Query 016166
Match_columns 394
No_of_seqs 193 out of 566
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:24:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016166.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016166hhsearch_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 97.5 4.1E-05 8.9E-10 56.7 1.6 24 361-384 1-24 (45)
2 cd00021 BBOX B-Box-type zinc f 97.3 0.00015 3.2E-09 50.0 2.1 38 47-90 2-39 (39)
3 cd00021 BBOX B-Box-type zinc f 97.1 0.00038 8.3E-09 47.9 2.3 39 3-47 1-39 (39)
4 smart00336 BBOX B-Box-type zin 96.8 0.0011 2.4E-08 46.2 2.7 41 44-90 2-42 (42)
5 PF00643 zf-B_box: B-box zinc 96.8 0.00057 1.2E-08 48.3 1.2 41 44-90 2-42 (42)
6 smart00336 BBOX B-Box-type zin 96.1 0.0044 9.5E-08 43.1 2.5 39 3-47 4-42 (42)
7 PF00643 zf-B_box: B-box zinc 95.9 0.0051 1.1E-07 43.4 2.0 40 2-47 3-42 (42)
8 KOG4367 Predicted Zn-finger pr 94.7 0.0092 2E-07 62.6 0.1 76 4-79 164-257 (699)
9 KOG4367 Predicted Zn-finger pr 61.8 2.9 6.4E-05 44.5 0.4 46 46-91 163-210 (699)
10 PF13248 zf-ribbon_3: zinc-rib 55.5 9.1 0.0002 24.9 1.7 26 1-32 1-26 (26)
11 cd02335 ZZ_ADA2 Zinc finger, Z 53.2 14 0.00031 27.3 2.7 32 47-78 2-37 (49)
12 PF15321 ATAD4: ATPase family 48.6 5 0.00011 33.7 -0.4 10 367-376 70-79 (84)
13 PF09425 CCT_2: Divergent CCT 47.0 12 0.00027 25.2 1.3 20 359-378 2-21 (27)
14 PRK14559 putative protein seri 44.7 19 0.00041 40.1 3.2 48 3-73 2-49 (645)
15 PF12773 DZR: Double zinc ribb 44.5 22 0.00048 25.7 2.6 31 18-54 8-38 (50)
16 PRK14873 primosome assembly pr 42.3 16 0.00034 40.8 2.1 46 13-63 382-428 (665)
17 cd02341 ZZ_ZZZ3 Zinc finger, Z 41.4 24 0.00051 26.4 2.3 28 48-75 3-36 (48)
18 KOG2807 RNA polymerase II tran 40.9 13 0.00029 38.3 1.2 66 12-77 274-365 (378)
19 PF04438 zf-HIT: HIT zinc fing 39.9 16 0.00034 24.8 1.1 23 46-69 3-25 (30)
20 KOG1601 GATA-4/5/6 transcripti 39.1 42 0.00091 30.6 4.1 87 4-91 7-99 (340)
21 COG1198 PriA Primosomal protei 38.3 21 0.00046 40.3 2.4 47 13-64 434-482 (730)
22 cd02334 ZZ_dystrophin Zinc fin 32.6 43 0.00093 25.2 2.5 32 47-78 2-37 (49)
23 COG5665 NOT5 CCR4-NOT transcri 31.2 53 0.0012 34.9 3.7 27 205-232 182-208 (548)
24 TIGR00595 priA primosomal prot 29.9 33 0.00071 36.8 2.0 39 13-56 212-251 (505)
25 KOG1601 GATA-4/5/6 transcripti 29.7 23 0.0005 32.3 0.7 28 358-385 290-317 (340)
26 PF03660 PHF5: PHF5-like prote 29.3 13 0.00028 32.4 -0.9 50 22-71 20-76 (106)
27 PF07649 C1_3: C1-like domain; 25.6 26 0.00057 23.2 0.3 26 4-34 2-27 (30)
28 TIGR00622 ssl1 transcription f 23.8 58 0.0013 28.7 2.1 21 57-77 81-101 (112)
29 KOG3576 Ovo and related transc 23.4 12 0.00027 36.5 -2.2 42 4-46 119-168 (267)
30 KOG1705 Uncharacterized conser 23.3 59 0.0013 28.1 2.0 53 10-62 4-60 (110)
31 KOG4571 Activating transcripti 22.6 47 0.001 33.8 1.5 19 358-376 232-250 (294)
32 cd02249 ZZ Zinc finger, ZZ typ 22.4 80 0.0017 22.8 2.3 30 47-76 2-34 (46)
33 PF07975 C1_4: TFIIH C1-like d 21.5 30 0.00065 26.4 -0.1 22 56-77 20-41 (51)
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=97.53 E-value=4.1e-05 Score=56.68 Aligned_cols=24 Identities=29% Similarity=0.300 Sum_probs=21.8
Q ss_pred hhHHHHHhHhhhhhccccccccee
Q 016166 361 RSKAVLRYKEKKKTRLTKECGMHL 384 (394)
Q Consensus 361 r~~a~~RYkeKkk~R~~~k~~~~~ 384 (394)
|..+++||+|||++|+|+|++.|-
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~ 24 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYE 24 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcc
