence 5778899999998764
No 29
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=63.65 E-value=3.8 Score=29.48 Aligned_cols=33 Identities=24% Similarity=0.505 Sum_probs=18.7
Q ss_pred CCCCeeeeccccccccCCCccccccCCCccccCC
Q psy2686 101 EHNPFQICARSYTPIYHGRESEACVYCGASYLPK 134 (139)
Q Consensus 101 ~~~~F~iC~~s~tPIy~g~~~v~Cp~cga~y~p~ 134 (139)
.-..|.-|+.||-||- .-..-.|+.||..++..
T Consensus 36 ~GH~w~RC~lT~l~i~-~~~~r~C~~C~~~~l~~ 68 (99)
T PF12660_consen 36 NGHVWPRCALTFLPIQ-TPGVRVCPVCGRRALDP 68 (99)
T ss_dssp TS-EEEB-SSS-SBS--SS-EEE-TTT--EEE-G
T ss_pred CCCEEeeeeeeeeeec-cCCeeEcCCCCCEEecC
Confidence 3346999999999996 23337899999998753
No 30
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=61.55 E-value=3.7 Score=24.57 Aligned_cols=23 Identities=26% Similarity=0.561 Sum_probs=13.7
Q ss_pred cccccCCCccccccCCCccccCC
Q psy2686 112 YTPIYHGRESEACVYCGASYLPK 134 (139)
Q Consensus 112 ~tPIy~g~~~v~Cp~cga~y~p~ 134 (139)
|+++..+...++|-+|+..+.-.
T Consensus 7 F~~~~~~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 7 FTKIPGDKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CEE--GCSS-EEETTTTEE----
T ss_pred EEEccCCcCeEEeCCCCeEEeeC
Confidence 45555789999999999888654
No 31
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=61.41 E-value=4.9 Score=22.65 Aligned_cols=13 Identities=31% Similarity=0.708 Sum_probs=11.9
Q ss_pred CCCccccccCCCc
Q psy2686 117 HGRESEACVYCGA 129 (139)
Q Consensus 117 ~g~~~v~Cp~cga 129 (139)
+|.++|+|+.|.+
T Consensus 12 ~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 12 RGAPSVRCACCHT 24 (25)
T ss_pred CCCCCeECCccCc
Confidence 6999999999975
No 32
>COG3931 Predicted N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=61.04 E-value=5 Score=34.03 Aligned_cols=20 Identities=40% Similarity=0.946 Sum_probs=17.5
Q ss_pred CCCeeeeccccccccCCCcc
Q psy2686 102 HNPFQICARSYTPIYHGRES 121 (139)
Q Consensus 102 ~~~F~iC~~s~tPIy~g~~~ 121 (139)
+.+|.|---||||+|+|.+.
T Consensus 143 ~~~~vvsvHSFTPvy~G~~R 162 (263)
T COG3931 143 RAPFVVSVHSFTPVYKGRPR 162 (263)
T ss_pred CCcEEEEEeccCccccCCCC
Confidence 46899999999999999763
No 33
>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=60.83 E-value=5 Score=23.40 Aligned_cols=16 Identities=19% Similarity=0.457 Sum_probs=12.0
Q ss_pred CCCccccccCCCcccc
Q psy2686 117 HGRESEACVYCGASYL 132 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~ 132 (139)
.+...|+||.||..+.
T Consensus 21 ~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 21 ANGGKVRCGKCGHVWY 36 (38)
T ss_pred CCCCEEECCCCCCEEE
Confidence 3445899999998763
No 34
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=60.30 E-value=4.7 Score=23.52 Aligned_cols=24 Identities=17% Similarity=0.581 Sum_probs=15.9
Q ss_pred eccccccccC--CCccccccCCCccc
Q psy2686 108 CARSYTPIYH--GRESEACVYCGASY 131 (139)
Q Consensus 108 C~~s~tPIy~--g~~~v~Cp~cga~y 131 (139)
|...|..+.. ....+.||.||+..
T Consensus 11 Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 11 CGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred CCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 5555655432 25788999999954
No 35
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=60.18 E-value=3.8 Score=40.10 Aligned_cols=14 Identities=29% Similarity=0.861 Sum_probs=11.7
Q ss_pred cccccCCCccccCC
Q psy2686 121 SEACVYCGASYLPK 134 (139)
Q Consensus 121 ~v~Cp~cga~y~p~ 134 (139)
-.-||.|||..||.
T Consensus 503 GePCPVCGS~~HP~ 516 (1047)
T PRK10246 503 GQPCPLCGSTSHPA 516 (1047)
T ss_pred CCCcCCCCcccCcC
Confidence 34499999999994
No 36
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=59.95 E-value=23 Score=21.74 Aligned_cols=22 Identities=27% Similarity=0.514 Sum_probs=10.8
Q ss_pred HhhhcHHHHHHHHHHHHhcCCC
Q psy2686 52 FKLKNYKTTASFAHRLLELGPS 73 (139)
Q Consensus 52 ~K~kN~~tAa~fArRLLel~p~ 73 (139)
++.|+|..|...-.+++...|+
T Consensus 36 ~~~g~~~~A~~~l~~~~~~~~~ 57 (68)
T PF14559_consen 36 LKQGQYDEAEELLERLLKQDPD 57 (68)
T ss_dssp HHTT-HHHHHHHHHCCHGGGTT
T ss_pred HHcCCHHHHHHHHHHHHHHCcC
Confidence 4445555555555555555544
No 37
>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=59.42 E-value=4.6 Score=25.49 Aligned_cols=9 Identities=56% Similarity=1.261 Sum_probs=6.7
Q ss_pred cccccCCCc
Q psy2686 121 SEACVYCGA 129 (139)
Q Consensus 121 ~v~Cp~cga 129 (139)
+..|||||.
T Consensus 2 ~f~CP~C~~ 10 (54)
T PF05605_consen 2 SFTCPYCGK 10 (54)
T ss_pred CcCCCCCCC
Confidence 457888887
No 38
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=59.24 E-value=4.2 Score=25.92 Aligned_cols=9 Identities=33% Similarity=1.206 Sum_probs=7.0
Q ss_pred cccCCCccc
Q psy2686 123 ACVYCGASY 131 (139)
Q Consensus 123 ~Cp~cga~y 131 (139)
-|||||..-
T Consensus 5 PCPFCG~~~ 13 (61)
T PF14354_consen 5 PCPFCGSAD 13 (61)
T ss_pred CCCCCCCcc
Confidence 499999654
No 39
>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=56.88 E-value=5 Score=24.16 Aligned_cols=11 Identities=18% Similarity=0.489 Sum_probs=9.3
Q ss_pred cccccCCCccc
Q psy2686 121 SEACVYCGASY 131 (139)
Q Consensus 121 ~v~Cp~cga~y 131 (139)
.|.||+|++.-
T Consensus 5 ~v~CP~C~s~~ 15 (36)
T PF03811_consen 5 DVHCPRCQSTE 15 (36)
T ss_pred eeeCCCCCCCC
Confidence 58999999865
No 40
>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=56.84 E-value=4.7 Score=20.12 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=6.6
Q ss_pred cccCCCcccc
Q psy2686 123 ACVYCGASYL 132 (139)
Q Consensus 123 ~Cp~cga~y~ 132 (139)
.|++||..|.
T Consensus 2 ~C~~C~~~~~ 11 (24)
T PF13894_consen 2 QCPICGKSFR 11 (24)
T ss_dssp E-SSTS-EES
T ss_pred CCcCCCCcCC
Confidence 6999998875
No 41
>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=56.76 E-value=5.6 Score=24.62 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=9.3
Q ss_pred CccccccCCCc
Q psy2686 119 RESEACVYCGA 129 (139)
Q Consensus 119 ~~~v~Cp~cga 129 (139)
.+.+.||.||+
T Consensus 24 ~~~~~CP~Cg~ 34 (52)
T TIGR02605 24 DPLATCPECGG 34 (52)
T ss_pred CCCCCCCCCCC
Confidence 46788999998
No 42
>COG3919 Predicted ATP-grasp enzyme [General function prediction only]
Probab=56.70 E-value=12 Score=33.26 Aligned_cols=52 Identities=21% Similarity=0.165 Sum_probs=42.9
Q ss_pred HhhhcHHHHHHHHHHHHhc-------------CCChHHHHHHHHHHHHhhcCCCCceeecCCCCC
Q psy2686 52 FKLKNYKTTASFAHRLLEL-------------GPSMEVATQARKLLAICNANPTDEHTIDYDEHN 103 (139)
Q Consensus 52 ~K~kN~~tAa~fArRLLel-------------~p~~~~~~qArkil~~~e~~~~da~~i~yD~~~ 103 (139)
+=.||..-|-..|||+++- ..+..+.++||++|...+-.+--+++..||++.
T Consensus 212 lw~~g~pvaeftarr~rqyPvdfgytst~vevvDn~Q~i~aar~~L~si~htGlvevefK~D~RD 276 (415)
T COG3919 212 LWDKGHPVAEFTARRLRQYPVDFGYTSTVVEVVDNQQVIQAARDFLESIEHTGLVEVEFKYDPRD 276 (415)
T ss_pred HHhCCCchhhhhcchhhcCCcccccccEEEEecCcHHHHHHHHHHHHhhcccceEEEEEEecCCC
Confidence 4456666688889999885 245778899999999999999999999999874
No 43
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.80 E-value=6.5 Score=29.92 Aligned_cols=26 Identities=27% Similarity=0.470 Sum_probs=19.9
Q ss_pred eeeccccccccC-CCccccccCCCccc
Q psy2686 106 QICARSYTPIYH-GRESEACVYCGASY 131 (139)
Q Consensus 106 ~iC~~s~tPIy~-g~~~v~Cp~cga~y 131 (139)
-||..+=...|- ....+.|||||.+|
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccCccccchhhccCCCccccCcccccc
Confidence 466666666674 56778899999999
No 44
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=54.54 E-value=5.6 Score=25.23 Aligned_cols=10 Identities=30% Similarity=1.125 Sum_probs=8.0
Q ss_pred cccCCCcccc
Q psy2686 123 ACVYCGASYL 132 (139)
Q Consensus 123 ~Cp~cga~y~ 132 (139)
-|||||..-.
T Consensus 3 PCPfCGg~~~ 12 (53)
T TIGR03655 3 PCPFCGGADV 12 (53)
T ss_pred CCCCCCCcce
Confidence 5999998754
No 45
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=54.45 E-value=69 Score=22.05 Aligned_cols=23 Identities=22% Similarity=0.216 Sum_probs=15.0
Q ss_pred HHhhhcHHHHHHHHHHHHhcCCC
Q psy2686 51 FFKLKNYKTTASFAHRLLELGPS 73 (139)
Q Consensus 51 ~~K~kN~~tAa~fArRLLel~p~ 73 (139)
.++.|+|..|....++.++++|.
T Consensus 61 ~~~~~~~~~A~~~~~~~~~~~p~ 83 (135)
T TIGR02552 61 CQMLKEYEEAIDAYALAAALDPD 83 (135)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCC
Confidence 34667777777666677666654
No 46
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=53.98 E-value=8.5 Score=23.50 Aligned_cols=15 Identities=33% Similarity=0.778 Sum_probs=12.6
Q ss_pred cccccCCCccccCCC
Q psy2686 121 SEACVYCGASYLPKY 135 (139)
Q Consensus 121 ~v~Cp~cga~y~p~~ 135 (139)
.++||.||=.|.|.-
T Consensus 13 ~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGS 27 (41)
T ss_pred CcCCCCCCCEECCCC
Confidence 489999999998753
No 47
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=53.37 E-value=8.4 Score=26.34 Aligned_cols=19 Identities=26% Similarity=0.763 Sum_probs=13.7
Q ss_pred CccccccCCCcc-ccCCCCC
Q psy2686 119 RESEACVYCGAS-YLPKYKG 137 (139)
Q Consensus 119 ~~~v~Cp~cga~-y~p~~kG 137 (139)
.....||.||+. +.-++.|
T Consensus 16 ~d~e~CP~Cgs~~~te~W~G 35 (64)
T COG2093 16 EDTEICPVCGSTDLTEEWFG 35 (64)
T ss_pred CCCccCCCCCCcccchhhcc
Confidence 455679999998 5555555
No 48
>PF04910 Tcf25: Transcriptional repressor TCF25; InterPro: IPR006994 This entry appears to represent a novel family of basic helix-loop-helix (bHLH) proteins that control differentiation and development of a variety of organs [, ]. Human Nulp1 (Q2MK75 from SWISSPROT) is a basic helix-loop-helix protein expressed broadly during early embryonic organogenesis. Over expression of human Nulp1 in COS-7 cells inhibits the transcriptional activity of serum response factor (SRF), suggesting that Nulp1 may act as a novel bHLH transcriptional repressor in the SRF signalling pathway to mediate cellular functions [].
Probab=51.61 E-value=22 Score=30.83 Aligned_cols=37 Identities=19% Similarity=0.217 Sum_probs=34.0
Q ss_pred hhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCC
Q psy2686 37 PVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPS 73 (139)
Q Consensus 37 p~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~ 73 (139)
.....|||-.=|....+-|.+.||..+||=||.|+|.
