Query 015947
Match_columns 397
No_of_seqs 183 out of 567
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 02:23:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015947.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015947hhsearch_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 98.5 3.4E-08 7.4E-13 73.0 1.1 28 361-388 1-28 (45)
2 cd00021 BBOX B-Box-type zinc f 97.2 0.00021 4.5E-09 49.3 2.2 38 47-90 2-39 (39)
3 cd00021 BBOX B-Box-type zinc f 97.1 0.00036 7.8E-09 48.1 2.4 39 3-47 1-39 (39)
4 PF00643 zf-B_box: B-box zinc 96.8 0.00053 1.1E-08 48.5 1.4 41 44-90 2-42 (42)
5 smart00336 BBOX B-Box-type zin 96.7 0.0012 2.7E-08 46.0 2.7 41 44-90 2-42 (42)
6 smart00336 BBOX B-Box-type zin 96.1 0.0045 9.7E-08 43.1 2.5 40 2-47 3-42 (42)
7 PF00643 zf-B_box: B-box zinc 95.8 0.0062 1.3E-07 43.0 2.1 40 2-47 3-42 (42)
8 KOG4367 Predicted Zn-finger pr 94.2 0.013 2.9E-07 61.5 0.2 76 4-79 164-257 (699)
9 KOG1601 GATA-4/5/6 transcripti 84.0 0.45 9.7E-06 43.4 0.9 83 4-87 7-95 (340)
10 PF09425 CCT_2: Divergent CCT 75.3 1.8 4E-05 29.2 1.4 20 359-378 2-21 (27)
11 KOG4367 Predicted Zn-finger pr 62.8 2.6 5.7E-05 45.0 0.2 46 46-91 163-210 (699)
12 PF13248 zf-ribbon_3: zinc-rib 53.9 10 0.00022 24.7 1.7 26 1-32 1-26 (26)
13 PF12773 DZR: Double zinc ribb 53.4 16 0.00034 26.5 2.9 31 18-54 8-38 (50)
14 cd02335 ZZ_ADA2 Zinc finger, Z 51.4 16 0.00034 27.1 2.7 31 47-77 2-36 (49)
15 PRK14559 putative protein seri 45.9 18 0.00039 40.3 3.2 48 3-73 2-49 (645)
16 PRK14873 primosome assembly pr 41.0 16 0.00035 40.7 2.0 45 13-62 382-427 (665)
17 PF04438 zf-HIT: HIT zinc fing 40.3 16 0.00035 24.9 1.2 24 45-69 2-25 (30)
18 PF15321 ATAD4: ATPase family 40.2 7.8 0.00017 32.6 -0.5 10 367-376 70-79 (84)
19 KOG2807 RNA polymerase II tran 38.8 15 0.00033 38.0 1.2 66 12-77 274-365 (378)
20 cd02341 ZZ_ZZZ3 Zinc finger, Z 38.3 28 0.0006 26.1 2.3 28 48-75 3-36 (48)
21 cd02334 ZZ_dystrophin Zinc fin 34.7 40 0.00086 25.4 2.6 32 47-78 2-37 (49)
22 COG1198 PriA Primosomal protei 31.9 31 0.00067 39.1 2.3 45 13-62 434-480 (730)
23 KOG4571 Activating transcripti 30.1 29 0.00063 35.3 1.6 19 358-376 232-250 (294)
24 TIGR00595 priA primosomal prot 28.1 36 0.00078 36.5 2.0 39 13-56 212-251 (505)
25 KOG1601 GATA-4/5/6 transcripti 27.4 85 0.0019 28.5 4.1 33 358-390 290-322 (340)
26 COG5665 NOT5 CCR4-NOT transcri 27.0 66 0.0014 34.3 3.5 27 205-232 182-208 (548)
27 PF14776 UNC-79: Cation-channe 25.2 32 0.00069 37.6 0.9 64 22-86 227-310 (525)
28 PF03660 PHF5: PHF5-like prote 23.2 20 0.00044 31.4 -0.8 50 22-71 20-76 (106)
29 KOG4301 Beta-dystrobrevin [Cyt 22.2 27 0.00058 36.6 -0.3 52 47-101 242-297 (434)
30 cd02338 ZZ_PCMF_like Zinc fing 21.5 1.1E+02 0.0024 22.7 3.0 31 47-77 2-36 (49)
31 PF07649 C1_3: C1-like domain; 21.3 35 0.00076 22.6 0.2 26 4-34 2-27 (30)
32 KOG1705 Uncharacterized conser 20.6 75 0.0016 27.6 2.1 53 10-62 4-60 (110)
33 PF07975 C1_4: TFIIH C1-like d 20.3 36 0.00077 26.1 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=98.50 E-value=3.4e-08 Score=73.03 Aligned_cols=28 Identities=25% Similarity=0.364 Sum_probs=26.2
Q ss_pred HHHHHHHhHHhhhhccccceeeeeeecC
Q 015947 361 RSKAVLRYKEKKKTRKLVLNRKLCLNLH 388 (397)
Q Consensus 361 r~~a~~ry~ekkk~r~~~k~i~~~~~~~ 388 (397)
|+++|+||+|||++|+|+|+|+|++|+.
