Query 033485
Match_columns 118
No_of_seqs 148 out of 331
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 02:49:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033485.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033485hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3408 U1-like Zn-finger-cont 100.0 1.8E-39 3.8E-44 238.5 6.0 105 12-117 11-117 (129)
2 COG5112 UFD2 U1-like Zn-finger 100.0 1.7E-35 3.6E-40 214.9 5.4 104 1-107 1-104 (126)
3 PF12171 zf-C2H2_jaz: Zinc-fin 99.1 2.8E-11 6.1E-16 66.7 1.6 27 57-83 1-27 (27)
4 smart00451 ZnF_U1 U1-like zinc 99.0 1.5E-10 3.2E-15 66.0 2.6 34 55-88 1-34 (35)
5 PF06220 zf-U1: U1 zinc finger 98.6 5.8E-08 1.2E-12 58.3 3.0 35 55-89 1-37 (38)
6 PF12874 zf-met: Zinc-finger o 98.5 9E-08 1.9E-12 51.0 1.8 25 58-82 1-25 (25)
7 KOG3454 U1 snRNP-specific prot 98.3 2E-07 4.3E-12 71.8 1.5 36 55-90 1-38 (165)
8 KOG0717 Molecular chaperone (D 98.2 6.3E-07 1.4E-11 78.4 1.9 35 57-91 292-326 (508)
9 KOG4727 U1-like Zn-finger prot 97.6 5.1E-05 1.1E-09 59.5 2.8 37 54-90 72-108 (193)
10 COG5188 PRP9 Splicing factor 3 97.3 7.6E-05 1.6E-09 64.3 1.0 32 57-88 238-269 (470)
11 PF00096 zf-C2H2: Zinc finger, 97.1 0.00024 5.2E-09 36.8 1.2 22 58-79 1-22 (23)
12 PF13912 zf-C2H2_6: C2H2-type 96.7 0.0011 2.4E-08 35.5 1.7 23 58-80 2-24 (27)
13 PF12756 zf-C2H2_2: C2H2 type 96.5 0.00086 1.9E-08 44.1 0.6 31 57-87 50-80 (100)
14 COG5136 U1 snRNP-specific prot 96.4 0.0012 2.6E-08 51.6 1.0 36 55-90 1-38 (188)
15 PF13894 zf-C2H2_4: C2H2-type 96.4 0.0016 3.5E-08 32.9 1.2 22 58-79 1-22 (24)
16 PLN02748 tRNA dimethylallyltra 96.4 0.0027 5.9E-08 55.5 3.2 36 56-91 417-453 (468)
17 PHA02768 hypothetical protein; 96.2 0.0026 5.7E-08 41.2 1.4 23 57-79 5-27 (55)
18 smart00355 ZnF_C2H2 zinc finge 95.9 0.0055 1.2E-07 31.0 1.6 21 58-78 1-21 (26)
19 KOG0150 Spliceosomal protein F 94.8 0.017 3.6E-07 48.9 2.0 34 55-88 8-42 (336)
20 KOG2384 Major histocompatibili 93.6 0.029 6.2E-07 45.2 0.9 41 48-89 75-115 (223)
21 PHA00616 hypothetical protein 93.3 0.033 7.1E-07 34.6 0.6 22 58-79 2-23 (44)
22 KOG2462 C2H2-type Zn-finger pr 93.1 0.052 1.1E-06 45.2 1.7 32 53-84 211-242 (279)
23 KOG2785 C2H2-type Zn-finger pr 93.0 0.043 9.3E-07 47.4 1.2 35 56-90 67-101 (390)
24 PF13913 zf-C2HC_2: zinc-finge 93.0 0.062 1.3E-06 29.2 1.4 20 58-78 3-22 (25)
25 PF07535 zf-DBF: DBF zinc fing 92.1 0.092 2E-06 33.2 1.5 26 58-86 6-31 (49)
26 KOG1994 Predicted RNA binding 91.8 0.091 2E-06 43.2 1.5 25 55-79 237-261 (268)
27 smart00586 ZnF_DBF Zinc finger 90.5 0.13 2.9E-06 32.5 1.1 25 59-86 7-31 (49)
28 KOG2837 Protein containing a U 90.0 0.077 1.7E-06 44.5 -0.4 34 57-90 25-58 (309)
29 KOG3032 Uncharacterized conser 89.0 0.4 8.6E-06 39.5 3.0 37 53-90 31-67 (264)
30 PTZ00448 hypothetical protein; 88.7 0.71 1.5E-05 39.9 4.5 49 56-104 313-362 (373)
31 PF13465 zf-H2C2_2: Zinc-finge 88.3 0.25 5.3E-06 26.7 1.0 16 54-69 11-26 (26)
32 PF13821 DUF4187: Domain of un 88.0 0.27 5.9E-06 31.5 1.2 23 57-79 27-49 (55)
33 KOG2482 Predicted C2H2-type Zn 87.7 0.21 4.7E-06 43.2 0.7 29 56-84 194-222 (423)
34 PHA00732 hypothetical protein 86.5 0.46 1E-05 32.3 1.7 22 58-79 2-23 (79)
35 PF13909 zf-H2C2_5: C2H2-type 85.9 0.41 8.8E-06 24.8 0.9 21 58-79 1-21 (24)
36 KOG2893 Zn finger protein [Gen 81.7 0.63 1.4E-05 39.0 0.8 23 59-81 12-34 (341)
37 PHA00733 hypothetical protein 81.0 0.99 2.1E-05 33.0 1.6 20 58-77 100-119 (128)
38 PHA00733 hypothetical protein 80.2 1.4 2.9E-05 32.2 2.1 25 55-79 71-95 (128)
39 KOG1074 Transcriptional repres 80.1 1.1 2.4E-05 42.6 1.9 32 49-80 871-902 (958)
40 KOG0227 Splicing factor 3a, su 79.7 1.3 2.8E-05 35.8 1.9 36 53-88 49-84 (222)
41 COG5246 PRP11 Splicing factor 79.2 1.5 3.2E-05 35.3 2.1 37 53-89 49-85 (222)
42 KOG3623 Homeobox transcription 79.2 0.82 1.8E-05 43.2 0.8 26 54-79 278-303 (1007)
43 PF12756 zf-C2H2_2: C2H2 type 79.2 0.61 1.3E-05 30.3 0.0 25 60-85 2-26 (100)
44 PF14968 CCDC84: Coiled coil p 78.6 1.4 3.1E-05 37.5 2.0 77 6-89 9-96 (336)
45 KOG2505 Ankyrin repeat protein 77.8 3.2 6.9E-05 37.7 4.0 49 56-104 65-114 (591)
46 PF05605 zf-Di19: Drought indu 77.4 1.7 3.6E-05 26.9 1.6 23 57-80 2-24 (54)
47 PF02892 zf-BED: BED zinc fing 74.9 1.9 4.1E-05 25.2 1.3 25 54-78 13-41 (45)
48 KOG1074 Transcriptional repres 73.0 1.3 2.8E-05 42.1 0.4 27 53-79 629-655 (958)
49 KOG2462 C2H2-type Zn-finger pr 71.9 2.1 4.5E-05 35.8 1.3 26 55-80 159-184 (279)
50 KOG3993 Transcription factor ( 71.2 2 4.2E-05 38.3 1.0 29 58-86 296-324 (500)
51 KOG2785 C2H2-type Zn-finger pr 70.8 4.2 9.2E-05 35.4 3.0 45 55-99 1-46 (390)
52 PF09237 GAGA: GAGA factor; I 69.4 3.3 7.1E-05 26.9 1.5 22 57-78 24-45 (54)
53 KOG4167 Predicted DNA-binding 68.3 2.2 4.7E-05 40.3 0.7 30 55-84 790-819 (907)
54 PHA00732 hypothetical protein 67.4 2.3 5E-05 28.8 0.6 21 58-81 28-48 (79)
55 KOG3576 Ovo and related transc 66.8 2.1 4.5E-05 35.2 0.3 37 52-88 168-207 (267)
56 smart00734 ZnF_Rad18 Rad18-lik 65.6 4.6 0.0001 22.0 1.5 19 59-78 3-21 (26)
57 smart00614 ZnF_BED BED zinc fi 60.2 4.4 9.5E-05 24.6 0.8 26 54-79 15-45 (50)
58 PF04988 AKAP95: A-kinase anch 57.1 7 0.00015 30.5 1.6 33 58-90 92-125 (165)
59 PF14968 CCDC84: Coiled coil p 56.6 4.8 0.0001 34.3 0.7 29 59-90 1-29 (336)
60 KOG3623 Homeobox transcription 55.4 4.2 9.1E-05 38.7 0.2 30 54-83 306-335 (1007)
61 PF11781 RRN7: RNA polymerase 55.3 4.8 0.0001 23.6 0.4 14 52-65 20-33 (36)
62 KOG3576 Ovo and related transc 54.9 5.1 0.00011 32.9 0.6 23 58-80 146-168 (267)
63 PRK09335 30S ribosomal protein 54.5 4.2 9.1E-05 29.1 0.0 14 55-68 65-78 (95)
64 PF02748 PyrI_C: Aspartate car 53.0 5.5 0.00012 25.2 0.4 19 54-72 32-50 (52)
65 PF08790 zf-LYAR: LYAR-type C2 53.0 2.8 6E-05 23.8 -0.9 19 58-77 1-19 (28)
66 PTZ00172 40S ribosomal protein 50.1 5.6 0.00012 29.1 0.1 15 55-69 69-83 (108)
67 PF12855 Ecl1: Life-span regul 49.5 4.3 9.3E-05 24.9 -0.5 11 58-68 7-17 (43)
68 PF03194 LUC7: LUC7 N_terminus 49.4 7.9 0.00017 31.3 0.9 29 56-84 189-220 (254)
69 KOG1146 Homeobox protein [Gene 49.0 18 0.00039 36.2 3.3 48 56-104 517-564 (1406)
70 PLN00186 ribosomal protein S26 47.2 6.7 0.00014 28.7 0.1 13 57-69 71-83 (109)
71 PF11931 DUF3449: Domain of un 47.0 6.4 0.00014 31.3 0.0 39 52-90 95-135 (196)
72 KOG3993 Transcription factor ( 46.2 8 0.00017 34.6 0.5 34 54-87 353-386 (500)
73 COG5067 DBF4 Protein kinase es 46.0 8.1 0.00017 34.2 0.5 24 59-85 424-447 (468)
74 PF12013 DUF3505: Protein of u 45.7 19 0.00041 24.8 2.3 32 49-80 72-107 (109)
75 KOG4722 Zn-finger protein [Gen 45.3 14 0.00029 33.5 1.7 37 54-90 490-526 (672)
76 PF13119 DUF3973: Domain of un 44.0 6.8 0.00015 24.1 -0.2 9 57-65 1-9 (41)
77 COG5189 SFP1 Putative transcri 43.4 5.7 0.00012 34.5 -0.8 23 56-78 397-419 (423)
78 PF04988 AKAP95: A-kinase anch 43.2 25 0.00054 27.4 2.7 32 58-89 1-32 (165)
79 COG4049 Uncharacterized protei 43.0 12 0.00025 24.9 0.8 31 52-82 12-43 (65)
80 TIGR03830 CxxCG_CxxCG_HTH puta 42.9 38 0.00082 23.2 3.4 52 56-107 30-91 (127)
81 KOG1146 Homeobox protein [Gene 42.3 9.6 0.00021 38.0 0.4 33 55-87 1326-1358(1406)
82 PLN03238 probable histone acet 40.1 18 0.00038 30.5 1.6 32 47-78 37-69 (290)
83 PF07295 DUF1451: Protein of u 39.6 11 0.00024 28.4 0.3 19 49-67 104-122 (146)
84 PF03966 Trm112p: Trm112p-like 39.5 11 0.00024 24.3 0.2 14 55-68 51-64 (68)
85 PF13462 Thioredoxin_4: Thiore 38.9 8.4 0.00018 26.9 -0.4 22 56-77 20-41 (162)
86 KOG0796 Spliceosome subunit [R 38.1 13 0.00029 31.6 0.6 37 48-84 172-216 (319)
87 PF04959 ARS2: Arsenite-resist 37.8 18 0.00038 29.0 1.2 32 56-88 76-107 (214)
88 COG5200 LUC7 U1 snRNP componen 37.0 15 0.00032 30.3 0.7 36 51-86 175-217 (258)
89 KOG3608 Zn finger proteins [Ge 34.9 17 0.00037 32.1 0.7 25 56-80 351-375 (467)
90 PF04423 Rad50_zn_hook: Rad50 34.8 16 0.00035 22.4 0.5 13 59-71 22-34 (54)
91 PLN03239 histone acetyltransfe 34.3 22 0.00047 30.7 1.3 22 57-78 106-127 (351)
92 PLN00104 MYST -like histone ac 34.1 21 0.00046 31.7 1.2 22 57-78 198-219 (450)
93 KOG3608 Zn finger proteins [Ge 33.3 23 0.00049 31.3 1.2 23 56-78 291-313 (467)
94 smart00834 CxxC_CXXC_SSSS Puta 32.8 16 0.00034 20.7 0.1 13 57-69 5-17 (41)
95 KOG3456 NADH:ubiquinone oxidor 32.5 15 0.00033 27.2 0.0 20 48-69 97-116 (120)
96 PF05443 ROS_MUCR: ROS/MUCR tr 32.3 24 0.00052 26.3 1.1 20 57-79 72-91 (132)
97 COG5034 TNG2 Chromatin remodel 31.5 18 0.00039 30.2 0.4 15 51-65 255-269 (271)
98 PF07895 DUF1673: Protein of u 31.4 19 0.00041 28.2 0.4 8 1-8 11-18 (205)
99 COG0492 TrxB Thioredoxin reduc 31.2 20 0.00043 29.6 0.6 19 51-69 125-143 (305)
100 PTZ00064 histone acetyltransfe 31.0 27 0.00058 31.8 1.4 22 57-78 280-301 (552)
101 PF05766 NinG: Bacteriophage L 30.7 85 0.0019 24.8 4.0 45 59-103 125-173 (189)
102 PF08209 Sgf11: Sgf11 (transcr 30.1 28 0.0006 20.2 0.9 20 57-77 4-23 (33)
103 COG5236 Uncharacterized conser 28.9 31 0.00068 30.5 1.4 25 57-81 220-244 (493)
104 PF09538 FYDLN_acid: Protein o 28.8 26 0.00057 25.1 0.8 13 57-69 9-21 (108)
105 COG4957 Predicted transcriptio 28.6 28 0.00061 26.7 0.9 21 57-80 76-96 (148)
106 PF07191 zinc-ribbons_6: zinc- 28.5 19 0.00042 24.3 0.0 14 56-69 16-29 (70)