T Consensus 99 NR~fflal~r~i~~L~~RG~~rTAlE~~KlLlsLdp~ 135 (360)
T PF04910_consen 99 NRQFFLALFRYIQSLGRRGCWRTALEWCKLLLSLDPD 135 (360)
T ss_pred chHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCC
Confidence 3456899999999999999999999999999999987
No 49
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=51.04 E-value=35 Score=21.02 Aligned_cols=37 Identities=22% Similarity=0.355 Sum_probs=19.2
Q ss_pred CchhhHHHHHHHHHHHHHhhh-cHHHHHHHHHHHHhcCC
Q psy2686 35 LQPVHQILTLRTATNLFFKLK-NYKTTASFAHRLLELGP 72 (139)
Q Consensus 35 Lqp~H~~LaLr~Am~~~~K~k-N~~tAa~fArRLLel~p 72 (139)
+.|.|-.+=.+.|.. .++.| ++..|.....+-|+++|
T Consensus 32 ~~p~~~~~~~~~g~~-~~~~~~~~~~A~~~~~~al~l~P 69 (69)
T PF13414_consen 32 LDPNNAEAYYNLGLA-YMKLGKDYEEAIEDFEKALKLDP 69 (69)
T ss_dssp HSTTHHHHHHHHHHH-HHHTTTHHHHHHHHHHHHHHHST
T ss_pred cCCCCHHHHHHHHHH-HHHhCccHHHHHHHHHHHHHcCc
Confidence 345554433333333 23334 56666666666666654
No 50
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=50.70 E-value=18 Score=22.59 Aligned_cols=25 Identities=24% Similarity=0.551 Sum_probs=22.4
Q ss_pred HHHhhhcHHHHHHHHHHHHhcCCCh
Q psy2686 50 LFFKLKNYKTTASFAHRLLELGPSM 74 (139)
Q Consensus 50 ~~~K~kN~~tAa~fArRLLel~p~~ 74 (139)
+.++.++|..|.....|+|+++|..
T Consensus 4 ~~~~~~~~~~A~~~~~~~l~~~p~~ 28 (73)
T PF13371_consen 4 IYLQQEDYEEALEVLERALELDPDD 28 (73)
T ss_pred HHHhCCCHHHHHHHHHHHHHhCccc
Confidence 4678999999999999999998873
No 51
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=49.52 E-value=84 Score=21.60 Aligned_cols=39 Identities=10% Similarity=0.146 Sum_probs=28.7
Q ss_pred CCchhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCC
Q psy2686 34 KLQPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPS 73 (139)
Q Consensus 34 ~Lqp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~ 73 (139)
.+.|.|. -++-.-....++.++|..|....+++++++|.
T Consensus 11 ~~~p~~~-~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~ 49 (135)
T TIGR02552 11 GLDSEQL-EQIYALAYNLYQQGRYDEALKLFQLLAAYDPY 49 (135)
T ss_pred cCChhhH-HHHHHHHHHHHHcccHHHHHHHHHHHHHhCCC
Confidence 4555553 33444445567899999999999999999885
No 52
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.28 E-value=10 Score=20.85 Aligned_cols=10 Identities=40% Similarity=0.963 Sum_probs=5.0
Q ss_pred cccccCCCcc
Q psy2686 121 SEACVYCGAS 130 (139)
Q Consensus 121 ~v~Cp~cga~ 130 (139)
...||.||++
T Consensus 16 ~~fC~~CG~~ 25 (26)
T PF13248_consen 16 AKFCPNCGAK 25 (26)
T ss_pred cccChhhCCC
Confidence 4445555543
No 53
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.26 E-value=10 Score=27.92 Aligned_cols=34 Identities=15% Similarity=0.386 Sum_probs=18.0
Q ss_pred eecCCCCCCeee---eccccccccCCCccccccCCCccc
Q psy2686 96 TIDYDEHNPFQI---CARSYTPIYHGRESEACVYCGASY 131 (139)
Q Consensus 96 ~i~yD~~~~F~i---C~~s~tPIy~g~~~v~Cp~cga~y 131 (139)
+|..+.--.-.- |...|.+ .+.....||.||+.-
T Consensus 62 ~L~Ie~vp~~~~C~~Cg~~~~~--~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 62 ILDIVDEKVELECKDCSHVFKP--NALDYGVCEKCHSKN 98 (117)
T ss_pred EEEEEecCCEEEhhhCCCcccc--CCccCCcCcCCCCCc
Confidence 555543333333 4444444 223445699999863
No 54
>PHA00159 endonuclease I
Probab=48.18 E-value=18 Score=28.41 Aligned_cols=35 Identities=23% Similarity=0.326 Sum_probs=27.4
Q ss_pred HHHHHHHhhcCCCCceeecCCCCCCeeeeccccccccCCCcccc
Q psy2686 80 ARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEA 123 (139)
Q Consensus 80 Arkil~~~e~~~~da~~i~yD~~~~F~iC~~s~tPIy~g~~~v~ 123 (139)
=+|++.+.||.|.=-+.+-| ..|-++||+|+++.-
T Consensus 75 R~K~lli~eQ~P~ldiR~VF---------s~s~~klyKgSkTtY 109 (148)
T PHA00159 75 RKKHLLIREQYPELDIRFVF---------SSSRTKLYKGSPTSY 109 (148)
T ss_pred HHHHHHHHHHCCCccEEEEE---------ecCCchhhcCCCCcH
Confidence 37899999999876555444 578999999998754
No 55
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=48.12 E-value=12 Score=21.89 Aligned_cols=15 Identities=27% Similarity=0.558 Sum_probs=12.9
Q ss_pred cCCCccccccCCCcc
Q psy2686 116 YHGRESEACVYCGAS 130 (139)
Q Consensus 116 y~g~~~v~Cp~cga~ 130 (139)
-+|.++|+|+.|.+.
T Consensus 14 P~gA~~vrCs~C~~v 28 (31)
T TIGR01053 14 PRGASSVRCALCQTV 28 (31)
T ss_pred CCCCCeEECCCCCeE
Confidence 379999999999864
No 56
>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=47.60 E-value=8.3 Score=29.68 Aligned_cols=12 Identities=33% Similarity=0.672 Sum_probs=10.2
Q ss_pred cccccCCCcccc
Q psy2686 121 SEACVYCGASYL 132 (139)
Q Consensus 121 ~v~Cp~cga~y~ 132 (139)
.|.||+|||..-
T Consensus 105 ~~~cp~c~s~~t 116 (146)
T TIGR02159 105 SVQCPRCGSADT 116 (146)
T ss_pred CCcCCCCCCCCc
Confidence 599999999764
No 57
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=47.42 E-value=1.5e+02 Score=23.96 Aligned_cols=53 Identities=9% Similarity=0.061 Sum_probs=40.6
Q ss_pred chhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhh
Q psy2686 36 QPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEVATQARKLLAICN 88 (139)
Q Consensus 36 qp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~~~qArkil~~~e 88 (139)
.+.+...++-.-...-|+.|+|..|....+|++++.|..+.++.|.=.+..|.
T Consensus 64 ~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~ 116 (243)
T PRK10866 64 FGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTN 116 (243)
T ss_pred CChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhh
Confidence 33444444333335568999999999999999999999888888888888774
No 58
>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=47.01 E-value=7.5 Score=22.64 Aligned_cols=10 Identities=40% Similarity=1.172 Sum_probs=2.9
Q ss_pred cccCCCcccc
Q psy2686 123 ACVYCGASYL 132 (139)
Q Consensus 123 ~Cp~cga~y~ 132 (139)
+||.||+.|-
T Consensus 4 ~Cp~C~se~~ 13 (30)
T PF08274_consen 4 KCPLCGSEYT 13 (30)
T ss_dssp --TTT-----
T ss_pred CCCCCCCcce
Confidence 7999999773
No 59
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=46.86 E-value=33 Score=16.15 Aligned_cols=24 Identities=29% Similarity=0.653 Sum_probs=18.1
Q ss_pred HHHhhhcHHHHHHHHHHHHhcCCC
Q psy2686 50 LFFKLKNYKTTASFAHRLLELGPS 73 (139)
Q Consensus 50 ~~~K~kN~~tAa~fArRLLel~p~ 73 (139)
..+..+||..|....++.+++.|.
T Consensus 10 ~~~~~~~~~~a~~~~~~~~~~~~~ 33 (34)
T smart00028 10 AYLKLGDYDEALEYYEKALELDPN 33 (34)
T ss_pred HHHHHhhHHHHHHHHHHHHccCCC
Confidence 346678899888888888877653
No 60
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=46.86 E-value=43 Score=17.49 Aligned_cols=23 Identities=26% Similarity=0.657 Sum_probs=19.4
Q ss_pred HHhhhcHHHHHHHHHHHHhcCCC
Q psy2686 51 FFKLKNYKTTASFAHRLLELGPS 73 (139)
Q Consensus 51 ~~K~kN~~tAa~fArRLLel~p~ 73 (139)
.++.|++..|...-+++++.-|+
T Consensus 10 ~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 10 YYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHCHHHHHHHHHHHHHHHSTT
T ss_pred HHHccCHHHHHHHHHHHHHHCcC
Confidence 45689999999999999987764
No 61
>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=46.68 E-value=9.7 Score=23.14 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=10.1
Q ss_pred CccccccCCCc
Q psy2686 119 RESEACVYCGA 129 (139)
Q Consensus 119 ~~~v~Cp~cga 129 (139)
.+.+.||-||+
T Consensus 24 ~~~~~CP~Cg~ 34 (42)
T PF09723_consen 24 DDPVPCPECGS 34 (42)
T ss_pred CCCCcCCCCCC
Confidence 67999999998
No 62
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=46.18 E-value=8.1 Score=26.32 Aligned_cols=16 Identities=19% Similarity=0.331 Sum_probs=13.3
Q ss_pred cccCCCccc-cCCCCCC
Q psy2686 123 ACVYCGASY-LPKYKGE 138 (139)
Q Consensus 123 ~Cp~cga~y-~p~~kG~ 138 (139)
.||.||+.- .++|.|-
T Consensus 19 ~Cp~Cgs~~~S~~w~G~ 35 (64)
T PRK06393 19 TCPVHGDEKTTTEWFGF 35 (64)
T ss_pred cCCCCCCCcCCcCcceE
Confidence 899999987 5778774
No 63
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=45.93 E-value=20 Score=27.70 Aligned_cols=35 Identities=17% Similarity=0.327 Sum_probs=27.0
Q ss_pred HHhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHHH
Q psy2686 51 FFKLKNYKTTASFAHRLLELGPSMEVATQARKLLA 85 (139)
Q Consensus 51 ~~K~kN~~tAa~fArRLLel~p~~~~~~qArkil~ 85 (139)
-||.++|..|..-+.|+|+|+|.-+.+.=|-=...
T Consensus 57 yy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~g 91 (142)
T PF13512_consen 57 YYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRG 91 (142)
T ss_pred HHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHH
Confidence 48999999999999999999997555444443333
No 64
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=45.78 E-value=35 Score=30.60 Aligned_cols=24 Identities=25% Similarity=0.527 Sum_probs=14.8
Q ss_pred eeccccccc--------cCCCcc------ccccCCCcc
Q psy2686 107 ICARSYTPI--------YHGRES------EACVYCGAS 130 (139)
Q Consensus 107 iC~~s~tPI--------y~g~~~------v~Cp~cga~ 130 (139)
+|..-|.|- -.|++. -.||.||+.
T Consensus 430 ~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 430 VCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 677666663 334444 578888864
No 65
>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=44.76 E-value=8.6 Score=19.63 Aligned_cols=11 Identities=36% Similarity=0.966 Sum_probs=9.0
Q ss_pred cccCCCccccC
Q psy2686 123 ACVYCGASYLP 133 (139)
Q Consensus 123 ~Cp~cga~y~p 133 (139)
+||.||..|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 69999998753
No 66
>PF14353 CpXC: CpXC protein
Probab=44.72 E-value=11 Score=27.46 Aligned_cols=15 Identities=33% Similarity=0.749 Sum_probs=12.6
Q ss_pred cccccCCCccccCCC
Q psy2686 121 SEACVYCGASYLPKY 135 (139)
Q Consensus 121 ~v~Cp~cga~y~p~~ 135 (139)
.++||.||..+..+|
T Consensus 38 ~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEY 52 (128)
T ss_pred EEECCCCCCceecCC
Confidence 689999999887665
No 67
>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=44.67 E-value=9.7 Score=29.70 Aligned_cols=16 Identities=25% Similarity=0.648 Sum_probs=12.5
Q ss_pred CCCccccccCCCcccc
Q psy2686 117 HGRESEACVYCGASYL 132 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~ 132 (139)
.....+.||+||+.-.
