Query 014667
Match_columns 420
No_of_seqs 294 out of 737
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 07:22:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014667.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014667hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06203 CCT: CCT motif; Inte 99.8 4.9E-20 1.1E-24 135.5 3.2 45 361-405 1-45 (45)
2 cd00021 BBOX B-Box-type zinc f 97.3 0.00019 4.1E-09 49.8 2.4 38 47-90 2-39 (39)
3 cd00021 BBOX B-Box-type zinc f 97.1 0.00034 7.4E-09 48.6 2.4 39 3-47 1-39 (39)
4 smart00336 BBOX B-Box-type zin 96.8 0.0013 2.7E-08 46.3 3.0 41 44-90 2-42 (42)
5 PF00643 zf-B_box: B-box zinc 96.7 0.00082 1.8E-08 47.9 1.5 41 44-90 2-42 (42)
6 smart00336 BBOX B-Box-type zin 96.1 0.0052 1.1E-07 43.2 2.7 40 2-47 3-42 (42)
7 PF00643 zf-B_box: B-box zinc 96.0 0.0039 8.5E-08 44.4 1.7 40 2-47 3-42 (42)
8 KOG1601 GATA-4/5/6 transcripti 95.8 0.0032 7E-08 58.5 0.8 42 357-398 289-330 (340)
9 PF09425 CCT_2: Divergent CCT 94.5 0.022 4.7E-07 38.2 1.6 25 359-384 2-26 (27)
10 KOG4367 Predicted Zn-finger pr 93.3 0.023 4.9E-07 60.0 -0.2 76 3-78 163-256 (699)
11 PF13248 zf-ribbon_3: zinc-rib 63.9 5.3 0.00011 26.1 1.7 26 1-32 1-26 (26)
12 KOG4367 Predicted Zn-finger pr 58.6 3.4 7.5E-05 44.2 0.2 46 46-91 163-210 (699)
13 cd02341 ZZ_ZZZ3 Zinc finger, Z 52.9 13 0.00027 28.1 2.4 29 47-75 2-36 (48)
14 PF12773 DZR: Double zinc ribb 52.8 15 0.00032 26.9 2.7 38 5-54 1-38 (50)
15 cd02335 ZZ_ADA2 Zinc finger, Z 50.3 19 0.00041 26.8 3.0 31 47-77 2-36 (49)
16 PRK14559 putative protein seri 45.6 19 0.00041 40.5 3.3 49 3-74 2-50 (645)
17 PRK14873 primosome assembly pr 42.5 16 0.00035 41.1 2.2 44 13-61 382-426 (665)
18 KOG1601 GATA-4/5/6 transcripti 39.2 42 0.0009 31.1 4.1 87 4-91 7-99 (340)
19 COG1198 PriA Primosomal protei 36.7 25 0.00054 40.1 2.6 44 13-61 434-479 (730)
20 PF04438 zf-HIT: HIT zinc fing 36.3 19 0.00042 24.5 1.0 24 45-69 2-25 (30)
21 PF07975 C1_4: TFIIH C1-like d 34.6 17 0.00037 27.9 0.6 23 13-35 20-42 (51)
22 PF07649 C1_3: C1-like domain; 34.0 13 0.00029 24.7 -0.0 26 4-34 2-27 (30)
23 cd02334 ZZ_dystrophin Zinc fin 31.3 49 0.0011 25.0 2.6 32 47-78 2-37 (49)
24 smart00521 CBF CCAAT-Binding t 30.3 65 0.0014 25.8 3.2 25 378-402 36-61 (62)
25 PF14776 UNC-79: Cation-channe 29.1 26 0.00057 38.4 1.1 57 22-78 227-303 (525)
26 TIGR00595 priA primosomal prot 27.8 39 0.00084 36.6 2.2 39 13-56 212-251 (505)
27 KOG3576 Ovo and related transc 27.7 7.5 0.00016 38.1 -2.9 43 3-46 118-168 (267)
28 PF14239 RRXRR: RRXRR protein 23.7 61 0.0013 30.9 2.4 38 363-402 88-126 (176)
29 cd02249 ZZ Zinc finger, ZZ typ 22.0 92 0.002 22.6 2.6 29 47-76 2-34 (46)
30 KOG4301 Beta-dystrobrevin [Cyt 21.9 28 0.00061 36.5 -0.2 51 47-100 242-296 (434)
31 KOG4571 Activating transcripti 21.3 75 0.0016 32.5 2.6 18 358-375 232-249 (294)
32 PF02045 CBFB_NFYA: CCAAT-bind 21.1 78 0.0017 25.1 2.1 22 379-400 36-58 (58)
33 PF03660 PHF5: PHF5-like prote 21.0 20 0.00043 31.4 -1.3 50 22-71 20-76 (106)
34 PF13240 zinc_ribbon_2: zinc-r 20.5 63 0.0014 20.7 1.3 22 5-32 2-23 (23)