Confidence 678999999999999999998764
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=97.30 E-value=0.00015 Score=49.99 Aligned_cols=38 Identities=32% Similarity=0.768 Sum_probs=33.5
Q ss_pred cccccCCCCceeeccCCccccccccccCCcCCCCCCCCCccccc
Q 016166 47 LCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (394)
Q Consensus 47 LCd~C~s~PA~v~C~~D~asLC~~CD~~~HsAN~la~rHqRvpl 90 (394)
+|+.|..+++.+||..|.+.+|..|++.+|. .|.++||
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 6888888899999999999999999988764 7888775
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=97.07 E-value=0.00038 Score=47.88 Aligned_cols=39 Identities=38% Similarity=0.809 Sum_probs=33.7
Q ss_pred CCCCccCCCCeeEEecCCccccccccccccccccchhhccccccc
Q 016166 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (394)
Q Consensus 3 ~lCd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~Rv~L 47 (394)
.+|+.++.+++.+||..|.+.+|..|+...|. .|.+++|
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 36999998899999999999999999988774 7777664
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.79 E-value=0.0011 Score=46.21 Aligned_cols=41 Identities=29% Similarity=0.545 Sum_probs=34.8
Q ss_pred ccccccccCCCCceeeccCCccccccccccCCcCCCCCCCCCccccc
Q 016166 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (394)
Q Consensus 44 Rv~LCd~C~s~PA~v~C~~D~asLC~~CD~~~HsAN~la~rHqRvpl 90 (394)
|..+|..|...++.+||..|...+|..|....| +.|.++||
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 567899999899999999999999999997755 46777664
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=96.78 E-value=0.00057 Score=48.30 Aligned_cols=41 Identities=27% Similarity=0.525 Sum_probs=34.6
Q ss_pred ccccccccCCCCceeeccCCccccccccccCCcCCCCCCCCCccccc
Q 016166 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (394)
Q Consensus 44 Rv~LCd~C~s~PA~v~C~~D~asLC~~CD~~~HsAN~la~rHqRvpl 90 (394)
+.++|..|...++.+||..|...||..|....|.. |..+||
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i 42 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI 42 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence 34689999998899999999999999999998763 887775
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.13 E-value=0.0044 Score=43.14 Aligned_cols=39 Identities=36% Similarity=0.718 Sum_probs=33.0
Q ss_pred CCCCccCCCCeeEEecCCccccccccccccccccchhhccccccc
Q 016166 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (394)
Q Consensus 3 ~lCd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~Rv~L 47 (394)
..|..++..++.+||..|.+.+|..|....| +.|.+++|
T Consensus 4 ~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 4 PKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred CcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 5799999889999999999999999998766 46666553
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=95.90 E-value=0.0051 Score=43.41 Aligned_cols=40 Identities=18% Similarity=0.337 Sum_probs=33.5
Q ss_pred CCCCCccCCCCeeEEecCCccccccccccccccccchhhccccccc
Q 016166 2 GYMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (394)
Q Consensus 2 ~~lCd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~Rv~L 47 (394)
...|..+...++.+||..+...+|..|....|.. |..++|
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 4679999998999999999999999999998854 766553
No 8
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=94.68 E-value=0.0092 Score=62.58 Aligned_cols=76 Identities=18% Similarity=0.433 Sum_probs=60.5