T Consensus 28 ~~~glv~CP~Cgs~~V 43 (148)
T PF06676_consen 28 QARGLVSCPVCGSTEV 43 (148)
T ss_pred HHcCCccCCCCCCCeE
Confidence 4567899999998643
No 68
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=44.60 E-value=9 Score=32.90 Aligned_cols=17 Identities=35% Similarity=0.856 Sum_probs=14.8
Q ss_pred CCCccccccCCCccccC
Q psy2686 117 HGRESEACVYCGASYLP 133 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~p 133 (139)
.|.-.|.|.|||.+|+=
T Consensus 262 dg~iev~C~FC~~~Y~f 278 (286)
T COG1281 262 DGGIEVTCEFCGTKYLF 278 (286)
T ss_pred CCCeEEEeeccCCEEec
Confidence 47889999999999973
No 69
>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=44.47 E-value=9.1 Score=27.61 Aligned_cols=19 Identities=26% Similarity=0.543 Sum_probs=16.1
Q ss_pred cCCCccccccCCCccccCC
Q psy2686 116 YHGRESEACVYCGASYLPK 134 (139)
Q Consensus 116 y~g~~~v~Cp~cga~y~p~ 134 (139)
-+..|...|+-||-.|+.+
T Consensus 30 IknVPa~~C~~CGe~y~~d 48 (89)
T TIGR03829 30 IKETPSISCSHCGMEYQDD 48 (89)
T ss_pred EecCCcccccCCCcEeecH
Confidence 3678999999999999753
No 70
>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=43.94 E-value=11 Score=23.86 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=6.4
Q ss_pred cccCCCccccCC
Q psy2686 123 ACVYCGASYLPK 134 (139)
Q Consensus 123 ~Cp~cga~y~p~ 134 (139)
.||+||..+.++
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 999999987654
No 71
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.91 E-value=94 Score=23.34 Aligned_cols=68 Identities=16% Similarity=0.188 Sum_probs=35.1
Q ss_pred HHHHHHHhcCCC----hHHHHHHHHHHHHhhcCCCCceeecCCCCCCeeee--cccccccc---CC--------------
Q psy2686 62 SFAHRLLELGPS----MEVATQARKLLAICNANPTDEHTIDYDEHNPFQIC--ARSYTPIY---HG-------------- 118 (139)
Q Consensus 62 ~fArRLLel~p~----~~~~~qArkil~~~e~~~~da~~i~yD~~~~F~iC--~~s~tPIy---~g-------------- 118 (139)
..++=.|+++.- ++..+.|-.++.. ..+-..-+|.++.-.....| |....++- ++
T Consensus 25 ~V~~V~l~IG~ls~V~pe~L~fafe~l~~--gt~~ega~L~i~~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (135)
T PRK03824 25 KVKALKVVLGELQDVDKEIVEFALNELLK--GTILEGAEIIFEEEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPE 102 (135)
T ss_pred hhHhHHhhHhhhhhhhHHHHHHHHHHHHc--CCcccCCEEEEEecceEEECCCCCCEEeccccccccccccccccccccc
Confidence 344444555442 5556667766543 22222226666554455555 33333322 00
Q ss_pred --CccccccCCCccc
Q psy2686 119 --RESEACVYCGASY 131 (139)
Q Consensus 119 --~~~v~Cp~cga~y 131 (139)
.....||.||+.-
T Consensus 103 ~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 103 VVHAFLKCPKCGSRD 117 (135)
T ss_pred ccccCcCCcCCCCCC
Confidence 4567899999863
No 72
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=43.62 E-value=8 Score=24.61 Aligned_cols=16 Identities=38% Similarity=0.667 Sum_probs=13.0
Q ss_pred cccCCCccccccCCCc
Q psy2686 114 PIYHGRESEACVYCGA 129 (139)
Q Consensus 114 PIy~g~~~v~Cp~cga 129 (139)
-|.+|...+.||.||.
T Consensus 39 ~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 39 EIRKGDEIVFCPNCGR 54 (56)
T ss_pred HHHcCCCeEECcCCCc
Confidence 3446889999999996
No 73
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=43.37 E-value=11 Score=22.74 Aligned_cols=9 Identities=33% Similarity=0.907 Sum_probs=7.6
Q ss_pred cccCCCccc
Q psy2686 123 ACVYCGASY 131 (139)
Q Consensus 123 ~Cp~cga~y 131 (139)
+||.||++.
T Consensus 2 ~Cp~Cg~~~ 10 (43)
T PF08271_consen 2 KCPNCGSKE 10 (43)
T ss_dssp SBTTTSSSE
T ss_pred CCcCCcCCc
Confidence 699999975
No 74
>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.
Probab=43.21 E-value=47 Score=19.41 Aligned_cols=30 Identities=13% Similarity=0.222 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHhhhcHHHHHHHHHHHHhc
Q psy2686 41 ILTLRTATNLFFKLKNYKTTASFAHRLLEL 70 (139)
Q Consensus 41 ~LaLr~Am~~~~K~kN~~tAa~fArRLLel 70 (139)
+--|+..|..|-+..+|..|+.+=.+|..|
T Consensus 4 i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l 33 (36)
T PF02151_consen 4 IKELEEKMEEAVENEDFEKAARLRDQIKAL 33 (36)
T ss_dssp HHHHHHHHHHHHHTT-CHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHHHHHHHH
Confidence 456889999999999999999998887665
No 75
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=42.69 E-value=41 Score=18.09 Aligned_cols=24 Identities=33% Similarity=0.742 Sum_probs=19.9
Q ss_pred HHHhhhcHHHHHHHHHHHHhcCCC
Q psy2686 50 LFFKLKNYKTTASFAHRLLELGPS 73 (139)
Q Consensus 50 ~~~K~kN~~tAa~fArRLLel~p~ 73 (139)
..+..|+|..|...-+|-|+++|.
T Consensus 10 ~~~~~~~~~~A~~~~~~al~~~p~ 33 (34)
T PF00515_consen 10 AYFQLGDYEEALEYYQRALELDPD 33 (34)
T ss_dssp HHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHhCCchHHHHHHHHHHHHCcC
Confidence 457889999999999999999875
No 76
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=41.76 E-value=62 Score=23.69 Aligned_cols=39 Identities=10% Similarity=0.043 Sum_probs=27.2
Q ss_pred hhcCCchhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCC
Q psy2686 31 THSKLQPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPS 73 (139)
Q Consensus 31 T~c~Lqp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~ 73 (139)
+-..++|.|.. ..|. ..+..|+|..|....+++++++|.
T Consensus 18 ~al~~~p~~~~---~~g~-~~~~~g~~~~A~~~~~~al~~~P~ 56 (144)
T PRK15359 18 QLLSVDPETVY---ASGY-ASWQEGDYSRAVIDFSWLVMAQPW 56 (144)
T ss_pred HHHHcCHHHHH---HHHH-HHHHcCCHHHHHHHHHHHHHcCCC
Confidence 44556666522 1232 347889999999999999999886
No 77
>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=41.50 E-value=12 Score=23.24 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=7.9
Q ss_pred cccCCCcccc
Q psy2686 123 ACVYCGASYL 132 (139)
Q Consensus 123 ~Cp~cga~y~ 132 (139)
.||.||++..
T Consensus 1 ~CP~Cg~~a~ 10 (47)
T PF04606_consen 1 RCPHCGSKAR 10 (47)
T ss_pred CcCCCCCeeE
Confidence 5999998753
No 78
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=40.83 E-value=31 Score=27.58 Aligned_cols=52 Identities=15% Similarity=0.342 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHHHhhcCCCCceeecCCCCCCeeeeccccccccCC---CccccccCCCccc
Q psy2686 74 MEVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHG---RESEACVYCGASY 131 (139)
Q Consensus 74 ~~~~~qArkil~~~e~~~~da~~i~yD~~~~F~iC~~s~tPIy~g---~~~v~Cp~cga~y 131 (139)
.....+.++++.+.... +.|+..++|-+|.....+.-=+ .---.||-||+..
T Consensus 88 ~~l~~~~~~~le~Lk~~------le~~~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L 142 (176)
T COG1675 88 EVLKGKKRKILEKLKRK------LEKETENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDL 142 (176)
T ss_pred HHHHHHHHHHHHHHHHH------HHhhccCCceeCCCCCCcccHHHHHHhCCCCCCCCchh
Confidence 34467788899888765 6777888899997777663111 2236899999864
No 79
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=40.28 E-value=24 Score=28.11 Aligned_cols=55 Identities=18% Similarity=0.307 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHHhhcCCCCceeecCCCCCCeeeeccccccccCCC--------------ccccccCCCccccC
Q psy2686 74 MEVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGR--------------ESEACVYCGASYLP 133 (139)
Q Consensus 74 ~~~~~qArkil~~~e~~~~da~~i~yD~~~~F~iC~~s~tPIy~g~--------------~~v~Cp~cga~y~p 133 (139)
.+.-+|...++..-.-++ ..+.+|+ -=-.|...+.++.++. ..-.||.||..|-+
T Consensus 74 ~s~~~Ql~e~~~~~~l~~--~~~~e~~---RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~ 142 (165)
T COG1656 74 DSIEEQLAEFLARLGLKP--RLFPEFS---RCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK 142 (165)
T ss_pred CCHHHHHHHHHHHhccch--hcccccc---cCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccC
Confidence 444556666666555444 3333332 1236777888776543 12349999999865
No 80
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=39.89 E-value=22 Score=23.06 Aligned_cols=25 Identities=20% Similarity=0.691 Sum_probs=16.5
Q ss_pred eeccccccccCC-CccccccCCCccccC
Q psy2686 107 ICARSYTPIYHG-RESEACVYCGASYLP 133 (139)
Q Consensus 107 iC~~s~tPIy~g-~~~v~Cp~cga~y~p 133 (139)
+.-+.| .|.| ...|+|.+||-.+..
T Consensus 23 LA~~Gf--yy~~~~d~v~C~~C~~~l~~ 48 (71)
T smart00238 23 LAEAGF--YYTGVGDEVKCFFCGGELDN 48 (71)
T ss_pred HHHcCC--eECCCCCEEEeCCCCCCcCC
Confidence 344444 2455 558999999987654
No 81
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=39.37 E-value=15 Score=27.20 Aligned_cols=31 Identities=26% Similarity=0.593 Sum_probs=21.5
Q ss_pred eeeeccccccc----cCCCccccccCCCccccCCCCC
Q psy2686 105 FQICARSYTPI----YHGRESEACVYCGASYLPKYKG 137 (139)
Q Consensus 105 F~iC~~s~tPI----y~g~~~v~Cp~cga~y~p~~kG 137 (139)
-.||++--.-+ | ...++||||.+.+.|.-+.
T Consensus 62 ~iiCGvC~~~LT~~EY--~~~~~Cp~C~spFNp~Ck~ 96 (105)
T COG4357 62 AIICGVCRKLLTRAEY--GMCGSCPYCQSPFNPGCKN 96 (105)
T ss_pred cEEhhhhhhhhhHHHH--hhcCCCCCcCCCCCccccc
Confidence 46776644333 4 4466799999999997653
No 82
>PF01430 HSP33: Hsp33 protein; InterPro: IPR000397 Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidizing conditions like H2O2 cause disulphide bonds to form in Hsp33, a process that leads to the activation of its chaperone function [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0005737 cytoplasm; PDB: 1VZY_B 1VQ0_A 1I7F_A 3M7M_X 1XJH_A 1HW7_A.
Probab=39.12 E-value=9.7 Score=31.66 Aligned_cols=16 Identities=31% Similarity=0.933 Sum_probs=10.8
Q ss_pred CCCccccccCCCcccc
Q psy2686 117 HGRESEACVYCGASYL 132 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~ 132 (139)
.|.-.|.|.|||.+|.
T Consensus 262 ~~~iev~C~fC~~~Y~ 277 (280)
T PF01430_consen 262 NGKIEVTCEFCGKKYR 277 (280)
T ss_dssp CSEEEEE-TTT--EEE
T ss_pred CCCEEEEeeCCCCEEE
Confidence 3677899999999995
No 83
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=39.05 E-value=1.1e+02 Score=21.68 Aligned_cols=36 Identities=19% Similarity=0.315 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHH
Q psy2686 41 ILTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEV 76 (139)
Q Consensus 41 ~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~ 76 (139)
+-+++.........+++..|...+++++++.|-.+.
T Consensus 62 ~~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~ 97 (146)
T PF03704_consen 62 LDALERLAEALLEAGDYEEALRLLQRALALDPYDEE 97 (146)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HH
T ss_pred HHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHH
Confidence 345566666778899999999999999999997654
No 84
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=38.81 E-value=14 Score=22.98 Aligned_cols=17 Identities=29% Similarity=0.862 Sum_probs=14.2
Q ss_pred CCCccccccCCCccccC
Q psy2686 117 HGRESEACVYCGASYLP 133 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~p 133 (139)
.|.+.+.|-+|+..|.-
T Consensus 14 ~g~~~a~C~~C~~~l~~ 30 (50)
T smart00614 14 NGKQRAKCKYCGKKLSR 30 (50)
T ss_pred CCCeEEEecCCCCEeee
Confidence 46689999999999863
No 85
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=38.37 E-value=43 Score=19.57 Aligned_cols=26 Identities=19% Similarity=0.278 Sum_probs=22.1
Q ss_pred HHhhhcHHHHHHHHHHHHhcCCChHH
Q psy2686 51 FFKLKNYKTTASFAHRLLELGPSMEV 76 (139)
Q Consensus 51 ~~K~kN~~tAa~fArRLLel~p~~~~ 76 (139)
-...|++..|...-+|.|++.|....
T Consensus 11 ~~~~G~~~~A~~~~~~~l~~~P~~~~ 36 (44)
T PF13428_consen 11 YRRLGQPDEAERLLRRALALDPDDPE 36 (44)
T ss_pred HHHcCCHHHHHHHHHHHHHHCcCCHH
Confidence 35789999999999999999987554
No 86
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=38.18 E-value=11 Score=25.26 Aligned_cols=26 Identities=19% Similarity=0.600 Sum_probs=22.4
Q ss_pred eeeccccccccCCCccccccCCCccc
Q psy2686 106 QICARSYTPIYHGRESEACVYCGASY 131 (139)
Q Consensus 106 ~iC~~s~tPIy~g~~~v~Cp~cga~y 131 (139)
.+|+..|.|.-.-+++-.||-|...|
T Consensus 29 ALCGk~wvp~rdp~~~PVCP~Ck~iy 54 (58)
T PF11238_consen 29 ALCGKVWVPTRDPKPFPVCPECKEIY 54 (58)
T ss_pred eeeCceeCCCCCCCCCCCCcCHHHHH
Confidence 48999999987778899999998766
No 87
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=37.91 E-value=19 Score=19.44 Aligned_cols=11 Identities=27% Similarity=0.912 Sum_probs=6.4
Q ss_pred ccccccCCCcc
Q psy2686 120 ESEACVYCGAS 130 (139)
Q Consensus 120 ~~v~Cp~cga~ 130 (139)
....||.||+.
