Query psy16400
Match_columns 145
No_of_seqs 116 out of 1121
Neff 9.5
Searched_HMMs 46136
Date Fri Aug 16 20:22:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16400.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16400hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 1.6E-21 3.4E-26 138.2 0.8 111 21-135 160-270 (279)
2 KOG2462|consensus 99.7 2.6E-18 5.6E-23 122.0 4.3 107 22-132 130-239 (279)
3 KOG3623|consensus 99.5 1.1E-14 2.4E-19 114.8 2.4 75 46-122 890-964 (1007)
4 KOG3576|consensus 99.4 2E-14 4.3E-19 98.4 -0.5 104 22-127 117-231 (267)
5 KOG3576|consensus 99.4 5.2E-14 1.1E-18 96.3 1.2 86 46-133 113-198 (267)
6 KOG3623|consensus 99.3 5.1E-13 1.1E-17 105.6 -0.2 78 22-101 894-971 (1007)
7 KOG1074|consensus 99.3 2.2E-12 4.8E-17 103.3 2.5 62 13-74 344-405 (958)
8 KOG3608|consensus 99.0 3.6E-11 7.8E-16 88.5 -0.0 110 19-132 204-316 (467)
9 PHA02768 hypothetical protein; 98.8 4.3E-09 9.2E-14 57.9 2.8 41 81-123 6-46 (55)
10 KOG1074|consensus 98.8 2E-09 4.4E-14 86.7 1.4 105 16-120 599-721 (958)
11 PHA00733 hypothetical protein 98.6 7.7E-09 1.7E-13 67.4 0.4 81 46-130 36-121 (128)
12 PHA00733 hypothetical protein 98.6 5.2E-08 1.1E-12 63.5 4.3 75 27-105 45-124 (128)
13 PHA02768 hypothetical protein; 98.6 3.3E-08 7.2E-13 54.3 2.1 43 51-97 6-48 (55)
14 PLN03086 PRLI-interacting fact 98.6 3.2E-08 6.8E-13 78.2 2.4 87 37-131 467-563 (567)
15 PF13465 zf-H2C2_2: Zinc-finge 98.5 5.3E-08 1.2E-12 45.8 0.7 24 95-118 1-24 (26)
16 PHA00616 hypothetical protein 98.4 9.4E-08 2E-12 50.1 1.5 33 80-112 1-33 (44)
17 KOG3608|consensus 98.4 3.8E-08 8.2E-13 72.9 -0.4 118 19-140 176-293 (467)
18 PF13465 zf-H2C2_2: Zinc-finge 98.4 3.4E-07 7.3E-12 43.0 2.3 26 65-92 1-26 (26)
19 PLN03086 PRLI-interacting fact 98.3 1.4E-06 3.1E-11 69.0 5.1 79 48-133 451-539 (567)
20 KOG3993|consensus 98.0 5.8E-07 1.3E-11 68.0 -2.2 86 51-138 268-386 (500)
21 PHA00732 hypothetical protein 98.0 6.3E-06 1.4E-10 49.2 2.4 46 50-103 1-47 (79)
22 PHA00616 hypothetical protein 97.9 7.7E-06 1.7E-10 42.9 1.5 34 50-85 1-34 (44)
23 PF05605 zf-Di19: Drought indu 97.8 5.2E-05 1.1E-09 41.9 4.5 53 50-105 2-54 (54)
24 PF00096 zf-C2H2: Zinc finger, 97.6 3.9E-05 8.5E-10 34.6 1.9 22 81-102 1-22 (23)
25 PHA00732 hypothetical protein 97.6 4.9E-05 1.1E-09 45.4 2.4 37 80-119 1-38 (79)
26 PF00096 zf-C2H2: Zinc finger, 97.4 0.00011 2.4E-09 33.0 2.0 23 51-73 1-23 (23)
27 PF13894 zf-C2H2_4: C2H2-type 97.2 0.00035 7.6E-09 31.3 2.1 23 81-103 1-23 (24)
28 KOG3993|consensus 97.1 0.00012 2.5E-09 55.9 0.3 78 28-105 273-381 (500)
29 PF13912 zf-C2H2_6: C2H2-type 97.0 0.00045 9.8E-09 32.3 1.7 24 51-74 2-25 (27)
30 COG5189 SFP1 Putative transcri 97.0 0.00066 1.4E-08 50.2 2.8 53 47-99 346-417 (423)
31 PF09237 GAGA: GAGA factor; I 96.9 0.00087 1.9E-08 36.1 2.4 31 78-108 22-52 (54)
32 PF13912 zf-C2H2_6: C2H2-type 96.9 0.00041 8.8E-09 32.4 0.9 26 80-105 1-26 (27)
33 PF13894 zf-C2H2_4: C2H2-type 96.9 0.00098 2.1E-08 29.8 2.1 23 51-73 1-23 (24)
34 smart00355 ZnF_C2H2 zinc finge 96.4 0.0035 7.6E-08 28.3 2.3 22 82-103 2-23 (26)
35 PRK04860 hypothetical protein; 96.4 0.0026 5.7E-08 43.0 2.4 38 80-121 119-156 (160)
36 COG5189 SFP1 Putative transcri 96.0 0.0044 9.6E-08 46.0 2.0 50 78-127 347-417 (423)
37 PF12756 zf-C2H2_2: C2H2 type 95.9 0.0072 1.6E-07 36.9 2.6 25 80-104 50-74 (100)
38 smart00355 ZnF_C2H2 zinc finge 95.7 0.0089 1.9E-07 26.9 1.9 24 51-74 1-24 (26)
39 PF12874 zf-met: Zinc-finger o 95.5 0.011 2.4E-07 26.8 1.7 21 51-71 1-21 (25)
40 PF09237 GAGA: GAGA factor; I 95.5 0.019 4.2E-07 30.9 2.7 33 46-80 20-52 (54)
41 PRK04860 hypothetical protein; 95.5 0.0097 2.1E-07 40.3 1.9 38 50-93 119-156 (160)
42 PF13909 zf-H2C2_5: C2H2-type 95.4 0.015 3.3E-07 26.1 1.9 23 81-104 1-23 (24)
43 PF12874 zf-met: Zinc-finger o 95.0 0.012 2.7E-07 26.7 1.0 23 81-103 1-23 (25)
44 PF12171 zf-C2H2_jaz: Zinc-fin 94.1 0.026 5.6E-07 26.2 1.0 22 51-72 2-23 (27)
45 PF05605 zf-Di19: Drought indu 94.1 0.084 1.8E-06 28.9 3.1 37 80-117 2-40 (54)
46 PF13909 zf-H2C2_5: C2H2-type 93.9 0.058 1.3E-06 24.1 1.9 23 51-74 1-23 (24)
47 PF13913 zf-C2HC_2: zinc-finge 92.5 0.12 2.7E-06 23.6 1.9 21 81-102 3-23 (25)
48 COG5048 FOG: Zn-finger [Genera 91.3 0.068 1.5E-06 40.7 0.4 66 49-116 288-359 (467)
49 KOG2893|consensus 90.6 0.079 1.7E-06 38.0 0.1 42 52-99 12-53 (341)
50 KOG2186|consensus 88.9 0.28 6.1E-06 35.4 1.8 50 50-104 3-52 (276)
51 smart00451 ZnF_U1 U1-like zinc 88.8 0.35 7.6E-06 23.5 1.7 22 50-71 3-24 (35)
52 cd00350 rubredoxin_like Rubred 87.7 0.46 1E-05 23.2 1.6 10 51-60 2-11 (33)
53 PF12756 zf-C2H2_2: C2H2 type 87.1 0.59 1.3E-05 28.2 2.3 25 50-74 50-74 (100)
54 KOG1146|consensus 86.4 1 2.2E-05 39.8 3.9 61 42-102 457-540 (1406)
55 PF09538 FYDLN_acid: Protein o 83.1 0.94 2E-05 28.6 1.8 15 79-93 25-39 (108)
56 COG1592 Rubrerythrin [Energy p 78.3 1.7 3.8E-05 29.6 2.0 10 78-87 147-156 (166)
57 COG5048 FOG: Zn-finger [Genera 75.5 2.8 6E-05 31.9 2.7 61 21-83 288-354 (467)
58 cd00729 rubredoxin_SM Rubredox 70.6 3.5 7.7E-05 20.2 1.5 10 50-59 2-11 (34)
59 PF09986 DUF2225: Uncharacteri 69.6 1.5 3.3E-05 31.1 0.1 45 48-93 3-61 (214)
60 PF13719 zinc_ribbon_5: zinc-r 69.5 3.7 8.1E-05 20.5 1.5 33 52-91 4-36 (37)
61 COG4049 Uncharacterized protei 68.5 2.6 5.7E-05 23.2 0.8 25 47-71 14-38 (65)
62 PF05443 ROS_MUCR: ROS/MUCR tr 68.2 2.9 6.4E-05 27.4 1.1 25 80-107 72-96 (132)
63 PF13717 zinc_ribbon_4: zinc-r 64.9 5 0.00011 19.9 1.4 33 51-90 3-35 (36)
64 KOG4173|consensus 62.9 2.6 5.6E-05 29.8 0.1 70 28-102 87-168 (253)
65 smart00614 ZnF_BED BED zinc fi 62.7 7.1 0.00015 20.7 1.8 20 82-101 20-44 (50)
66 COG2888 Predicted Zn-ribbon RN 62.5 8.3 0.00018 21.6 2.1 31 80-115 27-57 (61)
67 TIGR02098 MJ0042_CXXC MJ0042 f 61.4 6.3 0.00014 19.5 1.4 33 51-90 3-35 (38)
68 TIGR02300 FYDLN_acid conserved 61.1 6.7 0.00015 25.5 1.8 33 51-96 10-42 (129)
69 KOG4167|consensus 60.2 2 4.4E-05 35.8 -0.9 25 80-104 792-816 (907)
70 PF12013 DUF3505: Protein of u 59.9 8 0.00017 24.1 2.0 25 81-105 81-109 (109)
71 KOG2186|consensus 59.9 4.6 9.9E-05 29.4 0.9 46 80-128 3-48 (276)
72 smart00531 TFIIE Transcription 59.4 18 0.00039 24.0 3.7 37 78-118 97-133 (147)
73 TIGR00373 conserved hypothetic 58.9 12 0.00026 25.2 2.8 33 78-119 107-139 (158)
74 smart00734 ZnF_Rad18 Rad18-lik 55.7 11 0.00024 17.1 1.6 20 81-101 2-21 (26)
75 KOG0696|consensus 55.1 3.2 6.9E-05 32.9 -0.5 46 23-90 57-102 (683)
76 smart00834 CxxC_CXXC_SSSS Puta 54.5 4.8 0.0001 20.1 0.2 11 51-61 6-16 (41)
77 PRK06266 transcription initiat 53.7 14 0.00029 25.5 2.4 34 78-120 115-148 (178)
78 TIGR02605 CxxC_CxxC_SSSS putat 53.6 5 0.00011 21.4 0.3 11 51-61 6-16 (52)
79 KOG1146|consensus 51.8 3.5 7.6E-05 36.7 -0.8 63 56-120 442-530 (1406)
80 PF02892 zf-BED: BED zinc fing 51.5 16 0.00035 18.6 2.0 21 80-100 16-40 (45)
81 PF04959 ARS2: Arsenite-resist 50.0 5.9 0.00013 28.2 0.2 26 79-104 76-101 (214)
82 COG1997 RPL43A Ribosomal prote 49.6 7.6 0.00016 23.5 0.6 11 81-91 54-64 (89)
83 PRK00464 nrdR transcriptional 49.4 3.7 8.1E-05 27.7 -0.8 13 81-93 29-41 (154)
84 smart00659 RPOLCX RNA polymera 47.7 15 0.00033 19.1 1.5 26 51-89 3-28 (44)
85 PF06524 NOA36: NOA36 protein; 47.3 22 0.00048 26.2 2.7 85 23-119 126-220 (314)
86 PF09723 Zn-ribbon_8: Zinc rib 45.9 8.7 0.00019 19.7 0.4 12 51-62 6-17 (42)
87 KOG2593|consensus 45.4 20 0.00043 28.3 2.4 36 78-116 126-161 (436)
88 PRK00398 rpoP DNA-directed RNA 43.7 15 0.00033 19.0 1.1 12 50-61 3-14 (46)
89 PF04959 ARS2: Arsenite-resist 43.2 21 0.00045 25.5 2.1 30 46-75 73-102 (214)
90 TIGR00622 ssl1 transcription f 41.4 40 0.00088 21.5 3.0 76 50-127 15-100 (112)
91 PF05191 ADK_lid: Adenylate ki 41.2 16 0.00035 18.1 1.0 29 51-89 2-30 (36)
92 PF15269 zf-C2H2_7: Zinc-finge 41.1 26 0.00057 18.4 1.7 24 80-103 20-43 (54)
93 PF03604 DNA_RNApol_7kD: DNA d 38.4 28 0.00061 16.8 1.5 10 80-89 17-26 (32)
94 PRK14890 putative Zn-ribbon RN 37.8 34 0.00074 19.1 2.0 10 80-89 25-34 (59)
95 COG3357 Predicted transcriptio 37.8 18 0.0004 22.1 1.0 14 79-92 57-70 (97)
96 PF07754 DUF1610: Domain of un 37.7 16 0.00035 16.4 0.6 9 79-87 15-23 (24)
97 PRK03824 hypA hydrogenase nick 37.1 15 0.00033 24.0 0.6 15 48-62 68-82 (135)
98 KOG2785|consensus 36.8 36 0.00077 26.5 2.6 53 50-102 166-242 (390)
99 PF10571 UPF0547: Uncharacteri 36.2 20 0.00043 16.4 0.8 11 81-91 15-25 (26)
100 PF13878 zf-C2H2_3: zinc-finge 34.2 49 0.0011 16.8 2.1 23 81-103 14-38 (41)
101 PF11789 zf-Nse: Zinc-finger o 33.3 20 0.00043 19.8 0.6 32 80-115 24-55 (57)
102 COG4957 Predicted transcriptio 33.1 25 0.00055 23.2 1.1 22 51-75 77-98 (148)
103 PF10013 DUF2256: Uncharacteri 32.3 39 0.00085 17.5 1.5 12 53-64 11-22 (42)
104 PF01780 Ribosomal_L37ae: Ribo 32.1 14 0.0003 22.6 -0.2 30 50-91 35-64 (90)
105 PRK11823 DNA repair protein Ra 31.1 37 0.0008 27.0 2.0 25 48-88 5-29 (446)
106 COG1996 RPC10 DNA-directed RNA 30.6 27 0.00058 18.7 0.8 12 49-60 5-16 (49)
107 KOG4167|consensus 30.5 17 0.00038 30.7 0.1 28 48-75 790-817 (907)
108 TIGR00280 L37a ribosomal prote 29.9 16 0.00035 22.3 -0.2 10 81-90 54-63 (91)
109 PTZ00255 60S ribosomal protein 29.4 20 0.00043 21.9 0.2 11 108-118 54-64 (90)
110 PF08790 zf-LYAR: LYAR-type C2 28.7 20 0.00043 16.8 0.1 11 51-61 1-11 (28)
111 TIGR00416 sms DNA repair prote 28.5 38 0.00082 27.0 1.6 23 49-87 6-28 (454)
112 KOG3408|consensus 28.3 38 0.00083 21.9 1.3 27 46-72 53-79 (129)
113 PF02176 zf-TRAF: TRAF-type zi 27.2 35 0.00077 18.4 1.0 39 50-90 9-52 (60)
114 COG0068 HypF Hydrogenase matur 26.5 15 0.00033 30.8 -0.8 84 23-121 102-186 (750)
115 COG1198 PriA Primosomal protei 26.5 17 0.00037 30.8 -0.6 37 81-117 445-484 (730)
116 PF11672 DUF3268: Protein of u 26.3 27 0.00057 21.9 0.4 7 109-115 32-38 (102)
