Query 035649
Match_columns 163
No_of_seqs 164 out of 1047
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 04:58:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035649.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035649hhsearch_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 98.5 7.7E-08 1.7E-12 82.7 2.3 52 2-53 194-245 (279)
2 KOG1074 Transcriptional repres 97.8 3.8E-06 8.3E-11 81.1 -0.1 59 2-60 886-944 (958)
3 KOG3623 Homeobox transcription 97.8 5.1E-06 1.1E-10 79.6 0.7 46 8-53 907-952 (1007)
4 KOG1074 Transcriptional repres 97.8 1.2E-05 2.5E-10 77.8 2.7 44 9-52 619-662 (958)
5 PF13465 zf-H2C2_2: Zinc-finge 97.7 3.7E-06 8E-11 47.9 -1.8 25 11-35 2-26 (26)
6 KOG2462 C2H2-type Zn-finger pr 97.4 3.9E-05 8.5E-10 66.2 0.6 52 11-66 177-228 (279)
7 KOG3576 Ovo and related transc 97.4 5.6E-05 1.2E-09 63.6 1.0 59 2-60 152-211 (267)
8 PHA00616 hypothetical protein 97.2 9.6E-05 2.1E-09 47.6 0.5 31 23-53 1-31 (44)
9 PF00096 zf-C2H2: Zinc finger, 96.9 0.00045 9.7E-09 37.3 1.4 23 24-46 1-23 (23)
10 KOG3623 Homeobox transcription 96.6 0.00049 1.1E-08 66.4 -0.3 42 2-43 288-329 (1007)
11 PHA02768 hypothetical protein; 96.5 0.0011 2.5E-08 44.6 1.3 25 23-47 5-29 (55)
12 PF13912 zf-C2H2_6: C2H2-type 96.5 0.0014 3E-08 36.7 1.3 25 23-47 1-25 (27)
13 KOG3576 Ovo and related transc 96.4 0.00031 6.8E-09 59.2 -2.7 52 2-53 124-175 (267)
14 PF13894 zf-C2H2_4: C2H2-type 96.2 0.003 6.4E-08 33.4 1.7 23 24-46 1-23 (24)
15 PHA02768 hypothetical protein; 95.8 0.0015 3.3E-08 43.9 -1.0 37 2-40 12-48 (55)
16 smart00355 ZnF_C2H2 zinc finge 95.6 0.0084 1.8E-07 31.8 1.6 24 24-47 1-24 (26)
17 PF09237 GAGA: GAGA factor; I 95.0 0.03 6.4E-07 37.5 3.2 34 18-51 19-52 (54)
18 PHA00733 hypothetical protein 94.0 0.027 5.7E-07 43.3 1.3 35 11-46 62-96 (128)
19 PF12874 zf-met: Zinc-finger o 93.1 0.045 9.8E-07 29.8 1.0 23 24-46 1-23 (25)
20 PHA00733 hypothetical protein 92.1 0.091 2E-06 40.3 1.9 42 2-45 80-121 (128)
21 PHA00732 hypothetical protein 91.8 0.11 2.3E-06 37.0 1.7 26 23-48 1-27 (79)
22 PF12171 zf-C2H2_jaz: Zinc-fin 90.5 0.13 2.7E-06 28.9 0.9 22 24-45 2-23 (27)
23 PF13909 zf-H2C2_5: C2H2-type 89.4 0.23 5E-06 26.9 1.4 22 24-46 1-22 (24)
24 PF13913 zf-C2HC_2: zinc-finge 87.6 0.36 7.8E-06 27.1 1.4 21 24-45 3-23 (25)
25 smart00451 ZnF_U1 U1-like zinc 83.7 0.72 1.6E-05 26.7 1.4 23 23-45 3-25 (35)
26 KOG3608 Zn finger proteins [Ge 83.6 0.52 1.1E-05 42.9 1.1 38 10-47 278-316 (467)
27 KOG3993 Transcription factor ( 82.9 0.65 1.4E-05 42.9 1.5 38 11-48 283-320 (500)
28 PF12756 zf-C2H2_2: C2H2 type 80.9 1.1 2.4E-05 30.8 1.8 24 23-46 50-73 (100)
29 PHA00732 hypothetical protein 78.3 0.99 2.1E-05 32.1 0.9 38 2-45 8-46 (79)
30 PLN03086 PRLI-interacting fact 74.2 1.9 4.2E-05 40.9 1.9 39 11-53 468-506 (567)
31 KOG2893 Zn finger protein [Gen 66.9 1.4 3.1E-05 38.2 -0.6 40 3-46 18-58 (341)
32 PLN03086 PRLI-interacting fact 65.9 2.4 5.2E-05 40.3 0.6 27 20-47 450-476 (567)
33 KOG3608 Zn finger proteins [Ge 64.2 1.8 3.8E-05 39.5 -0.6 38 8-45 192-229 (467)
34 COG4049 Uncharacterized protei 63.1 3.8 8.3E-05 28.1 1.0 28 18-45 12-39 (65)
35 COG5048 FOG: Zn-finger [Genera 62.6 5.9 0.00013 33.0 2.3 50 4-53 298-353 (467)
36 PF05605 zf-Di19: Drought indu 59.9 7.3 0.00016 25.1 1.9 26 23-49 2-28 (54)
37 KOG3993 Transcription factor ( 59.6 3.9 8.4E-05 38.0 0.7 29 19-47 352-380 (500)