T Consensus 12 ~~~fC~~CG~~ 22 (23)
T PF13240_consen 12 DAKFCPNCGTP 22 (23)
T ss_pred cCcchhhhCCc
Confidence 35566666654
No 88
>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=37.66 E-value=16 Score=26.72 Aligned_cols=53 Identities=9% Similarity=0.157 Sum_probs=27.2
Q ss_pred hHHHHHHHHHHHHhhcCCCCceeecCCCCCCee---eeccccccccCCCccccccCCCccc
Q psy2686 74 MEVATQARKLLAICNANPTDEHTIDYDEHNPFQ---ICARSYTPIYHGRESEACVYCGASY 131 (139)
Q Consensus 74 ~~~~~qArkil~~~e~~~~da~~i~yD~~~~F~---iC~~s~tPIy~g~~~v~Cp~cga~y 131 (139)
++..+-|=.++. +..+-.--+|+.+.--.-. -|...|.+. .....||.||+.-
T Consensus 41 p~~L~faf~~~~--~~t~~ega~L~I~~~p~~~~C~~Cg~~~~~~---~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 41 PSQLQFAFEVVR--EGTVAEGAKLNIEDEPVECECEDCSEEVSPE---IDLYRCPKCHGIM 96 (115)
T ss_pred HHHHHHHHHHHh--CCCccCCCEEEEEeeCcEEEcccCCCEEecC---CcCccCcCCcCCC
Confidence 555555555442 2223222355554333333 355555553 3367899999853
No 89
>cd00498 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form.
Probab=37.63 E-value=13 Score=30.92 Aligned_cols=15 Identities=33% Similarity=0.902 Sum_probs=13.2
Q ss_pred CCccccccCCCcccc
Q psy2686 118 GRESEACVYCGASYL 132 (139)
Q Consensus 118 g~~~v~Cp~cga~y~ 132 (139)
|.-.|.|.|||..|.
T Consensus 259 g~iev~C~FC~~~Y~ 273 (275)
T cd00498 259 GGIEVTCEFCGEKYH 273 (275)
T ss_pred CCEEEEEeCCCCEEe
Confidence 667899999999996
No 90
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=37.39 E-value=16 Score=21.52 Aligned_cols=15 Identities=33% Similarity=1.114 Sum_probs=12.7
Q ss_pred CCCccccccCCCccc
Q psy2686 117 HGRESEACVYCGASY 131 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y 131 (139)
+-.....|++||++|
T Consensus 17 ~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 17 KEDDYEVCIFCGSSF 31 (33)
T ss_pred ecCCeEEcccCCcEe
Confidence 677788999999986
No 91
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=37.23 E-value=18 Score=31.52 Aligned_cols=26 Identities=19% Similarity=0.291 Sum_probs=20.2
Q ss_pred ccccCCCccccccCCCccccCCCCCC
Q psy2686 113 TPIYHGRESEACVYCGASYLPKYKGE 138 (139)
Q Consensus 113 tPIy~g~~~v~Cp~cga~y~p~~kG~ 138 (139)
.|=++-...-+||+||--+.|.|.|+
T Consensus 50 ~p~~~~~~pg~~p~~~m~lvp~y~~~ 75 (409)
T PRK09783 50 YPNTRFDKPGKSPFMDMDLVPKYADE 75 (409)
T ss_pred CCCcCCCCCCCCCCCCCeeeEEecCC
Confidence 46566666679999999999988764
No 92
>PF14122 YokU: YokU-like protein
Probab=37.09 E-value=16 Score=26.39 Aligned_cols=18 Identities=22% Similarity=0.523 Sum_probs=15.7
Q ss_pred CCCccccccCCCccccCC
Q psy2686 117 HGRESEACVYCGASYLPK 134 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~p~ 134 (139)
...|++.|.-||..|.++
T Consensus 31 ~~tP~i~C~~CgmvYq~d 48 (87)
T PF14122_consen 31 TDTPAIICSNCGMVYQDD 48 (87)
T ss_pred cCCceeeecCCCcEEehh
Confidence 567999999999999864
No 93
>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=36.70 E-value=12 Score=27.16 Aligned_cols=53 Identities=19% Similarity=0.253 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHHHhhcCCCCceeecCCCCCCee---eeccccccccCCCccccccCCCccc
Q psy2686 74 MEVATQARKLLAICNANPTDEHTIDYDEHNPFQ---ICARSYTPIYHGRESEACVYCGASY 131 (139)
Q Consensus 74 ~~~~~qArkil~~~e~~~~da~~i~yD~~~~F~---iC~~s~tPIy~g~~~v~Cp~cga~y 131 (139)
++..+.|=.++.. ..+-+--+|+.+.--.-. -|...|.|-. ....||.||+..
T Consensus 41 pe~L~f~f~~~~~--~T~~e~a~L~Ie~~p~~~~C~~Cg~~~~~~~---~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 41 PEALRFAFEVLAE--GTILEGAELEIEEVPARARCRDCGHEFEPDE---FDFSCPRCGSPD 96 (113)
T ss_dssp HHHHHHHHHHHHC--CSTTTT-EEEEEEE--EEEETTTS-EEECHH---CCHH-SSSSSS-
T ss_pred HHHHHHHHHHHhC--CCCccCCEEEEEecCCcEECCCCCCEEecCC---CCCCCcCCcCCC
Confidence 5666666665543 233333355554222222 4677777643 337799999974
No 94
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=36.33 E-value=15 Score=30.95 Aligned_cols=15 Identities=40% Similarity=1.081 Sum_probs=13.3
Q ss_pred CCccccccCCCcccc
Q psy2686 118 GRESEACVYCGASYL 132 (139)
Q Consensus 118 g~~~v~Cp~cga~y~ 132 (139)
|.-.|.|.|||.+|.
T Consensus 265 ~~iev~C~FC~~~Y~ 279 (293)
T PRK00114 265 GGAEMVCQFCGNKYL 279 (293)
T ss_pred CCEEEEEeCCCCEEE
Confidence 667899999999996
No 95
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=36.26 E-value=21 Score=21.11 Aligned_cols=16 Identities=25% Similarity=0.617 Sum_probs=12.5
Q ss_pred CCCccccccCCCcccc
Q psy2686 117 HGRESEACVYCGASYL 132 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~ 132 (139)
.+...|+||-||..+.
T Consensus 21 ~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 21 AGGRKVRCPKCGHVFR 36 (37)
T ss_pred cCCcEEECCCCCcEee
Confidence 4566999999998763
No 96
>PF13805 Pil1: Eisosome component PIL1; PDB: 3PLT_B.
Probab=36.24 E-value=1.1e+02 Score=26.07 Aligned_cols=48 Identities=29% Similarity=0.351 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhh-----hcHHHHHHHHHHHHhcCCChHH-----------HHHHHHHHHHhhcC
Q psy2686 43 TLRTATNLFFKL-----KNYKTTASFAHRLLELGPSMEV-----------ATQARKLLAICNAN 90 (139)
Q Consensus 43 aLr~Am~~~~K~-----kN~~tAa~fArRLLel~p~~~~-----------~~qArkil~~~e~~ 90 (139)
+|+.||+.-|.+ .-.+.-+.|+++||++-|...+ .+++++|++-|++.
T Consensus 195 ~lKEa~~~~f~Al~E~aEK~~Ila~~gk~Ll~lldd~pv~PG~~r~~Y~g~~~t~qIl~dAe~~ 258 (271)
T PF13805_consen 195 KLKEAYSLKFDALIERAEKQAILAEYGKRLLELLDDTPVVPGDTRPPYDGYEQTRQILNDAERA 258 (271)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS------TTS-------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCCCChhHHHHHHHHHHHH
Confidence 677777766653 3456678899999998553322 58899999998764
No 97
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.07 E-value=20 Score=26.16 Aligned_cols=20 Identities=20% Similarity=0.157 Sum_probs=16.0
Q ss_pred cccCCCccccccCCCccccC
Q psy2686 114 PIYHGRESEACVYCGASYLP 133 (139)
Q Consensus 114 PIy~g~~~v~Cp~cga~y~p 133 (139)
||-+|.+.+.||-||..|.-
T Consensus 35 ~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 35 KIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred ecCCCcceEECCCCCCccCE
Confidence 34568999999999988754
No 98
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=35.53 E-value=1.2e+02 Score=23.51 Aligned_cols=44 Identities=18% Similarity=0.271 Sum_probs=31.3
Q ss_pred HHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHHHHh
Q psy2686 44 LRTATNLFFKLKNYKTTASFAHRLLELGPSMEVATQARKLLAIC 87 (139)
Q Consensus 44 Lr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~~~qArkil~~~ 87 (139)
+-......|+.|+|..|..-..++++.-|..+.++.|.=++..|
T Consensus 45 ~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~ 88 (203)
T PF13525_consen 45 QLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLS 88 (203)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHH
Confidence 33344567999999999999999999999877777765555544
No 99
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=35.39 E-value=21 Score=23.79 Aligned_cols=16 Identities=25% Similarity=0.665 Sum_probs=11.4
Q ss_pred CccccccCCCccccCC
Q psy2686 119 RESEACVYCGASYLPK 134 (139)
Q Consensus 119 ~~~v~Cp~cga~y~p~ 134 (139)
+|.-.||+||...-|+
T Consensus 1 e~HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 1 EPHKHCPVCGKPIPPD 16 (59)
T ss_pred CCCCcCCcCCCcCCcc
Confidence 3566788888876664
No 100
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=35.10 E-value=92 Score=17.94 Aligned_cols=23 Identities=30% Similarity=0.483 Sum_probs=13.8
Q ss_pred HhhhcHHHHHHHHHHHHhcCCCh
Q psy2686 52 FKLKNYKTTASFAHRLLELGPSM 74 (139)
Q Consensus 52 ~K~kN~~tAa~fArRLLel~p~~ 74 (139)
+..+++..|.....+.+++.|..
T Consensus 45 ~~~~~~~~a~~~~~~~~~~~~~~ 67 (100)
T cd00189 45 YKLGKYEEALEDYEKALELDPDN 67 (100)
T ss_pred HHHHHHHHHHHHHHHHHhCCCcc
Confidence 34466666666666666665543
No 101
>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=34.47 E-value=24 Score=19.64 Aligned_cols=19 Identities=32% Similarity=0.791 Sum_probs=12.6
Q ss_pred eccccccccCC-CccccccCCC
Q psy2686 108 CARSYTPIYHG-RESEACVYCG 128 (139)
Q Consensus 108 C~~s~tPIy~g-~~~v~Cp~cg 128 (139)
|...+.| ++ .-.-.||-||
T Consensus 4 C~~~i~~--r~~~v~f~CPnCG 23 (24)
T PF07754_consen 4 CGRPIAP--REQAVPFPCPNCG 23 (24)
T ss_pred CCCcccC--cccCceEeCCCCC
Confidence 5566666 33 4556799998
No 102
>PRK01343 zinc-binding protein; Provisional
Probab=34.21 E-value=29 Score=23.14 Aligned_cols=18 Identities=22% Similarity=0.409 Sum_probs=13.1
Q ss_pred CCccccccCCCccccCCC
Q psy2686 118 GRESEACVYCGASYLPKY 135 (139)
Q Consensus 118 g~~~v~Cp~cga~y~p~~ 135 (139)
..|.+.||-||......|
T Consensus 6 ~~p~~~CP~C~k~~~~~~ 23 (57)
T PRK01343 6 LRPTRPCPECGKPSTREA 23 (57)
T ss_pred CCCCCcCCCCCCcCcCCC
Confidence 457889999998765433
No 103
>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=33.78 E-value=46 Score=30.78 Aligned_cols=45 Identities=20% Similarity=0.470 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhcCCCCceeecCCCCCCeeeecc-ccccccCCCcc-ccccCCCcc
Q psy2686 78 TQARKLLAICNANPTDEHTIDYDEHNPFQICAR-SYTPIYHGRES-EACVYCGAS 130 (139)
Q Consensus 78 ~qArkil~~~e~~~~da~~i~yD~~~~F~iC~~-s~tPIy~g~~~-v~Cp~cga~ 130 (139)
+..++|+..+-+++..=+.++. +|+||-. .| .|.-. -+||.||+.
T Consensus 501 eal~~lv~~a~~~~i~Y~~~n~----~~~~C~~CG~----~g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 501 EALKDITKKAMKNGIGYFGINP----PVDVCEDCGY----TGEGLNDKCPKCGSH 547 (579)
T ss_pred HHHHHHHHHHHhcCCceEEecc----CCccCCCCCC----CCCCCCCcCcCCCCc
Confidence 4566777666555434344443 4888874 33 45554 689999986
No 104
>PLN02294 cytochrome c oxidase subunit Vb
Probab=33.65 E-value=20 Score=28.86 Aligned_cols=26 Identities=15% Similarity=0.419 Sum_probs=20.1
Q ss_pred cccccc----CCCccccccCCCccccCCCCC
Q psy2686 111 SYTPIY----HGRESEACVYCGASYLPKYKG 137 (139)
Q Consensus 111 s~tPIy----~g~~~v~Cp~cga~y~p~~kG 137 (139)
+..+++ +|+|. +||-||..|.=+|-|
T Consensus 128 sh~v~Wf~L~kGkp~-RCpeCG~~fkL~~vG 157 (174)
T PLN02294 128 EHDVVWFWLEKGKSF-ECPVCTQYFELEVVG 157 (174)
T ss_pred CceeEEEEecCCCce-eCCCCCCEEEEEEeC
Confidence 566663 78755 499999999988876
No 105
>PF14863 Alkyl_sulf_dimr: Alkyl sulfatase dimerisation; PDB: 2YHE_C 2CG2_A 2CG3_A 2CFU_A 2CFZ_A.
