Query 017166
Match_columns 376
No_of_seqs 301 out of 885
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 06:11:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017166.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017166hhsearch_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 2.7E-20 5.9E-25 134.8 3.2 45 301-345 1-45 (45)
2 cd00021 BBOX B-Box-type zinc f 97.5 6.5E-05 1.4E-09 51.4 2.2 38 63-106 2-39 (39)
3 cd00021 BBOX B-Box-type zinc f 97.2 0.00035 7.5E-09 47.8 2.8 38 23-63 2-39 (39)
4 smart00336 BBOX B-Box-type zin 97.1 0.00041 8.9E-09 48.0 2.5 41 60-106 2-42 (42)
5 PF00643 zf-B_box: B-box zinc 96.9 0.0004 8.7E-09 48.7 1.1 40 61-106 3-42 (42)
6 KOG1601 GATA-4/5/6 transcripti 96.5 0.00083 1.8E-08 61.6 0.9 91 21-112 5-104 (340)
7 smart00336 BBOX B-Box-type zin 95.9 0.0081 1.8E-07 41.5 2.8 40 21-63 3-42 (42)
8 PF00643 zf-B_box: B-box zinc 95.5 0.01 2.2E-07 41.5 2.3 40 21-63 3-42 (42)
9 PF09425 CCT_2: Divergent CCT 95.4 0.0096 2.1E-07 39.2 1.6 25 299-324 2-26 (27)
10 KOG4367 Predicted Zn-finger pr 95.1 0.0044 9.5E-08 64.2 -0.8 75 21-95 162-257 (699)
11 KOG4367 Predicted Zn-finger pr 72.6 1.2 2.5E-05 46.9 -0.0 46 63-108 164-211 (699)
12 KOG1601 GATA-4/5/6 transcripti 59.9 11 0.00023 34.5 3.6 42 297-338 289-330 (340)
13 smart00521 CBF CCAAT-Binding t 52.3 20 0.00044 28.1 3.5 25 318-342 36-61 (62)
14 KOG0954 PHD finger protein [Ge 50.5 11 0.00023 42.3 2.3 54 21-77 271-330 (893)
15 PF02045 CBFB_NFYA: CCAAT-bind 49.6 12 0.00026 29.0 1.9 23 318-340 35-58 (58)
16 PF07649 C1_3: C1-like domain; 46.0 7.5 0.00016 25.5 0.2 26 23-53 2-27 (30)
17 cd02335 ZZ_ADA2 Zinc finger, Z 44.7 23 0.00051 25.8 2.7 40 63-102 2-45 (49)
18 PF13831 PHD_2: PHD-finger; PD 43.8 4.7 0.0001 28.0 -1.0 28 41-68 4-36 (36)
19 PF04438 zf-HIT: HIT zinc fing 42.1 17 0.00037 24.3 1.5 23 62-85 3-25 (30)
20 KOG0129 Predicted RNA-binding 39.7 8.7 0.00019 41.1 -0.3 74 31-107 415-505 (520)
21 smart00249 PHD PHD zinc finger 38.8 28 0.0006 23.4 2.2 26 24-54 2-27 (47)
22 TIGR00622 ssl1 transcription f 38.1 22 0.00048 30.9 2.0 31 63-93 57-101 (112)
23 PF09416 UPF1_Zn_bind: RNA hel 36.6 30 0.00065 31.7 2.6 66 23-88 2-94 (152)
24 PF13248 zf-ribbon_3: zinc-rib 35.4 25 0.00053 22.5 1.4 25 21-51 2-26 (26)
25 cd02334 ZZ_dystrophin Zinc fin 35.4 33 0.00072 25.4 2.3 33 63-95 2-38 (49)
26 PF03660 PHF5: PHF5-like prote 32.7 11 0.00024 32.4 -0.7 41 43-87 29-76 (106)
27 KOG1561 CCAAT-binding factor, 30.3 43 0.00093 33.9 2.8 48 300-347 191-246 (307)
28 PRK14873 primosome assembly pr 30.0 29 0.00064 38.4 1.7 46 34-89 384-430 (665)
29 KOG0956 PHD finger protein AF1 28.4 28 0.0006 38.9 1.2 48 24-77 8-66 (900)
30 PF12773 DZR: Double zinc ribb 27.6 55 0.0012 23.4 2.3 29 38-69 9-37 (50)
31 PF01286 XPA_N: XPA protein N- 26.1 29 0.00062 24.1 0.5 29 41-69 3-32 (34)
32 cd02341 ZZ_ZZZ3 Zinc finger, Z 24.6 66 0.0014 23.7 2.3 28 64-91 3-36 (48)
33 KOG3576 Ovo and related transc 24.6 13 0.00028 35.9 -1.9 49 21-69 117-181 (267)
34 KOG2807 RNA polymerase II tran 22.6 50 0.0011 33.9 1.7 46 20-71 329-377 (378)
35 KOG0129 Predicted RNA-binding 21.0 36 0.00079 36.6 0.4 42 17-58 451-499 (520)
36 PF07975 C1_4: TFIIH C1-like d 20.8 30 0.00065 26.1 -0.2 23 72-94 20-42 (51)