No 1
>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction. The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding
Probab=99.79 E-value=4.9e-20 Score=135.53 Aligned_cols=45 Identities=60% Similarity=0.961 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHhhccCCCCccchhhhhhhhhhcCCCCceeecCCC
Q 014667 361 RSKAVLRYKEKKKTRKFDKRVRYASRKARADVRRRVKGRFVKAGE 405 (420)
Q Consensus 361 R~~~~~ry~eKk~~R~f~kkirY~~Rk~~Ad~R~RvkGrFvk~~~ 405 (420)
|+++|+||+|||++|+|+|+|+|++||++||.|||||||||+..|
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~~e 45 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKKSE 45 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCCCC
Confidence 689999999999999999999999999999999999999999865
No 2
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=97.26 E-value=0.00019 Score=49.84 Aligned_cols=38 Identities=32% Similarity=0.768 Sum_probs=33.5
Q ss_pred ccCcCCCCCceeeccCCCcccCcccccCccCCCCCCCCCcceec
Q 014667 47 LCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (420)
Q Consensus 47 LCd~C~s~PA~v~C~~d~asLC~~CD~~~H~an~~a~rHqRvpv 90 (420)
+|+.|..+|+.+||..|.+.+|..|+..+|. .|.++||
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 6888988899999999999999999988763 7888875
No 3
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=97.11 E-value=0.00034 Score=48.56 Aligned_cols=39 Identities=38% Similarity=0.809 Sum_probs=33.8
Q ss_pred CCCCccCCCCeEEEecCCCcccCcccccccccccccccccccccc
Q 014667 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (420)
Q Consensus 3 ~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vHsaN~Ls~RH~Rv~L 47 (420)
..|+.++++++.+||..|.+.+|..|+...|. .|.+++|
T Consensus 1 ~~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 36999999899999999999999999988775 5887764
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.78 E-value=0.0013 Score=46.32 Aligned_cols=41 Identities=29% Similarity=0.545 Sum_probs=34.9
Q ss_pred cccccCcCCCCCceeeccCCCcccCcccccCccCCCCCCCCCcceec
Q 014667 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (420)
Q Consensus 44 Rv~LCd~C~s~PA~v~C~~d~asLC~~CD~~~H~an~~a~rHqRvpv 90 (420)
|...|+.|...++.+||..|...+|..|....| ..|.+.||
T Consensus 2 ~~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 2 RPPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred cCCcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 567899999999999999999999999997755 56777664
No 5
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=96.69 E-value=0.00082 Score=47.88 Aligned_cols=41 Identities=27% Similarity=0.537 Sum_probs=34.6
Q ss_pred cccccCcCCCCCceeeccCCCcccCcccccCccCCCCCCCCCcceec
Q 014667 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (420)
Q Consensus 44 Rv~LCd~C~s~PA~v~C~~d~asLC~~CD~~~H~an~~a~rHqRvpv 90 (420)
+...|..|...++.+||..|..+||..|....|. +|..+||
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~------~H~~~~i 42 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHK------GHKIVPI 42 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTT------TSEEEEC
