Query 024763
Match_columns 263
No_of_seqs 363 out of 1305
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 07:13:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024763.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024763hhsearch_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 98.6 9E-09 2E-13 94.7 -0.4 70 91-177 186-255 (279)
2 KOG2462 C2H2-type Zn-finger pr 98.5 3.1E-08 6.8E-13 91.2 -0.0 61 84-146 207-267 (279)
3 KOG3623 Homeobox transcription 98.2 4.5E-07 9.7E-12 92.5 0.8 70 88-159 890-967 (1007)
4 KOG1074 Transcriptional repres 97.9 4.7E-06 1E-10 86.2 2.3 66 84-156 625-693 (958)
5 KOG3623 Homeobox transcription 97.9 6.9E-06 1.5E-10 84.1 2.8 39 86-124 916-954 (1007)
6 PHA00616 hypothetical protein 97.4 3E-05 6.5E-10 53.3 -0.2 31 92-122 1-31 (44)
7 PHA02768 hypothetical protein; 97.3 6.6E-05 1.4E-09 53.9 0.6 29 92-122 5-33 (55)
8 KOG1074 Transcriptional repres 97.2 0.00012 2.6E-09 76.1 1.7 57 92-159 353-409 (958)
9 KOG3576 Ovo and related transc 97.0 0.00013 2.8E-09 65.4 -0.4 36 88-123 141-176 (267)
10 KOG3576 Ovo and related transc 96.8 0.0012 2.5E-08 59.4 3.6 74 88-178 113-186 (267)
11 PF00096 zf-C2H2: Zinc finger, 96.7 0.00041 8.9E-09 40.2 0.3 23 93-115 1-23 (23)
12 PF13465 zf-H2C2_2: Zinc-finge 96.6 0.00056 1.2E-08 41.5 0.2 19 86-104 8-26 (26)
13 PF13912 zf-C2H2_6: C2H2-type 96.1 0.0019 4.1E-08 38.8 0.5 25 92-116 1-25 (27)
14 PF13894 zf-C2H2_4: C2H2-type 95.7 0.004 8.7E-08 35.4 0.5 23 93-115 1-23 (24)
15 smart00355 ZnF_C2H2 zinc finge 95.1 0.009 1.9E-07 34.2 0.7 24 93-116 1-24 (26)
16 PF13465 zf-H2C2_2: Zinc-finge 94.3 0.012 2.5E-07 35.7 -0.1 18 107-124 1-18 (26)
17 PHA00733 hypothetical protein 93.9 0.016 3.5E-07 48.0 -0.1 29 87-115 68-96 (128)
18 PF09237 GAGA: GAGA factor; I 93.0 0.058 1.3E-06 38.4 1.6 34 87-120 19-52 (54)
19 PHA00732 hypothetical protein 91.5 0.085 1.8E-06 40.4 1.1 26 92-117 1-27 (79)
20 PF12874 zf-met: Zinc-finger o 91.0 0.065 1.4E-06 31.4 -0.0 23 93-115 1-23 (25)
21 COG5189 SFP1 Putative transcri 90.4 0.28 6.1E-06 47.0 3.6 66 89-154 346-421 (423)
22 PF12171 zf-C2H2_jaz: Zinc-fin 88.6 0.16 3.4E-06 30.6 0.3 22 93-114 2-23 (27)
23 PLN03086 PRLI-interacting fact 86.9 0.21 4.5E-06 51.0 0.2 54 90-146 451-510 (567)
24 PRK04860 hypothetical protein; 83.3 0.49 1.1E-05 40.8 0.8 30 91-124 118-147 (160)
25 KOG3608 Zn finger proteins [Ge 82.1 0.18 4E-06 48.8 -2.4 31 86-116 286-316 (467)
26 PF13909 zf-H2C2_5: C2H2-type 81.0 0.57 1.2E-05 27.2 0.3 23 93-116 1-23 (24)
27 COG5189 SFP1 Putative transcri 80.0 2.3 5E-05 40.9 4.1 24 89-112 395-418 (423)
28 PF13913 zf-C2HC_2: zinc-finge 78.1 0.91 2E-05 27.3 0.5 21 93-114 3-23 (25)
29 smart00451 ZnF_U1 U1-like zinc 73.9 1.4 3.1E-05 27.4 0.6 23 92-114 3-25 (35)
30 PF12756 zf-C2H2_2: C2H2 type 73.7 1.5 3.2E-05 32.8 0.8 24 92-115 50-73 (100)
31 PHA00733 hypothetical protein 73.1 1.6 3.6E-05 36.0 1.0 26 90-115 97-122 (128)
32 COG5048 FOG: Zn-finger [Genera 65.6 6.2 0.00013 36.0 3.2 39 86-124 313-355 (467)
33 PHA02768 hypothetical protein; 63.2 2.9 6.4E-05 30.1 0.5 24 85-110 26-49 (55)
34 KOG3993 Transcription factor ( 61.7 3.8 8.2E-05 40.7 1.1 25 92-116 295-319 (500)
35 KOG3993 Transcription factor ( 57.2 2.6 5.6E-05 41.9 -0.9 27 91-117 355-381 (500)
36 PLN03086 PRLI-interacting fact 57.1 5.6 0.00012 40.9 1.4 33 91-125 477-509 (567)
37 KOG3608 Zn finger proteins [Ge 51.9 9.3 0.0002 37.4 1.9 39 84-122 199-239 (467)
38 PF05443 ROS_MUCR: ROS/MUCR tr 45.7 13 0.00028 31.2 1.7 29 91-122 71-99 (132)
39 PF05605 zf-Di19: Drought indu 40.4 15 0.00032 25.5 1.0 26 92-118 2-28 (54)
40 PF02892 zf-BED: BED zinc fing 39.9 15 0.00032 24.2 0.9 23 90-112 14-40 (45)
41 smart00614 ZnF_BED BED zinc fi 39.7 16 0.00034 25.0 1.0 25 92-116 18-48 (50)
42 COG5112 UFD2 U1-like Zn-finger 34.8 7.5 0.00016 31.9 -1.3 36 88-127 51-86 (126)
43 COG5048 FOG: Zn-finger [Genera 33.7 17 0.00036 33.2 0.5 35 91-125 288-326 (467)
44 PRK04860 hypothetical protein; 33.1 19 0.0004 31.1 0.7 22 85-106 136-157 (160)
