Query 023005
Match_columns 289
No_of_seqs 162 out of 538
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:45:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023005.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023005hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00021 BBOX B-Box-type zinc f 97.5 8.6E-05 1.9E-09 49.0 2.3 38 47-90 2-39 (39)
2 cd00021 BBOX B-Box-type zinc f 97.2 0.00025 5.3E-09 46.8 2.4 39 3-47 1-39 (39)
3 PF00643 zf-B_box: B-box zinc 97.2 0.00015 3.3E-09 49.1 1.1 41 44-90 2-42 (42)
4 smart00336 BBOX B-Box-type zin 97.1 0.00048 1E-08 45.9 2.9 41 44-90 2-42 (42)
5 smart00336 BBOX B-Box-type zin 96.3 0.0034 7.4E-08 41.8 2.6 39 3-47 4-42 (42)
6 PF00643 zf-B_box: B-box zinc 96.3 0.0031 6.7E-08 42.6 2.2 40 2-47 3-42 (42)
7 KOG4367 Predicted Zn-finger pr 95.0 0.0061 1.3E-07 61.5 -0.1 74 3-76 163-254 (699)
8 KOG4367 Predicted Zn-finger pr 66.4 2.1 4.5E-05 43.9 0.2 46 46-91 163-210 (699)
9 PF13248 zf-ribbon_3: zinc-rib 58.9 7.7 0.00017 24.0 1.8 25 1-31 1-25 (26)
10 cd02335 ZZ_ADA2 Zinc finger, Z 57.2 13 0.00028 26.2 2.9 30 47-76 2-35 (49)
11 PF04438 zf-HIT: HIT zinc fing 53.8 6.9 0.00015 25.4 1.0 24 45-69 2-25 (30)
12 PF12773 DZR: Double zinc ribb 51.5 16 0.00034 25.3 2.6 30 19-54 9-38 (50)
13 KOG2807 RNA polymerase II tran 46.7 8.3 0.00018 38.2 0.7 66 12-77 274-365 (378)
14 PRK14559 putative protein seri 43.1 22 0.00047 37.9 3.2 35 3-54 2-36 (645)
15 cd02341 ZZ_ZZZ3 Zinc finger, Z 40.7 28 0.0006 24.9 2.5 41 47-90 2-48 (48)
16 PRK14873 primosome assembly pr 40.0 18 0.0004 38.5 2.1 46 13-63 382-428 (665)
17 cd02334 ZZ_dystrophin Zinc fin 33.4 46 0.001 23.9 2.7 31 47-77 2-36 (49)
18 PF14776 UNC-79: Cation-channe 33.2 19 0.00042 37.5 0.9 64 22-86 227-310 (525)
19 cd02249 ZZ Zinc finger, ZZ typ 32.3 47 0.001 22.9 2.5 30 47-76 2-34 (46)
20 COG1198 PriA Primosomal protei 29.5 37 0.0008 36.8 2.3 46 13-63 434-481 (730)
21 PF07975 C1_4: TFIIH C1-like d 29.0 24 0.00052 25.8 0.6 23 13-35 20-42 (51)
22 PF07649 C1_3: C1-like domain; 27.7 23 0.00049 22.4 0.2 26 4-34 2-27 (30)
23 TIGR00595 priA primosomal prot 25.2 45 0.00098 34.1 2.0 45 13-62 212-258 (505)
24 KOG1601 GATA-4/5/6 transcripti 24.0 1.2E+02 0.0025 26.3 4.1 86 5-91 8-99 (340)
25 PF03660 PHF5: PHF5-like prote 23.0 18 0.0004 30.2 -1.0 34 22-55 20-53 (106)
26 KOG1705 Uncharacterized conser 22.3 69 0.0015 26.5 2.2 50 10-63 4-61 (110)
27 KOG0129 Predicted RNA-binding 20.7 34 0.00073 35.7 0.1 33 3-35 456-495 (520)
No 1
>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=97.45 E-value=8.6e-05 Score=48.96 Aligned_cols=38 Identities=32% Similarity=0.768 Sum_probs=33.3
Q ss_pred cccccCCCCceeeccccccccccCcccCccCCCCCCCCCcceec
Q 023005 47 LCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (289)
Q Consensus 47 LCd~C~~~PA~v~C~~d~a~LC~~CD~~~H~an~~as~HqR~pL 90 (289)
+|+.|+.+++.+||..|.+.+|..|+..+|. .|.++||
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 5888988899999999999999999988763 7888775
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=97.22 E-value=0.00025 Score=46.75 Aligned_cols=39 Identities=38% Similarity=0.809 Sum_probs=33.5
Q ss_pred CCCCccCCCCeeEEecCCccccccccccccccccccccccccccc
Q 023005 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (289)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~RvpL 47 (289)