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~ 28 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKA 28 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHH
Confidence 6899999999999999999999999873
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=97.23 E-value=0.00021 Score=49.28 Aligned_cols=38 Identities=32% Similarity=0.768 Sum_probs=33.3
Q ss_pred cccccCCCCceeeecCCCcccCcccccCccCCCCCCCCCccccc
Q 015947 47 LCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (397)
Q Consensus 47 LCd~C~s~PA~v~C~~D~asLC~~CD~~~H~An~lA~~HqR~pl 90 (397)
+|+.|..+++.+||..|.+.+|..|+..+|. .|.++||
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 6888988899999999999999999988764 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=97.09 E-value=0.00036 Score=48.06 Aligned_cols=39 Identities=38% Similarity=0.809 Sum_probs=33.9
Q ss_pred CCCCccCCCCeeEEecCCccccccccccccccccchhhccccccc
Q 015947 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (397)
Q Consensus 3 ~~Cd~C~~a~A~VyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpL 47 (397)
.+|+.++.+++.+||..|.+.+|..|+...|. .|.++++
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 36999999899999999999999999988774 6777664
No 4
>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=96.83 E-value=0.00053 Score=48.53 Aligned_cols=41 Identities=27% Similarity=0.525 Sum_probs=34.6
Q ss_pred ccccccccCCCCceeeecCCCcccCcccccCccCCCCCCCCCccccc
Q 015947 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (397)
Q Consensus 44 RvpLCd~C~s~PA~v~C~~D~asLC~~CD~~~H~An~lA~~HqR~pl 90 (397)
+.+.|..|...++.+||..|...+|..|....|.. |..+||
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 35689999998899999999999999999998863 877765
No 5
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.75 E-value=0.0012 Score=45.99 Aligned_cols=41 Identities=29% Similarity=0.545 Sum_probs=34.7
Q ss_pred ccccccccCCCCceeeecCCCcccCcccccCccCCCCCCCCCccccc
Q 015947 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (397)
Q Consensus 44 RvpLCd~C~s~PA~v~C~~D~asLC~~CD~~~H~An~lA~~HqR~pl 90 (397)
|..+|..|...++.+||..|...+|..|....| +.|.+.+|
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 46777654
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.12 E-value=0.0045 Score=43.13 Aligned_cols=40 Identities=35% Similarity=0.687 Sum_probs=33.4
Q ss_pred CCCCCccCCCCeeEEecCCccccccccccccccccchhhccccccc
Q 015947 2 GYMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (397)
Q Consensus 2 ~~~Cd~C~~a~A~VyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpL 47 (397)
...|..++..++.+||..|.+.+|..|....| +.|.+++|
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 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=95.79 E-value=0.0062 Score=43.03 Aligned_cols=40 Identities=18% Similarity=0.337 Sum_probs=33.8