117 PRK03976 rpl37ae 50S ribosomal 25.5 21 0.00046 21.8 -0.2 9 81-89 55-63 (90)
118 PF01927 Mut7-C: Mut7-C RNAse 25.4 53 0.0012 21.7 1.7 20 80-99 124-143 (147)
119 cd01121 Sms Sms (bacterial rad 24.5 43 0.00093 26.0 1.3 21 51-87 1-21 (372)
120 COG4888 Uncharacterized Zn rib 24.3 11 0.00023 23.5 -1.6 39 47-91 19-57 (104)
121 KOG2893|consensus 24.0 40 0.00087 24.6 0.9 38 83-124 13-50 (341)
122 TIGR00143 hypF [NiFe] hydrogen 23.9 15 0.00032 31.0 -1.4 83 23-120 69-152 (711)
123 PLN02294 cytochrome c oxidase 22.6 54 0.0012 22.6 1.3 16 78-93 139-154 (174)
124 COG4530 Uncharacterized protei 22.2 51 0.0011 20.9 1.1 14 78-91 24-37 (129)
125 KOG2461|consensus 22.2 1.1E+02 0.0023 24.2 3.0 9 95-103 346-354 (396)
126 PF08274 PhnA_Zn_Ribbon: PhnA 21.7 41 0.0009 16.0 0.5 9 80-88 19-27 (30)
127 PF01363 FYVE: FYVE zinc finge 21.7 46 0.001 18.6 0.8 10 52-61 11-20 (69)
128 KOG2231|consensus 21.6 93 0.002 26.3 2.7 19 53-71 185-203 (669)
129 COG1773 Rubredoxin [Energy pro 21.3 43 0.00093 18.4 0.5 14 80-93 3-16 (55)
130 PF12760 Zn_Tnp_IS1595: Transp 20.6 1.1E+02 0.0025 15.6 2.1 11 106-116 35-45 (46)
131 PRK14873 primosome assembly pr 20.2 76 0.0016 26.8 2.0 12 107-118 421-432 (665)
132 PF01286 XPA_N: XPA protein N- 20.1 55 0.0012 16.1 0.7 11 52-62 5-15 (34)
No 1
>KOG2462|consensus
Probab=99.82 E-value=1.6e-21 Score=138.20 Aligned_cols=111 Identities=18% Similarity=0.218 Sum_probs=101.8
Q ss_pred cccccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHH
Q psy16400 21 FTAALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHI 100 (145)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~ 100 (145)
....|..|.........+.-|.++|+ -++.|.+|||.|...|.|..|+++|+| +|||.|+.|++.|...++|..|+
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTG--EKPF~C~hC~kAFADRSNLRAHm 235 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTG--EKPFSCPHCGKAFADRSNLRAHM 235 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccC--CCCccCCcccchhcchHHHHHHH
Confidence 34567778999999999999999887 468999999999999999999999999 88999999999999999999999
Q ss_pred HHhcCCCcccCCCCCCCCCCCCCchhhhhhcccCC
Q psy16400 101 RKYHTSIELQSPSPAPRKPIVNPMQTQQQASNLST 135 (145)
Q Consensus 101 ~~h~~~kp~~c~~c~~~~~~~~~~~~~~~~~~~~~ 135 (145)
++|.+.|.|+|..|++.|.+...|..|.|......
T Consensus 236 QTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~C~~~ 270 (279)
T KOG2462|consen 236 QTHSDVKKHQCPRCGKSFALKSYLNKHSESACLKY 270 (279)
T ss_pred HhhcCCccccCcchhhHHHHHHHHHHhhhhccccc
Confidence 99999999999999999999999999998876543
No 2
>KOG2462|consensus
Probab=99.73 E-value=2.6e-18 Score=121.98 Aligned_cols=107 Identities=16% Similarity=0.153 Sum_probs=96.5
Q ss_pred ccccchhhhccccCCCCCCCceeccC---CCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHH
Q psy16400 22 TAALSTLARFHWLNWDPNPKYVRTTQ---ENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRV 98 (145)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~ 98 (145)
...|..|.......+.|.+|...|-. .+.+.|..|++.|++-..|+.|+++|+- +.+|.+||+.|++..-|+-
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l----~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTL----PCECGICGKAFSRPWLLQG 205 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCC----CcccccccccccchHHhhc
Confidence 35677788888888889999888854 6789999999999999999999999964 7899999999999999999
Q ss_pred HHHHhcCCCcccCCCCCCCCCCCCCchhhhhhcc
Q psy16400 99 HIRKYHTSIELQSPSPAPRKPIVNPMQTQQQASN 132 (145)
Q Consensus 99 H~~~h~~~kp~~c~~c~~~~~~~~~~~~~~~~~~ 132 (145)
|+|+|||||||.|..|++.|--...|.+|.|.+-
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS 239 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHS 239 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhc
Confidence 9999999999999999999999999998888654
No 3
>KOG3623|consensus
Probab=99.48 E-value=1.1e-14 Score=114.84 Aligned_cols=75 Identities=25% Similarity=0.389 Sum_probs=70.2
Q ss_pred cCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCCCCC
Q psy16400 46 TQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKPIVN 122 (145)
Q Consensus 46 ~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~~~~ 122 (145)
+...+|.|+.|.+.|.-...|.+|.--|+| .+||.|.+|.+.|..+.+|..|.|.|.|||||+|+.|+++|...-
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsG--qRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSG 964 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSG--QRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSG 964 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcC--CCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhccccc
Confidence 446689999999999999999999999999 889999999999999999999999999999999999999998544
No 4
>KOG3576|consensus
Probab=99.42 E-value=2e-14 Score=98.37 Aligned_cols=104 Identities=17% Similarity=0.181 Sum_probs=75.9
Q ss_pred ccccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHHH
Q psy16400 22 TAALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIR 101 (145)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~ 101 (145)
...|..|...|.+...+++|+.-|..-+.|.|..||+.|.....|++|+++|+| .+||+|..|++.|.+..+|..|.+
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtg--vrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTG--VRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccC--ccccchhhhhHHHHhhccHHHHHH
Confidence 345566777777777788888888777778888888888877888888888888 778888888888888888888777
Q ss_pred HhcC-----------CCcccCCCCCCCCCCCCCchhh
Q psy16400 102 KYHT-----------SIELQSPSPAPRKPIVNPMQTQ 127 (145)
Q Consensus 102 ~h~~-----------~kp~~c~~c~~~~~~~~~~~~~ 127 (145)
.-+| +|-|.|..|+-........-.|
T Consensus 195 kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h 231 (267)
T KOG3576|consen 195 KVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLH 231 (267)
T ss_pred HHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHH
Confidence 5444 4567787777666555444333
No 5
>KOG3576|consensus
Probab=99.41 E-value=5.2e-14 Score=96.32 Aligned_cols=86 Identities=15% Similarity=0.303 Sum_probs=77.9
Q ss_pred cCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCCCCCCch
Q psy16400 46 TQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKPIVNPMQ 125 (145)
Q Consensus 46 ~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~~~~~~~ 125 (145)
.+...|+|.+|++.|...-.|.+|++.|.. .+.+.|..||+.|.....|++|.|+|+|.+||+|..|++.|...-.|.
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~--vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsle 190 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSD--VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLE 190 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccH--HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHH
Confidence 346789999999999999999999999988 789999999999999999999999999999999999999999998887
Q ss_pred hhhhhccc
Q psy16400 126 TQQQASNL 133 (145)
Q Consensus 126 ~~~~~~~~ 133 (145)
.|..-.+.
T Consensus 191 shl~kvhg 198 (267)
T KOG3576|consen 191 SHLKKVHG 198 (267)
T ss_pred HHHHHHcC
Confidence 77655444
No 6
>KOG3623|consensus
Probab=99.28 E-value=5.1e-13 Score=105.63 Aligned_cols=78 Identities=22% Similarity=0.362 Sum_probs=74.6
Q ss_pred ccccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHHH
Q psy16400 22 TAALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIR 101 (145)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~ 101 (145)
..+|+.|+..|...+.+.+|.=-|+|++||.|.+|.+.|..+..|..|++.|.| +|||.|+.|++.|+..++...|+.
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSG--EKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSG--EKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccC--CCcchhhhhhhhcccccchHhhhc
Confidence 468999999999999999999999999999999999999999999999999999 889999999999999999988875
No 7
>KOG1074|consensus
Probab=99.26 E-value=2.2e-12 Score=103.28 Aligned_cols=62 Identities=19% Similarity=0.171 Sum_probs=54.8
Q ss_pred eeccCCCCcccccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhc
Q psy16400 13 AFFFPRGVFTAALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFEC 74 (145)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~ 74 (145)
....+..+++..|--|.+.|+..+.+.-|+++|+|++||.|++||..|.++.+|+.|...|+
T Consensus 344 ~~~~~~~~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 344 EGPSEKPFFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred ccCCccccccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeecc
Confidence 44556677777888899999999999999999999999999999999999999998877664
No 8
>KOG3608|consensus
Probab=99.03 E-value=3.6e-11 Score=88.53 Aligned_cols=110 Identities=20% Similarity=0.281 Sum_probs=86.8
Q ss_pred CCcccccchhhhccccCCCCCCCceeccC--CCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhH
Q psy16400 19 GVFTAALSTLARFHWLNWDPNPKYVRTTQ--ENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNL 96 (145)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l 96 (145)
+.-..+|..|.++|.....+.+|.+..+. .++|.|..|.+.|.+...|..|++.|.. -|+|+.|+......++|
T Consensus 204 ~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn----~ykCplCdmtc~~~ssL 279 (467)
T KOG3608|consen 204 NEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN----CYKCPLCDMTCSSASSL 279 (467)
T ss_pred CCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh----cccccccccCCCChHHH
Confidence 34445666777777777777777766653 5677788888888888888888887755 68999999999999999
Q ss_pred HHHHHH-hcCCCcccCCCCCCCCCCCCCchhhhhhcc
Q psy16400 97 RVHIRK-YHTSIELQSPSPAPRKPIVNPMQTQQQASN 132 (145)
Q Consensus 97 ~~H~~~-h~~~kp~~c~~c~~~~~~~~~~~~~~~~~~ 132 (145)
..|++. |..+|||+|+.|...+.....|+.|-+.+.
