Query 043322
Match_columns 187
No_of_seqs 348 out of 1556
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 03:53:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043322.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043322hhsearch_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 99.4 1.8E-13 3.8E-18 113.1 3.7 86 40-125 136-239 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.3 7.2E-13 1.6E-17 109.5 1.8 82 40-123 167-265 (279)
3 KOG1074 Transcriptional repres 98.7 8.4E-09 1.8E-13 96.0 1.9 76 43-127 614-694 (958)
4 KOG3623 Homeobox transcription 98.5 1E-07 2.2E-12 87.9 3.3 34 57-90 890-923 (1007)
5 KOG3623 Homeobox transcription 98.4 3.6E-08 7.8E-13 90.8 -1.4 72 39-122 899-971 (1007)
6 KOG3576 Ovo and related transc 98.3 7.1E-08 1.5E-12 77.2 -0.7 59 32-90 115-174 (267)
7 KOG3576 Ovo and related transc 98.2 1.6E-07 3.6E-12 75.1 -0.5 63 59-121 115-193 (267)
8 PHA00616 hypothetical protein 98.2 5.2E-07 1.1E-11 55.2 1.2 30 61-90 1-30 (44)
9 PF13465 zf-H2C2_2: Zinc-finge 98.1 9.9E-08 2.1E-12 52.1 -3.3 24 50-73 2-26 (26)
10 PHA02768 hypothetical protein; 97.9 4.6E-06 9.9E-11 53.5 1.8 25 61-85 5-29 (55)
11 KOG1074 Transcriptional repres 97.9 2.4E-06 5.2E-11 80.0 0.6 68 61-140 879-946 (958)
12 PF00096 zf-C2H2: Zinc finger, 97.7 1.3E-05 2.8E-10 42.0 1.3 23 62-84 1-23 (23)
13 PHA00733 hypothetical protein 97.6 5.5E-05 1.2E-09 56.9 2.9 56 55-124 67-122 (128)
14 PF13912 zf-C2H2_6: C2H2-type 97.4 6.5E-05 1.4E-09 40.8 1.2 25 61-85 1-25 (27)
15 KOG3608 Zn finger proteins [Ge 97.4 4.8E-05 1E-09 65.6 0.7 124 41-166 186-338 (467)
16 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00015 3.2E-09 37.7 1.5 23 62-84 1-23 (24)
17 KOG3608 Zn finger proteins [Ge 97.0 0.00025 5.5E-09 61.2 1.4 81 43-124 272-376 (467)
18 PHA02768 hypothetical protein; 97.0 7.3E-05 1.6E-09 47.9 -1.9 38 39-78 10-48 (55)
19 smart00355 ZnF_C2H2 zinc finge 96.9 0.00068 1.5E-08 35.5 1.7 24 62-85 1-24 (26)
20 PF09237 GAGA: GAGA factor; I 96.5 0.0021 4.6E-08 40.4 2.2 34 56-89 19-52 (54)
21 PF13465 zf-H2C2_2: Zinc-finge 96.4 0.00092 2E-08 36.2 0.3 23 116-159 1-24 (26)
22 PHA00733 hypothetical protein 96.3 0.0014 3E-08 49.3 0.8 45 39-85 78-123 (128)
23 PHA00732 hypothetical protein 95.7 0.0061 1.3E-07 42.0 1.7 25 61-85 1-26 (79)
24 PF12874 zf-met: Zinc-finger o 95.6 0.0048 1E-07 32.6 0.8 23 62-84 1-23 (25)
25 KOG3993 Transcription factor ( 95.2 0.01 2.2E-07 52.5 1.7 93 32-125 266-380 (500)
26 PLN03086 PRLI-interacting fact 95.0 0.013 2.8E-07 54.1 1.8 55 58-129 450-504 (567)
27 PF12171 zf-C2H2_jaz: Zinc-fin 94.6 0.012 2.7E-07 31.8 0.4 22 62-83 2-23 (27)
28 PF13913 zf-C2HC_2: zinc-finge 94.4 0.025 5.4E-07 30.3 1.4 21 62-83 3-23 (25)
29 PF13909 zf-H2C2_5: C2H2-type 93.9 0.031 6.7E-07 29.2 1.1 23 62-85 1-23 (24)
30 PHA00732 hypothetical protein 93.0 0.024 5.3E-07 39.0 -0.3 41 39-85 6-48 (79)
31 smart00451 ZnF_U1 U1-like zinc 92.0 0.086 1.9E-06 29.8 1.2 23 61-83 3-25 (35)
32 COG5189 SFP1 Putative transcri 90.3 0.3 6.5E-06 42.1 3.3 25 58-82 346-372 (423)
33 PHA00616 hypothetical protein 90.2 0.1 2.2E-06 31.9 0.3 18 108-125 8-25 (44)
34 COG5189 SFP1 Putative transcri 89.6 0.1 2.3E-06 44.8 0.1 23 59-81 396-418 (423)
35 PF12756 zf-C2H2_2: C2H2 type 89.2 0.24 5.3E-06 34.1 1.7 24 61-84 50-73 (100)
36 PLN03086 PRLI-interacting fact 86.8 0.29 6.2E-06 45.4 1.0 47 41-92 460-507 (567)
37 PRK04860 hypothetical protein; 86.6 0.42 9.1E-06 37.3 1.7 27 60-90 118-144 (160)
38 KOG3993 Transcription factor ( 86.4 0.21 4.5E-06 44.5 -0.1 25 61-85 356-380 (500)
39 PF05605 zf-Di19: Drought indu 84.5 0.88 1.9E-05 28.6 2.2 26 61-87 2-28 (54)
40 COG5048 FOG: Zn-finger [Genera 84.1 0.68 1.5E-05 39.5 2.0 49 42-90 297-352 (467)
41 PF12756 zf-C2H2_2: C2H2 type 81.9 0.58 1.2E-05 32.2 0.6 62 63-124 1-73 (100)
42 COG4049 Uncharacterized protei 81.7 0.56 1.2E-05 30.2 0.4 29 55-83 11-39 (65)
43 PRK04860 hypothetical protein; 78.6 0.3 6.6E-06 38.0 -1.9 30 46-75 127-157 (160)
44 PF02892 zf-BED: BED zinc fing 70.8 3.3 7.1E-05 24.6 1.7 25 58-82 13-41 (45)
45 smart00614 ZnF_BED BED zinc fi 69.8 3.5 7.6E-05 25.4 1.7 25 61-85 18-48 (50)
46 PF05443 ROS_MUCR: ROS/MUCR tr 64.8 3.3 7.3E-05 31.2 1.1 26 61-89 72-97 (132)
47 COG4957 Predicted transcriptio 57.8 5 0.00011 30.4 0.9 25 62-89 77-101 (148)
48 PF11931 DUF3449: Domain of un 54.9 4.2 9.1E-05 32.8 0.1 45 35-81 77-122 (196)
49 smart00734 ZnF_Rad18 Rad18-lik 53.8 9.2 0.0002 20.4 1.3 20 62-82 2-21 (26)
50 KOG2636 Splicing factor 3a, su 53.5 14 0.00031 33.4 3.1 29 54-82 394-423 (497)
51 KOG4167 Predicted DNA-binding 49.9 3.6 7.8E-05 39.3 -1.1 25 61-85 792-816 (907)
52 COG5048 FOG: Zn-finger [Genera 47.8 8.8 0.00019 32.6 1.0 56 60-125 288-347 (467)
53 PF04959 ARS2: Arsenite-resist 46.5 5.5 0.00012 32.5 -0.5 27 58-84 74-100 (214)
54 smart00154 ZnF_AN1 AN1-like Zi 42.4 11 0.00025 22.1 0.6 15 61-75 12-26 (39)
55 PF12013 DUF3505: Protein of u 42.4 16 0.00036 26.0 1.6 25 62-86 81-109 (109)
56 smart00834 CxxC_CXXC_SSSS Puta 41.2 11 0.00024 21.6 0.4 15 61-75 5-19 (41)
57 KOG2893 Zn finger protein [Gen 39.6 7.8 0.00017 32.3 -0.6 42 42-86 18-60 (341)
58 PF07754 DUF1610: Domain of un 38.2 14 0.00031 19.5 0.5 10 60-69 15-24 (24)
59 PF09723 Zn-ribbon_8: Zinc rib 35.8 15 0.00032 21.8 0.4 16 61-76 5-20 (42)
60 KOG0717 Molecular chaperone (D 34.3 20 0.00043 32.6 1.1 22 62-83 293-314 (508)
61 PF09986 DUF2225: Uncharacteri 34.2 9.2 0.0002 31.0 -1.0 25 59-83 3-27 (214)