38 PRK04860 hypothetical protein; 57.4 14 0.00029 29.6 3.4 29 22-54 118-146 (160)
39 COG4957 Predicted transcriptio 48.0 22 0.00048 28.3 3.1 32 23-57 76-107 (148)
40 smart00614 ZnF_BED BED zinc fi 38.4 25 0.00055 22.2 1.8 26 22-47 17-48 (50)
41 PF05443 ROS_MUCR: ROS/MUCR tr 37.9 25 0.00055 27.4 2.1 30 21-53 70-99 (132)
42 COG5189 SFP1 Putative transcri 36.8 18 0.00039 32.7 1.2 24 21-44 347-372 (423)
43 PF02892 zf-BED: BED zinc fing 36.5 25 0.00055 21.3 1.5 24 20-43 13-40 (45)
44 KOG4167 Predicted DNA-binding 33.1 8.3 0.00018 38.1 -1.6 27 22-48 791-817 (907)
45 KOG2482 Predicted C2H2-type Zn 31.6 23 0.00049 32.4 1.0 23 23-45 195-217 (423)
46 KOG2071 mRNA cleavage and poly 28.9 33 0.00072 32.9 1.7 29 21-49 416-444 (579)
47 PF04959 ARS2: Arsenite-resist 27.8 23 0.0005 29.7 0.4 31 19-49 73-103 (214)
48 PF13878 zf-C2H2_3: zinc-finge 23.9 55 0.0012 20.2 1.5 25 23-47 13-39 (41)
49 smart00834 CxxC_CXXC_SSSS Puta 22.9 45 0.00097 19.6 0.9 16 22-37 4-19 (41)
50 PF12013 DUF3505: Protein of u 21.6 65 0.0014 23.3 1.7 25 23-47 80-108 (109)
51 PF09845 DUF2072: Zn-ribbon co 21.4 43 0.00094 26.2 0.8 15 23-37 1-15 (131)
52 PF08790 zf-LYAR: LYAR-type C2 20.6 45 0.00098 19.5 0.6 23 24-47 1-23 (28)
53 PF10276 zf-CHCC: Zinc-finger 20.2 54 0.0012 20.5 0.9 12 22-33 28-39 (40)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=98.46 E-value=7.7e-08 Score=82.66 Aligned_cols=52 Identities=17% Similarity=0.347 Sum_probs=49.4
Q ss_pred CCCCCCCcccccCCCCCCCCceeeCCCCCccccCchhhhhhhhhccCccchH
Q 035649 2 GDDHHRGKVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNAHKKERTAA 53 (163)
Q Consensus 2 g~~~~~~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~HqriHtgERp~a 53 (163)
|+.|-+-=.|+-|-|+|||+|||.|..|+|.|..+.+|..||++|.+.|.|.
T Consensus 194 GKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~q 245 (279)
T KOG2462|consen 194 GKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQ 245 (279)
T ss_pred cccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcccc
Confidence 7888888899999999999999999999999999999999999999988876
No 2
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.82 E-value=3.8e-06 Score=81.08 Aligned_cols=59 Identities=19% Similarity=0.318 Sum_probs=52.3
Q ss_pred CCCCCCCcccccCCCCCCCCceeeCCCCCccccCchhhhhhhhhccCccchHHhhhhcc
Q 035649 2 GDDHHRGKVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNAHKKERTAARKAKRVA 60 (163)
Q Consensus 2 g~~~~~~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~HqriHtgERp~a~r~~~~~ 60 (163)
|+-|-.-..|++|+++|+++|||.|.+|++.|.....|+.||..|.+..++++|+.+.+
T Consensus 886 gk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srrG~~~~ 944 (958)
T KOG1074|consen 886 GKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRRGPSPF 944 (958)
T ss_pred hhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccCCCCcc
Confidence 44455555689999999999999999999999999999999999999999999977655
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=97.82 E-value=5.1e-06 Score=79.59 Aligned_cols=46 Identities=22% Similarity=0.458 Sum_probs=43.9
Q ss_pred CcccccCCCCCCCCceeeCCCCCccccCchhhhhhhhhccCccchH
Q 035649 8 GKVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNAHKKERTAA 53 (163)
Q Consensus 8 ~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~HqriHtgERp~a 53 (163)
..+|.+|.=.|+|.+||+|.+|.|.|..+..|..|+|.|.|||||.