T Consensus 280 ~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 280 TTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 999995 788999999999999888777777666443
No 9
>PHA02768 hypothetical protein; Provisional
Probab=98.80 E-value=4.3e-09 Score=57.85 Aligned_cols=41 Identities=17% Similarity=0.240 Sum_probs=30.1
Q ss_pred cccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCCCCCC
Q psy16400 81 HQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKPIVNP 123 (145)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~~~~~ 123 (145)
|.|+.||+.|....+|..|+++|+ ++|+|..|++.|.....
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~ 46 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGE 46 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccce
Confidence 677777777777777777777777 67777777776665443
No 10
>KOG1074|consensus
Probab=98.77 E-value=2e-09 Score=86.72 Aligned_cols=105 Identities=20% Similarity=0.198 Sum_probs=80.4
Q ss_pred cCCCCcccccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCC--CCCCcccC---CCcccc
Q psy16400 16 FPRGVFTAALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGG--KEPVHQCP---HCDYRA 90 (145)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~--~~k~~~C~---~C~~~f 90 (145)
..+.....-|+.|.+.-.=.+.+.-|+++|+|++||.|.+||+.|.++.+|+.|+..|... -+.++.|+ +|-+.|
T Consensus 599 ~~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kf 678 (958)
T KOG1074|consen 599 ENKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKF 678 (958)
T ss_pred ccccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccc
Confidence 3344445667778888888888999999999999999999999999999999999988651 02356788 888999
Q ss_pred CCchhHHHHHHHhcC-CC------------cccCCCCCCCCCC
Q psy16400 91 KQSGNLRVHIRKYHT-SI------------ELQSPSPAPRKPI 120 (145)
Q Consensus 91 ~~~~~l~~H~~~h~~-~k------------p~~c~~c~~~~~~ 120 (145)
.+.-.|..|++.|.+ .. ..+|..|.+.|.-
T Consensus 679 tn~V~lpQhIriH~~~~~s~g~~a~e~~~~adq~~~~qk~~~~ 721 (958)
T KOG1074|consen 679 TNAVTLPQHIRIHLGGQISNGGTAAEGILAADQCSSCQKTFSD 721 (958)
T ss_pred cccccccceEEeecCCCCCCCcccccccchhcccchhhhcccc
Confidence 999999999999883 22 2456666666643
No 11
>PHA00733 hypothetical protein
Probab=98.62 E-value=7.7e-09 Score=67.42 Aligned_cols=81 Identities=12% Similarity=0.020 Sum_probs=58.6
Q ss_pred cCCCceecccccccccChhhHHHH--hh---hhcCCCCCCcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCCC
Q psy16400 46 TQENQYSCQHCGKRYRWKSTLKRH--EV---FECGGKEPVHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKPI 120 (145)
Q Consensus 46 ~~~k~~~C~~c~~~f~~~~~l~~h--~~---~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~~ 120 (145)
..++.+.|.+|...|.....|..+ .. .+.+ .++|.|..|++.|.....|..|++.+ +.+|.|..|++.|..
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~--~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~ 111 (128)
T PHA00733 36 PEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKA--VSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRN 111 (128)
T ss_pred hhhhhHHHHHHhhhccChhhhcchHHHHhhcccCC--CCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCC
Confidence 446778888888777766665554 11 2234 56888999999999888888888876 457899999988888
Q ss_pred CCCchhhhhh
Q psy16400 121 VNPMQTQQQA 130 (145)
Q Consensus 121 ~~~~~~~~~~ 130 (145)
...|..|...
T Consensus 112 ~~sL~~H~~~ 121 (128)
T PHA00733 112 TDSTLDHVCK 121 (128)
T ss_pred HHHHHHHHHH
Confidence 7777655443
No 12
>PHA00733 hypothetical protein
Probab=98.62 E-value=5.2e-08 Score=63.50 Aligned_cols=75 Identities=16% Similarity=0.298 Sum_probs=58.2
Q ss_pred hhhhccccCCCCCCC-----ceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHHH
Q psy16400 27 TLARFHWLNWDPNPK-----YVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIR 101 (145)
Q Consensus 27 ~~~~~~~~~~~~~~~-----~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~ 101 (145)
.|...+.....+..+ ...+.+.++|.|..|++.|.....|..|++.+. .+|.|..|++.|.....|..|+.
T Consensus 45 ~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~----~~~~C~~CgK~F~~~~sL~~H~~ 120 (128)
T PHA00733 45 VVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTE----HSKVCPVCGKEFRNTDSTLDHVC 120 (128)
T ss_pred HHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcCC----cCccCCCCCCccCCHHHHHHHHH
Confidence 355455554444443 233455889999999999999999999998763 36999999999999999999988
Q ss_pred HhcC
Q psy16400 102 KYHT 105 (145)
Q Consensus 102 ~h~~ 105 (145)
..++
T Consensus 121 ~~h~ 124 (128)
T PHA00733 121 KKHN 124 (128)
T ss_pred HhcC
Confidence 7664
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.58 E-value=3.3e-08 Score=54.33 Aligned_cols=43 Identities=19% Similarity=0.386 Sum_probs=38.3
Q ss_pred eecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHH
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLR 97 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~ 97 (145)
|.|+.||+.|.....|..|++.|. +++.|..|++.|...+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~----k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN----TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC----CcccCCcccceecccceeE
Confidence 799999999999999999999986 3789999999999876653
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.56 E-value=3.2e-08 Score=78.23 Aligned_cols=87 Identities=16% Similarity=0.197 Sum_probs=42.0
Q ss_pred CCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCC----------chhHHHHHHHhcCC
Q psy16400 37 DPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQ----------SGNLRVHIRKYHTS 106 (145)
Q Consensus 37 ~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~----------~~~l~~H~~~h~~~ 106 (145)
.+..|...++ +++.|. |+..+ .+..|..|+..|.+ .+++.|..|++.+.. ...|..|...+ |.
T Consensus 467 ~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp--~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~ 539 (567)
T PLN03086 467 EMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCP--LRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GS 539 (567)
T ss_pred HHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCC--CCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CC
Confidence 3444544442 455555 55433 34455555555555 445555555555421 12455554443 55
Q ss_pred CcccCCCCCCCCCCCCCchhhhhhc
Q psy16400 107 IELQSPSPAPRKPIVNPMQTQQQAS 131 (145)
Q Consensus 107 kp~~c~~c~~~~~~~~~~~~~~~~~ 131 (145)
+++.|..|++.+... .|..|..+.
T Consensus 540 rt~~C~~Cgk~Vrlr-dm~~H~~~~ 563 (567)
T PLN03086 540 RTAPCDSCGRSVMLK-EMDIHQIAV 563 (567)
T ss_pred cceEccccCCeeeeh-hHHHHHHHh
Confidence 555555555444333 444444433
No 15
>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=98.45 E-value=5.3e-08 Score=45.78 Aligned_cols=24 Identities=25% Similarity=0.257 Sum_probs=16.7
Q ss_pred hHHHHHHHhcCCCcccCCCCCCCC
Q psy16400 95 NLRVHIRKYHTSIELQSPSPAPRK 118 (145)
Q Consensus 95 ~l~~H~~~h~~~kp~~c~~c~~~~ 118 (145)
+|.+|+++|+|++||.|..|++.|
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEE
T ss_pred CHHHHhhhcCCCCCCCCCCCcCee
Confidence 366777777777777777777654
No 16
>PHA00616 hypothetical protein
Probab=98.44 E-value=9.4e-08 Score=50.10 Aligned_cols=33 Identities=18% Similarity=0.285 Sum_probs=25.1
Q ss_pred CcccCCCccccCCchhHHHHHHHhcCCCcccCC
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSP 112 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~ 112 (145)
||.|+.||+.|.+...|..|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 467777888888777888888777777777664
No 17
>KOG3608|consensus
Probab=98.42 E-value=3.8e-08 Score=72.89 Aligned_cols=118 Identities=16% Similarity=0.199 Sum_probs=94.8
Q ss_pred CCcccccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHH
Q psy16400 19 GVFTAALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRV 98 (145)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~ 98 (145)
.++.+.=..|...+...+.++.|.+.|+++|...|..||.-|..+..|..|.+.-+.....+|.|..|.+.|.....|..
T Consensus 176 pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~ 255 (467)
T KOG3608|consen 176 PVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKS 255 (467)
T ss_pred ceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHH
Confidence 34445566788889999999999999999999999999999999999999988666433679999999999999999999
Q ss_pred HHHHhcCCCcccCCCCCCCCCCCCCchhhhhhcccCCCCCCC
Q psy16400 99 HIRKYHTSIELQSPSPAPRKPIVNPMQTQQQASNLSTNQTPV 140 (145)
Q Consensus 99 H~~~h~~~kp~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 (145)
|+..|- .-|+|+.|.-.-+....|..|.--.+.. ..|+
T Consensus 256 Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~--dkpf 293 (467)
T KOG3608|consen 256 HVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSK--DKPF 293 (467)
T ss_pred HHHHhh--hcccccccccCCCChHHHHHHHHhhhcc--CCCc
Confidence 999997 5589988887666666665554444433 4444
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=98.36 E-value=3.4e-07 Score=43.00 Aligned_cols=26 Identities=31% Similarity=0.557 Sum_probs=21.4
Q ss_pred hHHHHhhhhcCCCCCCcccCCCccccCC
Q psy16400 65 TLKRHEVFECGGKEPVHQCPHCDYRAKQ 92 (145)
Q Consensus 65 ~l~~h~~~h~~~~~k~~~C~~C~~~f~~ 92 (145)
+|..|++.|++ +++|.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~--~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTG--EKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSS--SSSEEESSSSEEESS
T ss_pred CHHHHhhhcCC--CCCCCCCCCcCeeCc
Confidence 47788889988 779999999888863
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.27 E-value=1.4e-06 Score=69.03 Aligned_cols=79 Identities=14% Similarity=0.259 Sum_probs=62.5
Q ss_pred CCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCCCC------
Q psy16400 48 ENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKPIV------ 121 (145)
Q Consensus 48 ~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~~~------ 121 (145)
++.+.|..|++.|. ...|..|+..++ +++.|+ |++.+ ....|..|+.+|..++++.|..|+..+...
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H----kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~ 523 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH----EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDV 523 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC----CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccch
Confidence 44578999999996 677999999874 379999 99765 568999999999999999999999988532
Q ss_pred ----CCchhhhhhccc
Q psy16400 122 ----NPMQTQQQASNL 133 (145)
Q Consensus 122 ----~~~~~~~~~~~~ 133 (145)
..|..|...+..
T Consensus 524 ~d~~s~Lt~HE~~CG~ 539 (567)
T PLN03086 524 RDRLRGMSEHESICGS 539 (567)
T ss_pred hhhhhhHHHHHHhcCC
Confidence 246666666543
No 20
>KOG3993|consensus
Probab=97.97 E-value=5.8e-07 Score=68.01 Aligned_cols=86 Identities=20% Similarity=0.235 Sum_probs=68.5
Q ss_pred eecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHHHHhc--------CCC---------------
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIRKYH--------TSI--------------- 107 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~--------~~k--------------- 107 (145)
|.|+.|...|.....|.+|.-.--- ..-|.|+.|+++|+-..+|..|.|.|. +..
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV--~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIV--HVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeE--EeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 7899999999999899988654332 224899999999999999999999883 222
Q ss_pred ----------cccCCCCCCCCCCCCCchhhhhhcccCCCCC
Q psy16400 108 ----------ELQSPSPAPRKPIVNPMQTQQQASNLSTNQT 138 (145)
Q Consensus 108 ----------p~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~ 138 (145)
-|.|..|++.|..+..|..|+-.++...+..