Q ss_pred CCCCCccCCCCeeEEecCCccccccccccccccccchhhccccccc
Q 015947 2 GYMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (397)
Q Consensus 2 ~~~Cd~C~~a~A~VyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpL 47 (397)
...|+.+...++.+||..+...+|..|....|.. |..++|
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 4689999999999999999999999999999864 766554
No 8
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=94.24 E-value=0.013 Score=61.49 Aligned_cols=76 Identities=18% Similarity=0.437 Sum_probs=60.7
Q ss_pred CCCccCCC--CeeEEecCCccccccccccccccccchhhcccccc----------------cccccCCCCceeeecCCCc
Q 015947 4 MCDFCGDQ--RSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTL----------------LCERCNSQPALVRCAEERV 65 (397)
Q Consensus 4 ~Cd~C~~a--~A~VyC~aD~A~LC~~CD~~vHsAN~La~RH~Rvp----------------LCd~C~s~PA~v~C~~D~a 65 (397)
.|.+|+++ .|.|+|..+....|.-|..+.|-+-.-..+|.-++ .|.-+....-.+||..|++
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 58999988 48999999999999999999998766556665432 2555555567899999999
Q ss_pred ccCcccccCccCCC
Q 015947 66 SLCQNCDWIGHGTS 79 (397)
Q Consensus 66 sLC~~CD~~~H~An 79 (397)
++|-.|-..+.+++
T Consensus 244 pvc~~clee~khs~ 257 (699)
T KOG4367|consen 244 PVCYQCLEEGKHSS 257 (699)
T ss_pred hHHHHHHHhhcccc
Confidence 99999998764433
No 9
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=83.97 E-value=0.45 Score=43.39 Aligned_cols=83 Identities=19% Similarity=0.125 Sum_probs=50.7
Q ss_pred CCCccCCCCeeEEecCCccccccccccccccccchhhcccccccccccCCCCce--eeecCCCccc----CcccccCccC
Q 015947 4 MCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPAL--VRCAEERVSL----CQNCDWIGHG 77 (397)
Q Consensus 4 ~Cd~C~~a~A~VyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~s~PA~--v~C~~D~asL----C~~CD~~~H~ 77 (397)
.|+-|....... |..|.+.+|..++.++|..+.+...|.++.++..+...++. +.+..+...+ +..++...|.
T Consensus 7 ~~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (340)
T KOG1601|consen 7 DLDSCRFDDLLN-LNADDSLLDISVDARLSASNSLAFPHEPTRLSSSPESFVAATSFSIDLSVPSLDMPGLEGFSLFVSE 85 (340)
T ss_pred cccccCcccccc-cccccccCCcccccccccccccccccccccccchhhhhhcccccccccccccccccccccccccccc
Confidence 355555555555 99999999999999999988666677788887776522222 2233233333 4445555554
Q ss_pred CCCCCCCCcc
Q 015947 78 TSTSASSHKR 87 (397)
Q Consensus 78 An~lA~~HqR 87 (397)
.++...+|..
T Consensus 86 ~~~~~~~~~~ 95 (340)
T KOG1601|consen 86 NNPNSLRHPP 95 (340)
T ss_pred ccCCCCCCCC
Confidence 4444445544
No 10
>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=75.31 E-value=1.8 Score=29.21 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=9.8
Q ss_pred hhHHHHHHHhHHhhhhcccc
Q 015947 359 ASRSKAVLRYKEKKKTRKLV 378 (397)
Q Consensus 359 ~~r~~a~~ry~ekkk~r~~~ 378 (397)
.+|-..+.||-||+|.|...