37 PRK14714 DNA polymerase II lar 20.5 46 0.001 39.6 1.1 28 317-344 1151-1178(1337)
38 PF03833 PolC_DP2: DNA polymer 20.2 34 0.00074 39.0 0.0 26 83-113 694-719 (900)
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=2.7e-20 Score=134.75 Aligned_cols=45 Identities=67% Similarity=1.100 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHhhcccCCCcccccchhhhhhhCCCCCceeecCCC
Q 017166 301 REARVLRYREKRKNRKFEKTIRYHSRKAYAETRPRIKGRFAKRAE 345 (376)
Q Consensus 301 R~~~v~ry~eKr~~R~f~k~irY~~Rk~~A~~RpRvkGrF~k~~~ 345 (376)
|+++|+||+|||++|+|+|+|+|++||++|+.|||||||||+.++
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 789999999999999999999999999999999999999999864
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=97.49 E-value=6.5e-05 Score=51.41 Aligned_cols=38 Identities=39% Similarity=0.934 Sum_probs=33.7
Q ss_pred eeccccCcCceEEecCCccccccccCcCccCCCCCCCCcceeec
Q 017166 63 MCEVCEQAPAAVTCKADAAALCVTCDNDIHSANPLARRHERLPI 106 (376)
Q Consensus 63 LCd~C~~apA~v~C~~D~a~LC~~CD~~iH~aN~la~rH~Rvpv 106 (376)
+|+.|+.+++.+||..|...+|..|+...|. .|+++||
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 6889988899999999999999999988864 7988886
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=97.15 E-value=0.00035 Score=47.75 Aligned_cols=38 Identities=39% Similarity=0.885 Sum_probs=33.5
Q ss_pred CCCccCCCceeEEeecCCcccccccchhhhccccCCceeee
Q 017166 23 PCDTCKAAAAAVFCRVDSAFLCLNCDLRIHNCMNKHARVWM 63 (376)
Q Consensus 23 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~aasRH~Rv~L 63 (376)
.|+.+..+++.+||..|.+.+|..|+...|. .|.+++|
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 5999998899999999999999999988776 5888764
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.07 E-value=0.00041 Score=48.05 Aligned_cols=41 Identities=34% Similarity=0.599 Sum_probs=35.2
Q ss_pred eeeeeccccCcCceEEecCCccccccccCcCccCCCCCCCCcceeec
Q 017166 60 RVWMCEVCEQAPAAVTCKADAAALCVTCDNDIHSANPLARRHERLPI 106 (376)
Q Consensus 60 Rv~LCd~C~~apA~v~C~~D~a~LC~~CD~~iH~aN~la~rH~Rvpv 106 (376)
|..+|+.|+..++.+||..|...+|..|....| +.|.++||
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 567899999889999999999999999998765 56877765
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=96.88 E-value=0.0004 Score=48.70 Aligned_cols=40 Identities=25% Similarity=0.513 Sum_probs=34.2
Q ss_pred eeeeccccCcCceEEecCCccccccccCcCccCCCCCCCCcceeec
Q 017166 61 VWMCEVCEQAPAAVTCKADAAALCVTCDNDIHSANPLARRHERLPI 106 (376)
Q Consensus 61 v~LCd~C~~apA~v~C~~D~a~LC~~CD~~iH~aN~la~rH~Rvpv 106 (376)
.++|..|+..++.+||..|...||..|....|.. |..+||
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 4579999988899999999999999999999754 888876
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=96.55 E-value=0.00083 Score=61.64 Aligned_cols=91 Identities=21% Similarity=0.237 Sum_probs=66.0
Q ss_pred CCCCCccCCCceeEEeecCCcccccccchhhhcc---ccCCceeeeeccccCcCce--EEecCCcccc----ccccCcCc
Q 017166 21 AKPCDTCKAAAAAVFCRVDSAFLCLNCDLRIHNC---MNKHARVWMCEVCEQAPAA--VTCKADAAAL----CVTCDNDI 91 (376)
Q Consensus 21 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~a---asRH~Rv~LCd~C~~apA~--v~C~~D~a~L----C~~CD~~i 91 (376)
...|+.|....... |..|...+|..|+.++|.. ...|.++.+|..+....+. +.|..+...+ +..++...