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 2889999999999999988877777665554
No 21
>PHA00732 hypothetical protein
Probab=97.95 E-value=6.3e-06 Score=49.16 Aligned_cols=46 Identities=24% Similarity=0.422 Sum_probs=34.8
Q ss_pred ceecccccccccChhhHHHHhhh-hcCCCCCCcccCCCccccCCchhHHHHHHHh
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEVF-ECGGKEPVHQCPHCDYRAKQSGNLRVHIRKY 103 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~~-h~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h 103 (145)
+|.|..|++.|.....|..|++. |.+ +.|..|++.|. .+..|.++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~-----~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL-----TKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC-----CccCCCCCEeC---Chhhhhccc
Confidence 47788999999988889988874 433 47888988887 466676544
No 22
>PHA00616 hypothetical protein
Probab=97.86 E-value=7.7e-06 Score=42.91 Aligned_cols=34 Identities=21% Similarity=0.321 Sum_probs=30.9
Q ss_pred ceecccccccccChhhHHHHhhhhcCCCCCCcccCC
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPH 85 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~ 85 (145)
+|.|..||+.|..+..|..|++.|+| .+++.|..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg--~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK--QNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC--CCccceeE
Confidence 58999999999999999999999999 77888754
No 23
>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=97.82 E-value=5.2e-05 Score=41.89 Aligned_cols=53 Identities=30% Similarity=0.481 Sum_probs=39.3
Q ss_pred ceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHHHHhcC
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIRKYHT 105 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~~ 105 (145)
.|.|..|++ ..+...|..|....+....+.+.|++|...+. .+|..|+..+++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 488999999 55577899997754443345799999987544 488889887653
No 24
>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=97.64 E-value=3.9e-05 Score=34.58 Aligned_cols=22 Identities=32% Similarity=0.733 Sum_probs=12.3
Q ss_pred cccCCCccccCCchhHHHHHHH
Q psy16400 81 HQCPHCDYRAKQSGNLRVHIRK 102 (145)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~ 102 (145)
|.|+.|++.|.....|..|++.
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 3455555555555555555554
No 25
>PHA00732 hypothetical protein
Probab=97.60 E-value=4.9e-05 Score=45.35 Aligned_cols=37 Identities=19% Similarity=0.374 Sum_probs=32.6
Q ss_pred CcccCCCccccCCchhHHHHHHH-hcCCCcccCCCCCCCCC
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRK-YHTSIELQSPSPAPRKP 119 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~kp~~c~~c~~~~~ 119 (145)
||.|..|++.|.....|..|++. |.+ +.|..|++.|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~ 38 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR 38 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC
Confidence 58899999999999999999985 553 58999999887
No 26
>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=97.45 E-value=0.00011 Score=33.05 Aligned_cols=23 Identities=48% Similarity=0.821 Sum_probs=21.1
Q ss_pred eecccccccccChhhHHHHhhhh
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFE 73 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h 73 (145)
|.|..|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 68999999999999999999864
No 27
>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=97.19 E-value=0.00035 Score=31.34 Aligned_cols=23 Identities=35% Similarity=0.712 Sum_probs=12.1
Q ss_pred cccCCCccccCCchhHHHHHHHh
Q psy16400 81 HQCPHCDYRAKQSGNLRVHIRKY 103 (145)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h 103 (145)
|.|+.|++.|.....|..|++.+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 34555666666666666665554
No 28
>KOG3993|consensus
Probab=97.14 E-value=0.00012 Score=55.89 Aligned_cols=78 Identities=14% Similarity=0.242 Sum_probs=58.3
Q ss_pred hhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCC------C-----------------------
Q psy16400 28 LARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGK------E----------------------- 78 (145)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~------~----------------------- 78 (145)
|.-.+.....+.+|.=.-.-..-|.|.+|+|.|.-..+|..|.+.|.... .
T Consensus 273 CK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~ds 352 (500)
T KOG3993|consen 273 CKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDS 352 (500)
T ss_pred HHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcc
Confidence 44444455555555444444556999999999999999999999885310 0
Q ss_pred --CCcccCCCccccCCchhHHHHHHHhcC
Q psy16400 79 --PVHQCPHCDYRAKQSGNLRVHIRKYHT 105 (145)
Q Consensus 79 --k~~~C~~C~~~f~~~~~l~~H~~~h~~ 105 (145)
--|.|..|++.|.....|..|+-+|+.
T Consensus 353 s~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 353 SSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 137899999999999999999988874
No 29
>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=97.04 E-value=0.00045 Score=32.28 Aligned_cols=24 Identities=33% Similarity=0.873 Sum_probs=14.6
Q ss_pred eecccccccccChhhHHHHhhhhc
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFEC 74 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (145)
|.|..|++.|.+...|..|++.|.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 556666666666666666665543
No 30
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.96 E-value=0.00066 Score=50.18 Aligned_cols=53 Identities=30% Similarity=0.607 Sum_probs=31.9
Q ss_pred CCCceeccc--ccccccChhhHHHHhhhhc-C----------------CCCCCcccCCCccccCCchhHHHH
Q psy16400 47 QENQYSCQH--CGKRYRWKSTLKRHEVFEC-G----------------GKEPVHQCPHCDYRAKQSGNLRVH 99 (145)
Q Consensus 47 ~~k~~~C~~--c~~~f~~~~~l~~h~~~h~-~----------------~~~k~~~C~~C~~~f~~~~~l~~H 99 (145)
++|+|.|.+ |.|.|...-.|+-|+.--+ . .+.|||.|.+|++.|.+..-|+.|
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceec
Confidence 358888876 8888888777777765221 0 012455555555555555555544
No 31
>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=96.94 E-value=0.00087 Score=36.09 Aligned_cols=31 Identities=35% Similarity=0.517 Sum_probs=20.4
Q ss_pred CCCcccCCCccccCCchhHHHHHHHhcCCCc
Q psy16400 78 EPVHQCPHCDYRAKQSGNLRVHIRKYHTSIE 108 (145)
Q Consensus 78 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~kp 108 (145)
..|-.|++|+..+.+..+|.+|+.++++.||
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 5577888888888888888888888877765
No 32
>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=96.90 E-value=0.00041 Score=32.43 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=23.1
Q ss_pred CcccCCCccccCCchhHHHHHHHhcC
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYHT 105 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 105 (145)
+|.|..|++.|.....|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 58899999999999999999987753
No 33
>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=96.87 E-value=0.00098 Score=29.79 Aligned_cols=23 Identities=39% Similarity=0.807 Sum_probs=19.3
Q ss_pred eecccccccccChhhHHHHhhhh
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFE 73 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h 73 (145)
|.|..|++.|.....|..|+..+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 68999999999999999999876
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.43 E-value=0.0035 Score=28.29 Aligned_cols=22 Identities=32% Similarity=0.693 Sum_probs=13.1
Q ss_pred ccCCCccccCCchhHHHHHHHh
Q psy16400 82 QCPHCDYRAKQSGNLRVHIRKY 103 (145)
Q Consensus 82 ~C~~C~~~f~~~~~l~~H~~~h 103 (145)
.|..|++.|.....|..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4555666666666666666544
No 35
>PRK04860 hypothetical protein; Provisional
Probab=96.39 E-value=0.0026 Score=43.04 Aligned_cols=38 Identities=13% Similarity=0.132 Sum_probs=31.6
Q ss_pred CcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCCCC
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKPIV 121 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~~~ 121 (145)
+|.|. |+. ....+.+|.++|+++++|.|..|...+...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 68887 876 677788999999999999999999876544
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.98 E-value=0.0044 Score=45.96 Aligned_cols=50 Identities=18% Similarity=0.305 Sum_probs=39.4
Q ss_pred CCCcccCC--CccccCCchhHHHHHHHhc-------------------CCCcccCCCCCCCCCCCCCchhh
Q psy16400 78 EPVHQCPH--CDYRAKQSGNLRVHIRKYH-------------------TSIELQSPSPAPRKPIVNPMQTQ 127 (145)
Q Consensus 78 ~k~~~C~~--C~~~f~~~~~l~~H~~~h~-------------------~~kp~~c~~c~~~~~~~~~~~~~ 127 (145)
+|||+|++ |.+.|.+..-|+.|+.-.+ .+|||.|..|+++--..+-|.-|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceec
Confidence 47999975 9999999999999976533 14899999999987666665443
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.93 E-value=0.0072 Score=36.95 Aligned_cols=25 Identities=28% Similarity=0.651 Sum_probs=21.3
Q ss_pred CcccCCCccccCCchhHHHHHHHhc
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYH 104 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~ 104 (145)
.+.|..|++.|.....|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 5899999999999999999999753
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.75 E-value=0.0089 Score=26.86 Aligned_cols=24 Identities=42% Similarity=0.787 Sum_probs=21.2
Q ss_pred eecccccccccChhhHHHHhhhhc
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFEC 74 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (145)
|.|..|++.|.....|..|+..|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998654
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.53 E-value=0.011 Score=26.83 Aligned_cols=21 Identities=24% Similarity=0.681 Sum_probs=12.1
Q ss_pred eecccccccccChhhHHHHhh
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEV 71 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~ 71 (145)
|.|..|++.|.+...|..|++
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 345566666666665555554
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=95.47 E-value=0.019 Score=30.95 Aligned_cols=33 Identities=24% Similarity=0.370 Sum_probs=23.5
Q ss_pred cCCCceecccccccccChhhHHHHhhhhcCCCCCC
Q psy16400 46 TQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPV 80 (145)
Q Consensus 46 ~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~ 80 (145)
..+.+..|.+|+..+....+|.+|+...++ .||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~--~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHF--KKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTT--TS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhc--ccC
Confidence 456789999999999999999999988877 554
No 41
>PRK04860 hypothetical protein; Provisional
Probab=95.46 E-value=0.0097 Score=40.28 Aligned_cols=38 Identities=29% Similarity=0.623 Sum_probs=32.4
Q ss_pred ceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCc
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQS 93 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~ 93 (145)
+|.|. |+. ....+.+|.+++.+ .++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g--~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRG--EAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcC--CccEECCCCCceeEEe
Confidence 69998 987 46678999999999 7899999999887654
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.37 E-value=0.015 Score=26.13 Aligned_cols=23 Identities=39% Similarity=1.038 Sum_probs=12.3
Q ss_pred cccCCCccccCCchhHHHHHHHhc
Q psy16400 81 HQCPHCDYRAKQSGNLRVHIRKYH 104 (145)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h~ 104 (145)
|.|..|+.... ...|..|++.++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 45666665555 556666666543
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.03 E-value=0.012 Score=26.66 Aligned_cols=23 Identities=26% Similarity=0.528 Sum_probs=20.4
Q ss_pred cccCCCccccCCchhHHHHHHHh
Q psy16400 81 HQCPHCDYRAKQSGNLRVHIRKY 103 (145)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~h 103 (145)
|.|..|+..|.....+..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 57999999999999999998754
No 44
>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=94.14 E-value=0.026 Score=26.23 Aligned_cols=22 Identities=27% Similarity=0.602 Sum_probs=16.9
Q ss_pred eecccccccccChhhHHHHhhh
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVF 72 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~ 72 (145)
|.|..|++.|.+...+..|+..
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5688888888888887777654
No 45
>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=94.09 E-value=0.084 Score=28.88 Aligned_cols=37 Identities=24% Similarity=0.395 Sum_probs=28.6
Q ss_pred CcccCCCccccCCchhHHHHHHHhc-C-CCcccCCCCCCC
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYH-T-SIELQSPSPAPR 117 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~-~-~kp~~c~~c~~~ 117 (145)
.|.|+.|++. .....|..|....+ . .+.+.|+.|...