T Consensus 907 qSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQ 952 (1007)
T KOG3623|consen 907 QSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQ 952 (1007)
T ss_pred hHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcch
Confidence 4578999999999999999999999999999999999999999997
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=97.79 E-value=1.2e-05 Score=77.85 Aligned_cols=44 Identities=25% Similarity=0.424 Sum_probs=39.7
Q ss_pred cccccCCCCCCCCceeeCCCCCccccCchhhhhhhhhccCccch
Q 035649 9 KVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNAHKKERTA 52 (163)
Q Consensus 9 ~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~HqriHtgERp~ 52 (163)
..|+-|-|+|+++|||+|.+|++.|..+.+|+.|+.+|+..-++
T Consensus 619 saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~ 662 (958)
T KOG1074|consen 619 SALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA 662 (958)
T ss_pred hhhhhhhhcccCcCccccccccchhccccchhhcccccccCccc
Confidence 45788999999999999999999999999999999999865444
No 5
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=97.66 E-value=3.7e-06 Score=47.92 Aligned_cols=25 Identities=12% Similarity=0.466 Sum_probs=22.5
Q ss_pred cccCCCCCCCCceeeCCCCCccccC
Q 035649 11 SAEANVDDSSPRVFPCLFCSRKFYS 35 (163)
Q Consensus 11 ~~~h~~~HTg~KPfkC~~CgksFss 35 (163)
|..|.++|++++||+|++|++.|.+
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 5678899999999999999999863
No 6
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=97.43 E-value=3.9e-05 Score=66.16 Aligned_cols=52 Identities=15% Similarity=0.235 Sum_probs=40.7
Q ss_pred cccCCCCCCCCceeeCCCCCccccCchhhhhhhhhccCccchHHhhhhccccccCC
Q 035649 11 SAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNAHKKERTAARKAKRVASDHLHQ 66 (163)
Q Consensus 11 ~~~h~~~HTg~KPfkC~~CgksFsssqsL~~HqriHtgERp~a~r~~~~~~~~~~~ 66 (163)
|.-|-++|+ -+++|.+|+|.|...=-|.+|+|.|+|||||. +..++-+|+|+
T Consensus 177 LkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~--C~hC~kAFADR 228 (279)
T KOG2462|consen 177 LKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFS--CPHCGKAFADR 228 (279)
T ss_pred HhhHhhccC--CCcccccccccccchHHhhcccccccCCCCcc--CCcccchhcch
Confidence 455666666 78999999999999999999999999999997 33444344443
No 7
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=97.38 E-value=5.6e-05 Score=63.56 Aligned_cols=59 Identities=19% Similarity=0.321 Sum_probs=48.8
Q ss_pred CCCCCCCcccccCCCCCCCCceeeCCCCCccccCchhhhhhh-hhccCccchHHhhhhcc
Q 035649 2 GDDHHRGKVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQ-NAHKKERTAARKAKRVA 60 (163)
Q Consensus 2 g~~~~~~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~Hq-riHtgERp~a~r~~~~~ 60 (163)
|+-||----|.+|.++||+.+||+|..|++.|.+.-+|..|. ++|.....||-+.+|..
T Consensus 152 gkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~k 211 (267)
T KOG3576|consen 152 GKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAK 211 (267)
T ss_pred cCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhh
Confidence 566666667889999999999999999999999999999996 56766677776666654
No 8
>PHA00616 hypothetical protein
Probab=97.23 E-value=9.6e-05 Score=47.65 Aligned_cols=31 Identities=19% Similarity=0.397 Sum_probs=28.7
Q ss_pred eeeCCCCCccccCchhhhhhhhhccCccchH
Q 035649 23 VFPCLFCSRKFYSSQALGGHQNAHKKERTAA 53 (163)
Q Consensus 23 PfkC~~CgksFsssqsL~~HqriHtgERp~a 53 (163)
||+|..|++.|...+.|..|++.|++++++.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 6899999999999999999999999988764
No 9
>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=96.95 E-value=0.00045 Score=37.34 Aligned_cols=23 Identities=30% Similarity=0.714 Sum_probs=21.3
Q ss_pred eeCCCCCccccCchhhhhhhhhc
Q 035649 24 FPCLFCSRKFYSSQALGGHQNAH 46 (163)
Q Consensus 24 fkC~~CgksFsssqsL~~HqriH 46 (163)
|+|..|++.|.....|..|++.|
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 78999999999999999999864
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=96.57 E-value=0.00049 Score=66.36 Aligned_cols=42 Identities=21% Similarity=0.312 Sum_probs=28.8
Q ss_pred CCCCCCCcccccCCCCCCCCceeeCCCCCccccCchhhhhhh
Q 035649 2 GDDHHRGKVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQ 43 (163)
Q Consensus 2 g~~~~~~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~Hq 43 (163)
|+.|.|+-.|..|-|+|+|+|||.|..|.|.|+.+.++..||
T Consensus 288 gKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 288 GKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred chhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccc
Confidence 566666666666777777777777777777777666666665
No 11
>PHA02768 hypothetical protein; Provisional
Probab=96.54 E-value=0.0011 Score=44.55 Aligned_cols=25 Identities=16% Similarity=0.493 Sum_probs=23.8
Q ss_pred eeeCCCCCccccCchhhhhhhhhcc
Q 035649 23 VFPCLFCSRKFYSSQALGGHQNAHK 47 (163)
Q Consensus 23 PfkC~~CgksFsssqsL~~HqriHt 47 (163)
-|+|++|++.|...++|..|++.|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 4799999999999999999999998
No 12
>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=96.49 E-value=0.0014 Score=36.67 Aligned_cols=25 Identities=36% Similarity=0.602 Sum_probs=23.0
Q ss_pred eeeCCCCCccccCchhhhhhhhhcc
Q 035649 23 VFPCLFCSRKFYSSQALGGHQNAHK 47 (163)
Q Consensus 23 PfkC~~CgksFsssqsL~~HqriHt 47 (163)
||+|..|++.|.+...|..|++.|.