107 PF01283 Ribosomal_S26e: Ribos 28.0 14 0.00031 27.0 -0.7 17 52-68 64-82 (113)
108 PRK00893 aspartate carbamoyltr 27.3 30 0.00066 26.5 0.9 19 53-71 130-148 (152)
109 PF04780 DUF629: Protein of un 27.1 34 0.00074 30.5 1.3 27 58-85 58-84 (466)
110 PF09723 Zn-ribbon_8: Zinc rib 26.7 23 0.00049 21.0 0.1 14 57-70 5-18 (42)
111 smart00400 ZnF_CHCC zinc finge 26.5 1E+02 0.0022 18.7 3.0 35 54-89 20-54 (55)
112 PF06677 Auto_anti-p27: Sjogre 25.5 31 0.00066 20.8 0.5 10 55-64 32-41 (41)
113 PF05495 zf-CHY: CHY zinc fing 25.3 21 0.00046 23.4 -0.2 21 46-67 51-71 (71)
114 TIGR02605 CxxC_CxxC_SSSS putat 24.9 26 0.00057 20.9 0.2 14 57-70 5-18 (52)
115 cd00924 Cyt_c_Oxidase_Vb Cytoc 24.3 27 0.00058 24.7 0.1 14 56-69 78-91 (97)
116 KOG1280 Uncharacterized conser 24.3 43 0.00093 29.2 1.4 24 57-80 79-102 (381)
117 PF07492 Trehalase_Ca-bi: Neut 23.6 18 0.00039 20.9 -0.7 18 101-118 11-28 (30)
118 COG1781 PyrI Aspartate carbamo 23.5 31 0.00068 26.6 0.4 18 56-73 134-151 (153)
119 TIGR03831 YgiT_finger YgiT-typ 22.6 35 0.00077 19.4 0.4 17 54-70 29-45 (46)
120 PF08015 Pheromone: Fungal mat 22.6 53 0.0011 21.2 1.3 19 44-62 49-69 (69)
121 KOG1247 Methionyl-tRNA synthet 22.5 31 0.00067 31.2 0.2 16 55-70 134-149 (567)
122 PF11287 DUF3088: Protein of u 22.5 43 0.00094 24.5 0.9 9 57-65 21-29 (112)
123 cd02669 Peptidase_C19M A subfa 22.2 69 0.0015 27.4 2.2 29 55-83 26-57 (440)
124 PF10276 zf-CHCC: Zinc-finger 21.7 31 0.00068 20.8 0.0 13 56-68 28-40 (40)
125 KOG3792 Transcription factor N 21.1 41 0.0009 31.9 0.7 31 57-87 359-389 (816)
126 KOG2186 Cell growth-regulating 20.5 45 0.00098 28.0 0.7 21 56-77 28-48 (276)
127 PF05477 SURF2: Surfeit locus 20.5 1.1E+02 0.0023 25.2 2.9 37 54-90 76-113 (244)
128 PF08882 Acetone_carb_G: Aceto 20.2 44 0.00095 24.6 0.5 40 26-70 48-87 (112)
129 KOG2747 Histone acetyltransfer 20.2 43 0.00093 29.4 0.6 32 47-78 147-179 (396)
130 COG5027 SAS2 Histone acetyltra 20.1 43 0.00093 29.3 0.6 22 57-78 158-179 (395)
No 1
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=100.00 E-value=1.8e-39 Score=238.47 Aligned_cols=105 Identities=35% Similarity=0.590 Sum_probs=90.8
Q ss_pred cchhhhhhhhhcccCC-CchHHHHhhccCcCCCCCCCCCCCCCCCCcccccccccccCChHHHHHHhcchhhHHHHHHhh
Q 033485 12 RRYSHKTARLAKFLRK-GDDAVYDELQRSDSAKNPLPFDEDLPGMGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 12 ~~~~~kt~rrt~~~~k-D~DqI~~dl~~~~~~~~~~~~dedlpg~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~ 90 (118)
++.......|++-+++ |||||++||........++++|+||||+|||||++|+|||+++++|+.|++||.||||||+|+
T Consensus 11 ~~~~~hr~~r~r~~~r~dLDqi~~dl~~~~~kll~~~~D~dlPG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~ 90 (129)
T KOG3408|consen 11 HRSNRHRINRTRGRARKDLDQIDEDLETQKGKLLNQEIDPDLPGGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELR 90 (129)
T ss_pred ccchhHHHHhhhccCcccccccccccccccchhhcCcCCCCCCCCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcc
Confidence 3333344456666555 999999999765544568999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHHhcCCC-CCCCCCCCCC
Q 033485 91 GPKPHTQLDADLAAGMG-MPDNGPKLMP 117 (118)
Q Consensus 91 ~~~pytq~eAe~aag~g-~~dng~~l~~ 117 (118)
++||||+|||+|+||| +|++++++++
T Consensus 91 -~~PySQeeAe~A~G~g~vpp~~~~~~s 117 (129)
T KOG3408|consen 91 -EVPYSQEEAEAAAGMGFVPPKKLKVES 117 (129)
T ss_pred -cCCccHHHHHHhccCCcCCCcchhhhh
Confidence 6799999999999999 8899988765
No 2
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=100.00 E-value=1.7e-35 Score=214.91 Aligned_cols=104 Identities=38% Similarity=0.692 Sum_probs=88.5
Q ss_pred CCCCCcccccccchhhhhhhhhcccCCCchHHHHhhccCcCCCCCCCCCCCCCCCCcccccccccccCChHHHHHHhcch
Q 033485 1 MGKCPNRKVKKRRYSHKTARLAKFLRKGDDAVYDELQRSDSAKNPLPFDEDLPGMGQYYCLHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 1 ~~~~~~~~~k~~~~~~kt~rrt~~~~kD~DqI~~dl~~~~~~~~~~~~dedlpg~GqfYC~~Cdr~F~~~~~l~~H~ksK 80 (118)
||+- ..|+|+++.+.=.-.|||.+++|||||++||. ..+..+.+|+|++|||+|||||++|+|||+++.+|..|.+||
T Consensus 1 Mgr~-~~Krk~~~~~~~~i~rtr~~grDlDqi~nDls-~~Es~~Klp~Dp~lPGlGqhYCieCaryf~t~~aL~~Hkkgk 78 (126)
T COG5112 1 MGRS-DTKRKKRRSNRLRIKRTRLFGRDLDQIKNDLS-TKESQKKLPYDPELPGLGQHYCIECARYFITEKALMEHKKGK 78 (126)
T ss_pred CCch-hHhHhhhccchhHHHHHHHhcccHHHHHHhcc-hhhhhccCCCCCCCCCCceeeeehhHHHHHHHHHHHHHhccc
Confidence 4443 34666777666555678888889999999994 344456789999999999999999999999999999999999
Q ss_pred hhHHHHHHhhCCCCCCHHHHHHhcCCC
Q 033485 81 RHKKRVKEMMGPKPHTQLDADLAAGMG 107 (118)
Q Consensus 81 ~HKrrvK~l~~~~pytq~eAe~aag~g 107 (118)
+|+||+|+|+ +.||||++||||+|+.
T Consensus 79 vHkRR~KelR-evpytQe~aeaAvg~~ 104 (126)
T COG5112 79 VHKRRAKELR-EVPYTQEDAEAAVGLT 104 (126)
T ss_pred hhHHHHHHHh-cCcchhHHHHHHhccc
Confidence 9999999999 5699999999999954
No 3
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=99.11 E-value=2.8e-11 Score=66.67 Aligned_cols=27 Identities=48% Similarity=1.077 Sum_probs=25.5
Q ss_pred cccccccccccCChHHHHHHhcchhhH
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTKRHK 83 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK~HK 83 (118)
||||++|+++|.++.+|..|++|+.||
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence 699999999999999999999999996
No 4
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=99.04 E-value=1.5e-10 Score=65.96 Aligned_cols=34 Identities=41% Similarity=0.796 Sum_probs=31.6
Q ss_pred CCcccccccccccCChHHHHHHhcchhhHHHHHH
Q 033485 55 MGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKE 88 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~ 88 (118)
.|.|||++|+++|.++.++.+|++|+.|+++++.
T Consensus 1 ~~~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 1 TGGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CcCeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 3689999999999999999999999999999975
No 5
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=98.56 E-value=5.8e-08 Score=58.25 Aligned_cols=35 Identities=40% Similarity=0.841 Sum_probs=21.7
Q ss_pred CCcccccccccccCC--hHHHHHHhcchhhHHHHHHh
Q 033485 55 MGQYYCLHCDRYFAH--ESVRDEHFKTKRHKKRVKEM 89 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~--~~~l~~H~ksK~HKrrvK~l 89 (118)
|..|||.+|++||.+ .++.+.|..|..|+.+|++.
T Consensus 1 m~ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~ 37 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY 37 (38)
T ss_dssp --S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred CcCeecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence 457999999999954 36889999999999999864
No 6
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.46 E-value=9e-08 Score=51.03 Aligned_cols=25 Identities=32% Similarity=0.898 Sum_probs=24.3
Q ss_pred ccccccccccCChHHHHHHhcchhh
Q 033485 58 YYCLHCDRYFAHESVRDEHFKTKRH 82 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ksK~H 82 (118)
|||..|++.|.+..+|..|++|+.|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 7999999999999999999999998
No 7
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=98.32 E-value=2e-07 Score=71.84 Aligned_cols=36 Identities=44% Similarity=0.909 Sum_probs=32.6
Q ss_pred CCcccccccccccCCh--HHHHHHhcchhhHHHHHHhh
Q 033485 55 MGQYYCLHCDRYFAHE--SVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~--~~l~~H~ksK~HKrrvK~l~ 90 (118)
+..|||+|||.|..++ ++.++|+.|++|+++|+.+.
T Consensus 1 MpRYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~YY 38 (165)
T KOG3454|consen 1 MPRYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDYY 38 (165)
T ss_pred CCcchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHHH
Confidence 3579999999999875 99999999999999999984
No 8
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=6.3e-07 Score=78.43 Aligned_cols=35 Identities=31% Similarity=0.644 Sum_probs=33.2
Q ss_pred cccccccccccCChHHHHHHhcchhhHHHHHHhhC
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEMMG 91 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~~ 91 (118)
++||++|++.|.++.+|..|..||+|+++|.+|+.
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrq 326 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQ 326 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHHHHHHHH
Confidence 49999999999999999999999999999999973
No 9
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=97.57 E-value=5.1e-05 Score=59.54 Aligned_cols=37 Identities=27% Similarity=0.485 Sum_probs=33.6
Q ss_pred CCCcccccccccccCChHHHHHHhcchhhHHHHHHhh
Q 033485 54 GMGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~ 90 (118)
..|.|||.+||=-|.+.-+|..|+++|+|.+++..+.
T Consensus 72 q~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgmsm 108 (193)
T KOG4727|consen 72 QKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMSM 108 (193)
T ss_pred ccCceeeeecceeehhhHHHHHHhccHHHHHHHhhhh
Confidence 4578999999999999999999999999999887663
No 10
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=97.31 E-value=7.6e-05 Score=64.29 Aligned_cols=32 Identities=34% Similarity=0.678 Sum_probs=29.4
Q ss_pred cccccccccccCChHHHHHHhcchhhHHHHHH
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTKRHKKRVKE 88 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~ 88 (118)
.+||+.|+|||...++|..|+.||.|.+.++.