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 4899999995 44578999988744 3 357999999864
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.87 E-value=0.058 Score=24.15 Aligned_cols=23 Identities=43% Similarity=0.694 Sum_probs=17.7
Q ss_pred eecccccccccChhhHHHHhhhhc
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFEC 74 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~ 74 (145)
|.|..|+.... ...|..|+..++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 67999998887 889999988765
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.53 E-value=0.12 Score=23.58 Aligned_cols=21 Identities=24% Similarity=0.525 Sum_probs=13.3
Q ss_pred cccCCCccccCCchhHHHHHHH
Q psy16400 81 HQCPHCDYRAKQSGNLRVHIRK 102 (145)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~~ 102 (145)
..|+.|++.| ....|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4577777777 55566666553
No 48
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.33 E-value=0.068 Score=40.74 Aligned_cols=66 Identities=20% Similarity=0.279 Sum_probs=53.2
Q ss_pred CceecccccccccChhhHHHHhh--hhcCCCC--CCcccC--CCccccCCchhHHHHHHHhcCCCcccCCCCCC
Q psy16400 49 NQYSCQHCGKRYRWKSTLKRHEV--FECGGKE--PVHQCP--HCDYRAKQSGNLRVHIRKYHTSIELQSPSPAP 116 (145)
Q Consensus 49 k~~~C~~c~~~f~~~~~l~~h~~--~h~~~~~--k~~~C~--~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~ 116 (145)
.++.|..|...|.....+..|.. .|.+ . +++.|+ .|++.|.+...+..|...|++.+++.+..-..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~--~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 359 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSG--ESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNS 359 (467)
T ss_pred cCCCCccccCCcccccccccccccccccc--ccCCceeeeccCCCccccccccccCCcccccCCCccccccccC
Confidence 36778888888888888888888 6887 6 788888 68888999888888988888887777754433
No 49
>KOG2893|consensus
Probab=90.63 E-value=0.079 Score=37.99 Aligned_cols=42 Identities=19% Similarity=0.440 Sum_probs=30.5
Q ss_pred ecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHH
Q psy16400 52 SCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVH 99 (145)
Q Consensus 52 ~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H 99 (145)
.|..|++.|.....|..|++ .|-|+|-+|.+..-...-|..|
T Consensus 12 wcwycnrefddekiliqhqk------akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK------AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhh------hccceeeeehhhhccCCCceee
Confidence 58899999999999999877 4468888886653333333333
No 50
>KOG2186|consensus
Probab=88.87 E-value=0.28 Score=35.45 Aligned_cols=50 Identities=16% Similarity=0.414 Sum_probs=37.0
Q ss_pred ceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhHHHHHHHhc
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIRKYH 104 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l~~H~~~h~ 104 (145)
-|+|+.||.... +..+..|+...++ . .|.|.-|++.|..- ....|..=-+
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCrn--~-~fSCIDC~k~F~~~-sYknH~kCIT 52 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCRN--A-YFSCIDCGKTFERV-SYKNHTKCIT 52 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhccC--C-eeEEeecccccccc-hhhhhhhhcc
Confidence 378999997765 5677889888876 3 68999999999884 4556755333
No 51
>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=88.81 E-value=0.35 Score=23.51 Aligned_cols=22 Identities=14% Similarity=0.422 Sum_probs=15.3
Q ss_pred ceecccccccccChhhHHHHhh
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEV 71 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~ 71 (145)
.|.|+.|+..|.....+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777777766666655
No 52
>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=87.70 E-value=0.46 Score=23.16 Aligned_cols=10 Identities=50% Similarity=1.248 Sum_probs=5.9
Q ss_pred eecccccccc
Q psy16400 51 YSCQHCGKRY 60 (145)
Q Consensus 51 ~~C~~c~~~f 60 (145)
|.|..||..+
T Consensus 2 ~~C~~CGy~y 11 (33)
T cd00350 2 YVCPVCGYIY 11 (33)
T ss_pred EECCCCCCEE
Confidence 5566666544
No 53
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=87.05 E-value=0.59 Score=28.23 Aligned_cols=25 Identities=24% Similarity=0.588 Sum_probs=21.8
Q ss_pred ceecccccccccChhhHHHHhhhhc
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEVFEC 74 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~~h~ 74 (145)
.+.|..|++.|.+...|..|+..+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 6899999999999999999999753
No 54
>KOG1146|consensus
Probab=86.37 E-value=1 Score=39.83 Aligned_cols=61 Identities=23% Similarity=0.441 Sum_probs=48.2
Q ss_pred ceeccCCCceecccccccccChhhHHHHhhhhcCC-----------------------CCCCcccCCCccccCCchhHHH
Q psy16400 42 YVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGG-----------------------KEPVHQCPHCDYRAKQSGNLRV 98 (145)
Q Consensus 42 ~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~-----------------------~~k~~~C~~C~~~f~~~~~l~~ 98 (145)
...+.-.+.+.|..|+..|.....|..|++..+.. ..++|.|..|...+.-+.+|.+
T Consensus 457 ~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsi 536 (1406)
T KOG1146|consen 457 VVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSI 536 (1406)
T ss_pred eeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHH
Confidence 34445568899999999999999999999972110 1358889999999999999999
Q ss_pred HHHH
Q psy16400 99 HIRK 102 (145)
Q Consensus 99 H~~~ 102 (145)
|++.
T Consensus 537 hlqS 540 (1406)
T KOG1146|consen 537 HLQS 540 (1406)
T ss_pred HHHH
Confidence 9775
No 55
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=83.12 E-value=0.94 Score=28.64 Aligned_cols=15 Identities=20% Similarity=0.461 Sum_probs=8.9
Q ss_pred CCcccCCCccccCCc
Q psy16400 79 PVHQCPHCDYRAKQS 93 (145)
Q Consensus 79 k~~~C~~C~~~f~~~ 93 (145)
.|..|+.||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 356666666665544
No 56
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=78.28 E-value=1.7 Score=29.61 Aligned_cols=10 Identities=40% Similarity=0.983 Sum_probs=5.6
Q ss_pred CCCcccCCCc
Q psy16400 78 EPVHQCPHCD 87 (145)
Q Consensus 78 ~k~~~C~~C~ 87 (145)
+.|..||+|+
T Consensus 147 e~P~~CPiCg 156 (166)
T COG1592 147 EAPEVCPICG 156 (166)
T ss_pred CCCCcCCCCC
Confidence 4455666665
No 57
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=75.47 E-value=2.8 Score=31.87 Aligned_cols=61 Identities=16% Similarity=0.208 Sum_probs=51.4
Q ss_pred cccccchhhhccccCCCCCCCce--eccCC--Cceecc--cccccccChhhHHHHhhhhcCCCCCCccc
Q psy16400 21 FTAALSTLARFHWLNWDPNPKYV--RTTQE--NQYSCQ--HCGKRYRWKSTLKRHEVFECGGKEPVHQC 83 (145)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~--k~~~C~--~c~~~f~~~~~l~~h~~~h~~~~~k~~~C 83 (145)
....+..|...+.....+.+|.. .|+++ +++.|. .|++.|.+...+..|...|.+ ..++.+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~ 354 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS--ISPAKE 354 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccC--CCcccc
Confidence 35667778888888888999999 89999 999999 799999999999999998887 444444
No 58
>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=70.61 E-value=3.5 Score=20.18 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=6.4
Q ss_pred ceeccccccc
Q psy16400 50 QYSCQHCGKR 59 (145)
Q Consensus 50 ~~~C~~c~~~ 59 (145)
.|.|..||..
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 3667777754
No 59
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=69.62 E-value=1.5 Score=31.09 Aligned_cols=45 Identities=29% Similarity=0.601 Sum_probs=27.6
Q ss_pred CCceecccccccccChhhHHHHhhhhc---------CCCCC-----CcccCCCccccCCc
Q psy16400 48 ENQYSCQHCGKRYRWKSTLKRHEVFEC---------GGKEP-----VHQCPHCDYRAKQS 93 (145)
Q Consensus 48 ~k~~~C~~c~~~f~~~~~l~~h~~~h~---------~~~~k-----~~~C~~C~~~f~~~ 93 (145)
++...|.+|++.|..+....+..+.-. ++ .. .+.|+.||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~-vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKG-VNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCC-CCCeeeeEEECCCCCCccccc
Confidence 356789999999987765544433210 00 22 24799999775543
No 60
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=69.50 E-value=3.7 Score=20.46 Aligned_cols=33 Identities=24% Similarity=0.676 Sum_probs=17.7
Q ss_pred ecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccC
Q psy16400 52 SCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAK 91 (145)
Q Consensus 52 ~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~ 91 (145)
.|..|+..|..... +...+ .....|..|+..|.
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~--~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAG--GRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHH-----HcccC--CcEEECCCCCcEee
Confidence 56777766654432 11122 33567777776653
No 61
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=68.50 E-value=2.6 Score=23.20 Aligned_cols=25 Identities=28% Similarity=0.571 Sum_probs=11.5
Q ss_pred CCCceecccccccccChhhHHHHhh
Q psy16400 47 QENQYSCQHCGKRYRWKSTLKRHEV 71 (145)
Q Consensus 47 ~~k~~~C~~c~~~f~~~~~l~~h~~ 71 (145)
|+.-+.|..|+..|.....+.+|.-
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhh
Confidence 3444444445444444444444433
No 62
>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=68.25 E-value=2.9 Score=27.40 Aligned_cols=25 Identities=24% Similarity=0.397 Sum_probs=13.2
Q ss_pred CcccCCCccccCCchhHHHHHHHhcCCC
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYHTSI 107 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~k 107 (145)
...|..||+.|... ++|++.|+|..
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~glt 96 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHHGLT 96 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT-S-
T ss_pred eeEEccCCcccchH---HHHHHHccCCC
Confidence 35677788776644 77888886643
No 63
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=64.94 E-value=5 Score=19.90 Aligned_cols=33 Identities=15% Similarity=0.473 Sum_probs=18.0
Q ss_pred eecccccccccChhhHHHHhhhhcCCCCCCcccCCCcccc
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRA 90 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f 90 (145)
..|..|+..|..... +. -.. .....|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~----~i-p~~--g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDE----KI-PPK--GRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHH----HC-CCC--CcEEECCCCCCEe
Confidence 357777776664432 11 122 2356777777665
No 64
>KOG4173|consensus
Probab=62.92 E-value=2.6 Score=29.77 Aligned_cols=70 Identities=21% Similarity=0.288 Sum_probs=47.3
Q ss_pred hhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhh----------hcCCCCCCcccC--CCccccCCchh
Q psy16400 28 LARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVF----------ECGGKEPVHQCP--HCDYRAKQSGN 95 (145)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~----------h~~~~~k~~~C~--~C~~~f~~~~~ 95 (145)
|...+-.--+...|+...++ ..|.+|.+.|.+...|..|+.- ..| .-.|.|. .|+..|.....
T Consensus 87 c~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG--~dMy~ClvEgCt~KFkT~r~ 161 (253)
T KOG4173|consen 87 CCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERG--QDMYQCLVEGCTEKFKTSRD 161 (253)
T ss_pred hHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcC--ccHHHHHHHhhhhhhhhhhh
Confidence 33333333345566554444 4799999999999888888762 223 4468885 49888888878
Q ss_pred HHHHHHH
Q psy16400 96 LRVHIRK 102 (145)
Q Consensus 96 l~~H~~~ 102 (145)
.+.|+-.
T Consensus 162 RkdH~I~ 168 (253)
T KOG4173|consen 162 RKDHMIR 168 (253)
T ss_pred hhhHHHH
Confidence 7888654
No 65
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=62.74 E-value=7.1 Score=20.71 Aligned_cols=20 Identities=40% Similarity=0.823 Sum_probs=9.9
Q ss_pred ccCCCccccCCc-----hhHHHHHH
Q psy16400 82 QCPHCDYRAKQS-----GNLRVHIR 101 (145)
Q Consensus 82 ~C~~C~~~f~~~-----~~l~~H~~ 101 (145)
.|..|++.+... ++|.+|+.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 445555444332 45666655
No 66
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=62.51 E-value=8.3 Score=21.55 Aligned_cols=31 Identities=13% Similarity=0.171 Sum_probs=14.7
Q ss_pred CcccCCCccccCCchhHHHHHHHhcCCCcccCCCCC
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPA 115 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~ 115 (145)
.|.|+.||..-.......+ ....+|.|+.|+
T Consensus 27 ~F~CPnCGe~~I~Rc~~CR-----k~g~~Y~Cp~CG 57 (61)
T COG2888 27 KFPCPNCGEVEIYRCAKCR-----KLGNPYRCPKCG 57 (61)
T ss_pred EeeCCCCCceeeehhhhHH-----HcCCceECCCcC
Confidence 4666666654333322211 123456666665
No 67
>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=61.38 E-value=6.3 Score=19.46 Aligned_cols=33 Identities=15% Similarity=0.405 Sum_probs=16.1
Q ss_pred eecccccccccChhhHHHHhhhhcCCCCCCcccCCCcccc
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRA 90 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f 90 (145)
..|..|+..|...... .... .....|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~-----~~~~--~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ-----LGAN--GGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHH-----cCCC--CCEEECCCCCCEE
Confidence 4566777665543221 1111 1135677776654
No 68
>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=61.08 E-value=6.7 Score=25.50 Aligned_cols=33 Identities=12% Similarity=0.145 Sum_probs=21.6
Q ss_pred eecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCCchhH
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNL 96 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~~~~l 96 (145)
..|..||+.|-- .+ +.|..|+.||..|.....+
T Consensus 10 r~Cp~cg~kFYD-----------Ln--k~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 10 RICPNTGSKFYD-----------LN--RRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred ccCCCcCccccc-----------cC--CCCccCCCcCCccCcchhh
Confidence 468888877642 23 4577888888887655333
No 69
>KOG4167|consensus
Probab=60.21 E-value=2 Score=35.84 Aligned_cols=25 Identities=12% Similarity=0.309 Sum_probs=22.8
Q ss_pred CcccCCCccccCCchhHHHHHHHhc
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYH 104 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~ 104 (145)
-|.|..|++.|....+++.|+++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999999999999999985
No 70
>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=59.91 E-value=8 Score=24.14 Aligned_cols=25 Identities=40% Similarity=0.860 Sum_probs=21.3
Q ss_pred ccc----CCCccccCCchhHHHHHHHhcC
Q psy16400 81 HQC----PHCDYRAKQSGNLRVHIRKYHT 105 (145)
Q Consensus 81 ~~C----~~C~~~f~~~~~l~~H~~~h~~ 105 (145)
|.| ..|+..+.....+..|++.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 678 8899999999999999988764
No 71
>KOG2186|consensus
Probab=59.85 E-value=4.6 Score=29.44 Aligned_cols=46 Identities=9% Similarity=0.148 Sum_probs=35.1
Q ss_pred CcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCCCCCCchhhh
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKPIVNPMQTQQ 128 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~~~~~~~~~~ 128 (145)
-|.|..||.... +..+.+|+-+.++ .-|.|-.|+..|.. .....|-
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~ 48 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHT 48 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhh
Confidence 478999998854 4467789999888 66999999998887 3444443
No 72
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=59.36 E-value=18 Score=24.00 Aligned_cols=37 Identities=11% Similarity=0.186 Sum_probs=24.1
Q ss_pred CCCcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCC
Q psy16400 78 EPVHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRK 118 (145)
Q Consensus 78 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~ 118 (145)
..-|.|+.|+..|.....+.. .. .+..|.|+.|+..-
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~---~d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL---LD-MDGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh---cC-CCCcEECCCCCCEE
Confidence 446899999988886544321 01 13449999998743
No 73
>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=58.87 E-value=12 Score=25.23 Aligned_cols=33 Identities=12% Similarity=0.214 Sum_probs=25.7
Q ss_pred CCCcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCC
Q psy16400 78 EPVHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKP 119 (145)
Q Consensus 78 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~ 119 (145)
..-|.|+.|+..|+....+. .-|.|+.||..-.