..|+.++.+++.+||..|.+.+|..|+...|. .|.++++
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 36899998899999999999999999988775 5777664
No 3
>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=97.17 E-value=0.00015 Score=49.09 Aligned_cols=41 Identities=27% Similarity=0.537 Sum_probs=34.8
Q ss_pred ccccccccCCCCceeeccccccccccCcccCccCCCCCCCCCcceec
Q 023005 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (289)
Q Consensus 44 RvpLCd~C~~~PA~v~C~~d~a~LC~~CD~~~H~an~~as~HqR~pL 90 (289)
+.++|..|...++.+||..|..++|..|....|. +|+.+||
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~------~H~~~~i 42 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHK------GHKIVPI 42 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTT------TSEEEEC
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCC------CCEEeEC
Confidence 3568999999889999999999999999999875 3888775
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.09 E-value=0.00048 Score=45.95 Aligned_cols=41 Identities=29% Similarity=0.545 Sum_probs=34.8
Q ss_pred ccccccccCCCCceeeccccccccccCcccCccCCCCCCCCCcceec
Q 023005 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (289)
Q Consensus 44 RvpLCd~C~~~PA~v~C~~d~a~LC~~CD~~~H~an~~as~HqR~pL 90 (289)
|..+|..|...++.+||..|...+|..|....| ++|.+.||
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 567899999999999999999999999987655 57777664
No 5
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.29 E-value=0.0034 Score=41.78 Aligned_cols=39 Identities=36% Similarity=0.718 Sum_probs=32.7
Q ss_pred CCCCccCCCCeeEEecCCccccccccccccccccccccccccccc
Q 023005 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (289)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~RvpL 47 (289)
..|..++..++.+||..|.+.+|..|....| +.|.+.+|
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 34666553
No 6
>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=96.27 E-value=0.0031 Score=42.60 Aligned_cols=40 Identities=18% Similarity=0.337 Sum_probs=33.7
Q ss_pred CCCCCccCCCCeeEEecCCccccccccccccccccccccccccccc
Q 023005 2 GYMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (289)
Q Consensus 2 ~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~RvpL 47 (289)
...|..+...++.+||..+...+|..|....|.. |..++|
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 4679999999999999999999999999999865 666553
No 7
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=95.03 E-value=0.0061 Score=61.51 Aligned_cols=74 Identities=18% Similarity=0.434 Sum_probs=60.4
Q ss_pred CCCCccCCC--CeeEEecCCccccccccccccccccccccccccccc----------------ccccCCCCceeeccccc
Q 023005 3 YMCDFCGDQ--RSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL----------------CERCNSQPALVRCAEER 64 (289)
Q Consensus 3 ~~Cd~C~~a--~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~RvpL----------------Cd~C~~~PA~v~C~~d~ 64 (289)
..|.+|+++ .|.|+|..+..+.|.-|..+.|-+..-..+|.-++- |.-+..+.-.+||..|+
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~ck 242 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQCK 242 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEecC
Confidence 358999987 589999999999999999999988666667765432 55555556789999999
Q ss_pred cccccCcccCcc
Q 023005 65 VSLCQNCDWIGH 76 (289)
Q Consensus 65 a~LC~~CD~~~H 76 (289)
+++|-.|-..+.
