Query 047746
Match_columns 247
No_of_seqs 419 out of 2368
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 02:45:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047746.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047746hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.8 2.4E-19 5.1E-24 157.4 3.5 113 92-212 128-267 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.7 2.9E-18 6.3E-23 150.6 1.3 75 92-187 185-261 (279)
3 KOG3623 Homeobox transcription 99.5 9.5E-15 2.1E-19 141.6 1.1 74 89-183 889-963 (1007)
4 KOG3576 Ovo and related transc 99.4 4.7E-14 1E-18 119.4 2.3 96 91-207 114-231 (267)
5 KOG1074 Transcriptional repres 99.3 2.3E-12 4.9E-17 126.9 3.8 48 94-146 353-400 (958)
6 KOG3623 Homeobox transcription 99.1 1.9E-11 4.1E-16 119.0 0.5 82 94-183 240-322 (1007)
7 KOG1074 Transcriptional repres 98.9 1.1E-09 2.4E-14 108.3 3.0 74 92-183 603-681 (958)
8 KOG3576 Ovo and related transc 98.8 8.3E-10 1.8E-14 93.8 -0.5 70 90-180 141-222 (267)
9 PHA02768 hypothetical protein; 98.6 7.4E-09 1.6E-13 70.6 -0.1 34 94-131 5-38 (55)
10 PF13465 zf-H2C2_2: Zinc-finge 98.3 1.5E-07 3.3E-12 54.7 0.9 25 154-181 1-25 (26)
11 PLN03086 PRLI-interacting fact 98.3 4.5E-07 9.8E-12 88.3 2.8 84 92-200 451-553 (567)
12 PHA00733 hypothetical protein 98.2 6.5E-07 1.4E-11 71.7 2.5 55 90-164 69-124 (128)
13 PHA02768 hypothetical protein; 98.2 1.1E-06 2.4E-11 59.9 2.4 34 145-183 10-44 (55)
14 PHA00733 hypothetical protein 98.1 1.2E-06 2.6E-11 70.2 2.2 68 92-182 38-111 (128)
15 PHA00616 hypothetical protein 98.0 5E-07 1.1E-11 58.9 -1.6 33 94-126 1-33 (44)
16 PF13465 zf-H2C2_2: Zinc-finge 97.8 3E-06 6.4E-11 49.2 -0.7 25 109-138 1-25 (26)
17 KOG3608 Zn finger proteins [Ge 97.7 1.1E-05 2.4E-10 73.8 0.7 82 95-184 264-366 (467)
18 PLN03086 PRLI-interacting fact 97.7 2.2E-05 4.7E-10 76.7 2.6 67 93-183 477-554 (567)
19 KOG3608 Zn finger proteins [Ge 97.6 1.7E-06 3.8E-11 79.0 -5.2 36 94-131 177-214 (467)
20 PHA00732 hypothetical protein 97.5 3.6E-05 7.7E-10 56.7 1.0 33 94-131 1-34 (79)
21 PHA00616 hypothetical protein 97.4 6.1E-05 1.3E-09 49.1 0.9 26 145-170 6-32 (44)
22 PF00096 zf-C2H2: Zinc finger, 97.2 3.2E-05 7E-10 43.0 -1.9 23 95-117 1-23 (23)
23 KOG3993 Transcription factor ( 97.0 0.00022 4.8E-09 66.7 0.9 71 94-164 295-381 (500)
24 PF13912 zf-C2H2_6: C2H2-type 96.8 0.00017 3.8E-09 41.6 -0.9 26 94-119 1-26 (27)
25 PF13894 zf-C2H2_4: C2H2-type 96.3 0.00043 9.2E-09 38.2 -1.6 23 95-117 1-23 (24)
26 KOG3993 Transcription factor ( 96.3 0.00041 8.8E-09 65.0 -2.8 96 94-207 267-375 (500)
27 COG5189 SFP1 Putative transcri 96.1 0.0026 5.7E-08 57.8 1.8 51 91-146 346-417 (423)
28 PF05605 zf-Di19: Drought indu 96.1 0.0024 5.1E-08 43.3 1.0 50 94-163 2-53 (54)
29 PHA00732 hypothetical protein 96.1 0.0048 1E-07 45.3 2.5 32 145-182 6-39 (79)
30 smart00355 ZnF_C2H2 zinc finge 95.9 0.0015 3.2E-08 36.3 -0.7 25 95-119 1-25 (26)
31 PF00096 zf-C2H2: Zinc finger, 95.6 0.0047 1E-07 34.0 0.7 18 145-162 5-23 (23)
32 COG5189 SFP1 Putative transcri 95.5 0.016 3.5E-07 52.8 4.0 72 118-208 345-418 (423)
33 PRK04860 hypothetical protein; 95.3 0.0049 1.1E-07 51.2 0.2 33 93-131 118-150 (160)
34 COG5048 FOG: Zn-finger [Genera 95.1 0.017 3.8E-07 52.6 3.1 62 93-170 288-354 (467)
35 PF09237 GAGA: GAGA factor; I 94.4 0.0075 1.6E-07 40.5 -0.9 32 91-122 21-52 (54)
36 PF12874 zf-met: Zinc-finger o 93.6 0.007 1.5E-07 34.1 -1.9 23 95-117 1-23 (25)
37 PF12171 zf-C2H2_jaz: Zinc-fin 93.5 0.024 5.3E-07 32.7 0.2 22 95-116 2-23 (27)
38 PF12756 zf-C2H2_2: C2H2 type 93.3 0.041 8.8E-07 40.6 1.3 68 96-163 1-74 (100)
39 PRK04860 hypothetical protein; 93.2 0.051 1.1E-06 45.2 1.9 28 151-181 127-154 (160)
40 PF09237 GAGA: GAGA factor; I 92.6 0.098 2.1E-06 35.2 2.2 33 117-167 19-52 (54)
41 PF13912 zf-C2H2_6: C2H2-type 92.5 0.052 1.1E-06 31.0 0.7 20 145-164 6-26 (27)
42 PF13894 zf-C2H2_4: C2H2-type 92.3 0.073 1.6E-06 28.8 1.1 19 145-163 5-24 (24)
43 smart00355 ZnF_C2H2 zinc finge 90.4 0.2 4.3E-06 27.3 1.7 20 145-164 5-25 (26)
44 PF13913 zf-C2HC_2: zinc-finge 88.0 0.096 2.1E-06 29.9 -0.8 20 95-115 3-22 (25)
45 PF13909 zf-H2C2_5: C2H2-type 87.2 0.061 1.3E-06 29.9 -2.0 23 95-118 1-23 (24)
46 COG5048 FOG: Zn-finger [Genera 85.6 1.1 2.4E-05 40.7 4.3 44 88-131 313-360 (467)
47 smart00451 ZnF_U1 U1-like zinc 85.0 0.2 4.4E-06 30.1 -0.6 23 94-116 3-25 (35)
48 PF12756 zf-C2H2_2: C2H2 type 76.3 0.52 1.1E-05 34.5 -1.1 25 93-117 49-73 (100)
49 PF09538 FYDLN_acid: Protein o 76.3 2.2 4.7E-05 33.2 2.3 28 172-201 11-39 (108)
50 KOG2893 Zn finger protein [Gen 73.7 0.82 1.8E-05 40.4 -0.7 33 92-131 9-41 (341)
51 KOG1146 Homeobox protein [Gene 65.7 2.7 5.8E-05 45.2 0.9 94 96-209 438-539 (1406)
52 KOG4167 Predicted DNA-binding 62.3 2.2 4.9E-05 43.2 -0.4 28 92-119 790-817 (907)
53 KOG1146 Homeobox protein [Gene 61.1 4 8.7E-05 44.0 1.2 26 91-116 462-487 (1406)
54 TIGR02300 FYDLN_acid conserved 57.6 7.2 0.00016 31.2 1.8 26 173-200 12-38 (129)
55 PF07754 DUF1610: Domain of un 56.5 8.8 0.00019 21.7 1.6 23 174-196 2-24 (24)
56 smart00614 ZnF_BED BED zinc fi 53.7 3.9 8.5E-05 26.9 -0.2 24 95-118 19-48 (50)
57 PF02892 zf-BED: BED zinc fing 51.9 3.1 6.7E-05 26.4 -0.9 23 92-114 14-40 (45)
58 KOG2893 Zn finger protein [Gen 51.1 4.9 0.00011 35.7 -0.1 31 89-119 29-60 (341)
59 COG4049 Uncharacterized protei 46.4 2.9 6.2E-05 28.8 -1.8 28 89-116 12-39 (65)
60 TIGR02605 CxxC_CxxC_SSSS putat 46.0 10 0.00022 24.9 0.8 29 94-131 5-33 (52)
61 cd00350 rubredoxin_like Rubred 45.0 13 0.00028 22.3 1.2 23 95-131 2-24 (33)
62 smart00834 CxxC_CXXC_SSSS Puta 45.0 11 0.00023 23.2 0.8 29 94-131 5-33 (41)
63 PF09986 DUF2225: Uncharacteri 44.7 16 0.00034 31.6 2.1 25 92-116 3-27 (214)
64 PF05443 ROS_MUCR: ROS/MUCR tr 43.3 4.4 9.5E-05 32.7 -1.5 29 93-124 71-99 (132)
65 COG4530 Uncharacterized protei 40.5 12 0.00025 29.3 0.6 30 172-205 11-41 (129)
66 KOG4124 Putative transcription 40.4 56 0.0012 30.7 5.0 23 92-114 347-371 (442)
67 COG4957 Predicted transcriptio 38.3 10 0.00022 30.8 -0.1 54 95-159 77-132 (148)
68 PRK09678 DNA-binding transcrip 37.9 16 0.00035 26.3 0.9 35 95-131 2-36 (72)
69 PRK00464 nrdR transcriptional 36.6 18 0.00039 29.8 1.1 9 96-104 2-10 (154)
70 smart00659 RPOLCX RNA polymera 33.0 27 0.00059 22.5 1.3 25 94-131 2-26 (44)
71 PF08790 zf-LYAR: LYAR-type C2 32.2 19 0.00041 21.2 0.4 21 95-116 1-21 (28)
72 PF07981 Plasmod_MYXSPDY: Plas 31.6 19 0.00041 18.5 0.3 9 239-247 3-11 (17)
73 smart00154 ZnF_AN1 AN1-like Zi 31.4 23 0.00049 22.2 0.7 15 94-108 12-26 (39)
74 COG1996 RPC10 DNA-directed RNA 30.6 19 0.00041 24.0 0.3 28 167-197 6-33 (49)
75 PF09845 DUF2072: Zn-ribbon co 30.4 24 0.00052 28.4 0.9 27 167-196 1-27 (131)
76 COG2888 Predicted Zn-ribbon RN 29.2 31 0.00066 24.0 1.1 26 172-197 29-59 (61)
77 COG3357 Predicted transcriptio 29.0 44 0.00095 25.3 2.0 33 166-201 57-89 (97)
78 PF14353 CpXC: CpXC protein 28.4 29 0.00063 27.1 1.0 25 93-117 37-61 (128)
79 smart00531 TFIIE Transcription 27.4 27 0.00058 28.3 0.7 34 92-131 97-130 (147)
80 PF09723 Zn-ribbon_8: Zinc rib 27.3 25 0.00054 22.3 0.4 29 94-131 5-33 (42)
81 PRK06266 transcription initiat 26.3 21 0.00045 30.1 -0.2 29 92-131 115-143 (178)
82 PF13451 zf-trcl: Probable zin 25.9 22 0.00049 23.6 -0.0 17 187-203 3-19 (49)
83 COG1198 PriA Primosomal protei 24.6 67 0.0015 33.1 3.1 45 96-146 437-481 (730)
84 COG3364 Zn-ribbon containing p 24.5 24 0.00052 27.3 -0.1 27 167-196 2-28 (112)
85 KOG2186 Cell growth-regulating 24.0 34 0.00074 30.6 0.7 31 94-126 3-33 (276)
86 KOG1044 Actin-binding LIM Zn-f 23.7 1.7E+02 0.0036 29.5 5.4 131 93-228 132-279 (670)
87 TIGR00373 conserved hypothetic 23.5 25 0.00055 28.9 -0.1 29 92-131 107-135 (158)
88 cd00729 rubredoxin_SM Rubredox 23.3 48 0.001 20.0 1.1 24 94-131 2-25 (34)
89 PRK00398 rpoP DNA-directed RNA 23.1 39 0.00085 21.6 0.7 31 167-200 3-33 (46)