T Consensus 238 ~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~ 269 (470)
T COG5188 238 KVYCVKCGREFSRSKVFEYHLEGKRHCKEGQG 269 (470)
T ss_pred ceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhh
Confidence 68999999999999999999999999996544
No 11
>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=97.11 E-value=0.00024 Score=36.83 Aligned_cols=22 Identities=27% Similarity=0.652 Sum_probs=20.4
Q ss_pred ccccccccccCChHHHHHHhcc
Q 033485 58 YYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ks 79 (118)
|-|..|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 6799999999999999999875
No 12
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.68 E-value=0.0011 Score=35.49 Aligned_cols=23 Identities=26% Similarity=0.561 Sum_probs=21.0
Q ss_pred ccccccccccCChHHHHHHhcch
Q 033485 58 YYCLHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ksK 80 (118)
|.|..|++.|.+..+|..|.+..
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 78999999999999999999653
No 13
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.51 E-value=0.00086 Score=44.07 Aligned_cols=31 Identities=32% Similarity=0.697 Sum_probs=26.5
Q ss_pred cccccccccccCChHHHHHHhcchhhHHHHH
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTKRHKKRVK 87 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK 87 (118)
.+.|..|++.|.+...|..|++++.|.++..
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 6999999999999999999999999988653
No 14
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=96.43 E-value=0.0012 Score=51.61 Aligned_cols=36 Identities=31% Similarity=0.647 Sum_probs=32.5
Q ss_pred CCcccccccccccCCh--HHHHHHhcchhhHHHHHHhh
Q 033485 55 MGQYYCLHCDRYFAHE--SVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~--~~l~~H~ksK~HKrrvK~l~ 90 (118)
|..|||++|.+|..++ ++.+.|.-|+.|.+.++.+.
T Consensus 1 MpRY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~dYY 38 (188)
T COG5136 1 MPRYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDYY 38 (188)
T ss_pred CcchHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHHHH
Confidence 4579999999999985 89999999999999998874
No 15
>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=96.42 E-value=0.0016 Score=32.90 Aligned_cols=22 Identities=27% Similarity=0.644 Sum_probs=18.3
Q ss_pred ccccccccccCChHHHHHHhcc
Q 033485 58 YYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ks 79 (118)
|-|..|++.|.+...|..|+.+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 6799999999999999999864
No 16
>PLN02748 tRNA dimethylallyltransferase
Probab=96.40 E-value=0.0027 Score=55.53 Aligned_cols=36 Identities=25% Similarity=0.508 Sum_probs=32.7
Q ss_pred Cccccccccc-ccCChHHHHHHhcchhhHHHHHHhhC
Q 033485 56 GQYYCLHCDR-YFAHESVRDEHFKTKRHKKRVKEMMG 91 (118)
Q Consensus 56 GqfYC~~Cdr-~F~~~~~l~~H~ksK~HKrrvK~l~~ 91 (118)
-+|+|..|++ -|..+..-..|++|+.|+++++.++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 4678999998 89999999999999999999998853
No 17
>PHA02768 hypothetical protein; Provisional
Probab=96.15 E-value=0.0026 Score=41.19 Aligned_cols=23 Identities=17% Similarity=0.465 Sum_probs=21.8
Q ss_pred cccccccccccCChHHHHHHhcc
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ks 79 (118)
.|.|..|++.|...++|..|+++
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~ 27 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK 27 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh
Confidence 58999999999999999999988
No 18
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.90 E-value=0.0055 Score=30.97 Aligned_cols=21 Identities=33% Similarity=0.808 Sum_probs=19.6
Q ss_pred ccccccccccCChHHHHHHhc
Q 033485 58 YYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~k 78 (118)
|.|..|++.|.+...|..|++
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 579999999999999999987
No 19
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=94.84 E-value=0.017 Score=48.95 Aligned_cols=34 Identities=24% Similarity=0.411 Sum_probs=30.0
Q ss_pred CCcccccccccccCC-hHHHHHHhcchhhHHHHHH
Q 033485 55 MGQYYCLHCDRYFAH-ESVRDEHFKTKRHKKRVKE 88 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~-~~~l~~H~ksK~HKrrvK~ 88 (118)
.|.+||.+|-.||.+ ..+...|.+||.|+-+|..
T Consensus 8 ~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K 42 (336)
T KOG0150|consen 8 QPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAK 42 (336)
T ss_pred ccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence 578999999999998 5899999999999987654
No 20
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=93.57 E-value=0.029 Score=45.19 Aligned_cols=41 Identities=20% Similarity=0.466 Sum_probs=30.7
Q ss_pred CCCCCCCCCcccccccccccCChHHHHHHhcchhhHHHHHHh
Q 033485 48 FDEDLPGMGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEM 89 (118)
Q Consensus 48 ~dedlpg~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l 89 (118)
.++-.++...|||+.|+.||.+. .--.|++|-.|.-.++.+
T Consensus 75 p~nss~~e~lfyCE~Cd~~ip~~-~~snH~tSttHllsl~~~ 115 (223)
T KOG2384|consen 75 PMNSSRDEALFYCEVCDIYIPNS-KKSNHFTSTTHLLSLQHI 115 (223)
T ss_pred cccCCCCCccchhhhhhhhccCC-CCccchhhHHHHhhhccC
Confidence 34456677789999999999863 335688888887777665
No 21
>PHA00616 hypothetical protein
Probab=93.30 E-value=0.033 Score=34.63 Aligned_cols=22 Identities=32% Similarity=0.662 Sum_probs=20.2
Q ss_pred ccccccccccCChHHHHHHhcc
Q 033485 58 YYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ks 79 (118)
|-|..|++-|...+.|..|+++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~ 23 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLS 23 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHH
Confidence 6799999999999999999954
No 22
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=93.09 E-value=0.052 Score=45.16 Aligned_cols=32 Identities=31% Similarity=0.579 Sum_probs=27.4
Q ss_pred CCCCcccccccccccCChHHHHHHhcchhhHH
Q 033485 53 PGMGQYYCLHCDRYFAHESVRDEHFKTKRHKK 84 (118)
Q Consensus 53 pg~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKr 84 (118)
.|...|-|.+|+|-|.+.++|..|+.|--+-+
T Consensus 211 TGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 211 TGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred cCCCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 57778999999999999999999998765544
No 23
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=93.04 E-value=0.043 Score=47.44 Aligned_cols=35 Identities=26% Similarity=0.629 Sum_probs=32.0
Q ss_pred CcccccccccccCChHHHHHHhcchhhHHHHHHhh
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~ 90 (118)
--+||..|+|.|.+..+...|++||.|+.++....
T Consensus 67 ~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~ 101 (390)
T KOG2785|consen 67 SVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQ 101 (390)
T ss_pred cceehHHhhccccChhhHHHHHHHhhcchhhhhhh
Confidence 36899999999999999999999999999988754
No 24
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.98 E-value=0.062 Score=29.19 Aligned_cols=20 Identities=30% Similarity=0.504 Sum_probs=17.2
Q ss_pred ccccccccccCChHHHHHHhc
Q 033485 58 YYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~k 78 (118)
.-|..|+|.| ...+|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3699999999 6889999975
No 25
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=92.09 E-value=0.092 Score=33.16 Aligned_cols=26 Identities=27% Similarity=0.677 Sum_probs=23.1
Q ss_pred ccccccccccCChHHHHHHhcchhhHHHH
Q 033485 58 YYCLHCDRYFAHESVRDEHFKTKRHKKRV 86 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ksK~HKrrv 86 (118)
-||.-|-..|.+ |..|+.|..|++=.
T Consensus 6 GYCE~C~~ky~~---l~~Hi~s~~Hr~FA 31 (49)
T PF07535_consen 6 GYCENCRVKYDD---LEEHIQSEKHRKFA 31 (49)
T ss_pred ccCccccchhhh---HHHHhCCHHHHHHH
Confidence 399999999984 99999999998765
No 26
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=91.77 E-value=0.091 Score=43.18 Aligned_cols=25 Identities=28% Similarity=0.576 Sum_probs=22.7
Q ss_pred CCcccccccccccCChHHHHHHhcc
Q 033485 55 MGQYYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~~~l~~H~ks 79 (118)
.+.|||.+|+--|.+...|-.|.-|
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehCPG 261 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHCPG 261 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhCCC
Confidence 3689999999999999999999865
No 27
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=90.53 E-value=0.13 Score=32.54 Aligned_cols=25 Identities=20% Similarity=0.655 Sum_probs=22.3
Q ss_pred cccccccccCChHHHHHHhcchhhHHHH
Q 033485 59 YCLHCDRYFAHESVRDEHFKTKRHKKRV 86 (118)
Q Consensus 59 YC~~Cdr~F~~~~~l~~H~ksK~HKrrv 86 (118)
||.-|--.|. .|..|+.|..|++=.
T Consensus 7 YCE~Cr~kfd---~l~~Hi~s~~Hr~FA 31 (49)
T smart00586 7 YCENCREKYD---DLETHLLSEKHRRFA 31 (49)
T ss_pred ccccHhHHHh---hHHHHhccHHHHHHH
Confidence 9999999998 688999999998744
No 28
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=90.04 E-value=0.077 Score=44.47 Aligned_cols=34 Identities=18% Similarity=0.435 Sum_probs=31.7
Q ss_pred cccccccccccCChHHHHHHhcchhhHHHHHHhh
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~ 90 (118)
.|||..|-|.|.+++.|+.|..|--|.|.+-...
T Consensus 25 RwyCqmCQkQcrDeNGFkCH~~SeSHqRql~~~~ 58 (309)
T KOG2837|consen 25 RWYCQMCQKQCRDENGFKCHTMSESHQRQLLLFA 58 (309)
T ss_pred HHHHHHHHHHhccccccccccCCHHHHHHHHHHH
Confidence 5899999999999999999999999999887764
No 29
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.04 E-value=0.4 Score=39.52 Aligned_cols=37 Identities=24% Similarity=0.497 Sum_probs=34.2
Q ss_pred CCCCcccccccccccCChHHHHHHhcchhhHHHHHHhh
Q 033485 53 PGMGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 53 pg~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~ 90 (118)
-..|+.-|..|+--.. ++.-..|..||+|+-.|..|+
T Consensus 31 n~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lK 67 (264)
T KOG3032|consen 31 NESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLK 67 (264)
T ss_pred CCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHH
Confidence 3479999999999999 999999999999999999997
No 30
>PTZ00448 hypothetical protein; Provisional
Probab=88.74 E-value=0.71 Score=39.92 Aligned_cols=49 Identities=12% Similarity=0.221 Sum_probs=40.1
Q ss_pred CcccccccccccCChHHHHHHhcchhhHHHHHHh-hCCCCCCHHHHHHhc
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEM-MGPKPHTQLDADLAA 104 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l-~~~~pytq~eAe~aa 104 (118)
+.|-|..|+-.|.+......|++|=-|+=+||.- .+-.|-|.+|=+...
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~gLppvse~eF~~~i 362 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNARKMEPISEEEFLELQ 362 (373)
T ss_pred CCccccccccccCCHHHHHHHhhhhHHHHHHHHHhcCCCCCCHHHHHHHH
Confidence 3688999999999999999999999999888874 445578877765443
No 31
>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=88.35 E-value=0.25 Score=26.67 Aligned_cols=16 Identities=31% Similarity=0.785 Sum_probs=13.1
Q ss_pred CCCcccccccccccCC
Q 033485 54 GMGQYYCLHCDRYFAH 69 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~ 69 (118)
|...|-|..|++.|.+
T Consensus 11 ~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 11 GEKPYKCPYCGKSFSN 26 (26)
T ss_dssp SSSSEEESSSSEEESS
T ss_pred CCCCCCCCCCcCeeCc
Confidence 4456999999999974
No 32
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=87.97 E-value=0.27 Score=31.46 Aligned_cols=23 Identities=17% Similarity=0.512 Sum_probs=20.2
Q ss_pred cccccccccccCChHHHHHHhcc
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ks 79 (118)
-+||..|+-.|.+...|..|.-|
T Consensus 27 ~~YC~~Cg~~Y~d~~dL~~~CPG 49 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEEDLERNCPG 49 (55)
T ss_pred CceeeeeCCccCCHHHHHhCCCC
Confidence 57999999999999999887654
No 33
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=87.74 E-value=0.21 Score=43.23 Aligned_cols=29 Identities=31% Similarity=0.792 Sum_probs=27.2
Q ss_pred CcccccccccccCChHHHHHHhcchhhHH
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFKTKRHKK 84 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~ksK~HKr 84 (118)
..+.|.+|-+-|.+...|+.|++-|.|+|
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhccCcc
Confidence 35799999999999999999999999987
No 34
>PHA00732 hypothetical protein
Probab=86.54 E-value=0.46 Score=32.28 Aligned_cols=22 Identities=14% Similarity=0.226 Sum_probs=20.0
Q ss_pred ccccccccccCChHHHHHHhcc
Q 033485 58 YYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ks 79 (118)
|-|..|++.|.+..+|..|.+.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhc
Confidence 6799999999999999999863
No 35
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=85.90 E-value=0.41 Score=24.80 Aligned_cols=21 Identities=38% Similarity=0.781 Sum_probs=15.1
Q ss_pred ccccccccccCChHHHHHHhcc
Q 033485 58 YYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ks 79 (118)
|-|..|+ |..+.+.|..|++.