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCC------CCEEeEC
Confidence 3468999999889999999999999999999874 3888775
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.07 E-value=0.0052 Score=43.16 Aligned_cols=40 Identities=35% Similarity=0.687 Sum_probs=33.4
Q ss_pred CCCCCccCCCCeEEEecCCCcccCcccccccccccccccccccccc
Q 014667 2 GYMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (420)
Q Consensus 2 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vHsaN~Ls~RH~Rv~L 47 (420)
...|..++..++.+||..|.+.+|..|....| +.|.+++|
T Consensus 3 ~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 3 PPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred CCcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 36799999889999999999999999998766 35776654
No 7
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=95.97 E-value=0.0039 Score=44.36 Aligned_cols=40 Identities=18% Similarity=0.337 Sum_probs=33.8
Q ss_pred CCCCCccCCCCeEEEecCCCcccCcccccccccccccccccccccc
Q 014667 2 GYMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (420)
Q Consensus 2 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vHsaN~Ls~RH~Rv~L 47 (420)
...|+.|.+..+.+||..+...+|..|....|.. |..++|
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence 4689999998899999999999999999998865 766554
No 8
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=95.78 E-value=0.0032 Score=58.52 Aligned_cols=42 Identities=50% Similarity=0.784 Sum_probs=40.3
Q ss_pred CHHHHHHHHHHHHHHhhccCCCCccchhhhhhhhhhcCCCCc
Q 014667 357 TSASRSKAVLRYKEKKKTRKFDKRVRYASRKARADVRRRVKG 398 (420)
Q Consensus 357 ~~~~R~~~~~ry~eKk~~R~f~kkirY~~Rk~~Ad~R~RvkG 398 (420)
....|...+.||++|++.|.|.++|+|..||..|+.|+|+||
T Consensus 289 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 289 SSHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred ccchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 457899999999999999999999999999999999999999
No 9
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=94.54 E-value=0.022 Score=38.21 Aligned_cols=25 Identities=28% Similarity=0.465 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHhhccCCCCccchh
Q 014667 359 ASRSKAVLRYKEKKKTRKFDKRVRYA 384 (420)
Q Consensus 359 ~~R~~~~~ry~eKk~~R~f~kkirY~ 384 (420)
.+|.+.|+||.||||.|... +.-|.
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp ----HHHHHHHHHH------------
T ss_pred chHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 57999999999999999987 55553
No 10
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=93.29 E-value=0.023 Score=60.03 Aligned_cols=76 Identities=17% Similarity=0.423 Sum_probs=59.9
Q ss_pred CCCCccCCC--CeEEEecCCCcccCcccccccccccccccccccccc----------------cCcCCCCCceeeccCCC
Q 014667 3 YMCDFCGDQ--RSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL----------------CERCNSQPALVRCAEER 64 (420)
Q Consensus 3 ~~Cd~C~~~--~A~vyC~aD~A~LC~~CD~~vHsaN~Ls~RH~Rv~L----------------Cd~C~s~PA~v~C~~d~ 64 (420)
-.|.+|+++ .|.|+|+.+....|.-|-.+.|-+-.-..+|.-++- |..++...-..||..|.