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 44689999999888888875 3699999997533
No 74
>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=55.68 E-value=11 Score=17.15 Aligned_cols=20 Identities=25% Similarity=0.526 Sum_probs=12.8
Q ss_pred cccCCCccccCCchhHHHHHH
Q psy16400 81 HQCPHCDYRAKQSGNLRVHIR 101 (145)
Q Consensus 81 ~~C~~C~~~f~~~~~l~~H~~ 101 (145)
..|++|.+.+ ....++.|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3578887776 4456666654
No 75
>KOG0696|consensus
Probab=55.11 E-value=3.2 Score=32.90 Aligned_cols=46 Identities=22% Similarity=0.366 Sum_probs=29.0
Q ss_pred cccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCcccc
Q psy16400 23 AALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRA 90 (145)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f 90 (145)
.-|+.|.+++|- .|..-|.|++|. +..|.+.|. ...|.|+.-++.+
T Consensus 57 TfCsHCkDFiwG-----------fgKQGfQCqvC~--------fvvHkrChe---fVtF~CPGadkg~ 102 (683)
T KOG0696|consen 57 TFCSHCKDFIWG-----------FGKQGFQCQVCC--------FVVHKRCHE---FVTFSCPGADKGP 102 (683)
T ss_pred chhhhhhhheec-----------cccCceeeeEEe--------ehhhhhhcc---eEEEECCCCCCCC
Confidence 456777777765 566678999985 345666553 3456665544433
No 76
>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=54.51 E-value=4.8 Score=20.12 Aligned_cols=11 Identities=36% Similarity=1.367 Sum_probs=6.7
Q ss_pred eeccccccccc
Q psy16400 51 YSCQHCGKRYR 61 (145)
Q Consensus 51 ~~C~~c~~~f~ 61 (145)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 56666666554
No 77
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.65 E-value=14 Score=25.55 Aligned_cols=34 Identities=15% Similarity=0.293 Sum_probs=25.1
Q ss_pred CCCcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCCC
Q psy16400 78 EPVHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKPI 120 (145)
Q Consensus 78 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~~ 120 (145)
..-|.|+.|+..|+....+. .-|.|+.|+..-..
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 34688999998888777653 36999999875443
No 78
>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=53.59 E-value=5 Score=21.36 Aligned_cols=11 Identities=45% Similarity=1.428 Sum_probs=6.6
Q ss_pred eeccccccccc
Q psy16400 51 YSCQHCGKRYR 61 (145)
Q Consensus 51 ~~C~~c~~~f~ 61 (145)
|.|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 55666666554
No 79
>KOG1146|consensus
Probab=51.79 E-value=3.5 Score=36.73 Aligned_cols=63 Identities=17% Similarity=0.230 Sum_probs=42.8
Q ss_pred ccccccChhhHHHHhhh-hcCCCCCCcccCCCccccCCchhHHHHHHH-hc------------------------CCCcc
Q psy16400 56 CGKRYRWKSTLKRHEVF-ECGGKEPVHQCPHCDYRAKQSGNLRVHIRK-YH------------------------TSIEL 109 (145)
Q Consensus 56 c~~~f~~~~~l~~h~~~-h~~~~~k~~~C~~C~~~f~~~~~l~~H~~~-h~------------------------~~kp~ 109 (145)
|+..+.++..+..|+.. +.- .+-++|++|+..|.....|..|+|. |. +.++|
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~--~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~ 519 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSF--FKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPY 519 (1406)
T ss_pred hhhhhhhhcccccceeeeecc--cccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcc
Confidence 33344444444444432 333 4678999999999999999999998 10 23689
Q ss_pred cCCCCCCCCCC
Q psy16400 110 QSPSPAPRKPI 120 (145)
Q Consensus 110 ~c~~c~~~~~~ 120 (145)
.|..|.-++.-
T Consensus 520 ~C~~C~~sttt 530 (1406)
T KOG1146|consen 520 PCRACNYSTTT 530 (1406)
T ss_pred cceeeeeeeec
Confidence 99988877665
No 80
>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=51.52 E-value=16 Score=18.58 Aligned_cols=21 Identities=29% Similarity=0.558 Sum_probs=9.7
Q ss_pred CcccCCCccccCC----chhHHHHH
Q psy16400 80 VHQCPHCDYRAKQ----SGNLRVHI 100 (145)
Q Consensus 80 ~~~C~~C~~~f~~----~~~l~~H~ 100 (145)
...|..|++.+.. .++|.+|+
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 4456666655443 35566665
No 81
>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=49.99 E-value=5.9 Score=28.22 Aligned_cols=26 Identities=31% Similarity=0.456 Sum_probs=15.4
Q ss_pred CCcccCCCccccCCchhHHHHHHHhc
Q psy16400 79 PVHQCPHCDYRAKQSGNLRVHIRKYH 104 (145)
Q Consensus 79 k~~~C~~C~~~f~~~~~l~~H~~~h~ 104 (145)
..|.|+.|+|.|.-......|+..-|
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CEECCCCCCcccCChHHHHHHHhhcC
Confidence 35677777777777777777766533
No 82
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=49.58 E-value=7.6 Score=23.50 Aligned_cols=11 Identities=18% Similarity=0.646 Sum_probs=5.5
Q ss_pred cccCCCccccC
Q psy16400 81 HQCPHCDYRAK 91 (145)
Q Consensus 81 ~~C~~C~~~f~ 91 (145)
|.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 45555554443
No 83
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=49.39 E-value=3.7 Score=27.65 Aligned_cols=13 Identities=23% Similarity=0.511 Sum_probs=8.4
Q ss_pred cccCCCccccCCc
Q psy16400 81 HQCPHCDYRAKQS 93 (145)
Q Consensus 81 ~~C~~C~~~f~~~ 93 (145)
+.|+.||+.|..-
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 6677777666543
No 84
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.70 E-value=15 Score=19.12 Aligned_cols=26 Identities=38% Similarity=0.991 Sum_probs=15.7
Q ss_pred eecccccccccChhhHHHHhhhhcCCCCCCcccCCCccc
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYR 89 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~ 89 (145)
|.|..||..|... . .-+..|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~--~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------S--KDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------C--CCceECCCCCce
Confidence 6777887765421 1 225677777753
No 85
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=47.32 E-value=22 Score=26.20 Aligned_cols=85 Identities=14% Similarity=0.194 Sum_probs=45.9
Q ss_pred cccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccCC------chhH
Q psy16400 23 AALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQ------SGNL 96 (145)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~~------~~~l 96 (145)
..+..|.+..|. +|.+.|.|..|...+.-.. --.|+.+.--...-.|+|..|.+.=.+ ...-
T Consensus 126 a~C~EC~R~vw~-----------hGGrif~CsfC~~flCEDD-QFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfC 193 (314)
T PF06524_consen 126 AVCIECERGVWD-----------HGGRIFKCSFCDNFLCEDD-QFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFC 193 (314)
T ss_pred cEeeeeeccccc-----------CCCeEEEeecCCCeeeccc-hhhhhhhhhhhhcccccccccccccchhhhheeeeeh
Confidence 455667766665 7888999999986444332 233444211000124777666543111 1112
Q ss_pred HHHHHH----hcCCCcccCCCCCCCCC
Q psy16400 97 RVHIRK----YHTSIELQSPSPAPRKP 119 (145)
Q Consensus 97 ~~H~~~----h~~~kp~~c~~c~~~~~ 119 (145)
.-|.++ ....+++.|+.|+=...
T Consensus 194 ddHvrrKg~ky~k~k~~PCPKCg~et~ 220 (314)
T PF06524_consen 194 DDHVRRKGFKYEKGKPIPCPKCGYETQ 220 (314)
T ss_pred hhhhhhcccccccCCCCCCCCCCCccc
Confidence 234443 34468899999985433
No 86
>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=45.92 E-value=8.7 Score=19.67 Aligned_cols=12 Identities=33% Similarity=1.198 Sum_probs=8.2
Q ss_pred eecccccccccC
Q psy16400 51 YSCQHCGKRYRW 62 (145)
Q Consensus 51 ~~C~~c~~~f~~ 62 (145)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 677777776653
No 87
>KOG2593|consensus
Probab=45.43 E-value=20 Score=28.26 Aligned_cols=36 Identities=14% Similarity=0.180 Sum_probs=25.2
Q ss_pred CCCcccCCCccccCCchhHHHHHHHhcCCCcccCCCCCC
Q psy16400 78 EPVHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAP 116 (145)
Q Consensus 78 ~k~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~ 116 (145)
..-|.|+.|.+.|.....+. -.-.....|.|..|+.
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred cccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 45689999998888776543 2233356689988886
No 88
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=43.69 E-value=15 Score=19.04 Aligned_cols=12 Identities=33% Similarity=1.165 Sum_probs=7.1
Q ss_pred ceeccccccccc
Q psy16400 50 QYSCQHCGKRYR 61 (145)
Q Consensus 50 ~~~C~~c~~~f~ 61 (145)
.|.|..||..+.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 366666666543
No 89
>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=43.19 E-value=21 Score=25.50 Aligned_cols=30 Identities=20% Similarity=0.528 Sum_probs=23.5
Q ss_pred cCCCceecccccccccChhhHHHHhhhhcC
Q psy16400 46 TQENQYSCQHCGKRYRWKSTLKRHEVFECG 75 (145)
Q Consensus 46 ~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~ 75 (145)
..+..|.|..|+|.|.....+..|+..-+.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 456789999999999999999999987665
No 90
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.42 E-value=40 Score=21.45 Aligned_cols=76 Identities=13% Similarity=0.034 Sum_probs=34.9
Q ss_pred ceecccccccccChhhHHHHhhhhcCCC---CCC-------cccCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCC
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEVFECGGK---EPV-------HQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKP 119 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~---~k~-------~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~ 119 (145)
|-.|..|+-...+...|++.-.--.... +.+ ..|..|...|........ ..-.....|.|..|..-|=
T Consensus 15 P~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~FC 92 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVFC 92 (112)
T ss_pred CCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCccc
Confidence 4567777777766666664211100100 011 126666666654321110 0012234577777776665
Q ss_pred CCCCchhh
Q psy16400 120 IVNPMQTQ 127 (145)
Q Consensus 120 ~~~~~~~~ 127 (145)
..-.+..|
T Consensus 93 ~dCD~fiH 100 (112)
T TIGR00622 93 VDCDVFVH 100 (112)
T ss_pred cccchhhh
Confidence 54444443
No 91
>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=41.17 E-value=16 Score=18.09 Aligned_cols=29 Identities=24% Similarity=0.566 Sum_probs=14.9
Q ss_pred eecccccccccChhhHHHHhhhhcCCCCCCcccCCCccc
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYR 89 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~ 89 (145)
+.|..||..|.. ..... ...-.|..|+..