T Consensus 243 ~pvc~~clee~k 254 (699)
T KOG4367|consen 243 MPVCYQCLEEGK 254 (699)
T ss_pred ChHHHHHHHhhc
Confidence 999999988763
No 8
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=66.36 E-value=2.1 Score=43.92 Aligned_cols=46 Identities=26% Similarity=0.504 Sum_probs=39.8
Q ss_pred ccccccCCCC--ceeeccccccccccCcccCccCCCCCCCCCcceecc
Q 023005 46 LLCERCNSQP--ALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTIN 91 (289)
Q Consensus 46 pLCd~C~~~P--A~v~C~~d~a~LC~~CD~~~H~an~~as~HqR~pL~ 91 (289)
.-|..|...| |.|+|..|.++.|.-|....|-+-.+.++|..+|-+
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 4488998887 889999999999999999999887778889877755
No 9
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=58.94 E-value=7.7 Score=24.03 Aligned_cols=25 Identities=28% Similarity=0.703 Sum_probs=18.7
Q ss_pred CCCCCCccCCCCeeEEecCCccccccccccc
Q 023005 1 MGYMCDFCGDQRSIVYCRSDAACLCLSCDRN 31 (289)
Q Consensus 1 M~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~ 31 (289)
|...|-.|+... .+.+.+|..|.++
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 778888898742 5568888888765
No 10
>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=57.25 E-value=13 Score=26.24 Aligned_cols=30 Identities=30% Similarity=0.685 Sum_probs=24.3
Q ss_pred cccccCCCCce---eecccc-ccccccCcccCcc
Q 023005 47 LCERCNSQPAL---VRCAEE-RVSLCQNCDWIGH 76 (289)
Q Consensus 47 LCd~C~~~PA~---v~C~~d-~a~LC~~CD~~~H 76 (289)
.|+.|...+.. +.|..| .--||..|-..+.
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~ 35 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGA 35 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcC
Confidence 48888877754 779998 8899999988764
No 11
>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=53.84 E-value=6.9 Score=25.39 Aligned_cols=24 Identities=33% Similarity=0.771 Sum_probs=17.7
Q ss_pred cccccccCCCCceeecccccccccc
Q 023005 45 TLLCERCNSQPALVRCAEERVSLCQ 69 (289)
Q Consensus 45 vpLCd~C~~~PA~v~C~~d~a~LC~ 69 (289)
..+|.+|+. ++.+.|..|.+..|.
T Consensus 2 ~~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 2 RKLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp -EEETSSSS-EESEE-TTT--EESS
T ss_pred cCCCccCcC-CCEEECCCcCCceeC
Confidence 357999998 999999999999885
No 12
>PF12773 DZR: Double zinc ribbon
Probab=51.47 E-value=16 Score=25.28 Aligned_cols=30 Identities=20% Similarity=0.582 Sum_probs=20.0
Q ss_pred CCcccccccccccccccccccccccccccccccCCC
Q 023005 19 SDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQ 54 (289)
Q Consensus 19 aD~A~LC~~CD~~vHsaN~La~RH~RvpLCd~C~~~ 54 (289)
.+.+.+|..|...+- .......+|..|+..