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~ck 242 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQCK 242 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEecC
Confidence 368999987 599999999999999999999986555566655432 55555555679999999
Q ss_pred cccCcccccCccCC
Q 014667 65 VSLCQNCDWIGHGT 78 (420)
Q Consensus 65 asLC~~CD~~~H~a 78 (420)
+++|-.|-..+.++
T Consensus 243 ~pvc~~clee~khs 256 (699)
T KOG4367|consen 243 MPVCYQCLEEGKHS 256 (699)
T ss_pred ChHHHHHHHhhccc
Confidence 99999999876433
No 11
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=63.88 E-value=5.3 Score=26.08 Aligned_cols=26 Identities=27% Similarity=0.699 Sum_probs=20.2
Q ss_pred CCCCCCccCCCCeEEEecCCCcccCccccccc
Q 014667 1 MGYMCDFCGDQRSIVYCRSDAACLCLSCDRNV 32 (420)
Q Consensus 1 M~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 32 (420)
|...|-.|+... .+.+.+|..|.+++
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAKL 26 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCCC
Confidence 788899999842 56788999987653
No 12
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=58.64 E-value=3.4 Score=44.21 Aligned_cols=46 Identities=26% Similarity=0.504 Sum_probs=39.2
Q ss_pred cccCcCCCCC--ceeeccCCCcccCcccccCccCCCCCCCCCcceecc
Q 014667 46 LLCERCNSQP--ALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTIN 91 (420)
Q Consensus 46 ~LCd~C~s~P--A~v~C~~d~asLC~~CD~~~H~an~~a~rHqRvpv~ 91 (420)
+-|..|+..| |.|+|..|.++.|.-|....|-+-...++|..+|-+
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~ 210 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPA 210 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcc
Confidence 3588998887 889999999999999999999877767788877654
No 13
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=52.86 E-value=13 Score=28.06 Aligned_cols=29 Identities=34% Similarity=0.828 Sum_probs=22.9
Q ss_pred ccCcCCCCCce---eeccCCC---cccCcccccCc
Q 014667 47 LCERCNSQPAL---VRCAEER---VSLCQNCDWIG 75 (420)
Q Consensus 47 LCd~C~s~PA~---v~C~~d~---asLC~~CD~~~ 75 (420)
-|+.|...|.. +.|..|. --||+.|-..+
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 38889987743 6688776 78999998776
No 14
>PF12773 DZR: Double zinc ribbon
Probab=52.85 E-value=15 Score=26.87 Aligned_cols=38 Identities=24% Similarity=0.712 Sum_probs=25.6
Q ss_pred CCccCCCCeEEEecCCCcccCcccccccccccccccccccccccCcCCCC
Q 014667 5 CDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQ 54 (420)
Q Consensus 5 Cd~C~~~~A~vyC~aD~A~LC~~CD~~vHsaN~Ls~RH~Rv~LCd~C~s~ 54 (420)
|-.|+.. ..+.+.+|..|...+- .......+|..|...
T Consensus 1 Cp~Cg~~------~~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 1 CPHCGTP------NPDDAKFCPHCGTPLP------PPDQSKKICPNCGAE 38 (50)
T ss_pred CCCcCCc------CCccccCChhhcCChh------hccCCCCCCcCCcCC
Confidence 4456654 4567899999997666 334456678888765
No 15
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=50.26 E-value=19 Score=26.77 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=24.8
Q ss_pred ccCcCCCCCce---eeccCC-CcccCcccccCccC
Q 014667 47 LCERCNSQPAL---VRCAEE-RVSLCQNCDWIGHG 77 (420)
Q Consensus 47 LCd~C~s~PA~---v~C~~d-~asLC~~CD~~~H~ 77 (420)
.|+.|...+.. +.|..| ..-||..|-..+..
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~ 36 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAE 36 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCC
Confidence 48889887755 779988 67899999987643
No 16
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=45.63 E-value=19 Score=40.49 Aligned_cols=49 Identities=20% Similarity=0.590 Sum_probs=32.8
Q ss_pred CCCCccCCCCeEEEecCCCcccCcccccccccccccccccccccccCcCCCCCceeeccCCCcccCcccccC
Q 014667 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEERVSLCQNCDWI 74 (420)
Q Consensus 3 ~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vHsaN~Ls~RH~Rv~LCd~C~s~PA~v~C~~d~asLC~~CD~~ 74 (420)
..|-.|+.. -.+.|++|..|...+. | ..|..|+..- ...+.+|.+|...
T Consensus 2 ~~Cp~Cg~~------n~~~akFC~~CG~~l~--------~---~~Cp~CG~~~------~~~~~fC~~CG~~ 50 (645)
T PRK14559 2 LICPQCQFE------NPNNNRFCQKCGTSLT--------H---KPCPQCGTEV------PVDEAHCPNCGAE 50 (645)
T ss_pred CcCCCCCCc------CCCCCccccccCCCCC--------C---CcCCCCCCCC------CcccccccccCCc
Confidence 478889876 3578999999987652 1 2488888662 2345566666533
No 17
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.46 E-value=16 Score=41.09 Aligned_cols=44 Identities=20% Similarity=0.417 Sum_probs=28.9
Q ss_pred eEEEecCCC-cccCcccccccccccccccccccccccCcCCCCCceeecc
Q 014667 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCA 61 (420)
Q Consensus 13 A~vyC~aD~-A~LC~~CD~~vHsaN~Ls~RH~Rv~LCd~C~s~PA~v~C~ 61 (420)
..|+|+.+. ..-|..||..+.- ++..+.+.|..|+.......|.