Q ss_pred CCCccCCC--CeeEEecCCccccccccccccccccchhhccccccc----------------ccccCCCCceeeccCCcc
Q 016166 4 MCDFCGDQ--RSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL----------------CERCNSQPALVRCAEERV 65 (394)
Q Consensus 4 lCd~C~~a--~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~Rv~L----------------Cd~C~s~PA~v~C~~D~a 65 (394)
.|.+|+++ .|.|+|..+..+.|.-|..+.|-+-.-..+|.-++- |.-++-..-..||..|++
T Consensus 164 kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~ck~ 243 (699)
T KOG4367|consen 164 KCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQCKM 243 (699)
T ss_pred hhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEecCC
Confidence 58999987 489999999999999999999988666667765442 444444446799999999
Q ss_pred ccccccccCCcCCC
Q 016166 66 SLCQNCDWIGHGTS 79 (394)
Q Consensus 66 sLC~~CD~~~HsAN 79 (394)
++|-.|-..+.++|
T Consensus 244 pvc~~clee~khs~ 257 (699)
T KOG4367|consen 244 PVCYQCLEEGKHSS 257 (699)
T ss_pred hHHHHHHHhhcccc
Confidence 99999998764444
No 9
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=61.79 E-value=2.9 Score=44.51 Aligned_cols=46 Identities=26% Similarity=0.504 Sum_probs=39.6
Q ss_pred ccccccCCCC--ceeeccCCccccccccccCCcCCCCCCCCCcccccc
Q 016166 46 LLCERCNSQP--ALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTIN 91 (394)
Q Consensus 46 ~LCd~C~s~P--A~v~C~~D~asLC~~CD~~~HsAN~la~rHqRvpl~ 91 (394)
.-|..|+..| |.|+|..|.++.|.-|....|-+-...++|..+|-+
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 3588898887 889999999999999999999887778889887654
No 10
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=55.47 E-value=9.1 Score=24.85 Aligned_cols=26 Identities=27% Similarity=0.699 Sum_probs=19.5
Q ss_pred CCCCCCccCCCCeeEEecCCcccccccccccc
Q 016166 1 MGYMCDFCGDQRSIVYCRSDAACLCLSCDRNV 32 (394)
Q Consensus 1 M~~lCd~C~~a~A~vyC~aD~A~LC~~CD~~v 32 (394)
|...|-.|+.. ..+.+.+|..|.+++
T Consensus 1 m~~~Cp~Cg~~------~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 1 MEMFCPNCGAE------IDPDAKFCPNCGAKL 26 (26)
T ss_pred CcCCCcccCCc------CCcccccChhhCCCC
Confidence 77889999874 256788888887653
No 11
>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=53.17 E-value=14 Score=27.26 Aligned_cols=32 Identities=28% Similarity=0.627 Sum_probs=24.9
Q ss_pred cccccCCCCce---eeccCC-ccccccccccCCcCC
Q 016166 47 LCERCNSQPAL---VRCAEE-RVSLCQNCDWIGHGT 78 (394)
Q Consensus 47 LCd~C~s~PA~---v~C~~D-~asLC~~CD~~~HsA 78 (394)
.|+.|...+.. +.|..| ..-||..|-..+...
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~ 37 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEI 37 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCC
Confidence 48888877654 779988 889999999876443
No 12
>PF15321 ATAD4: ATPase family AAA domain containing 4
Probab=48.56 E-value=5 Score=33.69 Aligned_cols=10 Identities=60% Similarity=0.973 Sum_probs=8.9
Q ss_pred HhHhhhhhcc
Q 016166 367 RYKEKKKTRL 376 (394)
Q Consensus 367 RYkeKkk~R~ 376 (394)
|||||||.|.
T Consensus 70 RFKEKrKvRa 79 (84)
T PF15321_consen 70 RFKEKRKVRA 79 (84)
T ss_pred cccccccccc
Confidence 8999999884
No 13
>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=47.04 E-value=12 Score=25.20 Aligned_cols=20 Identities=35% Similarity=0.589 Sum_probs=9.7
Q ss_pred hhhhHHHHHhHhhhhhcccc
Q 016166 359 ASRSKAVLRYKEKKKTRLTK 378 (394)
Q Consensus 359 ~~r~~a~~RYkeKkk~R~~~ 378 (394)
.+|-..+-||-||+|-|.+.