45 KOG2893 Zn finger protein [Gen 32.7 17 0.00038 33.8 0.5 21 94-114 12-32 (341)
46 KOG3408 U1-like Zn-finger-cont 32.7 21 0.00046 29.8 1.0 37 88-128 53-89 (129)
47 COG4049 Uncharacterized protei 29.8 17 0.00037 26.6 -0.1 28 87-114 12-39 (65)
48 COG4957 Predicted transcriptio 26.7 33 0.00073 29.2 1.1 27 93-122 77-103 (148)
49 KOG4124 Putative transcription 25.3 76 0.0016 31.2 3.4 58 88-146 209-267 (442)
50 KOG4167 Predicted DNA-binding 22.9 16 0.00034 38.9 -1.8 26 91-116 791-816 (907)
51 KOG2893 Zn finger protein [Gen 21.0 33 0.00071 32.1 0.0 29 87-115 29-58 (341)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=98.57 E-value=9e-09 Score=94.67 Aligned_cols=70 Identities=24% Similarity=0.374 Sum_probs=57.7
Q ss_pred ceeecCccccccCCccchhhhhhhccCCCchhHHHhhhhhhhhcccCCCccccCCCCCcccccCCCCCCcccccCCCCCC
Q 024763 91 KKFECQYCFKEFANSQALGGHQNAHKKERMKKKRLQLQARKASLNSYLQPYQNMYNLSFNNTYHGSNTASTWFYDPSCYP 170 (263)
Q Consensus 91 Kpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR~~~~s~~~s~~~~l~p~~~~~~l~~~~y~h~~~~~sp~~y~~s~~~ 170 (263)
-+++|.+|||.|.+..-|++|+|+|||||||.| ..+.+.|.-+.+|..|.-+|.+... |. |-.
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C-----------~hC~kAFADRSNLRAHmQTHS~~K~----~q--C~~ 248 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSC-----------PHCGKAFADRSNLRAHMQTHSDVKK----HQ--CPR 248 (279)
T ss_pred CCcccccccccccchHHhhcccccccCCCCccC-----------CcccchhcchHHHHHHHHhhcCCcc----cc--Ccc
Confidence 578999999999999999999999999999974 3566777777777778888888877 44 778
Q ss_pred CCccccc
Q 024763 171 CDNQFTL 177 (263)
Q Consensus 171 ~~~~f~~ 177 (263)
|++.|.+
T Consensus 249 C~KsFsl 255 (279)
T KOG2462|consen 249 CGKSFAL 255 (279)
T ss_pred hhhHHHH
Confidence 8887754
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=98.46 E-value=3.1e-08 Score=91.16 Aligned_cols=61 Identities=23% Similarity=0.325 Sum_probs=50.3
Q ss_pred CCCCCCCceeecCccccccCCccchhhhhhhccCCCchhHHHhhhhhhhhcccCCCccccCCC
Q 024763 84 PTGESDYKKFECQYCFKEFANSQALGGHQNAHKKERMKKKRLQLQARKASLNSYLQPYQNMYN 146 (263)
Q Consensus 84 ~~tHTgeKpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR~~~~s~~~s~~~~l~p~~~~~~ 146 (263)
.++|||||||.|..|+|+|..+++|+.||++|.+.|+|+|- ++.+.|++-.||..|...-+
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~--~C~KsFsl~SyLnKH~ES~C 267 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCP--RCGKSFALKSYLNKHSESAC 267 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCc--chhhHHHHHHHHHHhhhhcc
Confidence 57899999999999999999999999999999999999843 45666666666666655444
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.18 E-value=4.5e-07 Score=92.53 Aligned_cols=70 Identities=20% Similarity=0.321 Sum_probs=50.7
Q ss_pred CCCceeecCccccccCCccchhhhhhhccCCCchh--------HHHhhhhhhhhcccCCCccccCCCCCcccccCCCCCC
Q 024763 88 SDYKKFECQYCFKEFANSQALGGHQNAHKKERMKK--------KRLQLQARKASLNSYLQPYQNMYNLSFNNTYHGSNTA 159 (263)
Q Consensus 88 TgeKpf~C~~CgKsF~ssssL~~HqR~HtGEKPyk--------kR~~~~s~~~s~~~~l~p~~~~~~l~~~~y~h~~~~~ 159 (263)
+.+..|.|..|.|.|...+.|.+|.--|+|.|||+ |..|..--+..+|++.+||+|+-+ +.+|.|.|++-
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKC--lKRFSHSGSYS 967 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKC--LKRFSHSGSYS 967 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhh--hhhcccccchH
Confidence 34567888888888888888888888888888887 233444455667788888888865 46677777543
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.91 E-value=4.7e-06 Score=86.23 Aligned_cols=66 Identities=18% Similarity=0.279 Sum_probs=53.4
Q ss_pred CCCCCCCceeecCccccccCCccchhhhhhhccCCCchhHHHhhhhhhhhcc---cCCCccccCCCCCcccccCCC
Q 024763 84 PTGESDYKKFECQYCFKEFANSQALGGHQNAHKKERMKKKRLQLQARKASLN---SYLQPYQNMYNLSFNNTYHGS 156 (263)
Q Consensus 84 ~~tHTgeKpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR~~~~s~~~s~~---~~l~p~~~~~~l~~~~y~h~~ 156 (263)
-++|+|||||+|++||++|.++.+|+.|+.+|.-.-++.- -++|. .+.++|.+.+.+-.|-..|.+
T Consensus 625 yrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~-------q~ScP~~~ic~~kftn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 625 YRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARV-------QFSCPSTFICQKKFTNAVTLPQHIRIHLG 693 (958)