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~ 21 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA 21 (27)
T ss_dssp ----HHHHHHHHHH------
T ss_pred chHHHHHHHHHHHHHHhhcc
Confidence 68999999999999999877
No 11
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=62.76 E-value=2.6 Score=44.96 Aligned_cols=46 Identities=26% Similarity=0.504 Sum_probs=39.5
Q ss_pred ccccccCCCC--ceeeecCCCcccCcccccCccCCCCCCCCCcccccc
Q 015947 46 LLCERCNSQP--ALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTIN 91 (397)
Q Consensus 46 pLCd~C~s~P--A~v~C~~D~asLC~~CD~~~H~An~lA~~HqR~pl~ 91 (397)
.-|..|+..| |.|+|..|.++.|.-|....|-+-.+.++|..+|-+
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 4589998887 889999999999999999999877778889877644
No 12
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=53.89 E-value=10 Score=24.73 Aligned_cols=26 Identities=27% Similarity=0.699 Sum_probs=19.7
Q ss_pred CCCCCCccCCCCeeEEecCCcccccccccccc
Q 015947 1 MGYMCDFCGDQRSIVYCRSDAACLCLSCDRNV 32 (397)
Q Consensus 1 M~~~Cd~C~~a~A~VyC~aD~A~LC~~CD~~v 32 (397)
|...|-.|+.. ..+.+.+|..|.+++
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 77889999885 256788888887653
No 13
>PF12773 DZR: Double zinc ribbon
Probab=53.36 E-value=16 Score=26.55 Aligned_cols=31 Identities=19% Similarity=0.566 Sum_probs=21.2
Q ss_pred cCCccccccccccccccccchhhcccccccccccCCC
Q 015947 18 RSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQ 54 (397)
Q Consensus 18 ~aD~A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~s~ 54 (397)
..+.+.+|..|...+- ........|..|+..
T Consensus 8 ~~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLP------PPDQSKKICPNCGAE 38 (50)
T ss_pred CCccccCChhhcCChh------hccCCCCCCcCCcCC
Confidence 4567888888887776 234445668777765
No 14
>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=51.41 E-value=16 Score=27.11 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=24.9
Q ss_pred cccccCCCCce---eeecCC-CcccCcccccCccC
Q 015947 47 LCERCNSQPAL---VRCAEE-RVSLCQNCDWIGHG 77 (397)
Q Consensus 47 LCd~C~s~PA~---v~C~~D-~asLC~~CD~~~H~ 77 (397)
.|+.|...+.. +.|..| .--||..|-..+..
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 48889887754 779998 77999999987643
No 15
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=45.92 E-value=18 Score=40.33 Aligned_cols=48 Identities=19% Similarity=0.567 Sum_probs=32.4
Q ss_pred CCCCccCCCCeeEEecCCccccccccccccccccchhhcccccccccccCCCCceeeecCCCcccCccccc
Q 015947 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEERVSLCQNCDW 73 (397)
Q Consensus 3 ~~Cd~C~~a~A~VyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~s~PA~v~C~~D~asLC~~CD~ 73 (397)
..|-.|+.. -.+.|++|..|...+.. ..|..|+..- .-.+.+|..|..
T Consensus 2 ~~Cp~Cg~~------n~~~akFC~~CG~~l~~-----------~~Cp~CG~~~------~~~~~fC~~CG~ 49 (645)
T PRK14559 2 LICPQCQFE------NPNNNRFCQKCGTSLTH-----------KPCPQCGTEV------PVDEAHCPNCGA 49 (645)
T ss_pred CcCCCCCCc------CCCCCccccccCCCCCC-----------CcCCCCCCCC------CcccccccccCC
Confidence 478888887 45788999999877631 2488888762 224556666643
No 16
>PRK14873 primosome assembly protein PriA; Provisional
Probab=41.03 E-value=16 Score=40.66 Aligned_cols=45 Identities=20% Similarity=0.417 Sum_probs=29.9
Q ss_pred eeEEecCCc-cccccccccccccccchhhcccccccccccCCCCceeeecC
Q 015947 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAE 62 (397)
Q Consensus 13 A~VyC~aD~-A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~s~PA~v~C~~ 62 (397)
..++|+.+. ..-|..||..+-.. +..+.+.|..|+.......|..
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L~~h-----~~~~~l~Ch~CG~~~~p~~Cp~ 427 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPLGLP-----SAGGTPRCRWCGRAAPDWRCPR 427 (665)
T ss_pred CeeEhhhCcCeeECCCCCCceeEe-----cCCCeeECCCCcCCCcCccCCC
Confidence 567888775 56699999765431 3456788999997543344443
No 17
>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=40.27 E-value=16 Score=24.86 Aligned_cols=24 Identities=33% Similarity=0.771 Sum_probs=17.7
Q ss_pred cccccccCCCCceeeecCCCcccCc
Q 015947 45 TLLCERCNSQPALVRCAEERVSLCQ 69 (397)
Q Consensus 45 vpLCd~C~s~PA~v~C~~D~asLC~ 69 (397)
..+|.+|+. ++.+.|..|.+..|.