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L~~-----h~~~~~l~Ch~CG~~~~p~~Cp 426 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPLGL-----PSAGGTPRCRWCGRAAPDWRCP 426 (665)
T ss_pred CeeEhhhCcCeeECCCCCCceeE-----ecCCCeeECCCCcCCCcCccCC
Confidence 467888775 5669999975542 1345678899999753333343
No 18
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=39.20 E-value=42 Score=31.08 Aligned_cols=87 Identities=18% Similarity=0.099 Sum_probs=56.0
Q ss_pred CCCccCCCCeEEEecCCCcccCcccccccccccccccccccccccCcCCCCCce--eeccCCCccc----CcccccCccC
Q 014667 4 MCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPAL--VRCAEERVSL----CQNCDWIGHG 77 (420)
Q Consensus 4 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vHsaN~Ls~RH~Rv~LCd~C~s~PA~--v~C~~d~asL----C~~CD~~~H~ 77 (420)
.|+.|....... |..|.+.+|..|+..+|..+.+...|.++.++..+...++. +.+..+...+ +..+....|.
T Consensus 7 ~~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (340)
T KOG1601|consen 7 DLDSCRFDDLLN-LNADDSLLDISVDARLSASNSLAFPHEPTRLSSSPESFVAATSFSIDLSVPSLDMPGLEGFSLFVSE 85 (340)
T ss_pred cccccCcccccc-cccccccCCcccccccccccccccccccccccchhhhhhcccccccccccccccccccccccccccc
Confidence 456666665556 99999999999999999988666688888888877622222 2333333333 4556555555
Q ss_pred CCCCCCCCcceecc
Q 014667 78 TSTSASSHKRQTIN 91 (420)
Q Consensus 78 an~~a~rHqRvpv~ 91 (420)
.+....+|..+++.
T Consensus 86 ~~~~~~~~~~~~~~ 99 (340)
T KOG1601|consen 86 NNPNSLRHPPVPSM 99 (340)
T ss_pred ccCCCCCCCCcccc
Confidence 55444555544333
No 19
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.75 E-value=25 Score=40.14 Aligned_cols=44 Identities=27% Similarity=0.662 Sum_probs=30.5
Q ss_pred eEEEecCCCc-ccCcccccccccccccccccccccccCcCCCC-Cceeecc
Q 014667 13 SIVYCRSDAA-CLCLSCDRNVHLANALSKRHSRTLLCERCNSQ-PALVRCA 61 (420)
Q Consensus 13 A~vyC~aD~A-~LC~~CD~~vHsaN~Ls~RH~Rv~LCd~C~s~-PA~v~C~ 61 (420)
..|.|+.+.- .=|..||..+-- +++.+.+.|..|+.+ +....|.
T Consensus 434 ~~l~C~~Cg~v~~Cp~Cd~~lt~-----H~~~~~L~CH~Cg~~~~~p~~Cp 479 (730)
T COG1198 434 PLLLCRDCGYIAECPNCDSPLTL-----HKATGQLRCHYCGYQEPIPQSCP 479 (730)
T ss_pred ceeecccCCCcccCCCCCcceEE-----ecCCCeeEeCCCCCCCCCCCCCC
Confidence 4677887764 459999976542 356689999999988 3334444
No 20
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=36.27 E-value=19 Score=24.51 Aligned_cols=24 Identities=33% Similarity=0.771 Sum_probs=17.5
Q ss_pred ccccCcCCCCCceeeccCCCcccCc
Q 014667 45 TLLCERCNSQPALVRCAEERVSLCQ 69 (420)
Q Consensus 45 v~LCd~C~s~PA~v~C~~d~asLC~ 69 (420)
..+|.+|+. ++.+.|..+.+..|.