T ss_pred hhcccCcCccccccccchhccccchhhcccccccCccccc-------cccCCchhhhcccccccccccceEEeecC
Confidence 3689999999999999999999999999999987655542 24555 677888888888777777764
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=97.88 E-value=6.9e-06 Score=84.07 Aligned_cols=39 Identities=23% Similarity=0.432 Sum_probs=37.2
Q ss_pred CCCCCceeecCccccccCCccchhhhhhhccCCCchhHH
Q 024763 86 GESDYKKFECQYCFKEFANSQALGGHQNAHKKERMKKKR 124 (263)
Q Consensus 86 tHTgeKpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR 124 (263)
-|+|.|||+|.+|.|+|..+.+|..|+|.|.|||||.|.
T Consensus 916 EHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCd 954 (1007)
T KOG3623|consen 916 EHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCD 954 (1007)
T ss_pred hhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhh
Confidence 489999999999999999999999999999999999965
No 6
>PHA00616 hypothetical protein
Probab=97.42 E-value=3e-05 Score=53.29 Aligned_cols=31 Identities=16% Similarity=0.262 Sum_probs=29.6
Q ss_pred eeecCccccccCCccchhhhhhhccCCCchh
Q 024763 92 KFECQYCFKEFANSQALGGHQNAHKKERMKK 122 (263)
Q Consensus 92 pf~C~~CgKsF~ssssL~~HqR~HtGEKPyk 122 (263)
||.|..||+.|...+.|..|++.|+|++++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 6899999999999999999999999999886
No 7
>PHA02768 hypothetical protein; Provisional
Probab=97.32 E-value=6.6e-05 Score=53.94 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=25.9
Q ss_pred eeecCccccccCCccchhhhhhhccCCCchh
Q 024763 92 KFECQYCFKEFANSQALGGHQNAHKKERMKK 122 (263)
Q Consensus 92 pf~C~~CgKsF~ssssL~~HqR~HtGEKPyk 122 (263)
-|+|..||+.|...++|..|+|+|+ ++|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~k 33 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLK 33 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cccc
Confidence 4899999999999999999999999 4553
No 8
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.24 E-value=0.00012 Score=76.05 Aligned_cols=57 Identities=25% Similarity=0.342 Sum_probs=43.9
Q ss_pred eeecCccccccCCccchhhhhhhccCCCchhHHHhhhhhhhhcccCCCccccCCCCCcccccCCCCCC
Q 024763 92 KFECQYCFKEFANSQALGGHQNAHKKERMKKKRLQLQARKASLNSYLQPYQNMYNLSFNNTYHGSNTA 159 (263)
Q Consensus 92 pf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR~~~~s~~~s~~~~l~p~~~~~~l~~~~y~h~~~~~ 159 (263)
+++|.+|.|.|...++|+.|.|.|||||||+|. .|.+.|-..-+|..|+..|+..++
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCn-----------vCG~~FSTkGNLKvH~~rH~e~~p 409 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCN-----------VCGNRFSTKGNLKVHFQRHREKYP 409 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeec-----------ccccccccccceeeeeeeccccCC
Confidence 578999999999999999999999999999954 344555555555555555555544
No 9
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=97.03 E-value=0.00013 Score=65.43 Aligned_cols=36 Identities=33% Similarity=0.502 Sum_probs=27.7
Q ss_pred CCCceeecCccccccCCccchhhhhhhccCCCchhH
Q 024763 88 SDYKKFECQYCFKEFANSQALGGHQNAHKKERMKKK 123 (263)
Q Consensus 88 TgeKpf~C~~CgKsF~ssssL~~HqR~HtGEKPykk 123 (263)
...|.|-|..|||.|..--.|.+|+|+|||-|||++
T Consensus 141 ~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc 176 (267)
T KOG3576|consen 141 SDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKC 176 (267)
T ss_pred cHHHHHHHhhccCcccchhhhhhhhccccCccccch
Confidence 345667777888888888888888888888888873
No 10
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=96.80 E-value=0.0012 Score=59.44 Aligned_cols=74 Identities=23% Similarity=0.443 Sum_probs=57.2
Q ss_pred CCCceeecCccccccCCccchhhhhhhccCCCchhHHHhhhhhhhhcccCCCccccCCCCCcccccCCCCCCcccccCCC
Q 024763 88 SDYKKFECQYCFKEFANSQALGGHQNAHKKERMKKKRLQLQARKASLNSYLQPYQNMYNLSFNNTYHGSNTASTWFYDPS 167 (263)
Q Consensus 88 TgeKpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR~~~~s~~~s~~~~l~p~~~~~~l~~~~y~h~~~~~sp~~y~~s 167 (263)
.+.-.|.|.+|+|.|....-|.+|++.|..-|.|-++ .+.+-|+....|.-|..+|.|..+ |.