T Consensus 1 y~C~~C~-y~t~~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCS-YSTSKSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS--EESHHHHHHHHHH
T ss_pred CCCCCCC-CcCCHHHHHHHHHh
Confidence 6799999 55558999999864
No 36
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=81.73 E-value=0.63 Score=38.98 Aligned_cols=23 Identities=35% Similarity=0.710 Sum_probs=21.5
Q ss_pred cccccccccCChHHHHHHhcchh
Q 033485 59 YCLHCDRYFAHESVRDEHFKTKR 81 (118)
Q Consensus 59 YC~~Cdr~F~~~~~l~~H~ksK~ 81 (118)
.|-||+|-|.++..|.+|++-|.
T Consensus 12 wcwycnrefddekiliqhqkakh 34 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAKH 34 (341)
T ss_pred eeeecccccchhhhhhhhhhhcc
Confidence 89999999999999999998874
No 37
>PHA00733 hypothetical protein
Probab=81.02 E-value=0.99 Score=32.95 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=10.4
Q ss_pred ccccccccccCChHHHHHHh
Q 033485 58 YYCLHCDRYFAHESVRDEHF 77 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ 77 (118)
|-|..|++.|.....|..|.
T Consensus 100 ~~C~~CgK~F~~~~sL~~H~ 119 (128)
T PHA00733 100 KVCPVCGKEFRNTDSTLDHV 119 (128)
T ss_pred ccCCCCCCccCCHHHHHHHH
Confidence 45555555555555555554
No 38
>PHA00733 hypothetical protein
Probab=80.18 E-value=1.4 Score=32.23 Aligned_cols=25 Identities=20% Similarity=0.433 Sum_probs=22.4
Q ss_pred CCcccccccccccCChHHHHHHhcc
Q 033485 55 MGQYYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~~~l~~H~ks 79 (118)
...|-|..|++.|.+...|..|.+.
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~ 95 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRY 95 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhc
Confidence 4569999999999999999999874
No 39
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=80.07 E-value=1.1 Score=42.61 Aligned_cols=32 Identities=19% Similarity=0.355 Sum_probs=26.5
Q ss_pred CCCCCCCCcccccccccccCChHHHHHHhcch
Q 033485 49 DEDLPGMGQYYCLHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 49 dedlpg~GqfYC~~Cdr~F~~~~~l~~H~ksK 80 (118)
-.+.|-...+||..|++.|.+.++|+.|.++-
T Consensus 871 ~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTH 902 (958)
T KOG1074|consen 871 GRPGPVNNAHVCNVCGKQFSSSAALEIHMRTH 902 (958)
T ss_pred CCCCcccchhhhccchhcccchHHHHHhhhcC
Confidence 34455556799999999999999999999874
No 40
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=79.70 E-value=1.3 Score=35.76 Aligned_cols=36 Identities=22% Similarity=0.430 Sum_probs=32.0
Q ss_pred CCCCcccccccccccCChHHHHHHhcchhhHHHHHH
Q 033485 53 PGMGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKE 88 (118)
Q Consensus 53 pg~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~ 88 (118)
.-.|.|-|..|.---.++.++..|..||+|+-+|..
T Consensus 49 Nh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlar 84 (222)
T KOG0227|consen 49 NHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLAR 84 (222)
T ss_pred ccCcceeehhhhhhhcchhhhhhhhccchhhHHHHH
Confidence 347899999999999999999999999999986643
No 41
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=79.21 E-value=1.5 Score=35.27 Aligned_cols=37 Identities=27% Similarity=0.439 Sum_probs=32.7
Q ss_pred CCCCcccccccccccCChHHHHHHhcchhhHHHHHHh
Q 033485 53 PGMGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEM 89 (118)
Q Consensus 53 pg~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l 89 (118)
.-.|.|-|..|.-.-.++.++..|.-||+|+-++..-
T Consensus 49 nh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rr 85 (222)
T COG5246 49 NHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRR 85 (222)
T ss_pred cCCCcEEeeeeccccccHHHHHHhhccchhhhhHHHH
Confidence 3468999999999999999999999999999877544
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=79.20 E-value=0.82 Score=43.17 Aligned_cols=26 Identities=19% Similarity=0.540 Sum_probs=22.1
Q ss_pred CCCcccccccccccCChHHHHHHhcc
Q 033485 54 GMGQYYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~~~l~~H~ks 79 (118)
++.+|-|.+|+|-|.-.++|+.|++-
T Consensus 278 ~lRKFKCtECgKAFKfKHHLKEHlRI 303 (1007)
T KOG3623|consen 278 LLRKFKCTECGKAFKFKHHLKEHLRI 303 (1007)
T ss_pred hhccccccccchhhhhHHHHHhhhee
Confidence 45689999999999999999988863
No 43
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=79.20 E-value=0.61 Score=30.29 Aligned_cols=25 Identities=36% Similarity=0.630 Sum_probs=0.0
Q ss_pred ccccccccCChHHHHHHhcchhhHHH
Q 033485 60 CLHCDRYFAHESVRDEHFKTKRHKKR 85 (118)
Q Consensus 60 C~~Cdr~F~~~~~l~~H~ksK~HKrr 85 (118)
|..|+..|.+...|..|+. ..|.-.
T Consensus 2 C~~C~~~f~~~~~l~~H~~-~~H~~~ 26 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMK-KKHGFD 26 (100)
T ss_dssp --------------------------
T ss_pred ccccccccccccccccccc-cccccc
Confidence 9999999999999999995 555443
No 44
>PF14968 CCDC84: Coiled coil protein 84
Probab=78.64 E-value=1.4 Score=37.47 Aligned_cols=77 Identities=21% Similarity=0.353 Sum_probs=50.8
Q ss_pred cccccccchhhhhhhhhcccCCCchHHHHhhccCc-----CCCCCCCCCCCCCCCCcccccccccccCCh------HHHH
Q 033485 6 NRKVKKRRYSHKTARLAKFLRKGDDAVYDELQRSD-----SAKNPLPFDEDLPGMGQYYCLHCDRYFAHE------SVRD 74 (118)
Q Consensus 6 ~~~~k~~~~~~kt~rrt~~~~kD~DqI~~dl~~~~-----~~~~~~~~dedlpg~GqfYC~~Cdr~F~~~------~~l~ 74 (118)
|--.++|+|+.+=+++.+ ++.+-+.+.- -....+.+..+..-...|-|+.|+--.... ..+.
T Consensus 9 h~~gr~H~Y~~~Hq~~L~-------~~L~rf~~Kl~d~R~~lk~p~v~~~~~~~~~~fWC~fC~~ev~~~~s~~~~~~ai 81 (336)
T PF14968_consen 9 HDQGRRHVYSPKHQKSLS-------AFLSRFRSKLSDARFFLKKPSVLRYDPEHRNRFWCVFCDCEVREHDSSFACGGAI 81 (336)
T ss_pred ccccCCCccCHHHHHHHH-------HHHHHHHHHHHHHHHHHhCCccCCCCccccceeEeeCccchhhhccchhhhccHH
Confidence 445788888887777553 3322221110 011233344555556789999999887754 5788
Q ss_pred HHhcchhhHHHHHHh
Q 033485 75 EHFKTKRHKKRVKEM 89 (118)
Q Consensus 75 ~H~ksK~HKrrvK~l 89 (118)
.|+-|-.|+++|+..
T Consensus 82 ~HLaS~eH~k~vk~F 96 (336)
T PF14968_consen 82 EHLASPEHRKNVKKF 96 (336)
T ss_pred hhcCCHHHHHHHHHH
Confidence 999999999999875
No 45
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=77.78 E-value=3.2 Score=37.70 Aligned_cols=49 Identities=20% Similarity=0.329 Sum_probs=41.7
Q ss_pred CcccccccccccCChHHHHHHhcchhhHHHHHH-hhCCCCCCHHHHHHhc
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKE-MMGPKPHTQLDADLAA 104 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~-l~~~~pytq~eAe~aa 104 (118)
....|..|+.-|-+......|+++=.|.-++|. |.+-.+++++|-|...
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krkl~~~~ils~edFe~i~ 114 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRKLRGKPILSEEDFEGII 114 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhh
Confidence 467999999999999999999999999988876 4555578998887654
No 46
>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=77.36 E-value=1.7 Score=26.88 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=18.5
Q ss_pred cccccccccccCChHHHHHHhcch
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK 80 (118)
.|-|.+|++. -+...|..|....
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~ 24 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDE 24 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhH
Confidence 5889999995 5578899998653
No 47
>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=74.88 E-value=1.9 Score=25.21 Aligned_cols=25 Identities=20% Similarity=0.317 Sum_probs=17.1
Q ss_pred CCCcccccccccccCCh----HHHHHHhc
Q 033485 54 GMGQYYCLHCDRYFAHE----SVRDEHFK 78 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~----~~l~~H~k 78 (118)
+.....|.+|++.|... +.|..|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 45678999999999874 89999993
No 48
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=73.01 E-value=1.3 Score=42.13 Aligned_cols=27 Identities=22% Similarity=0.501 Sum_probs=24.3
Q ss_pred CCCCcccccccccccCChHHHHHHhcc
Q 033485 53 PGMGQYYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 53 pg~GqfYC~~Cdr~F~~~~~l~~H~ks 79 (118)
.|...|.|..|+|-|.+.-+|++|+-.
T Consensus 629 tGERPFkCKiCgRAFtTkGNLkaH~~v 655 (958)
T KOG1074|consen 629 TGERPFKCKICGRAFTTKGNLKAHMSV 655 (958)
T ss_pred cCcCccccccccchhccccchhhcccc
Confidence 567789999999999999999999954
No 49
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=71.87 E-value=2.1 Score=35.83 Aligned_cols=26 Identities=15% Similarity=0.431 Sum_probs=19.3
Q ss_pred CCcccccccccccCChHHHHHHhcch
Q 033485 55 MGQYYCLHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~~~l~~H~ksK 80 (118)
..-|-|.+|+|-|.+.-+|+.|+++-
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH 184 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTH 184 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhcc
Confidence 34567888888888888888887764
No 50
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=71.19 E-value=2 Score=38.30 Aligned_cols=29 Identities=21% Similarity=0.496 Sum_probs=23.4
Q ss_pred ccccccccccCChHHHHHHhcchhhHHHH
Q 033485 58 YYCLHCDRYFAHESVRDEHFKTKRHKKRV 86 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ksK~HKrrv 86 (118)
|.|.+|||-|.-..+|.+|.+=.+=+...
T Consensus 296 YrCPEC~KVFsCPANLASHRRWHKPR~ea 324 (500)
T KOG3993|consen 296 YRCPECDKVFSCPANLASHRRWHKPRPEA 324 (500)
T ss_pred ecCCcccccccCchhhhhhhcccCCchhh
Confidence 68999999999999999999764443333
No 51
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=70.80 E-value=4.2 Score=35.44 Aligned_cols=45 Identities=20% Similarity=0.417 Sum_probs=35.9
Q ss_pred CCcccccccccccCChHHHHHHhcchhhHHHHHHhhC-CCCCCHHH
Q 033485 55 MGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEMMG-PKPHTQLD 99 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~~-~~pytq~e 99 (118)
++.|-|..|..-|.++..-..|.+|=-|+=+||.-.. -.|.|.++
T Consensus 1 st~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~ 46 (390)
T KOG2785|consen 1 STGFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEE 46 (390)
T ss_pred CCcceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHH
Confidence 3568999999999999999999999999888776422 23566554
No 52
>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=69.43 E-value=3.3 Score=26.88 Aligned_cols=22 Identities=14% Similarity=0.291 Sum_probs=16.4
Q ss_pred cccccccccccCChHHHHHHhc
Q 033485 57 QYYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~k 78 (118)
..-|.+|+.-+.++.+|..|+.
T Consensus 24 PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCcchhhccchhhHHHHHH
Confidence 3489999999999999999984
No 53
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=68.32 E-value=2.2 Score=40.31 Aligned_cols=30 Identities=30% Similarity=0.668 Sum_probs=25.2
Q ss_pred CCcccccccccccCChHHHHHHhcchhhHH
Q 033485 55 MGQYYCLHCDRYFAHESVRDEHFKTKRHKK 84 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKr 84 (118)
.|-|-|-+|+|-|.--++++.|+++..-+.