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 6899999999999999999998774
No 13
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=96.37 E-value=0.00031 Score=59.15 Aligned_cols=52 Identities=19% Similarity=0.294 Sum_probs=46.9
Q ss_pred CCCCCCCcccccCCCCCCCCceeeCCCCCccccCchhhhhhhhhccCccchH
Q 035649 2 GDDHHRGKVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNAHKKERTAA 53 (163)
Q Consensus 2 g~~~~~~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~HqriHtgERp~a 53 (163)
|+.|.+.-.|-+|-+-|+..+.+.|..|+++|...-.|++|+++|++-|||.
T Consensus 124 gK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpyk 175 (267)
T KOG3576|consen 124 GKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYK 175 (267)
T ss_pred hhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccc
Confidence 5666777778889999999999999999999999999999999999999986
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=96.24 E-value=0.003 Score=33.44 Aligned_cols=23 Identities=35% Similarity=0.772 Sum_probs=19.3
Q ss_pred eeCCCCCccccCchhhhhhhhhc
Q 035649 24 FPCLFCSRKFYSSQALGGHQNAH 46 (163)
Q Consensus 24 fkC~~CgksFsssqsL~~HqriH 46 (163)
|.|++|++.|.+...|..|+..|
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 78999999999999999998765
No 15
>PHA02768 hypothetical protein; Provisional
Probab=95.79 E-value=0.0015 Score=43.92 Aligned_cols=37 Identities=11% Similarity=-0.014 Sum_probs=32.8
Q ss_pred CCCCCCCcccccCCCCCCCCceeeCCCCCccccCchhhh
Q 035649 2 GDDHHRGKVSAEANVDDSSPRVFPCLFCSRKFYSSQALG 40 (163)
Q Consensus 2 g~~~~~~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~ 40 (163)
|+.|.+...|..|+++|+ ++++|..|++.|.....|.
T Consensus 12 GK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 12 GEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred CCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 788899999999999999 7999999999999776654
No 16
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.57 E-value=0.0084 Score=31.80 Aligned_cols=24 Identities=33% Similarity=0.632 Sum_probs=21.6
Q ss_pred eeCCCCCccccCchhhhhhhhhcc
Q 035649 24 FPCLFCSRKFYSSQALGGHQNAHK 47 (163)
Q Consensus 24 fkC~~CgksFsssqsL~~HqriHt 47 (163)
|+|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998764
No 17
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.02 E-value=0.03 Score=37.50 Aligned_cols=34 Identities=18% Similarity=0.304 Sum_probs=23.8
Q ss_pred CCCCceeeCCCCCccccCchhhhhhhhhccCccc
Q 035649 18 DSSPRVFPCLFCSRKFYSSQALGGHQNAHKKERT 51 (163)
Q Consensus 18 HTg~KPfkC~~CgksFsssqsL~~HqriHtgERp 51 (163)
...+.|-.|++|+..+.++.+|.+|+.++.+.+|
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 3457899999999999999999999988766554
No 18
>PHA00733 hypothetical protein
Probab=93.96 E-value=0.027 Score=43.32 Aligned_cols=35 Identities=20% Similarity=0.244 Sum_probs=27.8
Q ss_pred cccCCCCCCCCceeeCCCCCccccCchhhhhhhhhc
Q 035649 11 SAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNAH 46 (163)
Q Consensus 11 ~~~h~~~HTg~KPfkC~~CgksFsssqsL~~HqriH 46 (163)
+..+..++ ..+||.|..|++.|.+...|..|++.+
T Consensus 62 l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h 96 (128)
T PHA00733 62 LYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT 96 (128)
T ss_pred HHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC
Confidence 44454443 478999999999999999999999865
No 19
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.10 E-value=0.045 Score=29.82 Aligned_cols=23 Identities=30% Similarity=0.657 Sum_probs=20.6
Q ss_pred eeCCCCCccccCchhhhhhhhhc
Q 035649 24 FPCLFCSRKFYSSQALGGHQNAH 46 (163)
Q Consensus 24 fkC~~CgksFsssqsL~~HqriH 46 (163)
|.|..|.+.|.+...+..|++.+
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 68999999999999999998754
No 20
>PHA00733 hypothetical protein
Probab=92.15 E-value=0.091 Score=40.34 Aligned_cols=42 Identities=10% Similarity=0.044 Sum_probs=30.3
Q ss_pred CCCCCCCcccccCCCCCCCCceeeCCCCCccccCchhhhhhhhh
Q 035649 2 GDDHHRGKVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNA 45 (163)
Q Consensus 2 g~~~~~~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~Hqri 45 (163)
|..+.....|..|.+.+ ..+|.|..|++.|.....|..|+..