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct-----------~cgkgfndtfdlkrh~rthtgvrp----yk-- 175 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCT-----------FCGKGFNDTFDLKRHTRTHTGVRP----YK-- 175 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHh-----------hccCcccchhhhhhhhccccCccc----cc--
Confidence 4456799999999999999999999999876655544 555666666667777778888877 55
Q ss_pred CCCCCcccccc
Q 024763 168 CYPCDNQFTLY 178 (263)
Q Consensus 168 ~~~~~~~f~~~ 178 (263)
|.-|++.|+-+
T Consensus 176 c~~c~kaftqr 186 (267)
T KOG3576|consen 176 CSLCEKAFTQR 186 (267)
T ss_pred hhhhhHHHHhh
Confidence 77888877754
No 11
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.75 E-value=0.00041 Score=40.20 Aligned_cols=23 Identities=30% Similarity=0.699 Sum_probs=21.6
Q ss_pred eecCccccccCCccchhhhhhhc
Q 024763 93 FECQYCFKEFANSQALGGHQNAH 115 (263)
Q Consensus 93 f~C~~CgKsF~ssssL~~HqR~H 115 (263)
|.|.+|++.|.....|..|++.|
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 12
>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=96.61 E-value=0.00056 Score=41.50 Aligned_cols=19 Identities=37% Similarity=0.838 Sum_probs=17.2
Q ss_pred CCCCCceeecCccccccCC
Q 024763 86 GESDYKKFECQYCFKEFAN 104 (263)
Q Consensus 86 tHTgeKpf~C~~CgKsF~s 104 (263)
+|+++|||.|.+|++.|.+
T Consensus 8 ~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 8 THTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHSSSSSEEESSSSEEESS
T ss_pred hcCCCCCCCCCCCcCeeCc
Confidence 5899999999999999963
No 13
>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=96.10 E-value=0.0019 Score=38.79 Aligned_cols=25 Identities=40% Similarity=0.705 Sum_probs=23.3
Q ss_pred eeecCccccccCCccchhhhhhhcc
Q 024763 92 KFECQYCFKEFANSQALGGHQNAHK 116 (263)
Q Consensus 92 pf~C~~CgKsF~ssssL~~HqR~Ht 116 (263)
+|+|..|++.|.....|..|++.|.
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 5899999999999999999999875
No 14
>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=95.65 E-value=0.004 Score=35.43 Aligned_cols=23 Identities=35% Similarity=0.732 Sum_probs=19.5
Q ss_pred eecCccccccCCccchhhhhhhc
Q 024763 93 FECQYCFKEFANSQALGGHQNAH 115 (263)
Q Consensus 93 f~C~~CgKsF~ssssL~~HqR~H 115 (263)
|.|.+|++.|.+...|..|++.|
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 78999999999999999999876
No 15
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.05 E-value=0.009 Score=34.18 Aligned_cols=24 Identities=33% Similarity=0.628 Sum_probs=22.0
Q ss_pred eecCccccccCCccchhhhhhhcc
Q 024763 93 FECQYCFKEFANSQALGGHQNAHK 116 (263)
Q Consensus 93 f~C~~CgKsF~ssssL~~HqR~Ht 116 (263)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998775
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=94.30 E-value=0.012 Score=35.65 Aligned_cols=18 Identities=28% Similarity=0.259 Sum_probs=15.6
Q ss_pred chhhhhhhccCCCchhHH
Q 024763 107 ALGGHQNAHKKERMKKKR 124 (263)
Q Consensus 107 sL~~HqR~HtGEKPykkR 124 (263)
+|..|+++|+|+|||++.