62 PF10571 UPF0547: Uncharacteri 34.0 21 0.00045 19.1 0.7 11 62-72 15-25 (26)
63 PF10276 zf-CHCC: Zinc-finger 33.4 17 0.00037 21.6 0.4 13 60-72 28-40 (40)
64 PF01428 zf-AN1: AN1-like Zinc 33.2 15 0.00032 21.8 0.1 16 60-75 12-27 (43)
65 TIGR02605 CxxC_CxxC_SSSS putat 32.7 18 0.00039 22.1 0.4 14 61-74 5-18 (52)
66 KOG3408 U1-like Zn-finger-cont 32.1 24 0.00051 26.3 1.0 27 57-83 53-79 (129)
67 PF08790 zf-LYAR: LYAR-type C2 31.9 17 0.00038 19.9 0.2 20 62-82 1-20 (28)
68 PF09845 DUF2072: Zn-ribbon co 31.8 23 0.0005 26.7 0.9 15 61-75 1-15 (131)
69 KOG2482 Predicted C2H2-type Zn 31.7 25 0.00054 30.9 1.2 23 61-83 195-217 (423)
70 KOG1146 Homeobox protein [Gene 30.4 32 0.0007 35.2 1.9 52 32-83 434-487 (1406)
71 PLN02294 cytochrome c oxidase 30.2 31 0.00068 27.2 1.5 15 59-73 139-153 (174)
72 KOG2785 C2H2-type Zn-finger pr 29.9 58 0.0012 28.9 3.2 64 60-123 165-242 (390)
73 KOG2071 mRNA cleavage and poly 28.6 34 0.00073 32.0 1.6 29 58-86 415-443 (579)
74 PHA00626 hypothetical protein 28.0 27 0.00058 22.5 0.6 16 59-74 21-36 (59)
75 PF09538 FYDLN_acid: Protein o 27.9 24 0.00052 25.6 0.4 14 62-75 10-23 (108)
76 PRK00464 nrdR transcriptional 26.1 25 0.00053 27.2 0.2 18 61-78 28-45 (154)
77 COG1592 Rubrerythrin [Energy p 26.0 46 0.00099 26.1 1.7 23 33-68 134-156 (166)
78 PF13878 zf-C2H2_3: zinc-finge 25.9 51 0.0011 19.4 1.6 24 62-85 14-39 (41)
79 PF04423 Rad50_zn_hook: Rad50 25.5 25 0.00055 21.8 0.2 11 63-73 22-32 (54)
80 COG5188 PRP9 Splicing factor 3 25.2 45 0.00096 29.5 1.6 29 54-82 367-396 (470)
81 PF14353 CpXC: CpXC protein 24.5 17 0.00036 26.7 -1.0 22 61-82 38-59 (128)
82 cd00924 Cyt_c_Oxidase_Vb Cytoc 23.7 36 0.00078 24.3 0.7 17 55-72 74-90 (97)
83 PF13451 zf-trcl: Probable zin 22.9 35 0.00075 21.3 0.4 17 59-75 2-18 (49)
84 COG4391 Uncharacterized protei 22.4 33 0.00071 22.4 0.3 13 60-72 47-59 (62)
85 PF10013 DUF2256: Uncharacteri 20.5 45 0.00097 20.1 0.5 15 63-77 10-24 (42)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.39 E-value=1.8e-13 Score=113.14 Aligned_cols=86 Identities=26% Similarity=0.389 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCCC-CCCC---CCCccccCcccccccCchhHHHHHhhhcC-------CCCCcccccc-hhhHhhcCC-C
Q 043322 40 GGNSLSTSRDPDSP-ARPT---TAKVFSCNFCMRKFFSSQALGGHQNAHKR-------ERGAAKRYQS-QRMMTMMGL-P 106 (187)
Q Consensus 40 ~~~sF~~~~~L~~h-~~Ht---gekpf~C~~Cgk~F~~~~~L~~H~~~H~g-------ekp~~f~~~s-~l~r~Htge-p 106 (187)
.|+.+++.++|.+| ++|- ..+.+.|.+|+|.|.+..+|..|+++|+- .|.|...|.. -|+|+|||| |
T Consensus 136 Cgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP 215 (279)
T KOG2462|consen 136 CGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKP 215 (279)
T ss_pred cccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCC
Confidence 55677788888777 4553 35678888888888888888888888872 1222222222 237888888 7
Q ss_pred C-----CCCCCCchhhHhhhccCC
Q 043322 107 V-----HTNMVRSLGVRAHSLVHK 125 (187)
Q Consensus 107 ~-----gk~F~~~s~L~~H~riH~ 125 (187)
| +|+|..+++|+.||.+|.
T Consensus 216 F~C~hC~kAFADRSNLRAHmQTHS 239 (279)
T KOG2462|consen 216 FSCPHCGKAFADRSNLRAHMQTHS 239 (279)
T ss_pred ccCCcccchhcchHHHHHHHHhhc
Confidence 7 788888888888888873
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.30 E-value=7.2e-13 Score=109.53 Aligned_cols=82 Identities=20% Similarity=0.162 Sum_probs=66.6
Q ss_pred CCCCCCCCCCCCCC-CCCCCCCccccCcccccccCchhHHHHHhhhcCCCCC-------cccccchh---hHhhcCC-CC
Q 043322 40 GGNSLSTSRDPDSP-ARPTTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGA-------AKRYQSQR---MMTMMGL-PV 107 (187)
Q Consensus 40 ~~~sF~~~~~L~~h-~~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~-------~f~~~s~l---~r~Htge-p~ 107 (187)
.++.|..-..|..| ++|+ -+++|.+|||.|....-|++|+|+|+||||| +|..+++| |++|.+. +|
T Consensus 167 C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~ 244 (279)
T KOG2462|consen 167 CGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKH 244 (279)
T ss_pred CCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccc
Confidence 34455555566777 6776 6899999999999999999999999999999 66666665 8899887 77
Q ss_pred -----CCCCCCchhhHhhhcc
Q 043322 108 -----HTNMVRSLGVRAHSLV 123 (187)
Q Consensus 108 -----gk~F~~~s~L~~H~ri 123 (187)
+|.|...+-|.+|...
T Consensus 245 qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 245 QCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cCcchhhHHHHHHHHHHhhhh
Confidence 9999999999999743
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.66 E-value=8.4e-09 Score=96.00 Aligned_cols=76 Identities=24% Similarity=0.357 Sum_probs=59.6
Q ss_pred CCCCCCCCCCC-CCCCCCCccccCcccccccCchhHHHHHhhhcCCCCCcccccchhhHhhcCCCC----CCCCCCchhh
Q 043322 43 SLSTSRDPDSP-ARPTTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGAAKRYQSQRMMTMMGLPV----HTNMVRSLGV 117 (187)
Q Consensus 43 sF~~~~~L~~h-~~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~~f~~~s~l~r~Htgep~----gk~F~~~s~L 117 (187)
-.+..+.|+.| ++|+|||||+|.+||++|.++.+|+.|+.+|...-|+ |.... -|+ -+.|...-.|
T Consensus 614 VlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~--R~q~S-------cP~~~ic~~kftn~V~l 684 (958)
T KOG1074|consen 614 VLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA--RVQFS-------CPSTFICQKKFTNAVTL 684 (958)
T ss_pred cccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccc--ccccc-------CCchhhhcccccccccc
Confidence 34566778888 9999999999999999999999999999999865554 11100 021 4668888899
Q ss_pred HhhhccCCCC
Q 043322 118 RAHSLVHKPS 127 (187)
Q Consensus 118 ~~H~riH~p~ 127 (187)
..|+++|.+.