T Consensus 2 ~~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 2 RKLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp -EEETSSSS-EESEE-TTT--EESS
T ss_pred cCCCccCcC-CCEEECCCcCCceeC
Confidence 357999998 899999999998884
No 21
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=34.57 E-value=17 Score=27.92 Aligned_cols=23 Identities=26% Similarity=0.540 Sum_probs=15.2
Q ss_pred eEEEecCCCcccCcccccccccc
Q 014667 13 SIVYCRSDAACLCLSCDRNVHLA 35 (420)
Q Consensus 13 A~vyC~aD~A~LC~~CD~~vHsa 35 (420)
.+.-|......+|.+||.-||..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 56789999999999999998853
No 22
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=34.02 E-value=13 Score=24.71 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=9.0
Q ss_pred CCCccCCCCeEEEecCCCcccCccccccccc
Q 014667 4 MCDFCGDQRSIVYCRSDAACLCLSCDRNVHL 34 (420)
Q Consensus 4 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vHs 34 (420)
.|+.|+..... +..+-|..||..+|.
T Consensus 2 ~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 2 RCDACGKPIDG-----GWFYRCSECDFDLHE 27 (30)
T ss_dssp --TTTS----S-------EEE-TTT-----H
T ss_pred cCCcCCCcCCC-----CceEECccCCCccCh
Confidence 58888886432 245679999998884
No 23
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=31.27 E-value=49 Score=24.99 Aligned_cols=32 Identities=31% Similarity=0.735 Sum_probs=24.1
Q ss_pred ccCcCCCCCce---eeccCC-CcccCcccccCccCC
Q 014667 47 LCERCNSQPAL---VRCAEE-RVSLCQNCDWIGHGT 78 (420)
Q Consensus 47 LCd~C~s~PA~---v~C~~d-~asLC~~CD~~~H~a 78 (420)
.|+.|...|.. +.|..| .--||+.|-+.++..
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~ 37 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTS 37 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcC
Confidence 48899987743 668777 457999999887543
No 24
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=30.35 E-value=65 Score=25.81 Aligned_cols=25 Identities=36% Similarity=0.376 Sum_probs=21.7
Q ss_pred CCccchhhhhhhhhhcCC-CCceeec
Q 014667 378 DKRVRYASRKARADVRRR-VKGRFVK 402 (420)
Q Consensus 378 ~kkirY~~Rk~~Ad~R~R-vkGrFvk 402 (420)
.|+.-+++|-.-|-.|+| --|||.+
T Consensus 36 rkpYlhESRH~HAm~R~Rg~gGRFl~ 61 (62)
T smart00521 36 RKPYLHESRHLHAMRRPRGSGGRFLN 61 (62)
T ss_pred cCCcccchhHHHHHccCcCCCCCCCC
Confidence 567899999999999999 5589975
No 25
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=29.13 E-value=26 Score=38.38 Aligned_cols=57 Identities=28% Similarity=0.602 Sum_probs=37.8
Q ss_pred cccCcccccccccccccccc-cccc------cccC--cCCCC--Cceeecc---------CCCcccCcccccCccCC
Q 014667 22 ACLCLSCDRNVHLANALSKR-HSRT------LLCE--RCNSQ--PALVRCA---------EERVSLCQNCDWIGHGT 78 (420)
Q Consensus 22 A~LC~~CD~~vHsaN~Ls~R-H~Rv------~LCd--~C~s~--PA~v~C~---------~d~asLC~~CD~~~H~a 78 (420)
.+||..|...||+.-+.... +.-. ..|+ .|.++ .|++.|- .-.+-+|+.|....|+.