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 378999999999999999999997754433
No 54
>PHA00732 hypothetical protein
Probab=67.38 E-value=2.3 Score=28.82 Aligned_cols=21 Identities=19% Similarity=0.540 Sum_probs=17.9
Q ss_pred ccccccccccCChHHHHHHhcchh
Q 033485 58 YYCLHCDRYFAHESVRDEHFKTKR 81 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ksK~ 81 (118)
+-|..|++.|. .|..|+.+|.
T Consensus 28 ~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 28 TKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCEeC---ChhhhhcccC
Confidence 46999999998 5899998774
No 55
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=66.82 E-value=2.1 Score=35.17 Aligned_cols=37 Identities=27% Similarity=0.564 Sum_probs=28.8
Q ss_pred CCCCCcccccccccccCChHHHHHHhc---chhhHHHHHH
Q 033485 52 LPGMGQYYCLHCDRYFAHESVRDEHFK---TKRHKKRVKE 88 (118)
Q Consensus 52 lpg~GqfYC~~Cdr~F~~~~~l~~H~k---sK~HKrrvK~ 88 (118)
-.|...|.|..|++.|...-+|.+|++ |-.|+=..++
T Consensus 168 htgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yayke 207 (267)
T KOG3576|consen 168 HTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKE 207 (267)
T ss_pred ccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHH
Confidence 468889999999999999999999984 3444443333
No 56
>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=65.58 E-value=4.6 Score=22.00 Aligned_cols=19 Identities=26% Similarity=0.497 Sum_probs=16.6
Q ss_pred cccccccccCChHHHHHHhc
Q 033485 59 YCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 59 YC~~Cdr~F~~~~~l~~H~k 78 (118)
-|..|++.+ ++..++.|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 599999999 7789999985
No 57
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=60.22 E-value=4.4 Score=24.61 Aligned_cols=26 Identities=19% Similarity=0.425 Sum_probs=21.2
Q ss_pred CCCcccccccccccCCh-----HHHHHHhcc
Q 033485 54 GMGQYYCLHCDRYFAHE-----SVRDEHFKT 79 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~-----~~l~~H~ks 79 (118)
|...-.|.+|.+-+... ++|..|+++
T Consensus 15 g~~~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 15 GKQRAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred CCeEEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 33467999999999765 799999986
No 58
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=57.10 E-value=7 Score=30.46 Aligned_cols=33 Identities=30% Similarity=0.593 Sum_probs=28.4
Q ss_pred ccccccccccCC-hHHHHHHhcchhhHHHHHHhh
Q 033485 58 YYCLHCDRYFAH-ESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 58 fYC~~Cdr~F~~-~~~l~~H~ksK~HKrrvK~l~ 90 (118)
++|..||-+-.. .++++.|++|-.|.++.+...
T Consensus 92 ~hCsACd~~IP~~~~~vQ~Hl~S~~H~~Nrr~~~ 125 (165)
T PF04988_consen 92 AHCSACDVFIPMQHSSVQKHLKSQDHNKNRRAMM 125 (165)
T ss_pred hhhhHhhhhccCcHHHHHHHhccHHHHhhHHHHH
Confidence 499999998887 499999999999998877553
No 59
>PF14968 CCDC84: Coiled coil protein 84
Probab=56.65 E-value=4.8 Score=34.31 Aligned_cols=29 Identities=24% Similarity=0.613 Sum_probs=25.6
Q ss_pred cccccccccCChHHHHHHhcchhhHHHHHHhh
Q 033485 59 YCLHCDRYFAHESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 59 YC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~ 90 (118)
||..|.+.+.. -..|.-+..|+++|..+.
T Consensus 1 yC~vCr~~h~~---gr~H~Y~~~Hq~~L~~~L 29 (336)
T PF14968_consen 1 YCEVCRRNHDQ---GRRHVYSPKHQKSLSAFL 29 (336)
T ss_pred CcchhhCcccc---cCCCccCHHHHHHHHHHH
Confidence 89999998765 789999999999998873
No 60
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=55.37 E-value=4.2 Score=38.67 Aligned_cols=30 Identities=23% Similarity=0.593 Sum_probs=27.7
Q ss_pred CCCcccccccccccCChHHHHHHhcchhhH
Q 033485 54 GMGQYYCLHCDRYFAHESVRDEHFKTKRHK 83 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~~~l~~H~ksK~HK 83 (118)
|...|-|.-|.|.|.+.-++-+|+.||+=.
T Consensus 306 GEKPfeCpnCkKRFSHSGSySSHmSSKKCI 335 (1007)
T KOG3623|consen 306 GEKPFECPNCKKRFSHSGSYSSHMSSKKCI 335 (1007)
T ss_pred CCCCcCCcccccccccCCcccccccccchh
Confidence 566899999999999999999999999876
No 61
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=55.25 E-value=4.8 Score=23.62 Aligned_cols=14 Identities=36% Similarity=0.890 Sum_probs=11.1
Q ss_pred CCCCCccccccccc
Q 033485 52 LPGMGQYYCLHCDR 65 (118)
Q Consensus 52 lpg~GqfYC~~Cdr 65 (118)
.+..|.|||..|+-
T Consensus 20 ~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 20 YSDDGFYYCDRCGH 33 (36)
T ss_pred EccCCEEEhhhCce
Confidence 45579999999973
No 62
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=54.88 E-value=5.1 Score=32.92 Aligned_cols=23 Identities=22% Similarity=0.404 Sum_probs=13.1
Q ss_pred ccccccccccCChHHHHHHhcch
Q 033485 58 YYCLHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ksK 80 (118)
|.|..|++-|.+...|+.|.++.
T Consensus 146 ~lct~cgkgfndtfdlkrh~rth 168 (267)
T KOG3576|consen 146 HLCTFCGKGFNDTFDLKRHTRTH 168 (267)
T ss_pred HHHhhccCcccchhhhhhhhccc
Confidence 45555555555555566555554
No 63
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=54.51 E-value=4.2 Score=29.09 Aligned_cols=14 Identities=21% Similarity=0.793 Sum_probs=11.7
Q ss_pred CCcccccccccccC
Q 033485 55 MGQYYCLHCDRYFA 68 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~ 68 (118)
...+||+.|+.++.
T Consensus 65 ~k~~YCvSCAiH~~ 78 (95)
T PRK09335 65 VTKCYCVNCAVHLG 78 (95)
T ss_pred eeeEEechhhhhcc
Confidence 34799999999875
No 64
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=53.01 E-value=5.5 Score=25.18 Aligned_cols=19 Identities=16% Similarity=0.450 Sum_probs=13.4
Q ss_pred CCCcccccccccccCChHH
Q 033485 54 GMGQYYCLHCDRYFAHESV 72 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~~~ 72 (118)
+.++|.|.||++.|..+..
T Consensus 32 ~~~~~rC~YCe~~~~~~eI 50 (52)
T PF02748_consen 32 EPIKLRCHYCERIITEDEI 50 (52)
T ss_dssp TTCEEEETTT--EEEHHHH
T ss_pred CCCEEEeeCCCCEecccEE
Confidence 4578999999999986544
No 65
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=52.96 E-value=2.8 Score=23.79 Aligned_cols=19 Identities=21% Similarity=0.677 Sum_probs=13.1
Q ss_pred ccccccccccCChHHHHHHh
Q 033485 58 YYCLHCDRYFAHESVRDEHF 77 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ 77 (118)
|-|+-|.+.| +....+.|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 5799999999 455556654
No 66
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=50.13 E-value=5.6 Score=29.05 Aligned_cols=15 Identities=33% Similarity=0.585 Sum_probs=11.9
Q ss_pred CCcccccccccccCC
Q 033485 55 MGQYYCLHCDRYFAH 69 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~ 69 (118)
.-.+||+.|+.++.-
T Consensus 69 ~k~~YCVSCAIH~~i 83 (108)
T PTZ00172 69 MKQQYCVSCAIHSRV 83 (108)
T ss_pred eeeEEeeehhhcCCe
Confidence 347899999998863
No 67
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=49.47 E-value=4.3 Score=24.91 Aligned_cols=11 Identities=36% Similarity=1.065 Sum_probs=9.5
Q ss_pred ccccccccccC
Q 033485 58 YYCLHCDRYFA 68 (118)
Q Consensus 58 fYC~~Cdr~F~ 68 (118)
-||+.|+|.|.
T Consensus 7 ~yC~~Cdk~~~ 17 (43)
T PF12855_consen 7 DYCIVCDKQID 17 (43)
T ss_pred hHHHHhhcccc
Confidence 39999999994
No 68
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=49.43 E-value=7.9 Score=31.34 Aligned_cols=29 Identities=21% Similarity=0.419 Sum_probs=24.2
Q ss_pred CcccccccccccCC---hHHHHHHhcchhhHH
Q 033485 56 GQYYCLHCDRYFAH---ESVRDEHFKTKRHKK 84 (118)
Q Consensus 56 GqfYC~~Cdr~F~~---~~~l~~H~ksK~HKr 84 (118)
...-|.+|+-+.+. +.-|..|+.||.|.-
T Consensus 189 kl~VCeVCGA~Ls~~D~d~RladH~~GK~HlG 220 (254)
T PF03194_consen 189 KLEVCEVCGAFLSVGDNDRRLADHFGGKQHLG 220 (254)
T ss_pred CccchhhhhhHHhccchHHHHHHHhccchhhh
Confidence 35789999988854 577999999999965
No 69
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=48.99 E-value=18 Score=36.21 Aligned_cols=48 Identities=17% Similarity=0.245 Sum_probs=38.2
Q ss_pred CcccccccccccCChHHHHHHhcchhhHHHHHHhhCCCCCCHHHHHHhc
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEMMGPKPHTQLDADLAA 104 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~~~~pytq~eAe~aa 104 (118)
+.|-|..|+-.|....+|-.|+.+=.|+..++++.+. .-.|..++.|+
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~-~g~~v~~~~~~ 564 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEEN-AGEQVRLLPAS 564 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhc-cccchhhhhhh
Confidence 4789999999999999999999999999998887643 34444444433
No 70
>PLN00186 ribosomal protein S26; Provisional
Probab=47.17 E-value=6.7 Score=28.72 Aligned_cols=13 Identities=23% Similarity=0.511 Sum_probs=11.1
Q ss_pred cccccccccccCC
Q 033485 57 QYYCLHCDRYFAH 69 (118)
Q Consensus 57 qfYC~~Cdr~F~~ 69 (118)
.+||+.|+.++.-
T Consensus 71 ~~YCVSCAIH~~i 83 (109)
T PLN00186 71 VQYCISCAIHSRV 83 (109)
T ss_pred eEEEEeehhccce
Confidence 5999999998863
No 71
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=47.02 E-value=6.4 Score=31.26 Aligned_cols=39 Identities=26% Similarity=0.502 Sum_probs=0.0
Q ss_pred CCCCC-ccccccccccc-CChHHHHHHhcchhhHHHHHHhh
Q 033485 52 LPGMG-QYYCLHCDRYF-AHESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 52 lpg~G-qfYC~~Cdr~F-~~~~~l~~H~ksK~HKrrvK~l~ 90 (118)
|-|++ .|+|..|+=+. .-..+|..|+..-.|..=++-|-
T Consensus 95 LhGL~~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLG 135 (196)
T PF11931_consen 95 LHGLGVEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLG 135 (196)
T ss_dssp -----------------------------------------
T ss_pred HhCCCCeeeeEeCCCcceecHHHHHHhcChhHHHccChhcC
Confidence 55777 69999998654 46899999999999998777773
No 72
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=46.21 E-value=8 Score=34.56 Aligned_cols=34 Identities=21% Similarity=0.417 Sum_probs=26.7
Q ss_pred CCCcccccccccccCChHHHHHHhcchhhHHHHH
Q 033485 54 GMGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVK 87 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK 87 (118)
..|.|-|.+|++-|..+.-|..|+-+-.-.-..+
T Consensus 353 s~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 353 SSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred cCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 3569999999999999999999987654433444
No 73
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=46.02 E-value=8.1 Score=34.25 Aligned_cols=24 Identities=21% Similarity=0.728 Sum_probs=21.1
Q ss_pred cccccccccCChHHHHHHhcchhhHHH
Q 033485 59 YCLHCDRYFAHESVRDEHFKTKRHKKR 85 (118)
Q Consensus 59 YC~~Cdr~F~~~~~l~~H~ksK~HKrr 85 (118)
||.-|--.|. +|.+|+.|+.|.|=
T Consensus 424 YCENCreky~---~lE~Hi~s~~HrrF 447 (468)
T COG5067 424 YCENCREKYE---SLEQHIVSEKHRRF 447 (468)
T ss_pred hhHHHHHHHH---HHHHHhhhhhhhhh
Confidence 9999998886 68999999999763
No 74
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=45.71 E-value=19 Score=24.83 Aligned_cols=32 Identities=22% Similarity=0.463 Sum_probs=26.5
Q ss_pred CCCCCCCCcccc----cccccccCChHHHHHHhcch
Q 033485 49 DEDLPGMGQYYC----LHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 49 dedlpg~GqfYC----~~Cdr~F~~~~~l~~H~ksK 80 (118)
-+-||--..|-| ..|.-.+.+...+..|++..