90 PF01428 zf-AN1: AN1-like Zinc 22.4 31 0.00068 21.9 0.1 15 93-107 12-26 (43)
91 PF10276 zf-CHCC: Zinc-finger 22.1 33 0.00072 21.8 0.2 13 93-105 28-40 (40)
92 KOG2071 mRNA cleavage and poly 21.5 31 0.00068 34.3 0.0 28 92-119 416-443 (579)
93 PHA00626 hypothetical protein 21.4 44 0.00096 23.0 0.7 15 93-107 22-36 (59)
94 PF01286 XPA_N: XPA protein N- 21.3 72 0.0016 19.6 1.6 22 173-194 6-27 (34)
95 PF10571 UPF0547: Uncharacteri 21.2 49 0.0011 18.9 0.8 11 95-105 15-25 (26)
96 PF02701 zf-Dof: Dof domain, z 20.8 47 0.001 23.3 0.8 48 165-212 3-54 (63)
97 TIGR00595 priA primosomal prot 20.2 85 0.0018 30.7 2.7 47 96-148 215-261 (505)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.76 E-value=2.4e-19 Score=157.38 Aligned_cols=113 Identities=19% Similarity=0.320 Sum_probs=98.8
Q ss_pred CcccccCcCCcccCCCccccccccccCC---CccccccccccCcccccccCCCC-------------CCCCCCCc-Cchh
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKR---ERTMAKRAMRMGIFSDRYTSLAS-------------LPLHGSAF-RSLG 154 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htg---ekp~~C~~~~Cg~~~k~F~~~s~-------------L~~hgk~F-~~~~ 154 (247)
...|+|..|||.+...++|.+|+.+|.. .+.+.|. .|+ |.|.+... +.+|||.| |++-
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~--~C~---K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWL 202 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCK--YCG---KVYVSMPALKMHIRTHTLPCECGICGKAFSRPWL 202 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCC--CCC---ceeeehHHHhhHhhccCCCcccccccccccchHH
Confidence 4569999999999999999999999975 5778899 999 88865443 35679999 9999
Q ss_pred HHHHhhhcCCCCCCCCCCCCcccccccCC-CC--------C-CCccccCCCCccccCCCceecCCCCC
Q 047746 155 IKAHAAMHQGVVPPQRPPDMRGGARFEQG-YF--------A-MPMFMEDDDIDLFWPGSFRQVSEAVR 212 (247)
Q Consensus 155 L~~H~riHtgekPy~~~~~~~cg~~f~~~-~l--------~-~P~~~~~c~~~f~~~~s~~~~~~~~~ 212 (247)
|+.|+|+|||||||.| ..|+|.|.+. +| + ++|.|..|+|.|...+.|.+|.+.+=
T Consensus 203 LQGHiRTHTGEKPF~C---~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~C 267 (279)
T KOG2462|consen 203 LQGHIRTHTGEKPFSC---PHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESAC 267 (279)
T ss_pred hhcccccccCCCCccC---CcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhcc
Confidence 9999999999999998 6999999985 44 2 89999999999999999999988654
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.70 E-value=2.9e-18 Score=150.56 Aligned_cols=75 Identities=27% Similarity=0.422 Sum_probs=67.9
Q ss_pred CcccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCCCCCCCC
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQGVVPPQR 170 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtgekPy~~ 170 (247)
.-+++|.+|||.|.+.+-|.+|+|+|||||||.|. .|+|+| .+++|+.||.+|.+.|+|+|
T Consensus 185 ~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~------------------hC~kAFADRSNLRAHmQTHS~~K~~qC 246 (279)
T KOG2462|consen 185 TLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCP------------------HCGKAFADRSNLRAHMQTHSDVKKHQC 246 (279)
T ss_pred CCCcccccccccccchHHhhcccccccCCCCccCC------------------cccchhcchHHHHHHHHhhcCCccccC
Confidence 34788999999999999999999999999999998 677999 89999999999999999998
Q ss_pred CCCCcccccccCC-CCCC
Q 047746 171 PPDMRGGARFEQG-YFAM 187 (247)
Q Consensus 171 ~~~~~cg~~f~~~-~l~~ 187 (247)
.+|+|.|.+. ||++
T Consensus 247 ---~~C~KsFsl~SyLnK 261 (279)
T KOG2462|consen 247 ---PRCGKSFALKSYLNK 261 (279)
T ss_pred ---cchhhHHHHHHHHHH
Confidence 9999999985 5653
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.47 E-value=9.5e-15 Score=141.58 Aligned_cols=74 Identities=23% Similarity=0.416 Sum_probs=68.9
Q ss_pred CCCCcccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCCCCC
Q 047746 89 ATVPRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQGVVP 167 (247)
Q Consensus 89 ~tgekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtgekP 167 (247)
.+.+..|.|+.|.|.|...+.|.+|.--|+|.|||+|. +|.|+| .+.+|..|+|.|.||||
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~------------------iCkKAFKHKHHLtEHkRLHSGEKP 950 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCI------------------ICKKAFKHKHHLTEHKRLHSGEKP 950 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccc------------------hhhHhhhhhhhhhhhhhhccCCCc
Confidence 45567899999999999999999999999999999998 777999 89999999999999999
Q ss_pred CCCCCCCcccccccCC
Q 047746 168 PQRPPDMRGGARFEQG 183 (247)
Q Consensus 168 y~~~~~~~cg~~f~~~ 183 (247)
|+| ..|+|||++.
T Consensus 951 fQC---dKClKRFSHS 963 (1007)
T KOG3623|consen 951 FQC---DKCLKRFSHS 963 (1007)
T ss_pred chh---hhhhhhcccc
Confidence 998 9999999983
No 4
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.43 E-value=4.7e-14 Score=119.42 Aligned_cols=96 Identities=23% Similarity=0.318 Sum_probs=82.7
Q ss_pred CCcccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCCCCCCC
Q 047746 91 VPRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQGVVPPQ 169 (247)
Q Consensus 91 gekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtgekPy~ 169 (247)
+...|.|.+|+|+|....-|.+|++.|...|.|.|. .|||.| ....|++|+|+|||.+||.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct------------------~cgkgfndtfdlkrh~rthtgvrpyk 175 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCT------------------FCGKGFNDTFDLKRHTRTHTGVRPYK 175 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHh------------------hccCcccchhhhhhhhccccCccccc
Confidence 356799999999999999999999999999999998 788999 7889999999999999999
Q ss_pred CCCCCcccccccCC-CC--------------------CCCccccCCCCccccCCCceec
Q 047746 170 RPPDMRGGARFEQG-YF--------------------AMPMFMEDDDIDLFWPGSFRQV 207 (247)
Q Consensus 170 ~~~~~~cg~~f~~~-~l--------------------~~P~~~~~c~~~f~~~~s~~~~ 207 (247)
| ..|+|.|.+. .| .+-|.|+|||.....+..+-.|
T Consensus 176 c---~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h 231 (267)
T KOG3576|consen 176 C---SLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLH 231 (267)
T ss_pred h---hhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHH
Confidence 8 8999999984 21 1578999999877666555444
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.27 E-value=2.3e-12 Score=126.94 Aligned_cols=48 Identities=29% Similarity=0.565 Sum_probs=43.8
Q ss_pred ccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLH 146 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~h 146 (247)
+++|.+|.|.|.+.++|..|.|.|||||||+|. .|| .+|..+..|..|
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCn--vCG---~~FSTkGNLKvH 400 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCN--VCG---NRFSTKGNLKVH 400 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeec--ccc---cccccccceeee
Confidence 478999999999999999999999999999999 999 888888777554
No 6
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.09 E-value=1.9e-11 Score=118.99 Aligned_cols=82 Identities=24% Similarity=0.293 Sum_probs=52.4
Q ss_pred ccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCCCCCCCCCC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQGVVPPQRPP 172 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtgekPy~~~~ 172 (247)
.|.|..|..+|.++..|.+|+.+|.-..+-.-...+ -...++..+..|||+| .+.+|+.|.|||.|||||+|
T Consensus 240 nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltq-----sa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeC-- 312 (1007)
T KOG3623|consen 240 NFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQ-----SALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFEC-- 312 (1007)
T ss_pred CCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccc-----hhhhccccccccchhhhhHHHHHhhheeecCCCCcCC--
Confidence 456666666666666666666665432211000000 0001122234678999 89999999999999999998
Q ss_pred CCcccccccCC
Q 047746 173 DMRGGARFEQG 183 (247)
Q Consensus 173 ~~~cg~~f~~~ 183 (247)
..|+|||++.