T Consensus 80 gk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~ 121 (128)
T PHA00733 80 LMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCK 121 (128)
T ss_pred CCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHH
Confidence 44556666677777765 3568888888888888888888754
No 21
>PHA00732 hypothetical protein
Probab=91.76 E-value=0.11 Score=37.01 Aligned_cols=26 Identities=27% Similarity=0.441 Sum_probs=21.7
Q ss_pred eeeCCCCCccccCchhhhhhhhh-ccC
Q 035649 23 VFPCLFCSRKFYSSQALGGHQNA-HKK 48 (163)
Q Consensus 23 PfkC~~CgksFsssqsL~~Hqri-Htg 48 (163)
||.|..|++.|.+...|..|++. |.+
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 57899999999999999999874 654
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=90.54 E-value=0.13 Score=28.91 Aligned_cols=22 Identities=32% Similarity=0.584 Sum_probs=20.0
Q ss_pred eeCCCCCccccCchhhhhhhhh
Q 035649 24 FPCLFCSRKFYSSQALGGHQNA 45 (163)
Q Consensus 24 fkC~~CgksFsssqsL~~Hqri 45 (163)
|.|..|++.|.+...+..|++.
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 6899999999999999999864
No 23
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=89.41 E-value=0.23 Score=26.87 Aligned_cols=22 Identities=27% Similarity=0.516 Sum_probs=17.2
Q ss_pred eeCCCCCccccCchhhhhhhhhc
Q 035649 24 FPCLFCSRKFYSSQALGGHQNAH 46 (163)
Q Consensus 24 fkC~~CgksFsssqsL~~HqriH 46 (163)
|+|..|..... ...|..|++.+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 78999998887 88999998764
No 24
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=87.60 E-value=0.36 Score=27.12 Aligned_cols=21 Identities=38% Similarity=0.890 Sum_probs=17.2
Q ss_pred eeCCCCCccccCchhhhhhhhh
Q 035649 24 FPCLFCSRKFYSSQALGGHQNA 45 (163)
Q Consensus 24 fkC~~CgksFsssqsL~~Hqri 45 (163)
..|..|++.| ....|..|+.+
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 67778888754
No 25
>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=83.69 E-value=0.72 Score=26.68 Aligned_cols=23 Identities=22% Similarity=0.504 Sum_probs=19.8
Q ss_pred eeeCCCCCccccCchhhhhhhhh
Q 035649 23 VFPCLFCSRKFYSSQALGGHQNA 45 (163)
Q Consensus 23 PfkC~~CgksFsssqsL~~Hqri 45 (163)
+|.|.+|.+.|.+...+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999888888753
No 26
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=83.59 E-value=0.52 Score=42.85 Aligned_cols=38 Identities=18% Similarity=0.280 Sum_probs=31.3
Q ss_pred ccccCCC-CCCCCceeeCCCCCccccCchhhhhhhhhcc
Q 035649 10 VSAEANV-DDSSPRVFPCLFCSRKFYSSQALGGHQNAHK 47 (163)
Q Consensus 10 ~~~~h~~-~HTg~KPfkC~~CgksFsssqsL~~HqriHt 47 (163)
+|..|-+ .|+.+|||+|+.|.+.|.....|..|..+|+
T Consensus 278 sL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 278 SLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 4455544 3677899999999999999999999998887
No 27
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=82.93 E-value=0.65 Score=42.92 Aligned_cols=38 Identities=21% Similarity=0.335 Sum_probs=32.6
Q ss_pred cccCCCCCCCCceeeCCCCCccccCchhhhhhhhhccC
Q 035649 11 SAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNAHKK 48 (163)
Q Consensus 11 ~~~h~~~HTg~KPfkC~~CgksFsssqsL~~HqriHtg 48 (163)
|.+|.....-..-|+|.+|+|.|....+|..|++-|.-
T Consensus 283 LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 283 LAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred HhhccCCeeEEeeecCCcccccccCchhhhhhhcccCC
Confidence 56777776667789999999999999999999988853
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=80.87 E-value=1.1 Score=30.77 Aligned_cols=24 Identities=33% Similarity=0.765 Sum_probs=21.2
Q ss_pred eeeCCCCCccccCchhhhhhhhhc
Q 035649 23 VFPCLFCSRKFYSSQALGGHQNAH 46 (163)
Q Consensus 23 PfkC~~CgksFsssqsL~~HqriH 46 (163)
.+.|..|++.|.+...|..|++.+
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 699999999999999999999864
No 29
>PHA00732 hypothetical protein
Probab=78.27 E-value=0.99 Score=32.05 Aligned_cols=38 Identities=13% Similarity=0.164 Sum_probs=28.5
Q ss_pred CCCCCCCcccccCCCC-CCCCceeeCCCCCccccCchhhhhhhhh
Q 035649 2 GDDHHRGKVSAEANVD-DSSPRVFPCLFCSRKFYSSQALGGHQNA 45 (163)
Q Consensus 2 g~~~~~~~~~~~h~~~-HTg~KPfkC~~CgksFsssqsL~~Hqri 45 (163)
|..+.....|..|.+. |++ +.|..|++.|. .+..|...