T Consensus 9 ~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP------PPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCChh------hccCCCCCCcCCcCC
Confidence 456888888887666 234445667777764
No 13
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=46.69 E-value=8.3 Score=38.17 Aligned_cols=66 Identities=23% Similarity=0.455 Sum_probs=44.0
Q ss_pred CeeEEecCCcccc------cccccccccccccccc-ccccccc----------------ccccCCCC---ceeecccccc
Q 023005 12 RSIVYCRSDAACL------CLSCDRNVHLANALSK-RHSRTLL----------------CERCNSQP---ALVRCAEERV 65 (289)
Q Consensus 12 ~A~vyC~aD~A~L------C~~CD~~vHsaN~La~-RH~RvpL----------------Cd~C~~~P---A~v~C~~d~a 65 (289)
.+.++|..+.|+. |.-|+..+=++.-|++ -|.-.|| |-.|+... -.++|..|+-
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 4566777777665 4567766555544544 2333333 77884332 4588999999
Q ss_pred ccccCcccCccC
Q 023005 66 SLCQNCDWIGHG 77 (289)
Q Consensus 66 ~LC~~CD~~~H~ 77 (289)
.+|..||.-.|.
T Consensus 354 ~FCldCDv~iHe 365 (378)
T KOG2807|consen 354 VFCLDCDVFIHE 365 (378)
T ss_pred eeeccchHHHHh
Confidence 999999999886
No 14
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=43.07 E-value=22 Score=37.91 Aligned_cols=35 Identities=20% Similarity=0.700 Sum_probs=24.1
Q ss_pred CCCCccCCCCeeEEecCCcccccccccccccccccccccccccccccccCCC
Q 023005 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQ 54 (289)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~RvpLCd~C~~~ 54 (289)
..|-.|+.. -.+.|++|..|...+. + ..|..|+..
T Consensus 2 ~~Cp~Cg~~------n~~~akFC~~CG~~l~--------~---~~Cp~CG~~ 36 (645)
T PRK14559 2 LICPQCQFE------NPNNNRFCQKCGTSLT--------H---KPCPQCGTE 36 (645)
T ss_pred CcCCCCCCc------CCCCCccccccCCCCC--------C---CcCCCCCCC
Confidence 368888876 2467888888876652 1 248888765
No 15
>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=40.69 E-value=28 Score=24.88 Aligned_cols=41 Identities=29% Similarity=0.628 Sum_probs=27.5
Q ss_pred cccccCCCCce---eeccccc---cccccCcccCccCCCCCCCCCcceec
Q 023005 47 LCERCNSQPAL---VRCAEER---VSLCQNCDWIGHGTSTSASSHKRQTI 90 (289)
Q Consensus 47 LCd~C~~~PA~---v~C~~d~---a~LC~~CD~~~H~an~~as~HqR~pL 90 (289)
-|+.|+..|.. +.|..|. --||+.|-..+. .-...|..++|
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~---~H~~~H~~~~i 48 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE---SHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC---CCCCCCceeeC
Confidence 38888887743 6688877 899999987762 11235655543
No 16
>PRK14873 primosome assembly protein PriA; Provisional
Probab=40.02 E-value=18 Score=38.50 Aligned_cols=46 Identities=20% Similarity=0.380 Sum_probs=30.5
Q ss_pred eeEEecCCc-ccccccccccccccccccccccccccccccCCCCceeecccc
Q 023005 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEE 63 (289)
Q Consensus 13 A~vyC~aD~-A~LC~~CD~~vHsaN~La~RH~RvpLCd~C~~~PA~v~C~~d 63 (289)
..++|+.+. ..-|..||...-. ++..+.+.|..|+.......|..|
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 5569999965542 134457889999975444445443
No 17
>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=33.36 E-value=46 Score=23.85 Aligned_cols=31 Identities=32% Similarity=0.733 Sum_probs=23.5
Q ss_pred cccccCCCCc---eeecccc-ccccccCcccCccC
Q 023005 47 LCERCNSQPA---LVRCAEE-RVSLCQNCDWIGHG 77 (289)
Q Consensus 47 LCd~C~~~PA---~v~C~~d-~a~LC~~CD~~~H~ 77 (289)
.|+.|+..|. -+.|..| .--||+.|-+.++.