Probab=33.28 E-value=1.4e+02 Score=22.79 Aligned_cols=31 Identities=16% Similarity=0.193 Sum_probs=23.2
Q ss_pred HHHHHHHhhhcHHHHHHHHHHHHhcCCChHH
Q psy2686 46 TATNLFFKLKNYKTTASFAHRLLELGPSMEV 76 (139)
Q Consensus 46 ~Am~~~~K~kN~~tAa~fArRLLel~p~~~~ 76 (139)
.....++..++|.-|+.++.-|+..+|..+.
T Consensus 75 ~~A~~~~~~gd~~wA~~L~d~l~~adp~n~~ 105 (141)
T PF14863_consen 75 ERAQAALAAGDYQWAAELLDHLVFADPDNEE 105 (141)
T ss_dssp HHHHHHHHCT-HHHHHHHHHHHHHH-TT-HH
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHcCCCcHH
Confidence 3344578999999999999999999987654
No 106
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=33.22 E-value=15 Score=24.91 Aligned_cols=16 Identities=31% Similarity=0.667 Sum_probs=13.5
Q ss_pred CCCccccccCCCcccc
Q psy2686 117 HGRESEACVYCGASYL 132 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~ 132 (139)
-|+...+||-||+.+-
T Consensus 13 DGE~~lrCPRC~~~FR 28 (65)
T COG4049 13 DGEEFLRCPRCGMVFR 28 (65)
T ss_pred CCceeeeCCchhHHHH
Confidence 4899999999998753
No 107
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=33.09 E-value=1.2e+02 Score=25.06 Aligned_cols=33 Identities=18% Similarity=0.176 Sum_probs=18.5
Q ss_pred HhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHH
Q psy2686 52 FKLKNYKTTASFAHRLLELGPSMEVATQARKLL 84 (139)
Q Consensus 52 ~K~kN~~tAa~fArRLLel~p~~~~~~qArkil 84 (139)
.+.|++..|..+-+++++.-|..+.+.+|++-|
T Consensus 228 ~~~g~~~~A~~~~~~vi~~yP~s~~a~~A~~rL 260 (263)
T PRK10803 228 QDKGDTAKAKAVYQQVIKKYPGTDGAKQAQKRL 260 (263)
T ss_pred HHcCCHHHHHHHHHHHHHHCcCCHHHHHHHHHH
Confidence 355555555555555555555555555555544
No 108
>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=32.99 E-value=20 Score=20.28 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=5.7
Q ss_pred cccCCCcccc
Q psy2686 123 ACVYCGASYL 132 (139)
Q Consensus 123 ~Cp~cga~y~ 132 (139)
.||.||+...
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 5999999877
No 109
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.72 E-value=20 Score=21.20 Aligned_cols=11 Identities=36% Similarity=0.733 Sum_probs=9.2
Q ss_pred ccccCCCcccc
Q psy2686 122 EACVYCGASYL 132 (139)
Q Consensus 122 v~Cp~cga~y~ 132 (139)
+.||-|+++|.
T Consensus 3 i~Cp~C~~~y~ 13 (36)
T PF13717_consen 3 ITCPNCQAKYE 13 (36)
T ss_pred EECCCCCCEEe
Confidence 67999999886
No 110
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=31.96 E-value=36 Score=31.23 Aligned_cols=48 Identities=27% Similarity=0.480 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHhhc-CCCCceeecCCCCCCeeeeccccccccCCCccccccCCCcc
Q psy2686 76 VATQARKLLAICNA-NPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGAS 130 (139)
Q Consensus 76 ~~~qArkil~~~e~-~~~da~~i~yD~~~~F~iC~~s~tPIy~g~~~v~Cp~cga~ 130 (139)
-.+..++++..+=. ....=+.|+. ||++|..=- |.+...-.||.||+.
T Consensus 465 n~~al~~lv~~~~~~~~i~Y~~in~----~~~~C~~CG---~~~~~~~~CP~CGs~ 513 (546)
T PF13597_consen 465 NPEALEKLVRYAMENTGIPYFTINP----PIDICPDCG---YIGGEGDKCPKCGSE 513 (546)
T ss_dssp -HHHHHHHHHHHHH--H-SEEEEE------EEEETTT------S--EEE-CCC---
T ss_pred CHHHHHHHHHHHHHhCCCCeEEEec----CcccccCCC---cCCCCCCCCCCCCCc
Confidence 44556666655544 3333344444 488997654 344448899999997
No 111
>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]
Probab=31.84 E-value=88 Score=27.77 Aligned_cols=51 Identities=22% Similarity=0.257 Sum_probs=39.6
Q ss_pred HHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhhcCCCCceee
Q psy2686 44 LRTATNLFFKLKNYKTTASFAHRLLELGPSMEVATQARKLLAICNANPTDEHTI 97 (139)
Q Consensus 44 Lr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~~~qArkil~~~e~~~~da~~i 97 (139)
|..+-+-+-++++|..|.++.+|+|.++| ..++-.|++.+.-..-.|.|.+
T Consensus 282 lgkva~~yle~g~~neAi~l~qr~ltldp---L~e~~nk~lm~~la~~gD~is~ 332 (361)
T COG3947 282 LGKVARAYLEAGKPNEAIQLHQRALTLDP---LSEQDNKGLMASLATLGDEISA 332 (361)
T ss_pred HHHHHHHHHHcCChHHHHHHHHHHhhcCh---hhhHHHHHHHHHHHHhccchhh
Confidence 44566677889999999999999999976 4456777777777666776654
No 112
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=31.74 E-value=1.8e+02 Score=23.68 Aligned_cols=59 Identities=20% Similarity=0.213 Sum_probs=37.4
Q ss_pred chhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHH-------------HHHHHHHHH-HhhcCCCCc
Q psy2686 36 QPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEV-------------ATQARKLLA-ICNANPTDE 94 (139)
Q Consensus 36 qp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~-------------~~qArkil~-~~e~~~~da 94 (139)
.|.+...++........+.|++..|..+.++++++.|+... .++|.+++. .-+..|.+.
T Consensus 244 ~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~ 316 (389)
T PRK11788 244 DPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLR 316 (389)
T ss_pred ChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHH
Confidence 34444444555556677888999999999998888776433 334666664 334445543
No 113
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=31.68 E-value=1.5e+02 Score=19.35 Aligned_cols=45 Identities=13% Similarity=0.087 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHHHHh
Q psy2686 43 TLRTATNLFFKLKNYKTTASFAHRLLELGPSMEVATQARKLLAIC 87 (139)
Q Consensus 43 aLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~~~qArkil~~~ 87 (139)
++...-...++.++|..|...-++++...|.......+.-.+..+
T Consensus 41 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~ 85 (119)
T TIGR02795 41 AHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMS 85 (119)
T ss_pred HHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHH
Confidence 344445556677777777777777777666544434444443333
No 114
>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=31.68 E-value=22 Score=21.81 Aligned_cols=9 Identities=33% Similarity=0.903 Sum_probs=7.7
Q ss_pred ccccCCCcc
Q psy2686 122 EACVYCGAS 130 (139)
Q Consensus 122 v~Cp~cga~ 130 (139)
+.||.||+.
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 569999986
No 115
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=31.50 E-value=1.3e+02 Score=18.60 Aligned_cols=33 Identities=18% Similarity=0.295 Sum_probs=26.4
Q ss_pred HhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHHH
Q psy2686 52 FKLKNYKTTASFAHRLLELGPSMEVATQARKLLA 85 (139)
Q Consensus 52 ~K~kN~~tAa~fArRLLel~p~~~~~~qArkil~ 85 (139)
.+.|.+..|-..-..+|+ .++++..++|+++++
T Consensus 10 ie~Gd~e~Ar~lL~evl~-~~~~~q~~eA~~LL~ 42 (44)
T TIGR03504 10 IEMGDLEGARELLEEVIE-EGDEAQRQEARALLA 42 (44)
T ss_pred HHcCChHHHHHHHHHHHH-cCCHHHHHHHHHHHh
Confidence 577888888888888885 566888888888875
No 116
>PF11475 VP_N-CPKC: Virion protein N terminal domain ; InterPro: IPR021573 This is the N-terminal domain of a family of virion proteins which contains a zinc finger domain. Currently no function is known. ; PDB: 2BAI_A.
Probab=31.49 E-value=8.5 Score=22.68 Aligned_cols=18 Identities=50% Similarity=0.833 Sum_probs=9.9
Q ss_pred eeeeccccccccCCCccccccCCCc
Q psy2686 105 FQICARSYTPIYHGRESEACVYCGA 129 (139)
Q Consensus 105 F~iC~~s~tPIy~g~~~v~Cp~cga 129 (139)
-+||+-|++ .+.||-|+|
T Consensus 7 qeicahslt-------f~ecpkcsa 24 (32)
T PF11475_consen 7 QEICAHSLT-------FEECPKCSA 24 (32)
T ss_dssp S---SSSS--------GGGHHHHH-
T ss_pred HHHHhcccc-------cccCcchhH
Confidence 358988886 467888876
No 117
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=31.38 E-value=37 Score=21.82 Aligned_cols=15 Identities=20% Similarity=0.676 Sum_probs=12.2
Q ss_pred CccccccCCCccccC
Q psy2686 119 RESEACVYCGASYLP 133 (139)
Q Consensus 119 ~~~v~Cp~cga~y~p 133 (139)
...|+|.+||-.+..
T Consensus 32 ~d~v~C~~C~~~~~~ 46 (69)
T cd00022 32 GDEVKCFFCGLELKN 46 (69)
T ss_pred CCEEEeCCCCCCccC
Confidence 468999999987754
No 118
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=30.77 E-value=30 Score=23.17 Aligned_cols=19 Identities=16% Similarity=0.335 Sum_probs=13.8
Q ss_pred CCCccccccCCCccccCCC
Q psy2686 117 HGRESEACVYCGASYLPKY 135 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~p~~ 135 (139)
..+..-.||+|++.-..+.
T Consensus 35 s~~~~p~CPlC~s~M~~~~ 53 (59)
T PF14169_consen 35 SFEEEPVCPLCKSPMVSGT 53 (59)
T ss_pred ccCCCccCCCcCCccccce
Confidence 3466678999999866543
No 119
>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=30.40 E-value=20 Score=26.02 Aligned_cols=26 Identities=27% Similarity=0.428 Sum_probs=19.6
Q ss_pred ccccc----cCCCccccccCCCccccCCCCC
Q psy2686 111 SYTPI----YHGRESEACVYCGASYLPKYKG 137 (139)
Q Consensus 111 s~tPI----y~g~~~v~Cp~cga~y~p~~kG 137 (139)
++.++ .+| +..+||-||..|.=.+.|
T Consensus 66 ~h~v~W~~l~~g-~~~rC~eCG~~fkL~~v~ 95 (97)
T cd00924 66 SHDVIWMWLEKG-KPKRCPECGHVFKLVDVG 95 (97)
T ss_pred CceEEEEEEeCC-CceeCCCCCcEEEEEECC
Confidence 45555 478 789999999999766554
No 120
>PF15616 TerY-C: TerY-C metal binding domain
Probab=30.39 E-value=38 Score=25.95 Aligned_cols=28 Identities=21% Similarity=0.533 Sum_probs=22.3
Q ss_pred CeeeeccccccccCCCccccccCCCccc
Q psy2686 104 PFQICARSYTPIYHGRESEACVYCGASY 131 (139)
Q Consensus 104 ~F~iC~~s~tPIy~g~~~v~Cp~cga~y 131 (139)
-|.+|.=.-..=|.|+..|.||-||..-
T Consensus 88 ~fa~C~CGkl~Ci~g~~~~~CPwCg~~g 115 (131)
T PF15616_consen 88 AFAVCGCGKLFCIDGEGEVTCPWCGNEG 115 (131)
T ss_pred cEEEecCCCEEEeCCCCCEECCCCCCee
Confidence 5888865555558999999999999764
No 121
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=30.37 E-value=21 Score=24.35 Aligned_cols=10 Identities=30% Similarity=1.142 Sum_probs=7.4
Q ss_pred cccccCCCcc
Q psy2686 121 SEACVYCGAS 130 (139)
Q Consensus 121 ~v~Cp~cga~ 130 (139)
..-|||||-.
T Consensus 6 lKPCPFCG~~ 15 (64)
T PRK09710 6 VKPCPFCGCP 15 (64)
T ss_pred ccCCCCCCCc
Confidence 3459999964
No 122
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.95 E-value=28 Score=25.85 Aligned_cols=12 Identities=25% Similarity=0.584 Sum_probs=9.0
Q ss_pred ccccccCCCccc
Q psy2686 120 ESEACVYCGASY 131 (139)
Q Consensus 120 ~~v~Cp~cga~y 131 (139)
+...||.||+.-
T Consensus 91 ~~~~CP~Cgs~~ 102 (124)
T PRK00762 91 AVIECPVCGNKR 102 (124)
T ss_pred cCCcCcCCCCCC
Confidence 347899999754
No 123
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=29.79 E-value=26 Score=20.92 Aligned_cols=11 Identities=27% Similarity=0.742 Sum_probs=8.5
Q ss_pred cccccCCCccc
Q psy2686 121 SEACVYCGASY 131 (139)
Q Consensus 121 ~v~Cp~cga~y 131 (139)
...||.||+.-
T Consensus 2 ~~~Cp~Cg~~~ 12 (47)
T PF14690_consen 2 PPRCPHCGSPS 12 (47)
T ss_pred CccCCCcCCCc
Confidence 35799999764
No 124
>PF14788 EF-hand_10: EF hand; PDB: 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B 1DJZ_B 1DJY_B 1DJX_B 1QAT_A 1DJH_A ....