T Consensus 8 gk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~---~l~~H~~~ 46 (79)
T PHA00732 8 GFTTVTLFALKQHARRNHTL---TKCPVCNKSYR---RLNQHFYS 46 (79)
T ss_pred CCccCCHHHHHHHhhcccCC---CccCCCCCEeC---Chhhhhcc
Confidence 5667778889999874 553 58999999998 46667643
No 30
>PLN03086 PRLI-interacting factor K; Provisional
Probab=74.23 E-value=1.9 Score=40.94 Aligned_cols=39 Identities=13% Similarity=0.120 Sum_probs=18.4
Q ss_pred cccCCCCCCCCceeeCCCCCccccCchhhhhhhhhccCccchH
Q 035649 11 SAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNAHKKERTAA 53 (163)
Q Consensus 11 ~~~h~~~HTg~KPfkC~~CgksFsssqsL~~HqriHtgERp~a 53 (163)
+..|..+++ +++.|. |++.+ .+..|..|+..|..++++.
T Consensus 468 LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~ 506 (567)
T PLN03086 468 MEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLIT 506 (567)
T ss_pred HHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCcee
Confidence 344444432 455555 55432 3345555555555444443
No 31
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=66.87 E-value=1.4 Score=38.24 Aligned_cols=40 Identities=23% Similarity=0.511 Sum_probs=30.8
Q ss_pred CCCCCCcccccCCCCCCCCceeeCCCCCccccCchhhhhh-hhhc
Q 035649 3 DDHHRGKVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGH-QNAH 46 (163)
Q Consensus 3 ~~~~~~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~H-qriH 46 (163)
.+|.-|+.|-+||+. |.|+|.+|.+++.+--.|..| |++|
T Consensus 18 refddekiliqhqka----khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 18 REFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred cccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhh
Confidence 356677888888875 889999999988887777666 4555
No 32
>PLN03086 PRLI-interacting factor K; Provisional
Probab=65.88 E-value=2.4 Score=40.33 Aligned_cols=27 Identities=15% Similarity=0.347 Sum_probs=19.6
Q ss_pred CCceeeCCCCCccccCchhhhhhhhhcc
Q 035649 20 SPRVFPCLFCSRKFYSSQALGGHQNAHK 47 (163)
Q Consensus 20 g~KPfkC~~CgksFsssqsL~~HqriHt 47 (163)
.++.+.|..|++.|. ...|..|+.+++
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~~H 476 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKVFH 476 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHhcC
Confidence 345678888888885 566888887764
No 33
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=64.24 E-value=1.8 Score=39.52 Aligned_cols=38 Identities=21% Similarity=0.250 Sum_probs=31.5
Q ss_pred CcccccCCCCCCCCceeeCCCCCccccCchhhhhhhhh
Q 035649 8 GKVSAEANVDDSSPRVFPCLFCSRKFYSSQALGGHQNA 45 (163)
Q Consensus 8 ~~~~~~h~~~HTg~KPfkC~~CgksFsssqsL~~Hqri 45 (163)
+..|..|-++|+++|.+.|..|+.-|.....|-.|.+-
T Consensus 192 k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rR 229 (467)
T KOG3608|consen 192 KYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRR 229 (467)
T ss_pred HHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHh
Confidence 34577888999999999999999999988888888643
No 34
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=63.08 E-value=3.8 Score=28.07 Aligned_cols=28 Identities=18% Similarity=0.294 Sum_probs=24.5
Q ss_pred CCCCceeeCCCCCccccCchhhhhhhhh
Q 035649 18 DSSPRVFPCLFCSRKFYSSQALGGHQNA 45 (163)
Q Consensus 18 HTg~KPfkC~~CgksFsssqsL~~Hqri 45 (163)
..++..+.|+-|+..|.....+.+|.+.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 4577889999999999999999999764
No 35
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=62.62 E-value=5.9 Score=32.98 Aligned_cols=50 Identities=22% Similarity=0.333 Sum_probs=39.2
Q ss_pred CCCCCcccccCCC--CCCCC--ceeeCC--CCCccccCchhhhhhhhhccCccchH
Q 035649 4 DHHRGKVSAEANV--DDSSP--RVFPCL--FCSRKFYSSQALGGHQNAHKKERTAA 53 (163)
Q Consensus 4 ~~~~~~~~~~h~~--~HTg~--KPfkC~--~CgksFsssqsL~~HqriHtgERp~a 53 (163)
.+.....+..|.+ .|+.+ +++.|. .|++.|.....+..|...|...++..