T Consensus 1 ~l~~H~~~H~~~k~~~C~ 18 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCP 18 (26)
T ss_dssp HHHHHHHHHSSSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCC
Confidence 478999999999999853
No 17
>PHA00733 hypothetical protein
Probab=93.86 E-value=0.016 Score=48.01 Aligned_cols=29 Identities=21% Similarity=0.450 Sum_probs=26.0
Q ss_pred CCCCceeecCccccccCCccchhhhhhhc
Q 024763 87 ESDYKKFECQYCFKEFANSQALGGHQNAH 115 (263)
Q Consensus 87 HTgeKpf~C~~CgKsF~ssssL~~HqR~H 115 (263)
+.++++|.|..|++.|.....|..|++.|
T Consensus 68 ~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 68 SKAVSPYVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred cCCCCCccCCCCCCcCCCHHHHHHHHhcC
Confidence 34578999999999999999999999977
No 18
>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=92.97 E-value=0.058 Score=38.45 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=24.8
Q ss_pred CCCCceeecCccccccCCccchhhhhhhccCCCc
Q 024763 87 ESDYKKFECQYCFKEFANSQALGGHQNAHKKERM 120 (263)
Q Consensus 87 HTgeKpf~C~~CgKsF~ssssL~~HqR~HtGEKP 120 (263)
+..+.|-.|++|+..+.+..+|.+|+.++.+.||
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 4557899999999999999999999988888776
No 19
>PHA00732 hypothetical protein
Probab=91.52 E-value=0.085 Score=40.39 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=23.0
Q ss_pred eeecCccccccCCccchhhhhhh-ccC
Q 024763 92 KFECQYCFKEFANSQALGGHQNA-HKK 117 (263)
Q Consensus 92 pf~C~~CgKsF~ssssL~~HqR~-HtG 117 (263)
||.|..|++.|.....|..|++. |++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~ 27 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL 27 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC
Confidence 58999999999999999999984 653
No 20
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=91.01 E-value=0.065 Score=31.36 Aligned_cols=23 Identities=30% Similarity=0.684 Sum_probs=21.1
Q ss_pred eecCccccccCCccchhhhhhhc
Q 024763 93 FECQYCFKEFANSQALGGHQNAH 115 (263)
Q Consensus 93 f~C~~CgKsF~ssssL~~HqR~H 115 (263)
|.|..|.+.|.....+..|++.+
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 68999999999999999998765
No 21
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=90.45 E-value=0.28 Score=46.96 Aligned_cols=66 Identities=18% Similarity=0.395 Sum_probs=45.7
Q ss_pred CCceeecCc--cccccCCccchhhhhhh-ccCCCchh-------HHHhhhhhhhhcccCCCccccCCCCCcccccC
Q 024763 89 DYKKFECQY--CFKEFANSQALGGHQNA-HKKERMKK-------KRLQLQARKASLNSYLQPYQNMYNLSFNNTYH 154 (263)
Q Consensus 89 geKpf~C~~--CgKsF~ssssL~~HqR~-HtGEKPyk-------kR~~~~s~~~s~~~~l~p~~~~~~l~~~~y~h 154 (263)
++|||+|.+ |.|.+.....|+-|+.- |...+... .-|....+.+.|..|.++|.+-.+|.+|+-+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~Hs 421 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKHS 421 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccccc
Confidence 359999997 99999999999988642 31111111 12344455666777888999988888887543
No 22
>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=88.55 E-value=0.16 Score=30.64 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=20.3
Q ss_pred eecCccccccCCccchhhhhhh
Q 024763 93 FECQYCFKEFANSQALGGHQNA 114 (263)
Q Consensus 93 f~C~~CgKsF~ssssL~~HqR~ 114 (263)
|.|..|++.|.+...+..|++.
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 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=86.88 E-value=0.21 Score=51.05 Aligned_cols=54 Identities=9% Similarity=0.147 Sum_probs=33.5
Q ss_pred CceeecCccccccCCccchhhhhhhccCCCchhHH------HhhhhhhhhcccCCCccccCCC
Q 024763 90 YKKFECQYCFKEFANSQALGGHQNAHKKERMKKKR------LQLQARKASLNSYLQPYQNMYN 146 (263)
Q Consensus 90 eKpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR------~~~~s~~~s~~~~l~p~~~~~~ 146 (263)
++.+.|.+|++.|. ...|..|+++|+ +++.|. ......|...+...+++.|.++
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~CpCg~~~~R~~L~~H~~thCp~Kpi~C~fC 510 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCPCGVVLEKEQMVQHQASTCPLRLITCRFC 510 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCCCCCCcchhHHHhhhhccCCCCceeCCCC
Confidence 45678999999986 567899988874 555542 0122223333455566666655
No 24
>PRK04860 hypothetical protein; Provisional
Probab=83.26 E-value=0.49 Score=40.84 Aligned_cols=30 Identities=17% Similarity=0.431 Sum_probs=26.3
Q ss_pred ceeecCccccccCCccchhhhhhhccCCCchhHH
Q 024763 91 KKFECQYCFKEFANSQALGGHQNAHKKERMKKKR 124 (263)
Q Consensus 91 Kpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR 124 (263)
-+|.|. |++ ....+.+|.++|+|+++|.|+
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~ 147 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCR 147 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECC
Confidence 479998 988 666789999999999999976
No 25
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=82.07 E-value=0.18 Score=48.81 Aligned_cols=31 Identities=26% Similarity=0.450 Sum_probs=28.1
Q ss_pred CCCCCceeecCccccccCCccchhhhhhhcc
Q 024763 86 GESDYKKFECQYCFKEFANSQALGGHQNAHK 116 (263)
Q Consensus 86 tHTgeKpf~C~~CgKsF~ssssL~~HqR~Ht 116 (263)
.|...|||+|..|.+.|.+.+.|.+|..+|.
T Consensus 286 rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 286 RHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred hhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 4677899999999999999999999999987
No 26
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=80.99 E-value=0.57 Score=27.16 Aligned_cols=23 Identities=22% Similarity=0.496 Sum_probs=17.6
Q ss_pred eecCccccccCCccchhhhhhhcc
Q 024763 93 FECQYCFKEFANSQALGGHQNAHK 116 (263)
Q Consensus 93 f~C~~CgKsF~ssssL~~HqR~Ht 116 (263)
|.|..|..... ...|..|++.|.