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 358999998 899999999999885
No 18
>PF15321 ATAD4: ATPase family AAA domain containing 4
Probab=40.20 E-value=7.8 Score=32.61 Aligned_cols=10 Identities=60% Similarity=0.999 Sum_probs=8.7
Q ss_pred HhHHhhhhcc
Q 015947 367 RYKEKKKTRK 376 (397)
Q Consensus 367 ry~ekkk~r~ 376 (397)
|||||||-|.
T Consensus 70 RFKEKrKvRa 79 (84)
T PF15321_consen 70 RFKEKRKVRA 79 (84)
T ss_pred cccccccccc
Confidence 8999999884
No 19
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=38.80 E-value=15 Score=38.03 Aligned_cols=66 Identities=23% Similarity=0.455 Sum_probs=45.8
Q ss_pred CeeEEecCCcccc------ccccccccccccchhh-ccccccc----------------ccccCCCC---ceeeecCCCc
Q 015947 12 RSIVYCRSDAACL------CLSCDRNVHLANALSK-RHSRTLL----------------CERCNSQP---ALVRCAEERV 65 (397)
Q Consensus 12 ~A~VyC~aD~A~L------C~~CD~~vHsAN~La~-RH~RvpL----------------Cd~C~s~P---A~v~C~~D~a 65 (397)
.+..+|..+.|+. |.-|+..+=++.-|++ =|.-.|| |-.|+... ..++|..|.-
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 4667787777775 5577776666655553 2222232 77884332 4588999999
Q ss_pred ccCcccccCccC
Q 015947 66 SLCQNCDWIGHG 77 (397)
Q Consensus 66 sLC~~CD~~~H~ 77 (397)
.+|..||.-+|.
T Consensus 354 ~FCldCDv~iHe 365 (378)
T KOG2807|consen 354 VFCLDCDVFIHE 365 (378)
T ss_pred eeeccchHHHHh
Confidence 999999999986
No 20
>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=38.31 E-value=28 Score=26.15 Aligned_cols=28 Identities=36% Similarity=0.883 Sum_probs=22.3
Q ss_pred ccccCCCCce---eeecCCC---cccCcccccCc
Q 015947 48 CERCNSQPAL---VRCAEER---VSLCQNCDWIG 75 (397)
Q Consensus 48 Cd~C~s~PA~---v~C~~D~---asLC~~CD~~~ 75 (397)
|+.|+..|-. +.|..|. --||+.|-..+
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 8889887743 6688776 89999998776
No 21
>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=34.67 E-value=40 Score=25.44 Aligned_cols=32 Identities=31% Similarity=0.726 Sum_probs=24.2
Q ss_pred cccccCCCCc---eeeecCC-CcccCcccccCccCC
Q 015947 47 LCERCNSQPA---LVRCAEE-RVSLCQNCDWIGHGT 78 (397)
Q Consensus 47 LCd~C~s~PA---~v~C~~D-~asLC~~CD~~~H~A 78 (397)
.|+.|+..|. -+.|..| .--||+.|-+.++..
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 4889998774 3668877 568999999887543
No 22
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=31.91 E-value=31 Score=39.12 Aligned_cols=45 Identities=29% Similarity=0.674 Sum_probs=31.0
Q ss_pred eeEEecCCcc-ccccccccccccccchhhcccccccccccCCC-CceeeecC
Q 015947 13 SIVYCRSDAA-CLCLSCDRNVHLANALSKRHSRTLLCERCNSQ-PALVRCAE 62 (397)
Q Consensus 13 A~VyC~aD~A-~LC~~CD~~vHsAN~La~RH~RvpLCd~C~s~-PA~v~C~~ 62 (397)
..|.|+.+.- .=|..||...-. +++.+.+.|..|+.+ +....|..