T Consensus 313 -pnCkKRFSHS 322 (1007)
T KOG3623|consen 313 -PNCKKRFSHS 322 (1007)
T ss_pred -cccccccccC
Confidence 8899999983
No 7
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.86 E-value=1.1e-09 Score=108.31 Aligned_cols=74 Identities=26% Similarity=0.399 Sum_probs=63.2
Q ss_pred CcccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCCCCC---
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQGVVP--- 167 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtgekP--- 167 (247)
..|-.|-+|.|.....++|+-|.|+|+|||||+|+ +||++| ++.+|+.||-+|....|
T Consensus 603 TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCK------------------iCgRAFtTkGNLkaH~~vHka~p~~R~ 664 (958)
T KOG1074|consen 603 TDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCK------------------ICGRAFTTKGNLKAHMSVHKAKPPARV 664 (958)
T ss_pred CCccceeeeeecccchhhhhhhhhcccCcCccccc------------------cccchhccccchhhcccccccCccccc
Confidence 34679999999999999999999999999999999 788999 89999999999986544
Q ss_pred -CCCCCCCcccccccCC
Q 047746 168 -PQRPPDMRGGARFEQG 183 (247)
Q Consensus 168 -y~~~~~~~cg~~f~~~ 183 (247)
+.||+...|-+.|..+
T Consensus 665 q~ScP~~~ic~~kftn~ 681 (958)
T KOG1074|consen 665 QFSCPSTFICQKKFTNA 681 (958)
T ss_pred cccCCchhhhccccccc
Confidence 3465555788888875
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.78 E-value=8.3e-10 Score=93.80 Aligned_cols=70 Identities=19% Similarity=0.255 Sum_probs=57.5
Q ss_pred CCCcccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhh-hcCC---
Q 047746 90 TVPRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAA-MHQG--- 164 (247)
Q Consensus 90 tgekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~r-iHtg--- 164 (247)
..-|.|-|..|||.|..-..|++|.|+|||.|||+|. .|+|+| +...|..|.+ +|.-
T Consensus 141 ~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~------------------~c~kaftqrcsleshl~kvhgv~~~ 202 (267)
T KOG3576|consen 141 SDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCS------------------LCEKAFTQRCSLESHLKKVHGVQHQ 202 (267)
T ss_pred cHHHHHHHhhccCcccchhhhhhhhccccCccccchh------------------hhhHHHHhhccHHHHHHHHcCchHH
Confidence 3457899999999999999999999999999999999 667889 7889999976 6643
Q ss_pred -------CCCCCCCCCCcccccc
Q 047746 165 -------VVPPQRPPDMRGGARF 180 (247)
Q Consensus 165 -------ekPy~~~~~~~cg~~f 180 (247)
+|-|.| .+||..-
T Consensus 203 yaykerr~kl~vc---edcg~t~ 222 (267)
T KOG3576|consen 203 YAYKERRAKLYVC---EDCGYTS 222 (267)
T ss_pred HHHHHhhhheeee---cccCCCC
Confidence 456666 6777543
No 9
>PHA02768 hypothetical protein; Provisional
Probab=98.60 E-value=7.4e-09 Score=70.61 Aligned_cols=34 Identities=12% Similarity=0.340 Sum_probs=30.7
Q ss_pred ccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
-|+|++|||.|...++|..|+++|+ ++|+|. .|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~--~C~ 38 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLS--NCK 38 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCC--ccc
Confidence 3899999999999999999999999 688887 555
No 10
>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=98.34 E-value=1.5e-07 Score=54.70 Aligned_cols=25 Identities=24% Similarity=0.390 Sum_probs=22.7
Q ss_pred hHHHHhhhcCCCCCCCCCCCCccccccc
Q 047746 154 GIKAHAAMHQGVVPPQRPPDMRGGARFE 181 (247)
Q Consensus 154 ~L~~H~riHtgekPy~~~~~~~cg~~f~ 181 (247)
+|.+|+++|+|+|||.| ..|+++|.
T Consensus 1 ~l~~H~~~H~~~k~~~C---~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKC---PYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEE---SSSSEEES
T ss_pred CHHHHhhhcCCCCCCCC---CCCcCeeC
Confidence 58999999999999987 88999986
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.26 E-value=4.5e-07 Score=88.28 Aligned_cols=84 Identities=11% Similarity=0.115 Sum_probs=65.0
Q ss_pred CcccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCcCchhHHHHhhhcCCCCCCCCC
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAFRSLGIKAHAAMHQGVVPPQRP 171 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F~~~~L~~H~riHtgekPy~~~ 171 (247)
++.+.|.+|++.|. ...|..|+++|+ +++.|. | |+.|.+..|..|+++|.++||+.|
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp---C----------------g~~~~R~~L~~H~~thCp~Kpi~C- 507 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP---C----------------GVVLEKEQMVQHQASTCPLRLITC- 507 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC---C----------------CCCcchhHHHhhhhccCCCCceeC-
Confidence 45678899999885 567899988875 788885 4 444566899999999999999987
Q ss_pred CCCcccccccCC-----------CC--------CCCccccCCCCcccc
Q 047746 172 PDMRGGARFEQG-----------YF--------AMPMFMEDDDIDLFW 200 (247)
Q Consensus 172 ~~~~cg~~f~~~-----------~l--------~~P~~~~~c~~~f~~ 200 (247)
..|++.|..+ .| .+|+.|..|++.+..
T Consensus 508 --~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 508 --RFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVML 553 (567)
T ss_pred --CCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeee
Confidence 6799888532 11 379999999987653
No 12
>PHA00733 hypothetical protein
Probab=98.22 E-value=6.5e-07 Score=71.73 Aligned_cols=55 Identities=20% Similarity=0.295 Sum_probs=46.4
Q ss_pred CCCcccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCC
Q 047746 90 TVPRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQG 164 (247)
Q Consensus 90 tgekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtg 164 (247)
.+.++|.|+.|++.|.....|..|++.| +++|.|. .|++.| ....|..|++...+
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~------------------~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCP------------------VCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCC------------------CCCCccCCHHHHHHHHHHhcC
Confidence 3478999999999999999999999987 4578887 677899 78899999886543
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.17 E-value=1.1e-06 Score=59.94 Aligned_cols=34 Identities=9% Similarity=0.077 Sum_probs=29.7
Q ss_pred CCCCCc-CchhHHHHhhhcCCCCCCCCCCCCcccccccCC
Q 047746 145 LHGSAF-RSLGIKAHAAMHQGVVPPQRPPDMRGGARFEQG 183 (247)
Q Consensus 145 ~hgk~F-~~~~L~~H~riHtgekPy~~~~~~~cg~~f~~~ 183 (247)
.|||.| +..+|+.|||+|+ +||.| ..|++.|.+.
T Consensus 10 ~CGK~Fs~~~~L~~H~r~H~--k~~kc---~~C~k~f~~~ 44 (55)
T PHA02768 10 ICGEIYIKRKSMITHLRKHN--TNLKL---SNCKRISLRT 44 (55)
T ss_pred hhCCeeccHHHHHHHHHhcC--CcccC---Ccccceeccc
Confidence 778999 8999999999999 78876 8888888864
No 14
>PHA00733 hypothetical protein
Probab=98.13 E-value=1.2e-06 Score=70.22 Aligned_cols=68 Identities=16% Similarity=0.118 Sum_probs=50.7
Q ss_pred CcccccCcCCcccCCCcccccc--c---cccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCCC
Q 047746 92 PRVFSCNYCRRKFYSSQALGGH--Q---NAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQGV 165 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H--~---r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtge 165 (247)
.+++.|.+|.+.|.....|..| . ..+.+++||.|. .||+.| ....|..|+++| +
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~------------------~Cgk~Fss~s~L~~H~r~h--~ 97 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCP------------------LCLMPFSSSVSLKQHIRYT--E 97 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCC------------------CCCCcCCCHHHHHHHHhcC--C
Confidence 6789999999999988887765 1 133458899998 567889 788999999987 3
Q ss_pred CCCCCCCCCcccccccC
Q 047746 166 VPPQRPPDMRGGARFEQ 182 (247)
Q Consensus 166 kPy~~~~~~~cg~~f~~ 182 (247)
++|.| ..|++.|..
T Consensus 98 ~~~~C---~~CgK~F~~ 111 (128)
T PHA00733 98 HSKVC---PVCGKEFRN 111 (128)
T ss_pred cCccC---CCCCCccCC
Confidence 46654 555555543
No 15
>PHA00616 hypothetical protein
Probab=98.01 E-value=5e-07 Score=58.85 Aligned_cols=33 Identities=12% Similarity=0.325 Sum_probs=31.8
Q ss_pred ccccCcCCcccCCCccccccccccCCCcccccc
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKR 126 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~ 126 (247)
||+|..||+.|...+.|..|++.|+|++++.|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 699999999999999999999999999999887
No 16
>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=97.81 E-value=3e-06 Score=49.20 Aligned_cols=25 Identities=20% Similarity=0.343 Sum_probs=20.5
Q ss_pred cccccccccCCCccccccccccCccccccc
Q 047746 109 ALGGHQNAHKRERTMAKRAMRMGIFSDRYT 138 (247)
Q Consensus 109 ~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~ 138 (247)
+|..|+++|+++|||.|. .|+ +.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~--~C~---k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCP--YCG---KSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEES--SSS---EEES
T ss_pred CHHHHhhhcCCCCCCCCC--CCc---CeeC
Confidence 477899999999999999 776 5553
No 17
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=97.68 E-value=1.1e-05 Score=73.81 Aligned_cols=82 Identities=16% Similarity=0.227 Sum_probs=51.8
Q ss_pred cccCcCCcccCCCccccccccc-cCCCccccccccccCcccccccCCCCCCC----------------CCCCc-CchhHH
Q 047746 95 FSCNYCRRKFYSSQALGGHQNA-HKRERTMAKRAMRMGIFSDRYTSLASLPL----------------HGSAF-RSLGIK 156 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~-Htgekp~~C~~~~Cg~~~k~F~~~s~L~~----------------hgk~F-~~~~L~ 156 (247)
|+|+.|.-+....+.|..|+|. |.+.|||+|. .|. +.|...+.|.. |...| ....|+
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd--~Cd---~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~ 338 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCD--ECD---TRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMR 338 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCcccc--chh---hhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHH
Confidence 5566666666666666667663 6777888887 777 55554444322 23445 456788
Q ss_pred HHhhh-cCCC--CCCCCCCCCcccccccCCC
Q 047746 157 AHAAM-HQGV--VPPQRPPDMRGGARFEQGY 184 (247)
Q Consensus 157 ~H~ri-Htge--kPy~~~~~~~cg~~f~~~~ 184 (247)
+|++- |-|. .+|.| --|.+-|..|.