Probab=29.48 E-value=87 Score=20.34 Aligned_cols=32 Identities=19% Similarity=0.270 Sum_probs=18.4
Q ss_pred HHHHhcCCChHHHHHHHHHHHHhhcCCCCcee
Q psy2686 65 HRLLELGPSMEVATQARKLLAICNANPTDEHT 96 (139)
Q Consensus 65 rRLLel~p~~~~~~qArkil~~~e~~~~da~~ 96 (139)
++||..---.-.-+.|+.+.+.||++.++..+
T Consensus 8 k~lLk~~NI~~~~~yA~~LFq~~D~s~~g~Le 39 (51)
T PF14788_consen 8 KKLLKMMNIEMDDEYARQLFQECDKSQSGRLE 39 (51)
T ss_dssp HHHHHHTT----HHHHHHHHHHH-SSSSSEBE
T ss_pred HHHHHHHccCcCHHHHHHHHHHhcccCCCCcc
Confidence 34444332233345699999999999877654
No 125
>KOG3352|consensus
Probab=29.05 E-value=26 Score=27.70 Aligned_cols=63 Identities=17% Similarity=0.252 Sum_probs=38.5
Q ss_pred hHHHHHH---HHHHHHhhcCCCCceeecCCCC------CCee------------eeccc-----cccccCCCccccccCC
Q psy2686 74 MEVATQA---RKLLAICNANPTDEHTIDYDEH------NPFQ------------ICARS-----YTPIYHGRESEACVYC 127 (139)
Q Consensus 74 ~~~~~qA---rkil~~~e~~~~da~~i~yD~~------~~F~------------iC~~s-----~tPIy~g~~~v~Cp~c 127 (139)
++..+|| .|---.++..+.|.++++|+.. +|-. +|... |--|++|+..- ||-|
T Consensus 61 pddle~aTGlEk~eLla~l~G~d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c~eD~~~V~Wmwl~Kge~~r-c~eC 139 (153)
T KOG3352|consen 61 PDDLEQATGLEKEELLAELEGRDPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGCEEDSHAVVWMWLEKGETQR-CPEC 139 (153)
T ss_pred CCchhhhhhHHHHHHHHHhhCCCccccccccCCCCcccCCccccccCCceEEeecccCCCcceEEEEEEcCCccc-CCcc
Confidence 3444553 3334456777889888888743 2222 23333 22357887765 9999
Q ss_pred CccccCCCCC
Q psy2686 128 GASYLPKYKG 137 (139)
Q Consensus 128 ga~y~p~~kG 137 (139)
|..|.=...|
T Consensus 140 G~~fkL~~v~ 149 (153)
T KOG3352|consen 140 GHYFKLVPVG 149 (153)
T ss_pred cceEEeeecC
Confidence 9999866554
No 126
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.61 E-value=31 Score=25.20 Aligned_cols=55 Identities=11% Similarity=0.286 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHHHhhcCCCCceeecCCCCCCeeee--ccccccccCCCccccccCCCccc
Q psy2686 74 MEVATQARKLLAICNANPTDEHTIDYDEHNPFQIC--ARSYTPIYHGRESEACVYCGASY 131 (139)
Q Consensus 74 ~~~~~qArkil~~~e~~~~da~~i~yD~~~~F~iC--~~s~tPIy~g~~~v~Cp~cga~y 131 (139)
++..+-|=.++. +..+-.--+|..+.--.-.-| |..+.|+. +.....||.||+.-
T Consensus 41 p~~L~f~f~~~~--~~t~~egA~L~i~~~p~~~~C~~Cg~~~~~~-~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 41 TSSLAFCFDLVC--RGTVAEGCKLHLEEQEAECWCETCQQYVTLL-TQRVRRCPQCHGDM 97 (114)
T ss_pred HHHHHHHHHHHh--CCCccCCCEEEEEeeCcEEEcccCCCeeecC-CccCCcCcCcCCCC
Confidence 455555555532 222323334444333233333 34444432 22337799999764
No 127
>COG1143 NuoI Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]
Probab=28.34 E-value=40 Score=26.70 Aligned_cols=41 Identities=20% Similarity=0.478 Sum_probs=28.0
Q ss_pred HhhcC-CCCceeecCCCCCCeeeeccccccccCCCccccccCCCcc
Q psy2686 86 ICNAN-PTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGAS 130 (139)
Q Consensus 86 ~~e~~-~~da~~i~yD~~~~F~iC~~s~tPIy~g~~~v~Cp~cga~ 130 (139)
.|++- |+|++++.-++..+ -.+-.+-+.+-...+|-|||=.
T Consensus 62 lCa~iCP~~aI~m~~~~~~~----~g~~~~~~~~In~grCIfCg~C 103 (172)
T COG1143 62 LCANICPANAITMETAERKV----DGRKKPKRPDINLGRCIFCGLC 103 (172)
T ss_pred HHHhhCCcCceEEEEcccCC----CCccccccceeccccccccCch
Confidence 34433 99999999987765 3444444446677889999843
No 128
>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=27.78 E-value=27 Score=22.84 Aligned_cols=12 Identities=42% Similarity=0.706 Sum_probs=10.2
Q ss_pred ccccccCCCccc
Q psy2686 120 ESEACVYCGASY 131 (139)
Q Consensus 120 ~~v~Cp~cga~y 131 (139)
..|.||-||+.+
T Consensus 21 eiV~Cp~CGael 32 (54)
T TIGR01206 21 ELVICDECGAEL 32 (54)
T ss_pred CEEeCCCCCCEE
Confidence 478999999976
No 129
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=27.62 E-value=1.5e+02 Score=19.55 Aligned_cols=31 Identities=16% Similarity=0.172 Sum_probs=23.8
Q ss_pred hhHHHHHHHHHHHHHhhhcHHHHHHHHHHHH
Q psy2686 38 VHQILTLRTATNLFFKLKNYKTTASFAHRLL 68 (139)
Q Consensus 38 ~H~~LaLr~Am~~~~K~kN~~tAa~fArRLL 68 (139)
.-.+-.+..-+..+|+.++|..|+...+||-
T Consensus 37 ~~~~~~~~~~l~~~f~~~d~~~A~~~~~kLk 67 (78)
T PF07743_consen 37 EERIKELIKELAEAFDAKDWEEAKEALRKLK 67 (78)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHccCcHHHHHHHHHHHH
Confidence 3455666777888889999999999999873
No 130
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Probab=27.18 E-value=41 Score=25.12 Aligned_cols=33 Identities=27% Similarity=0.373 Sum_probs=26.2
Q ss_pred ceeecCCCCCCeeeeccccccccCCCccccccCC
Q psy2686 94 EHTIDYDEHNPFQICARSYTPIYHGRESEACVYC 127 (139)
Q Consensus 94 a~~i~yD~~~~F~iC~~s~tPIy~g~~~v~Cp~c 127 (139)
-+.|++| -|.-++-+.|..||-.|.-..+|||=
T Consensus 18 gv~ie~d-cnakvvvats~dpvts~klyfscpye 50 (122)
T PF05325_consen 18 GVPIECD-CNAKVVVATSRDPVTSGKLYFSCPYE 50 (122)
T ss_pred Ccceecc-CCceEEEEeccCCcccceeeecCccc
Confidence 3566775 35567778999999999999999983
No 131
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=26.97 E-value=1.1e+02 Score=16.05 Aligned_cols=29 Identities=14% Similarity=0.087 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhhhcHHHHHHHHHHHHhcC
Q psy2686 43 TLRTATNLFFKLKNYKTTASFAHRLLELG 71 (139)
Q Consensus 43 aLr~Am~~~~K~kN~~tAa~fArRLLel~ 71 (139)
+....|..+.|.|++..|...-+.+.+.+
T Consensus 3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~g 31 (34)
T PF13812_consen 3 TYNALLRACAKAGDPDAALQLFDEMKEQG 31 (34)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence 45677888999999998887777776643
No 132
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.64 E-value=40 Score=25.35 Aligned_cols=32 Identities=22% Similarity=0.456 Sum_probs=23.4
Q ss_pred eecccc----ccccCCCccccccCCCccccCCCCCC
Q psy2686 107 ICARSY----TPIYHGRESEACVYCGASYLPKYKGE 138 (139)
Q Consensus 107 iC~~s~----tPIy~g~~~v~Cp~cga~y~p~~kG~ 138 (139)
.|..++ -++.+|.+.-+|+-|+..+.-++.+.
T Consensus 35 ~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~~~~ 70 (129)
T COG3677 35 RCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVETGSP 70 (129)
T ss_pred CCCccceeeECCccccccccccCCcCcceeeeccCc
Confidence 466655 45567888899999999987766543
No 133
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=26.55 E-value=2.6e+02 Score=23.82 Aligned_cols=44 Identities=25% Similarity=0.299 Sum_probs=32.3
Q ss_pred CCchhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHHHH
Q psy2686 34 KLQPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEVAT 78 (139)
Q Consensus 34 ~Lqp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~~~ 78 (139)
.|.|.+...-++.| ...++.|+|..|....++.|++.|....+.
T Consensus 64 ~l~P~~~~a~~~lg-~~~~~lg~~~eA~~~~~~al~l~P~~~~~~ 107 (356)
T PLN03088 64 ELDPSLAKAYLRKG-TACMKLEEYQTAKAALEKGASLAPGDSRFT 107 (356)
T ss_pred HhCcCCHHHHHHHH-HHHHHhCCHHHHHHHHHHHHHhCCCCHHHH
Confidence 45666555555555 455789999999999999999998755543
No 134
>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=26.27 E-value=22 Score=27.43 Aligned_cols=36 Identities=22% Similarity=0.462 Sum_probs=23.3
Q ss_pred eecCCCCCCeeeeccccccc---cCCCccccccCCCccc
Q psy2686 96 TIDYDEHNPFQICARSYTPI---YHGRESEACVYCGASY 131 (139)
Q Consensus 96 ~i~yD~~~~F~iC~~s~tPI---y~g~~~v~Cp~cga~y 131 (139)
++.++..+.|-+|..-..-. --=+-.-.||.||+..
T Consensus 100 ~l~~e~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 100 KLEFETNNMFFICPNMCVRFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred HHhhccCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCEe
Confidence 46677778899996544321 0112367999999864
No 135
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.20 E-value=27 Score=27.58 Aligned_cols=37 Identities=19% Similarity=0.275 Sum_probs=22.9
Q ss_pred eecCCCCCCeeeecccccc---ccCCCccccccCCCcccc
Q psy2686 96 TIDYDEHNPFQICARSYTP---IYHGRESEACVYCGASYL 132 (139)
Q Consensus 96 ~i~yD~~~~F~iC~~s~tP---Iy~g~~~v~Cp~cga~y~ 132 (139)
+++|+..+.|-+|..-..- .--=+-.-.||.||....
T Consensus 108 ~l~~e~~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 108 QLEEEENNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred HhhhccCCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCe
Confidence 4566667789999653322 111134678999998653
No 136
>PF05367 Phage_endo_I: Phage endonuclease I; InterPro: IPR008029 Endonuclease I (3.1.21.2 from EC) is a junction-resolving enzyme encoded by bacteriophage T7, that selectively binds and cleaves four-way Holliday DNA junctions []. The structure of the enzyme shows that it forms a symmetric homodimer arranged in two well-separated domains. Each domain, however, is composed of elements from both subunits, and amino acid side chains from both protomers contribute to the active site []. ; GO: 0008833 deoxyribonuclease IV (phage-T4-induced) activity, 0015074 DNA integration, 0016032 viral reproduction; PDB: 3CAE_A 1M0D_A 1M0I_C 1FZR_B 2PFJ_B.
Probab=25.90 E-value=90 Score=24.58 Aligned_cols=37 Identities=30% Similarity=0.382 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhhcCCCCceeecCCCCCCeeeeccccccccCCCccc
Q psy2686 77 ATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESE 122 (139)
Q Consensus 77 ~~qArkil~~~e~~~~da~~i~yD~~~~F~iC~~s~tPIy~g~~~v 122 (139)
.+--||++..=+++|.=.+.+ |=..+.++||+|+++.
T Consensus 72 ~~DR~K~l~Ik~q~P~LDIR~---------VFq~~~~Ki~K~SkTT 108 (149)
T PF05367_consen 72 AEDRRKHLLIKEQYPELDIRF---------VFQSSRTKIYKGSKTT 108 (149)
T ss_dssp HHHHHHHHHHHHH-TTSEEEE---------EES-TTSBSSTT-SSB
T ss_pred cchhHHHHHHHHhCCCccEEE---------EEecCCCcccCCCCcc
Confidence 455799999999999844444 4456788999998764
No 137
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=25.70 E-value=23 Score=23.74 Aligned_cols=12 Identities=25% Similarity=0.620 Sum_probs=7.0
Q ss_pred ccccCCCccccC
Q psy2686 122 EACVYCGASYLP 133 (139)
Q Consensus 122 v~Cp~cga~y~p 133 (139)
..||+|.+...-
T Consensus 56 G~CP~C~~~i~~ 67 (70)
T PF11793_consen 56 GECPYCSSPISW 67 (70)
T ss_dssp EE-TTT-SEEEG
T ss_pred cCCcCCCCeeeE
Confidence 469999887643
No 138
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=25.70 E-value=32 Score=21.00 Aligned_cols=15 Identities=20% Similarity=0.430 Sum_probs=12.1
Q ss_pred ccccccCCCccccCC
Q psy2686 120 ESEACVYCGASYLPK 134 (139)
Q Consensus 120 ~~v~Cp~cga~y~p~ 134 (139)
..+.|+.||..+...