T Consensus 434 ~~l~C~~Cg~v~~Cp~Cd~~lt~-----H~~~~~L~CH~Cg~~~~~p~~Cp~ 480 (730)
T COG1198 434 PLLLCRDCGYIAECPNCDSPLTL-----HKATGQLRCHYCGYQEPIPQSCPE 480 (730)
T ss_pred ceeecccCCCcccCCCCCcceEE-----ecCCCeeEeCCCCCCCCCCCCCCC
Confidence 4678887754 449999976543 366688999999987 34444443
No 23
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=30.06 E-value=29 Score=35.27 Aligned_cols=19 Identities=32% Similarity=0.548 Sum_probs=14.8
Q ss_pred hhhHHHHHHHhHHhhhhcc
Q 015947 358 SASRSKAVLRYKEKKKTRK 376 (397)
Q Consensus 358 ~~~r~~a~~ry~ekkk~r~ 376 (397)
.+.|..|-.||++|||..+
T Consensus 232 r~qnk~AAtRYRqKkRae~ 250 (294)
T KOG4571|consen 232 RQQNKAAATRYRQKKRAEK 250 (294)
T ss_pred HHHhHHHHHHHHHHHHHHH
Confidence 4566678899999998754
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=28.12 E-value=36 Score=36.53 Aligned_cols=39 Identities=26% Similarity=0.559 Sum_probs=26.9
Q ss_pred eeEEecCCc-cccccccccccccccchhhcccccccccccCCCCc
Q 015947 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPA 56 (397)
Q Consensus 13 A~VyC~aD~-A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~s~PA 56 (397)
..++|+.+. ..-|..||..+-. +++.+.+.|..|+....
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 456787774 5569999965543 24566788999986643
No 25
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=27.40 E-value=85 Score=28.51 Aligned_cols=33 Identities=21% Similarity=0.247 Sum_probs=30.1
Q ss_pred hhhHHHHHHHhHHhhhhccccceeeeeeecCCc
Q 015947 358 SASRSKAVLRYKEKKKTRKLVLNRKLCLNLHGV 390 (397)
Q Consensus 358 ~~~r~~a~~ry~ekkk~r~~~k~i~~~~~~~~~ 390 (397)
...|...+.||+||++.|.|+|.|+|..++...
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 322 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNA 322 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccc
Confidence 578999999999999999999999999887654
No 26
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=27.04 E-value=66 Score=34.30 Aligned_cols=27 Identities=37% Similarity=0.503 Sum_probs=18.6
Q ss_pred ccccccCCcccccCCCCCcccccccchh
Q 015947 205 KDLAFCEDDDLYEDFNMDEMDLNFENYE 232 (397)
Q Consensus 205 ~~~~iced~dl~edfnmDDvdL~fENyE 232 (397)
++.+.-|++.|||+++ |++.-.=-|.+
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 27
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=25.22 E-value=32 Score=37.56 Aligned_cols=64 Identities=28% Similarity=0.579 Sum_probs=40.9
Q ss_pred cccccccccccccccchhhc-ccc------ccccc--ccCCC--Cceeeec---------CCCcccCcccccCccCCCCC
Q 015947 22 ACLCLSCDRNVHLANALSKR-HSR------TLLCE--RCNSQ--PALVRCA---------EERVSLCQNCDWIGHGTSTS 81 (397)
Q Consensus 22 A~LC~~CD~~vHsAN~La~R-H~R------vpLCd--~C~s~--PA~v~C~---------~D~asLC~~CD~~~H~An~l 81 (397)
..||..|...||..-+.... +.- ...|+ .|.++ .|++.|- +-.+.+|+.|....|+.. .
T Consensus 227 LylC~~Ca~~i~~e~~~~~~~~il~P~~~vS~~CenK~C~S~~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~~~H~n~-~ 305 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNNR-R 305 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCCCCCeEEEEechhhccccCCCcchhHHHHhhhhcccc-c
Confidence 45999999999985442222 111 23365 67655 3777774 347899999999988643 3
Q ss_pred CCCCc
Q 015947 82 ASSHK 86 (397)
Q Consensus 82 A~~Hq 86 (397)
...|.