T Consensus 72 i~gLp~~~G~~C~~~~~~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 72 IPGLPVYDGYRCQCDPPHCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred CCCCCCCCCeeeecCCCCCCcEeccHHHHHHHHHHh
Confidence 345666678999 99999999999999999753
No 75
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=45.29 E-value=14 Score=33.52 Aligned_cols=37 Identities=19% Similarity=0.367 Sum_probs=32.7
Q ss_pred CCCcccccccccccCChHHHHHHhcchhhHHHHHHhh
Q 033485 54 GMGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l~ 90 (118)
-..+-.|-.|+.-..++-.|-+|.+|++|.+.|.++.
T Consensus 490 yerkkqcslcnvlissevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 490 YERKKQCSLCNVLISSEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred HHhhhccchhhhhhhhhhhhhhhhcchhHHHHHHHHh
Confidence 3345689999999999999999999999999999873
No 76
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=44.03 E-value=6.8 Score=24.07 Aligned_cols=9 Identities=44% Similarity=1.571 Sum_probs=7.4
Q ss_pred ccccccccc
Q 033485 57 QYYCLHCDR 65 (118)
Q Consensus 57 qfYC~~Cdr 65 (118)
.|||+.|.+
T Consensus 1 MyYCi~Cs~ 9 (41)
T PF13119_consen 1 MYYCINCSE 9 (41)
T ss_pred CEEEEEhHH
Confidence 489999965
No 77
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=43.40 E-value=5.7 Score=34.50 Aligned_cols=23 Identities=26% Similarity=0.447 Sum_probs=20.2
Q ss_pred CcccccccccccCChHHHHHHhc
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~k 78 (118)
..|.|++|+|.+.+.+.|+-|.+
T Consensus 397 KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 397 KPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceeccccchhhccCccceeccc
Confidence 45899999999999999988864
No 78
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=43.22 E-value=25 Score=27.43 Aligned_cols=32 Identities=25% Similarity=0.463 Sum_probs=26.0
Q ss_pred ccccccccccCChHHHHHHhcchhhHHHHHHh
Q 033485 58 YYCLHCDRYFAHESVRDEHFKTKRHKKRVKEM 89 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l 89 (118)
|.|-.|-=.--.+..+..|+.|+.|+--++-+
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i 32 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYI 32 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHH
Confidence 67899975555689999999999999766655
No 79
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=43.03 E-value=12 Score=24.93 Aligned_cols=31 Identities=19% Similarity=0.251 Sum_probs=23.8
Q ss_pred CCCCCcccccccccccCChHHHHHHh-cchhh
Q 033485 52 LPGMGQYYCLHCDRYFAHESVRDEHF-KTKRH 82 (118)
Q Consensus 52 lpg~GqfYC~~Cdr~F~~~~~l~~H~-ksK~H 82 (118)
--|.--+.|.-|+.-|-....+..|. ++.-|
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 33555689999999999999999887 33333
No 80
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=42.93 E-value=38 Score=23.24 Aligned_cols=52 Identities=13% Similarity=0.189 Sum_probs=30.8
Q ss_pred CcccccccccccCChHHHHHHhc----------chhhHHHHHHhhCCCCCCHHHHHHhcCCC
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFK----------TKRHKKRVKEMMGPKPHTQLDADLAAGMG 107 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~k----------sK~HKrrvK~l~~~~pytq~eAe~aag~g 107 (118)
..++|..|+-.|.+......-.+ +-.--.+++.++...=.||.++-...|++
T Consensus 30 ~~~~C~~CGe~~~~~e~~~~~~~~i~~~~~~~~~~~~~~~i~~~r~~~gltq~~lA~~lg~~ 91 (127)
T TIGR03830 30 PGWYCPACGEELLDPEESKRNSAALADFYRKVDGLLTPPEIRRIRKKLGLSQREAAELLGGG 91 (127)
T ss_pred eeeECCCCCCEEEcHHHHHHHHHHHHHHHHHccCCcCHHHHHHHHHHcCCCHHHHHHHhCCC
Confidence 35799999999988643332221 11112245555444447888877777765
No 81
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=42.31 E-value=9.6 Score=38.03 Aligned_cols=33 Identities=18% Similarity=0.515 Sum_probs=29.5
Q ss_pred CCcccccccccccCChHHHHHHhcchhhHHHHH
Q 033485 55 MGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVK 87 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK 87 (118)
+.++||..|.+-|.+..+|+.|+++--|+++..
T Consensus 1326 d~~~~c~~c~~~~~~~~alqihm~~~~~~~kt~ 1358 (1406)
T KOG1146|consen 1326 DCTYHCLACEVLLSGREALQIHMRSSAHRRKTA 1358 (1406)
T ss_pred cccccchHHHhhcchhHHHHHHHHHhhhcccCC
Confidence 357789999999999999999999999988753
No 82
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=40.09 E-value=18 Score=30.52 Aligned_cols=32 Identities=22% Similarity=0.493 Sum_probs=24.8
Q ss_pred CCCCCCCCCC-cccccccccccCChHHHHHHhc
Q 033485 47 PFDEDLPGMG-QYYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 47 ~~dedlpg~G-qfYC~~Cdr~F~~~~~l~~H~k 78 (118)
|+.+++-... -|-|.+|=+||.+...|..|..
T Consensus 37 PyP~e~~~~~~lyiCe~Clky~~~~~~l~~H~~ 69 (290)
T PLN03238 37 PYPEPYASCTKLYICEYCLKYMRKKKSLLRHLA 69 (290)
T ss_pred CCChHHcCCCeEEEcCCCcchhCCHHHHHHHHH
Confidence 4444443333 6899999999999999999986
No 83
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=39.63 E-value=11 Score=28.37 Aligned_cols=19 Identities=21% Similarity=0.555 Sum_probs=16.1
Q ss_pred CCCCCCCCccccccccccc
Q 033485 49 DEDLPGMGQYYCLHCDRYF 67 (118)
Q Consensus 49 dedlpg~GqfYC~~Cdr~F 67 (118)
.-+++|.|.|.|..|+...
T Consensus 104 sGE~~g~G~l~C~~Cg~~~ 122 (146)
T PF07295_consen 104 SGEVVGPGTLVCENCGHEV 122 (146)
T ss_pred cCcEecCceEecccCCCEE
Confidence 5679999999999999643
No 84
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=39.54 E-value=11 Score=24.29 Aligned_cols=14 Identities=29% Similarity=0.814 Sum_probs=12.5
Q ss_pred CCcccccccccccC
Q 033485 55 MGQYYCLHCDRYFA 68 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~ 68 (118)
.|..+|..|+++|.
T Consensus 51 eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 51 EGELICPECGREYP 64 (68)
T ss_dssp TTEEEETTTTEEEE
T ss_pred CCEEEcCCCCCEEe
Confidence 48999999999994
No 85
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=38.85 E-value=8.4 Score=26.89 Aligned_cols=22 Identities=14% Similarity=0.455 Sum_probs=18.1
Q ss_pred CcccccccccccCChHHHHHHh
Q 033485 56 GQYYCLHCDRYFAHESVRDEHF 77 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~ 77 (118)
.-|+|.+|.+++..-..+..++
T Consensus 20 ~d~~Cp~C~~~~~~~~~~~~~~ 41 (162)
T PF13462_consen 20 FDFQCPHCAKFHEELEKLLKKY 41 (162)
T ss_dssp E-TTSHHHHHHHHHHHHHHHHH
T ss_pred ECCCCHhHHHHHHHHhhhhhhc
Confidence 4689999999998877888887
No 86
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=38.09 E-value=13 Score=31.62 Aligned_cols=37 Identities=22% Similarity=0.529 Sum_probs=28.9
Q ss_pred CCCCCCCCC-----cccccccccccCC---hHHHHHHhcchhhHH
Q 033485 48 FDEDLPGMG-----QYYCLHCDRYFAH---ESVRDEHFKTKRHKK 84 (118)
Q Consensus 48 ~dedlpg~G-----qfYC~~Cdr~F~~---~~~l~~H~ksK~HKr 84 (118)
.....|+.. .--|.+|+-|..- +.-|..|+.||.|.-
T Consensus 172 ~~~~~~~~~~~~qkl~VCeVCGa~L~~~D~d~RlaDHf~GKlHlG 216 (319)
T KOG0796|consen 172 YNTTMPGASAQQQKLRVCEVCGAFLSVNDADRRLADHFGGKLHLG 216 (319)
T ss_pred HccCcchhhhhhhhhhHHHhhhHHHhccchHHHHHHhhcchHHHH
Confidence 345566554 3489999999873 688999999999975
No 87
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=37.83 E-value=18 Score=29.01 Aligned_cols=32 Identities=25% Similarity=0.566 Sum_probs=22.2
Q ss_pred CcccccccccccCChHHHHHHhcchhhHHHHHH
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKE 88 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~ 88 (118)
.+|.|..|+|-|.-..=-..|+..| |---|.+
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nK-H~e~ve~ 107 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNK-HPEKVEE 107 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH--HHHHHH
T ss_pred CEECCCCCCcccCChHHHHHHHhhc-CHHHHHH
Confidence 4899999999999988888888765 4444433
No 88
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=37.03 E-value=15 Score=30.25 Aligned_cols=36 Identities=25% Similarity=0.475 Sum_probs=28.8
Q ss_pred CCCCCC----cccccccccccCC---hHHHHHHhcchhhHHHH
Q 033485 51 DLPGMG----QYYCLHCDRYFAH---ESVRDEHFKTKRHKKRV 86 (118)
Q Consensus 51 dlpg~G----qfYC~~Cdr~F~~---~~~l~~H~ksK~HKrrv 86 (118)
+.||.| .--|..|+-|... +.-|..|+.||.|.--+
T Consensus 175 en~gq~thqklqvC~iCgayLsrlDtdrrladHf~GklHlGy~ 217 (258)
T COG5200 175 ENNGQGTHQKLQVCGICGAYLSRLDTDRRLADHFNGKLHLGYL 217 (258)
T ss_pred hCcchhhhhhhhhhhhhhhHHHhcchhhHHHHHhccchhhhHH
Confidence 367777 4589999999874 68899999999997533
No 89
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=34.86 E-value=17 Score=32.10 Aligned_cols=25 Identities=32% Similarity=0.636 Sum_probs=22.1
Q ss_pred CcccccccccccCChHHHHHHhcch
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~ksK 80 (118)
..|-|-.|||.|++-.+|..|+.-|
T Consensus 351 ~~Y~CH~Cdr~ft~G~~L~~HL~kk 375 (467)
T KOG3608|consen 351 ILYACHCCDRFFTSGKSLSAHLMKK 375 (467)
T ss_pred CceeeecchhhhccchhHHHHHHHh
Confidence 3689999999999999999999643
No 90
>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=34.84 E-value=16 Score=22.39 Aligned_cols=13 Identities=31% Similarity=0.654 Sum_probs=7.5
Q ss_pred cccccccccCChH
Q 033485 59 YCLHCDRYFAHES 71 (118)
Q Consensus 59 YC~~Cdr~F~~~~ 71 (118)
-|+.|+|-|..++
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999999999763
No 91
>PLN03239 histone acetyltransferase; Provisional
Probab=34.35 E-value=22 Score=30.70 Aligned_cols=22 Identities=23% Similarity=0.244 Sum_probs=20.2
Q ss_pred cccccccccccCChHHHHHHhc
Q 033485 57 QYYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~k 78 (118)
-|-|.+|=+||.+...|..|..
T Consensus 106 lYiCE~Clky~~~~~~l~~H~~ 127 (351)
T PLN03239 106 LYVCEFSFGFFARKSELLRFQA 127 (351)
T ss_pred EEEeccchhhhcCHHHHHHHHH
Confidence 6899999999999999999964
No 92
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=34.13 E-value=21 Score=31.68 Aligned_cols=22 Identities=23% Similarity=0.709 Sum_probs=20.7
Q ss_pred cccccccccccCChHHHHHHhc
Q 033485 57 QYYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~k 78 (118)
-|-|.+|=+||.+...|..|+.
T Consensus 198 lyiCe~Cl~y~~~~~~~~~H~~ 219 (450)
T PLN00104 198 LYFCEFCLKFMKRKEQLQRHMK 219 (450)
T ss_pred EEEchhhhhhhcCHHHHHHHHh
Confidence 6899999999999999999985
No 93
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=33.31 E-value=23 Score=31.32 Aligned_cols=23 Identities=26% Similarity=0.478 Sum_probs=20.9
Q ss_pred CcccccccccccCChHHHHHHhc
Q 033485 56 GQYYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~k 78 (118)
..|-|..||..|.+++.|+.|..