T Consensus 227 LylC~~Ca~~i~~e~~~~~~~~il~P~~~vS~~CenK~C~S~~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~~~H~n 303 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNN 303 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCCCCCeEEEEechhhccccCCCcchhHHHHhhhhccc
Confidence 46999999999985433222 1111 2376 67766 3777773 23667999999988864
No 26
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.83 E-value=39 Score=36.62 Aligned_cols=39 Identities=26% Similarity=0.559 Sum_probs=27.1
Q ss_pred eEEEecCCC-cccCcccccccccccccccccccccccCcCCCCCc
Q 014667 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPA 56 (420)
Q Consensus 13 A~vyC~aD~-A~LC~~CD~~vHsaN~Ls~RH~Rv~LCd~C~s~PA 56 (420)
..|+|+.+. ..-|..||..+-- +++.+.+.|..|+....
T Consensus 212 ~~~~C~~Cg~~~~C~~C~~~l~~-----h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 212 KNLLCRSCGYILCCPNCDVSLTY-----HKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CeeEhhhCcCccCCCCCCCceEE-----ecCCCeEEcCCCcCcCC
Confidence 456788764 5669999965432 24566788999997743
No 27
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=27.70 E-value=7.5 Score=38.09 Aligned_cols=43 Identities=33% Similarity=0.671 Sum_probs=34.0
Q ss_pred CCCCccCCC-------CeEEEecCC-CcccCccccccccccccccccccccc
Q 014667 3 YMCDFCGDQ-------RSIVYCRSD-AACLCLSCDRNVHLANALSKRHSRTL 46 (420)
Q Consensus 3 ~~Cd~C~~~-------~A~vyC~aD-~A~LC~~CD~~vHsaN~Ls~RH~Rv~ 46 (420)
..|++|++. .-.+-|++| .-+||..|..-.|-+ +=..||.|..
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndt-fdlkrh~rth 168 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDT-FDLKRHTRTH 168 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccch-hhhhhhhccc
Confidence 358899886 345789998 578999999988876 4468999864
No 28
>PF14239 RRXRR: RRXRR protein
Probab=23.69 E-value=61 Score=30.88 Aligned_cols=38 Identities=32% Similarity=0.622 Sum_probs=29.6
Q ss_pred HHH-HHHHHHhhccCCCCccchhhhhhhhhhcCCCCceeec
Q 014667 363 KAV-LRYKEKKKTRKFDKRVRYASRKARADVRRRVKGRFVK 402 (420)
Q Consensus 363 ~~~-~ry~eKk~~R~f~kkirY~~Rk~~Ad~R~RvkGrFvk 402 (420)
++| ...+.-|..|.|.+|.|| ||++=+.|.|-+|++..
T Consensus 88 ~~lr~~RR~~RR~RR~~rk~Ry--R~~RF~NR~r~~gwL~P 126 (176)
T PF14239_consen 88 DRLRTQRRAYRRGRRYNRKTRY--RKARFDNRKRPKGWLPP 126 (176)
T ss_pred HHHHHHHHHHhhhccccccccc--ccccccccCCCCCCcCc
Confidence 444 666777778888888888 88888899998888763
No 29
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=22.04 E-value=92 Score=22.64 Aligned_cols=29 Identities=28% Similarity=0.666 Sum_probs=22.3
Q ss_pred ccCcCCCCC---ceeeccCCC-cccCcccccCcc
Q 014667 47 LCERCNSQP---ALVRCAEER-VSLCQNCDWIGH 76 (420)
Q Consensus 47 LCd~C~s~P---A~v~C~~d~-asLC~~CD~~~H 76 (420)
.|+.|.. + ..+.|..|. --||..|-...+
T Consensus 2 ~C~~C~~-~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLK-PIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCC-CCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 4788887 4 457788886 789999987764
No 30
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=21.94 E-value=28 Score=36.50 Aligned_cols=51 Identities=31% Similarity=0.716 Sum_probs=34.9
Q ss_pred ccCcCCCCCce---eeccCCCc-ccCcccccCccCCCCCCCCCcceeccccCCCCChh
Q 014667 47 LCERCNSQPAL---VRCAEERV-SLCQNCDWIGHGTSTSASSHKRQTINCYSGCPSAS 100 (420)
Q Consensus 47 LCd~C~s~PA~---v~C~~d~a-sLC~~CD~~~H~an~~a~rHqRvpv~~~sGCps~~ 100 (420)
