Query psy3946
Match_columns 127
No_of_seqs 112 out of 1220
Neff 9.5
Searched_HMMs 46136
Date Fri Aug 16 21:24:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3946.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3946hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.7 1.6E-18 3.5E-23 119.5 4.6 91 21-116 160-250 (279)
2 KOG2462|consensus 99.7 3.5E-17 7.6E-22 112.9 2.6 78 23-103 188-265 (279)
3 KOG3576|consensus 99.6 1.1E-15 2.4E-20 101.7 2.5 97 21-120 116-223 (267)
4 KOG3623|consensus 99.4 5.5E-14 1.2E-18 107.7 2.9 77 23-102 895-971 (1007)
5 KOG3623|consensus 99.3 7.4E-13 1.6E-17 101.7 1.8 69 46-116 889-957 (1007)
6 KOG3576|consensus 99.2 4.4E-12 9.4E-17 84.6 0.9 67 48-116 114-180 (267)
7 KOG1074|consensus 99.0 2.4E-10 5.3E-15 89.1 1.8 58 51-110 605-662 (958)
8 PHA02768 hypothetical protein; 98.9 1.1E-09 2.4E-14 58.6 1.9 42 52-97 6-47 (55)
9 KOG1074|consensus 98.8 7.8E-10 1.7E-14 86.3 0.9 85 19-106 602-693 (958)
10 PHA00733 hypothetical protein 98.8 1E-08 2.2E-13 64.9 5.4 58 46-107 68-125 (128)
11 PF13465 zf-H2C2_2: Zinc-finge 98.7 8.6E-09 1.9E-13 47.4 2.1 25 68-92 1-25 (26)
12 KOG3608|consensus 98.7 1.8E-08 4E-13 72.4 3.6 92 21-116 206-299 (467)
13 PHA00616 hypothetical protein 98.6 1.4E-08 3E-13 52.0 1.6 33 81-113 1-33 (44)
14 KOG3608|consensus 98.6 1.7E-07 3.7E-12 67.6 5.7 86 22-113 237-323 (467)
15 PHA02768 hypothetical protein; 98.3 8.5E-07 1.9E-11 47.6 2.5 34 81-114 5-39 (55)
16 PLN03086 PRLI-interacting fact 98.2 2.4E-06 5.3E-11 65.7 5.4 84 23-115 454-547 (567)
17 KOG3993|consensus 98.2 1.5E-06 3.2E-11 64.0 3.2 77 28-107 273-382 (500)
18 PF13465 zf-H2C2_2: Zinc-finge 98.2 1.7E-06 3.7E-11 39.5 2.2 26 37-65 1-26 (26)
19 PHA00616 hypothetical protein 98.1 1.7E-06 3.6E-11 44.3 1.3 34 51-86 1-34 (44)
20 PHA00732 hypothetical protein 98.0 4.7E-06 1E-10 48.4 2.7 46 51-104 1-47 (79)
21 COG5189 SFP1 Putative transcri 98.0 2.4E-06 5.2E-11 61.0 1.2 54 49-102 347-419 (423)
22 PHA00733 hypothetical protein 97.9 6.4E-06 1.4E-10 52.2 2.0 63 49-115 38-105 (128)
23 PF00096 zf-C2H2: Zinc finger, 97.8 1.3E-05 2.9E-10 35.3 1.9 22 82-103 1-22 (23)
24 PLN03086 PRLI-interacting fact 97.8 4.7E-05 1E-09 58.8 4.9 60 49-115 451-510 (567)
25 PF13894 zf-C2H2_4: C2H2-type 97.6 5.2E-05 1.1E-09 33.3 2.2 24 82-105 1-24 (24)
26 PF13912 zf-C2H2_6: C2H2-type 97.5 6E-05 1.3E-09 34.5 1.8 25 81-105 1-25 (27)
27 PF05605 zf-Di19: Drought indu 97.5 0.00026 5.6E-09 38.0 4.3 51 51-106 2-54 (54)
28 PF00096 zf-C2H2: Zinc finger, 97.4 0.00014 3.1E-09 31.9 1.8 23 52-76 1-23 (23)
29 PF09237 GAGA: GAGA factor; I 97.4 0.00026 5.7E-09 37.2 2.9 32 78-109 21-52 (54)
30 smart00355 ZnF_C2H2 zinc finge 97.1 0.00069 1.5E-08 30.0 2.5 24 82-105 1-24 (26)
31 PRK04860 hypothetical protein; 96.7 0.0016 3.5E-08 42.8 3.0 36 51-92 119-154 (160)
32 KOG3993|consensus 96.7 0.00019 4.2E-09 53.2 -1.4 53 51-105 267-319 (500)
33 PF13912 zf-C2H2_6: C2H2-type 96.7 0.0011 2.4E-08 30.1 1.5 25 51-77 1-25 (27)
34 PF13909 zf-H2C2_5: C2H2-type 96.7 0.0013 2.8E-08 29.1 1.6 24 82-106 1-24 (24)
35 PF13894 zf-C2H2_4: C2H2-type 96.6 0.0026 5.7E-08 27.6 2.2 23 52-76 1-23 (24)
36 PHA00732 hypothetical protein 96.3 0.005 1.1E-07 35.7 2.9 27 81-107 1-28 (79)
37 PF12756 zf-C2H2_2: C2H2 type 96.1 0.0067 1.4E-07 36.0 3.0 72 26-105 3-74 (100)
38 PF12874 zf-met: Zinc-finger o 95.8 0.0063 1.4E-07 26.9 1.5 21 82-102 1-21 (25)
39 smart00355 ZnF_C2H2 zinc finge 95.7 0.012 2.5E-07 25.7 2.2 24 52-77 1-24 (26)
40 PF09237 GAGA: GAGA factor; I 95.4 0.024 5.2E-07 29.9 2.9 34 46-81 19-52 (54)
41 KOG2893|consensus 94.8 0.0062 1.3E-07 42.3 -0.4 47 47-100 7-53 (341)
42 PRK04860 hypothetical protein; 94.8 0.017 3.8E-07 37.9 1.7 33 80-116 118-150 (160)
43 PF12874 zf-met: Zinc-finger o 94.4 0.026 5.7E-07 24.9 1.3 22 52-75 1-22 (25)
44 COG5048 FOG: Zn-finger [Genera 94.0 0.012 2.7E-07 43.2 -0.4 64 50-115 288-357 (467)
45 PF13913 zf-C2HC_2: zinc-finge 94.0 0.06 1.3E-06 24.0 2.0 19 83-102 4-22 (25)
46 PF12171 zf-C2H2_jaz: Zinc-fin 94.0 0.016 3.6E-07 26.2 0.1 21 82-102 2-22 (27)
47 KOG1146|consensus 92.8 0.094 2E-06 44.5 2.7 74 28-103 442-540 (1406)
48 smart00451 ZnF_U1 U1-like zinc 91.6 0.19 4.2E-06 23.8 2.1 22 81-102 3-24 (35)
49 PF05605 zf-Di19: Drought indu 91.3 0.47 1E-05 25.2 3.5 49 23-76 3-52 (54)
50 cd00350 rubredoxin_like Rubred 87.5 0.56 1.2E-05 22.3 1.8 24 52-89 2-25 (33)
51 KOG2186|consensus 86.2 0.71 1.5E-05 32.5 2.4 46 52-102 4-49 (276)
52 COG4049 Uncharacterized protei 85.1 0.42 9.2E-06 25.6 0.7 25 79-103 15-39 (65)
53 COG5189 SFP1 Putative transcri 83.0 0.41 8.9E-06 34.9 0.2 47 26-74 355-419 (423)
54 PF05443 ROS_MUCR: ROS/MUCR tr 82.5 0.62 1.4E-05 29.7 0.8 25 82-109 73-97 (132)
55 PF09986 DUF2225: Uncharacteri 82.3 0.44 9.6E-06 32.8 0.1 41 50-92 4-59 (214)
56 PF12756 zf-C2H2_2: C2H2 type 81.5 1.6 3.5E-05 25.4 2.4 24 51-76 50-73 (100)
57 PF09538 FYDLN_acid: Protein o 80.5 1.5 3.2E-05 27.0 2.0 31 51-94 9-39 (108)
58 smart00614 ZnF_BED BED zinc fi 77.0 2.6 5.6E-05 21.8 2.0 20 83-102 20-44 (50)
59 PF12013 DUF3505: Protein of u 76.0 2.7 6E-05 25.5 2.3 25 82-106 81-109 (109)
60 cd00729 rubredoxin_SM Rubredox 72.5 3.6 7.8E-05 19.6 1.7 25 51-89 2-26 (34)
61 PF13717 zinc_ribbon_4: zinc-r 72.0 5.4 0.00012 19.3 2.3 33 52-91 3-35 (36)
62 PF13719 zinc_ribbon_5: zinc-r 71.5 5.7 0.00012 19.2 2.4 34 52-92 3-36 (37)
63 TIGR02300 FYDLN_acid conserved 71.5 3.3 7.2E-05 26.2 1.8 35 51-98 9-43 (129)
64 PRK00464 nrdR transcriptional 71.3 0.95 2.1E-05 29.6 -0.6 14 81-94 28-41 (154)
65 COG1592 Rubrerythrin [Energy p 71.0 3.6 7.8E-05 27.3 2.0 24 51-89 134-157 (166)
66 PF02892 zf-BED: BED zinc fing 69.9 5.9 0.00013 19.7 2.3 24 79-102 14-41 (45)
67 smart00659 RPOLCX RNA polymera 68.7 6.2 0.00013 20.1 2.2 27 51-90 2-28 (44)
68 TIGR00373 conserved hypothetic 68.6 8.3 0.00018 25.3 3.3 37 46-93 104-140 (158)
69 COG5048 FOG: Zn-finger [Genera 67.8 6.4 0.00014 28.8 3.0 61 49-111 31-93 (467)
70 COG2888 Predicted Zn-ribbon RN 67.7 4.3 9.4E-05 22.1 1.5 32 51-89 27-58 (61)
71 TIGR02098 MJ0042_CXXC MJ0042 f 67.0 6.8 0.00015 18.8 2.1 34 52-92 3-36 (38)
72 PHA00626 hypothetical protein 66.9 3 6.6E-05 22.4 0.8 16 79-94 21-36 (59)
73 PF04959 ARS2: Arsenite-resist 65.8 5.2 0.00011 27.7 2.0 27 47-75 73-99 (214)
74 KOG4167|consensus 65.1 1.2 2.6E-05 36.1 -1.3 25 81-105 792-816 (907)
75 smart00734 ZnF_Rad18 Rad18-lik 62.4 10 0.00022 16.9 2.0 19 83-102 3-21 (26)
76 PRK06266 transcription initiat 61.6 14 0.0003 24.7 3.4 36 47-93 113-148 (178)
77 PF04959 ARS2: Arsenite-resist 60.3 3.1 6.7E-05 28.8 0.2 31 78-108 74-104 (214)
78 PRK00398 rpoP DNA-directed RNA 59.9 7.9 0.00017 19.6 1.6 29 51-91 3-31 (46)
79 COG1996 RPC10 DNA-directed RNA 57.7 8.1 0.00018 20.2 1.4 29 50-90 5-33 (49)
80 PF10571 UPF0547: Uncharacteri 57.3 6.5 0.00014 17.6 0.9 11 82-92 15-25 (26)
81 COG3357 Predicted transcriptio 56.4 6.7 0.00015 23.3 1.1 28 49-88 56-83 (97)
82 PF03604 DNA_RNApol_7kD: DNA d 56.4 11 0.00025 17.7 1.7 26 52-90 1-26 (32)
83 smart00834 CxxC_CXXC_SSSS Puta 55.1 5.4 0.00012 19.4 0.5 30 51-89 5-34 (41)
84 TIGR02605 CxxC_CxxC_SSSS putat 54.9 5.2 0.00011 20.7 0.5 30 51-89 5-34 (52)
85 smart00531 TFIIE Transcription 52.0 62 0.0013 20.8 5.5 39 47-91 95-133 (147)
86 PF13878 zf-C2H2_3: zinc-finge 51.0 21 0.00046 17.7 2.3 24 82-105 14-39 (41)
87 KOG4167|consensus 46.4 4.4 9.5E-05 33.0 -1.0 24 52-77 793-816 (907)
88 PF02176 zf-TRAF: TRAF-type zi 45.5 27 0.00058 18.3 2.4 42 49-91 7-52 (60)
89 COG4530 Uncharacterized protei 45.3 21 0.00046 22.1 2.0 26 53-91 11-36 (129)
90 PRK14890 putative Zn-ribbon RN 45.1 27 0.00058 19.0 2.2 33 50-89 24-56 (59)
91 KOG2593|consensus 43.9 52 0.0011 25.3 4.3 39 46-89 123-161 (436)
92 KOG4173|consensus 43.8 16 0.00035 25.2 1.5 72 28-105 87-170 (253)
93 KOG3408|consensus 43.5 17 0.00036 22.9 1.4 23 80-102 56-78 (129)
94 PF10013 DUF2256: Uncharacteri 43.0 18 0.0004 18.2 1.3 17 82-98 9-25 (42)
95 PF07754 DUF1610: Domain of un 42.6 14 0.00031 16.2 0.8 8 81-88 16-23 (24)
96 KOG2893|consensus 42.1 7.7 0.00017 27.4 -0.2 43 28-77 16-59 (341)
97 PF15269 zf-C2H2_7: Zinc-finge 41.9 24 0.00051 18.1 1.6 23 82-104 21-43 (54)
98 COG3091 SprT Zn-dependent meta 41.9 16 0.00035 23.9 1.2 8 81-88 140-147 (156)
99 PF09723 Zn-ribbon_8: Zinc rib 41.4 13 0.00028 18.5 0.6 15 81-95 5-19 (42)
100 PRK03824 hypA hydrogenase nick 40.5 13 0.00029 23.6 0.7 39 50-90 69-116 (135)
101 COG1997 RPL43A Ribosomal prote 38.6 26 0.00055 20.7 1.6 32 49-92 33-64 (89)
102 COG3677 Transposase and inacti 37.2 18 0.00039 22.9 1.0 15 78-92 50-64 (129)
103 COG4957 Predicted transcriptio 37.1 27 0.00058 22.5 1.6 20 57-79 80-99 (148)
104 smart00154 ZnF_AN1 AN1-like Zi 36.0 23 0.00049 17.4 1.0 14 81-94 12-25 (39)
105 COG1773 Rubredoxin [Energy pro 34.9 19 0.00042 19.3 0.7 13 80-92 2-14 (55)
106 KOG2295|consensus 32.5 44 0.00096 26.6 2.5 29 46-74 504-532 (648)
107 PRK09678 DNA-binding transcrip 32.3 18 0.0004 20.5 0.4 40 52-95 2-43 (72)
108 PF07975 C1_4: TFIIH C1-like d 32.2 8.1 0.00018 20.4 -1.0 25 80-104 20-44 (51)
109 KOG0717|consensus 30.2 31 0.00067 26.8 1.3 21 82-102 293-313 (508)
110 PLN03238 probable histone acet 30.1 75 0.0016 23.2 3.2 31 79-109 46-76 (290)
111 PF01428 zf-AN1: AN1-like Zinc 30.0 19 0.00042 17.9 0.2 15 80-94 12-26 (43)
112 KOG4124|consensus 29.7 6.4 0.00014 29.3 -2.2 52 49-100 347-417 (442)
113 KOG2071|consensus 29.5 39 0.00084 27.0 1.8 26 79-104 416-441 (579)
114 PF08209 Sgf11: Sgf11 (transcr 29.3 57 0.0012 15.4 1.7 22 82-104 5-26 (33)
115 COG4338 Uncharacterized protei 29.1 23 0.0005 18.4 0.4 17 82-98 13-29 (54)
116 PF08790 zf-LYAR: LYAR-type C2 29.1 12 0.00026 17.1 -0.6 7 57-63 4-10 (28)
117 TIGR00622 ssl1 transcription f 29.0 46 0.001 20.6 1.8 49 53-105 57-105 (112)
118 KOG2231|consensus 28.8 85 0.0018 25.7 3.5 17 57-73 186-202 (669)
119 PF13451 zf-trcl: Probable zin 28.4 28 0.0006 18.2 0.6 17 79-95 2-18 (49)
120 PF04423 Rad50_zn_hook: Rad50 28.3 22 0.00047 18.6 0.2 12 83-94 22-33 (54)
121 KOG2231|consensus 28.0 81 0.0018 25.8 3.3 78 30-108 122-209 (669)
122 KOG2785|consensus 27.8 59 0.0013 24.6 2.4 25 79-103 66-90 (390)
123 KOG0978|consensus 27.6 24 0.00051 28.9 0.4 23 78-100 675-697 (698)
124 TIGR00100 hypA hydrogenase nic 27.5 40 0.00086 20.8 1.3 26 51-90 70-95 (115)