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~ 36 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRT 36 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCc
Confidence 4888987774 3668776 57899999888754
No 18
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=33.17 E-value=19 Score=37.46 Aligned_cols=64 Identities=28% Similarity=0.565 Sum_probs=40.8
Q ss_pred cccccccccccccccccccc-cccc------cccc--ccCCCC--ceeecc---------ccccccccCcccCccCCCCC
Q 023005 22 ACLCLSCDRNVHLANALSKR-HSRT------LLCE--RCNSQP--ALVRCA---------EERVSLCQNCDWIGHGTSTS 81 (289)
Q Consensus 22 A~LC~~CD~~vHsaN~La~R-H~Rv------pLCd--~C~~~P--A~v~C~---------~d~a~LC~~CD~~~H~an~~ 81 (289)
.+||..|...+|+.-+.... +.-. ..|+ .|.++. |++.|. +-.+.+|+.|....|+...
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 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNNRR- 305 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCCCCCeEEEEechhhccccCCCcchhHHHHhhhhccccc-
Confidence 45999999999986443222 2222 2365 666553 777774 3478899999999886542
Q ss_pred CCCCc
Q 023005 82 ASSHK 86 (289)
Q Consensus 82 as~Hq 86 (289)
...|.
T Consensus 306 ~~dHi 310 (525)
T PF14776_consen 306 GSDHI 310 (525)
T ss_pred cccee
Confidence 33344
No 19
>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=32.30 E-value=47 Score=22.90 Aligned_cols=30 Identities=23% Similarity=0.528 Sum_probs=22.2
Q ss_pred cccccCCCC--ceeeccccc-cccccCcccCcc
Q 023005 47 LCERCNSQP--ALVRCAEER-VSLCQNCDWIGH 76 (289)
Q Consensus 47 LCd~C~~~P--A~v~C~~d~-a~LC~~CD~~~H 76 (289)
.|+.|+..- .-+.|..|. --||..|-...+
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 478887721 456788886 899999987764
No 20
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=29.49 E-value=37 Score=36.81 Aligned_cols=46 Identities=28% Similarity=0.638 Sum_probs=32.1
Q ss_pred eeEEecCCcccc-cccccccccccccccccccccccccccCCC-Cceeecccc
Q 023005 13 SIVYCRSDAACL-CLSCDRNVHLANALSKRHSRTLLCERCNSQ-PALVRCAEE 63 (289)
Q Consensus 13 A~vyC~aD~A~L-C~~CD~~vHsaN~La~RH~RvpLCd~C~~~-PA~v~C~~d 63 (289)
..+.|+.++-.+ |..||...-. +++.+.+.|..|+.+ +....|..|
T Consensus 434 ~~l~C~~Cg~v~~Cp~Cd~~lt~-----H~~~~~L~CH~Cg~~~~~p~~Cp~C 481 (730)
T COG1198 434 PLLLCRDCGYIAECPNCDSPLTL-----HKATGQLRCHYCGYQEPIPQSCPEC 481 (730)
T ss_pred ceeecccCCCcccCCCCCcceEE-----ecCCCeeEeCCCCCCCCCCCCCCCC
Confidence 467888886444 9999966532 356688999999987 444555543
No 21
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=28.99 E-value=24 Score=25.76 Aligned_cols=23 Identities=26% Similarity=0.540 Sum_probs=15.5
Q ss_pred eeEEecCCccccccccccccccc
Q 023005 13 SIVYCRSDAACLCLSCDRNVHLA 35 (289)
Q Consensus 13 A~vyC~aD~A~LC~~CD~~vHsa 35 (289)
.++-|......+|.+||.-||..
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 56889999999999999998854
No 22
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=27.66 E-value=23 Score=22.37 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=8.5
Q ss_pred CCCccCCCCeeEEecCCcccccccccccccc
Q 023005 4 MCDFCGDQRSIVYCRSDAACLCLSCDRNVHL 34 (289)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHs 34 (289)
.|+.|+..... +..+-|..||..+|.