T Consensus 685 pQhIriH~~~ 694 (958)
T KOG1074|consen 685 PQHIRIHLGG 694 (958)
T ss_pred cceEEeecCC
Confidence 9999999744
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.46 E-value=1e-07 Score=87.85 Aligned_cols=34 Identities=24% Similarity=0.530 Sum_probs=28.7
Q ss_pred CCCCccccCcccccccCchhHHHHHhhhcCCCCC
Q 043322 57 TTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGA 90 (187)
Q Consensus 57 tgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~ 90 (187)
+.+.+|.|+.|.|.|...+.|.+|.--|+|.|||
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPy 923 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPY 923 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCc
Confidence 4456888999998888888888888888888887
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.39 E-value=3.6e-08 Score=90.81 Aligned_cols=72 Identities=13% Similarity=0.176 Sum_probs=61.7
Q ss_pred cCCCCCCCCCCCCCCC-CCCCCCccccCcccccccCchhHHHHHhhhcCCCCCcccccchhhHhhcCCCCCCCCCCchhh
Q 043322 39 LGGNSLSTSRDPDSPA-RPTTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGAAKRYQSQRMMTMMGLPVHTNMVRSLGV 117 (187)
Q Consensus 39 ~~~~sF~~~~~L~~h~-~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~~f~~~s~l~r~Htgep~gk~F~~~s~L 117 (187)
++++.|...+.|.+|+ -|+|.|||+|.+|.|+|..+..|..|+|.|.|||||.+.. .+|.|..+...
T Consensus 899 qCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdK------------ClKRFSHSGSY 966 (1007)
T KOG3623|consen 899 QCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDK------------CLKRFSHSGSY 966 (1007)
T ss_pred HHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhh------------hhhhcccccch
Confidence 3566898889999996 5999999999999999999999999999999999983221 26788888889
Q ss_pred Hhhhc
Q 043322 118 RAHSL 122 (187)
Q Consensus 118 ~~H~r 122 (187)
.+||.
T Consensus 967 SQHMN 971 (1007)
T KOG3623|consen 967 SQHMN 971 (1007)
T ss_pred Hhhhc
Confidence 99983
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.33 E-value=7.1e-08 Score=77.19 Aligned_cols=59 Identities=19% Similarity=0.298 Sum_probs=38.3
Q ss_pred CcceeeccCCCCCCCCCCCCCC-CCCCCCCccccCcccccccCchhHHHHHhhhcCCCCC
Q 043322 32 GEWLNLKLGGNSLSTSRDPDSP-ARPTTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGA 90 (187)
Q Consensus 32 ~~~l~l~~~~~sF~~~~~L~~h-~~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~ 90 (187)
.+-+.-.++++.|....-|++| +.|...|.|-|..|||.|...-.|.+|.|+|+|-|||
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpy 174 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPY 174 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCcccc
Confidence 3344445566666665556666 4566666677777777777777777777777777776
No 7
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.25 E-value=1.6e-07 Score=75.15 Aligned_cols=63 Identities=19% Similarity=0.358 Sum_probs=41.2
Q ss_pred CCccccCcccccccCchhHHHHHhhhcCCCCC-------ccccc---chhhHhhcCC-CC-----CCCCCCchhhHhhh
Q 043322 59 AKVFSCNFCMRKFFSSQALGGHQNAHKRERGA-------AKRYQ---SQRMMTMMGL-PV-----HTNMVRSLGVRAHS 121 (187)
Q Consensus 59 ekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~-------~f~~~---s~l~r~Htge-p~-----gk~F~~~s~L~~H~ 121 (187)
...|.|.+|+|+|.-..-|.+|++.|..-|.| .|... ..++|+|+|- || +|+|++...|..|.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 45699999999999999999999999865544 11111 1124555555 55 55555555555553
No 8
>PHA00616 hypothetical protein
Probab=98.20 E-value=5.2e-07 Score=55.16 Aligned_cols=30 Identities=13% Similarity=0.253 Sum_probs=28.9
Q ss_pred ccccCcccccccCchhHHHHHhhhcCCCCC
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNAHKRERGA 90 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~H~gekp~ 90 (187)
||+|..||+.|...+.|..|++.|+|++++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~ 30 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKL 30 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcc
Confidence 699999999999999999999999999987
No 9
>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=98.09 E-value=9.9e-08 Score=52.11 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=19.9
Q ss_pred CCCC-CCCCCCCccccCcccccccC
Q 043322 50 PDSP-ARPTTAKVFSCNFCMRKFFS 73 (187)
Q Consensus 50 L~~h-~~Htgekpf~C~~Cgk~F~~ 73 (187)
|..| ++|++++||.|++|++.|.+
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 3445 67999999999999999964
No 10
>PHA02768 hypothetical protein; Provisional
Probab=97.94 E-value=4.6e-06 Score=53.45 Aligned_cols=25 Identities=16% Similarity=0.491 Sum_probs=23.8
Q ss_pred ccccCcccccccCchhHHHHHhhhc
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNAHK 85 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~H~ 85 (187)
-|+|+.||+.|...++|..|+++|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 4899999999999999999999998
No 11
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.94 E-value=2.4e-06 Score=80.02 Aligned_cols=68 Identities=19% Similarity=0.200 Sum_probs=52.1
Q ss_pred ccccCcccccccCchhHHHHHhhhcCCCCCcccccchhhHhhcCCCCCCCCCCchhhHhhhccCCCCCCCCCCccCCCCC
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNAHKRERGAAKRYQSQRMMTMMGLPVHTNMVRSLGVRAHSLVHKPSRDGAGVGARFNDA 140 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~H~gekp~~f~~~s~l~r~Htgep~gk~F~~~s~L~~H~riH~p~~~~~~~~~~f~~~ 140 (187)
...|..||+.|.++.+|..|+++|+++|||...+ .++.|..+..|+.||.+|.-.....+.|.+-..+
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~f------------C~~aFttrgnLKvHMgtH~w~q~~srrG~~~~~~ 946 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHF------------CEEAFTTRGNLKVHMGTHMWVQPPSRRGPSPFIG 946 (958)
T ss_pred hhhhccchhcccchHHHHHhhhcCCCCCCccchh------------hhhhhhhhhhhhhhhccccccCCCccCCCCcccC
Confidence 3679999999999999999999999999984333 2678999999999999996443333335554433
No 12
>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=97.75 E-value=1.3e-05 Score=41.96 Aligned_cols=23 Identities=30% Similarity=0.675 Sum_probs=21.5
Q ss_pred cccCcccccccCchhHHHHHhhh
Q 043322 62 FSCNFCMRKFFSSQALGGHQNAH 84 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~~H 84 (187)
|.|+.|++.|.+...|..|++.|
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 78999999999999999999875
No 13
>PHA00733 hypothetical protein
Probab=97.57 E-value=5.5e-05 Score=56.86 Aligned_cols=56 Identities=14% Similarity=0.194 Sum_probs=39.2
Q ss_pred CCCCCCccccCcccccccCchhHHHHHhhhcCCCCCcccccchhhHhhcCCCCCCCCCCchhhHhhhccC
Q 043322 55 RPTTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGAAKRYQSQRMMTMMGLPVHTNMVRSLGVRAHSLVH 124 (187)
Q Consensus 55 ~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~~f~~~s~l~r~Htgep~gk~F~~~s~L~~H~riH 124 (187)
.+.+.+||.|+.|++.|.+...|..|+++|. .+|.. ...++.|.....|..|++..