T Consensus 5 ~~~~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (340)
T KOG1601|consen 5 AEDLDSCRFDDLLN-LNADDSLLDISVDARLSASNSLAFPHEPTRLSSSPESFVAATSFSIDLSVPSLDMPGLEGFSLFV 83 (340)
T ss_pred cccccccCcccccc-cccccccCCcccccccccccccccccccccccchhhhhhcccccccccccccccccccccccccc
Confidence 44567776655555 9999999999999999987 2478888898888733333 4555555555 56688888
Q ss_pred cCCCCCCCCcceeeccCCCCC
Q 017166 92 HSANPLARRHERLPIEPFFDS 112 (376)
Q Consensus 92 H~aN~la~rH~Rvpv~~~~~~ 112 (376)
|..++...+|..+++.+....
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~ 104 (340)
T KOG1601|consen 84 SENNPNSLRHPPVPSMPSSNS 104 (340)
T ss_pred ccccCCCCCCCCccccccccc
Confidence 888888888887777665543
No 7
>smart00336 BBOX B-Box-type zinc finger.
Probab=95.85 E-value=0.0081 Score=41.48 Aligned_cols=40 Identities=33% Similarity=0.623 Sum_probs=33.4
Q ss_pred CCCCCccCCCceeEEeecCCcccccccchhhhccccCCceeee
Q 017166 21 AKPCDTCKAAAAAVFCRVDSAFLCLNCDLRIHNCMNKHARVWM 63 (376)
Q Consensus 21 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~aasRH~Rv~L 63 (376)
.+.|..+...++.+||..|.+.+|..|....|. .|.+++|
T Consensus 3 ~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H~---~H~~~~l 42 (42)
T smart00336 3 PPKCDSHGDEPAEFFCEECGALLCRTCDEAEHR---GHTVVLL 42 (42)
T ss_pred CCcCCCCCCCceEEECCCCCcccccccChhhcC---CCceecC
Confidence 456999998899999999999999999987664 5766553
No 8
>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=95.51 E-value=0.01 Score=41.50 Aligned_cols=40 Identities=23% Similarity=0.428 Sum_probs=33.9
Q ss_pred CCCCCccCCCceeEEeecCCcccccccchhhhccccCCceeee
Q 017166 21 AKPCDTCKAAAAAVFCRVDSAFLCLNCDLRIHNCMNKHARVWM 63 (376)
Q Consensus 21 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~aasRH~Rv~L 63 (376)
...|+.|....+.+||..+...||..|....|.. |..++|
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 4579999998899999999999999999988874 777654
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=95.36 E-value=0.0096 Score=39.16 Aligned_cols=25 Identities=40% Similarity=0.577 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHhhcccCCCccccc
Q 017166 299 IDREARVLRYREKRKNRKFEKTIRYH 324 (376)
Q Consensus 299 ~~R~~~v~ry~eKr~~R~f~k~irY~ 324 (376)
..|.+.|+||.||||.|... +..|.
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 66664
No 10
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=95.13 E-value=0.0044 Score=64.24 Aligned_cols=75 Identities=28% Similarity=0.524 Sum_probs=63.2
Q ss_pred CCCCCccCCCc--eeEEeecCCcccccccchhhhcc---ccCCceee----------------eeccccCcCceEEecCC
Q 017166 21 AKPCDTCKAAA--AAVFCRVDSAFLCLNCDLRIHNC---MNKHARVW----------------MCEVCEQAPAAVTCKAD 79 (376)
Q Consensus 21 ~~~Cd~C~~~~--A~vyC~aD~A~LC~~CD~~vH~a---asRH~Rv~----------------LCd~C~~apA~v~C~~D 79 (376)
.-.|..|++++ |+|+|.....|.|.-|-.+.|-+ .++|.-++ -|.-++...-.+||.+|
T Consensus 162 a~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~c 241 (699)
T KOG4367|consen 162 ALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQC 241 (699)
T ss_pred hhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEec
Confidence 45699998764 89999999999999999999977 56665443 28888887889999999
Q ss_pred ccccccccCcCccCCC
Q 017166 80 AAALCVTCDNDIHSAN 95 (376)
Q Consensus 80 ~a~LC~~CD~~iH~aN 95 (376)
.+++|..|-.+..++|
T Consensus 242 k~pvc~~clee~khs~ 257 (699)
T KOG4367|consen 242 KMPVCYQCLEEGKHSS 257 (699)
T ss_pred CChHHHHHHHhhcccc
Confidence 9999999999887665
No 11
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=72.55 E-value=1.2 Score=46.93 Aligned_cols=46 Identities=28% Similarity=0.603 Sum_probs=40.2
Q ss_pred eeccccCcC--ceEEecCCccccccccCcCccCCCCCCCCcceeeccC
Q 017166 63 MCEVCEQAP--AAVTCKADAAALCVTCDNDIHSANPLARRHERLPIEP 108 (376)
Q Consensus 63 LCd~C~~ap--A~v~C~~D~a~LC~~CD~~iH~aN~la~rH~Rvpv~~ 108 (376)
.|..|+.+| |.++|..|.+..|.-|....|-+-...++|..+|-..