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~ 21 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA 21 (27)
T ss_dssp ----HHHHHHHHHH------
T ss_pred chHHHHHHHHHHHHHHhhcc
Confidence 57888999999999999877
No 14
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=44.68 E-value=19 Score=40.06 Aligned_cols=48 Identities=19% Similarity=0.572 Sum_probs=31.2
Q ss_pred CCCCccCCCCeeEEecCCccccccccccccccccchhhcccccccccccCCCCceeeccCCcccccccccc
Q 016166 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEERVSLCQNCDW 73 (394)
Q Consensus 3 ~lCd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~Rv~LCd~C~s~PA~v~C~~D~asLC~~CD~ 73 (394)
..|-.|+.. -.+.|++|..|...+.. ..|..|+..-. ..+.+|..|..
T Consensus 2 ~~Cp~Cg~~------n~~~akFC~~CG~~l~~-----------~~Cp~CG~~~~------~~~~fC~~CG~ 49 (645)
T PRK14559 2 LICPQCQFE------NPNNNRFCQKCGTSLTH-----------KPCPQCGTEVP------VDEAHCPNCGA 49 (645)
T ss_pred CcCCCCCCc------CCCCCccccccCCCCCC-----------CcCCCCCCCCC------cccccccccCC
Confidence 368899876 45788899999877631 24888876632 23445555543
No 15
>PF12773 DZR: Double zinc ribbon
Probab=44.53 E-value=22 Score=25.71 Aligned_cols=31 Identities=19% Similarity=0.566 Sum_probs=20.6
Q ss_pred cCCccccccccccccccccchhhcccccccccccCCC
Q 016166 18 RSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQ 54 (394)
Q Consensus 18 ~aD~A~LC~~CD~~vHsaN~La~RH~Rv~LCd~C~s~ 54 (394)
..+.+.+|..|...+- .......+|..|+..
T Consensus 8 ~~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLP------PPDQSKKICPNCGAE 38 (50)
T ss_pred CCccccCChhhcCChh------hccCCCCCCcCCcCC
Confidence 4567888888887766 233445667777764
No 16
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.29 E-value=16 Score=40.75 Aligned_cols=46 Identities=20% Similarity=0.380 Sum_probs=30.4
Q ss_pred eeEEecCCc-cccccccccccccccchhhcccccccccccCCCCceeeccCC
Q 016166 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEE 63 (394)
Q Consensus 13 A~vyC~aD~-A~LC~~CD~~vHsaN~La~RH~Rv~LCd~C~s~PA~v~C~~D 63 (394)
..|+|+.+. ..-|..||..+-. ++..+.+.|..|+.......|..|
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L~~-----h~~~~~l~Ch~CG~~~~p~~Cp~C 428 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPLGL-----PSAGGTPRCRWCGRAAPDWRCPRC 428 (665)
T ss_pred CeeEhhhCcCeeECCCCCCceeE-----ecCCCeeECCCCcCCCcCccCCCC
Confidence 567888885 5669999976542 134557889999875434444433
No 17
>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=41.43 E-value=24 Score=26.45 Aligned_cols=28 Identities=36% Similarity=0.884 Sum_probs=21.9
Q ss_pred ccccCCCCc---eeeccCCc---cccccccccCC
Q 016166 48 CERCNSQPA---LVRCAEER---VSLCQNCDWIG 75 (394)
Q Consensus 48 Cd~C~s~PA---~v~C~~D~---asLC~~CD~~~ 75 (394)
|+.|+..|. .+.|..|. --||+.|-..+
T Consensus 3 Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 3 CDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 788887663 36688776 89999998776
No 18
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=40.88 E-value=13 Score=38.34 Aligned_cols=66 Identities=23% Similarity=0.463 Sum_probs=46.4
Q ss_pred CeeEEecCCcccc------ccccccccccccchhhc-cccccc----------------ccccCCCC---ceeeccCCcc
Q 016166 12 RSIVYCRSDAACL------CLSCDRNVHLANALSKR-HSRTLL----------------CERCNSQP---ALVRCAEERV 65 (394)
Q Consensus 12 ~A~vyC~aD~A~L------C~~CD~~vHsaN~La~R-H~Rv~L----------------Cd~C~s~P---A~v~C~~D~a 65 (394)
.+..+|..+.|+. |.-|+-.+=++-.|++- |.-.|| |-.|+... ..++|..|.-
T Consensus 274 ~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~ 353 (378)
T KOG2807|consen 274 GGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKN 353 (378)
T ss_pred cCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccc
Confidence 4667777777775 56788776666666642 333343 77884332 4588999999
Q ss_pred ccccccccCCcC
Q 016166 66 SLCQNCDWIGHG 77 (394)
Q Consensus 66 sLC~~CD~~~Hs 77 (394)
.+|..||.-+|.