T Consensus 67 ~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~--~~~~C------------~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 67 TSKAVSPYVCPLCLMPFSSSVSLKQHIRYTE--HSKVC------------PVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred ccCCCCCccCCCCCCcCCCHHHHHHHHhcCC--cCccC------------CCCCCccCCHHHHHHHHHHh
Confidence 4455788888888888888888888887652 22210 01278888888888887543
No 14
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.42 E-value=6.5e-05 Score=40.80 Aligned_cols=25 Identities=36% Similarity=0.630 Sum_probs=23.4
Q ss_pred ccccCcccccccCchhHHHHHhhhc
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNAHK 85 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~H~ 85 (187)
||.|..|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6899999999999999999998875
No 15
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=97.39 E-value=4.8e-05 Score=65.57 Aligned_cols=124 Identities=16% Similarity=0.195 Sum_probs=78.7
Q ss_pred CCCCCCCCCCCCC-CCCCCCCccccCcccccccCchhHHHHHhhhc--CCCCC-----ccccc-----chhhHhhcCC--
Q 043322 41 GNSLSTSRDPDSP-ARPTTAKVFSCNFCMRKFFSSQALGGHQNAHK--RERGA-----AKRYQ-----SQRMMTMMGL-- 105 (187)
Q Consensus 41 ~~sF~~~~~L~~h-~~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~--gekp~-----~f~~~-----s~l~r~Htge-- 105 (187)
-+.|..++.|+.| +.|+++|...|+.||.-|.+...|-.|.+..+ ...+| .+++. ..+++.|..-
T Consensus 186 t~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~yk 265 (467)
T KOG3608|consen 186 TKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYK 265 (467)
T ss_pred hhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhccc
Confidence 3478888899988 88999999999999999999999999987554 23456 12221 1124444332
Q ss_pred -CC-CCCCCCchhhHhhhcc-C---CCCCCCCCCccCCCCC-----CCCCCCCCCcccccc--c-CCCcCCCCcc
Q 043322 106 -PV-HTNMVRSLGVRAHSLV-H---KPSRDGAGVGARFNDA-----DTGFGMAWTPYVLEE--A-TDVMWPGSFR 166 (187)
Q Consensus 106 -p~-gk~F~~~s~L~~H~ri-H---~p~~~~~~~~~~f~~~-----~~~~~~~~~p~~~~~--~-~~~~wp~s~~ 166 (187)
|. .......+.|..|++. | +|.+|.. |..+|..- +..+|. ..-|.|+- + -+++|--+++
T Consensus 266 CplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~-Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~ 338 (467)
T KOG3608|consen 266 CPLCDMTCSSASSLTTHIRYRHSKDKPFKCDE-CDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMR 338 (467)
T ss_pred ccccccCCCChHHHHHHHHhhhccCCCccccc-hhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHH
Confidence 33 6677788889999876 3 3445532 34443322 223444 44577775 2 2556654443
No 16
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.28 E-value=0.00015 Score=37.67 Aligned_cols=23 Identities=35% Similarity=0.722 Sum_probs=19.6
Q ss_pred cccCcccccccCchhHHHHHhhh
Q 043322 62 FSCNFCMRKFFSSQALGGHQNAH 84 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~~H 84 (187)
|.|++|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 68999999999999999999876
No 17
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=97.04 E-value=0.00025 Score=61.22 Aligned_cols=81 Identities=19% Similarity=0.260 Sum_probs=59.9
Q ss_pred CCCCCCCCCCC-C-CCCCCCccccCcccccccCchhHHHHHhhhcCCCCC---------cccccchh---hH-hhcCC--
Q 043322 43 SLSTSRDPDSP-A-RPTTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGA---------AKRYQSQR---MM-TMMGL-- 105 (187)
Q Consensus 43 sF~~~~~L~~h-~-~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~---------~f~~~s~l---~r-~Htge-- 105 (187)
+....++|..| + .|...|||+|+.|.+.|.+.+.|.+|..+|+ +..| .+++..++ ++ .|-|.
T Consensus 272 tc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np 350 (467)
T KOG3608|consen 272 TCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNP 350 (467)
T ss_pred CCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCC
Confidence 55566778888 3 4888999999999999999999999999998 3334 33333222 33 34454
Q ss_pred -CC-----CCCCCCchhhHhhhc-cC
Q 043322 106 -PV-----HTNMVRSLGVRAHSL-VH 124 (187)
Q Consensus 106 -p~-----gk~F~~~s~L~~H~r-iH 124 (187)
+| .+.|++-.+|..|.+ .|
T Consensus 351 ~~Y~CH~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 351 ILYACHCCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred CceeeecchhhhccchhHHHHHHHhh
Confidence 45 889999999999964 44
No 18
>PHA02768 hypothetical protein; Provisional
Probab=96.96 E-value=7.3e-05 Score=47.91 Aligned_cols=38 Identities=8% Similarity=0.068 Sum_probs=32.9
Q ss_pred cCCCCCCCCCCCCCC-CCCCCCCccccCcccccccCchhHH
Q 043322 39 LGGNSLSTSRDPDSP-ARPTTAKVFSCNFCMRKFFSSQALG 78 (187)
Q Consensus 39 ~~~~sF~~~~~L~~h-~~Htgekpf~C~~Cgk~F~~~~~L~ 78 (187)
..|+.|+...+|..| ++|+ ++|+|..|+|.|...+.|.
T Consensus 10 ~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 10 ICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred hhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 468899999999988 6888 7999999999999877664
No 19
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.87 E-value=0.00068 Score=35.45 Aligned_cols=24 Identities=33% Similarity=0.591 Sum_probs=22.0
Q ss_pred cccCcccccccCchhHHHHHhhhc
Q 043322 62 FSCNFCMRKFFSSQALGGHQNAHK 85 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~~H~ 85 (187)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 679999999999999999998775
No 20
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.49 E-value=0.0021 Score=40.42 Aligned_cols=34 Identities=15% Similarity=0.259 Sum_probs=24.5
Q ss_pred CCCCCccccCcccccccCchhHHHHHhhhcCCCC
Q 043322 56 PTTAKVFSCNFCMRKFFSSQALGGHQNAHKRERG 89 (187)
Q Consensus 56 Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp 89 (187)
+..+.|-.|++|+..+.++.+|++|+.++.+.||
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 4567899999999999999999999988777665
No 21
>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=96.42 E-value=0.00092 Score=36.19 Aligned_cols=23 Identities=22% Similarity=0.300 Sum_probs=18.3
Q ss_pred hhHhhhccCCCCCCCCCCccCCCCCCCCCCCCCCcccccc-cCCC
Q 043322 116 GVRAHSLVHKPSRDGAGVGARFNDADTGFGMAWTPYVLEE-ATDV 159 (187)
Q Consensus 116 ~L~~H~riH~p~~~~~~~~~~f~~~~~~~~~~~~p~~~~~-~~~~ 159 (187)
+|..|+++| +|++||.|+. ++.|
T Consensus 1 ~l~~H~~~H---------------------~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 1 NLRRHMRTH---------------------TGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHH---------------------SSSSSEEESSSSEEE
T ss_pred CHHHHhhhc---------------------CCCCCCCCCCCcCee
Confidence 478899888 8889999998 4454
No 22
>PHA00733 hypothetical protein
Probab=96.32 E-value=0.0014 Score=49.25 Aligned_cols=45 Identities=16% Similarity=0.159 Sum_probs=37.0
Q ss_pred cCCCCCCCCCCCCCC-CCCCCCCccccCcccccccCchhHHHHHhhhc
Q 043322 39 LGGNSLSTSRDPDSP-ARPTTAKVFSCNFCMRKFFSSQALGGHQNAHK 85 (187)
Q Consensus 39 ~~~~sF~~~~~L~~h-~~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~ 85 (187)
..++.|.....|..| +.| +.+|.|..|++.|.....|..|+....
T Consensus 78 ~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 78 LCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 367789998888887 444 467999999999999999999987543
No 23
>PHA00732 hypothetical protein
Probab=95.70 E-value=0.0061 Score=42.01 Aligned_cols=25 Identities=28% Similarity=0.478 Sum_probs=19.2
Q ss_pred ccccCcccccccCchhHHHHHhh-hc
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNA-HK 85 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~-H~ 85 (187)
||.|..|++.|.+...|..|++. |.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC
Confidence 57788888888888888888763 54
No 24
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.64 E-value=0.0048 Score=32.59 Aligned_cols=23 Identities=30% Similarity=0.706 Sum_probs=20.8
Q ss_pred cccCcccccccCchhHHHHHhhh
Q 043322 62 FSCNFCMRKFFSSQALGGHQNAH 84 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~~H 84 (187)
|.|..|.+.|.+...|..|++.+
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 67999999999999999998754
No 25
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=95.17 E-value=0.01 Score=52.48 Aligned_cols=93 Identities=20% Similarity=0.265 Sum_probs=56.7
Q ss_pred CcceeeccCCCCCCCCCCCCCCCCC-CCCCccccCcccccccCchhHHHHHhhhcCCCCCc-------ccccch--h--h
Q 043322 32 GEWLNLKLGGNSLSTSRDPDSPARP-TTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGAA-------KRYQSQ--R--M 99 (187)
Q Consensus 32 ~~~l~l~~~~~sF~~~~~L~~h~~H-tgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~~-------f~~~s~--l--~ 99 (187)
|++++- |+.-.|...-.|..|+.- .-.--|+|++|+|.|....+|..|.|-|+-...-+ ...... . .