T Consensus 164 kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~ 211 (699)
T KOG4367|consen 164 KCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQ 211 (699)
T ss_pred hhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCccc
Confidence 499998877 8999999999999999999999887888998777543
No 12
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=59.86 E-value=11 Score=34.53 Aligned_cols=42 Identities=57% Similarity=0.869 Sum_probs=40.7
Q ss_pred ChHHHHHHHHHHHHHhhcccCCCcccccchhhhhhhCCCCCc
Q 017166 297 CGIDREARVLRYREKRKNRKFEKTIRYHSRKAYAETRPRIKG 338 (376)
Q Consensus 297 ~~~~R~~~v~ry~eKr~~R~f~k~irY~~Rk~~A~~RpRvkG 338 (376)
....|+..+.||++|++.|.|.|+|+|..||..|+.|||+||
T Consensus 289 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 289 SSHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred ccchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 578999999999999999999999999999999999999999
No 13
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=52.29 E-value=20 Score=28.08 Aligned_cols=25 Identities=40% Similarity=0.472 Sum_probs=21.9
Q ss_pred CCcccccchhhhhhhCCC-CCceeec
Q 017166 318 EKTIRYHSRKAYAETRPR-IKGRFAK 342 (376)
Q Consensus 318 ~k~irY~~Rk~~A~~RpR-vkGrF~k 342 (376)
.|..-++||-..|-.||| --|||.+
T Consensus 36 rkpYlhESRH~HAm~R~Rg~gGRFl~ 61 (62)
T smart00521 36 RKPYLHESRHLHAMRRPRGSGGRFLN 61 (62)
T ss_pred cCCcccchhHHHHHccCcCCCCCCCC
Confidence 567789999999999999 6789975
No 14
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=50.46 E-value=11 Score=42.30 Aligned_cols=54 Identities=22% Similarity=0.762 Sum_probs=38.9
Q ss_pred CCCCCccCCCceeEEeecCCcccccccchhhhcc----ccCCceeeeeccccC--cCceEEec
Q 017166 21 AKPCDTCKAAAAAVFCRVDSAFLCLNCDLRIHNC----MNKHARVWMCEVCEQ--APAAVTCK 77 (376)
Q Consensus 21 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~a----asRH~Rv~LCd~C~~--apA~v~C~ 77 (376)
..+||+|+..-.. .++..-+|..|..-||.+ ..-..--|||.-|.. .|.-|.|.
T Consensus 271 dviCDvCrspD~e---~~neMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg~~ppCvLCP 330 (893)
T KOG0954|consen 271 DVICDVCRSPDSE---EANEMVFCDKCNICVHQACYGILEVPEGPWLCRTCALGIEPPCVLCP 330 (893)
T ss_pred cceeceecCCCcc---ccceeEEeccchhHHHHhhhceeecCCCCeeehhccccCCCCeeecc
Confidence 6789999976443 256778899999999998 445557799988864 33444444
No 15
>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=49.59 E-value=12 Score=28.97 Aligned_cols=23 Identities=43% Similarity=0.518 Sum_probs=18.9
Q ss_pred CCcccccchhhhhhhCCC-CCcee
Q 017166 318 EKTIRYHSRKAYAETRPR-IKGRF 340 (376)
Q Consensus 318 ~k~irY~~Rk~~A~~RpR-vkGrF 340 (376)
.|+.-++||-..|-.||| -.|||
T Consensus 35 rk~YlheSRH~HA~~R~Rg~gGRF 58 (58)
T PF02045_consen 35 RKPYLHESRHKHAMRRPRGPGGRF 58 (58)
T ss_pred hHHHHHHHHHHHHHcCccCCCCCC
Confidence 344578999999999999 67787
No 16
>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=46.02 E-value=7.5 Score=25.47 Aligned_cols=26 Identities=27% Similarity=0.781 Sum_probs=9.0
Q ss_pred CCCccCCCceeEEeecCCcccccccchhhhc
Q 017166 23 PCDTCKAAAAAVFCRVDSAFLCLNCDLRIHN 53 (376)
Q Consensus 23 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~ 53 (376)
.|+.|+...-. +..|-|..||-.+|.