T Consensus 339 ~H~~evhEg~np~~Y~C---H~Cdr~ft~G~ 366 (467)
T KOG3608|consen 339 RHFLEVHEGNNPILYAC---HCCDRFFTSGK 366 (467)
T ss_pred HHHHHhccCCCCCceee---ecchhhhccch
Confidence 88874 4454 45766 77888888763
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.68 E-value=2.2e-05 Score=76.72 Aligned_cols=67 Identities=16% Similarity=0.220 Sum_probs=55.2
Q ss_pred cccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc-C----------chhHHHHhhh
Q 047746 93 RVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-R----------SLGIKAHAAM 161 (247)
Q Consensus 93 kpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~----------~~~L~~H~ri 161 (247)
++|.|. |++.| .+..|..|+++|..+|++.|. . |++.| . ...|+.|.++
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~--f----------------C~~~v~~g~~~~d~~d~~s~Lt~HE~~ 536 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCR--F----------------CGDMVQAGGSAMDVRDRLRGMSEHESI 536 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCC--C----------------CCCccccCccccchhhhhhhHHHHHHh
Confidence 678999 99765 668999999999999999999 4 44444 1 3489999999
Q ss_pred cCCCCCCCCCCCCcccccccCC
Q 047746 162 HQGVVPPQRPPDMRGGARFEQG 183 (247)
Q Consensus 162 HtgekPy~~~~~~~cg~~f~~~ 183 (247)
+ |.+++.| ..||+.|...
T Consensus 537 C-G~rt~~C---~~Cgk~Vrlr 554 (567)
T PLN03086 537 C-GSRTAPC---DSCGRSVMLK 554 (567)
T ss_pred c-CCcceEc---cccCCeeeeh
Confidence 7 9999987 8999988754
No 19
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=97.64 E-value=1.7e-06 Score=79.03 Aligned_cols=36 Identities=28% Similarity=0.525 Sum_probs=28.3
Q ss_pred ccccCc--CCcccCCCccccccccccCCCccccccccccC
Q 047746 94 VFSCNY--CRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 94 pf~C~~--Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
.+.|+. |-+.|..+..|..|.|.|++||-.+|. .||
T Consensus 177 v~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp--~Cg 214 (467)
T KOG3608|consen 177 VTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACP--HCG 214 (467)
T ss_pred eeeccchhhhhhhccHHHHHHHHHhcCCCeEEecc--hHH
Confidence 466765 778888888888888888888888887 776
No 20
>PHA00732 hypothetical protein
Probab=97.49 E-value=3.6e-05 Score=56.65 Aligned_cols=33 Identities=21% Similarity=0.264 Sum_probs=27.6
Q ss_pred ccccCcCCcccCCCccccccccc-cCCCccccccccccC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNA-HKRERTMAKRAMRMG 131 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~-Htgekp~~C~~~~Cg 131 (247)
||.|.+|++.|.....|..|++. |++ +.|. .|+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~--~Cg 34 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCP--VCN 34 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccC--CCC
Confidence 58999999999999999999984 764 5687 554
No 21
>PHA00616 hypothetical protein
Probab=97.38 E-value=6.1e-05 Score=49.11 Aligned_cols=26 Identities=12% Similarity=0.029 Sum_probs=23.5
Q ss_pred CCCCCc-CchhHHHHhhhcCCCCCCCC
Q 047746 145 LHGSAF-RSLGIKAHAAMHQGVVPPQR 170 (247)
Q Consensus 145 ~hgk~F-~~~~L~~H~riHtgekPy~~ 170 (247)
.||+.| .++.|..|++.|+|++|+.|
T Consensus 6 ~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 6 RCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred hhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 677899 89999999999999999865
No 22
>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=97.17 E-value=3.2e-05 Score=43.04 Aligned_cols=23 Identities=30% Similarity=0.700 Sum_probs=21.4
Q ss_pred cccCcCCcccCCCcccccccccc
Q 047746 95 FSCNYCRRKFYSSQALGGHQNAH 117 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~H 117 (247)
|.|.+|++.|.....|..|++.|
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 78999999999999999999865
No 23
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.01 E-value=0.00022 Score=66.74 Aligned_cols=71 Identities=24% Similarity=0.358 Sum_probs=45.1
Q ss_pred ccccCcCCcccCCCccccccccccCCCcccccc-------ccccCc----ccc----cccCCCCCCCCCCCc-CchhHHH
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKR-------AMRMGI----FSD----RYTSLASLPLHGSAF-RSLGIKA 157 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~-------~~~Cg~----~~k----~F~~~s~L~~hgk~F-~~~~L~~ 157 (247)
-|+|.+|+|.|....+|..|+|-|+-..--.-. ..+-+. -.+ .-.....+..|+|.| +...|++
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 489999999999999999999988643211100 000000 000 011123456789999 8889999
Q ss_pred HhhhcCC
Q 047746 158 HAAMHQG 164 (247)
Q Consensus 158 H~riHtg 164 (247)
|+.+|..
T Consensus 375 Hqlthq~ 381 (500)
T KOG3993|consen 375 HQLTHQR 381 (500)
T ss_pred hHHhhhc
Confidence 9988864
No 24
>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=96.83 E-value=0.00017 Score=41.63 Aligned_cols=26 Identities=35% Similarity=0.662 Sum_probs=23.8
Q ss_pred ccccCcCCcccCCCccccccccccCC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKR 119 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htg 119 (247)
+|.|..|++.|....+|..|++.|.+
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 68999999999999999999998753
No 25
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.29 E-value=0.00043 Score=38.16 Aligned_cols=23 Identities=35% Similarity=0.753 Sum_probs=19.4
Q ss_pred cccCcCCcccCCCcccccccccc
Q 047746 95 FSCNYCRRKFYSSQALGGHQNAH 117 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~H 117 (247)
|.|++|++.|.....|..|++.|
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 78999999999999999999875
No 26
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=96.27 E-value=0.00041 Score=65.03 Aligned_cols=96 Identities=15% Similarity=0.163 Sum_probs=61.6
Q ss_pred ccccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCCCCCCC--C
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQGVVPPQ--R 170 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtgekPy~--~ 170 (247)
-|.|..|...|.....|.+|+-...-.--|+|. .|+|.| -..+|..|.|.|.-.+-.. -
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCP------------------EC~KVFsCPANLASHRRWHKPR~eaa~a~ 328 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCP------------------ECDKVFSCPANLASHRRWHKPRPEAAKAG 328 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCC------------------cccccccCchhhhhhhcccCCchhhhhcC
Confidence 499999999999999999996433333457787 556889 7999999999996322111 0
Q ss_pred -CCCC-c-----ccccccC-C--CCCCCccccCCCCccccCCCceec
Q 047746 171 -PPDM-R-----GGARFEQ-G--YFAMPMFMEDDDIDLFWPGSFRQV 207 (247)
Q Consensus 171 -~~~~-~-----cg~~f~~-~--~l~~P~~~~~c~~~f~~~~s~~~~ 207 (247)
+|.. . .++.-.+ | .-.-=|.|.+|+|.|.+..+||.|
T Consensus 329 ~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKH 375 (500)
T KOG3993|consen 329 SPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKH 375 (500)
T ss_pred CCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHh
Confidence 0100 0 0000000 0 001146888888888888888887
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.14 E-value=0.0026 Score=57.85 Aligned_cols=51 Identities=22% Similarity=0.455 Sum_probs=37.6
Q ss_pred CCcccccCc--CCcccCCCccccccccc-c------------------CCCccccccccccCcccccccCCCCCCCC
Q 047746 91 VPRVFSCNY--CRRKFYSSQALGGHQNA-H------------------KRERTMAKRAMRMGIFSDRYTSLASLPLH 146 (247)
Q Consensus 91 gekpf~C~~--Cgk~F~~~~~L~~H~r~-H------------------tgekp~~C~~~~Cg~~~k~F~~~s~L~~h 146 (247)
++|||+|++ |.|+|...-.|+-|+.- | ...|||+|. .|+ |+|.....|.+|
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCe--vC~---KRYKNlNGLKYH 417 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCE--VCD---KRYKNLNGLKYH 417 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceecc--ccc---hhhccCccceec
Confidence 469999987 99999998888877542 2 124899999 677 666666666655
No 28
>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=96.09 E-value=0.0024 Score=43.28 Aligned_cols=50 Identities=22% Similarity=0.440 Sum_probs=35.8
Q ss_pred ccccCcCCcccCCCcccccccc-ccCCC-ccccccccccCcccccccCCCCCCCCCCCcCchhHHHHhhhcC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQN-AHKRE-RTMAKRAMRMGIFSDRYTSLASLPLHGSAFRSLGIKAHAAMHQ 163 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r-~Htge-kp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F~~~~L~~H~riHt 163 (247)
.|.|++|++ ..+...|..|.. .|..+ +.+.|. +|...+. .+|..|++++.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CP------------------iC~~~~~-~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCP------------------ICSSRVT-DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCC------------------Cchhhhh-hHHHHHHHHhc
Confidence 489999999 455678999965 46665 567787 4444442 38899998764
No 29
>PHA00732 hypothetical protein
Probab=96.06 E-value=0.0048 Score=45.33 Aligned_cols=32 Identities=16% Similarity=0.181 Sum_probs=25.9
Q ss_pred CCCCCc-CchhHHHHhhh-cCCCCCCCCCCCCcccccccC
Q 047746 145 LHGSAF-RSLGIKAHAAM-HQGVVPPQRPPDMRGGARFEQ 182 (247)
Q Consensus 145 ~hgk~F-~~~~L~~H~ri-HtgekPy~~~~~~~cg~~f~~ 182 (247)
.||+.| +...|+.|++. |++ +.| ..|++.|.+
T Consensus 6 ~Cgk~F~s~s~Lk~H~r~~H~~---~~C---~~CgKsF~~ 39 (79)
T PHA00732 6 ICGFTTVTLFALKQHARRNHTL---TKC---PVCNKSYRR 39 (79)
T ss_pred CCCCccCCHHHHHHHhhcccCC---Ccc---CCCCCEeCC
Confidence 677899 88999999984 764 455 889999975
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.86 E-value=0.0015 Score=36.29 Aligned_cols=25 Identities=32% Similarity=0.628 Sum_probs=22.4
Q ss_pred cccCcCCcccCCCccccccccccCC
Q 047746 95 FSCNYCRRKFYSSQALGGHQNAHKR 119 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~Htg 119 (247)
|.|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999987753