T Consensus 2 r~C~~Cg~~Yh~--------~~~pP--~~~~~Cd~cg~~ 30 (36)
T PF05191_consen 2 RICPKCGRIYHI--------EFNPP--KVEGVCDNCGGE 30 (36)
T ss_dssp EEETTTTEEEET--------TTB----SSTTBCTTTTEB
T ss_pred cCcCCCCCcccc--------ccCCC--CCCCccCCCCCe
Confidence 357777776642 22223 334567777653
No 92
>PF15269 zf-C2H2_7: Zinc-finger
Probab=41.06 E-value=26 Score=18.39 Aligned_cols=24 Identities=17% Similarity=0.455 Sum_probs=17.8
Q ss_pred CcccCCCccccCCchhHHHHHHHh
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKY 103 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h 103 (145)
.|.|-+|......+++|-.|+.-.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHH
Confidence 367888887777788888887643
No 93
>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=38.38 E-value=28 Score=16.78 Aligned_cols=10 Identities=40% Similarity=1.036 Sum_probs=6.1
Q ss_pred CcccCCCccc
Q psy16400 80 VHQCPHCDYR 89 (145)
Q Consensus 80 ~~~C~~C~~~ 89 (145)
+..|+.||..
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 4677777754
No 94
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=37.82 E-value=34 Score=19.11 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=6.2
Q ss_pred CcccCCCccc
Q psy16400 80 VHQCPHCDYR 89 (145)
Q Consensus 80 ~~~C~~C~~~ 89 (145)
.|.|+.||..
T Consensus 25 ~F~CPnCG~~ 34 (59)
T PRK14890 25 KFLCPNCGEV 34 (59)
T ss_pred EeeCCCCCCe
Confidence 4666666655
No 95
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=37.81 E-value=18 Score=22.07 Aligned_cols=14 Identities=14% Similarity=0.665 Sum_probs=8.5
Q ss_pred CCcccCCCccccCC
Q psy16400 79 PVHQCPHCDYRAKQ 92 (145)
Q Consensus 79 k~~~C~~C~~~f~~ 92 (145)
.|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 35566667666655
No 96
>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=37.67 E-value=16 Score=16.44 Aligned_cols=9 Identities=33% Similarity=1.036 Sum_probs=6.0
Q ss_pred CCcccCCCc
Q psy16400 79 PVHQCPHCD 87 (145)
Q Consensus 79 k~~~C~~C~ 87 (145)
..|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 357777776
No 97
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.11 E-value=15 Score=24.05 Aligned_cols=15 Identities=27% Similarity=0.857 Sum_probs=10.2
Q ss_pred CCceecccccccccC
Q psy16400 48 ENQYSCQHCGKRYRW 62 (145)
Q Consensus 48 ~k~~~C~~c~~~f~~ 62 (145)
...+.|..||..|..
T Consensus 68 p~~~~C~~CG~~~~~ 82 (135)
T PRK03824 68 EAVLKCRNCGNEWSL 82 (135)
T ss_pred ceEEECCCCCCEEec
Confidence 345778888876654
No 98
>KOG2785|consensus
Probab=36.79 E-value=36 Score=26.47 Aligned_cols=53 Identities=21% Similarity=0.304 Sum_probs=41.1
Q ss_pred ceecccccccccChhhHHHHhhhhcCC---------------------CCCCcccCCCc---cccCCchhHHHHHHH
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEVFECGG---------------------KEPVHQCPHCD---YRAKQSGNLRVHIRK 102 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~~h~~~---------------------~~k~~~C~~C~---~~f~~~~~l~~H~~~ 102 (145)
|-.|-.|++.+.....-..||..++|- ...-+.|..|. +.|........|+..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 456888999999888888899988772 12356888887 788888888888774
No 99
>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=36.25 E-value=20 Score=16.40 Aligned_cols=11 Identities=45% Similarity=1.244 Sum_probs=7.6
Q ss_pred cccCCCccccC
Q psy16400 81 HQCPHCDYRAK 91 (145)
Q Consensus 81 ~~C~~C~~~f~ 91 (145)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 36777887764
No 100
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=34.22 E-value=49 Score=16.78 Aligned_cols=23 Identities=17% Similarity=0.453 Sum_probs=11.7
Q ss_pred cccCCCccccCCc--hhHHHHHHHh
Q psy16400 81 HQCPHCDYRAKQS--GNLRVHIRKY 103 (145)
Q Consensus 81 ~~C~~C~~~f~~~--~~l~~H~~~h 103 (145)
..|+.|+..|... ..-..|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 4666676665532 3334444443
No 101
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=33.30 E-value=20 Score=19.77 Aligned_cols=32 Identities=13% Similarity=0.180 Sum_probs=13.7
Q ss_pred CcccCCCccccCCchhHHHHHHHhcCCCcccCCCCC
Q psy16400 80 VHQCPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPA 115 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~ 115 (145)
|+....|+.+|.....+. ++ ...+..+|+..|
T Consensus 24 PV~s~~C~H~fek~aI~~-~i---~~~~~~~CPv~G 55 (57)
T PF11789_consen 24 PVKSKKCGHTFEKEAILQ-YI---QRNGSKRCPVAG 55 (57)
T ss_dssp EEEESSS--EEEHHHHHH-HC---TTTS-EE-SCCC
T ss_pred CcCcCCCCCeecHHHHHH-HH---HhcCCCCCCCCC
Confidence 455556666666554433 22 234455665543
No 102
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=33.13 E-value=25 Score=23.15 Aligned_cols=22 Identities=36% Similarity=0.694 Sum_probs=18.5
Q ss_pred eecccccccccChhhHHHHhhhhcC
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFECG 75 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~ 75 (145)
..|-++|+.|. .|++|..+|.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~g 98 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYG 98 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccC
Confidence 46889999886 58899999887
No 103
>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=32.30 E-value=39 Score=17.47 Aligned_cols=12 Identities=33% Similarity=1.417 Sum_probs=7.0
Q ss_pred cccccccccChh
Q psy16400 53 CQHCGKRYRWKS 64 (145)
Q Consensus 53 C~~c~~~f~~~~ 64 (145)
|..|++.|....
T Consensus 11 C~~C~rpf~WRK 22 (42)
T PF10013_consen 11 CPVCGRPFTWRK 22 (42)
T ss_pred CcccCCcchHHH
Confidence 666666665543
No 104
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=32.05 E-value=14 Score=22.58 Aligned_cols=30 Identities=27% Similarity=0.771 Sum_probs=15.3
Q ss_pred ceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccC
Q psy16400 50 QYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAK 91 (145)
Q Consensus 50 ~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~ 91 (145)
.|.|..|++.-. .+...| -|.|..|++.|.
T Consensus 35 ky~Cp~Cgk~~v--------kR~a~G----IW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSV--------KRVATG----IWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEE--------EEEETT----EEEETTTTEEEE
T ss_pred CCcCCCCCCcee--------EEeeeE----EeecCCCCCEEe
Confidence 466777765421 122333 266777766543
No 105
>PRK11823 DNA repair protein RadA; Provisional
Probab=31.12 E-value=37 Score=26.96 Aligned_cols=25 Identities=32% Similarity=0.860 Sum_probs=17.7
Q ss_pred CCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCcc
Q psy16400 48 ENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDY 88 (145)
Q Consensus 48 ~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~ 88 (145)
...|.|..||..+ . .+.+.|+.|+.
T Consensus 5 ~~~y~C~~Cg~~~--------------~--~~~g~Cp~C~~ 29 (446)
T PRK11823 5 KTAYVCQECGAES--------------P--KWLGRCPECGA 29 (446)
T ss_pred CCeEECCcCCCCC--------------c--ccCeeCcCCCC
Confidence 3469999999643 2 55678888853
No 106
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=30.58 E-value=27 Score=18.73 Aligned_cols=12 Identities=33% Similarity=1.093 Sum_probs=8.8
Q ss_pred Cceecccccccc
Q psy16400 49 NQYSCQHCGKRY 60 (145)
Q Consensus 49 k~~~C~~c~~~f 60 (145)
..|.|..|++.|
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 357888888776
No 107
>KOG4167|consensus
Probab=30.49 E-value=17 Score=30.66 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=24.3
Q ss_pred CCceecccccccccChhhHHHHhhhhcC
Q psy16400 48 ENQYSCQHCGKRYRWKSTLKRHEVFECG 75 (145)
Q Consensus 48 ~k~~~C~~c~~~f~~~~~l~~h~~~h~~ 75 (145)
...|.|.+|++.|--...+..||++|.-
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 4579999999999988889999998863
No 108
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=29.94 E-value=16 Score=22.34 Aligned_cols=10 Identities=20% Similarity=0.674 Sum_probs=4.7
Q ss_pred cccCCCcccc
Q psy16400 81 HQCPHCDYRA 90 (145)
Q Consensus 81 ~~C~~C~~~f 90 (145)
|.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (91)
T TIGR00280 54 WTCRKCGAKF 63 (91)
T ss_pred EEcCCCCCEE
Confidence 4455554443
No 109
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.44 E-value=20 Score=21.89 Aligned_cols=11 Identities=0% Similarity=-0.239 Sum_probs=4.9
Q ss_pred cccCCCCCCCC
Q psy16400 108 ELQSPSPAPRK 118 (145)
Q Consensus 108 p~~c~~c~~~~ 118 (145)
.|.|..|+..+
T Consensus 54 IW~C~~C~~~~ 64 (90)
T PTZ00255 54 IWRCKGCKKTV 64 (90)
T ss_pred EEEcCCCCCEE
Confidence 34444444433
No 110
>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=28.66 E-value=20 Score=16.83 Aligned_cols=11 Identities=36% Similarity=1.117 Sum_probs=7.1
Q ss_pred eeccccccccc
Q psy16400 51 YSCQHCGKRYR 61 (145)
Q Consensus 51 ~~C~~c~~~f~ 61 (145)
|.|..|++.|.
T Consensus 1 ~sCiDC~~~F~ 11 (28)
T PF08790_consen 1 FSCIDCSKDFD 11 (28)
T ss_dssp EEETTTTEEEE
T ss_pred CeeecCCCCcC
Confidence 45667777773
No 111
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=28.47 E-value=38 Score=27.01 Aligned_cols=23 Identities=35% Similarity=0.950 Sum_probs=16.8
Q ss_pred CceecccccccccChhhHHHHhhhhcCCCCCCcccCCCc
Q psy16400 49 NQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCD 87 (145)
Q Consensus 49 k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~ 87 (145)
..|.|..||... . .+.+.|+.|+
T Consensus 6 ~~y~C~~Cg~~~--------------~--~~~g~Cp~C~ 28 (454)
T TIGR00416 6 SKFVCQHCGADS--------------P--KWQGKCPACH 28 (454)
T ss_pred CeEECCcCCCCC--------------c--cccEECcCCC
Confidence 359999999643 2 5567898885
No 112
>KOG3408|consensus
Probab=28.31 E-value=38 Score=21.89 Aligned_cols=27 Identities=22% Similarity=0.378 Sum_probs=20.5
Q ss_pred cCCCceecccccccccChhhHHHHhhh
Q psy16400 46 TQENQYSCQHCGKRYRWKSTLKRHEVF 72 (145)
Q Consensus 46 ~~~k~~~C~~c~~~f~~~~~l~~h~~~ 72 (145)
.|...|.|.+|.+-|.....|..|.++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 345568888888888888888777664
No 113
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=27.18 E-value=35 Score=18.36 Aligned_cols=39 Identities=26% Similarity=0.519 Sum_probs=17.7
Q ss_pred ceeccc-ccccccChhhHHHHhhhhcCCCCCCcccCC----Ccccc
Q psy16400 50 QYSCQH-CGKRYRWKSTLKRHEVFECGGKEPVHQCPH----CDYRA 90 (145)
Q Consensus 50 ~~~C~~-c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~----C~~~f 90 (145)
+..|.. |+..-..+..|..|....-. ..+..|.. |...+
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~--~~~v~C~~~~~GC~~~~ 52 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECP--KRPVPCPYSPYGCKERV 52 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTST--TSEEE-SS----S--EE
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCC--CCcEECCCCCCCCCCcc
Confidence 345655 33222235567777775555 44666766 65544
No 114
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=26.55 E-value=15 Score=30.85 Aligned_cols=84 Identities=21% Similarity=0.288 Sum_probs=49.8
Q ss_pred cccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCc-ccCCCccccCCchhHHHHHH
Q psy16400 23 AALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVH-QCPHCDYRAKQSGNLRVHIR 101 (145)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~-~C~~C~~~f~~~~~l~~H~~ 101 (145)
+.|..|..-...+.+.+=++.= -.|..||-.|+....|- +.+-++. .+.| .|+.|.+-|....+..-|
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~YPF------~~CT~CGPRfTIi~alP-YDR~nTs--M~~F~lC~~C~~EY~dP~nRRfH-- 170 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYLYPF------INCTNCGPRFTIIEALP-YDRENTS--MADFPLCPFCDKEYKDPLNRRFH-- 170 (750)
T ss_pred hhhHHHHHHhcCCCCcceeccc------cccCCCCcceeeeccCC-CCcccCc--cccCcCCHHHHHHhcCccccccc--
Confidence 4556666555554444333221 24999999888654432 2233343 3344 588898887777664333
Q ss_pred HhcCCCcccCCCCCCCCCCC
Q psy16400 102 KYHTSIELQSPSPAPRKPIV 121 (145)
Q Consensus 102 ~h~~~kp~~c~~c~~~~~~~ 121 (145)
. .|..|+.|++.-...