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 58888754332 346778888888885
No 17
>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=44.73 E-value=23 Score=25.82 Aligned_cols=40 Identities=18% Similarity=0.455 Sum_probs=27.2
Q ss_pred eeccccCcCce---EEecCC-ccccccccCcCccCCCCCCCCcc
Q 017166 63 MCEVCEQAPAA---VTCKAD-AAALCVTCDNDIHSANPLARRHE 102 (376)
Q Consensus 63 LCd~C~~apA~---v~C~~D-~a~LC~~CD~~iH~aN~la~rH~ 102 (376)
.|+.|...+-. +.|..| .--||..|-......+.--..|.
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~ 45 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHN 45 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCC
Confidence 37777766544 788887 68999999887755444344443
No 18
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=43.78 E-value=4.7 Score=27.96 Aligned_cols=28 Identities=29% Similarity=0.975 Sum_probs=12.5
Q ss_pred cccccccchhhhcc---ccCCce--eeeecccc
Q 017166 41 AFLCLNCDLRIHNC---MNKHAR--VWMCEVCE 68 (376)
Q Consensus 41 A~LC~~CD~~vH~a---asRH~R--v~LCd~C~ 68 (376)
-..|..|+-.||.. ...... .|+|+.|+
T Consensus 4 ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 4 LLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp EEE-SSS--EEEHHHHT-SS--SS-----HHH-
T ss_pred eEEeCCCCCcCChhhCCcccCCCCCcEECCcCC
Confidence 35688999999988 333222 39999885
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=42.14 E-value=17 Score=24.32 Aligned_cols=23 Identities=35% Similarity=0.782 Sum_probs=17.1
Q ss_pred eeeccccCcCceEEecCCcccccc
Q 017166 62 WMCEVCEQAPAAVTCKADAAALCV 85 (376)
Q Consensus 62 ~LCd~C~~apA~v~C~~D~a~LC~ 85 (376)
.+|.+|+. ++...|..+.+..|.
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 899999999888874
No 20
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=39.74 E-value=8.7 Score=41.13 Aligned_cols=74 Identities=22% Similarity=0.322 Sum_probs=48.9
Q ss_pred ceeEEeecCCcccccccchhhhcc-ccCCceee---------eeccccC-----cCceEEec--CCccccccccCcCccC
Q 017166 31 AAAVFCRVDSAFLCLNCDLRIHNC-MNKHARVW---------MCEVCEQ-----APAAVTCK--ADAAALCVTCDNDIHS 93 (376)
Q Consensus 31 ~A~vyC~aD~A~LC~~CD~~vH~a-asRH~Rv~---------LCd~C~~-----apA~v~C~--~D~a~LC~~CD~~iH~ 93 (376)
.++|--.++.||+=+-=.+-|+-. ..=+.||. +|+.|+. ..|-+||. .|--..|..|-+.+|+
T Consensus 415 aGRVtFsnqqsYi~AIsarFvql~h~d~~KRVEIkPYv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS 494 (520)
T KOG0129|consen 415 AGRVTFSNQQAYIKAISARFVQLDHTDIDKRVEIKPYVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHS 494 (520)
T ss_pred cceeeecccHHHHHHHhhheEEEeccccceeeeecceeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhc
Confidence 345555556666533333333333 33344664 4999988 88999999 5889999999999998
Q ss_pred CCCCCCCcceeecc
Q 017166 94 ANPLARRHERLPIE 107 (376)
Q Consensus 94 aN~la~rH~Rvpv~ 107 (376)
- ..++...||.