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 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=79.99 E-value=2.3 Score=40.91 Aligned_cols=24 Identities=29% Similarity=0.591 Sum_probs=21.6
Q ss_pred CCceeecCccccccCCccchhhhh
Q 024763 89 DYKKFECQYCFKEFANSQALGGHQ 112 (263)
Q Consensus 89 geKpf~C~~CgKsF~ssssL~~Hq 112 (263)
..|||+|.+|+|++.....|+-|+
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred cCCceeccccchhhccCccceecc
Confidence 459999999999999999998884
No 28
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=78.10 E-value=0.91 Score=27.27 Aligned_cols=21 Identities=29% Similarity=0.662 Sum_probs=17.1
Q ss_pred eecCccccccCCccchhhhhhh
Q 024763 93 FECQYCFKEFANSQALGGHQNA 114 (263)
Q Consensus 93 f~C~~CgKsF~ssssL~~HqR~ 114 (263)
..|..||+.| ....|..|+.+
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 66778888764
No 29
>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=73.90 E-value=1.4 Score=27.39 Aligned_cols=23 Identities=22% Similarity=0.569 Sum_probs=19.8
Q ss_pred eeecCccccccCCccchhhhhhh
Q 024763 92 KFECQYCFKEFANSQALGGHQNA 114 (263)
Q Consensus 92 pf~C~~CgKsF~ssssL~~HqR~ 114 (263)
+|.|.+|.+.|.....+..|.+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999988888888753
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=73.69 E-value=1.5 Score=32.81 Aligned_cols=24 Identities=38% Similarity=0.812 Sum_probs=21.5
Q ss_pred eeecCccccccCCccchhhhhhhc
Q 024763 92 KFECQYCFKEFANSQALGGHQNAH 115 (263)
Q Consensus 92 pf~C~~CgKsF~ssssL~~HqR~H 115 (263)
.+.|.+|++.|.....|..|++.+
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 699999999999999999999865
No 31
>PHA00733 hypothetical protein
Probab=73.09 E-value=1.6 Score=36.05 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=22.9
Q ss_pred CceeecCccccccCCccchhhhhhhc
Q 024763 90 YKKFECQYCFKEFANSQALGGHQNAH 115 (263)
Q Consensus 90 eKpf~C~~CgKsF~ssssL~~HqR~H 115 (263)
+++|.|..|++.|.....|..|++..
T Consensus 97 ~~~~~C~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 97 EHSKVCPVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred CcCccCCCCCCccCCHHHHHHHHHHh
Confidence 46799999999999999999998654
No 32
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=65.56 E-value=6.2 Score=36.02 Aligned_cols=39 Identities=31% Similarity=0.430 Sum_probs=31.3
Q ss_pred CCCCC--ceeecC--ccccccCCccchhhhhhhccCCCchhHH
Q 024763 86 GESDY--KKFECQ--YCFKEFANSQALGGHQNAHKKERMKKKR 124 (263)
Q Consensus 86 tHTge--Kpf~C~--~CgKsF~ssssL~~HqR~HtGEKPykkR 124 (263)
.|+++ +++.|. .|++.|.+...+..|...|++.++++..
T Consensus 313 ~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 313 NHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred ccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 57788 888888 6888888888888888888887766633
No 33
>PHA02768 hypothetical protein; Provisional
Probab=63.24 E-value=2.9 Score=30.08 Aligned_cols=24 Identities=4% Similarity=0.018 Sum_probs=19.7
Q ss_pred CCCCCCceeecCccccccCCccchhh
Q 024763 85 TGESDYKKFECQYCFKEFANSQALGG 110 (263)
Q Consensus 85 ~tHTgeKpf~C~~CgKsF~ssssL~~ 110 (263)
.+|+ ++|+|..|++.|.+.+.|..
T Consensus 26 r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 26 RKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred HhcC--CcccCCcccceecccceeEE
Confidence 3466 79999999999998887763
No 34
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=61.65 E-value=3.8 Score=40.74 Aligned_cols=25 Identities=32% Similarity=0.642 Sum_probs=23.4
Q ss_pred eeecCccccccCCccchhhhhhhcc
Q 024763 92 KFECQYCFKEFANSQALGGHQNAHK 116 (263)
Q Consensus 92 pf~C~~CgKsF~ssssL~~HqR~Ht 116 (263)
-|+|.+|+|.|.-..+|..|.|-|.
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred eecCCcccccccCchhhhhhhcccC
Confidence 4999999999999999999999885
No 35
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=57.21 E-value=2.6 Score=41.88 Aligned_cols=27 Identities=33% Similarity=0.598 Sum_probs=24.3
Q ss_pred ceeecCccccccCCccchhhhhhhccC
Q 024763 91 KKFECQYCFKEFANSQALGGHQNAHKK 117 (263)
Q Consensus 91 Kpf~C~~CgKsF~ssssL~~HqR~HtG 117 (263)
.-|.|.+|+|.|.+...|+.|+.+|..