125 PRK12380 hydrogenase nickel in 27.3 44 0.00095 20.5 1.5 25 51-89 70-94 (113)
126 PF01363 FYVE: FYVE zinc finge 27.3 39 0.00085 18.3 1.2 25 53-91 11-35 (69)
127 KOG2482|consensus 26.8 49 0.0011 24.8 1.8 67 35-103 128-217 (423)
128 COG0068 HypF Hydrogenase matur 25.5 7.2 0.00016 31.7 -2.7 27 57-89 155-181 (750)
129 KOG1146|consensus 25.0 19 0.00041 31.6 -0.6 47 57-103 440-487 (1406)
130 PRK04351 hypothetical protein; 23.2 62 0.0013 21.0 1.6 11 80-90 131-141 (149)
131 PF12760 Zn_Tnp_IS1595: Transp 22.9 95 0.0021 15.5 2.0 27 52-89 19-45 (46)
132 PF10537 WAC_Acf1_DNA_bd: ATP- 22.9 1.5E+02 0.0032 18.0 3.1 47 50-99 2-49 (102)
133 KOG2636|consensus 22.1 73 0.0016 24.8 2.0 48 50-102 375-423 (497)
134 cd00065 FYVE FYVE domain; Zinc 22.0 81 0.0018 16.2 1.7 24 57-92 6-29 (57)
135 PF14787 zf-CCHC_5: GAG-polypr 21.6 50 0.0011 16.0 0.7 15 83-97 4-18 (36)
136 COG1571 Predicted DNA-binding 21.0 69 0.0015 24.7 1.7 32 53-97 352-383 (421)
137 PF05191 ADK_lid: Adenylate ki 20.8 34 0.00074 16.5 0.1 32 52-93 2-33 (36)
138 KOG1280|consensus 20.7 1.2E+02 0.0026 22.8 2.8 33 81-113 79-111 (381)
139 PRK00432 30S ribosomal protein 20.6 70 0.0015 16.6 1.2 12 80-91 36-47 (50)
140 smart00064 FYVE Protein presen 20.5 84 0.0018 16.9 1.6 26 53-92 12-37 (68)
141 PLN00104 MYST -like histone ac 20.2 96 0.0021 24.1 2.3 31 79-109 196-226 (450)
142 PTZ00064 histone acetyltransfe 20.1 1.1E+02 0.0024 24.3 2.6 31 79-109 278-308 (552)
No 1
>KOG2462|consensus
Probab=99.74 E-value=1.6e-18 Score=119.49 Aligned_cols=91 Identities=16% Similarity=0.209 Sum_probs=80.7
Q ss_pred ccccccchhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHH
Q psy3946 21 EVLSVLDFEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSH 100 (127)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H 100 (127)
....+..|.+.+..-..|+-|++. |+ -++.| .+|||.|.+.=.|+.|+++|||+|||.|..|+|+|.-+++|+.|
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirT-H~--l~c~C--~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAH 234 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRT-HT--LPCEC--GICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAH 234 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhc-cC--CCccc--ccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHH
Confidence 345667788888888888888765 76 36899 99999999999999999999999999999999999999999999
Q ss_pred HHhcCCCCCCCchhhh
Q psy3946 101 MKHGHKLEHITEDQII 116 (127)
Q Consensus 101 ~~~h~g~k~~~c~~~~ 116 (127)
+++|.+.|+|.|..+.
T Consensus 235 mQTHS~~K~~qC~~C~ 250 (279)
T KOG2462|consen 235 MQTHSDVKKHQCPRCG 250 (279)
T ss_pred HHhhcCCccccCcchh
Confidence 9999999999997654
No 2
>KOG2462|consensus
Probab=99.66 E-value=3.5e-17 Score=112.92 Aligned_cols=78 Identities=17% Similarity=0.344 Sum_probs=71.2
Q ss_pred ccccchhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHH
Q psy3946 23 LSVLDFEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~ 102 (127)
..+..|.+.|...=.|+.|++. |+|||||.| ..|++.|...++|+.|+++|.+.++|+|..|+|+|...+.|++|..
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRT-HTGEKPF~C--~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRT-HTGEKPFSC--PHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred cccccccccccchHHhhccccc-ccCCCCccC--CcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 3566799998877777888765 999999999 9999999999999999999999999999999999999999999987
Q ss_pred h
Q psy3946 103 H 103 (127)
Q Consensus 103 ~ 103 (127)
.
T Consensus 265 S 265 (279)
T KOG2462|consen 265 S 265 (279)
T ss_pred h
Confidence 4
No 3
>KOG3576|consensus
Probab=99.57 E-value=1.1e-15 Score=101.66 Aligned_cols=97 Identities=21% Similarity=0.335 Sum_probs=85.7
Q ss_pred ccccccchhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHH
Q psy3946 21 EVLSVLDFEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSH 100 (127)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H 100 (127)
..+++..|.+.|....-|++|++. |...+.|.| ..||+.|...-.|++|+++|+|.+||+|..|+|+|.++-+|..|
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kc-h~~vkr~lc--t~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKC-HSDVKRHLC--TFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhh-ccHHHHHHH--hhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 446677799999999999999998 999999999 99999999999999999999999999999999999999999999
Q ss_pred HHhcCC-----------CCCCCchhhhhcCC
Q psy3946 101 MKHGHK-----------LEHITEDQIIVRKD 120 (127)
Q Consensus 101 ~~~h~g-----------~k~~~c~~~~~~~~ 120 (127)
++.-+| +|.|-|.++-.+..
T Consensus 193 l~kvhgv~~~yaykerr~kl~vcedcg~t~~ 223 (267)
T KOG3576|consen 193 LKKVHGVQHQYAYKERRAKLYVCEDCGYTSE 223 (267)
T ss_pred HHHHcCchHHHHHHHhhhheeeecccCCCCC
Confidence 987665 46666766655443
No 4
>KOG3623|consensus
Probab=99.43 E-value=5.5e-14 Score=107.72 Aligned_cols=77 Identities=16% Similarity=0.352 Sum_probs=70.7
Q ss_pred ccccchhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHH
Q psy3946 23 LSVLDFEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~ 102 (127)
+.|..|.+.|.-..+|.||.=. |+|.+||+| .+|.|.|..+.+|..|.+.|.|++||+|..|+|.|+...++..|+-
T Consensus 895 yaCDqCDK~FqKqSSLaRHKYE-HsGqRPyqC--~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 895 YACDQCDKAFQKQSSLARHKYE-HSGQRPYQC--IICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred chHHHHHHHHHhhHHHHHhhhh-hcCCCCccc--chhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 4566699999999999999755 999999999 9999999999999999999999999999999999999999999885
No 5
>KOG3623|consensus
Probab=99.30 E-value=7.4e-13 Score=101.66 Aligned_cols=69 Identities=20% Similarity=0.519 Sum_probs=64.9
Q ss_pred cCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHHhcCCCCCCCchhhh
Q psy3946 46 FNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMKHGHKLEHITEDQII 116 (127)
Q Consensus 46 h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~~~c~~~~ 116 (127)
.+...+|.| ..|.|.|...+.|.+|.--|+|.+||+|..|.|.|.....|.-|.|.|.|||||.|+.+.
T Consensus 889 kte~gmyaC--DqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKCl 957 (1007)
T KOG3623|consen 889 KTEDGMYAC--DQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCL 957 (1007)
T ss_pred cCccccchH--HHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhh
Confidence 344568999 999999999999999999999999999999999999999999999999999999998775
No 6
>KOG3576|consensus
Probab=99.19 E-value=4.4e-12 Score=84.64 Aligned_cols=67 Identities=21% Similarity=0.356 Sum_probs=62.5
Q ss_pred CCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHHhcCCCCCCCchhhh
Q psy3946 48 DTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMKHGHKLEHITEDQII 116 (127)
Q Consensus 48 ~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~~~c~~~~ 116 (127)
+...|.| .+|+|.|.....|.+|++.|..-+.+-|..|||.|...-.|++|.++|+|.+||+|..+.
T Consensus 114 d~d~ftC--rvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~ 180 (267)
T KOG3576|consen 114 DQDSFTC--RVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCE 180 (267)
T ss_pred CCCeeee--ehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhh
Confidence 3556999 999999999999999999999999999999999999999999999999999999997654
No 7
>KOG1074|consensus
Probab=98.95 E-value=2.4e-10 Score=89.09 Aligned_cols=58 Identities=26% Similarity=0.336 Sum_probs=43.6
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHHhcCCCCCC
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMKHGHKLEHI 110 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~~ 110 (127)
|-+| .+|.+++...+.|+.|.++|+|++||+|+.||+.|.++.+|+.|+.+|.-.-++
T Consensus 605 PNqC--iiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~ 662 (958)
T KOG1074|consen 605 PNQC--IICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA 662 (958)
T ss_pred ccce--eeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccc
Confidence 5577 777777777777888877888888888888888888888888777777654443
No 8
>PHA02768 hypothetical protein; Provisional
Probab=98.87 E-value=1.1e-09 Score=58.62 Aligned_cols=42 Identities=26% Similarity=0.578 Sum_probs=37.8
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHH
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLL 97 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l 97 (127)
|.| ..||+.|....+|..|+++|+ ++++|..|++.|.+.+.|
T Consensus 6 y~C--~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YEC--PICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCc--chhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 789 999999999999999999998 689999999999877655
No 9
>KOG1074|consensus
Probab=98.84 E-value=7.8e-10 Score=86.34 Aligned_cols=85 Identities=15% Similarity=0.307 Sum_probs=73.6
Q ss_pred ccccccccchhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHHHcCCCC----ceecC---CCCccC
Q psy3946 19 SEEVLSVLDFEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLP----RFHCS---LCPYKS 91 (127)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~----~~~C~---~C~k~f 91 (127)
..+...|.-|.+.-.+...|+-|++. |+|++||+| .+||+.|..+.+|+.|+.+|.... ++.|+ .|-+.|
T Consensus 602 ~TdPNqCiiC~rVlSC~saLqmHyrt-HtGERPFkC--KiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kf 678 (958)
T KOG1074|consen 602 RTDPNQCIICLRVLSCPSALQMHYRT-HTGERPFKC--KICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKF 678 (958)
T ss_pred cCCccceeeeeecccchhhhhhhhhc-ccCcCcccc--ccccchhccccchhhcccccccCccccccccCCchhhhcccc
Confidence 33445677788888899999999976 999999999 999999999999999999887654 46788 888999
Q ss_pred CChHHHHHHHHhcCC
Q psy3946 92 KRRDLLKSHMKHGHK 106 (127)
Q Consensus 92 ~~~~~l~~H~~~h~g 106 (127)
...-.|..|++.|.+
T Consensus 679 tn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 679 TNAVTLPQHIRIHLG 693 (958)
T ss_pred cccccccceEEeecC
Confidence 999999999999983
No 10
>PHA00733 hypothetical protein
Probab=98.82 E-value=1e-08 Score=64.90 Aligned_cols=58 Identities=21% Similarity=0.360 Sum_probs=51.5
Q ss_pred cCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHHhcCCC
Q psy3946 46 FNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMKHGHKL 107 (127)
Q Consensus 46 h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h~g~ 107 (127)
+.+.+||.| ..|++.|.....|..|++.+ ..+|.|..|++.|.....|..|+...++.