T Consensus 354 ~FCldCDv~iHe 365 (378)
T KOG2807|consen 354 VFCLDCDVFIHE 365 (378)
T ss_pred eeeccchHHHHh
Confidence 999999999885
No 19
>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=39.93 E-value=16 Score=24.85 Aligned_cols=23 Identities=35% Similarity=0.807 Sum_probs=17.5
Q ss_pred ccccccCCCCceeeccCCcccccc
Q 016166 46 LLCERCNSQPALVRCAEERVSLCQ 69 (394)
Q Consensus 46 ~LCd~C~s~PA~v~C~~D~asLC~ 69 (394)
.+|.+|+. ++.+.|..+.+..|.
T Consensus 3 ~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSS-EESEE-TTT--EESS
T ss_pred CCCccCcC-CCEEECCCcCCceeC
Confidence 58999998 999999999998885
No 20
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=39.08 E-value=42 Score=30.56 Aligned_cols=87 Identities=18% Similarity=0.099 Sum_probs=56.8
Q ss_pred CCCccCCCCeeEEecCCccccccccccccccccchhhcccccccccccCCCCce--eeccCCcccc----ccccccCCcC
Q 016166 4 MCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPAL--VRCAEERVSL----CQNCDWIGHG 77 (394)
Q Consensus 4 lCd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~Rv~LCd~C~s~PA~--v~C~~D~asL----C~~CD~~~Hs 77 (394)
.|+.|....... |..|.+.+|..++.++|..+.+...|.++.++..+...++. +.+..+...+ +..++...|.
T Consensus 7 ~~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (340)
T KOG1601|consen 7 DLDSCRFDDLLN-LNADDSLLDISVDARLSASNSLAFPHEPTRLSSSPESFVAATSFSIDLSVPSLDMPGLEGFSLFVSE 85 (340)
T ss_pred cccccCcccccc-cccccccCCcccccccccccccccccccccccchhhhhhcccccccccccccccccccccccccccc
Confidence 356666665555 99999999999999999988666788888888877622222 2333333333 4556666666
Q ss_pred CCCCCCCCcccccc
Q 016166 78 TSTSASSHKRQTIN 91 (394)
Q Consensus 78 AN~la~rHqRvpl~ 91 (394)
.+....+|..+++.
T Consensus 86 ~~~~~~~~~~~~~~ 99 (340)
T KOG1601|consen 86 NNPNSLRHPPVPSM 99 (340)
T ss_pred ccCCCCCCCCcccc
Confidence 66555566554433
No 21
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.29 E-value=21 Score=40.31 Aligned_cols=47 Identities=28% Similarity=0.606 Sum_probs=32.8
Q ss_pred eeEEecCCccc-cccccccccccccchhhcccccccccccCCC-CceeeccCCc
Q 016166 13 SIVYCRSDAAC-LCLSCDRNVHLANALSKRHSRTLLCERCNSQ-PALVRCAEER 64 (394)
Q Consensus 13 A~vyC~aD~A~-LC~~CD~~vHsaN~La~RH~Rv~LCd~C~s~-PA~v~C~~D~ 64 (394)
..|.|+.+.-. =|..||...-- +++.+.+.|..|+.+ +....|..|.