T Consensus 355 gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 355 GIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 379999999999999999999988853
No 36
>PLN03086 PRLI-interacting factor K; Provisional
Probab=57.11 E-value=5.6 Score=40.89 Aligned_cols=33 Identities=18% Similarity=0.342 Sum_probs=28.8
Q ss_pred ceeecCccccccCCccchhhhhhhccCCCchhHHH
Q 024763 91 KKFECQYCFKEFANSQALGGHQNAHKKERMKKKRL 125 (263)
Q Consensus 91 Kpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR~ 125 (263)
+++.|. |++.+ .+..|..|++.|..+|++.|++
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~f 509 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRF 509 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCC
Confidence 789999 99765 6689999999999999999774
No 37
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=51.86 E-value=9.3 Score=37.42 Aligned_cols=39 Identities=18% Similarity=0.196 Sum_probs=31.4
Q ss_pred CCCCCCCceeecCccccccCCccchhhhhhhccC--CCchh
Q 024763 84 PTGESDYKKFECQYCFKEFANSQALGGHQNAHKK--ERMKK 122 (263)
Q Consensus 84 ~~tHTgeKpf~C~~CgKsF~ssssL~~HqR~HtG--EKPyk 122 (263)
.++|+++|...|..||.-|.+...|-.|.|..+. ..+|.
T Consensus 199 ~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fq 239 (467)
T KOG3608|consen 199 IRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQ 239 (467)
T ss_pred HHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchH
Confidence 4678999999999999999999999999876543 34555
No 38
>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=45.69 E-value=13 Score=31.22 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=18.7
Q ss_pred ceeecCccccccCCccchhhhhhhccCCCchh
Q 024763 91 KKFECQYCFKEFANSQALGGHQNAHKKERMKK 122 (263)
Q Consensus 91 Kpf~C~~CgKsF~ssssL~~HqR~HtGEKPyk 122 (263)
.-..|-+|||.|. .|.+|.+.|.|--|-.
T Consensus 71 d~i~clecGk~~k---~LkrHL~~~~gltp~e 99 (132)
T PF05443_consen 71 DYIICLECGKKFK---TLKRHLRTHHGLTPEE 99 (132)
T ss_dssp S-EE-TBT--EES---BHHHHHHHTT-S-HHH
T ss_pred CeeEEccCCcccc---hHHHHHHHccCCCHHH
Confidence 4568999999998 5799999998876633
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=40.41 E-value=15 Score=25.51 Aligned_cols=26 Identities=38% Similarity=0.782 Sum_probs=19.2
Q ss_pred eeecCccccccCCccchhhhhh-hccCC
Q 024763 92 KFECQYCFKEFANSQALGGHQN-AHKKE 118 (263)
Q Consensus 92 pf~C~~CgKsF~ssssL~~HqR-~HtGE 118 (263)
.|.|++|++.| ....|..|.. .|..+
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSE 28 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCC
Confidence 48999999954 4577999954 45554
No 40
>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=39.89 E-value=15 Score=24.21 Aligned_cols=23 Identities=39% Similarity=0.569 Sum_probs=14.1
Q ss_pred CceeecCccccccCCc----cchhhhh
Q 024763 90 YKKFECQYCFKEFANS----QALGGHQ 112 (263)
Q Consensus 90 eKpf~C~~CgKsF~ss----ssL~~Hq 112 (263)
.....|.+|++.+... +.|..|+
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 4567899999988875 5677776
No 41
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=39.68 E-value=16 Score=25.03 Aligned_cols=25 Identities=32% Similarity=0.671 Sum_probs=18.5
Q ss_pred eeecCccccccCCc-----cchhhhhh-hcc
Q 024763 92 KFECQYCFKEFANS-----QALGGHQN-AHK 116 (263)
Q Consensus 92 pf~C~~CgKsF~ss-----ssL~~HqR-~Ht 116 (263)
.-.|.+|++.+... ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 45799999998765 47778876 453
No 42
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=34.84 E-value=7.5 Score=31.86 Aligned_cols=36 Identities=22% Similarity=0.420 Sum_probs=27.1
Q ss_pred CCCceeecCccccccCCccchhhhhhhccCCCchhHHHhh
Q 024763 88 SDYKKFECQYCFKEFANSQALGGHQNAHKKERMKKKRLQL 127 (263)
Q Consensus 88 TgeKpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR~~~ 127 (263)
.|-..|-|-.|.+-|.+...|..|.+ .+++++|...
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~Hkk----gkvHkRR~Ke 86 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKK----GKVHKRRAKE 86 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhc----cchhHHHHHH
Confidence 45557899999999999999988765 3566666443
No 43
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=33.71 E-value=17 Score=33.20 Aligned_cols=35 Identities=20% Similarity=0.243 Sum_probs=31.2
Q ss_pred ceeecCccccccCCccchhhhhh--hccCC--CchhHHH
Q 024763 91 KKFECQYCFKEFANSQALGGHQN--AHKKE--RMKKKRL 125 (263)
Q Consensus 91 Kpf~C~~CgKsF~ssssL~~HqR--~HtGE--KPykkR~ 125 (263)
.++.|..|...|.....|..|.+ .|+++ +++.+-.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~ 326 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPY 326 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeec
Confidence 47899999999999999999999 89999 8887553
No 44
>PRK04860 hypothetical protein; Provisional
Probab=33.12 E-value=19 Score=31.11 Aligned_cols=22 Identities=9% Similarity=0.182 Sum_probs=18.1
Q ss_pred CCCCCCceeecCccccccCCcc
Q 024763 85 TGESDYKKFECQYCFKEFANSQ 106 (263)
Q Consensus 85 ~tHTgeKpf~C~~CgKsF~sss 106 (263)
.+|+++++|.|..|+..|....