T Consensus 68 ~~~~kPy~C--~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 68 SKAVSPYVC--PLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred cCCCCCccC--CCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcCc
Confidence 456889999 99999999999999999876 35799999999999999999999877653
No 11
>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=98.73 E-value=8.6e-09 Score=47.35 Aligned_cols=25 Identities=20% Similarity=0.404 Sum_probs=19.1
Q ss_pred HHHHHHHHcCCCCceecCCCCccCC
Q psy3946 68 SLSRHRQECGQLPRFHCSLCPYKSK 92 (127)
Q Consensus 68 ~l~~h~~~h~~~~~~~C~~C~k~f~ 92 (127)
+|..|+++|++++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 3677778888888888888887775
No 12
>KOG3608|consensus
Probab=98.67 E-value=1.8e-08 Score=72.41 Aligned_cols=92 Identities=17% Similarity=0.315 Sum_probs=54.1
Q ss_pred ccccccchhhHhHhhHHHHHhHHh-hcCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHH
Q psy3946 21 EVLSVLDFEKEERMNDVYNRNMKK-NFNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKS 99 (127)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~-~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~ 99 (127)
+++-+..|..-|..+..|-.|+++ +-....+|+| ..|.|.|.....|..|+..|.. .|+|+.|.-+....+.|..
T Consensus 206 KvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC--~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL~~ 281 (467)
T KOG3608|consen 206 KVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQC--AQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSLTT 281 (467)
T ss_pred eEEecchHHHHhccccHHHHHHHhhhhhcCCchHH--HHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCChHHHHH
Confidence 334444455555555444444322 1222345555 5555666655556666555533 4677777777777788888
Q ss_pred HHHh-cCCCCCCCchhhh
Q psy3946 100 HMKH-GHKLEHITEDQII 116 (127)
Q Consensus 100 H~~~-h~g~k~~~c~~~~ 116 (127)
|+++ |...|||+|++..
T Consensus 282 H~r~rHs~dkpfKCd~Cd 299 (467)
T KOG3608|consen 282 HIRYRHSKDKPFKCDECD 299 (467)
T ss_pred HHHhhhccCCCccccchh
Confidence 8774 5678888887665
No 13
>PHA00616 hypothetical protein
Probab=98.64 E-value=1.4e-08 Score=51.96 Aligned_cols=33 Identities=18% Similarity=0.365 Sum_probs=25.1
Q ss_pred ceecCCCCccCCChHHHHHHHHhcCCCCCCCch
Q psy3946 81 RFHCSLCPYKSKRRDLLKSHMKHGHKLEHITED 113 (127)
Q Consensus 81 ~~~C~~C~k~f~~~~~l~~H~~~h~g~k~~~c~ 113 (127)
||+|..||+.|.+.+.|..|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 577777777777777778888777777777664
No 14
>KOG3608|consensus
Probab=98.55 E-value=1.7e-07 Score=67.58 Aligned_cols=86 Identities=16% Similarity=0.304 Sum_probs=58.3
Q ss_pred cccccchhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHH-HcCCCCceecCCCCccCCChHHHHHH
Q psy3946 22 VLSVLDFEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQ-ECGQLPRFHCSLCPYKSKRRDLLKSH 100 (127)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~-~h~~~~~~~C~~C~k~f~~~~~l~~H 100 (127)
.+.+..|.+.|.....|..|+.+ |.. -|.| +.|.-.....+.|..|++ .|..++||+|..|.+.|...+.|++|
T Consensus 237 ~fqC~~C~KrFaTeklL~~Hv~r-Hvn--~ykC--plCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH 311 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLKSHVVR-HVN--CYKC--PLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKH 311 (467)
T ss_pred chHHHHHHHHHhHHHHHHHHHHH-hhh--cccc--cccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHH
Confidence 45566677777777777777655 443 3667 777777777777777766 46667777777777777777777777
Q ss_pred HHhcCCCCCCCch
Q psy3946 101 MKHGHKLEHITED 113 (127)
Q Consensus 101 ~~~h~g~k~~~c~ 113 (127)
..+|. +-.|.|+
T Consensus 312 ~~~HS-~~~y~C~ 323 (467)
T KOG3608|consen 312 VQVHS-KTVYQCE 323 (467)
T ss_pred HHhcc-ccceecC
Confidence 77666 4445554
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.25 E-value=8.5e-07 Score=47.55 Aligned_cols=34 Identities=15% Similarity=0.413 Sum_probs=27.8
Q ss_pred ceecCCCCccCCChHHHHHHHHhcC-CCCCCCchh
Q psy3946 81 RFHCSLCPYKSKRRDLLKSHMKHGH-KLEHITEDQ 114 (127)
Q Consensus 81 ~~~C~~C~k~f~~~~~l~~H~~~h~-g~k~~~c~~ 114 (127)
-|.|+.||+.|...+.|..|+++|+ +.+...|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCcccCCcccc
Confidence 3899999999999999999999999 444444443
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.22 E-value=2.4e-06 Score=65.68 Aligned_cols=84 Identities=17% Similarity=0.296 Sum_probs=64.6
Q ss_pred ccccchhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCC---------
Q psy3946 23 LSVLDFEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKR--------- 93 (127)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~--------- 93 (127)
+.|..|...+. ...+..|+.. ++ .++.| . |++.+ ....|..|+.+|.+.+++.|..|++.|..
T Consensus 454 ~~C~~Cgk~f~-~s~LekH~~~-~H--kpv~C--p-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d 525 (567)
T PLN03086 454 VHCEKCGQAFQ-QGEMEKHMKV-FH--EPLQC--P-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRD 525 (567)
T ss_pred ccCCCCCCccc-hHHHHHHHHh-cC--CCccC--C-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhh
Confidence 34555766664 4667888766 43 78999 7 99755 56789999999999999999999988842
Q ss_pred -hHHHHHHHHhcCCCCCCCchhh
Q psy3946 94 -RDLLKSHMKHGHKLEHITEDQI 115 (127)
Q Consensus 94 -~~~l~~H~~~h~g~k~~~c~~~ 115 (127)
...|..|...+ |.+++.|..+
T Consensus 526 ~~s~Lt~HE~~C-G~rt~~C~~C 547 (567)
T PLN03086 526 RLRGMSEHESIC-GSRTAPCDSC 547 (567)
T ss_pred hhhhHHHHHHhc-CCcceEcccc
Confidence 35789998886 8899988544
No 17
>KOG3993|consensus
Probab=98.17 E-value=1.5e-06 Score=64.02 Aligned_cols=77 Identities=21% Similarity=0.365 Sum_probs=56.7
Q ss_pred hhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHHHcCCC--------C-------------------
Q psy3946 28 FEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQL--------P------------------- 80 (127)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~--------~------------------- 80 (127)
|...+.-.--|.+|.-. -.-...|.| ..|+|.|....+|..|.++|..+ .
T Consensus 273 CK~kYeD~F~LAQHrC~-RIV~vEYrC--PEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg 349 (500)
T KOG3993|consen 273 CKEKYEDAFALAQHRCP-RIVHVEYRC--PECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSG 349 (500)
T ss_pred HHHhhhhHHHHhhccCC-eeEEeeecC--CcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccC
Confidence 33333333345555321 333456999 99999999999999999998421 1
Q ss_pred ------ceecCCCCccCCChHHHHHHHHhcCCC
Q psy3946 81 ------RFHCSLCPYKSKRRDLLKSHMKHGHKL 107 (127)
Q Consensus 81 ------~~~C~~C~k~f~~~~~l~~H~~~h~g~ 107 (127)
-|.|..|+|.|.....|+.|+.+|+..
T Consensus 350 ~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 350 DDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred CcccCceeecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 278999999999999999999988753
No 18
>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=98.16 E-value=1.7e-06 Score=39.55 Aligned_cols=26 Identities=23% Similarity=0.694 Sum_probs=22.7
Q ss_pred HHHHhHHhhcCCCcceeCCCCCCCccccC
Q psy3946 37 VYNRNMKKNFNDTGVFQCPVPNCNRVYSR 65 (127)
Q Consensus 37 ~~~~~~~~~h~~~~p~~C~~~~C~~~f~~ 65 (127)
+|.+|++. |++++||.| ..|++.|..
T Consensus 1 ~l~~H~~~-H~~~k~~~C--~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRT-HTGEKPYKC--PYCGKSFSN 26 (26)
T ss_dssp HHHHHHHH-HSSSSSEEE--SSSSEEESS
T ss_pred CHHHHhhh-cCCCCCCCC--CCCcCeeCc
Confidence 47889876 999999999 999999863
No 19
>PHA00616 hypothetical protein
Probab=98.07 E-value=1.7e-06 Score=44.31 Aligned_cols=34 Identities=12% Similarity=0.487 Sum_probs=31.4
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCC
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSL 86 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~ 86 (127)
||+| ..||+.|...+.+..|++.|+++.++.|..
T Consensus 1 pYqC--~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQC--LRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCcc--chhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6899 999999999999999999999999988764
No 20
>PHA00732 hypothetical protein
Probab=98.02 E-value=4.7e-06 Score=48.36 Aligned_cols=46 Identities=22% Similarity=0.477 Sum_probs=37.5
Q ss_pred ceeCCCCCCCccccCchHHHHHHH-HcCCCCceecCCCCccCCChHHHHHHHHhc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQ-ECGQLPRFHCSLCPYKSKRRDLLKSHMKHG 104 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~-~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h 104 (127)
||.| ..|++.|.....|..|++ .|.+ +.|..|++.|. .+..|..+.
T Consensus 1 py~C--~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKC--PICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccC--CCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhhccc
Confidence 5789 999999999999999998 4653 58999999997 467777543
No 21
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.99 E-value=2.4e-06 Score=60.96 Aligned_cols=54 Identities=28% Similarity=0.565 Sum_probs=46.5
Q ss_pred CcceeCCCCCCCccccCchHHHHHHHH-cC------------------CCCceecCCCCccCCChHHHHHHHH
Q psy3946 49 TGVFQCPVPNCNRVYSRRRSLSRHRQE-CG------------------QLPRFHCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 49 ~~p~~C~~~~C~~~f~~~~~l~~h~~~-h~------------------~~~~~~C~~C~k~f~~~~~l~~H~~ 102 (127)
++||.||...|.|.+..+.-|+.|+.. |. ..+||+|.+|+|.+.....|+.|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 599999999999999999999999862 30 2389999999999999999988865
No 22
>PHA00733 hypothetical protein
Probab=97.91 E-value=6.4e-06 Score=52.17 Aligned_cols=63 Identities=11% Similarity=0.086 Sum_probs=48.8
Q ss_pred CcceeCCCCCCCccccCchHHHHH--HH---HcCCCCceecCCCCccCCChHHHHHHHHhcCCCCCCCchhh
Q psy3946 49 TGVFQCPVPNCNRVYSRRRSLSRH--RQ---ECGQLPRFHCSLCPYKSKRRDLLKSHMKHGHKLEHITEDQI 115 (127)
Q Consensus 49 ~~p~~C~~~~C~~~f~~~~~l~~h--~~---~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~~~c~~~ 115 (127)
.+++.| ..|.+.|.....|..+ .. .+.+.+||.|..|++.|.....|..|++.+ +.++.|...
T Consensus 38 ~~~~~~--~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~C 105 (128)
T PHA00733 38 QKRLIR--AVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVC 105 (128)
T ss_pred hhhHHH--HHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCC
Confidence 456889 8898888877766665 11 334578999999999999999999999976 456777654
No 23
>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=97.84 E-value=1.3e-05 Score=35.26 Aligned_cols=22 Identities=27% Similarity=0.700 Sum_probs=14.1
Q ss_pred eecCCCCccCCChHHHHHHHHh
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMKH 103 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~~ 103 (127)
|.|..|++.|.....|..|++.