T Consensus 495 ~---~~r~~HkPlv 505 (520)
T KOG0129|consen 495 G---PGREHHKPLV 505 (520)
T ss_pred C---CchhcCCcee
Confidence 6 4455555654
No 21
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.06 E-value=22 Score=30.92 Aligned_cols=31 Identities=26% Similarity=0.639 Sum_probs=25.3
Q ss_pred eeccccCc--------------CceEEecCCccccccccCcCccC
Q 017166 63 MCEVCEQA--------------PAAVTCKADAAALCVTCDNDIHS 93 (376)
Q Consensus 63 LCd~C~~a--------------pA~v~C~~D~a~LC~~CD~~iH~ 93 (376)
.|-.|+.. ...+.|..|.-.+|.+||.-+|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh
Confidence 48888762 23477999999999999999996
No 23
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=36.62 E-value=30 Score=31.66 Aligned_cols=66 Identities=21% Similarity=0.498 Sum_probs=36.6
Q ss_pred CCCccC--CCceeEEeecCCcccccccchhhhcc------ccCCceeee------------eccccCcCc----eEEecC
Q 017166 23 PCDTCK--AAAAAVFCRVDSAFLCLNCDLRIHNC------MNKHARVWM------------CEVCEQAPA----AVTCKA 78 (376)
Q Consensus 23 ~Cd~C~--~~~A~vyC~aD~A~LC~~CD~~vH~a------asRH~Rv~L------------Cd~C~~apA----~v~C~~ 78 (376)
.|.+|+ ...++|.|....-.+|.+=+..-.+. .+||.-+-| |-.|+.... .+-.++
T Consensus 2 aC~YCG~~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~NvF~LGFipak~ 81 (152)
T PF09416_consen 2 ACAYCGIHDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKS 81 (152)
T ss_dssp S-TTT----CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT----TTTEEEEEETT
T ss_pred CccccCCCCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCCceeeEEEEEecc
Confidence 599998 88899999999999998655422111 567776544 999987653 455556
Q ss_pred Cc--cccccc-cC
Q 017166 79 DA--AALCVT-CD 88 (376)
Q Consensus 79 D~--a~LC~~-CD 88 (376)
|. +.||.. |-
T Consensus 82 d~vvvllCR~pC~ 94 (152)
T PF09416_consen 82 DSVVVLLCRQPCA 94 (152)
T ss_dssp SCEEEEEETTTTT
T ss_pred CCeEEEEeCCchh
Confidence 65 578877 75
No 24
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.44 E-value=25 Score=22.46 Aligned_cols=25 Identities=28% Similarity=0.600 Sum_probs=16.4
Q ss_pred CCCCCccCCCceeEEeecCCcccccccchhh
Q 017166 21 AKPCDTCKAAAAAVFCRVDSAFLCLNCDLRI 51 (376)
Q Consensus 21 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 51 (376)
.+.|-.|+... .+++..|..|.+++
T Consensus 2 ~~~Cp~Cg~~~------~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEI------DPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcC------CcccccChhhCCCC
Confidence 45678887521 55678888887653
No 25
>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=35.42 E-value=33 Score=25.43 Aligned_cols=33 Identities=21% Similarity=0.526 Sum_probs=23.2
Q ss_pred eeccccCcC---ceEEecCC-ccccccccCcCccCCC
Q 017166 63 MCEVCEQAP---AAVTCKAD-AAALCVTCDNDIHSAN 95 (376)
Q Consensus 63 LCd~C~~ap---A~v~C~~D-~a~LC~~CD~~iH~aN 95 (376)
.|+.|+..| ..+.|..| .--||..|-+..+...
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~ 38 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSK 38 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCC
Confidence 477887655 45667766 4789999998776543
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=32.72 E-value=11 Score=32.42 Aligned_cols=41 Identities=24% Similarity=0.566 Sum_probs=16.8
Q ss_pred cccccchhhhccccCCceeeeeccccCcCceEEecCCc-------ccccccc
Q 017166 43 LCLNCDLRIHNCMNKHARVWMCEVCEQAPAAVTCKADA-------AALCVTC 87 (376)
Q Consensus 43 LC~~CD~~vH~aasRH~Rv~LCd~C~~apA~v~C~~D~-------a~LC~~C 87 (376)
-|.-||.-|+- ...|.+|+.|.--.-.-.|-.|. |..|..|
T Consensus 29 kCpiCDS~Vrp----~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC~eC 76 (106)
T PF03660_consen 29 KCPICDSYVRP----CTKVRICDECSFGSLQGRCIICGSGPGVSDAYYCWEC 76 (106)
T ss_dssp --TTT-----------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-HHH
T ss_pred cccccCCccCC----cceEEECCcCCCCCcCceEEEecCCCCcccceehhhh
Confidence 47778877755 36677888876544433443333 5556666
No 27
>KOG1561 consensus CCAAT-binding factor, subunit B (HAP2) [Transcription]
Probab=30.28 E-value=43 Score=33.91 Aligned_cols=48 Identities=33% Similarity=0.358 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhhc-------ccCCCcccccchhhhhhhCCC-CCceeecCCCcc
Q 017166 300 DREARVLRYREKRKN-------RKFEKTIRYHSRKAYAETRPR-IKGRFAKRAEAD 347 (376)
Q Consensus 300 ~R~~~v~ry~eKr~~-------R~f~k~irY~~Rk~~A~~RpR-vkGrF~k~~~~~ 347 (376)
.--.+|+|-|+-|.+ .|=.|+---++|-..|-+||| --|||....+.+
T Consensus 191 KQY~~IlrRRq~RaKlEa~~klik~RkpYLHESRH~HAmkR~RG~GGRFln~k~~~ 246 (307)
T KOG1561|consen 191 KQYHRILRRRQARAKLEATTKLIKARKPYLHESRHLHAMKRARGEGGRFLNTKEYH 246 (307)
T ss_pred HHHHHHHHHHHHHhhhhhcccchhhcCccccchhhHHHhhcccCCCCCCCchhhhh
Confidence 344455555544432 123344557899999999999 999999988755
No 28
>PRK14873 primosome assembly protein PriA; Provisional
Probab=29.99 E-value=29 Score=38.43 Aligned_cols=46 Identities=17% Similarity=0.358 Sum_probs=27.5
Q ss_pred EEeecC-CcccccccchhhhccccCCceeeeeccccCcCceEEecCCccccccccCc
Q 017166 34 VFCRVD-SAFLCLNCDLRIHNCMNKHARVWMCEVCEQAPAAVTCKADAAALCVTCDN 89 (376)
Q Consensus 34 vyC~aD-~A~LC~~CD~~vH~aasRH~Rv~LCd~C~~apA~v~C~~D~a~LC~~CD~ 89 (376)
|+|+.+ ...-|..||..+-- .+..+...|..|+.... -..|..|..