T Consensus 291 kpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 291 KPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred CCccccchhhhhccHHHHHHHHH
Confidence 45899999999999999999986
No 94
>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=32.85 E-value=16 Score=20.65 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=11.0
Q ss_pred cccccccccccCC
Q 033485 57 QYYCLHCDRYFAH 69 (118)
Q Consensus 57 qfYC~~Cdr~F~~ 69 (118)
.|.|..|+..|.-
T Consensus 5 ~y~C~~Cg~~fe~ 17 (41)
T smart00834 5 EYRCEDCGHTFEV 17 (41)
T ss_pred EEEcCCCCCEEEE
Confidence 5899999998874
No 95
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=32.45 E-value=15 Score=27.17 Aligned_cols=20 Identities=30% Similarity=0.545 Sum_probs=17.1
Q ss_pred CCCCCCCCCcccccccccccCC
Q 033485 48 FDEDLPGMGQYYCLHCDRYFAH 69 (118)
Q Consensus 48 ~dedlpg~GqfYC~~Cdr~F~~ 69 (118)
|+.|+||. +-|-||+-.|..
T Consensus 97 InLDk~~~--~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 97 INLDKPGP--HICGYCGLRFVQ 116 (120)
T ss_pred EEcCCCCC--cccccchhhhhh
Confidence 67888876 889999999986
No 96
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=32.31 E-value=24 Score=26.29 Aligned_cols=20 Identities=30% Similarity=0.710 Sum_probs=11.6
Q ss_pred cccccccccccCChHHHHHHhcc
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKT 79 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ks 79 (118)
...|.+|++.|.+- +.|+++
T Consensus 72 ~i~clecGk~~k~L---krHL~~ 91 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRT 91 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHH
T ss_pred eeEEccCCcccchH---HHHHHH
Confidence 56999999999974 555543
No 97
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=31.47 E-value=18 Score=30.19 Aligned_cols=15 Identities=33% Similarity=1.034 Sum_probs=11.8
Q ss_pred CCCCCCccccccccc
Q 033485 51 DLPGMGQYYCLHCDR 65 (118)
Q Consensus 51 dlpg~GqfYC~~Cdr 65 (118)
--|..|.+||..|-+
T Consensus 255 k~pPKG~WYC~eCk~ 269 (271)
T COG5034 255 KEPPKGKWYCPECKK 269 (271)
T ss_pred CCCCCCcEeCHHhHh
Confidence 357789999999954
No 98
>PF07895 DUF1673: Protein of unknown function (DUF1673); InterPro: IPR012874 This family contains hypothetical proteins of unknown function found in Methanosarcina acetivorans and Methanosarcina mazei.
Probab=31.37 E-value=19 Score=28.20 Aligned_cols=8 Identities=75% Similarity=1.369 Sum_probs=6.9
Q ss_pred CCCCCccc
Q 033485 1 MGKCPNRK 8 (118)
Q Consensus 1 ~~~~~~~~ 8 (118)
||-||+.|
T Consensus 11 MGWCPnak 18 (205)
T PF07895_consen 11 MGWCPNAK 18 (205)
T ss_pred hCcCcCcC
Confidence 89999875
No 99
>COG0492 TrxB Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]
Probab=31.18 E-value=20 Score=29.56 Aligned_cols=19 Identities=37% Similarity=0.980 Sum_probs=15.9
Q ss_pred CCCCCCcccccccccccCC
Q 033485 51 DLPGMGQYYCLHCDRYFAH 69 (118)
Q Consensus 51 dlpg~GqfYC~~Cdr~F~~ 69 (118)
++-|.|-+||..||-+|.+
T Consensus 125 e~~g~gv~yc~~cdg~~~~ 143 (305)
T COG0492 125 EFEGKGVSYCATCDGFFKG 143 (305)
T ss_pred hhcCCceEEeeecCccccC
Confidence 5677889999999997765
No 100
>PTZ00064 histone acetyltransferase; Provisional
Probab=31.04 E-value=27 Score=31.84 Aligned_cols=22 Identities=23% Similarity=0.489 Sum_probs=20.5
Q ss_pred cccccccccccCChHHHHHHhc
Q 033485 57 QYYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~k 78 (118)
-|-|.+|=+||.+...|..|..
T Consensus 280 LYICEfCLkY~~s~~~l~rH~~ 301 (552)
T PTZ00064 280 LHFCEYCLDFFCFEDELIRHLS 301 (552)
T ss_pred EEEccchhhhhCCHHHHHHHHh
Confidence 5789999999999999999985
No 101
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=30.67 E-value=85 Score=24.76 Aligned_cols=45 Identities=22% Similarity=0.304 Sum_probs=30.4
Q ss_pred cccccccccCC-hHHHHHHhcchhhHHHHHHhhC---CCCCCHHHHHHh
Q 033485 59 YCLHCDRYFAH-ESVRDEHFKTKRHKKRVKEMMG---PKPHTQLDADLA 103 (118)
Q Consensus 59 YC~~Cdr~F~~-~~~l~~H~ksK~HKrrvK~l~~---~~pytq~eAe~a 103 (118)
-|..|++++.. ...+..++..|.=..+|..|.. +..||.+|-++.
T Consensus 125 qC~~CN~~~sgn~~~Yr~~Li~kiG~~~ve~Le~~~~~~k~~~~el~~i 173 (189)
T PF05766_consen 125 QCKHCNRHLSGNIVEYRIGLIEKIGQERVEWLEGPHEPRKWTIEELKAI 173 (189)
T ss_pred cCCccccccccCHHHHHHHHHHHHhHHHHHHHhcCCCCCCCCHHHHHHH
Confidence 58888888775 3667777777777778877743 234677765543
No 102
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=30.13 E-value=28 Score=20.21 Aligned_cols=20 Identities=30% Similarity=0.414 Sum_probs=14.8
Q ss_pred cccccccccccCChHHHHHHh
Q 033485 57 QYYCLHCDRYFAHESVRDEHF 77 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ 77 (118)
.|.|.-|+|.+. .+-|..|+
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHL 23 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHH
T ss_pred eEECCCCcCCcc-hhhhHHHH
Confidence 478999999887 56677776
No 103
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=28.86 E-value=31 Score=30.46 Aligned_cols=25 Identities=20% Similarity=0.587 Sum_probs=21.9
Q ss_pred cccccccccccCChHHHHHHhcchh
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTKR 81 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK~ 81 (118)
.=-|++|..+|-++-.|-.|.+.+.
T Consensus 220 HP~C~FC~~~FYdDDEL~~HcR~~H 244 (493)
T COG5236 220 HPLCIFCKIYFYDDDELRRHCRLRH 244 (493)
T ss_pred CchhhhccceecChHHHHHHHHhhh
Confidence 4489999999999999999998764
No 104
>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=28.80 E-value=26 Score=25.11 Aligned_cols=13 Identities=23% Similarity=0.536 Sum_probs=7.3
Q ss_pred cccccccccccCC
Q 033485 57 QYYCLHCDRYFAH 69 (118)
Q Consensus 57 qfYC~~Cdr~F~~ 69 (118)
+.-|..|++.|-+
T Consensus 9 KR~Cp~CG~kFYD 21 (108)
T PF09538_consen 9 KRTCPSCGAKFYD 21 (108)
T ss_pred cccCCCCcchhcc
Confidence 4556666655554
No 105
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=28.62 E-value=28 Score=26.67 Aligned_cols=21 Identities=24% Similarity=0.423 Sum_probs=16.2
Q ss_pred cccccccccccCChHHHHHHhcch
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK 80 (118)
-.-|.+|++-|.+ |+.|+.++
T Consensus 76 ~IicLEDGkkfKS---LKRHL~t~ 96 (148)
T COG4957 76 YIICLEDGKKFKS---LKRHLTTH 96 (148)
T ss_pred eEEEeccCcchHH---HHHHHhcc
Confidence 3589999999975 66777664
No 106
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=28.45 E-value=19 Score=24.33 Aligned_cols=14 Identities=29% Similarity=0.925 Sum_probs=10.3
Q ss_pred CcccccccccccCC
Q 033485 56 GQYYCLHCDRYFAH 69 (118)
Q Consensus 56 GqfYC~~Cdr~F~~ 69 (118)
+.|+|..|++.|.-
T Consensus 16 ~~~~C~~C~~~~~~ 29 (70)
T PF07191_consen 16 GHYHCEACQKDYKK 29 (70)
T ss_dssp TEEEETTT--EEEE
T ss_pred CEEECcccccccee
Confidence 79999999998863
No 107
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=27.95 E-value=14 Score=27.04 Aligned_cols=17 Identities=35% Similarity=0.837 Sum_probs=11.0
Q ss_pred CCCC--CcccccccccccC
Q 033485 52 LPGM--GQYYCLHCDRYFA 68 (118)
Q Consensus 52 lpg~--GqfYC~~Cdr~F~ 68 (118)
||-+ -.|||+.|+.+..
T Consensus 64 lPKlyvK~~YCvSCAIH~~ 82 (113)
T PF01283_consen 64 LPKLYVKLYYCVSCAIHSK 82 (113)
T ss_dssp S-EEEEEEEE-CHHHHHTT
T ss_pred cccceeEEEEeeeeeeecc
Confidence 4533 3789999998765
No 108
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=27.27 E-value=30 Score=26.49 Aligned_cols=19 Identities=16% Similarity=0.390 Sum_probs=15.1
Q ss_pred CCCCcccccccccccCChH
Q 033485 53 PGMGQYYCLHCDRYFAHES 71 (118)
Q Consensus 53 pg~GqfYC~~Cdr~F~~~~ 71 (118)
...+.|.|.||++.|..+.
T Consensus 130 ~~~~~~rC~YCe~~~~~~~ 148 (152)
T PRK00893 130 KEPIKLRCKYCEKEFSEDI 148 (152)
T ss_pred CCCCEEEeeCCCCEechhh
Confidence 4556899999999998643
No 109
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=27.05 E-value=34 Score=30.49 Aligned_cols=27 Identities=19% Similarity=0.513 Sum_probs=22.1
Q ss_pred ccccccccccCChHHHHHHhcchhhHHH
Q 033485 58 YYCLHCDRYFAHESVRDEHFKTKRHKKR 85 (118)
Q Consensus 58 fYC~~Cdr~F~~~~~l~~H~ksK~HKrr 85 (118)
+-|..|.+-|.+...+..|+-.+ |-..
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~e-H~~~ 84 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQE-HPAG 84 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHh-hhhh
Confidence 47999999999999999999754 4433
No 110
>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=26.72 E-value=23 Score=20.97 Aligned_cols=14 Identities=29% Similarity=0.679 Sum_probs=11.7
Q ss_pred cccccccccccCCh
Q 033485 57 QYYCLHCDRYFAHE 70 (118)
Q Consensus 57 qfYC~~Cdr~F~~~ 70 (118)
.|.|..|+..|+-.
T Consensus 5 ey~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 5 EYRCEECGHEFEVL 18 (42)
T ss_pred EEEeCCCCCEEEEE
Confidence 58999999999754
No 111
>smart00400 ZnF_CHCC zinc finger.
Probab=26.47 E-value=1e+02 Score=18.75 Aligned_cols=35 Identities=11% Similarity=0.122 Sum_probs=23.9
Q ss_pred CCCcccccccccccCChHHHHHHhcchhhHHHHHHh
Q 033485 54 GMGQYYCLHCDRYFAHESVRDEHFKTKRHKKRVKEM 89 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK~l 89 (118)
..+.|||-.|++.- +.-.|-.++.+...+..++.|
T Consensus 20 ~kn~~~Cf~cg~gG-d~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 20 DKQFFHCFGCGAGG-NVISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred CCCEEEEeCCCCCC-CHHHHHHHHHCcCHHHHHHHh
Confidence 35789999999876 566677776665555555443
No 112
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=25.46 E-value=31 Score=20.84 Aligned_cols=10 Identities=40% Similarity=1.228 Sum_probs=8.2
Q ss_pred CCcccccccc
Q 033485 55 MGQYYCLHCD 64 (118)
Q Consensus 55 ~GqfYC~~Cd 64 (118)
.|+.||+.|+
T Consensus 32 ~g~~~Cv~C~ 41 (41)
T PF06677_consen 32 DGKIYCVSCG 41 (41)
T ss_pred CCCEECCCCC
Confidence 4688999996
No 113
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=25.28 E-value=21 Score=23.36 Aligned_cols=21 Identities=43% Similarity=0.942 Sum_probs=12.8
Q ss_pred CCCCCCCCCCCccccccccccc
Q 033485 46 LPFDEDLPGMGQYYCLHCDRYF 67 (118)
Q Consensus 46 ~~~dedlpg~GqfYC~~Cdr~F 67 (118)
|.+++-.-+ +.++|..|+-+|
T Consensus 51 ~~~~~~~c~-~~~~C~~C~~~~ 71 (71)
T PF05495_consen 51 QPIDEYSCG-ADYFCPICGLYF 71 (71)
T ss_dssp EES-SBTT---SEEETTTTEEE
T ss_pred cChhhhhcC-CCccCcCcCCCC
Confidence 445544333 789999998877
No 114
>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=24.87 E-value=26 Score=20.95 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=11.7
Q ss_pred cccccccccccCCh
Q 033485 57 QYYCLHCDRYFAHE 70 (118)
Q Consensus 57 qfYC~~Cdr~F~~~ 70 (118)
.|.|..|+..|+-.