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 4566666666666666666654
No 24
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.76 E-value=4.7e-05 Score=58.77 Aligned_cols=60 Identities=15% Similarity=0.368 Sum_probs=50.9
Q ss_pred CcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHHhcCCCCCCCchhh
Q psy3946 49 TGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMKHGHKLEHITEDQI 115 (127)
Q Consensus 49 ~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~~~c~~~ 115 (127)
.+.|.| ..|++.|. ...+..|+..|. +++.|+ |++.+ ....|..|+.+|-+++++.|.-+
T Consensus 451 ~~H~~C--~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC 510 (567)
T PLN03086 451 KNHVHC--EKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFC 510 (567)
T ss_pred ccCccC--CCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCC
Confidence 456789 99999996 577999999874 789999 99755 67899999999999999999744
No 25
>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=97.64 E-value=5.2e-05 Score=33.34 Aligned_cols=24 Identities=29% Similarity=0.765 Sum_probs=15.6
Q ss_pred eecCCCCccCCChHHHHHHHHhcC
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMKHGH 105 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~~h~ 105 (127)
|.|..|++.|.....|..|++.++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 567777777777777777777653
No 26
>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=97.54 E-value=6e-05 Score=34.48 Aligned_cols=25 Identities=20% Similarity=0.389 Sum_probs=17.5
Q ss_pred ceecCCCCccCCChHHHHHHHHhcC
Q psy3946 81 RFHCSLCPYKSKRRDLLKSHMKHGH 105 (127)
Q Consensus 81 ~~~C~~C~k~f~~~~~l~~H~~~h~ 105 (127)
+|.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 4667777777777777777776654
No 27
>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=97.52 E-value=0.00026 Score=38.01 Aligned_cols=51 Identities=27% Similarity=0.563 Sum_probs=39.4
Q ss_pred ceeCCCCCCCccccCchHHHHHHH-HcCCC-CceecCCCCccCCChHHHHHHHHhcCC
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQ-ECGQL-PRFHCSLCPYKSKRRDLLKSHMKHGHK 106 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~-~h~~~-~~~~C~~C~k~f~~~~~l~~H~~~h~g 106 (127)
.|.| +.|++ ......|..|.. .|..+ +.+.|+.|...+. .+|..|+..+++
T Consensus 2 ~f~C--P~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTC--PYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCC--CCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 4889 99999 455678999976 56654 5799999987544 489999988764
No 28
>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=97.38 E-value=0.00014 Score=31.86 Aligned_cols=23 Identities=30% Similarity=0.879 Sum_probs=21.0
Q ss_pred eeCCCCCCCccccCchHHHHHHHHc
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQEC 76 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h 76 (127)
|.| ..|++.|.....|..|++.|
T Consensus 1 y~C--~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKC--PICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEE--TTTTEEESSHHHHHHHHHHH
T ss_pred CCC--CCCCCccCCHHHHHHHHhHC
Confidence 689 99999999999999999864
No 29
>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=97.35 E-value=0.00026 Score=37.17 Aligned_cols=32 Identities=16% Similarity=0.286 Sum_probs=22.2
Q ss_pred CCCceecCCCCccCCChHHHHHHHHhcCCCCC
Q psy3946 78 QLPRFHCSLCPYKSKRRDLLKSHMKHGHKLEH 109 (127)
Q Consensus 78 ~~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~ 109 (127)
...|-.|+.|+..+.+..+|.+|++++++.||
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 45678899999888888999999988888876
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.09 E-value=0.00069 Score=29.97 Aligned_cols=24 Identities=29% Similarity=0.570 Sum_probs=16.4
Q ss_pred eecCCCCccCCChHHHHHHHHhcC
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMKHGH 105 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~~h~ 105 (127)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 456777777777777777776543
No 31
>PRK04860 hypothetical protein; Provisional
Probab=96.74 E-value=0.0016 Score=42.77 Aligned_cols=36 Identities=17% Similarity=0.498 Sum_probs=19.0
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCC
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSK 92 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~ 92 (127)
+|.| . |+. ....+..|.++|++.++|.|..|+..|.
T Consensus 119 ~Y~C--~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 119 PYRC--K-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEc--C-CCC---eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 3555 4 554 3334555555555555555555555443
No 32
>KOG3993|consensus
Probab=96.74 E-value=0.00019 Score=53.17 Aligned_cols=53 Identities=21% Similarity=0.325 Sum_probs=47.1
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHHhcC
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMKHGH 105 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h~ 105 (127)
.|.| +.|.-.|-..-.|.+|....-...-|+|+.|+|.|+...+|..|+|-|.
T Consensus 267 dyiC--qLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 267 DYIC--QLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHH--HHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccC
Confidence 4889 9999999999999999875555667999999999999999999999774
No 33
>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=96.69 E-value=0.0011 Score=30.10 Aligned_cols=25 Identities=24% Similarity=0.671 Sum_probs=22.5
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcC
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECG 77 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~ 77 (127)
||.| ..|++.|.....|..|++.|.
T Consensus 1 ~~~C--~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFEC--DECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEE--TTTTEEESSHHHHHHHHCTTT
T ss_pred CCCC--CccCCccCChhHHHHHhHHhc
Confidence 5899 999999999999999998663
No 34
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.68 E-value=0.0013 Score=29.06 Aligned_cols=24 Identities=33% Similarity=0.845 Sum_probs=16.9
Q ss_pred eecCCCCccCCChHHHHHHHHhcCC
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMKHGHK 106 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~~h~g 106 (127)
|+|..|++... ...|..|++.+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 67888887777 7788888887653
No 35
>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=96.56 E-value=0.0026 Score=27.57 Aligned_cols=23 Identities=30% Similarity=0.821 Sum_probs=19.0
Q ss_pred eeCCCCCCCccccCchHHHHHHHHc
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQEC 76 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h 76 (127)
|.| ..|++.|.....|..|+..+
T Consensus 1 ~~C--~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQC--PICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE---SSTS-EESSHHHHHHHHHHH
T ss_pred CCC--cCCCCcCCcHHHHHHHHHhh
Confidence 689 99999999999999998864
No 36
>PHA00732 hypothetical protein
Probab=96.30 E-value=0.005 Score=35.70 Aligned_cols=27 Identities=22% Similarity=0.474 Sum_probs=23.5
Q ss_pred ceecCCCCccCCChHHHHHHHHh-cCCC
Q psy3946 81 RFHCSLCPYKSKRRDLLKSHMKH-GHKL 107 (127)
Q Consensus 81 ~~~C~~C~k~f~~~~~l~~H~~~-h~g~ 107 (127)
||.|..|++.|.+...|..|++. |.+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~ 28 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLT 28 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCC
Confidence 58999999999999999999985 6543
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.13 E-value=0.0067 Score=35.96 Aligned_cols=72 Identities=21% Similarity=0.215 Sum_probs=22.2
Q ss_pred cchhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHHhcC
Q psy3946 26 LDFEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMKHGH 105 (127)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h~ 105 (127)
.-|...+.....+..|+...|.-..+-. ..+.....+..+.... ....+.|..|++.|.....|..|++.+.
T Consensus 3 ~~C~~~f~~~~~l~~H~~~~H~~~~~~~-------~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 3 LFCDESFSSVDDLLQHMKKKHGFDIPDQ-------KYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred cccccccccccccccccccccccccccc-------cccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 3456666666777777766554432210 1111222222232211 1236999999999999999999999753
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.83 E-value=0.0063 Score=26.94 Aligned_cols=21 Identities=24% Similarity=0.702 Sum_probs=13.1
Q ss_pred eecCCCCccCCChHHHHHHHH
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~ 102 (127)
|.|..|.+.|.....|..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 456666666666666666655
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.73 E-value=0.012 Score=25.74 Aligned_cols=24 Identities=25% Similarity=0.851 Sum_probs=21.0
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcC
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECG 77 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~ 77 (127)
|.| ..|++.|.....+..|++.|.
T Consensus 1 ~~C--~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRC--PECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCC--CCCcchhCCHHHHHHHHHHhc
Confidence 568 999999999999999998664
No 40
>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=95.43 E-value=0.024 Score=29.85 Aligned_cols=34 Identities=24% Similarity=0.312 Sum_probs=23.7
Q ss_pred cCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCc
Q psy3946 46 FNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPR 81 (127)
Q Consensus 46 h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~ 81 (127)
+..+.|..| +.|+..+....+|.+|+..+.+.+|
T Consensus 19 ~~S~~PatC--P~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATC--PICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE---TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCC--CcchhhccchhhHHHHHHHHhcccC
Confidence 566789999 9999999999999999986656554
No 41
>KOG2893|consensus
Probab=94.84 E-value=0.0062 Score=42.33 Aligned_cols=47 Identities=26% Similarity=0.495 Sum_probs=36.1
Q ss_pred CCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHH
Q psy3946 47 NDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSH 100 (127)
Q Consensus 47 ~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H 100 (127)
...+|| | ..|++.|.....|..|++ -+.|+|-.|-|.+-+...|..|
T Consensus 7 k~~kpw-c--wycnrefddekiliqhqk----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 7 KVDKPW-C--WYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ccCCce-e--eecccccchhhhhhhhhh----hccceeeeehhhhccCCCceee
Confidence 345677 5 689999999999999987 4679999998765555555444
No 42
>PRK04860 hypothetical protein; Provisional
Probab=94.84 E-value=0.017 Score=37.94 Aligned_cols=33 Identities=9% Similarity=0.102 Sum_probs=28.1
Q ss_pred CceecCCCCccCCChHHHHHHHHhcCCCCCCCchhhh
Q psy3946 80 PRFHCSLCPYKSKRRDLLKSHMKHGHKLEHITEDQII 116 (127)
Q Consensus 80 ~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~~~c~~~~ 116 (127)
-+|.|. |+. ....+.+|.++|+|+++|.|..+.
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~ 150 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCG 150 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCC
Confidence 369998 987 677889999999999999997654
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.43 E-value=0.026 Score=24.85 Aligned_cols=22 Identities=36% Similarity=0.774 Sum_probs=19.9
Q ss_pred eeCCCCCCCccccCchHHHHHHHH
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQE 75 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~ 75 (127)
|.| ..|+..|.....+..|++.
T Consensus 1 ~~C--~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYC--DICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEE--TTTTEEESSHHHHHHHHTT
T ss_pred CCC--CCCCCCcCCHHHHHHHHCc
Confidence 679 9999999999999999874
No 44
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.04 E-value=0.012 Score=43.23 Aligned_cols=64 Identities=27% Similarity=0.424 Sum_probs=55.8
Q ss_pred cceeCCCCCCCccccCchHHHHHHH--HcCCC--CceecC--CCCccCCChHHHHHHHHhcCCCCCCCchhh
Q psy3946 50 GVFQCPVPNCNRVYSRRRSLSRHRQ--ECGQL--PRFHCS--LCPYKSKRRDLLKSHMKHGHKLEHITEDQI 115 (127)
Q Consensus 50 ~p~~C~~~~C~~~f~~~~~l~~h~~--~h~~~--~~~~C~--~C~k~f~~~~~l~~H~~~h~g~k~~~c~~~ 115 (127)
.++.| ..|...|.....+..|.+ .|+++ +++.|. .|++.|.+...+..|..+|.+..+..+...
T Consensus 288 ~~~~~--~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 357 (467)
T COG5048 288 LPIKS--KQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLL 357 (467)
T ss_pred cCCCC--ccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccc
Confidence 36778 999999999999999999 89999 999999 799999999999999999998887765433
No 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.00 E-value=0.06 Score=24.03 Aligned_cols=19 Identities=37% Similarity=0.641 Sum_probs=10.4
Q ss_pred ecCCCCccCCChHHHHHHHH
Q psy3946 83 HCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 83 ~C~~C~k~f~~~~~l~~H~~ 102 (127)
.|..||+.| ..+.|.+|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455666666 4445555554
No 46
>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=93.97 E-value=0.016 Score=26.23 Aligned_cols=21 Identities=38% Similarity=0.654 Sum_probs=14.0
Q ss_pred eecCCCCccCCChHHHHHHHH
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~ 102 (127)
|-|..|++.|.....+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 556777777777777666654
No 47
>KOG1146|consensus
Probab=92.79 E-value=0.094 Score=44.45 Aligned_cols=74 Identities=18% Similarity=0.300 Sum_probs=56.4
Q ss_pred hhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHHH-c------------------------CCCCce
Q psy3946 28 FEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQE-C------------------------GQLPRF 82 (127)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~-h------------------------~~~~~~ 82 (127)
++..+.....+..++...+.--+.+.| +.|+-.|.....|..|++. | .+.++|
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~~kt~~c--pkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~ 519 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSFFKTLKC--PKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPY 519 (1406)
T ss_pred hhhhhhhhcccccceeeeecccccccC--CccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcc
Confidence 444444444555555455666688999 9999999999999999986 1 123678
Q ss_pred ecCCCCccCCChHHHHHHHHh
Q psy3946 83 HCSLCPYKSKRRDLLKSHMKH 103 (127)
Q Consensus 83 ~C~~C~k~f~~~~~l~~H~~~ 103 (127)
.|..|...+.....|.+|+..
T Consensus 520 ~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 520 PCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cceeeeeeeecchHHHHHHHH
Confidence 999999999999999999874
No 48
>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=91.62 E-value=0.19 Score=23.80 Aligned_cols=22 Identities=27% Similarity=0.555 Sum_probs=15.9
Q ss_pred ceecCCCCccCCChHHHHHHHH
Q psy3946 81 RFHCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 81 ~~~C~~C~k~f~~~~~l~~H~~ 102 (127)
+|.|..|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4677778777777777777765
No 49
>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=91.26 E-value=0.47 Score=25.15 Aligned_cols=49 Identities=14% Similarity=0.197 Sum_probs=34.5
Q ss_pred ccccchhhHhHhhHHHHHhHHhhcCCC-cceeCCCCCCCccccCchHHHHHHHHc
Q psy3946 23 LSVLDFEKEERMNDVYNRNMKKNFNDT-GVFQCPVPNCNRVYSRRRSLSRHRQEC 76 (127)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~h~~~-~p~~C~~~~C~~~f~~~~~l~~h~~~h 76 (127)
+.+.-|.+ ......|..|....|..+ +.+.| ++|...+. ..|..|+..+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~C--PiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVC--PICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccC--CCchhhhh--hHHHHHHHHh
Confidence 34455666 344567888987778764 57899 99998655 3788888743
No 50
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=87.50 E-value=0.56 Score=22.27 Aligned_cols=24 Identities=25% Similarity=0.891 Sum_probs=17.7
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
|.| ..||..+.-.. .++.|+.|+.
T Consensus 2 ~~C--~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVC--PVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EEC--CCCCCEECCCc------------CCCcCcCCCC
Confidence 788 89987655332 6789999975
No 51
>KOG2186|consensus
Probab=86.17 E-value=0.71 Score=32.53 Aligned_cols=46 Identities=26% Similarity=0.567 Sum_probs=33.3
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHH
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~ 102 (127)
|.| ..||...... .+..|+....+ ..|.|..|++.|-. ..+..|..