No 31
>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=95.58 E-value=0.0047 Score=34.05 Aligned_cols=18 Identities=28% Similarity=0.536 Sum_probs=16.1
Q ss_pred CCCCCc-CchhHHHHhhhc
Q 047746 145 LHGSAF-RSLGIKAHAAMH 162 (247)
Q Consensus 145 ~hgk~F-~~~~L~~H~riH 162 (247)
.|++.| +...|..|+++|
T Consensus 5 ~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 5 ICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp TTTEEESSHHHHHHHHHHH
T ss_pred CCCCccCCHHHHHHHHhHC
Confidence 788999 899999999986
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.48 E-value=0.016 Score=52.83 Aligned_cols=72 Identities=15% Similarity=0.054 Sum_probs=44.1
Q ss_pred CCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhh-cCCCCCCCCCCCCcccccccCCCCCCCccccCCC
Q 047746 118 KRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAM-HQGVVPPQRPPDMRGGARFEQGYFAMPMFMEDDD 195 (247)
Q Consensus 118 tgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~ri-HtgekPy~~~~~~~cg~~f~~~~l~~P~~~~~c~ 195 (247)
.++|||+|.... |.|.+ ..-+|+-|+.- |...|-..- |..+-...|. .-.+||.|+-|+
T Consensus 345 ~d~KpykCpV~g----------------C~K~YknqnGLKYH~lhGH~~~~~~~~-p~p~~~~~F~--~~~KPYrCevC~ 405 (423)
T COG5189 345 KDGKPYKCPVEG----------------CNKKYKNQNGLKYHMLHGHQNQKLHEN-PSPEKMNIFS--AKDKPYRCEVCD 405 (423)
T ss_pred ecCceecCCCCC----------------chhhhccccchhhhhhccccCcccCCC-CCcccccccc--ccCCceeccccc
Confidence 346999999444 55666 55577777652 544443332 2222223342 135899999999
Q ss_pred CccccCCCceecC
Q 047746 196 IDLFWPGSFRQVS 208 (247)
Q Consensus 196 ~~f~~~~s~~~~~ 208 (247)
|.+.--..|+-|-
T Consensus 406 KRYKNlNGLKYHr 418 (423)
T COG5189 406 KRYKNLNGLKYHR 418 (423)
T ss_pred hhhccCccceecc
Confidence 9988777777653
No 33
>PRK04860 hypothetical protein; Provisional
Probab=95.32 E-value=0.0049 Score=51.22 Aligned_cols=33 Identities=21% Similarity=0.463 Sum_probs=29.4
Q ss_pred cccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 93 RVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 93 kpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
-+|.|. |++ ....+.+|.++|+++++|.|. .|+
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~--~C~ 150 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCR--RCG 150 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECC--CCC
Confidence 479998 998 677789999999999999999 676
No 34
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.09 E-value=0.017 Score=52.58 Aligned_cols=62 Identities=24% Similarity=0.401 Sum_probs=54.1
Q ss_pred cccccCcCCcccCCCcccccccc--ccCCC--ccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCCCCC
Q 047746 93 RVFSCNYCRRKFYSSQALGGHQN--AHKRE--RTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQGVVP 167 (247)
Q Consensus 93 kpf~C~~Cgk~F~~~~~L~~H~r--~Htge--kp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtgekP 167 (247)
.++.|..|.+.|.....|..|.+ .|+++ +|+.|... .|++.| +...|..|..+|++-++
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~----------------~~~~~~~~~~~~~~~~~~~~~~~~ 351 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYS----------------LCGKLFSRNDALKRHILLHTSISP 351 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeecc----------------CCCccccccccccCCcccccCCCc
Confidence 47999999999999999999999 89999 99999721 577888 88889999999998887
Q ss_pred CCC
Q 047746 168 PQR 170 (247)
Q Consensus 168 y~~ 170 (247)
+.+
T Consensus 352 ~~~ 354 (467)
T COG5048 352 AKE 354 (467)
T ss_pred ccc
Confidence 765
No 35
>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=94.38 E-value=0.0075 Score=40.51 Aligned_cols=32 Identities=16% Similarity=0.281 Sum_probs=23.6
Q ss_pred CCcccccCcCCcccCCCccccccccccCCCcc
Q 047746 91 VPRVFSCNYCRRKFYSSQALGGHQNAHKRERT 122 (247)
Q Consensus 91 gekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp 122 (247)
.+.|..|++|+..+.+..+|.+|+.++.+.||
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 36789999999999999999999998888776
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.63 E-value=0.007 Score=34.06 Aligned_cols=23 Identities=30% Similarity=0.730 Sum_probs=20.9
Q ss_pred cccCcCCcccCCCcccccccccc
Q 047746 95 FSCNYCRRKFYSSQALGGHQNAH 117 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~H 117 (247)
|.|..|++.|.+...|..|++.+
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 68999999999999999998764
No 37
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=93.45 E-value=0.024 Score=32.66 Aligned_cols=22 Identities=32% Similarity=0.685 Sum_probs=20.5
Q ss_pred cccCcCCcccCCCccccccccc
Q 047746 95 FSCNYCRRKFYSSQALGGHQNA 116 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~ 116 (247)
|.|..|+|.|.....|..|++.
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 7899999999999999999875
No 38
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=93.33 E-value=0.041 Score=40.60 Aligned_cols=68 Identities=15% Similarity=0.268 Sum_probs=18.2
Q ss_pred ccCcCCcccCCCccccccccccCC-Ccc---ccccccccCcc-cccccCCCCCCCCCCCc-CchhHHHHhhhcC
Q 047746 96 SCNYCRRKFYSSQALGGHQNAHKR-ERT---MAKRAMRMGIF-SDRYTSLASLPLHGSAF-RSLGIKAHAAMHQ 163 (247)
Q Consensus 96 ~C~~Cgk~F~~~~~L~~H~r~Htg-ekp---~~C~~~~Cg~~-~k~F~~~s~L~~hgk~F-~~~~L~~H~riHt 163 (247)
+|.+|+..|.....|..|+....+ ..+ +.........+ .........+..|++.| ....|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 599999999999999999865433 222 00000000000 01111224467889999 7889999999753
No 39
>PRK04860 hypothetical protein; Provisional
Probab=93.20 E-value=0.051 Score=45.17 Aligned_cols=28 Identities=18% Similarity=0.261 Sum_probs=24.4
Q ss_pred CchhHHHHhhhcCCCCCCCCCCCCccccccc
Q 047746 151 RSLGIKAHAAMHQGVVPPQRPPDMRGGARFE 181 (247)
Q Consensus 151 ~~~~L~~H~riHtgekPy~~~~~~~cg~~f~ 181 (247)
....+.+|.|+|+|+++|.| ..|+..|.
T Consensus 127 ~~~~~rrH~ri~~g~~~YrC---~~C~~~l~ 154 (160)
T PRK04860 127 HQLTVRRHNRVVRGEAVYRC---RRCGETLV 154 (160)
T ss_pred eeCHHHHHHHHhcCCccEEC---CCCCceeE
Confidence 46788999999999999988 88888875
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=92.64 E-value=0.098 Score=35.20 Aligned_cols=33 Identities=15% Similarity=0.281 Sum_probs=21.9
Q ss_pred cCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhhcCCCCC
Q 047746 117 HKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAMHQGVVP 167 (247)
Q Consensus 117 Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~riHtgekP 167 (247)
+..+.|..|. .|+..+ +..+|++|+.++++.||
T Consensus 19 ~~S~~PatCP------------------~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCP------------------ICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-T------------------TT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCC------------------cchhhccchhhHHHHHHHHhcccC
Confidence 4456788887 566777 67899999999998887
No 41
>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=92.54 E-value=0.052 Score=30.95 Aligned_cols=20 Identities=20% Similarity=0.325 Sum_probs=16.7
Q ss_pred CCCCCc-CchhHHHHhhhcCC
Q 047746 145 LHGSAF-RSLGIKAHAAMHQG 164 (247)
Q Consensus 145 ~hgk~F-~~~~L~~H~riHtg 164 (247)
.|++.| ....|..|++.|.+
T Consensus 6 ~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 6 ECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp TTTEEESSHHHHHHHHCTTTT
T ss_pred ccCCccCChhHHHHHhHHhcC
Confidence 677889 78899999998853
No 42
>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=92.28 E-value=0.073 Score=28.82 Aligned_cols=19 Identities=21% Similarity=0.525 Sum_probs=15.5
Q ss_pred CCCCCc-CchhHHHHhhhcC
Q 047746 145 LHGSAF-RSLGIKAHAAMHQ 163 (247)
Q Consensus 145 ~hgk~F-~~~~L~~H~riHt 163 (247)
+|++.| ....|..|+++|.
T Consensus 5 ~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 5 ICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp STS-EESSHHHHHHHHHHHS
T ss_pred CCCCcCCcHHHHHHHHHhhC
Confidence 788999 8899999999873
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=90.40 E-value=0.2 Score=27.28 Aligned_cols=20 Identities=25% Similarity=0.390 Sum_probs=16.9
Q ss_pred CCCCCc-CchhHHHHhhhcCC
Q 047746 145 LHGSAF-RSLGIKAHAAMHQG 164 (247)
Q Consensus 145 ~hgk~F-~~~~L~~H~riHtg 164 (247)
.|++.| ....|..|+++|..
T Consensus 5 ~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 5 ECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCcchhCCHHHHHHHHHHhcc
Confidence 678899 78899999998853
No 44
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=87.99 E-value=0.096 Score=29.88 Aligned_cols=20 Identities=35% Similarity=0.800 Sum_probs=16.3
Q ss_pred cccCcCCcccCCCcccccccc
Q 047746 95 FSCNYCRRKFYSSQALGGHQN 115 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r 115 (247)
..|..||+.| ....|..|++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4799999999 6667888865
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.22 E-value=0.061 Score=29.91 Aligned_cols=23 Identities=22% Similarity=0.467 Sum_probs=17.5
Q ss_pred cccCcCCcccCCCccccccccccC
Q 047746 95 FSCNYCRRKFYSSQALGGHQNAHK 118 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~Ht 118 (247)
|+|..|..... ...|..|++.|.
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 78999998887 888999988753
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=85.61 E-value=1.1 Score=40.68 Aligned_cols=44 Identities=20% Similarity=0.351 Sum_probs=38.3
Q ss_pred CCCCC--cccccC--cCCcccCCCccccccccccCCCccccccccccC
Q 047746 88 AATVP--RVFSCN--YCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 88 ~~tge--kpf~C~--~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
.++++ ++|.|. .|++.|.+...+.+|..+|++-+++.|....|.