T Consensus 4 g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRR 18 (58)
T ss_pred CcEEcccCCcEeEEE
Confidence 468999999988754
No 139
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=25.28 E-value=65 Score=19.82 Aligned_cols=18 Identities=28% Similarity=0.599 Sum_probs=13.6
Q ss_pred CCCccccccCCCccccCC
Q psy2686 117 HGRESEACVYCGASYLPK 134 (139)
Q Consensus 117 ~g~~~v~Cp~cga~y~p~ 134 (139)
.|.+.|+||.||..+.-.
T Consensus 36 ~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 36 EGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CCCCeeECCCCCCeECCC
Confidence 378889999888777543
No 140
>cd03532 Rieske_RO_Alpha_VanA_DdmC Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degrad
Probab=24.89 E-value=52 Score=23.42 Aligned_cols=31 Identities=23% Similarity=0.542 Sum_probs=22.6
Q ss_pred eeeccccccccCC---CccccccCCCccccCCCCCC
Q psy2686 106 QICARSYTPIYHG---RESEACVYCGASYLPKYKGE 138 (139)
Q Consensus 106 ~iC~~s~tPIy~g---~~~v~Cp~cga~y~p~~kG~ 138 (139)
++|.---.|+..| ...+.|||.|..|.. .|+
T Consensus 44 n~CpH~g~~L~~G~~~~~~i~Cp~Hg~~fd~--~G~ 77 (116)
T cd03532 44 DRCPHRSAPLSKGSVEGGGLVCGYHGLEFDS--DGR 77 (116)
T ss_pred CcCCCCCCCccCCcccCCEEEeCCCCcEEcC--CCC
Confidence 3677766677544 457999999999984 454
No 141
>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=24.69 E-value=15 Score=28.30 Aligned_cols=27 Identities=33% Similarity=0.626 Sum_probs=17.5
Q ss_pred cccccc----cCCCccccccCCCccccCCCCC
Q psy2686 110 RSYTPI----YHGRESEACVYCGASYLPKYKG 137 (139)
Q Consensus 110 ~s~tPI----y~g~~~v~Cp~cga~y~p~~kG 137 (139)
.|+..+ .+|+| .+||-||..|.-++-|
T Consensus 98 ~sH~v~W~~l~~g~~-~RCpeCG~~fkL~~vg 128 (136)
T PF01215_consen 98 DSHDVIWFWLHKGKP-QRCPECGQVFKLKYVG 128 (136)
T ss_dssp -SSS-EEEEEETTSE-EEETTTEEEEEEEE--
T ss_pred CcceeEEEEEeCCCc-cCCCCCCeEEEEEEcC
Confidence 344554 37875 6999999999866655
No 142
>PRK01402 hslO Hsp33-like chaperonin; Reviewed
Probab=24.64 E-value=32 Score=29.80 Aligned_cols=15 Identities=33% Similarity=0.846 Sum_probs=13.5
Q ss_pred CCccccccCCCcccc
Q psy2686 118 GRESEACVYCGASYL 132 (139)
Q Consensus 118 g~~~v~Cp~cga~y~ 132 (139)
|.-.|.|-|||.+|.
T Consensus 305 g~iev~CeFC~~~Y~ 319 (328)
T PRK01402 305 GKISVTCEFCSRVYR 319 (328)
T ss_pred CCEEEEeeCCCCEEE
Confidence 677899999999996
No 143
>cd03469 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the i
Probab=24.32 E-value=56 Score=22.73 Aligned_cols=31 Identities=19% Similarity=0.442 Sum_probs=23.0
Q ss_pred eeeccccccccC----CCccccccCCCccccCCCCCC
Q psy2686 106 QICARSYTPIYH----GRESEACVYCGASYLPKYKGE 138 (139)
Q Consensus 106 ~iC~~s~tPIy~----g~~~v~Cp~cga~y~p~~kG~ 138 (139)
++|.---.|+-. +...+.||+-|+.|..+ |+
T Consensus 41 n~CpH~g~~L~~g~~~~~~~i~Cp~Hg~~Fd~~--G~ 75 (118)
T cd03469 41 NVCPHRGARLCEGRGGNAGRLVCPYHGWTYDLD--GK 75 (118)
T ss_pred EeCCCCCCEeeeccCCCCCEEECCCCCCEECCC--Cc
Confidence 467666666654 34589999999999887 64
No 144
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.94 E-value=32 Score=26.77 Aligned_cols=14 Identities=29% Similarity=0.627 Sum_probs=11.2
Q ss_pred CCccccccCCCccc
Q psy2686 118 GRESEACVYCGASY 131 (139)
Q Consensus 118 g~~~v~Cp~cga~y 131 (139)
-..-|.||.||+.-
T Consensus 29 ~rgLv~CPvCgs~~ 42 (142)
T COG5319 29 ERGLVTCPVCGSTE 42 (142)
T ss_pred HcCceeCCCCCcHH
Confidence 45679999999864
No 145
>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=23.81 E-value=32 Score=22.70 Aligned_cols=9 Identities=44% Similarity=1.051 Sum_probs=2.9
Q ss_pred ccccCCCcc
Q psy2686 122 EACVYCGAS 130 (139)
Q Consensus 122 v~Cp~cga~ 130 (139)
..||.|||.
T Consensus 34 y~Cp~CgAt 42 (55)
T PF05741_consen 34 YVCPICGAT 42 (55)
T ss_dssp ---TTT---
T ss_pred CcCCCCcCc
Confidence 589999994
No 146
>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=23.60 E-value=1.1e+02 Score=28.78 Aligned_cols=46 Identities=24% Similarity=0.452 Sum_probs=26.1
Q ss_pred HHHHHHHHHhhcCCCCceeecCCCCCCeeeecc-ccccccCCCccccccCCCcc
Q psy2686 78 TQARKLLAICNANPTDEHTIDYDEHNPFQICAR-SYTPIYHGRESEACVYCGAS 130 (139)
Q Consensus 78 ~qArkil~~~e~~~~da~~i~yD~~~~F~iC~~-s~tPIy~g~~~v~Cp~cga~ 130 (139)
+..++++...-++...=+.|+. +|+||.. .| | .|.-...||.||+.
T Consensus 509 ea~~~lv~~~~~~~i~Y~tin~----~~siC~~CGy--~-~g~~~~~CP~CGs~ 555 (586)
T TIGR02827 509 DGYRKLLRVAADTGCNYFCFNI----KITICNDCHH--I-DKRTLHRCPVCGSA 555 (586)
T ss_pred HHHHHHHHHHHhcCCceEEeCC----CCeecCCCCC--c-CCCcCCcCcCCCCc
Confidence 4455566554333223233332 5889974 23 2 45556899999964
No 147
>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=23.58 E-value=45 Score=19.46 Aligned_cols=22 Identities=23% Similarity=0.454 Sum_probs=16.4
Q ss_pred cccccCCCccccccCCCccccC
Q psy2686 112 YTPIYHGRESEACVYCGASYLP 133 (139)
Q Consensus 112 ~tPIy~g~~~v~Cp~cga~y~p 133 (139)
..-+.++-|...|+-||-.|..
T Consensus 23 ~~~~i~~vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 23 ELIVIENVPALVCPQCGEEYLD 44 (46)
T ss_pred EEEEEeCCCccccccCCCEeeC
Confidence 3334467788899999998864
No 148
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=23.39 E-value=47 Score=26.66 Aligned_cols=12 Identities=33% Similarity=0.924 Sum_probs=10.3
Q ss_pred cccCCCccccCC
Q psy2686 123 ACVYCGASYLPK 134 (139)
Q Consensus 123 ~Cp~cga~y~p~ 134 (139)
.||+||....|+
T Consensus 156 ~CPlCg~PlDP~ 167 (171)
T PF11290_consen 156 PCPLCGEPLDPE 167 (171)
T ss_pred CCCCCCCCCCCC
Confidence 599999988876
No 149
>PRK00420 hypothetical protein; Validated
Probab=23.36 E-value=48 Score=24.71 Aligned_cols=26 Identities=19% Similarity=0.488 Sum_probs=17.3
Q ss_pred eccccccccC-CCccccccCCCccccC
Q psy2686 108 CARSYTPIYH-GRESEACVYCGASYLP 133 (139)
Q Consensus 108 C~~s~tPIy~-g~~~v~Cp~cga~y~p 133 (139)
|..=-+|+++ -...+.||-||..+.-
T Consensus 26 CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 26 CPVCGLPLFELKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCcceecCCCceECCCCCCeeee
Confidence 3333355554 4568999999997764
No 150
>TIGR02378 nirD_assim_sml nitrite reductase [NAD(P)H], small subunit. This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused.
Probab=23.34 E-value=45 Score=23.07 Aligned_cols=28 Identities=14% Similarity=0.253 Sum_probs=18.9
Q ss_pred eeccc-cccccCC-------CccccccCCCccccCC
Q psy2686 107 ICARS-YTPIYHG-------RESEACVYCGASYLPK 134 (139)
Q Consensus 107 iC~~s-~tPIy~g-------~~~v~Cp~cga~y~p~ 134 (139)
.|.-. -.|+-.| ...+.||+.|+.|..+
T Consensus 42 ~CpH~g~~~L~~g~~~~~~~~~~i~Cp~Hg~~Fdl~ 77 (105)
T TIGR02378 42 MCPHKRAFVLSRGIVGDAQGELWVACPLHKRNFRLE 77 (105)
T ss_pred cCCCCCCccccceEEccCCCcEEEECCcCCCEEEcC
Confidence 56665 5554322 2249999999999865
No 151
>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=23.24 E-value=42 Score=20.12 Aligned_cols=19 Identities=21% Similarity=0.692 Sum_probs=12.0
Q ss_pred cccccCCCccccccCCCcc
Q psy2686 112 YTPIYHGRESEACVYCGAS 130 (139)
Q Consensus 112 ~tPIy~g~~~v~Cp~cga~ 130 (139)
|..|-.+...-+|++|+..
T Consensus 15 ~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 15 FCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp TSEEETTTTEEEETTT--E
T ss_pred cceEcCCCCEEECcCCCCc
Confidence 3344457778999999874
No 152
>PF02489 Herpes_glycop_H: Herpesvirus glycoprotein H; InterPro: IPR003493 Herpesviruses are enveloped by a lipid bilayer that contains at least a dozen glycoproteins. The virion surface glycoproteins mediate recognition of susceptible cells and promote fusion of the viral envelope with the cell membrane, leading to virus entry. No single glycoprotein associated with the virion membrane has been identified as the fusogen []. Glycoprotein L (gL) forms a non-covalently linked heterodimer with glycoprotein H (gH). This heterodimer is essential for virus-cell and cell-cell fusion since the association of gH and gL is necessary for correct localisation of gH to the virion or cell surface. gH anchoring the heterodimer to the plasma membrane through its transmembrane domain. gL lacks a transmembrane domain and is secreted from cells when expressed in the absence of gH []. This entry represents Herpesvirus glycoprotein H (gH), which is a virion associated envelope glycoprotein []. Heterodimer formation between gH and gL has been demonstrated in both virions and infected cells []. Heterodimer formation between gL and gH is important for the proper folding of gH and its insertion into the membrane because the anti-gH conformation-dependent monoclonal antibodies (mAbs) 53S and LP11 bind gH only when gL is present [, ].; PDB: 3PHF_S 3M1C_A 2LQY_A 2XQY_A.
Probab=23.00 E-value=34 Score=31.79 Aligned_cols=19 Identities=32% Similarity=0.882 Sum_probs=9.2
Q ss_pred cccCCCccccccCCCcccc
Q psy2686 114 PIYHGRESEACVYCGASYL 132 (139)
Q Consensus 114 PIy~g~~~v~Cp~cga~y~ 132 (139)
-+|.-++...|+|||+..+
T Consensus 554 ~~~Nit~~~~C~~Cgsv~l 572 (657)
T PF02489_consen 554 VVYNITPSKDCPFCGSVFL 572 (657)
T ss_dssp EE--SSS-SS-STTT-EEE
T ss_pred CCcCCCCCCCCCCCCcEEE
Confidence 3454446778999988654
No 153
>PF12475 Amdo_NSP: Amdovirus non-structural protein ; InterPro: IPR020960 This domain family is found in viruses, and is approximately 50 amino acids in length. This family contains proteins of each of the three types of Amdovirus non-structural protein [].