T Consensus 4 FtC--nvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTC--NVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eeh--hhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 678 8888776655 46668876666 56888889988866 56666654
No 52
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=85.12 E-value=0.42 Score=25.65 Aligned_cols=25 Identities=20% Similarity=0.352 Sum_probs=12.2
Q ss_pred CCceecCCCCccCCChHHHHHHHHh
Q psy3946 79 LPRFHCSLCPYKSKRRDLLKSHMKH 103 (127)
Q Consensus 79 ~~~~~C~~C~k~f~~~~~l~~H~~~ 103 (127)
+.-++|+-|+..|.....+.+|...
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3344555555555555555555443
No 53
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=82.99 E-value=0.41 Score=34.92 Aligned_cols=47 Identities=17% Similarity=0.381 Sum_probs=37.4
Q ss_pred cchhhHhHhhHHHHHhHHhhcCC------------------CcceeCCCCCCCccccCchHHHHHHH
Q psy3946 26 LDFEKEERMNDVYNRNMKKNFND------------------TGVFQCPVPNCNRVYSRRRSLSRHRQ 74 (127)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~h~~------------------~~p~~C~~~~C~~~f~~~~~l~~h~~ 74 (127)
..|++..+.+.-|+.|+...|.. .+||.| ..|+|.+....-|+.|+.
T Consensus 355 ~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrC--evC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 355 EGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRC--EVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceec--cccchhhccCccceeccc
Confidence 44888888888888887665511 379999 999999999888888764
No 54
>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=82.47 E-value=0.62 Score=29.67 Aligned_cols=25 Identities=32% Similarity=0.466 Sum_probs=14.0
Q ss_pred eecCCCCccCCChHHHHHHHHhcCCCCC
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMKHGHKLEH 109 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~~h~g~k~ 109 (127)
..|..||+.|... ++|++.|+|.-|
T Consensus 73 i~clecGk~~k~L---krHL~~~~gltp 97 (132)
T PF05443_consen 73 IICLECGKKFKTL---KRHLRTHHGLTP 97 (132)
T ss_dssp EE-TBT--EESBH---HHHHHHTT-S-H
T ss_pred eEEccCCcccchH---HHHHHHccCCCH
Confidence 5677788776543 788888877654
No 55
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=82.27 E-value=0.44 Score=32.80 Aligned_cols=41 Identities=17% Similarity=0.463 Sum_probs=28.6
Q ss_pred cceeCCCCCCCccccCchHHHHHHHH---cC-------CCCc-----eecCCCCccCC
Q psy3946 50 GVFQCPVPNCNRVYSRRRSLSRHRQE---CG-------QLPR-----FHCSLCPYKSK 92 (127)
Q Consensus 50 ~p~~C~~~~C~~~f~~~~~l~~h~~~---h~-------~~~~-----~~C~~C~k~f~ 92 (127)
+...| +.|++.|..........+. .+ +..| +.|+.||.++.
T Consensus 4 k~~~C--PvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~ 59 (214)
T PF09986_consen 4 KKITC--PVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAF 59 (214)
T ss_pred CceEC--CCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccc
Confidence 56789 9999999988766655442 11 1222 47999998765
No 56
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=81.48 E-value=1.6 Score=25.40 Aligned_cols=24 Identities=33% Similarity=0.859 Sum_probs=21.2
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQEC 76 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h 76 (127)
.+.| ..|++.|.....|..|++.+
T Consensus 50 ~~~C--~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRC--PYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEB--SSSS-EESSHHHHHHHHHHT
T ss_pred CCCC--CccCCCCcCHHHHHHHHcCc
Confidence 6999 99999999999999999854
No 57
>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=80.49 E-value=1.5 Score=26.95 Aligned_cols=31 Identities=16% Similarity=0.394 Sum_probs=24.2
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCCh
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRR 94 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~ 94 (127)
...| +.||+.|.-. +..|..|+.||..|.-.
T Consensus 9 KR~C--p~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTC--PSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccC--CCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 4579 9999988743 35788999999887655
No 58
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=76.96 E-value=2.6 Score=21.84 Aligned_cols=20 Identities=30% Similarity=0.687 Sum_probs=10.7
Q ss_pred ecCCCCccCCCh-----HHHHHHHH
Q psy3946 83 HCSLCPYKSKRR-----DLLKSHMK 102 (127)
Q Consensus 83 ~C~~C~k~f~~~-----~~l~~H~~ 102 (127)
.|..|++.+... +.|.+|+.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 455555544433 46666665
No 59
>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=76.01 E-value=2.7 Score=25.51 Aligned_cols=25 Identities=20% Similarity=0.736 Sum_probs=22.9
Q ss_pred eec----CCCCccCCChHHHHHHHHhcCC
Q psy3946 82 FHC----SLCPYKSKRRDLLKSHMKHGHK 106 (127)
Q Consensus 82 ~~C----~~C~k~f~~~~~l~~H~~~h~g 106 (127)
|.| ..|++.+.+...+..|.+.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 8999999999999999998775
No 60
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=72.48 E-value=3.6 Score=19.62 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=17.5
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
.|.| ..||..+.-. ..|..|+.|+.
T Consensus 2 ~~~C--~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVC--PVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEEC--CCCCCEeECC------------cCCCcCcCCCC
Confidence 4789 9998654422 25678999985
No 61
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=72.00 E-value=5.4 Score=19.27 Aligned_cols=33 Identities=24% Similarity=0.444 Sum_probs=21.1
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccC
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKS 91 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f 91 (127)
..| +.|+..|...... +.......+|..|+..|
T Consensus 3 i~C--p~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITC--PNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEC--CCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 467 8888877765431 22334457888888765
No 62
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=71.53 E-value=5.7 Score=19.24 Aligned_cols=34 Identities=18% Similarity=0.442 Sum_probs=22.2
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCC
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSK 92 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~ 92 (127)
..| +.|+..|..... +...+.+..+|..|+..|.
T Consensus 3 i~C--P~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITC--PNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EEC--CCCCceEEcCHH-----HcccCCcEEECCCCCcEee
Confidence 468 888888876543 1223345688888887663
No 63
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=71.49 E-value=3.3 Score=26.16 Aligned_cols=35 Identities=14% Similarity=0.090 Sum_probs=25.5
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHH
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLK 98 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~ 98 (127)
...| +.||+.|... ++.|..|+.||..|.-...++
T Consensus 9 Kr~C--p~cg~kFYDL-----------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 9 KRIC--PNTGSKFYDL-----------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cccC--CCcCcccccc-----------CCCCccCCCcCCccCcchhhc
Confidence 4579 9999988742 357899999998875553433
No 64
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=71.31 E-value=0.95 Score=29.62 Aligned_cols=14 Identities=21% Similarity=0.346 Sum_probs=10.1
Q ss_pred ceecCCCCccCCCh
Q psy3946 81 RFHCSLCPYKSKRR 94 (127)
Q Consensus 81 ~~~C~~C~k~f~~~ 94 (127)
.++|+.||++|...
T Consensus 28 ~~~c~~c~~~f~~~ 41 (154)
T PRK00464 28 RRECLACGKRFTTF 41 (154)
T ss_pred eeeccccCCcceEe
Confidence 47888888887543
No 65
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=71.00 E-value=3.6 Score=27.30 Aligned_cols=24 Identities=25% Similarity=0.591 Sum_probs=19.1
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
-|.| ..||.. +-++.|.+|+.||-
T Consensus 134 ~~vC--~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVC--PVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEc--CCCCCc-------------ccCCCCCcCCCCCC
Confidence 6999 999853 44577999999983
No 66
>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=69.92 E-value=5.9 Score=19.71 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=12.4
Q ss_pred CCceecCCCCccCCCh----HHHHHHHH
Q psy3946 79 LPRFHCSLCPYKSKRR----DLLKSHMK 102 (127)
Q Consensus 79 ~~~~~C~~C~k~f~~~----~~l~~H~~ 102 (127)
.....|..|++.+... ..|.+|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 3445677777665543 56777774
No 67
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=68.74 E-value=6.2 Score=20.05 Aligned_cols=27 Identities=22% Similarity=0.690 Sum_probs=19.4
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCcc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYK 90 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~ 90 (127)
.|.| ..||..|... ...+.+|+.||..
T Consensus 2 ~Y~C--~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYIC--GECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EEEC--CCCCCEeecC-----------CCCceECCCCCce
Confidence 3789 9999877643 2346889999854
No 68
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=68.62 E-value=8.3 Score=25.26 Aligned_cols=37 Identities=19% Similarity=0.386 Sum_probs=27.6
Q ss_pred cCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCC
Q psy3946 46 FNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKR 93 (127)
Q Consensus 46 h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~ 93 (127)
.....-|.| +.|+..|....++. .-|.|+.||..+..
T Consensus 104 e~~~~~Y~C--p~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 104 ETNNMFFIC--PNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred ccCCCeEEC--CCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 455566899 99999888766653 25999999976543
No 69
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=67.80 E-value=6.4 Score=28.85 Aligned_cols=61 Identities=26% Similarity=0.391 Sum_probs=45.6
Q ss_pred CcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCC--CCccCCChHHHHHHHHhcCCCCCCC
Q psy3946 49 TGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSL--CPYKSKRRDLLKSHMKHGHKLEHIT 111 (127)
Q Consensus 49 ~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~--C~k~f~~~~~l~~H~~~h~g~k~~~ 111 (127)
.+.+.| ..|...|........|...+++.+++.|.. |...+.....+..|...++......
T Consensus 31 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (467)
T COG5048 31 PRPDSC--PNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSDL 93 (467)
T ss_pred Cchhhc--ccccccccccchhhhhcccccccCCccccccccccccCCcchhhhhccccccccccc
Confidence 345678 888888888888888888888888888876 5566777777777777776554443
No 70
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=67.67 E-value=4.3 Score=22.10 Aligned_cols=32 Identities=28% Similarity=0.596 Sum_probs=18.8
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
.|.| +.||......- .+......+|+|+.||.
T Consensus 27 ~F~C--PnCGe~~I~Rc-----~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPC--PNCGEVEIYRC-----AKCRKLGNPYRCPKCGF 58 (61)
T ss_pred EeeC--CCCCceeeehh-----hhHHHcCCceECCCcCc
Confidence 4788 88886544321 12222346788888873
No 71
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=67.01 E-value=6.8 Score=18.81 Aligned_cols=34 Identities=24% Similarity=0.430 Sum_probs=21.3
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCC
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSK 92 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~ 92 (127)
+.| +.|+..|....... ........|+.|+..|.
T Consensus 3 ~~C--P~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQC--PNCKTSFRVVDSQL-----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEC--CCCCCEEEeCHHHc-----CCCCCEEECCCCCCEEE
Confidence 568 88888777654321 12223578999987663
No 72
>PHA00626 hypothetical protein
Probab=66.90 E-value=3 Score=22.41 Aligned_cols=16 Identities=19% Similarity=0.607 Sum_probs=12.5
Q ss_pred CCceecCCCCccCCCh
Q psy3946 79 LPRFHCSLCPYKSKRR 94 (127)
Q Consensus 79 ~~~~~C~~C~k~f~~~ 94 (127)
...|.|..||+.|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 4579999999888654
No 73
>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=65.81 E-value=5.2 Score=27.69 Aligned_cols=27 Identities=19% Similarity=0.601 Sum_probs=21.6
Q ss_pred CCCcceeCCCCCCCccccCchHHHHHHHH
Q psy3946 47 NDTGVFQCPVPNCNRVYSRRRSLSRHRQE 75 (127)
Q Consensus 47 ~~~~p~~C~~~~C~~~f~~~~~l~~h~~~ 75 (127)
..+..|.| ..|+|.|.-...+..|+..
T Consensus 73 ~~~~K~~C--~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 73 EDEDKWRC--PLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSSEEEEE---SSS-EESSHHHHHHHHHH
T ss_pred HcCCEECC--CCCCcccCChHHHHHHHhh
Confidence 45678999 9999999999999999874
No 74
>KOG4167|consensus
Probab=65.11 E-value=1.2 Score=36.07 Aligned_cols=25 Identities=24% Similarity=0.305 Sum_probs=22.6
Q ss_pred ceecCCCCccCCChHHHHHHHHhcC
Q psy3946 81 RFHCSLCPYKSKRRDLLKSHMKHGH 105 (127)
Q Consensus 81 ~~~C~~C~k~f~~~~~l~~H~~~h~ 105 (127)
-|.|..|+|.|....+++.|+++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3899999999999999999999885
No 75
>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=62.36 E-value=10 Score=16.86 Aligned_cols=19 Identities=26% Similarity=0.733 Sum_probs=11.5
Q ss_pred ecCCCCccCCChHHHHHHHH
Q psy3946 83 HCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 83 ~C~~C~k~f~~~~~l~~H~~ 102 (127)
.|+.|++.+ ....++.|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 466676665 4456666654
No 76
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=61.56 E-value=14 Score=24.74 Aligned_cols=36 Identities=22% Similarity=0.579 Sum_probs=26.5
Q ss_pred CCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCC
Q psy3946 47 NDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKR 93 (127)
Q Consensus 47 ~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~ 93 (127)
....-|.| +.|+..|.....+. .-|.|+.||..+..