T Consensus 266 GdyiCq-LCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~e 344 (500)
T KOG3993|consen 266 GDYICQ-LCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQE 344 (500)
T ss_pred HHHHHH-HHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhh
Confidence 455442 223356555667777421 11124999999999999999999999997322111 111000 1 0
Q ss_pred HhhcCC-----CC-----CCCCCCchhhHhhhccCC
Q 043322 100 MTMMGL-----PV-----HTNMVRSLGVRAHSLVHK 125 (187)
Q Consensus 100 r~Htge-----p~-----gk~F~~~s~L~~H~riH~ 125 (187)
..-.|. -| +|.|.+..-|++|+.+|.
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 010111 12 999999999999999885
No 26
>PLN03086 PRLI-interacting factor K; Provisional
Probab=94.95 E-value=0.013 Score=54.07 Aligned_cols=55 Identities=13% Similarity=0.148 Sum_probs=35.8
Q ss_pred CCCccccCcccccccCchhHHHHHhhhcCCCCCcccccchhhHhhcCCCCCCCCCCchhhHhhhccCCCCCC
Q 043322 58 TAKVFSCNFCMRKFFSSQALGGHQNAHKRERGAAKRYQSQRMMTMMGLPVHTNMVRSLGVRAHSLVHKPSRD 129 (187)
Q Consensus 58 gekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~~f~~~s~l~r~Htgep~gk~F~~~s~L~~H~riH~p~~~ 129 (187)
.++.+.|+.|++.|. ...|..|+.+|+ +++.+. .|+.+ .+..|..|+.+|.|.+.
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-------------Cg~~~-~R~~L~~H~~thCp~Kp 504 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-------------CGVVL-EKEQMVQHQASTCPLRL 504 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-------------CCCCc-chhHHHhhhhccCCCCc
Confidence 345678999999996 577999998874 454221 13323 34667777777765543
No 27
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=94.56 E-value=0.012 Score=31.80 Aligned_cols=22 Identities=32% Similarity=0.629 Sum_probs=20.1
Q ss_pred cccCcccccccCchhHHHHHhh
Q 043322 62 FSCNFCMRKFFSSQALGGHQNA 83 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~~ 83 (187)
|.|..|++.|.+...+..|++.
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 7899999999999999999864
No 28
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.43 E-value=0.025 Score=30.28 Aligned_cols=21 Identities=33% Similarity=0.736 Sum_probs=17.6
Q ss_pred cccCcccccccCchhHHHHHhh
Q 043322 62 FSCNFCMRKFFSSQALGGHQNA 83 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~~ 83 (187)
..|+.||+.| ....|..|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 67789999864
No 29
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.91 E-value=0.031 Score=29.18 Aligned_cols=23 Identities=22% Similarity=0.468 Sum_probs=17.9
Q ss_pred cccCcccccccCchhHHHHHhhhc
Q 043322 62 FSCNFCMRKFFSSQALGGHQNAHK 85 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~~H~ 85 (187)
|.|+.|..... ...|..|++.|.
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 889999988754
No 30
>PHA00732 hypothetical protein
Probab=93.01 E-value=0.024 Score=38.99 Aligned_cols=41 Identities=20% Similarity=0.255 Sum_probs=31.3
Q ss_pred cCCCCCCCCCCCCCCC--CCCCCCccccCcccccccCchhHHHHHhhhc
Q 043322 39 LGGNSLSTSRDPDSPA--RPTTAKVFSCNFCMRKFFSSQALGGHQNAHK 85 (187)
Q Consensus 39 ~~~~sF~~~~~L~~h~--~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~ 85 (187)
..+..|.....|..|. .|. ++.|+.|++.|. .|..|.+++.
T Consensus 6 ~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 6 ICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 3577899999999884 355 468999999998 4778876544
No 31
>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=92.01 E-value=0.086 Score=29.82 Aligned_cols=23 Identities=22% Similarity=0.514 Sum_probs=20.4
Q ss_pred ccccCcccccccCchhHHHHHhh
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNA 83 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~ 83 (187)
+|.|.+|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999763
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=90.32 E-value=0.3 Score=42.08 Aligned_cols=25 Identities=24% Similarity=0.507 Sum_probs=22.4
Q ss_pred CCCccccCc--ccccccCchhHHHHHh
Q 043322 58 TAKVFSCNF--CMRKFFSSQALGGHQN 82 (187)
Q Consensus 58 gekpf~C~~--Cgk~F~~~~~L~~H~~ 82 (187)
++|||+|++ |.|++.....|+.|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhh
Confidence 469999998 9999999999999965
No 33
>PHA00616 hypothetical protein
Probab=90.18 E-value=0.1 Score=31.90 Aligned_cols=18 Identities=17% Similarity=0.015 Sum_probs=16.6
Q ss_pred CCCCCCchhhHhhhccCC
Q 043322 108 HTNMVRSLGVRAHSLVHK 125 (187)
Q Consensus 108 gk~F~~~s~L~~H~riH~ 125 (187)
|+.|..++.|..|++.|+
T Consensus 8 G~~F~~~s~l~~H~r~~h 25 (44)
T PHA00616 8 GGIFRKKKEVIEHLLSVH 25 (44)
T ss_pred hHHHhhHHHHHHHHHHhc
Confidence 889999999999999983
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=89.62 E-value=0.1 Score=44.82 Aligned_cols=23 Identities=22% Similarity=0.589 Sum_probs=21.0
Q ss_pred CCccccCcccccccCchhHHHHH
Q 043322 59 AKVFSCNFCMRKFFSSQALGGHQ 81 (187)
Q Consensus 59 ekpf~C~~Cgk~F~~~~~L~~H~ 81 (187)
.|||.|++|+|++.....|+.|.
T Consensus 396 ~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 396 DKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CCceeccccchhhccCccceecc
Confidence 48999999999999999999885
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=89.24 E-value=0.24 Score=34.10 Aligned_cols=24 Identities=33% Similarity=0.732 Sum_probs=21.3
Q ss_pred ccccCcccccccCchhHHHHHhhh
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNAH 84 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~H 84 (187)
.+.|..|++.|.+...|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 689999999999999999999864
No 36
>PLN03086 PRLI-interacting factor K; Provisional
Probab=86.80 E-value=0.29 Score=45.39 Aligned_cols=47 Identities=13% Similarity=0.173 Sum_probs=36.0
Q ss_pred CCCCCCCCCCCCC-CCCCCCCccccCcccccccCchhHHHHHhhhcCCCCCcc
Q 043322 41 GNSLSTSRDPDSP-ARPTTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGAAK 92 (187)
Q Consensus 41 ~~sF~~~~~L~~h-~~Htgekpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~~f 92 (187)
+..|. ...|..| .+|+ +++.|+ ||+.+ .+..|..|+.+|.+++++.+
T Consensus 460 gk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C 507 (567)
T PLN03086 460 GQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITC 507 (567)
T ss_pred CCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeC
Confidence 44564 4667777 4553 899999 99755 67899999999999999833
No 37
>PRK04860 hypothetical protein; Provisional
Probab=86.55 E-value=0.42 Score=37.25 Aligned_cols=27 Identities=15% Similarity=0.324 Sum_probs=23.7
Q ss_pred CccccCcccccccCchhHHHHHhhhcCCCCC
Q 043322 60 KVFSCNFCMRKFFSSQALGGHQNAHKRERGA 90 (187)
Q Consensus 60 kpf~C~~Cgk~F~~~~~L~~H~~~H~gekp~ 90 (187)
-+|.|. |++ ....+.+|.++|+++++|
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~Y 144 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVY 144 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccE
Confidence 479998 998 677789999999999998
No 38
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=86.35 E-value=0.21 Score=44.48 Aligned_cols=25 Identities=40% Similarity=0.717 Sum_probs=23.1
Q ss_pred ccccCcccccccCchhHHHHHhhhc
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNAHK 85 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~H~ 85 (187)
.|.|.+|+|+|.....|+.|+.+|.