T Consensus 313 ~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 360 (467)
T COG5048 313 NHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSS 360 (467)
T ss_pred ccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCc
Confidence 47788 999999 799999999999999999999998888744444
No 47
>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=84.98 E-value=0.2 Score=30.10 Aligned_cols=23 Identities=22% Similarity=0.525 Sum_probs=19.9
Q ss_pred ccccCcCCcccCCCccccccccc
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNA 116 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~ 116 (247)
+|.|.+|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999888888753
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=76.30 E-value=0.52 Score=34.53 Aligned_cols=25 Identities=36% Similarity=0.796 Sum_probs=21.6
Q ss_pred cccccCcCCcccCCCcccccccccc
Q 047746 93 RVFSCNYCRRKFYSSQALGGHQNAH 117 (247)
Q Consensus 93 kpf~C~~Cgk~F~~~~~L~~H~r~H 117 (247)
..|.|.+|++.|.+...|..|++.+
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCc
Confidence 3699999999999999999999864
No 49
>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=76.30 E-value=2.2 Score=33.21 Aligned_cols=28 Identities=14% Similarity=0.108 Sum_probs=22.2
Q ss_pred CCCcccccccCCCCC-CCccccCCCCccccC
Q 047746 172 PDMRGGARFEQGYFA-MPMFMEDDDIDLFWP 201 (247)
Q Consensus 172 ~~~~cg~~f~~~~l~-~P~~~~~c~~~f~~~ 201 (247)
.|..||+||-. |+ .|..|..||..|.-.
T Consensus 11 ~Cp~CG~kFYD--Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYD--LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhcc--CCCCCccCCCCCCccCcc
Confidence 35899999954 55 799999999987655
No 50
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=73.73 E-value=0.82 Score=40.44 Aligned_cols=33 Identities=27% Similarity=0.505 Sum_probs=26.0
Q ss_pred CcccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
.|+| |=+|+|.|....-|.+||+. |-|+|. .|.
T Consensus 9 ~kpw-cwycnrefddekiliqhqka----khfkch--ich 41 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKA----KHFKCH--ICH 41 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhh----ccceee--eeh
Confidence 3454 99999999999999999864 567887 554
No 51
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=65.69 E-value=2.7 Score=45.22 Aligned_cols=94 Identities=12% Similarity=0.044 Sum_probs=59.3
Q ss_pred ccCcCCcccCCCcccccccc-ccCCCccccccccccCcccccccCCCCCCCCCCCc-CchhHHHHhhh-cC-CCCCCCCC
Q 047746 96 SCNYCRRKFYSSQALGGHQN-AHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF-RSLGIKAHAAM-HQ-GVVPPQRP 171 (247)
Q Consensus 96 ~C~~Cgk~F~~~~~L~~H~r-~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F-~~~~L~~H~ri-Ht-gekPy~~~ 171 (247)
.|.-|+..|.+...+..|+. .|...|.|+|. .|+..| ....|..|||. |. ++.-| |
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cp------------------kc~~~yk~a~~L~vhmRskhp~~~~~~-c- 497 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVLHSFFKTLKCP------------------KCNWHYKLAQTLGVHMRSKHPESQSAY-C- 497 (1406)
T ss_pred cccchhhhhhhhcccccceeeeecccccccCC------------------ccchhhhhHHHhhhcccccccccchhH-h-
Confidence 35556777777778888865 47778899998 445567 67789999996 32 22222 1
Q ss_pred CCCcccccccCC-C---CCCCccccCCCCccccCCCceecCC
Q 047746 172 PDMRGGARFEQG-Y---FAMPMFMEDDDIDLFWPGSFRQVSE 209 (247)
Q Consensus 172 ~~~~cg~~f~~~-~---l~~P~~~~~c~~~f~~~~s~~~~~~ 209 (247)
....-+.+-.++ . -+.||.|..|..++...++|-+|-+
T Consensus 498 ~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 498 KAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred HhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 000000011111 1 2489999999999999888876644
No 52
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=62.26 E-value=2.2 Score=43.16 Aligned_cols=28 Identities=21% Similarity=0.697 Sum_probs=25.1
Q ss_pred CcccccCcCCcccCCCccccccccccCC
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKR 119 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htg 119 (247)
..-|.|.+|+|.|.....+..||+.|.-
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 4579999999999999999999999964
No 53
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=61.08 E-value=4 Score=43.95 Aligned_cols=26 Identities=23% Similarity=0.506 Sum_probs=24.0
Q ss_pred CCcccccCcCCcccCCCccccccccc
Q 047746 91 VPRVFSCNYCRRKFYSSQALGGHQNA 116 (247)
Q Consensus 91 gekpf~C~~Cgk~F~~~~~L~~H~r~ 116 (247)
-.|.|+|+.|+-.|...+.|..|+|.
T Consensus 462 ~~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 462 FFKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred ccccccCCccchhhhhHHHhhhcccc
Confidence 35889999999999999999999997
No 54
>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=57.61 E-value=7.2 Score=31.20 Aligned_cols=26 Identities=12% Similarity=0.041 Sum_probs=20.3
Q ss_pred CCcccccccCCCCC-CCccccCCCCcccc
Q 047746 173 DMRGGARFEQGYFA-MPMFMEDDDIDLFW 200 (247)
Q Consensus 173 ~~~cg~~f~~~~l~-~P~~~~~c~~~f~~ 200 (247)
|..||+||-. |+ .|..|..||..|.-
T Consensus 12 Cp~cg~kFYD--Lnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 12 CPNTGSKFYD--LNRRPAVSPYTGEQFPP 38 (129)
T ss_pred CCCcCccccc--cCCCCccCCCcCCccCc
Confidence 5889999954 54 69999999988543
No 55
>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=56.52 E-value=8.8 Score=21.75 Aligned_cols=23 Identities=13% Similarity=0.073 Sum_probs=14.7
Q ss_pred CcccccccCCCCCCCccccCCCC
Q 047746 174 MRGGARFEQGYFAMPMFMEDDDI 196 (247)
Q Consensus 174 ~~cg~~f~~~~l~~P~~~~~c~~ 196 (247)
..|+........+.+|.|+.||+
T Consensus 2 ~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 2 TSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred ccCCCcccCcccCceEeCCCCCC
Confidence 45655554434467888888874
No 56
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=53.68 E-value=3.9 Score=26.88 Aligned_cols=24 Identities=33% Similarity=0.667 Sum_probs=18.2
Q ss_pred cccCcCCcccCCC-----cccccccc-ccC
Q 047746 95 FSCNYCRRKFYSS-----QALGGHQN-AHK 118 (247)
Q Consensus 95 f~C~~Cgk~F~~~-----~~L~~H~r-~Ht 118 (247)
-.|.+|++.+... ++|.+|++ .|.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 4799999999776 46777776 453
No 57
>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=51.88 E-value=3.1 Score=26.41 Aligned_cols=23 Identities=26% Similarity=0.511 Sum_probs=14.3
Q ss_pred CcccccCcCCcccCCC----ccccccc
Q 047746 92 PRVFSCNYCRRKFYSS----QALGGHQ 114 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~----~~L~~H~ 114 (247)
....+|.+|++.+... +.|..|+
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 4557999999998875 5677776
No 58
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=51.12 E-value=4.9 Score=35.66 Aligned_cols=31 Identities=29% Similarity=0.655 Sum_probs=24.8
Q ss_pred CCCCcccccCcCCcccCCCcccccc-ccccCC
Q 047746 89 ATVPRVFSCNYCRRKFYSSQALGGH-QNAHKR 119 (247)
Q Consensus 89 ~tgekpf~C~~Cgk~F~~~~~L~~H-~r~Htg 119 (247)
|...|-|+|.+|.|+.++--.|..| +.+|+.
T Consensus 29 hqkakhfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 29 HQKAKHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred hhhhccceeeeehhhhccCCCceeehhhhhhh
Confidence 3445789999999999999999998 456653
No 59
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=46.38 E-value=2.9 Score=28.75 Aligned_cols=28 Identities=18% Similarity=0.266 Sum_probs=24.0
Q ss_pred CCCCcccccCcCCcccCCCccccccccc
Q 047746 89 ATVPRVFSCNYCRRKFYSSQALGGHQNA 116 (247)
Q Consensus 89 ~tgekpf~C~~Cgk~F~~~~~L~~H~r~ 116 (247)
..||.-+.|+-|+..|.......+|.+.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 4567789999999999999999999764
No 60
>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=46.03 E-value=10 Score=24.88 Aligned_cols=29 Identities=17% Similarity=0.415 Sum_probs=19.5
Q ss_pred ccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
.|+|..||..|...... +. +.+-.|. .||
T Consensus 5 ey~C~~Cg~~fe~~~~~------~~-~~~~~CP--~Cg 33 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKM------SD-DPLATCP--ECG 33 (52)
T ss_pred EEEeCCCCCEeEEEEec------CC-CCCCCCC--CCC
Confidence 48999999998754322 11 3455688 777
No 61
>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=45.03 E-value=13 Score=22.29 Aligned_cols=23 Identities=13% Similarity=0.340 Sum_probs=16.4
Q ss_pred cccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 95 FSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
|.|..||..+.... .++.|. .|+
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP--~Cg 24 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCP--VCG 24 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCc--CCC
Confidence 78999987654332 678888 777
No 62
>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=44.96 E-value=11 Score=23.23 Aligned_cols=29 Identities=17% Similarity=0.385 Sum_probs=19.3
Q ss_pred ccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
.|+|..||+.|........ .....|. .||
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~-------~~~~~CP--~Cg 33 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD-------DPLATCP--ECG 33 (41)
T ss_pred EEEcCCCCCEEEEEEecCC-------CCCCCCC--CCC
Confidence 5899999998875543321 3455677 666
No 63
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=44.66 E-value=16 Score=31.62 Aligned_cols=25 Identities=16% Similarity=0.517 Sum_probs=20.2
Q ss_pred CcccccCcCCcccCCCccccccccc
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNA 116 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~ 116 (247)
+|.+.|++|++.|....-..+..|+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 4678999999999998777766654
No 64
>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=43.30 E-value=4.4 Score=32.65 Aligned_cols=29 Identities=24% Similarity=0.395 Sum_probs=18.1
Q ss_pred cccccCcCCcccCCCccccccccccCCCcccc
Q 047746 93 RVFSCNYCRRKFYSSQALGGHQNAHKRERTMA 124 (247)
Q Consensus 93 kpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~ 124 (247)
.--.|-+|||.|.. |++|.+.|.|-.|-.