T Consensus 113 ~~~~~Y~C--p~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 113 ENNMFFFC--PNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred cCCCEEEC--CCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 44456899 99999888765542 36999999976643
No 77
>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=60.29 E-value=3.1 Score=28.76 Aligned_cols=31 Identities=19% Similarity=0.461 Sum_probs=22.6
Q ss_pred CCCceecCCCCccCCChHHHHHHHHhcCCCC
Q psy3946 78 QLPRFHCSLCPYKSKRRDLLKSHMKHGHKLE 108 (127)
Q Consensus 78 ~~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k 108 (127)
.+..|.|..|+|.|.-..-..+|+..=|.++
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHH
Confidence 3456999999999999999999988766544
No 78
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=59.94 E-value=7.9 Score=19.58 Aligned_cols=29 Identities=21% Similarity=0.604 Sum_probs=20.2
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccC
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKS 91 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f 91 (127)
.|.| ..||..|..... ...+.|+.||..+
T Consensus 3 ~y~C--~~CG~~~~~~~~----------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKC--ARCGREVELDEY----------GTGVRCPYCGYRI 31 (46)
T ss_pred EEEC--CCCCCEEEECCC----------CCceECCCCCCeE
Confidence 5889 999987765331 1168899998654
No 79
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=57.65 E-value=8.1 Score=20.20 Aligned_cols=29 Identities=17% Similarity=0.533 Sum_probs=19.0
Q ss_pred cceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCcc
Q psy3946 50 GVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYK 90 (127)
Q Consensus 50 ~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~ 90 (127)
.-|.| ..|++.|... ......+|+.||..
T Consensus 5 ~~Y~C--~~Cg~~~~~~----------~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKC--ARCGREVELD----------QETRGIRCPYCGSR 33 (49)
T ss_pred EEEEh--hhcCCeeehh----------hccCceeCCCCCcE
Confidence 35889 9999887311 12345789999853
No 80
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=57.31 E-value=6.5 Score=17.58 Aligned_cols=11 Identities=27% Similarity=0.703 Sum_probs=8.4
Q ss_pred eecCCCCccCC
Q psy3946 82 FHCSLCPYKSK 92 (127)
Q Consensus 82 ~~C~~C~k~f~ 92 (127)
-.|+.||+.|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 46888988874
No 81
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=56.45 E-value=6.7 Score=23.30 Aligned_cols=28 Identities=14% Similarity=0.417 Sum_probs=19.8
Q ss_pred CcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCC
Q psy3946 49 TGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCP 88 (127)
Q Consensus 49 ~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~ 88 (127)
.+|-.| ..||..|.... -.+|.+|+.|.
T Consensus 56 v~Pa~C--kkCGfef~~~~----------ik~pSRCP~CK 83 (97)
T COG3357 56 VRPARC--KKCGFEFRDDK----------IKKPSRCPKCK 83 (97)
T ss_pred ecChhh--cccCccccccc----------cCCcccCCcch
Confidence 367789 99998887632 13577888884
No 82
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=56.41 E-value=11 Score=17.71 Aligned_cols=26 Identities=15% Similarity=0.478 Sum_probs=15.5
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCcc
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYK 90 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~ 90 (127)
|.| ..|+..+.... ..+.+|..||..
T Consensus 1 Y~C--~~Cg~~~~~~~-----------~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YIC--GECGAEVELKP-----------GDPIRCPECGHR 26 (32)
T ss_dssp EBE--SSSSSSE-BST-----------SSTSSBSSSS-S
T ss_pred CCC--CcCCCeeEcCC-----------CCcEECCcCCCe
Confidence 567 77887665321 235788888854
No 83
>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=55.12 E-value=5.4 Score=19.36 Aligned_cols=30 Identities=17% Similarity=0.555 Sum_probs=19.6
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
.|.| ..|+..|...... .. .....|+.||.
T Consensus 5 ~y~C--~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRC--EDCGHTFEVLQKI------SD-DPLATCPECGG 34 (41)
T ss_pred EEEc--CCCCCEEEEEEec------CC-CCCCCCCCCCC
Confidence 4789 9999888754322 11 34567888886
No 84
>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=54.91 E-value=5.2 Score=20.69 Aligned_cols=30 Identities=17% Similarity=0.512 Sum_probs=19.2
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
.|.| ..|+..|.....+ .. .....|+.||.
T Consensus 5 ey~C--~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRC--TACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEEe--CCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 4789 9999877754221 11 34457888885
No 85
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=51.98 E-value=62 Score=20.78 Aligned_cols=39 Identities=21% Similarity=0.430 Sum_probs=25.9
Q ss_pred CCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccC
Q psy3946 47 NDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKS 91 (127)
Q Consensus 47 ~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f 91 (127)
....-|.| +.|+..|.....+.. ... ...|.|+.||...
T Consensus 95 ~~~~~Y~C--p~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKC--PNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEEC--cCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 44557999 999999885443221 112 3349999999765
No 86
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=50.96 E-value=21 Score=17.68 Aligned_cols=24 Identities=21% Similarity=0.217 Sum_probs=14.1
Q ss_pred eecCCCCcc--CCChHHHHHHHHhcC
Q psy3946 82 FHCSLCPYK--SKRRDLLKSHMKHGH 105 (127)
Q Consensus 82 ~~C~~C~k~--f~~~~~l~~H~~~h~ 105 (127)
-.|..||=. ......-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 467777733 344556666766664
No 87
>KOG4167|consensus
Probab=46.38 E-value=4.4 Score=33.02 Aligned_cols=24 Identities=25% Similarity=0.630 Sum_probs=22.3
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcC
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECG 77 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~ 77 (127)
|.| ..|++.|..-..+..||++|.
T Consensus 793 FpC--reC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPC--RECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeh--HHHHHHHHHHhhhhHHHHHHH
Confidence 889 999999999999999999885
No 88
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=45.51 E-value=27 Score=18.31 Aligned_cols=42 Identities=21% Similarity=0.440 Sum_probs=23.2
Q ss_pred CcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCC----CCccC
Q psy3946 49 TGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSL----CPYKS 91 (127)
Q Consensus 49 ~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~----C~k~f 91 (127)
..+..||...|...+. ...|..|+...-..++..|.. |...+
T Consensus 7 ~~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~ 52 (60)
T PF02176_consen 7 FRPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERV 52 (60)
T ss_dssp TSEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EE
T ss_pred CCEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCcc
Confidence 3456783333655555 446889988655667788888 76654
No 89
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.32 E-value=21 Score=22.05 Aligned_cols=26 Identities=4% Similarity=-0.084 Sum_probs=19.5
Q ss_pred eCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccC
Q psy3946 53 QCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKS 91 (127)
Q Consensus 53 ~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f 91 (127)
.| +.|++.|.. ..+.|..|+.||++|
T Consensus 11 id--Petg~KFYD-----------LNrdPiVsPytG~s~ 36 (129)
T COG4530 11 ID--PETGKKFYD-----------LNRDPIVSPYTGKSY 36 (129)
T ss_pred cC--ccccchhhc-----------cCCCccccCcccccc
Confidence 46 788877763 236788899999988
No 90
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=45.07 E-value=27 Score=19.03 Aligned_cols=33 Identities=30% Similarity=0.618 Sum_probs=18.6
Q ss_pred cceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 50 GVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 50 ~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
-.|.| +.||......- .+-.....+|.|+.||.
T Consensus 24 ~~F~C--PnCG~~~I~RC-----~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLC--PNCGEVIIYRC-----EKCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeC--CCCCCeeEeec-----hhHHhcCCceECCCCCC
Confidence 35788 88887522221 11122246788888874
No 91
>KOG2593|consensus
Probab=43.94 E-value=52 Score=25.33 Aligned_cols=39 Identities=26% Similarity=0.576 Sum_probs=27.0
Q ss_pred cCCCcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 46 FNDTGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 46 h~~~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
.+...-|.| +.|.+.|.....+. ..-...-.|.|..|+-
T Consensus 123 ~t~~~~Y~C--p~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 123 DTNVAGYVC--PNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred ccccccccC--CccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 455667999 99999998655433 3333344699999874
No 92
>KOG4173|consensus
Probab=43.84 E-value=16 Score=25.23 Aligned_cols=72 Identities=21% Similarity=0.286 Sum_probs=49.8
Q ss_pred hhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHHHH-Hc---------CCCCceecCC--CCccCCChH
Q psy3946 28 FEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRHRQ-EC---------GQLPRFHCSL--CPYKSKRRD 95 (127)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h~~-~h---------~~~~~~~C~~--C~k~f~~~~ 95 (127)
|-..+..-+.+..|....|+. .| ..|.+.|.....|..|+. .| .|.-=|.|.+ |+--|.+..
T Consensus 87 c~~~~d~lD~~E~hY~~~h~~----sC--s~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r 160 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHGN----SC--SFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSR 160 (253)
T ss_pred hHHHHhhhhhHHHhhhhcccc----hh--HHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhh
Confidence 555555556666666554544 58 999999999998988875 33 2333478854 888888887
Q ss_pred HHHHHHHhcC
Q psy3946 96 LLKSHMKHGH 105 (127)
Q Consensus 96 ~l~~H~~~h~ 105 (127)
..+.|+-..|
T Consensus 161 ~RkdH~I~~H 170 (253)
T KOG4173|consen 161 DRKDHMIRMH 170 (253)
T ss_pred hhhhHHHHhc
Confidence 7788875443
No 93
>KOG3408|consensus
Probab=43.48 E-value=17 Score=22.88 Aligned_cols=23 Identities=30% Similarity=0.472 Sum_probs=14.3
Q ss_pred CceecCCCCccCCChHHHHHHHH
Q psy3946 80 PRFHCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 80 ~~~~C~~C~k~f~~~~~l~~H~~ 102 (127)
-.|-|..|.+-|.....|..|.+
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHh
Confidence 34666666666666666666654
No 94
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=42.99 E-value=18 Score=18.22 Aligned_cols=17 Identities=18% Similarity=0.264 Sum_probs=12.0
Q ss_pred eecCCCCccCCChHHHH
Q psy3946 82 FHCSLCPYKSKRRDLLK 98 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~ 98 (127)
-.|..|++.|.++....
T Consensus 9 K~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWA 25 (42)
T ss_pred CcCcccCCcchHHHHHH
Confidence 35888888888775543
No 95
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=42.64 E-value=14 Score=16.23 Aligned_cols=8 Identities=38% Similarity=0.991 Sum_probs=4.9
Q ss_pred ceecCCCC
Q psy3946 81 RFHCSLCP 88 (127)
Q Consensus 81 ~~~C~~C~ 88 (127)
.|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 46666665
No 96
>KOG2893|consensus
Probab=42.06 E-value=7.7 Score=27.39 Aligned_cols=43 Identities=19% Similarity=0.253 Sum_probs=29.9
Q ss_pred hhhHhHhhHHHHHhHHhhcCCCcceeCCCCCCCccccCchHHHHH-HHHcC
Q psy3946 28 FEKEERMNDVYNRNMKKNFNDTGVFQCPVPNCNRVYSRRRSLSRH-RQECG 77 (127)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~~~~~l~~h-~~~h~ 77 (127)
|..+|.-...|.+|. ..+-|.| .+|.+.+.+-.-|..| +++|.
T Consensus 16 cnrefddekiliqhq-----kakhfkc--hichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 16 CNREFDDEKILIQHQ-----KAKHFKC--HICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred cccccchhhhhhhhh-----hhcccee--eeehhhhccCCCceeehhhhhh
Confidence 777777777776654 4466899 9999877666666666 45553
No 97
>PF15269 zf-C2H2_7: Zinc-finger
Probab=41.93 E-value=24 Score=18.11 Aligned_cols=23 Identities=30% Similarity=0.768 Sum_probs=15.9
Q ss_pred eecCCCCccCCChHHHHHHHHhc
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMKHG 104 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~~h 104 (127)
|+|-+|+.+..-.+.|-.|++..
T Consensus 21 ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred ceeecCCcccchHHHHHHHHHHH
Confidence 56777777766777777777643
No 98
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=41.89 E-value=16 Score=23.92 Aligned_cols=8 Identities=25% Similarity=0.974 Sum_probs=4.0
Q ss_pred ceecCCCC
Q psy3946 81 RFHCSLCP 88 (127)
Q Consensus 81 ~~~C~~C~ 88 (127)
.|.|..|+
T Consensus 140 ~YrC~~C~ 147 (156)
T COG3091 140 VYRCGKCG 147 (156)
T ss_pred eEEeccCC
Confidence 45555554
No 99
>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=41.38 E-value=13 Score=18.52 Aligned_cols=15 Identities=13% Similarity=0.423 Sum_probs=11.1
Q ss_pred ceecCCCCccCCChH
Q psy3946 81 RFHCSLCPYKSKRRD 95 (127)
Q Consensus 81 ~~~C~~C~k~f~~~~ 95 (127)
.|+|..||..|....
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ 19 (42)
T ss_pred EEEeCCCCCEEEEEE
Confidence 488999998876543
No 100
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.47 E-value=13 Score=23.63 Aligned_cols=39 Identities=26% Similarity=0.472 Sum_probs=22.2
Q ss_pred cceeCCCCCCCccccCch---HH------HHHHHHcCCCCceecCCCCcc
Q psy3946 50 GVFQCPVPNCNRVYSRRR---SL------SRHRQECGQLPRFHCSLCPYK 90 (127)
Q Consensus 50 ~p~~C~~~~C~~~f~~~~---~l------~~h~~~h~~~~~~~C~~C~k~ 90 (127)
..|.| ..||..|.... .| .-|...-+....+.|+.||..
T Consensus 69 ~~~~C--~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKC--RNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEEC--CCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 45889 99998887641 11 011111112344779999853
No 101
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=38.57 E-value=26 Score=20.72 Aligned_cols=32 Identities=22% Similarity=0.456 Sum_probs=21.7
Q ss_pred CcceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCC
Q psy3946 49 TGVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSK 92 (127)
Q Consensus 49 ~~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~ 92 (127)
..+|.| +.|++.- +.+..+ .-|.|..|+..|.