T Consensus 298 ~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 298 SFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred CccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccc
Confidence 3455666778888 78888 899999 79999999999998888887665443
No 36
>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=59.92 E-value=7.3 Score=25.10 Aligned_cols=26 Identities=31% Similarity=0.710 Sum_probs=19.5
Q ss_pred eeeCCCCCccccCchhhhhhhh-hccCc
Q 035649 23 VFPCLFCSRKFYSSQALGGHQN-AHKKE 49 (163)
Q Consensus 23 PfkC~~CgksFsssqsL~~Hqr-iHtgE 49 (163)
.|.|++|++ ..+...|..|.. .|..+
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 556778999964 45543
No 37
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=59.63 E-value=3.9 Score=38.00 Aligned_cols=29 Identities=38% Similarity=0.667 Sum_probs=24.8
Q ss_pred CCCceeeCCCCCccccCchhhhhhhhhcc
Q 035649 19 SSPRVFPCLFCSRKFYSSQALGGHQNAHK 47 (163)
Q Consensus 19 Tg~KPfkC~~CgksFsssqsL~~HqriHt 47 (163)
+.+--|.|.+|+++|.....|+.|+-.|.
T Consensus 352 ss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 352 SSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred ccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 34457999999999999999999987764
No 38
>PRK04860 hypothetical protein; Provisional
Probab=57.39 E-value=14 Score=29.60 Aligned_cols=29 Identities=14% Similarity=0.280 Sum_probs=24.4
Q ss_pred ceeeCCCCCccccCchhhhhhhhhccCccchHH
Q 035649 22 RVFPCLFCSRKFYSSQALGGHQNAHKKERTAAR 54 (163)
Q Consensus 22 KPfkC~~CgksFsssqsL~~HqriHtgERp~a~ 54 (163)
.+|.|. |+. ....+..|.++|+++++|..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC 146 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRC 146 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEEC
Confidence 589998 987 66678999999999998863
No 39
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=47.98 E-value=22 Score=28.29 Aligned_cols=32 Identities=28% Similarity=0.329 Sum_probs=25.7
Q ss_pred eeeCCCCCccccCchhhhhhhhhccCccchHHhhh
Q 035649 23 VFPCLFCSRKFYSSQALGGHQNAHKKERTAARKAK 57 (163)
Q Consensus 23 PfkC~~CgksFsssqsL~~HqriHtgERp~a~r~~ 57 (163)
-..|.+||++|. +|++|..+|-+..|-.-|.+
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~gmTPd~YR~K 107 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHYGLTPDEYRAK 107 (148)
T ss_pred eEEEeccCcchH---HHHHHHhcccCCCHHHHHHh
Confidence 357999999997 68999999988877665554
No 40
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=38.39 E-value=25 Score=22.19 Aligned_cols=26 Identities=27% Similarity=0.547 Sum_probs=19.1
Q ss_pred ceeeCCCCCccccCc-----hhhhhhhh-hcc
Q 035649 22 RVFPCLFCSRKFYSS-----QALGGHQN-AHK 47 (163)
Q Consensus 22 KPfkC~~CgksFsss-----qsL~~Hqr-iHt 47 (163)
.--.|.+|++.+... ..|..|++ .|.
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 456799999988765 47888876 443
No 41
>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=37.87 E-value=25 Score=27.37 Aligned_cols=30 Identities=30% Similarity=0.548 Sum_probs=18.4
Q ss_pred CceeeCCCCCccccCchhhhhhhhhccCccchH
Q 035649 21 PRVFPCLFCSRKFYSSQALGGHQNAHKKERTAA 53 (163)
Q Consensus 21 ~KPfkC~~CgksFsssqsL~~HqriHtgERp~a 53 (163)
+....|-+||+.|. .|++|...|.+..+-.
T Consensus 70 ~d~i~clecGk~~k---~LkrHL~~~~gltp~e 99 (132)
T PF05443_consen 70 PDYIICLECGKKFK---TLKRHLRTHHGLTPEE 99 (132)
T ss_dssp SS-EE-TBT--EES---BHHHHHHHTT-S-HHH
T ss_pred cCeeEEccCCcccc---hHHHHHHHccCCCHHH
Confidence 34578999999988 4689999997766644
No 42
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=36.80 E-value=18 Score=32.74 Aligned_cols=24 Identities=21% Similarity=0.523 Sum_probs=21.3
Q ss_pred CceeeCCC--CCccccCchhhhhhhh
Q 035649 21 PRVFPCLF--CSRKFYSSQALGGHQN 44 (163)
Q Consensus 21 ~KPfkC~~--CgksFsssqsL~~Hqr 44 (163)
+|||+|++ |.|+|.+...|+=|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhh
Confidence 49999987 9999999999998874
No 43
>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=36.47 E-value=25 Score=21.28 Aligned_cols=24 Identities=21% Similarity=0.429 Sum_probs=15.0
Q ss_pred CCceeeCCCCCccccCc----hhhhhhh
Q 035649 20 SPRVFPCLFCSRKFYSS----QALGGHQ 43 (163)
Q Consensus 20 g~KPfkC~~CgksFsss----qsL~~Hq 43 (163)
.+.-.+|.+|++.+... ..|..|+
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 45678899999988764 5677776
No 44
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=33.06 E-value=8.3 Score=38.13 Aligned_cols=27 Identities=26% Similarity=0.781 Sum_probs=24.2
Q ss_pred ceeeCCCCCccccCchhhhhhhhhccC
Q 035649 22 RVFPCLFCSRKFYSSQALGGHQNAHKK 48 (163)
Q Consensus 22 KPfkC~~CgksFsssqsL~~HqriHtg 48 (163)
--|.|.+|++.|..-.++..||+.|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 369999999999999999999999863
No 45
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=31.61 E-value=23 Score=32.35 Aligned_cols=23 Identities=26% Similarity=0.668 Sum_probs=21.2
Q ss_pred eeeCCCCCccccCchhhhhhhhh
Q 035649 23 VFPCLFCSRKFYSSQALGGHQNA 45 (163)
Q Consensus 23 PfkC~~CgksFsssqsL~~Hqri 45 (163)
.+.|.+|.+.|..+..|+.||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 57899999999999999999975
No 46
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=28.92 E-value=33 Score=32.91 Aligned_cols=29 Identities=21% Similarity=0.321 Sum_probs=25.8
Q ss_pred CceeeCCCCCccccCchhhhhhhhhccCc
Q 035649 21 PRVFPCLFCSRKFYSSQALGGHQNAHKKE 49 (163)
Q Consensus 21 ~KPfkC~~CgksFsssqsL~~HqriHtgE 49 (163)
.+|.+|..||..|...+....||..|...