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhhh
Confidence 4899999999999999999998875
No 39
>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=84.45 E-value=0.88 Score=28.59 Aligned_cols=26 Identities=35% Similarity=0.713 Sum_probs=20.0
Q ss_pred ccccCcccccccCchhHHHHHhh-hcCC
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNA-HKRE 87 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~-H~ge 87 (187)
.|.|++|++ -.+...|..|... |..+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSE 28 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCC
Confidence 489999999 5567889999664 5544
No 40
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=84.10 E-value=0.68 Score=39.51 Aligned_cols=49 Identities=29% Similarity=0.312 Sum_probs=40.5
Q ss_pred CCCCCCCCCCCC-C--CCCCC--CccccC--cccccccCchhHHHHHhhhcCCCCC
Q 043322 42 NSLSTSRDPDSP-A--RPTTA--KVFSCN--FCMRKFFSSQALGGHQNAHKRERGA 90 (187)
Q Consensus 42 ~sF~~~~~L~~h-~--~Htge--kpf~C~--~Cgk~F~~~~~L~~H~~~H~gekp~ 90 (187)
..|+....|..| + .|+++ +|+.|+ .|++.|.....+..|...|.+-+++
T Consensus 297 ~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (467)
T COG5048 297 ISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPA 352 (467)
T ss_pred CCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcc
Confidence 367777888877 5 68888 899999 7999999999999999888876654
No 41
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=81.92 E-value=0.58 Score=32.17 Aligned_cols=62 Identities=16% Similarity=0.199 Sum_probs=15.7
Q ss_pred ccCcccccccCchhHHHHHhh-hcCCCCC--cccccchh---h--HhhcCC--CC-CCCCCCchhhHhhhccC
Q 043322 63 SCNFCMRKFFSSQALGGHQNA-HKRERGA--AKRYQSQR---M--MTMMGL--PV-HTNMVRSLGVRAHSLVH 124 (187)
Q Consensus 63 ~C~~Cgk~F~~~~~L~~H~~~-H~gekp~--~f~~~s~l---~--r~Htge--p~-gk~F~~~s~L~~H~riH 124 (187)
+|..|+..|.+...|..|+.. |.-..+- .......+ . .+.... ++ ++.|.....|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 599999999999999999864 4322221 00011111 1 111101 33 88899999999999875
No 42
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=81.74 E-value=0.56 Score=30.15 Aligned_cols=29 Identities=17% Similarity=0.229 Sum_probs=25.6
Q ss_pred CCCCCCccccCcccccccCchhHHHHHhh
Q 043322 55 RPTTAKVFSCNFCMRKFFSSQALGGHQNA 83 (187)
Q Consensus 55 ~Htgekpf~C~~Cgk~F~~~~~L~~H~~~ 83 (187)
...||--+.|+-|+..|.......+|.+.
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 45678889999999999999999999874
No 43
>PRK04860 hypothetical protein; Provisional
Probab=78.57 E-value=0.3 Score=38.04 Aligned_cols=30 Identities=10% Similarity=0.135 Sum_probs=23.3
Q ss_pred CCCCCCCC-CCCCCCCccccCcccccccCch
Q 043322 46 TSRDPDSP-ARPTTAKVFSCNFCMRKFFSSQ 75 (187)
Q Consensus 46 ~~~~L~~h-~~Htgekpf~C~~Cgk~F~~~~ 75 (187)
....+.+| ++|+++++|.|..|++.|....
T Consensus 127 ~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 127 HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 34445567 7899999999999999887543
No 44
>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=70.80 E-value=3.3 Score=24.62 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=15.9
Q ss_pred CCCccccCcccccccCc----hhHHHHHh
Q 043322 58 TAKVFSCNFCMRKFFSS----QALGGHQN 82 (187)
Q Consensus 58 gekpf~C~~Cgk~F~~~----~~L~~H~~ 82 (187)
+.....|.+|++.+... +.|.+|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 34567899999988764 68888873
No 45
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=69.77 E-value=3.5 Score=25.37 Aligned_cols=25 Identities=28% Similarity=0.533 Sum_probs=19.0
Q ss_pred ccccCcccccccCc-----hhHHHHHh-hhc
Q 043322 61 VFSCNFCMRKFFSS-----QALGGHQN-AHK 85 (187)
Q Consensus 61 pf~C~~Cgk~F~~~-----~~L~~H~~-~H~ 85 (187)
.-.|.+|++.+... +.|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 35699999988765 58888887 554
No 46
>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=64.84 E-value=3.3 Score=31.23 Aligned_cols=26 Identities=27% Similarity=0.386 Sum_probs=16.4
Q ss_pred ccccCcccccccCchhHHHHHhhhcCCCC
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNAHKRERG 89 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~H~gekp 89 (187)
--.|-+|||.|.. |.+|.+.|.|-.|
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCCcccch---HHHHHHHccCCCH
Confidence 3579999999986 6999999976544
No 47
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=57.76 E-value=5 Score=30.43 Aligned_cols=25 Identities=28% Similarity=0.196 Sum_probs=20.8
Q ss_pred cccCcccccccCchhHHHHHhhhcCCCC
Q 043322 62 FSCNFCMRKFFSSQALGGHQNAHKRERG 89 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~~H~gekp 89 (187)
..|-+|||.|.+ |.+|..+|.|-.|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 469999999974 8999999987554
No 48
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=54.92 E-value=4.2 Score=32.77 Aligned_cols=45 Identities=20% Similarity=0.265 Sum_probs=0.0
Q ss_pred eeeccCCCCCCCCCCCCCCCCCCCCCccccCccccc-ccCchhHHHHH
Q 043322 35 LNLKLGGNSLSTSRDPDSPARPTTAKVFSCNFCMRK-FFSSQALGGHQ 81 (187)
Q Consensus 35 l~l~~~~~sF~~~~~L~~h~~Htgekpf~C~~Cgk~-F~~~~~L~~H~ 81 (187)
++|.|+-..---..-|.+ .|-=.+.|.|.+||-. |.-+.++.+|-
T Consensus 77 ~~lPLG~DGkPIPyWLYK--LhGL~~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 77 LNLPLGWDGKPIPYWLYK--LHGLGVEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp ------------------------------------------------
T ss_pred ccCCCCCCCCcccHHHHH--HhCCCCeeeeEeCCCcceecHHHHHHhc
Confidence 777777554433333332 2333467999999954 33455555553
No 49
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=53.82 E-value=9.2 Score=20.41 Aligned_cols=20 Identities=20% Similarity=0.674 Sum_probs=15.1
Q ss_pred cccCcccccccCchhHHHHHh
Q 043322 62 FSCNFCMRKFFSSQALGGHQN 82 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~ 82 (187)
..|+.|++.+ ....+..|.-
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999998 5566777764
No 50
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=53.50 E-value=14 Score=33.40 Aligned_cols=29 Identities=17% Similarity=0.320 Sum_probs=23.5
Q ss_pred CCCCCCCccccCccc-ccccCchhHHHHHh
Q 043322 54 ARPTTAKVFSCNFCM-RKFFSSQALGGHQN 82 (187)
Q Consensus 54 ~~Htgekpf~C~~Cg-k~F~~~~~L~~H~~ 82 (187)
+.|--.+.|.|.+|| +++.-..++.+|-+
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 445557789999999 88888888988865
No 51
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=49.90 E-value=3.6 Score=39.28 Aligned_cols=25 Identities=28% Similarity=0.748 Sum_probs=22.9
Q ss_pred ccccCcccccccCchhHHHHHhhhc
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNAHK 85 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~H~ 85 (187)
.|.|.+|+|.|..-..+..|++.|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999886
No 52
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=47.79 E-value=8.8 Score=32.58 Aligned_cols=56 Identities=21% Similarity=0.267 Sum_probs=40.3
Q ss_pred CccccCcccccccCchhHHHHHh--hhcCC--CCCcccccchhhHhhcCCCCCCCCCCchhhHhhhccCC
Q 043322 60 KVFSCNFCMRKFFSSQALGGHQN--AHKRE--RGAAKRYQSQRMMTMMGLPVHTNMVRSLGVRAHSLVHK 125 (187)
Q Consensus 60 kpf~C~~Cgk~F~~~~~L~~H~~--~H~ge--kp~~f~~~s~l~r~Htgep~gk~F~~~s~L~~H~riH~ 125 (187)
.++.|..|...|.....|..|.+ .|.++ +|+..... .+++.|.+...+..|..+|.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~----------~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYS----------LCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeecc----------CCCccccccccccCCccccc
Confidence 47899999999999999999999 89998 77622210 12555555566666665554
No 53
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=46.50 E-value=5.5 Score=32.53 Aligned_cols=27 Identities=15% Similarity=0.351 Sum_probs=21.0
Q ss_pred CCCccccCcccccccCchhHHHHHhhh
Q 043322 58 TAKVFSCNFCMRKFFSSQALGGHQNAH 84 (187)
Q Consensus 58 gekpf~C~~Cgk~F~~~~~L~~H~~~H 84 (187)
.+..|.|..|+|.|.-..-+..|+..-
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhc
Confidence 345699999999999999999998653
No 54
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=42.39 E-value=11 Score=22.06 Aligned_cols=15 Identities=27% Similarity=0.660 Sum_probs=13.0
Q ss_pred ccccCcccccccCch
Q 043322 61 VFSCNFCMRKFFSSQ 75 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~ 75 (187)
||.|..|++.|-...