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~--h~~~~~l~Ch~CG~~~~--------p~~Cp~Cgs 430 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGL--PSAGGTPRCRWCGRAAP--------DWRCPRCGS 430 (665)
T ss_pred eEhhhCcCeeECCCCCCceeE--ecCCCeeECCCCcCCCc--------CccCCCCcC
Confidence 344433 26778999876432 12355778999987432 346667743
No 29
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=28.38 E-value=28 Score=38.95 Aligned_cols=48 Identities=27% Similarity=0.799 Sum_probs=35.1
Q ss_pred CCccCC-----CceeEEeecCCcccccccchhhhcc----ccCCceeeeeccccCcCc--eEEec
Q 017166 24 CDTCKA-----AAAAVFCRVDSAFLCLNCDLRIHNC----MNKHARVWMCEVCEQAPA--AVTCK 77 (376)
Q Consensus 24 Cd~C~~-----~~A~vyC~aD~A~LC~~CD~~vH~a----asRH~Rv~LCd~C~~apA--~v~C~ 77 (376)
|=+|.. ....|||... .|...||.| +.-..=-|.|..|+++.. .|+|.
T Consensus 8 CCVCSDErGWaeNPLVYCDG~------nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCe 66 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGH------NCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCE 66 (900)
T ss_pred eeeecCcCCCccCceeeecCC------CceeeeehhcceeEecCCCchhhhhhhhhhhhccceee
Confidence 556643 3568999875 488999999 667777799999997664 45554
No 30
>PF12773 DZR: Double zinc ribbon
Probab=27.60 E-value=55 Score=23.36 Aligned_cols=29 Identities=21% Similarity=0.473 Sum_probs=16.0
Q ss_pred cCCcccccccchhhhccccCCceeeeeccccC
Q 017166 38 VDSAFLCLNCDLRIHNCMNKHARVWMCEVCEQ 69 (376)
Q Consensus 38 aD~A~LC~~CD~~vH~aasRH~Rv~LCd~C~~ 69 (376)
.+.+..|..|...+- .......+|..|+.
T Consensus 9 ~~~~~fC~~CG~~l~---~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP---PPDQSKKICPNCGA 37 (50)
T ss_pred CccccCChhhcCChh---hccCCCCCCcCCcC
Confidence 355677777776664 11233445666664
No 31
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=26.08 E-value=29 Score=24.13 Aligned_cols=29 Identities=14% Similarity=0.390 Sum_probs=16.3
Q ss_pred cccccccchhhhcc-ccCCceeeeeccccC
Q 017166 41 AFLCLNCDLRIHNC-MNKHARVWMCEVCEQ 69 (376)
Q Consensus 41 A~LC~~CD~~vH~a-asRH~Rv~LCd~C~~ 69 (376)
+-.|..|+....-+ ...|-...+|+.|..
T Consensus 3 ~~~C~eC~~~f~dSyL~~~F~~~VCD~CRD 32 (34)
T PF01286_consen 3 YPKCDECGKPFMDSYLLNNFDLPVCDKCRD 32 (34)
T ss_dssp -EE-TTT--EES-SSCCCCTS-S--TTT-S
T ss_pred CchHhHhCCHHHHHHHHHhCCccccccccC
Confidence 45688888887777 888888999999975
No 32
>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=24.64 E-value=66 Score=23.73 Aligned_cols=28 Identities=25% Similarity=0.597 Sum_probs=19.6
Q ss_pred eccccCcC---ceEEecCCc---cccccccCcCc
Q 017166 64 CEVCEQAP---AAVTCKADA---AALCVTCDNDI 91 (376)
Q Consensus 64 Cd~C~~ap---A~v~C~~D~---a~LC~~CD~~i 91 (376)
|+.|+..| ..+.|..|. --||..|-...