T Consensus 33 ~~~~~C--p~C~~~~--------VkR~a~--GIW~C~kCg~~fA 64 (89)
T COG1997 33 RAKHVC--PFCGRTT--------VKRIAT--GIWKCRKCGAKFA 64 (89)
T ss_pred hcCCcC--CCCCCcc--------eeeecc--CeEEcCCCCCeec
Confidence 346899 9998651 223333 3589999998874
No 102
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.20 E-value=18 Score=22.88 Aligned_cols=15 Identities=20% Similarity=0.494 Sum_probs=12.4
Q ss_pred CCCceecCCCCccCC
Q psy3946 78 QLPRFHCSLCPYKSK 92 (127)
Q Consensus 78 ~~~~~~C~~C~k~f~ 92 (127)
+...|+|..|+++|.
T Consensus 50 ~~qRyrC~~C~~tf~ 64 (129)
T COG3677 50 GHQRYKCKSCGSTFT 64 (129)
T ss_pred cccccccCCcCccee
Confidence 356799999999885
No 103
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=37.08 E-value=27 Score=22.46 Aligned_cols=20 Identities=25% Similarity=0.242 Sum_probs=9.9
Q ss_pred CCCCccccCchHHHHHHHHcCCC
Q psy3946 57 PNCNRVYSRRRSLSRHRQECGQL 79 (127)
Q Consensus 57 ~~C~~~f~~~~~l~~h~~~h~~~ 79 (127)
-.+|+.|. .|++|..+|-+.
T Consensus 80 LEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 80 LEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred eccCcchH---HHHHHHhcccCC
Confidence 55555554 355555554443
No 104
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=36.00 E-value=23 Score=17.39 Aligned_cols=14 Identities=21% Similarity=0.387 Sum_probs=11.1
Q ss_pred ceecCCCCccCCCh
Q psy3946 81 RFHCSLCPYKSKRR 94 (127)
Q Consensus 81 ~~~C~~C~k~f~~~ 94 (127)
|+.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 78999999888544
No 105
>COG1773 Rubredoxin [Energy production and conversion]
Probab=34.95 E-value=19 Score=19.29 Aligned_cols=13 Identities=38% Similarity=0.984 Sum_probs=9.3
Q ss_pred CceecCCCCccCC
Q psy3946 80 PRFHCSLCPYKSK 92 (127)
Q Consensus 80 ~~~~C~~C~k~f~ 92 (127)
+.|+|..||..|.
T Consensus 2 ~~~~C~~CG~vYd 14 (55)
T COG1773 2 KRWRCSVCGYVYD 14 (55)
T ss_pred CceEecCCceEec
Confidence 3578888887664
No 106
>KOG2295|consensus
Probab=32.46 E-value=44 Score=26.64 Aligned_cols=29 Identities=17% Similarity=0.537 Sum_probs=25.3
Q ss_pred cCCCcceeCCCCCCCccccCchHHHHHHH
Q psy3946 46 FNDTGVFQCPVPNCNRVYSRRRSLSRHRQ 74 (127)
Q Consensus 46 h~~~~p~~C~~~~C~~~f~~~~~l~~h~~ 74 (127)
..++..|.||..+|.|.|.-...+..|+.
T Consensus 504 e~~kdKy~C~lsgc~KlF~gpEFvrKHi~ 532 (648)
T KOG2295|consen 504 ELDKDKYLCPLSGCAKLFKGPEFVRKHIN 532 (648)
T ss_pred HhhcccccCCCcchHhhccCHHHHHHHHH
Confidence 45667899988999999999999999986
No 107
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=32.33 E-value=18 Score=20.49 Aligned_cols=40 Identities=20% Similarity=0.389 Sum_probs=21.1
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecC--CCCccCCChH
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCS--LCPYKSKRRD 95 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~--~C~k~f~~~~ 95 (127)
+.| +.|+..-......... ..+-+..++|. .||.+|....
T Consensus 2 m~C--P~Cg~~a~irtSr~~s--~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 2 FHC--PLCQHAAHARTSRYIT--DTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred ccC--CCCCCccEEEEChhcC--hhhheeeeecCCCCCCCEEEEEE
Confidence 357 7777644322221111 11335567787 7888876543
No 108
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=32.25 E-value=8.1 Score=20.37 Aligned_cols=25 Identities=16% Similarity=0.171 Sum_probs=9.7
Q ss_pred CceecCCCCccCCChHHHHHHHHhc
Q psy3946 80 PRFHCSLCPYKSKRRDLLKSHMKHG 104 (127)
Q Consensus 80 ~~~~C~~C~k~f~~~~~l~~H~~~h 104 (127)
..|+|+.|...|-..=..-.|..+|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 3567777766665444444444333
No 109
>KOG0717|consensus
Probab=30.16 E-value=31 Score=26.83 Aligned_cols=21 Identities=29% Similarity=0.526 Sum_probs=16.3
Q ss_pred eecCCCCccCCChHHHHHHHH
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMK 102 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~ 102 (127)
+-|..|.|+|.+...+..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 668888888888888877754
No 110
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=30.09 E-value=75 Score=23.15 Aligned_cols=31 Identities=13% Similarity=0.281 Sum_probs=24.0
Q ss_pred CCceecCCCCccCCChHHHHHHHHhcCCCCC
Q psy3946 79 LPRFHCSLCPYKSKRRDLLKSHMKHGHKLEH 109 (127)
Q Consensus 79 ~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~ 109 (127)
..-|.|..|-+-|.....+.+|+....-..|
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C~~r~P 76 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKCDIRQP 76 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhCCCCCC
Confidence 4568999999999999999999886553333
No 111
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=30.03 E-value=19 Score=17.89 Aligned_cols=15 Identities=20% Similarity=0.377 Sum_probs=9.3
Q ss_pred CceecCCCCccCCCh
Q psy3946 80 PRFHCSLCPYKSKRR 94 (127)
Q Consensus 80 ~~~~C~~C~k~f~~~ 94 (127)
.++.|..|++.|-..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 478999999888544
No 112
>KOG4124|consensus
Probab=29.68 E-value=6.4 Score=29.32 Aligned_cols=52 Identities=29% Similarity=0.694 Sum_probs=34.5
Q ss_pred CcceeCCCCCCCccccCchHHHHHHH-Hc--------------C----CCCceecCCCCccCCChHHHHHH
Q psy3946 49 TGVFQCPVPNCNRVYSRRRSLSRHRQ-EC--------------G----QLPRFHCSLCPYKSKRRDLLKSH 100 (127)
Q Consensus 49 ~~p~~C~~~~C~~~f~~~~~l~~h~~-~h--------------~----~~~~~~C~~C~k~f~~~~~l~~H 100 (127)
.++|.|+.+.|.+.+....-|..|.. .| + ..|+|+|+.|.+.++-...|+.|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 46788988889888887766665532 11 1 23678999998776655555443
No 113
>KOG2071|consensus
Probab=29.53 E-value=39 Score=27.00 Aligned_cols=26 Identities=15% Similarity=0.233 Sum_probs=17.0
Q ss_pred CCceecCCCCccCCChHHHHHHHHhc
Q psy3946 79 LPRFHCSLCPYKSKRRDLLKSHMKHG 104 (127)
Q Consensus 79 ~~~~~C~~C~k~f~~~~~l~~H~~~h 104 (127)
..+-+|..||..|........|+..|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 34567888888777666665555554
No 114
>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=29.34 E-value=57 Score=15.45 Aligned_cols=22 Identities=14% Similarity=0.359 Sum_probs=9.6
Q ss_pred eecCCCCccCCChHHHHHHHHhc
Q psy3946 82 FHCSLCPYKSKRRDLLKSHMKHG 104 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~~H~~~h 104 (127)
+.|+.|++.. ....+..|+...
T Consensus 5 ~~C~nC~R~v-~a~RfA~HLekC 26 (33)
T PF08209_consen 5 VECPNCGRPV-AASRFAPHLEKC 26 (33)
T ss_dssp EE-TTTSSEE-EGGGHHHHHHHH
T ss_pred EECCCCcCCc-chhhhHHHHHHH
Confidence 4555555543 233445555443
No 115
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.15 E-value=23 Score=18.44 Aligned_cols=17 Identities=18% Similarity=0.292 Sum_probs=12.1
Q ss_pred eecCCCCccCCChHHHH
Q psy3946 82 FHCSLCPYKSKRRDLLK 98 (127)
Q Consensus 82 ~~C~~C~k~f~~~~~l~ 98 (127)
-.|+.|++.|.++....
T Consensus 13 KICpvCqRPFsWRkKW~ 29 (54)
T COG4338 13 KICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhhcCchHHHHHHH
Confidence 36888888888765443
No 116
>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=29.06 E-value=12 Score=17.15 Aligned_cols=7 Identities=14% Similarity=0.804 Sum_probs=3.9
Q ss_pred CCCCccc
Q psy3946 57 PNCNRVY 63 (127)
Q Consensus 57 ~~C~~~f 63 (127)
..|++.|
T Consensus 4 iDC~~~F 10 (28)
T PF08790_consen 4 IDCSKDF 10 (28)
T ss_dssp TTTTEEE
T ss_pred ecCCCCc
Confidence 5555555
No 117
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.03 E-value=46 Score=20.61 Aligned_cols=49 Identities=12% Similarity=0.160 Sum_probs=31.4
Q ss_pred eCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHHHHHHHhcC
Q psy3946 53 QCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLLKSHMKHGH 105 (127)
Q Consensus 53 ~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~h~ 105 (127)
.| -.|...|........-. -.....|+|..|...|-..-+.-.|..+|.
T Consensus 57 ~C--~~C~~~f~~~~~~~~~~--~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 57 FC--FGCQGPFPKPPVSPFDE--LKDSHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cc--cCcCCCCCCcccccccc--cccccceeCCCCCCccccccchhhhhhccC
Confidence 38 88888887543111000 112346899999998887777777877765
No 118
>KOG2231|consensus
Probab=28.76 E-value=85 Score=25.72 Aligned_cols=17 Identities=24% Similarity=0.399 Sum_probs=7.2
Q ss_pred CCCCccccCchHHHHHH
Q psy3946 57 PNCNRVYSRRRSLSRHR 73 (127)
Q Consensus 57 ~~C~~~f~~~~~l~~h~ 73 (127)
..|...|.....|..|+
T Consensus 186 ~~C~~~fld~~el~rH~ 202 (669)
T KOG2231|consen 186 KFCHERFLDDDELYRHL 202 (669)
T ss_pred hhhhhhhccHHHHHHhh
Confidence 34444444444444443
No 119
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=28.41 E-value=28 Score=18.20 Aligned_cols=17 Identities=12% Similarity=0.104 Sum_probs=13.0
Q ss_pred CCceecCCCCccCCChH
Q psy3946 79 LPRFHCSLCPYKSKRRD 95 (127)
Q Consensus 79 ~~~~~C~~C~k~f~~~~ 95 (127)
++.+.|..||..|....
T Consensus 2 Dk~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTA 18 (49)
T ss_pred CeeEEcccCCCeEEEeh
Confidence 46789999998876543
No 120
>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=28.29 E-value=22 Score=18.59 Aligned_cols=12 Identities=25% Similarity=0.592 Sum_probs=5.7
Q ss_pred ecCCCCccCCCh
Q psy3946 83 HCSLCPYKSKRR 94 (127)
Q Consensus 83 ~C~~C~k~f~~~ 94 (127)
.|++|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 788888877533
No 121
>KOG2231|consensus
Probab=27.96 E-value=81 Score=25.83 Aligned_cols=78 Identities=18% Similarity=0.229 Sum_probs=43.5
Q ss_pred hHhHhhHHHHHhHHhhcCCCcceeCC-----CCCCCccccCchHHHHHHHHcCC-CC----ceecCCCCccCCChHHHHH
Q psy3946 30 KEERMNDVYNRNMKKNFNDTGVFQCP-----VPNCNRVYSRRRSLSRHRQECGQ-LP----RFHCSLCPYKSKRRDLLKS 99 (127)
Q Consensus 30 ~~~~~~~~~~~~~~~~h~~~~p~~C~-----~~~C~~~f~~~~~l~~h~~~h~~-~~----~~~C~~C~k~f~~~~~l~~ 99 (127)
..+..-..|++|+...|..-.-..|- ...+.+.|. ...|..|+...-. ++ .-.|..|-..|.....|.+
T Consensus 122 ~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt-~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~r 200 (669)
T KOG2231|consen 122 TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYT-RAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYR 200 (669)
T ss_pred cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeeheh-HHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHH
Confidence 34445677888887666653322220 012233333 3445566552211 11 2457788888888888888
Q ss_pred HHHhcCCCC
Q psy3946 100 HMKHGHKLE 108 (127)
Q Consensus 100 H~~~h~g~k 108 (127)
|++.++-..
T Consensus 201 H~~~~h~~c 209 (669)
T KOG2231|consen 201 HLRFDHEFC 209 (669)
T ss_pred hhccceehe
Confidence 888766444
No 122
>KOG2785|consensus
Probab=27.77 E-value=59 Score=24.61 Aligned_cols=25 Identities=16% Similarity=0.263 Sum_probs=20.3
Q ss_pred CCceecCCCCccCCChHHHHHHHHh
Q psy3946 79 LPRFHCSLCPYKSKRRDLLKSHMKH 103 (127)
Q Consensus 79 ~~~~~C~~C~k~f~~~~~l~~H~~~ 103 (127)
.-++.|..|.+.|........|+..