T Consensus 434 ~~l~C~~Cg~v~~Cp~Cd~~lt~-----H~~~~~L~CH~Cg~~~~~p~~Cp~Cg 482 (730)
T COG1198 434 PLLLCRDCGYIAECPNCDSPLTL-----HKATGQLRCHYCGYQEPIPQSCPECG 482 (730)
T ss_pred ceeecccCCCcccCCCCCcceEE-----ecCCCeeEeCCCCCCCCCCCCCCCCC
Confidence 46788888644 49999976542 466688999999987 4445555443
No 22
>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=32.60 E-value=43 Score=25.17 Aligned_cols=32 Identities=31% Similarity=0.726 Sum_probs=23.9
Q ss_pred cccccCCCCc---eeeccCC-ccccccccccCCcCC
Q 016166 47 LCERCNSQPA---LVRCAEE-RVSLCQNCDWIGHGT 78 (394)
Q Consensus 47 LCd~C~s~PA---~v~C~~D-~asLC~~CD~~~HsA 78 (394)
.|+.|...|. .+.|..| .--||+.|-+.++..
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 4888887763 3667766 578999999887653
No 23
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=31.23 E-value=53 Score=34.87 Aligned_cols=27 Identities=37% Similarity=0.503 Sum_probs=18.5
Q ss_pred ccccccCCcccccCCCCCcccccccchh
Q 016166 205 KDLAFCEDDDLYEDFNMDEMDLNFENYE 232 (394)
Q Consensus 205 ~~~~~ced~dl~edfnmDDvdL~fENyE 232 (394)
++.+.-|++.|||+++ |++.-.=-|.+
T Consensus 182 ~~~df~e~~~~y~~~~-~e~~~sss~~~ 208 (548)
T COG5665 182 DDPDFIEYDTIYEDMG-CEIQPSSSNNE 208 (548)
T ss_pred CCcchhhhhhHHHhhc-cccCCccCCCC
Confidence 3455778888999988 88875444433
No 24
>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=29.91 E-value=33 Score=36.81 Aligned_cols=39 Identities=26% Similarity=0.559 Sum_probs=27.1
Q ss_pred eeEEecCCc-cccccccccccccccchhhcccccccccccCCCCc
Q 016166 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPA 56 (394)
Q Consensus 13 A~vyC~aD~-A~LC~~CD~~vHsaN~La~RH~Rv~LCd~C~s~PA 56 (394)
..|+|+.+. ..-|..||..+-. +++.+.+.|..|+....
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 457888775 5569999966542 24566788999987654
No 25
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=29.69 E-value=23 Score=32.30 Aligned_cols=28 Identities=25% Similarity=0.249 Sum_probs=24.8
Q ss_pred hhhhhHHHHHhHhhhhhcccccccceee
Q 016166 358 SASRSKAVLRYKEKKKTRLTKECGMHLA 385 (394)
Q Consensus 358 ~~~r~~a~~RYkeKkk~R~~~k~~~~~~ 385 (394)
...|...+.||+||++.|.|++++.+..
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~ 317 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYAS 317 (340)
T ss_pred cchHHHHHhhccCccCCccccccccccc
Confidence 5789999999999999999999987653
No 26
>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=29.28 E-value=13 Score=32.44 Aligned_cols=50 Identities=20% Similarity=0.551 Sum_probs=19.3
Q ss_pred cccccccccccccccchhhcccccccccccCCCCceeeccCCc-------ccccccc
Q 016166 22 ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEER-------VSLCQNC 71 (394)
Q Consensus 22 A~LC~~CD~~vHsaN~La~RH~Rv~LCd~C~s~PA~v~C~~D~-------asLC~~C 71 (394)
+.||..||-+--.-....+-...+.+|+.|..-.-.-+|..|. |..|..|
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 4566666655444444444456677777665544444444443 5566666
No 27
>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=25.58 E-value=26 Score=23.15 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=8.8
Q ss_pred CCCccCCCCeeEEecCCcccccccccccccc
Q 016166 4 MCDFCGDQRSIVYCRSDAACLCLSCDRNVHL 34 (394)
Q Consensus 4 lCd~C~~a~A~vyC~aD~A~LC~~CD~~vHs 34 (394)
.|+.|+..... +..+-|..||..+|.