T Consensus 171 --A--Qp~aCp~CGP~~~l~ 186 (750)
T COG0068 171 --A--QPIACPKCGPHLFLV 186 (750)
T ss_pred --c--ccccCcccCCCeEEE
Confidence 3 578999999855544
No 115
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=26.55 E-value=17 Score=30.83 Aligned_cols=37 Identities=30% Similarity=0.634 Sum_probs=22.3
Q ss_pred cccCCCccccC---CchhHHHHHHHhcCCCcccCCCCCCC
Q psy16400 81 HQCPHCDYRAK---QSGNLRVHIRKYHTSIELQSPSPAPR 117 (145)
Q Consensus 81 ~~C~~C~~~f~---~~~~l~~H~~~h~~~kp~~c~~c~~~ 117 (145)
+.|+.|+..+. ....|..|.--+....|..|+.|+..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 35555554322 23455555555566778888888875
No 116
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.27 E-value=27 Score=21.88 Aligned_cols=7 Identities=0% Similarity=-0.202 Sum_probs=3.2
Q ss_pred ccCCCCC
Q psy16400 109 LQSPSPA 115 (145)
Q Consensus 109 ~~c~~c~ 115 (145)
|.|..|+
T Consensus 32 y~C~~C~ 38 (102)
T PF11672_consen 32 YVCTPCD 38 (102)
T ss_pred EECCCCC
Confidence 4444443
No 117
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=25.54 E-value=21 Score=21.75 Aligned_cols=9 Identities=22% Similarity=0.896 Sum_probs=4.2
Q ss_pred cccCCCccc
Q psy16400 81 HQCPHCDYR 89 (145)
Q Consensus 81 ~~C~~C~~~ 89 (145)
|.|..|++.
T Consensus 55 W~C~~C~~~ 63 (90)
T PRK03976 55 WECRKCGAK 63 (90)
T ss_pred EEcCCCCCE
Confidence 444444443
No 118
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=25.43 E-value=53 Score=21.69 Aligned_cols=20 Identities=20% Similarity=0.406 Sum_probs=16.3
Q ss_pred CcccCCCccccCCchhHHHH
Q psy16400 80 VHQCPHCDYRAKQSGNLRVH 99 (145)
Q Consensus 80 ~~~C~~C~~~f~~~~~l~~H 99 (145)
-+.|+.|++.|...++..+-
T Consensus 124 f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred EEECCCCCCEecccccHHHH
Confidence 57899999999988776543
No 119
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=24.47 E-value=43 Score=25.95 Aligned_cols=21 Identities=33% Similarity=0.929 Sum_probs=13.5
Q ss_pred eecccccccccChhhHHHHhhhhcCCCCCCcccCCCc
Q psy16400 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCD 87 (145)
Q Consensus 51 ~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~ 87 (145)
|.|..||... . .+...|+.|+
T Consensus 1 ~~c~~cg~~~--------------~--~~~g~cp~c~ 21 (372)
T cd01121 1 YVCSECGYVS--------------P--KWLGKCPECG 21 (372)
T ss_pred CCCCCCCCCC--------------C--CccEECcCCC
Confidence 5788887542 1 4456788775
No 120
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=24.32 E-value=11 Score=23.50 Aligned_cols=39 Identities=18% Similarity=0.472 Sum_probs=21.5
Q ss_pred CCCceecccccccccChhhHHHHhhhhcCCCCCCcccCCCccccC
Q psy16400 47 QENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAK 91 (145)
Q Consensus 47 ~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~~C~~C~~~f~ 91 (145)
-.+.|+|..|+..-.+.-.++. ... .-...|..||.+|.
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk--~~~----~g~~~Cg~CGls~e 57 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKK--TVN----IGTAVCGNCGLSFE 57 (104)
T ss_pred CCceEecCccCCeeeeEEEEEe--cCc----eeEEEcccCcceEE
Confidence 3567999999875443222110 111 12357788887654
No 121
>KOG2893|consensus
Probab=24.01 E-value=40 Score=24.58 Aligned_cols=38 Identities=11% Similarity=0.059 Sum_probs=27.2
Q ss_pred cCCCccccCCchhHHHHHHHhcCCCcccCCCCCCCCCCCCCc
Q psy16400 83 CPHCDYRAKQSGNLRVHIRKYHTSIELQSPSPAPRKPIVNPM 124 (145)
Q Consensus 83 C~~C~~~f~~~~~l~~H~~~h~~~kp~~c~~c~~~~~~~~~~ 124 (145)
|=.|.+-|.....|..|++ -|-|+|..|-+..+.-.-|
T Consensus 13 cwycnrefddekiliqhqk----akhfkchichkkl~sgpgl 50 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGL 50 (341)
T ss_pred eeecccccchhhhhhhhhh----hccceeeeehhhhccCCCc
Confidence 5568888888888876654 4669999999765544443
No 122
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=23.91 E-value=15 Score=31.05 Aligned_cols=83 Identities=22% Similarity=0.285 Sum_probs=46.7
Q ss_pred cccchhhhccccCCCCCCCceeccCCCceecccccccccChhhHHHHhhhhcCCCCCCc-ccCCCccccCCchhHHHHHH
Q psy16400 23 AALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVH-QCPHCDYRAKQSGNLRVHIR 101 (145)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~C~~c~~~f~~~~~l~~h~~~h~~~~~k~~-~C~~C~~~f~~~~~l~~H~~ 101 (145)
..|..|..-...+.+.+-++.= -.|..||-.|.....|- ..+.++. .+.| .|+.|-+-+....+...
T Consensus 69 a~C~~Cl~E~~dp~~Rry~YpF------~nCt~CGPr~~i~~~lp-ydr~~t~--m~~f~~C~~C~~ey~~p~~rr~--- 136 (711)
T TIGR00143 69 ATCSDCLEEMLDKNDRRYLYPF------ISCTHCGPRFTIIEALP-YDRENTS--MADFPLCPDCAKEYKDPLDRRF--- 136 (711)
T ss_pred hhHHHHHHHhcCCCcccccCCc------ccccCCCCCeEEeecCC-CCCCCcC--CCCCcCCHHHHHHhcCCccccC---
Confidence 4555566555444444333221 24899998887665433 1222333 2233 57888777766644322
Q ss_pred HhcCCCcccCCCCCCCCCC
Q psy16400 102 KYHTSIELQSPSPAPRKPI 120 (145)
Q Consensus 102 ~h~~~kp~~c~~c~~~~~~ 120 (145)
.-.+-.|..|+++-..
T Consensus 137 ---h~~~~~C~~Cgp~l~l 152 (711)
T TIGR00143 137 ---HAQPIACPRCGPQLNF 152 (711)
T ss_pred ---CCCCccCCCCCcEEEE
Confidence 2466789999986544
No 123
>PLN02294 cytochrome c oxidase subunit Vb
Probab=22.58 E-value=54 Score=22.57 Aligned_cols=16 Identities=19% Similarity=0.455 Sum_probs=11.4
Q ss_pred CCCcccCCCccccCCc
Q psy16400 78 EPVHQCPHCDYRAKQS 93 (145)
Q Consensus 78 ~k~~~C~~C~~~f~~~ 93 (145)
.++..|+.||..|.-.
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 3478888888877643
No 124
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.19 E-value=51 Score=20.94 Aligned_cols=14 Identities=7% Similarity=-0.135 Sum_probs=10.3
Q ss_pred CCCcccCCCccccC
Q psy16400 78 EPVHQCPHCDYRAK 91 (145)
Q Consensus 78 ~k~~~C~~C~~~f~ 91 (145)
+.|..|+.||++|.
T Consensus 24 rdPiVsPytG~s~P 37 (129)
T COG4530 24 RDPIVSPYTGKSYP 37 (129)
T ss_pred CCccccCcccccch
Confidence 45778888888874
No 125
>KOG2461|consensus
Probab=22.15 E-value=1.1e+02 Score=24.17 Aligned_cols=9 Identities=0% Similarity=-0.411 Sum_probs=3.3
Q ss_pred hHHHHHHHh
Q psy16400 95 NLRVHIRKY 103 (145)
Q Consensus 95 ~l~~H~~~h 103 (145)
.+..+...+
T Consensus 346 ~~~~~~~~~ 354 (396)
T KOG2461|consen 346 IYTQSHSME 354 (396)
T ss_pred chhhhhhcc
Confidence 333333333
No 126
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=21.73 E-value=41 Score=15.96 Aligned_cols=9 Identities=33% Similarity=1.010 Sum_probs=5.8
Q ss_pred CcccCCCcc
Q psy16400 80 VHQCPHCDY 88 (145)
Q Consensus 80 ~~~C~~C~~ 88 (145)
.+.|+.|+.
T Consensus 19 ~~vCp~C~~ 27 (30)
T PF08274_consen 19 LLVCPECGH 27 (30)
T ss_dssp SEEETTTTE
T ss_pred EEeCCcccc
Confidence 567777754
No 127
>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=21.66 E-value=46 Score=18.59 Aligned_cols=10 Identities=40% Similarity=1.268 Sum_probs=3.2
Q ss_pred eccccccccc
Q psy16400 52 SCQHCGKRYR 61 (145)
Q Consensus 52 ~C~~c~~~f~ 61 (145)
.|..|++.|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 4555665553
No 128
>KOG2231|consensus
Probab=21.55 E-value=93 Score=26.27 Aligned_cols=19 Identities=32% Similarity=0.620 Sum_probs=8.9
Q ss_pred cccccccccChhhHHHHhh
Q psy16400 53 CQHCGKRYRWKSTLKRHEV 71 (145)
Q Consensus 53 C~~c~~~f~~~~~l~~h~~ 71 (145)
|..|...|.....|..|++
T Consensus 185 C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLR 203 (669)
T ss_pred chhhhhhhccHHHHHHhhc
Confidence 4444444444444444444
No 129
>COG1773 Rubredoxin [Energy production and conversion]
Probab=21.34 E-value=43 Score=18.44 Aligned_cols=14 Identities=21% Similarity=0.579 Sum_probs=10.6
Q ss_pred CcccCCCccccCCc
Q psy16400 80 VHQCPHCDYRAKQS 93 (145)
Q Consensus 80 ~~~C~~C~~~f~~~ 93 (145)
.|.|..|+..|.-.
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 58899998887643
No 130
>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=20.60 E-value=1.1e+02 Score=15.65 Aligned_cols=11 Identities=0% Similarity=-0.194 Sum_probs=6.8
Q ss_pred CCcccCCCCCC
Q psy16400 106 SIELQSPSPAP 116 (145)
Q Consensus 106 ~kp~~c~~c~~ 116 (145)
...|.|..|..
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 45677776653
No 131
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.20 E-value=76 Score=26.77 Aligned_cols=12 Identities=8% Similarity=0.241 Sum_probs=8.1
Q ss_pred CcccCCCCCCCC
Q psy16400 107 IELQSPSPAPRK 118 (145)
Q Consensus 107 kp~~c~~c~~~~ 118 (145)
.|+.|+.|+...
T Consensus 421 ~p~~Cp~Cgs~~ 432 (665)
T PRK14873 421 PDWRCPRCGSDR 432 (665)
T ss_pred cCccCCCCcCCc
Confidence 467787777643
No 132
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=20.11 E-value=55 Score=16.06 Aligned_cols=11 Identities=36% Similarity=0.954 Sum_probs=4.7
Q ss_pred ecccccccccC
Q psy16400 52 SCQHCGKRYRW 62 (145)
Q Consensus 52 ~C~~c~~~f~~ 62 (145)
.|.+|++.|..
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 57777776653
Done!