T Consensus 66 ~~~~~c~~c~k~~~s~~a~~~hl~S 90 (390)
T KOG2785|consen 66 ESVVYCEACNKSFASPKAHENHLKS 90 (390)
T ss_pred ccceehHHhhccccChhhHHHHHHH
Confidence 4568899999999988888888764
No 123
>KOG0978|consensus
Probab=27.55 E-value=24 Score=28.87 Aligned_cols=23 Identities=17% Similarity=0.342 Sum_probs=17.0
Q ss_pred CCCceecCCCCccCCChHHHHHH
Q psy3946 78 QLPRFHCSLCPYKSKRRDLLKSH 100 (127)
Q Consensus 78 ~~~~~~C~~C~k~f~~~~~l~~H 100 (127)
..+.-+|+.|+.+|...+.+..|
T Consensus 675 etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 675 ETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred HHhcCCCCCCCCCCCcccccccC
Confidence 44667899999999877665443
No 124
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=27.51 E-value=40 Score=20.79 Aligned_cols=26 Identities=19% Similarity=0.491 Sum_probs=18.3
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCcc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYK 90 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~ 90 (127)
...| ..|+..|.... ..+.|+.||..
T Consensus 70 ~~~C--~~Cg~~~~~~~------------~~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECEC--EDCSEEVSPEI------------DLYRCPKCHGI 95 (115)
T ss_pred EEEc--ccCCCEEecCC------------cCccCcCCcCC
Confidence 4679 99998776542 14679999853
No 125
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=27.33 E-value=44 Score=20.55 Aligned_cols=25 Identities=20% Similarity=0.430 Sum_probs=17.7
Q ss_pred ceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 51 VFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 51 p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
.+.| ..|+..|.... ..+.|+.||.
T Consensus 70 ~~~C--~~Cg~~~~~~~------------~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWC--WDCSQVVEIHQ------------HDAQCPHCHG 94 (113)
T ss_pred EEEc--ccCCCEEecCC------------cCccCcCCCC
Confidence 4779 99997776432 3467999984
No 126
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=27.31 E-value=39 Score=18.34 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=10.5
Q ss_pred eCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccC
Q psy3946 53 QCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKS 91 (127)
Q Consensus 53 ~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f 91 (127)
.| ..|++.|... .+.+.|..||..|
T Consensus 11 ~C--~~C~~~F~~~------------~rrhhCr~CG~~v 35 (69)
T PF01363_consen 11 NC--MICGKKFSLF------------RRRHHCRNCGRVV 35 (69)
T ss_dssp B---TTT--B-BSS------------S-EEE-TTT--EE
T ss_pred cC--cCcCCcCCCc------------eeeEccCCCCCEE
Confidence 57 7888888531 3456777777655
No 127
>KOG2482|consensus
Probab=26.84 E-value=49 Score=24.80 Aligned_cols=67 Identities=22% Similarity=0.365 Sum_probs=42.0
Q ss_pred hHHHHHhHHhhcCCCcceeCCCCCCCcccc-CchHHHHHHH-HcC---C--C----------------CceecCCCCccC
Q psy3946 35 NDVYNRNMKKNFNDTGVFQCPVPNCNRVYS-RRRSLSRHRQ-ECG---Q--L----------------PRFHCSLCPYKS 91 (127)
Q Consensus 35 ~~~~~~~~~~~h~~~~p~~C~~~~C~~~f~-~~~~l~~h~~-~h~---~--~----------------~~~~C~~C~k~f 91 (127)
++.|.++.+........-+| -.|+..+. ..+....|+- .|. | + ..++|..|-+.|
T Consensus 128 ~eaLeqqQ~Eredt~fslqC--lFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekif 205 (423)
T KOG2482|consen 128 KEALEQQQKEREDTIFSLQC--LFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIF 205 (423)
T ss_pred HHHHHHHHHHhcCCeeeeEE--EEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeecccc
Confidence 34455555443222334568 88876443 3455556654 332 1 1 136899999999
Q ss_pred CChHHHHHHHHh
Q psy3946 92 KRRDLLKSHMKH 103 (127)
Q Consensus 92 ~~~~~l~~H~~~ 103 (127)
..+..|+-|++.
T Consensus 206 rdkntLkeHMrk 217 (423)
T KOG2482|consen 206 RDKNTLKEHMRK 217 (423)
T ss_pred CCcHHHHHHHHh
Confidence 999999999984
No 128
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=25.50 E-value=7.2 Score=31.73 Aligned_cols=27 Identities=22% Similarity=0.486 Sum_probs=13.4
Q ss_pred CCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 57 PNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 57 ~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
..|.+.|....+.+-| -.|..|+.||.
T Consensus 155 ~~C~~EY~dP~nRRfH------AQp~aCp~CGP 181 (750)
T COG0068 155 PFCDKEYKDPLNRRFH------AQPIACPKCGP 181 (750)
T ss_pred HHHHHHhcCccccccc------cccccCcccCC
Confidence 5555555444432222 13556777774
No 129
>KOG1146|consensus
Probab=24.97 E-value=19 Score=31.56 Aligned_cols=47 Identities=19% Similarity=0.362 Sum_probs=35.7
Q ss_pred CCCCccccCchHHHHHHH-HcCCCCceecCCCCccCCChHHHHHHHHh
Q psy3946 57 PNCNRVYSRRRSLSRHRQ-ECGQLPRFHCSLCPYKSKRRDLLKSHMKH 103 (127)
Q Consensus 57 ~~C~~~f~~~~~l~~h~~-~h~~~~~~~C~~C~k~f~~~~~l~~H~~~ 103 (127)
..|+..+.+...+..|+. .+.-.+.++|+.|+-.|.+...|..|+|.
T Consensus 440 ~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 440 TKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred cchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccc
Confidence 555555665555555544 45556889999999999999999999987
No 130
>PRK04351 hypothetical protein; Provisional
Probab=23.17 E-value=62 Score=21.04 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=5.4
Q ss_pred CceecCCCCcc
Q psy3946 80 PRFHCSLCPYK 90 (127)
Q Consensus 80 ~~~~C~~C~k~ 90 (127)
..|.|..|+-.
T Consensus 131 ~~yrCg~C~g~ 141 (149)
T PRK04351 131 KRYRCGKCRGK 141 (149)
T ss_pred CcEEeCCCCcE
Confidence 34555555543
No 131
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=22.90 E-value=95 Score=15.51 Aligned_cols=27 Identities=30% Similarity=0.797 Sum_probs=16.0
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCc
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPY 89 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k 89 (127)
+.| +.|+.. . ...+ .....|+|..|.+
T Consensus 19 ~~C--P~Cg~~-~-~~~~-------~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVC--PHCGST-K-HYRL-------KTRGRYRCKACRK 45 (46)
T ss_pred CCC--CCCCCe-e-eEEe-------CCCCeEECCCCCC
Confidence 678 888853 1 1111 1146788888875
No 132
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=22.90 E-value=1.5e+02 Score=17.99 Aligned_cols=47 Identities=13% Similarity=0.171 Sum_probs=29.8
Q ss_pred cceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCcc-CCChHHHHH
Q psy3946 50 GVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYK-SKRRDLLKS 99 (127)
Q Consensus 50 ~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~-f~~~~~l~~ 99 (127)
.-|.| +..+..|.........+.... .+-|.|...|+. +.+...|..
T Consensus 2 eVf~i--~~T~EiF~dYe~Y~~R~~~y~-~~vwtC~~TGk~~LTy~eAl~S 49 (102)
T PF10537_consen 2 EVFYI--PFTGEIFRDYEEYLKRMILYN-QRVWTCEITGKSNLTYFEALES 49 (102)
T ss_pred ceEEe--CCCCcccCCHHHHHHHHHHHh-CCeeEEecCCCCCCCHHHHHHH
Confidence 34677 777888888766666655443 456888887764 344444433
No 133
>KOG2636|consensus
Probab=22.07 E-value=73 Score=24.77 Aligned_cols=48 Identities=17% Similarity=0.261 Sum_probs=30.9
Q ss_pred cceeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCC-ccCCChHHHHHHHH
Q psy3946 50 GVFQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCP-YKSKRRDLLKSHMK 102 (127)
Q Consensus 50 ~p~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~-k~f~~~~~l~~H~~ 102 (127)
+|+.-|..+=|+..+.. .-+.|.-.+-|.|..|| +++.=+..+.+|-.
T Consensus 375 np~~lPLGwDGkPiPyW-----LyKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 375 NPKNLPLGWDGKPIPYW-----LYKLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred CcccCCCCCCCCcCchH-----HHhhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 44555445555544322 12467778899999999 77777777777743
No 134
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=22.02 E-value=81 Score=16.20 Aligned_cols=24 Identities=21% Similarity=0.434 Sum_probs=13.7
Q ss_pred CCCCccccCchHHHHHHHHcCCCCceecCCCCccCC
Q psy3946 57 PNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSK 92 (127)
Q Consensus 57 ~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~ 92 (127)
..|++.|... .+.+.|..||+.|-
T Consensus 6 ~~C~~~F~~~------------~rk~~Cr~Cg~~~C 29 (57)
T cd00065 6 MGCGKPFTLT------------RRRHHCRNCGRIFC 29 (57)
T ss_pred cccCccccCC------------ccccccCcCcCCcC
Confidence 6677666641 23456666666654
No 135
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=21.58 E-value=50 Score=16.04 Aligned_cols=15 Identities=13% Similarity=0.142 Sum_probs=8.0
Q ss_pred ecCCCCccCCChHHH
Q psy3946 83 HCSLCPYKSKRRDLL 97 (127)
Q Consensus 83 ~C~~C~k~f~~~~~l 97 (127)
.|..|++.|.+.+..
T Consensus 4 ~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 4 LCPRCGKGFHWASEC 18 (36)
T ss_dssp C-TTTSSSCS-TTT-
T ss_pred cCcccCCCcchhhhh
Confidence 467777777666544
No 136
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.03 E-value=69 Score=24.65 Aligned_cols=32 Identities=19% Similarity=0.514 Sum_probs=21.9
Q ss_pred eCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCChHHH
Q psy3946 53 QCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKRRDLL 97 (127)
Q Consensus 53 ~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~l 97 (127)
.| +.||..+.+. |..-|+|+.||+.+......
T Consensus 352 ~C--p~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VC--PRCGGRMKSA-----------GRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CC--CccCCchhhc-----------CCCCcccccccccCCccccc
Confidence 58 8888765432 33479999999887655443
No 137
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=20.82 E-value=34 Score=16.48 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=17.6
Q ss_pred eeCCCCCCCccccCchHHHHHHHHcCCCCceecCCCCccCCC
Q psy3946 52 FQCPVPNCNRVYSRRRSLSRHRQECGQLPRFHCSLCPYKSKR 93 (127)
Q Consensus 52 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~ 93 (127)
+.| ..||+.|-... ......-.|..||-.+.+
T Consensus 2 r~C--~~Cg~~Yh~~~--------~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RIC--PKCGRIYHIEF--------NPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEE--TTTTEEEETTT--------B--SSTTBCTTTTEBEBE
T ss_pred cCc--CCCCCcccccc--------CCCCCCCccCCCCCeeEe
Confidence 457 77877765332 223445677777754433
No 138
>KOG1280|consensus
Probab=20.69 E-value=1.2e+02 Score=22.84 Aligned_cols=33 Identities=15% Similarity=0.263 Sum_probs=20.8
Q ss_pred ceecCCCCccCCChHHHHHHHHhcCCCCCCCch
Q psy3946 81 RFHCSLCPYKSKRRDLLKSHMKHGHKLEHITED 113 (127)
Q Consensus 81 ~~~C~~C~k~f~~~~~l~~H~~~h~g~k~~~c~ 113 (127)
-|.|++|++.--....|..|....|.+-++.+.
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~i 111 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVI 111 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccCccee
Confidence 467777776666666667776666665554443
No 139
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.64 E-value=70 Score=16.61 Aligned_cols=12 Identities=42% Similarity=1.149 Sum_probs=8.7
Q ss_pred CceecCCCCccC
Q psy3946 80 PRFHCSLCPYKS 91 (127)
Q Consensus 80 ~~~~C~~C~k~f 91 (127)
..+.|..||..+
T Consensus 36 ~r~~C~~Cgyt~ 47 (50)
T PRK00432 36 DRWHCGKCGYTE 47 (50)
T ss_pred CcEECCCcCCEE
Confidence 468888888653
No 140
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=20.18 E-value=96 Score=24.15 Aligned_cols=31 Identities=26% Similarity=0.440 Sum_probs=24.7
Q ss_pred CCceecCCCCccCCChHHHHHHHHhcCCCCC
Q psy3946 79 LPRFHCSLCPYKSKRRDLLKSHMKHGHKLEH 109 (127)
Q Consensus 79 ~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~ 109 (127)
..-|.|..|-+-|.....|.+|+....-..|
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~C~~~~P 226 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKKCDLKHP 226 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhcCCCCCC
Confidence 3468999999999999999999986553333
No 142
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.12 E-value=1.1e+02 Score=24.30 Aligned_cols=31 Identities=16% Similarity=0.082 Sum_probs=24.9
Q ss_pred CCceecCCCCccCCChHHHHHHHHhcCCCCC
Q psy3946 79 LPRFHCSLCPYKSKRRDLLKSHMKHGHKLEH 109 (127)
Q Consensus 79 ~~~~~C~~C~k~f~~~~~l~~H~~~h~g~k~ 109 (127)
..-|.|..|-+-|.....|.+|+....-..|
T Consensus 278 d~LYICEfCLkY~~s~~~l~rH~~~C~~rhP 308 (552)
T PTZ00064 278 DTLHFCEYCLDFFCFEDELIRHLSRCQLRHP 308 (552)
T ss_pred CeEEEccchhhhhCCHHHHHHHHhcCCCCCC
Confidence 4568999999999999999999986653333
Done!