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 58888876432 245668999998884
No 28
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.81 E-value=58 Score=28.71 Aligned_cols=21 Identities=29% Similarity=0.539 Sum_probs=18.9
Q ss_pred eeeccCCccccccccccCCcC
Q 016166 57 LVRCAEERVSLCQNCDWIGHG 77 (394)
Q Consensus 57 ~v~C~~D~asLC~~CD~~~Hs 77 (394)
.+.|..|.-.+|..||.-+|.
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred ceeCCCCCCccccccchhhhh
Confidence 367999999999999999986
No 29
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=23.38 E-value=12 Score=36.47 Aligned_cols=42 Identities=33% Similarity=0.646 Sum_probs=32.5
Q ss_pred CCCccCCC-------CeeEEecCC-ccccccccccccccccchhhcccccc
Q 016166 4 MCDFCGDQ-------RSIVYCRSD-AACLCLSCDRNVHLANALSKRHSRTL 46 (394)
Q Consensus 4 lCd~C~~a-------~A~vyC~aD-~A~LC~~CD~~vHsaN~La~RH~Rv~ 46 (394)
.|++|++. .-.+-|++| ..+||.-|....|-+ .=..||.|..
T Consensus 119 tCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndt-fdlkrh~rth 168 (267)
T KOG3576|consen 119 TCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDT-FDLKRHTRTH 168 (267)
T ss_pred eeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccch-hhhhhhhccc
Confidence 58888875 335789999 688999999998875 3357898864
No 30
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=23.33 E-value=59 Score=28.06 Aligned_cols=53 Identities=21% Similarity=0.556 Sum_probs=30.9
Q ss_pred CCCeeEEecCC----ccccccccccccccccchhhcccccccccccCCCCceeeccC
Q 016166 10 DQRSIVYCRSD----AACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAE 62 (394)
Q Consensus 10 ~a~A~vyC~aD----~A~LC~~CD~~vHsaN~La~RH~Rv~LCd~C~s~PA~v~C~~ 62 (394)
+.|-.|.|+-- -..||..||.+----....+--.-+.+|+.|....-.-+|..
T Consensus 4 HhpDLi~CrkQPGi~~G~LCEkCDgkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~cii 60 (110)
T KOG1705|consen 4 HHPDLIMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVI 60 (110)
T ss_pred cCCcEEEEecCCCchhhhhHHhcCCcccccccccccceeeeeehhcCCccccCceEE
Confidence 34667778654 367999999765433222222222667888876655444443
No 31
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=22.61 E-value=47 Score=33.79 Aligned_cols=19 Identities=26% Similarity=0.455 Sum_probs=15.1
Q ss_pred hhhhhHHHHHhHhhhhhcc
Q 016166 358 SASRSKAVLRYKEKKKTRL 376 (394)
Q Consensus 358 ~~~r~~a~~RYkeKkk~R~ 376 (394)
.+.|.-|-.||++|||.-+
T Consensus 232 r~qnk~AAtRYRqKkRae~ 250 (294)
T KOG4571|consen 232 RQQNKAAATRYRQKKRAEK 250 (294)
T ss_pred HHHhHHHHHHHHHHHHHHH
Confidence 4566678899999999765
No 32
>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=22.43 E-value=80 Score=22.82 Aligned_cols=30 Identities=23% Similarity=0.540 Sum_probs=21.9
Q ss_pred cccccCCC--CceeeccCCc-cccccccccCCc
Q 016166 47 LCERCNSQ--PALVRCAEER-VSLCQNCDWIGH 76 (394)
Q Consensus 47 LCd~C~s~--PA~v~C~~D~-asLC~~CD~~~H 76 (394)
.|+.|... ...+.|..|. --||..|-...+
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 47777762 1456788876 899999987764
No 33
>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=21.46 E-value=30 Score=26.44 Aligned_cols=22 Identities=27% Similarity=0.635 Sum_probs=14.9
Q ss_pred ceeeccCCccccccccccCCcC
Q 016166 56 ALVRCAEERVSLCQNCDWIGHG 77 (394)
Q Consensus 56 A~v~C~~D~asLC~~CD~~~Hs 77 (394)
..++|..|+..+|..||.-+|.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTT
T ss_pred CeEECCCCCCccccCcChhhhc
Confidence 5678999999999999999885
Done!