T Consensus 136 ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 136 RVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred HHhcCCccEECCCCCceeEEec
Confidence 4678999999999999887543
No 45
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=32.68 E-value=17 Score=33.84 Aligned_cols=21 Identities=43% Similarity=0.749 Sum_probs=17.0
Q ss_pred ecCccccccCCccchhhhhhh
Q 024763 94 ECQYCFKEFANSQALGGHQNA 114 (263)
Q Consensus 94 ~C~~CgKsF~ssssL~~HqR~ 114 (263)
.|-+|.+.|....-|.+||+.
T Consensus 12 wcwycnrefddekiliqhqka 32 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA 32 (341)
T ss_pred eeeecccccchhhhhhhhhhh
Confidence 588888888888888888763
No 46
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=32.65 E-value=21 Score=29.80 Aligned_cols=37 Identities=24% Similarity=0.467 Sum_probs=29.4
Q ss_pred CCCceeecCccccccCCccchhhhhhhccCCCchhHHHhhh
Q 024763 88 SDYKKFECQYCFKEFANSQALGGHQNAHKKERMKKKRLQLQ 128 (263)
Q Consensus 88 TgeKpf~C~~CgKsF~ssssL~~HqR~HtGEKPykkR~~~~ 128 (263)
.|-..|.|-.|.+-|.....|..|.++ |.+++|....
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~kt----K~HKrRvK~l 89 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKT----KVHKRRVKEL 89 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhc----cHHHHHHHhc
Confidence 455679999999999999999888764 6677775544
No 47
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=29.81 E-value=17 Score=26.59 Aligned_cols=28 Identities=18% Similarity=0.254 Sum_probs=24.5
Q ss_pred CCCCceeecCccccccCCccchhhhhhh
Q 024763 87 ESDYKKFECQYCFKEFANSQALGGHQNA 114 (263)
Q Consensus 87 HTgeKpf~C~~CgKsF~ssssL~~HqR~ 114 (263)
..||.-+.|+-|+..|...-...+|.+.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 4678889999999999999999999764
No 48
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=26.70 E-value=33 Score=29.22 Aligned_cols=27 Identities=22% Similarity=0.196 Sum_probs=22.8
Q ss_pred eecCccccccCCccchhhhhhhccCCCchh
Q 024763 93 FECQYCFKEFANSQALGGHQNAHKKERMKK 122 (263)
Q Consensus 93 f~C~~CgKsF~ssssL~~HqR~HtGEKPyk 122 (263)
..|-+|||.|. .|++|..+|-|--|-.
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTPd~ 103 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTPDE 103 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCHHH
Confidence 57999999998 6999999998876644
No 49
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=25.30 E-value=76 Score=31.20 Aligned_cols=58 Identities=16% Similarity=0.159 Sum_probs=46.1
Q ss_pred CCCceeecCccccccCCccchhhh-hhhccCCCchhHHHhhhhhhhhcccCCCccccCCC
Q 024763 88 SDYKKFECQYCFKEFANSQALGGH-QNAHKKERMKKKRLQLQARKASLNSYLQPYQNMYN 146 (263)
Q Consensus 88 TgeKpf~C~~CgKsF~ssssL~~H-qR~HtGEKPykkR~~~~s~~~s~~~~l~p~~~~~~ 146 (263)
+..+||+|. |++...+.+.|..| +++|-++..---|+..+.....-..++++|+..+.
T Consensus 209 t~~~p~k~~-~~~~~~T~~~l~~HS~N~~~~~Sa~n~~~~~Q~~~~~~st~~~~~~~~h~ 267 (442)
T KOG4124|consen 209 TTGTPKKMP-ESLVMDTSSPLSDHSMNIDVGESAANNVFAFQQKDMVDSTYLPPFNYDHD 267 (442)
T ss_pred cccCCccCc-ccccccccchhhhccccCCCCccHHHHHHHHhhcccccccccCCcCccch
Confidence 456799985 89999999999988 56777776555677788777777889998887755
No 50
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=22.89 E-value=16 Score=38.87 Aligned_cols=26 Identities=27% Similarity=0.530 Sum_probs=23.7
Q ss_pred ceeecCccccccCCccchhhhhhhcc
Q 024763 91 KKFECQYCFKEFANSQALGGHQNAHK 116 (263)
Q Consensus 91 Kpf~C~~CgKsF~ssssL~~HqR~Ht 116 (263)
.-|.|.+|+|.|-.--.+..||+.|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 45999999999999999999999995
No 51
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=20.98 E-value=33 Score=32.09 Aligned_cols=29 Identities=28% Similarity=0.595 Sum_probs=23.2
Q ss_pred CCCCceeecCccccccCCccchhhh-hhhc
Q 024763 87 ESDYKKFECQYCFKEFANSQALGGH-QNAH 115 (263)
Q Consensus 87 HTgeKpf~C~~CgKsF~ssssL~~H-qR~H 115 (263)
|...|-|+|.+|.|.+.+.-.|..| +.+|
T Consensus 29 hqkakhfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 29 HQKAKHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred hhhhccceeeeehhhhccCCCceeehhhhh
Confidence 5666889999999988888888877 4555
Done!