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp~e 99 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTPEE 99 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-HHH
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCHHH
Confidence 34679999999876 599999998876633
No 65
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.51 E-value=12 Score=29.34 Aligned_cols=30 Identities=20% Similarity=0.296 Sum_probs=22.0
Q ss_pred CCCcccccccCCCCC-CCccccCCCCccccCCCce
Q 047746 172 PDMRGGARFEQGYFA-MPMFMEDDDIDLFWPGSFR 205 (247)
Q Consensus 172 ~~~~cg~~f~~~~l~-~P~~~~~c~~~f~~~~s~~ 205 (247)
.+..||++|-. |+ .|..|..||++| |.++-
T Consensus 11 idPetg~KFYD--LNrdPiVsPytG~s~--P~s~f 41 (129)
T COG4530 11 IDPETGKKFYD--LNRDPIVSPYTGKSY--PRSYF 41 (129)
T ss_pred cCccccchhhc--cCCCccccCcccccc--hHHHH
Confidence 35688888854 55 799999999987 55543
No 66
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=40.35 E-value=56 Score=30.71 Aligned_cols=23 Identities=17% Similarity=0.582 Sum_probs=17.5
Q ss_pred CcccccCc--CCcccCCCccccccc
Q 047746 92 PRVFSCNY--CRRKFYSSQALGGHQ 114 (247)
Q Consensus 92 ekpf~C~~--Cgk~F~~~~~L~~H~ 114 (247)
.++|+|.+ |.+.+...-.|+.|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~ 371 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHK 371 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeecc
Confidence 57899975 888888777776664
No 67
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=38.31 E-value=10 Score=30.75 Aligned_cols=54 Identities=17% Similarity=0.207 Sum_probs=35.6
Q ss_pred cccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCCCc--CchhHHHHh
Q 047746 95 FSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGSAF--RSLGIKAHA 159 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk~F--~~~~L~~H~ 159 (247)
..|-+|||+|.+ |++|.++|.+--|-.-+ ..|-....+|.--..+ .++.|.+-|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTPd~YR--------~KW~LP~dYPMvAPnYAa~RS~LAK~m 132 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTPDEYR--------AKWGLPPDYPMVAPNYAAARSQLAKAM 132 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCHHHHH--------HhcCCCCCCCccchHHHHHHHHHHHHh
Confidence 469999999975 89999999998775444 4444445555544444 345555443
No 68
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=37.94 E-value=16 Score=26.32 Aligned_cols=35 Identities=14% Similarity=0.242 Sum_probs=19.0
Q ss_pred cccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 95 FSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
+.|+.||........-..+. -+.++-+.|.-.+||
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~Y~qC~N~eCg 36 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKERYHQCQNVNCS 36 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhheeeeecCCCCCC
Confidence 57888887653332222221 245666777654555
No 69
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=36.62 E-value=18 Score=29.85 Aligned_cols=9 Identities=22% Similarity=0.796 Sum_probs=4.7
Q ss_pred ccCcCCccc
Q 047746 96 SCNYCRRKF 104 (247)
Q Consensus 96 ~C~~Cgk~F 104 (247)
+|++||-.+
T Consensus 2 ~cp~c~~~~ 10 (154)
T PRK00464 2 RCPFCGHPD 10 (154)
T ss_pred cCCCCCCCC
Confidence 466665433
No 70
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=32.99 E-value=27 Score=22.55 Aligned_cols=25 Identities=20% Similarity=0.457 Sum_probs=18.4
Q ss_pred ccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
.|.|..||..|... ...+..|+ +||
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~--~CG 26 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCR--ECG 26 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECC--CCC
Confidence 48999999988754 22467888 777
No 71
>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=32.16 E-value=19 Score=21.20 Aligned_cols=21 Identities=29% Similarity=0.733 Sum_probs=13.2
Q ss_pred cccCcCCcccCCCccccccccc
Q 047746 95 FSCNYCRRKFYSSQALGGHQNA 116 (247)
Q Consensus 95 f~C~~Cgk~F~~~~~L~~H~r~ 116 (247)
|.|-.|++.| .....+.|..-
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~C 21 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTSC 21 (28)
T ss_dssp EEETTTTEEE-EGGGTTT----
T ss_pred CeeecCCCCc-CcCCcCCCCcc
Confidence 6799999999 55566667543
No 72
>PF07981 Plasmod_MYXSPDY: Plasmodium repeat_MYXSPDY; InterPro: IPR012598 This repeat is found in two hypothetical Plasmodium proteins.
Probab=31.64 E-value=19 Score=18.48 Aligned_cols=9 Identities=56% Similarity=0.881 Sum_probs=7.1
Q ss_pred CCCCccccC
Q 047746 239 SAPDLTLKL 247 (247)
Q Consensus 239 ~~~~l~~~~ 247 (247)
.+||.||+|
T Consensus 3 ~SPdytL~~ 11 (17)
T PF07981_consen 3 FSPDYTLRL 11 (17)
T ss_pred cCCCceEEE
Confidence 468999986
No 73
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=31.37 E-value=23 Score=22.22 Aligned_cols=15 Identities=27% Similarity=0.676 Sum_probs=12.7
Q ss_pred ccccCcCCcccCCCc
Q 047746 94 VFSCNYCRRKFYSSQ 108 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~ 108 (247)
+|+|..|++.|-...
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 799999999997653
No 74
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=30.56 E-value=19 Score=24.01 Aligned_cols=28 Identities=11% Similarity=-0.141 Sum_probs=19.7
Q ss_pred CCCCCCCCcccccccCCCCCCCccccCCCCc
Q 047746 167 PPQRPPDMRGGARFEQGYFAMPMFMEDDDID 197 (247)
Q Consensus 167 Py~~~~~~~cg~~f~~~~l~~P~~~~~c~~~ 197 (247)
-|.| ..||+.|........+.|.+|+.-
T Consensus 6 ~Y~C---~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKC---ARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEh---hhcCCeeehhhccCceeCCCCCcE
Confidence 4656 899999964334466789999754
No 75
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=30.43 E-value=24 Score=28.39 Aligned_cols=27 Identities=22% Similarity=0.142 Sum_probs=17.8
Q ss_pred CCCCCCCCcccccccCCCCCCCccccCCCC
Q 047746 167 PPQRPPDMRGGARFEQGYFAMPMFMEDDDI 196 (247)
Q Consensus 167 Py~~~~~~~cg~~f~~~~l~~P~~~~~c~~ 196 (247)
|++| ..||+.|..+...+---|.+||-
T Consensus 1 PH~C---t~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 1 PHQC---TKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred Cccc---CcCCCCcCCCcHHHHccCcccCC
Confidence 5666 89999999875222234777753
No 76
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=29.15 E-value=31 Score=24.01 Aligned_cols=26 Identities=12% Similarity=0.077 Sum_probs=16.6
Q ss_pred CCCccccc-ccC----CCCCCCccccCCCCc
Q 047746 172 PDMRGGAR-FEQ----GYFAMPMFMEDDDID 197 (247)
Q Consensus 172 ~~~~cg~~-f~~----~~l~~P~~~~~c~~~ 197 (247)
+|..||+. ..+ ..+|.||.|+.||+.
T Consensus 29 ~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 29 PCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eCCCCCceeeehhhhHHHcCCceECCCcCcc
Confidence 44667743 222 137889999999863
No 77
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=29.04 E-value=44 Score=25.28 Aligned_cols=33 Identities=12% Similarity=0.108 Sum_probs=24.8
Q ss_pred CCCCCCCCCcccccccCCCCCCCccccCCCCccccC
Q 047746 166 VPPQRPPDMRGGARFEQGYFAMPMFMEDDDIDLFWP 201 (247)
Q Consensus 166 kPy~~~~~~~cg~~f~~~~l~~P~~~~~c~~~f~~~ 201 (247)
+|..| ..||.-|...-..+|-.|..|...-.-+
T Consensus 57 ~Pa~C---kkCGfef~~~~ik~pSRCP~CKSE~Ie~ 89 (97)
T COG3357 57 RPARC---KKCGFEFRDDKIKKPSRCPKCKSEWIEE 89 (97)
T ss_pred cChhh---cccCccccccccCCcccCCcchhhcccC
Confidence 45544 9999999886677899999997654433
No 78
>PF14353 CpXC: CpXC protein
Probab=28.36 E-value=29 Score=27.12 Aligned_cols=25 Identities=28% Similarity=0.420 Sum_probs=19.6
Q ss_pred cccccCcCCcccCCCcccccccccc
Q 047746 93 RVFSCNYCRRKFYSSQALGGHQNAH 117 (247)
Q Consensus 93 kpf~C~~Cgk~F~~~~~L~~H~r~H 117 (247)
-.|.|+.||+.|.-...+.-|...|
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~~~ 61 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDPEK 61 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcCCC
Confidence 3589999999998888777775543
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.43 E-value=27 Score=28.28 Aligned_cols=34 Identities=21% Similarity=0.315 Sum_probs=23.4
Q ss_pred CcccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
..-|.|+.|++.|....++..- +. ..-|.|. .||
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp--~Cg 130 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCP--RCG 130 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhc---CC-CCcEECC--CCC
Confidence 4579999999999976655431 11 2348998 676
No 80
>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=27.32 E-value=25 Score=22.26 Aligned_cols=29 Identities=17% Similarity=0.474 Sum_probs=20.2
Q ss_pred ccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
.|+|..||..|-...... . ..+..|. .||
T Consensus 5 ey~C~~Cg~~fe~~~~~~------~-~~~~~CP--~Cg 33 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSIS------E-DDPVPCP--ECG 33 (42)
T ss_pred EEEeCCCCCEEEEEEEcC------C-CCCCcCC--CCC
Confidence 489999999987654332 2 4566787 676
No 81
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.27 E-value=21 Score=30.08 Aligned_cols=29 Identities=21% Similarity=0.390 Sum_probs=23.0
Q ss_pred CcccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
..-|.|+.|++.|+...++. .-|.|. .||
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp--~Cg 143 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCP--QCG 143 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCC--CCC
Confidence 35699999999999888763 368898 776
No 82
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=25.90 E-value=22 Score=23.65 Aligned_cols=17 Identities=6% Similarity=0.194 Sum_probs=12.7
Q ss_pred CCccccCCCCccccCCC
Q 047746 187 MPMFMEDDDIDLFWPGS 203 (247)
Q Consensus 187 ~P~~~~~c~~~f~~~~s 203 (247)
+++.|.+||..|.|-..