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 899999999998654
No 55
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=42.38 E-value=16 Score=26.00 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=22.1
Q ss_pred ccc----CcccccccCchhHHHHHhhhcC
Q 043322 62 FSC----NFCMRKFFSSQALGGHQNAHKR 86 (187)
Q Consensus 62 f~C----~~Cgk~F~~~~~L~~H~~~H~g 86 (187)
|.| ..|+..+.+...+..|.+.+.|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999887543
No 56
>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=41.18 E-value=11 Score=21.64 Aligned_cols=15 Identities=27% Similarity=0.496 Sum_probs=11.4
Q ss_pred ccccCcccccccCch
Q 043322 61 VFSCNFCMRKFFSSQ 75 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~ 75 (187)
.|.|..||+.|.-..
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 478999999886443
No 57
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=39.57 E-value=7.8 Score=32.32 Aligned_cols=42 Identities=29% Similarity=0.500 Sum_probs=29.0
Q ss_pred CCCCCCCCCCCCCCCCCCCccccCcccccccCchhHHHH-HhhhcC
Q 043322 42 NSLSTSRDPDSPARPTTAKVFSCNFCMRKFFSSQALGGH-QNAHKR 86 (187)
Q Consensus 42 ~sF~~~~~L~~h~~Htgekpf~C~~Cgk~F~~~~~L~~H-~~~H~g 86 (187)
..|....-|.. |...|-|+|.+|-|+..+--.|..| +.+|+.
T Consensus 18 refddekiliq---hqkakhfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 18 REFDDEKILIQ---HQKAKHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred cccchhhhhhh---hhhhccceeeeehhhhccCCCceeehhhhhhh
Confidence 35554444433 4446779999999998888888888 566753
No 58
>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=38.22 E-value=14 Score=19.50 Aligned_cols=10 Identities=30% Similarity=0.541 Sum_probs=8.4
Q ss_pred CccccCcccc
Q 043322 60 KVFSCNFCMR 69 (187)
Q Consensus 60 kpf~C~~Cgk 69 (187)
-+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4799999985
No 59
>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=35.82 E-value=15 Score=21.82 Aligned_cols=16 Identities=25% Similarity=0.524 Sum_probs=12.1
Q ss_pred ccccCcccccccCchh
Q 043322 61 VFSCNFCMRKFFSSQA 76 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~ 76 (187)
-|.|..||..|-....
T Consensus 5 ey~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQS 20 (42)
T ss_pred EEEeCCCCCEEEEEEE
Confidence 4889999988865543
No 60
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=34.28 E-value=20 Score=32.65 Aligned_cols=22 Identities=32% Similarity=0.680 Sum_probs=19.5
Q ss_pred cccCcccccccCchhHHHHHhh
Q 043322 62 FSCNFCMRKFFSSQALGGHQNA 83 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~~ 83 (187)
+-|..|.|+|.+.-+|..|.+.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6699999999999999999763
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=34.20 E-value=9.2 Score=31.02 Aligned_cols=25 Identities=20% Similarity=0.495 Sum_probs=18.9
Q ss_pred CCccccCcccccccCchhHHHHHhh
Q 043322 59 AKVFSCNFCMRKFFSSQALGGHQNA 83 (187)
Q Consensus 59 ekpf~C~~Cgk~F~~~~~L~~H~~~ 83 (187)
++.+.|++|++.|....-..+..++
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 4568899999999988766555543
No 62
>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=33.96 E-value=21 Score=19.13 Aligned_cols=11 Identities=27% Similarity=0.431 Sum_probs=8.6
Q ss_pred cccCccccccc
Q 043322 62 FSCNFCMRKFF 72 (187)
Q Consensus 62 f~C~~Cgk~F~ 72 (187)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 35999998884
No 63
>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=33.41 E-value=17 Score=21.60 Aligned_cols=13 Identities=15% Similarity=0.708 Sum_probs=10.6
Q ss_pred CccccCccccccc
Q 043322 60 KVFSCNFCMRKFF 72 (187)
Q Consensus 60 kpf~C~~Cgk~F~ 72 (187)
++-.|++|+..|.
T Consensus 28 ~~~~CpYCg~~yv 40 (40)
T PF10276_consen 28 GPVVCPYCGTRYV 40 (40)
T ss_dssp CEEEETTTTEEEE
T ss_pred CeEECCCCCCEEC
Confidence 4678999999873
No 64
>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=33.18 E-value=15 Score=21.85 Aligned_cols=16 Identities=25% Similarity=0.658 Sum_probs=10.7
Q ss_pred CccccCcccccccCch
Q 043322 60 KVFSCNFCMRKFFSSQ 75 (187)
Q Consensus 60 kpf~C~~Cgk~F~~~~ 75 (187)
-||.|..|++.|-...
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 5899999999998654
No 65
>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=32.69 E-value=18 Score=22.10 Aligned_cols=14 Identities=21% Similarity=0.572 Sum_probs=11.0
Q ss_pred ccccCcccccccCc
Q 043322 61 VFSCNFCMRKFFSS 74 (187)
Q Consensus 61 pf~C~~Cgk~F~~~ 74 (187)
-|.|..||..|-..
T Consensus 5 ey~C~~Cg~~fe~~ 18 (52)
T TIGR02605 5 EYRCTACGHRFEVL 18 (52)
T ss_pred EEEeCCCCCEeEEE
Confidence 37899999988754
No 66
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=32.07 E-value=24 Score=26.32 Aligned_cols=27 Identities=30% Similarity=0.498 Sum_probs=23.2
Q ss_pred CCCCccccCcccccccCchhHHHHHhh
Q 043322 57 TTAKVFSCNFCMRKFFSSQALGGHQNA 83 (187)
Q Consensus 57 tgekpf~C~~Cgk~F~~~~~L~~H~~~ 83 (187)
.|...|-|-.|.+-|.+..+|..|.+.
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc
Confidence 455678999999999999999999763
No 67
>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=31.95 E-value=17 Score=19.93 Aligned_cols=20 Identities=30% Similarity=0.713 Sum_probs=12.4
Q ss_pred cccCcccccccCchhHHHHHh
Q 043322 62 FSCNFCMRKFFSSQALGGHQN 82 (187)
Q Consensus 62 f~C~~Cgk~F~~~~~L~~H~~ 82 (187)
|.|-.|++.| .......|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 5789999999 4445555543
No 68
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=31.77 E-value=23 Score=26.70 Aligned_cols=15 Identities=27% Similarity=0.494 Sum_probs=12.9
Q ss_pred ccccCcccccccCch
Q 043322 61 VFSCNFCMRKFFSSQ 75 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~ 75 (187)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998765
No 69
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=31.75 E-value=25 Score=30.87 Aligned_cols=23 Identities=22% Similarity=0.525 Sum_probs=21.1
Q ss_pred ccccCcccccccCchhHHHHHhh
Q 043322 61 VFSCNFCMRKFFSSQALGGHQNA 83 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~~ 83 (187)
.+.|-+|.|.|..+..|..|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999974
No 70
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=30.40 E-value=32 Score=35.21 Aligned_cols=52 Identities=21% Similarity=0.330 Sum_probs=38.4
Q ss_pred CcceeeccCCCCCCCCCCCCCC--CCCCCCCccccCcccccccCchhHHHHHhh
Q 043322 32 GEWLNLKLGGNSLSTSRDPDSP--ARPTTAKVFSCNFCMRKFFSSQALGGHQNA 83 (187)
Q Consensus 32 ~~~l~l~~~~~sF~~~~~L~~h--~~Htgekpf~C~~Cgk~F~~~~~L~~H~~~ 83 (187)
+--..+.-.+..+..+..+..| ..|.-.+.|.|+.|+..|.....|..|+|.