Probab=22.91 E-value=44 Score=21.64 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=13.7
Q ss_pred HHHHHhh--hcCCchhhHH
Q psy2686 25 ELAAYFT--HSKLQPVHQI 41 (139)
Q Consensus 25 ELaAYFT--~c~Lqp~H~~ 41 (139)
+|+.+|+ ||++|.++.-
T Consensus 25 DLa~~~sn~~c~~q~i~d~ 43 (48)
T PF12475_consen 25 DLALIFSNHHCDQQDIKDP 43 (48)
T ss_pred HHHHHHcccccchhhccCh
Confidence 8999997 7998887643
No 154
>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=22.73 E-value=74 Score=19.50 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=15.1
Q ss_pred ccccccCCCcc--ccccCCCccccCCC
Q psy2686 111 SYTPIYHGRES--EACVYCGASYLPKY 135 (139)
Q Consensus 111 s~tPIy~g~~~--v~Cp~cga~y~p~~ 135 (139)
.+..+-.|... |.||.||..+.-.-
T Consensus 28 ~~~~~~~~~~~~~~~C~~C~~~fC~~C 54 (64)
T PF01485_consen 28 YIIEKDDGCNSPIVTCPSCGTEFCFKC 54 (64)
T ss_dssp --ECS-SSTTS--CCTTSCCSEECSSS
T ss_pred ccEEecCCCCCCeeECCCCCCcCcccc
Confidence 44444455555 99999998876443
No 155
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=22.58 E-value=46 Score=20.99 Aligned_cols=15 Identities=33% Similarity=0.461 Sum_probs=12.5
Q ss_pred CCCeeeecccccccc
Q psy2686 102 HNPFQICARSYTPIY 116 (139)
Q Consensus 102 ~~~F~iC~~s~tPIy 116 (139)
...|++|+.|=.||-
T Consensus 4 pG~~V~CAVTg~~Ip 18 (42)
T PF09866_consen 4 PGSFVRCAVTGQPIP 18 (42)
T ss_pred CCCEEEEEeeCCccc
Confidence 357999999999984
No 156
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=22.10 E-value=51 Score=26.65 Aligned_cols=12 Identities=33% Similarity=0.869 Sum_probs=10.4
Q ss_pred cccCCCccccCC
Q psy2686 123 ACVYCGASYLPK 134 (139)
Q Consensus 123 ~Cp~cga~y~p~ 134 (139)
.||+||....|+
T Consensus 158 ~CPlCg~PldP~ 169 (177)
T TIGR03847 158 PCPLCGRPIDPD 169 (177)
T ss_pred CCCCCCCCCCCC
Confidence 599999998876
No 157
>PF13041 PPR_2: PPR repeat family
Probab=22.04 E-value=1.8e+02 Score=17.04 Aligned_cols=35 Identities=11% Similarity=0.167 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHH
Q psy2686 42 LTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEV 76 (139)
Q Consensus 42 LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~ 76 (139)
.+..+-|....|.+++..|-.+=+++.+.+-.|+.
T Consensus 4 ~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~ 38 (50)
T PF13041_consen 4 VTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDS 38 (50)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCH
Confidence 45677889999999999999999999998765554
No 158
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=21.84 E-value=2.1e+02 Score=20.10 Aligned_cols=76 Identities=20% Similarity=0.283 Sum_probs=51.4
Q ss_pred HHHhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhhcCCCCceeecCCCCCCeeeeccccccccCCCccccccCCCc
Q psy2686 50 LFFKLKNYKTTASFAHRLLELGPSMEVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGA 129 (139)
Q Consensus 50 ~~~K~kN~~tAa~fArRLLel~p~~~~~~qArkil~~~e~~~~da~~i~yD~~~~F~iC~~s~tPIy~g~~~v~Cp~cga 129 (139)
.........||-.+-++|-+.+|....+.-=|-+-...+..--..++.+ |...-|+++. -.......|--||.
T Consensus 16 ~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~-~~~~~Y~~~~------~~~h~h~iC~~Cg~ 88 (120)
T PF01475_consen 16 LLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG-DGESRYELST------CHHHHHFICTQCGK 88 (120)
T ss_dssp HHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET-TSEEEEEESS------SSSCEEEEETTTS-
T ss_pred HHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC-CCcceEeecC------CCcceEEEECCCCC
Confidence 3345556899999999999988888777777777777777755555555 4445566665 12356789999998
Q ss_pred ccc
Q psy2686 130 SYL 132 (139)
Q Consensus 130 ~y~ 132 (139)
...
T Consensus 89 v~~ 91 (120)
T PF01475_consen 89 VID 91 (120)
T ss_dssp EEE
T ss_pred EEE
Confidence 753
No 159
>PF12773 DZR: Double zinc ribbon
Probab=21.67 E-value=69 Score=19.35 Aligned_cols=18 Identities=28% Similarity=0.626 Sum_probs=13.2
Q ss_pred CCccccccCCCccccCCC
Q psy2686 118 GRESEACVYCGASYLPKY 135 (139)
Q Consensus 118 g~~~v~Cp~cga~y~p~~ 135 (139)
....+.||.||+...+..
T Consensus 26 ~~~~~~C~~Cg~~~~~~~ 43 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNA 43 (50)
T ss_pred cCCCCCCcCCcCCCcCCc
Confidence 456778999999866543
No 160
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=21.37 E-value=43 Score=22.16 Aligned_cols=14 Identities=29% Similarity=0.745 Sum_probs=6.8
Q ss_pred CCccccccCCCccc
Q psy2686 118 GRESEACVYCGASY 131 (139)
Q Consensus 118 g~~~v~Cp~cga~y 131 (139)
....-+||.|++..
T Consensus 21 S~~PatCP~C~a~~ 34 (54)
T PF09237_consen 21 SEQPATCPICGAVI 34 (54)
T ss_dssp TS--EE-TTT--EE
T ss_pred cCCCCCCCcchhhc
Confidence 45667999999864
No 161
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=21.36 E-value=44 Score=18.46 Aligned_cols=10 Identities=20% Similarity=0.378 Sum_probs=8.5
Q ss_pred ccccCCCccc
Q psy2686 122 EACVYCGASY 131 (139)
Q Consensus 122 v~Cp~cga~y 131 (139)
|.||.|+...
T Consensus 2 v~CPiC~~~v 11 (26)
T smart00734 2 VQCPVCFREV 11 (26)
T ss_pred CcCCCCcCcc
Confidence 7899998875
No 162
>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 PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=21.13 E-value=37 Score=22.49 Aligned_cols=13 Identities=23% Similarity=0.447 Sum_probs=6.8
Q ss_pred cccccCCCccccC
Q psy2686 121 SEACVYCGASYLP 133 (139)
Q Consensus 121 ~v~Cp~cga~y~p 133 (139)
.|+||-||.....
T Consensus 2 ~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 2 TVKCPICGKPVEW 14 (57)
T ss_dssp EEE-TTT--EEE-
T ss_pred cccCCCCCCeecc
Confidence 4788999887665
No 164
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=21.10 E-value=48 Score=19.74 Aligned_cols=14 Identities=29% Similarity=0.719 Sum_probs=8.3
Q ss_pred CCccccccCCCccc
Q psy2686 118 GRESEACVYCGASY 131 (139)
Q Consensus 118 g~~~v~Cp~cga~y 131 (139)
.-+.+.|+-||-.|
T Consensus 18 ~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 18 HYQFISCTNCGPRY 31 (35)
T ss_dssp T-TT--BTTCC-SC
T ss_pred cCcCccCCCCCCCE
Confidence 56889999999766
No 165
>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=21.10 E-value=46 Score=21.06 Aligned_cols=13 Identities=38% Similarity=0.866 Sum_probs=10.4
Q ss_pred cccCCCccccCCC
Q psy2686 123 ACVYCGASYLPKY 135 (139)
Q Consensus 123 ~Cp~cga~y~p~~ 135 (139)
+|+.||-.|.|+.
T Consensus 3 ~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 3 QCPVCGYVYDPEK 15 (47)
T ss_dssp EETTTSBEEETTT
T ss_pred CCCCCCEEEcCCc
Confidence 6888888888765
No 166
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=20.59 E-value=1.4e+02 Score=15.12 Aligned_cols=28 Identities=11% Similarity=0.233 Sum_probs=22.2
Q ss_pred HHHHHHHHHhhhcHHHHHHHHHHHHhcC
Q psy2686 44 LRTATNLFFKLKNYKTTASFAHRLLELG 71 (139)
Q Consensus 44 Lr~Am~~~~K~kN~~tAa~fArRLLel~ 71 (139)
..+-|+...+.+++..|..+-+++.+.+
T Consensus 3 y~~li~~~~~~~~~~~a~~~~~~M~~~g 30 (31)
T PF01535_consen 3 YNSLISGYCKMGQFEEALEVFDEMRERG 30 (31)
T ss_pred HHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence 4566788889999999988888887653
No 167
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.53 E-value=1.1e+02 Score=28.95 Aligned_cols=91 Identities=18% Similarity=0.186 Sum_probs=45.8
Q ss_pred HhhhcCCchhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhhcCCCCceeecCCCCCCeeee
Q psy2686 29 YFTHSKLQPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEVATQARKLLAICNANPTDEHTIDYDEHNPFQIC 108 (139)
Q Consensus 29 YFT~c~Lqp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~~~qArkil~~~e~~~~da~~i~yD~~~~F~iC 108 (139)
|+|..- +|+..-..+--++..--+...+.|...+.-=-|.-.|++ +..++|+....+....=..|+. +|++|
T Consensus 500 yYTNS~-~pv~~~i~~~eki~~e~~~~~~~~GG~i~hi~l~E~pn~---~al~~lv~~~~~~~i~Y~~inp----~~~~C 571 (625)
T PRK08579 500 IYSTSI-APYYGPLELWDRIEIEEKVQQEFTGGVMMHIFLGEEPDP---EALAKLTKRIMNTKLVYWSYTP----AITVC 571 (625)
T ss_pred ceeCce-eeCCCCCCHHHHHHhhccccccccCceEEEEEeCCCCCH---HHHHHHHHHHHhcCCceEEeCC----CCccC
Confidence 777655 366555555544444444444444443221111111443 4566777776432222223322 48888
Q ss_pred cc-ccccccCCCccccccCCCcc
Q psy2686 109 AR-SYTPIYHGRESEACVYCGAS 130 (139)
Q Consensus 109 ~~-s~tPIy~g~~~v~Cp~cga~ 130 (139)
-. .+ .+.|. ...||.||+.
T Consensus 572 ~~CG~--~~~g~-~~~CP~CGs~ 591 (625)
T PRK08579 572 NKCGR--STTGL-YTRCPRCGSE 591 (625)
T ss_pred CCCCC--ccCCC-CCcCcCCCCc
Confidence 64 33 12333 6799999974
No 168
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=20.49 E-value=2.9e+02 Score=23.56 Aligned_cols=42 Identities=17% Similarity=0.169 Sum_probs=30.4
Q ss_pred CCchhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChH
Q psy2686 34 KLQPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSME 75 (139)
Q Consensus 34 ~Lqp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~ 75 (139)
+..|.+..-..-.+-.+....|++..|...++++++.+|...
T Consensus 146 ~~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~~~ 187 (398)
T PRK10747 146 ELADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPRHP 187 (398)
T ss_pred hcCCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCH
Confidence 445555433333446677889999999999999999998643
No 169
>KOG0547|consensus
Probab=20.42 E-value=1.7e+02 Score=27.71 Aligned_cols=63 Identities=22% Similarity=0.367 Sum_probs=46.6
Q ss_pred hcCCchhhHHHHHHHHHHHHHhhhcHHHHHHHHHHHHhcCCChHH-----------HHHHHHHHHHhhcCCCCceeec
Q psy2686 32 HSKLQPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSMEV-----------ATQARKLLAICNANPTDEHTID 98 (139)
Q Consensus 32 ~c~Lqp~H~~LaLr~Am~~~~K~kN~~tAa~fArRLLel~p~~~~-----------~~qArkil~~~e~~~~da~~i~ 98 (139)
+.+.+..-...+|.+==|.+|++|+|..|-.+=..=|++.|+..+ ...-.+|++-| |-+++|+
T Consensus 106 ~~~e~~~k~A~~lK~~GN~~f~~kkY~eAIkyY~~AI~l~p~epiFYsNraAcY~~lgd~~~Vied~----TkALEl~ 179 (606)
T KOG0547|consen 106 MLKEERLKYAAALKTKGNKFFRNKKYDEAIKYYTQAIELCPDEPIFYSNRAACYESLGDWEKVIEDC----TKALELN 179 (606)
T ss_pred cChHHHHHHHHHHHhhhhhhhhcccHHHHHHHHHHHHhcCCCCchhhhhHHHHHHHHhhHHHHHHHH----HHHhhcC
Confidence 344555667788888889999999999999999999999998433 23355666665 4445543
No 170
>TIGR02710 CRISPR-associated protein, TIGR02710 family. Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Archaea), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia).
Probab=20.35 E-value=4e+02 Score=23.74 Aligned_cols=54 Identities=9% Similarity=-0.097 Sum_probs=40.3
Q ss_pred CchhhHHHHHHHHHH--HHHhhhcHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhh
Q psy2686 35 LQPVHQILTLRTATN--LFFKLKNYKTTASFAHRLLELGPSMEVATQARKLLAICN 88 (139)
Q Consensus 35 Lqp~H~~LaLr~Am~--~~~K~kN~~tAa~fArRLLel~p~~~~~~qArkil~~~e 88 (139)
++.+|.+...+...- .+|+..||..|...-..|+.-.++++....-..+...|+
T Consensus 122 ~~nP~~v~~~~e~~~~r~l~n~~dy~aA~~~~~~L~~r~l~~~~~~~~~~~~~l~~ 177 (380)
T TIGR02710 122 PSDPYNVEGNTEQGYARRAINAFDYLFAHARLETLLRRLLSAVNHTFYEAMIKLTR 177 (380)
T ss_pred cCCHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHhcccChhhhhHHHHHHHHHH
Confidence 677888888888766 899999999999988888887666665444444444443
No 171
>TIGR00618 sbcc exonuclease SbcC. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.14 E-value=46 Score=32.48 Aligned_cols=17 Identities=29% Similarity=0.692 Sum_probs=13.5
Q ss_pred CccccccCCCccccCCC
Q psy2686 119 RESEACVYCGASYLPKY 135 (139)
Q Consensus 119 ~~~v~Cp~cga~y~p~~ 135 (139)
.+-..||+||+.-||.-
T Consensus 499 ~~~~~cplcgs~~hp~~ 515 (1042)
T TIGR00618 499 LQEEPCPLCGSCIHPNP 515 (1042)
T ss_pred CCCCCCCCCCCCCCCCh
Confidence 45567999999999943
Done!