T Consensus 3 k~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAG 19 (49)
T ss_pred eeEEcccCCCeEEEehh
Confidence 35678999999887643
No 83
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.60 E-value=67 Score=33.09 Aligned_cols=45 Identities=16% Similarity=0.096 Sum_probs=22.5
Q ss_pred ccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCC
Q 047746 96 SCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLH 146 (247)
Q Consensus 96 ~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~h 146 (247)
.|..||..|.... -..-+..|...+-..|. .|| +.-.....|+.|
T Consensus 437 ~C~~Cg~v~~Cp~-Cd~~lt~H~~~~~L~CH--~Cg---~~~~~p~~Cp~C 481 (730)
T COG1198 437 LCRDCGYIAECPN-CDSPLTLHKATGQLRCH--YCG---YQEPIPQSCPEC 481 (730)
T ss_pred ecccCCCcccCCC-CCcceEEecCCCeeEeC--CCC---CCCCCCCCCCCC
Confidence 4777776665432 12223344445566777 666 333333444444
No 84
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=24.48 E-value=24 Score=27.25 Aligned_cols=27 Identities=22% Similarity=0.170 Sum_probs=16.4
Q ss_pred CCCCCCCCcccccccCCCCCCCccccCCCC
Q 047746 167 PPQRPPDMRGGARFEQGYFAMPMFMEDDDI 196 (247)
Q Consensus 167 Py~~~~~~~cg~~f~~~~l~~P~~~~~c~~ 196 (247)
|++| ++||+.|..+..-.---|.+||-
T Consensus 2 pH~C---trCG~vf~~g~~~il~GCp~CG~ 28 (112)
T COG3364 2 PHQC---TRCGEVFDDGSEEILSGCPKCGC 28 (112)
T ss_pred Ccee---cccccccccccHHHHccCccccc
Confidence 5555 89999998863111124666654
No 85
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=24.04 E-value=34 Score=30.63 Aligned_cols=31 Identities=16% Similarity=0.367 Sum_probs=21.3
Q ss_pred ccccCcCCcccCCCccccccccccCCCcccccc
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKR 126 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~ 126 (247)
-|.|+.||-..... .+.+|+-.-++ .-|.|-
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~fSCI 33 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AYFSCI 33 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-CeeEEe
Confidence 38899999876655 46668766555 456666
No 86
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=23.70 E-value=1.7e+02 Score=29.47 Aligned_cols=131 Identities=14% Similarity=0.132 Sum_probs=69.4
Q ss_pred cccccCcCCcccCCCcccccccc-ccCCCccccccccccCc-ccccccCCCCCCCCCCC----c-CchhHHHH----hhh
Q 047746 93 RVFSCNYCRRKFYSSQALGGHQN-AHKRERTMAKRAMRMGI-FSDRYTSLASLPLHGSA----F-RSLGIKAH----AAM 161 (247)
Q Consensus 93 kpf~C~~Cgk~F~~~~~L~~H~r-~Htgekp~~C~~~~Cg~-~~k~F~~~s~L~~hgk~----F-~~~~L~~H----~ri 161 (247)
-+-.|--|+.....-++|..--+ -|. --|+|. .|+. .+-.|..+...++|.+. | -+..--.+ ...
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv--~cfkc~--~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvL 207 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHV--SCFKCK--SCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVL 207 (670)
T ss_pred CCccccchhhhhhccceeeeeccceee--eeeehh--hhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhh
Confidence 45578888888777777654322 122 357777 6764 44456677777777332 3 22211111 123
Q ss_pred cCCCCCCC--CCCCCcccccccCC---CC-CCCccccCCCCccccCCCceecCCCCCCCCccccCCCCCCCcc
Q 047746 162 HQGVVPPQ--RPPDMRGGARFEQG---YF-AMPMFMEDDDIDLFWPGSFRQVSEAVRGNPTLDFAQGSNGNFA 228 (247)
Q Consensus 162 HtgekPy~--~~~~~~cg~~f~~~---~l-~~P~~~~~c~~~f~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (247)
-.|.|-|- |+-|.+||--|..| || |--+=-.+|+-+-.- ..+..+..++..++.-...||.+.|+.
T Consensus 208 qag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~qa~~t-E~i~~~~rtst~Si~~~~~~Ss~Gsp~ 279 (670)
T KOG1044|consen 208 QAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQATKT-EEILKPGRTSTESIYSRPGSSTPGSPG 279 (670)
T ss_pred hccCcccCcchhhhhhhccccccchheeeccccccCCccccccch-hhcccCCCCCcccccCCCCCCCCCCCC
Confidence 34556553 77789999999987 34 311112334333222 233333444444554444566666654
No 87
>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=23.46 E-value=25 Score=28.90 Aligned_cols=29 Identities=21% Similarity=0.300 Sum_probs=23.7
Q ss_pred CcccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
..-|.|+.|+++|+...++. .-|.|. .||
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp--~Cg 135 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAME---------LNFTCP--RCG 135 (158)
T ss_pred CCeEECCCCCcEeeHHHHHH---------cCCcCC--CCC
Confidence 45699999999999988885 268898 776
No 88
>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=23.31 E-value=48 Score=20.04 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=16.1
Q ss_pred ccccCcCCcccCCCccccccccccCCCccccccccccC
Q 047746 94 VFSCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMG 131 (247)
Q Consensus 94 pf~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg 131 (247)
.|.|..||..+... +.|..|. .|+
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP--~Cg 25 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCP--ICG 25 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCc--CCC
Confidence 48899998754322 2467888 776
No 89
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=23.06 E-value=39 Score=21.60 Aligned_cols=31 Identities=10% Similarity=0.061 Sum_probs=20.1
Q ss_pred CCCCCCCCcccccccCCCCCCCccccCCCCcccc
Q 047746 167 PPQRPPDMRGGARFEQGYFAMPMFMEDDDIDLFW 200 (247)
Q Consensus 167 Py~~~~~~~cg~~f~~~~l~~P~~~~~c~~~f~~ 200 (247)
.|.| ..||+.|.-......+.|+.||..+.+
T Consensus 3 ~y~C---~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKC---ARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EEEC---CCCCCEEEECCCCCceECCCCCCeEEE
Confidence 4555 788888764322236789999876543
No 90
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=22.37 E-value=31 Score=21.85 Aligned_cols=15 Identities=27% Similarity=0.689 Sum_probs=10.0
Q ss_pred cccccCcCCcccCCC
Q 047746 93 RVFSCNYCRRKFYSS 107 (247)
Q Consensus 93 kpf~C~~Cgk~F~~~ 107 (247)
-+|.|..|++.|=..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 479999999999765
No 91
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=22.11 E-value=33 Score=21.79 Aligned_cols=13 Identities=23% Similarity=0.812 Sum_probs=10.6
Q ss_pred cccccCcCCcccC
Q 047746 93 RVFSCNYCRRKFY 105 (247)
Q Consensus 93 kpf~C~~Cgk~F~ 105 (247)
++-.|.+|++.|.
T Consensus 28 ~~~~CpYCg~~yv 40 (40)
T PF10276_consen 28 GPVVCPYCGTRYV 40 (40)
T ss_dssp CEEEETTTTEEEE
T ss_pred CeEECCCCCCEEC
Confidence 4679999999873
No 92
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=21.46 E-value=31 Score=34.32 Aligned_cols=28 Identities=21% Similarity=0.407 Sum_probs=23.5
Q ss_pred CcccccCcCCcccCCCccccccccccCC
Q 047746 92 PRVFSCNYCRRKFYSSQALGGHQNAHKR 119 (247)
Q Consensus 92 ekpf~C~~Cgk~F~~~~~L~~H~r~Htg 119 (247)
.++..|..||++|........||.+|-.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhh
Confidence 4578999999999999988888877754
No 93
>PHA00626 hypothetical protein
Probab=21.43 E-value=44 Score=22.98 Aligned_cols=15 Identities=13% Similarity=0.257 Sum_probs=12.5
Q ss_pred cccccCcCCcccCCC
Q 047746 93 RVFSCNYCRRKFYSS 107 (247)
Q Consensus 93 kpf~C~~Cgk~F~~~ 107 (247)
..|+|..||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 469999999988764
No 94
>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=21.32 E-value=72 Score=19.56 Aligned_cols=22 Identities=14% Similarity=0.042 Sum_probs=9.9
Q ss_pred CCcccccccCCCCCCCccccCC
Q 047746 173 DMRGGARFEQGYFAMPMFMEDD 194 (247)
Q Consensus 173 ~~~cg~~f~~~~l~~P~~~~~c 194 (247)
|.+|++.|...+|-.-|-+.-|
T Consensus 6 C~eC~~~f~dSyL~~~F~~~VC 27 (34)
T PF01286_consen 6 CDECGKPFMDSYLLNNFDLPVC 27 (34)
T ss_dssp -TTT--EES-SSCCCCTS-S--
T ss_pred HhHhCCHHHHHHHHHhCCcccc
Confidence 5899999998875433333333
No 95
>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=21.16 E-value=49 Score=18.93 Aligned_cols=11 Identities=27% Similarity=0.479 Sum_probs=9.0
Q ss_pred cccCcCCcccC
Q 047746 95 FSCNYCRRKFY 105 (247)
Q Consensus 95 f~C~~Cgk~F~ 105 (247)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 47999999885
No 96
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=20.76 E-value=47 Score=23.26 Aligned_cols=48 Identities=17% Similarity=0.145 Sum_probs=31.5
Q ss_pred CCCCCCCCCCcccccccC-CC--CCCC-ccccCCCCccccCCCceecCCCCC
Q 047746 165 VVPPQRPPDMRGGARFEQ-GY--FAMP-MFMEDDDIDLFWPGSFRQVSEAVR 212 (247)
Q Consensus 165 ekPy~~~~~~~cg~~f~~-~~--l~~P-~~~~~c~~~f~~~~s~~~~~~~~~ 212 (247)
+.+..||-|..-.-+|-. .+ +..| |+|..|..-+..-|.||.++-+++
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg 54 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGG 54 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCC
Confidence 345556444444445543 11 3345 799999999999999999876655
No 97
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.16 E-value=85 Score=30.69 Aligned_cols=47 Identities=19% Similarity=0.232 Sum_probs=32.0
Q ss_pred ccCcCCcccCCCccccccccccCCCccccccccccCcccccccCCCCCCCCCC
Q 047746 96 SCNYCRRKFYSSQALGGHQNAHKRERTMAKRAMRMGIFSDRYTSLASLPLHGS 148 (247)
Q Consensus 96 ~C~~Cgk~F~~~~~L~~H~r~Htgekp~~C~~~~Cg~~~k~F~~~s~L~~hgk 148 (247)
.|..||....... -...+..|..+....|. .|| ....-...||.||.
T Consensus 215 ~C~~Cg~~~~C~~-C~~~l~~h~~~~~l~Ch--~Cg---~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 215 LCRSCGYILCCPN-CDVSLTYHKKEGKLRCH--YCG---YQEPIPKTCPQCGS 261 (505)
T ss_pred EhhhCcCccCCCC-CCCceEEecCCCeEEcC--CCc---CcCCCCCCCCCCCC
Confidence 6888887765542 34456667777778888 888 56555667788854
Done!