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 67777644 346676665 78999997765
No 33
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=24.63 E-value=13 Score=35.94 Aligned_cols=49 Identities=24% Similarity=0.665 Sum_probs=38.2
Q ss_pred CCCCCccCCCc-------eeEEeecC-Ccccccccchhhhcc--ccCCceee------eeccccC
Q 017166 21 AKPCDTCKAAA-------AAVFCRVD-SAFLCLNCDLRIHNC--MNKHARVW------MCEVCEQ 69 (376)
Q Consensus 21 ~~~Cd~C~~~~-------A~vyC~aD-~A~LC~~CD~~vH~a--asRH~Rv~------LCd~C~~ 69 (376)
.-.|++|++.- --+-|++| .-+||..|..-.|-+ ..||.|.. .|..|+.
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~k 181 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEK 181 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhH
Confidence 55699998753 34789999 589999999999988 88999853 3666664
No 34
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=22.62 E-value=50 Score=33.95 Aligned_cols=46 Identities=28% Similarity=0.730 Sum_probs=34.2
Q ss_pred CCCCCCccC---CCceeEEeecCCcccccccchhhhccccCCceeeeeccccCcC
Q 017166 20 AAKPCDTCK---AAAAAVFCRVDSAFLCLNCDLRIHNCMNKHARVWMCEVCEQAP 71 (376)
Q Consensus 20 ~~~~Cd~C~---~~~A~vyC~aD~A~LC~~CD~~vH~aasRH~Rv~LCd~C~~ap 71 (376)
+.+.|=.|. .....+-|....-.+|.+||.-+|-. ...|..|+..|
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHes------Lh~CpgCeh~~ 377 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHES------LHNCPGCEHKP 377 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccceeeccchHHHHhh------hhcCCCcCCCC
Confidence 456688992 24567788889999999999999754 34688888654
No 35
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=21.01 E-value=36 Score=36.60 Aligned_cols=42 Identities=26% Similarity=0.621 Sum_probs=34.5
Q ss_pred cccCCCCCCccCC-----CceeEEeec--CCcccccccchhhhccccCC
Q 017166 17 WSVAAKPCDTCKA-----AAAAVFCRV--DSAFLCLNCDLRIHNCMNKH 58 (376)
Q Consensus 17 w~~~~~~Cd~C~~-----~~A~vyC~a--D~A~LC~~CD~~vH~aasRH 58 (376)
.-|-..+||.|+. ..|-+||++ +--|.|..|=+.+|+-..|+
T Consensus 451 Yv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~~r~ 499 (520)
T KOG0129|consen 451 YVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGPGRE 499 (520)
T ss_pred eeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCCchh
Confidence 3456788999998 789999996 56899999999999973333
No 36
>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=20.84 E-value=30 Score=26.06 Aligned_cols=23 Identities=26% Similarity=0.608 Sum_probs=15.3
Q ss_pred ceEEecCCccccccccCcCccCC
Q 017166 72 AAVTCKADAAALCVTCDNDIHSA 94 (376)
Q Consensus 72 A~v~C~~D~a~LC~~CD~~iH~a 94 (376)
..+.|..|.-.+|.+||.=||..
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 56889999999999999999853
No 37
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=20.49 E-value=46 Score=39.59 Aligned_cols=28 Identities=18% Similarity=0.340 Sum_probs=19.5
Q ss_pred CCCcccccchhhhhhhCCCCCceeecCC
Q 017166 317 FEKTIRYHSRKAYAETRPRIKGRFAKRA 344 (376)
Q Consensus 317 f~k~irY~~Rk~~A~~RpRvkGrF~k~~ 344 (376)
|+++.+|+.=|.+.+.--||+-|.-+..
T Consensus 1151 Yeat~~~~~p~ev~~~i~~ve~rlg~~~ 1178 (1337)
T PRK14714 1151 YEATLEMADPKDVEDLIERVEDRLGTPE 1178 (1337)
T ss_pred HHHHhccCCHHHHHHHHHHHHHhcCCch
Confidence 5677777777777776667777766644
No 38
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=20.21 E-value=34 Score=39.02 Aligned_cols=26 Identities=15% Similarity=0.494 Sum_probs=0.0
Q ss_pred cccccCcCccCCCCCCCCcceeeccCCCCCC
Q 017166 83 LCVTCDNDIHSANPLARRHERLPIEPFFDSA 113 (376)
Q Consensus 83 LC~~CD~~iH~aN~la~rH~Rvpv~~~~~~~ 113 (376)
.|..|....- ...++.++|..++..+
T Consensus 694 ~C~~C~~~~~-----~~~~~~i~l~~~~~~A 719 (900)
T PF03833_consen 694 ECPKCGRETT-----SYSKQKIDLKEEYDRA 719 (900)
T ss_dssp -------------------------------
T ss_pred ccccccccCc-----ccceeecCHHHHHHHH
Confidence 5788876643 4467788888887653
Done!