T Consensus 306 ~~dHi 310 (525)
T PF14776_consen 306 GSDHI 310 (525)
T ss_pred cccee
Confidence 44454
No 28
>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=23.21 E-value=20 Score=31.36 Aligned_cols=50 Identities=20% Similarity=0.551 Sum_probs=19.7
Q ss_pred cccccccccccccccchhhcccccccccccCCCCceeeecCCC-------cccCccc
Q 015947 22 ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEER-------VSLCQNC 71 (397)
Q Consensus 22 A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~s~PA~v~C~~D~-------asLC~~C 71 (397)
+.||..||.+--.-...++-...+.+|+.|..-.-.-+|..|. |..|..|
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 4566666654444333444456677777665554444444443 5566666
No 29
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=22.16 E-value=27 Score=36.57 Aligned_cols=52 Identities=31% Similarity=0.720 Sum_probs=36.3
Q ss_pred cccccCCCCce---eeecCCCc-ccCcccccCccCCCCCCCCCcccccccCCCCCChhh
Q 015947 47 LCERCNSQPAL---VRCAEERV-SLCQNCDWIGHGTSTSASSHKRQTINCYSGCPSASE 101 (397)
Q Consensus 47 LCd~C~s~PA~---v~C~~D~a-sLC~~CD~~~H~An~lA~~HqR~pl~~ysgcPs~~e 101 (397)
.|..|..++-. ++|..|+. .||+.|-|.+|..+.-.-+|+ +..|+.=.+++.
T Consensus 242 ~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~---mke~Ss~ksp~k 297 (434)
T KOG4301|consen 242 ECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQ---MKEYSSWKSPAK 297 (434)
T ss_pred cCcceecccccchhhhHhhcCCccccchhhccccCCCCcchHHH---HHHhhcccChHH
Confidence 39999988753 45888865 899999999997655344454 455655555543
No 30
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=21.54 E-value=1.1e+02 Score=22.71 Aligned_cols=31 Identities=23% Similarity=0.504 Sum_probs=23.0
Q ss_pred cccccCCCCce---eeecCC-CcccCcccccCccC
Q 015947 47 LCERCNSQPAL---VRCAEE-RVSLCQNCDWIGHG 77 (397)
Q Consensus 47 LCd~C~s~PA~---v~C~~D-~asLC~~CD~~~H~ 77 (397)
.|+.|...|.. +.|..| ..-||..|-..++.
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~ 36 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVT 36 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCc
Confidence 48888876643 678877 56899999877643
No 31
>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=21.31 E-value=35 Score=22.61 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=8.6
Q ss_pred CCCccCCCCeeEEecCCcccccccccccccc
Q 015947 4 MCDFCGDQRSIVYCRSDAACLCLSCDRNVHL 34 (397)
Q Consensus 4 ~Cd~C~~a~A~VyC~aD~A~LC~~CD~~vHs 34 (397)
.|+.|+...-. +...-|..||..+|.
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 58888887432 234568899988884
No 32
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=20.55 E-value=75 Score=27.57 Aligned_cols=53 Identities=21% Similarity=0.556 Sum_probs=30.7
Q ss_pred CCCeeEEecCC----ccccccccccccccccchhhcccccccccccCCCCceeeecC
Q 015947 10 DQRSIVYCRSD----AACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAE 62 (397)
Q Consensus 10 ~a~A~VyC~aD----~A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~s~PA~v~C~~ 62 (397)
..|-.|.|+-- -..||..||.+----...++--.-+.+|+.|.-..-.-+|..
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 34667777643 467999999765432221222223677888876655444443
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=20.32 E-value=36 Score=26.13 Aligned_cols=22 Identities=27% Similarity=0.635 Sum_probs=15.0
Q ss_pred ceeeecCCCcccCcccccCccC
Q 015947 56 ALVRCAEERVSLCQNCDWIGHG 77 (397)
Q Consensus 56 A~v~C~~D~asLC~~CD~~~H~ 77 (397)
..++|..|+..+|..||.-+|.
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 4578999999999999999985
Done!