T Consensus 5 ey~C~~Cg~~fe~~ 18 (52)
T TIGR02605 5 EYRCTACGHRFEVL 18 (52)
T ss_pred EEEeCCCCCEeEEE
Confidence 58999999999854
No 115
>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=24.31 E-value=27 Score=24.72 Aligned_cols=14 Identities=21% Similarity=0.482 Sum_probs=11.6
Q ss_pred CcccccccccccCC
Q 033485 56 GQYYCLHCDRYFAH 69 (118)
Q Consensus 56 GqfYC~~Cdr~F~~ 69 (118)
..++|.+|+-||.-
T Consensus 78 ~~~rC~eCG~~fkL 91 (97)
T cd00924 78 KPKRCPECGHVFKL 91 (97)
T ss_pred CceeCCCCCcEEEE
Confidence 46799999999973
No 116
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=24.28 E-value=43 Score=29.23 Aligned_cols=24 Identities=17% Similarity=0.242 Sum_probs=21.1
Q ss_pred cccccccccccCChHHHHHHhcch
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTK 80 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK 80 (118)
-|-|.||++|=-++..|..|..+.
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~ 102 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQ 102 (381)
T ss_pred cccCCcccccccchhHHHHHhhhc
Confidence 588999999999999999998654
No 117
>PF07492 Trehalase_Ca-bi: Neutral trehalase Ca2+ binding domain; InterPro: IPR011120 Neutral trehalases mobilise trehalose accumulated by fungal cells as a protective and storage carbohydrate. This family represents a calcium-binding domain similar to EF hand. Residues 97 and 108 in O42893 from SWISSPROT have been implicated in this interaction. It is thought that this domain may provide a general mechanism for regulating neutral trehalase activity in yeasts and filamentous fungi [].; GO: 0004555 alpha,alpha-trehalase activity, 0005509 calcium ion binding, 0005993 trehalose catabolic process, 0005737 cytoplasm
Probab=23.63 E-value=18 Score=20.90 Aligned_cols=18 Identities=28% Similarity=0.547 Sum_probs=11.9
Q ss_pred HHhcCCCCCCCCCCCCCC
Q 033485 101 DLAAGMGMPDNGPKLMPV 118 (118)
Q Consensus 101 e~aag~g~~dng~~l~~~ 118 (118)
..-.-+...|+|||++++
T Consensus 11 Dgn~qITIeD~GPKv~~l 28 (30)
T PF07492_consen 11 DGNFQITIEDTGPKVLSL 28 (30)
T ss_pred CCCcEEEEecCCCeEEec
Confidence 333345567889998875
No 118
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=23.51 E-value=31 Score=26.60 Aligned_cols=18 Identities=22% Similarity=0.527 Sum_probs=14.7
Q ss_pred CcccccccccccCChHHH
Q 033485 56 GQYYCLHCDRYFAHESVR 73 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l 73 (118)
..|.|.||.+.|..+..+
T Consensus 134 ~~lrC~YCe~~~~~~~v~ 151 (153)
T COG1781 134 LALRCKYCEKTFSEDEVL 151 (153)
T ss_pred cEEEEEecCcEechhhhh
Confidence 568999999999876554
No 119
>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=22.65 E-value=35 Score=19.37 Aligned_cols=17 Identities=12% Similarity=0.454 Sum_probs=12.4
Q ss_pred CCCcccccccccccCCh
Q 033485 54 GMGQYYCLHCDRYFAHE 70 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~~ 70 (118)
+..-++|..|+-.|.+.
T Consensus 29 ~vp~~~C~~CGE~~~~~ 45 (46)
T TIGR03831 29 NVPALVCPQCGEEYLDA 45 (46)
T ss_pred CCCccccccCCCEeeCC
Confidence 34457999999877653
No 120
>PF08015 Pheromone: Fungal mating-type pheromone; InterPro: IPR012597 This family corresponds to mating-type pheromone proteins. The homobasidiomycetes, or mushroom fungi, have arguably the most complex mating system of all known organisms. Many species possess a mating system known as bifactorial incompatibility, where two unlinked loci control the mating-type of an individual incompatibility loci (the A and B mating-type loci). Each A mating-type sublocus encodes a pair of divergently transcribed homeodomain transcription factors while the genes responsible for B mating-type activity encode lipopeptide pheromones and G-protein -coupled pheromone receptors [].; GO: 0000772 mating pheromone activity, 0016020 membrane
Probab=22.58 E-value=53 Score=21.17 Aligned_cols=19 Identities=26% Similarity=0.599 Sum_probs=15.6
Q ss_pred CCCCCCCCCCCCC--cccccc
Q 033485 44 NPLPFDEDLPGMG--QYYCLH 62 (118)
Q Consensus 44 ~~~~~dedlpg~G--qfYC~~ 62 (118)
..+++|.|-+|.| ..|||.
T Consensus 49 ~~vpvd~Er~~~g~~~~fCVI 69 (69)
T PF08015_consen 49 DDVPVDFERRGGGGAGAFCVI 69 (69)
T ss_pred cccccCccccCCCCceEEEeC
Confidence 4578999999999 789974
No 121
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=22.54 E-value=31 Score=31.22 Aligned_cols=16 Identities=38% Similarity=0.916 Sum_probs=14.0
Q ss_pred CCcccccccccccCCh
Q 033485 55 MGQYYCLHCDRYFAHE 70 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~~ 70 (118)
+.|+||.+|+++|.+.
T Consensus 134 v~qLyC~vc~~fladr 149 (567)
T KOG1247|consen 134 VKQLYCEVCDTFLADR 149 (567)
T ss_pred eeeEEehhhcccccch
Confidence 5699999999999874
No 122
>PF11287 DUF3088: Protein of unknown function (DUF3088); InterPro: IPR021439 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=22.46 E-value=43 Score=24.55 Aligned_cols=9 Identities=44% Similarity=1.486 Sum_probs=7.9
Q ss_pred ccccccccc
Q 033485 57 QYYCLHCDR 65 (118)
Q Consensus 57 qfYC~~Cdr 65 (118)
.|||.+|+.
T Consensus 21 ~f~Cp~c~~ 29 (112)
T PF11287_consen 21 RFYCPHCAA 29 (112)
T ss_pred eEECCchHH
Confidence 599999985
No 123
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=22.18 E-value=69 Score=27.35 Aligned_cols=29 Identities=31% Similarity=0.605 Sum_probs=17.7
Q ss_pred CCcccccccccccCC---hHHHHHHhcchhhH
Q 033485 55 MGQYYCLHCDRYFAH---ESVRDEHFKTKRHK 83 (118)
Q Consensus 55 ~GqfYC~~Cdr~F~~---~~~l~~H~ksK~HK 83 (118)
..-|-|..|+++|.- .+.--.|.....|.
T Consensus 26 ~n~~~CL~cg~~~~g~~~~~ha~~H~~~~~H~ 57 (440)
T cd02669 26 LNVYACLVCGKYFQGRGKGSHAYTHSLEDNHH 57 (440)
T ss_pred CcEEEEcccCCeecCCCCCcHHHHHhhccCCC
Confidence 335788888887763 24455566555553
No 124
>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=21.68 E-value=31 Score=20.76 Aligned_cols=13 Identities=23% Similarity=0.667 Sum_probs=10.7
Q ss_pred CcccccccccccC
Q 033485 56 GQYYCLHCDRYFA 68 (118)
Q Consensus 56 GqfYC~~Cdr~F~ 68 (118)
+.-.|.+|+..|.
T Consensus 28 ~~~~CpYCg~~yv 40 (40)
T PF10276_consen 28 GPVVCPYCGTRYV 40 (40)
T ss_dssp CEEEETTTTEEEE
T ss_pred CeEECCCCCCEEC
Confidence 3679999999884
No 125
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=21.13 E-value=41 Score=31.92 Aligned_cols=31 Identities=29% Similarity=0.672 Sum_probs=28.4
Q ss_pred cccccccccccCChHHHHHHhcchhhHHHHH
Q 033485 57 QYYCLHCDRYFAHESVRDEHFKTKRHKKRVK 87 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~ksK~HKrrvK 87 (118)
+|-|..|+=-|.+..+-..|+++..|.-..|
T Consensus 359 ~f~cKlcdckf~d~nak~mhl~grRhrLQYk 389 (816)
T KOG3792|consen 359 RFHCKLCDCKFNDPNAKEMHLKGRRHRLQYK 389 (816)
T ss_pred hhhhhhhcCCCCCcchHHhhhhcccccceec
Confidence 7999999999999999999999999976555
No 126
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=20.46 E-value=45 Score=27.95 Aligned_cols=21 Identities=19% Similarity=0.605 Sum_probs=17.7
Q ss_pred CcccccccccccCChHHHHHHh
Q 033485 56 GQYYCLHCDRYFAHESVRDEHF 77 (118)
Q Consensus 56 GqfYC~~Cdr~F~~~~~l~~H~ 77 (118)
.-|.|+-|++.|.. ..+..|.
T Consensus 28 ~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 28 AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred CeeEEeeccccccc-chhhhhh
Confidence 57899999999998 6777775
No 127
>PF05477 SURF2: Surfeit locus protein 2 (SURF2); InterPro: IPR008833 Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown [].
Probab=20.46 E-value=1.1e+02 Score=25.16 Aligned_cols=37 Identities=16% Similarity=0.295 Sum_probs=32.1
Q ss_pred CCCcccccccccccCC-hHHHHHHhcchhhHHHHHHhh
Q 033485 54 GMGQYYCLHCDRYFAH-ESVRDEHFKTKRHKKRVKEMM 90 (118)
Q Consensus 54 g~GqfYC~~Cdr~F~~-~~~l~~H~ksK~HKrrvK~l~ 90 (118)
.-.++||....++..- ..+...|..||..++.|..+.
T Consensus 76 ~~~~LfCkLT~~~iNk~pe~V~rHv~GKRf~kaLek~e 113 (244)
T PF05477_consen 76 NPHKLFCKLTGRHINKSPEHVERHVNGKRFQKALEKYE 113 (244)
T ss_pred CCceeEEechHhHhccCHHHHHHHhhhHHHHHHHHHHH
Confidence 3468999999999875 699999999999999998774
No 128
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=20.17 E-value=44 Score=24.59 Aligned_cols=40 Identities=18% Similarity=0.370 Sum_probs=25.3
Q ss_pred CCCchHHHHhhccCcCCCCCCCCCCCCCCCCcccccccccccCCh
Q 033485 26 RKGDDAVYDELQRSDSAKNPLPFDEDLPGMGQYYCLHCDRYFAHE 70 (118)
Q Consensus 26 ~kD~DqI~~dl~~~~~~~~~~~~dedlpg~GqfYC~~Cdr~F~~~ 70 (118)
.||--+|+..|.+ . ....|.+---...|||..|+.....+
T Consensus 48 vRd~~E~~~~iYp-~----~~aPdp~w~~irEyyCP~Cgt~levE 87 (112)
T PF08882_consen 48 VRDPEEIHPEIYP-F----TMAPDPEWQVIREYYCPGCGTQLEVE 87 (112)
T ss_pred ecChHHhhhhhcc-c----ccCCCCCcEEEEEEECCCCcceeEEc
Confidence 4477888888843 1 12234444445679999999876543
No 129
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=20.16 E-value=43 Score=29.37 Aligned_cols=32 Identities=25% Similarity=0.674 Sum_probs=24.4
Q ss_pred CCCCCCCCCC-cccccccccccCChHHHHHHhc
Q 033485 47 PFDEDLPGMG-QYYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 47 ~~dedlpg~G-qfYC~~Cdr~F~~~~~l~~H~k 78 (118)
|+.+++--.. -|-|.+|=+|+.+...|..|+.
T Consensus 147 PyP~e~~~~~~lYiCEfCLkY~~s~~~l~rH~~ 179 (396)
T KOG2747|consen 147 PYPEEYAKLDKLYICEFCLKYMKSRTSLQRHLK 179 (396)
T ss_pred CCchhhccCCeEEEehHHHhHhchHHHHHHHHH
Confidence 3344444433 5789999999999999999984
No 130
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=20.08 E-value=43 Score=29.33 Aligned_cols=22 Identities=27% Similarity=0.623 Sum_probs=20.1
Q ss_pred cccccccccccCChHHHHHHhc
Q 033485 57 QYYCLHCDRYFAHESVRDEHFK 78 (118)
Q Consensus 57 qfYC~~Cdr~F~~~~~l~~H~k 78 (118)
-|-|.+|=+||.++.+|..|.+
T Consensus 158 vyICefClkY~~s~~~~~rH~~ 179 (395)
T COG5027 158 VYICEFCLKYYGSQTSLVRHRK 179 (395)
T ss_pred EEEhhhhHHHhcchhHHHHHHh
Confidence 4789999999999999999974
Done!