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhhh
Confidence 56899999999999999999999998654
No 47
>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=27.83 E-value=23 Score=29.71 Aligned_cols=31 Identities=16% Similarity=0.370 Sum_probs=22.5
Q ss_pred CCCceeeCCCCCccccCchhhhhhhhhccCc
Q 035649 19 SSPRVFPCLFCSRKFYSSQALGGHQNAHKKE 49 (163)
Q Consensus 19 Tg~KPfkC~~CgksFsssqsL~~HqriHtgE 49 (163)
..+..|.|..|+|.|.-...+..|+..-..|
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 4556799999999999999999998654333
No 48
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=23.87 E-value=55 Score=20.22 Aligned_cols=25 Identities=16% Similarity=0.305 Sum_probs=17.9
Q ss_pred eeeCCCCCccccC--chhhhhhhhhcc
Q 035649 23 VFPCLFCSRKFYS--SQALGGHQNAHK 47 (163)
Q Consensus 23 PfkC~~CgksFss--sqsL~~HqriHt 47 (163)
...|..|+..|.. ...-..|.+.|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 3589999998874 555566776664
No 49
>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=22.91 E-value=45 Score=19.60 Aligned_cols=16 Identities=25% Similarity=0.443 Sum_probs=12.4
Q ss_pred ceeeCCCCCccccCch
Q 035649 22 RVFPCLFCSRKFYSSQ 37 (163)
Q Consensus 22 KPfkC~~CgksFsssq 37 (163)
..|+|..|+..|....
T Consensus 4 Y~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 4 YEYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEEcCCCCCEEEEEE
Confidence 4689999999887443
No 50
>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=21.61 E-value=65 Score=23.32 Aligned_cols=25 Identities=16% Similarity=0.312 Sum_probs=21.4
Q ss_pred eeeC----CCCCccccCchhhhhhhhhcc
Q 035649 23 VFPC----LFCSRKFYSSQALGGHQNAHK 47 (163)
Q Consensus 23 PfkC----~~CgksFsssqsL~~HqriHt 47 (163)
-|.| ..|+..+.+...+..|.+.+.
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 4889 999999999999999987643
No 51
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=21.39 E-value=43 Score=26.25 Aligned_cols=15 Identities=27% Similarity=0.558 Sum_probs=12.8
Q ss_pred eeeCCCCCccccCch
Q 035649 23 VFPCLFCSRKFYSSQ 37 (163)
Q Consensus 23 PfkC~~CgksFsssq 37 (163)
|++|..|++.|....
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 689999999999654
No 52
>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=20.64 E-value=45 Score=19.48 Aligned_cols=23 Identities=26% Similarity=0.704 Sum_probs=13.5
Q ss_pred eeCCCCCccccCchhhhhhhhhcc
Q 035649 24 FPCLFCSRKFYSSQALGGHQNAHK 47 (163)
Q Consensus 24 fkC~~CgksFsssqsL~~HqriHt 47 (163)
|.|-.|++.| .......|...-+
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~CIt 23 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTSCIT 23 (28)
T ss_dssp EEETTTTEEE-EGGGTTT-----S
T ss_pred CeeecCCCCc-CcCCcCCCCcccC
Confidence 5799999999 4555666754433
No 53
>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=20.18 E-value=54 Score=20.49 Aligned_cols=12 Identities=17% Similarity=0.814 Sum_probs=10.4
Q ss_pred ceeeCCCCCccc
Q 035649 22 RVFPCLFCSRKF 33 (163)
Q Consensus 22 KPfkC~~CgksF 33 (163)
++..|.+|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 478999999887
Done!