.|..|.+.+-. ++|..|+. -||++|-|.+|......-.| .+..|+--.+++
T Consensus 242 ~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~hsnqh---~mke~Ss~ksp~ 296 (434)
T KOG4301|consen 242 ECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSHSNQH---QMKEYSSWKSPA 296 (434)
T ss_pred cCcceecccccchhhhHhhcCCccccchhhccccCCCCcchHH---HHHHhhcccChH
Confidence 49999988854 56888866 79999999999754322233 344555555555
No 31
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=21.32 E-value=75 Score=32.55 Aligned_cols=18 Identities=28% Similarity=0.519 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHhhcc
Q 014667 358 SASRSKAVLRYKEKKKTR 375 (420)
Q Consensus 358 ~~~R~~~~~ry~eKk~~R 375 (420)
.+.|+.|-.|||+|||.-
T Consensus 232 r~qnk~AAtRYRqKkRae 249 (294)
T KOG4571|consen 232 RQQNKAAATRYRQKKRAE 249 (294)
T ss_pred HHHhHHHHHHHHHHHHHH
Confidence 456666779999999864
No 32
>PF02045 CBFB_NFYA: CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B; InterPro: IPR001289 The CCAAT-binding factor (CBFB/NF-YA) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin []. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding []. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The B subunit contains a region of similarity with the yeast protein HAP2 []. For the B subunit it has been suggested that the N-terminal portion of the conserved region is involved in subunit interaction and the C-terminal region involved in DNA-binding [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.11 E-value=78 Score=25.09 Aligned_cols=22 Identities=41% Similarity=0.392 Sum_probs=18.6
Q ss_pred CccchhhhhhhhhhcCC-CCcee
Q 014667 379 KRVRYASRKARADVRRR-VKGRF 400 (420)
Q Consensus 379 kkirY~~Rk~~Ad~R~R-vkGrF 400 (420)
|+.-+++|-.=|-.|+| --|||
T Consensus 36 k~YlheSRH~HA~~R~Rg~gGRF 58 (58)
T PF02045_consen 36 KPYLHESRHKHAMRRPRGPGGRF 58 (58)
T ss_pred HHHHHHHHHHHHHcCccCCCCCC
Confidence 55688999999999999 55787
No 33
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=21.00 E-value=20 Score=31.44 Aligned_cols=50 Identities=20% Similarity=0.551 Sum_probs=17.1
Q ss_pred cccCcccccccccccccccccccccccCcCCCCCceeeccCCC-------cccCccc
Q 014667 22 ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEER-------VSLCQNC 71 (420)
Q Consensus 22 A~LC~~CD~~vHsaN~Ls~RH~Rv~LCd~C~s~PA~v~C~~d~-------asLC~~C 71 (420)
+.||..||.+-=.-...++-...+.+|+.|..-.-.-+|..|. |..|..|
T Consensus 20 G~lC~kCdGkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC~eC 76 (106)
T PF03660_consen 20 GRLCEKCDGKCPICDSYVRPCTKVRICDECSFGSLQGRCIICGSGPGVSDAYYCWEC 76 (106)
T ss_dssp -EE-GGGTT--TTT-------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-HHH
T ss_pred hhhhhhcCCcccccCCccCCcceEEECCcCCCCCcCceEEEecCCCCcccceehhhh
Confidence 3444444433222222233345566776555444333443333 5566666
No 34
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.53 E-value=63 Score=20.67 Aligned_cols=22 Identities=32% Similarity=0.809 Sum_probs=13.7
Q ss_pred CCccCCCCeEEEecCCCcccCccccccc
Q 014667 5 CDFCGDQRSIVYCRSDAACLCLSCDRNV 32 (420)
Q Consensus 5 Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 32 (420)
|-.|+.. -.|.+.+|..|...+
T Consensus 2 Cp~CG~~------~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAE------IEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCC------CCCcCcchhhhCCcC
Confidence 4555554 246788888887643
Done!