T Consensus 434 ~~l~e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRs 487 (1406)
T KOG1146|consen 434 GTLVELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRS 487 (1406)
T ss_pred CccccccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccc
Confidence 4444444455556555555555 357777999999999999999999999986
No 71
>PLN02294 cytochrome c oxidase subunit Vb
Probab=30.16 E-value=31 Score=27.18 Aligned_cols=15 Identities=33% Similarity=0.709 Sum_probs=12.4
Q ss_pred CCccccCcccccccC
Q 043322 59 AKVFSCNFCMRKFFS 73 (187)
Q Consensus 59 ekpf~C~~Cgk~F~~ 73 (187)
.+|+.|..||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 479999999988753
No 72
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=29.90 E-value=58 Score=28.94 Aligned_cols=64 Identities=19% Similarity=0.087 Sum_probs=40.9
Q ss_pred CccccCcccccccCchhHHHHHhhhcC----CCCCc--ccc-cchh-hHhhcCC--CC----CCCCCCchhhHhhhcc
Q 043322 60 KVFSCNFCMRKFFSSQALGGHQNAHKR----ERGAA--KRY-QSQR-MMTMMGL--PV----HTNMVRSLGVRAHSLV 123 (187)
Q Consensus 60 kpf~C~~Cgk~F~~~~~L~~H~~~H~g----ekp~~--f~~-~s~l-~r~Htge--p~----gk~F~~~s~L~~H~ri 123 (187)
-|-.|-+|++.|.+.-.-..|+..++| ++.|. ... ...+ .++-.+. -| ++.|.+-...+.||.-
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 356799999999999999999987765 22220 000 0111 2222222 12 6889999999999864
No 73
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=28.62 E-value=34 Score=32.02 Aligned_cols=29 Identities=21% Similarity=0.344 Sum_probs=24.9
Q ss_pred CCCccccCcccccccCchhHHHHHhhhcC
Q 043322 58 TAKVFSCNFCMRKFFSSQALGGHQNAHKR 86 (187)
Q Consensus 58 gekpf~C~~Cgk~F~~~~~L~~H~~~H~g 86 (187)
..+|-.|..||.+|........|+..|..
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhh
Confidence 35678999999999999999999988863
No 74
>PHA00626 hypothetical protein
Probab=28.00 E-value=27 Score=22.47 Aligned_cols=16 Identities=13% Similarity=0.175 Sum_probs=12.8
Q ss_pred CCccccCcccccccCc
Q 043322 59 AKVFSCNFCMRKFFSS 74 (187)
Q Consensus 59 ekpf~C~~Cgk~F~~~ 74 (187)
...|.|+.||..|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 3579999999988643
No 75
>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=27.94 E-value=24 Score=25.63 Aligned_cols=14 Identities=29% Similarity=0.664 Sum_probs=11.2
Q ss_pred cccCcccccccCch
Q 043322 62 FSCNFCMRKFFSSQ 75 (187)
Q Consensus 62 f~C~~Cgk~F~~~~ 75 (187)
..|+.||++|+-..
T Consensus 10 R~Cp~CG~kFYDLn 23 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN 23 (108)
T ss_pred ccCCCCcchhccCC
Confidence 46999999998643
No 76
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=26.12 E-value=25 Score=27.22 Aligned_cols=18 Identities=17% Similarity=0.375 Sum_probs=14.2
Q ss_pred ccccCcccccccCchhHH
Q 043322 61 VFSCNFCMRKFFSSQALG 78 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~ 78 (187)
.++|+.||+.|...-.+.
T Consensus 28 ~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 28 RRECLACGKRFTTFERVE 45 (154)
T ss_pred eeeccccCCcceEeEecc
Confidence 489999999998765443
No 77
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=26.04 E-value=46 Score=26.12 Aligned_cols=23 Identities=17% Similarity=0.309 Sum_probs=16.7
Q ss_pred cceeeccCCCCCCCCCCCCCCCCCCCCCccccCccc
Q 043322 33 EWLNLKLGGNSLSTSRDPDSPARPTTAKVFSCNFCM 68 (187)
Q Consensus 33 ~~l~l~~~~~sF~~~~~L~~h~~Htgekpf~C~~Cg 68 (187)
+|.+.-++ -+|.|+-|-.|+.||
T Consensus 134 ~~vC~vCG-------------y~~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCG-------------YTHEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCC-------------CcccCCCCCcCCCCC
Confidence 78777653 345567788899998
No 78
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=25.87 E-value=51 Score=19.43 Aligned_cols=24 Identities=17% Similarity=0.289 Sum_probs=16.9
Q ss_pred cccCcccccccC--chhHHHHHhhhc
Q 043322 62 FSCNFCMRKFFS--SQALGGHQNAHK 85 (187)
Q Consensus 62 f~C~~Cgk~F~~--~~~L~~H~~~H~ 85 (187)
-.|..||-.|.. ...-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 479999988764 445566776664
No 79
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=25.51 E-value=25 Score=21.81 Aligned_cols=11 Identities=27% Similarity=0.682 Sum_probs=6.0
Q ss_pred ccCcccccccC
Q 043322 63 SCNFCMRKFFS 73 (187)
Q Consensus 63 ~C~~Cgk~F~~ 73 (187)
.|+.|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 79999999874
No 80
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=25.15 E-value=45 Score=29.50 Aligned_cols=29 Identities=14% Similarity=0.355 Sum_probs=22.2
Q ss_pred CCCCCCCccccCccc-ccccCchhHHHHHh
Q 043322 54 ARPTTAKVFSCNFCM-RKFFSSQALGGHQN 82 (187)
Q Consensus 54 ~~Htgekpf~C~~Cg-k~F~~~~~L~~H~~ 82 (187)
+.|--.+-|.|.+|| +.+.-...+.+|..
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhhhh
Confidence 456667889999999 77777777777743
No 81
>PF14353 CpXC: CpXC protein
Probab=24.47 E-value=17 Score=26.72 Aligned_cols=22 Identities=32% Similarity=0.443 Sum_probs=16.7
Q ss_pred ccccCcccccccCchhHHHHHh
Q 043322 61 VFSCNFCMRKFFSSQALGGHQN 82 (187)
Q Consensus 61 pf~C~~Cgk~F~~~~~L~~H~~ 82 (187)
.|.|+.||..|.-...+..|-.
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred EEECCCCCCceecCCCEEEEcC
Confidence 5889999999987666655543
No 82
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=23.72 E-value=36 Score=24.26 Aligned_cols=17 Identities=24% Similarity=0.227 Sum_probs=13.5
Q ss_pred CCCCCCccccCccccccc
Q 043322 55 RPTTAKVFSCNFCMRKFF 72 (187)
Q Consensus 55 ~Htgekpf~C~~Cgk~F~ 72 (187)
.+.+ +|+.|..||.-|.
T Consensus 74 l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 74 LEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EeCC-CceeCCCCCcEEE
Confidence 3455 7999999998875
No 83
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=22.88 E-value=35 Score=21.27 Aligned_cols=17 Identities=24% Similarity=0.557 Sum_probs=13.6
Q ss_pred CCccccCcccccccCch
Q 043322 59 AKVFSCNFCMRKFFSSQ 75 (187)
Q Consensus 59 ekpf~C~~Cgk~F~~~~ 75 (187)
.+++.|..||..|....
T Consensus 2 Dk~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTA 18 (49)
T ss_pred CeeEEcccCCCeEEEeh
Confidence 46789999999987654
No 84
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.42 E-value=33 Score=22.42 Aligned_cols=13 Identities=15% Similarity=0.674 Sum_probs=10.3
Q ss_pred CccccCccccccc
Q 043322 60 KVFSCNFCMRKFF 72 (187)
Q Consensus 60 kpf~C~~Cgk~F~ 72 (187)
.--.|++|++.|.
T Consensus 47 gev~CPYC~t~y~ 59 (62)
T COG4391 47 GEVVCPYCSTRYR 59 (62)
T ss_pred CcEecCccccEEE
Confidence 4457999999885
No 85
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.52 E-value=45 Score=20.11 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=11.5
Q ss_pred ccCcccccccCchhH
Q 043322 63 SCNFCMRKFFSSQAL 77 (187)
Q Consensus 63 ~C~~Cgk~F~~~~~L 77 (187)
.|..||+.|...-..
T Consensus 10 ~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKW 24 (42)
T ss_pred cCcccCCcchHHHHH
Confidence 499999999865443
Done!