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 58888876532 234668889988884
No 23
>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=25.17 E-value=45 Score=34.13 Aligned_cols=45 Identities=24% Similarity=0.553 Sum_probs=29.2
Q ss_pred eeEEecCCc-ccccccccccccccccccccccccccccccCCCCc-eeeccc
Q 023005 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPA-LVRCAE 62 (289)
Q Consensus 13 A~vyC~aD~-A~LC~~CD~~vHsaN~La~RH~RvpLCd~C~~~PA-~v~C~~ 62 (289)
..++|+.+. ..-|..||...-. +++.+.+.|..|+.... ...|..
T Consensus 212 ~~~~C~~Cg~~~~C~~C~~~l~~-----h~~~~~l~Ch~Cg~~~~~~~~Cp~ 258 (505)
T TIGR00595 212 KNLLCRSCGYILCCPNCDVSLTY-----HKKEGKLRCHYCGYQEPIPKTCPQ 258 (505)
T ss_pred CeeEhhhCcCccCCCCCCCceEE-----ecCCCeEEcCCCcCcCCCCCCCCC
Confidence 457788775 5559999965432 24566788999987654 334443
No 24
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=24.01 E-value=1.2e+02 Score=26.31 Aligned_cols=86 Identities=19% Similarity=0.112 Sum_probs=55.0
Q ss_pred CCccCCCCeeEEecCCcccccccccccccccccccccccccccccccCCCCce--eecccccccc----ccCcccCccCC
Q 023005 5 CDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPAL--VRCAEERVSL----CQNCDWIGHGT 78 (289)
Q Consensus 5 Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsaN~La~RH~RvpLCd~C~~~PA~--v~C~~d~a~L----C~~CD~~~H~a 78 (289)
++.+....... |..|.+.+|..++.++|..+.+...|.+..++..+...++. +.+......+ +..+....|..
T Consensus 8 ~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (340)
T KOG1601|consen 8 LDSCRFDDLLN-LNADDSLLDISVDARLSASNSLAFPHEPTRLSSSPESFVAATSFSIDLSVPSLDMPGLEGFSLFVSEN 86 (340)
T ss_pred ccccCcccccc-cccccccCCcccccccccccccccccccccccchhhhhhccccccccccccccccccccccccccccc
Confidence 55555555555 99999999999999999998666678888888776522222 3333333333 44565555555
Q ss_pred CCCCCCCcceecc
Q 023005 79 STSASSHKRQTIN 91 (289)
Q Consensus 79 n~~as~HqR~pL~ 91 (289)
+.....|..+++.
T Consensus 87 ~~~~~~~~~~~~~ 99 (340)
T KOG1601|consen 87 NPNSLRHPPVPSM 99 (340)
T ss_pred cCCCCCCCCcccc
Confidence 5555556554443
No 25
>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=23.00 E-value=18 Score=30.18 Aligned_cols=34 Identities=18% Similarity=0.594 Sum_probs=11.2
Q ss_pred ccccccccccccccccccccccccccccccCCCC
Q 023005 22 ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQP 55 (289)
Q Consensus 22 A~LC~~CD~~vHsaN~La~RH~RvpLCd~C~~~P 55 (289)
+.||..||-+--.-....+-...+.+|+.|..-.
T Consensus 20 G~lC~kCdGkCpiCDS~Vrp~~~VrICdeCs~G~ 53 (106)
T PF03660_consen 20 GRLCEKCDGKCPICDSYVRPCTKVRICDECSFGS 53 (106)
T ss_dssp -EE-GGGTT--TTT-------EE-EEEHHHHTSS
T ss_pred hhhhhhcCCcccccCCccCCcceEEECCcCCCCC
Confidence 3455555544333333334455566766554433
No 26
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=22.35 E-value=69 Score=26.50 Aligned_cols=50 Identities=24% Similarity=0.565 Sum_probs=30.5
Q ss_pred CCCeeEEecCC----cccccccccccccccccccccccc----cccccccCCCCceeecccc
Q 023005 10 DQRSIVYCRSD----AACLCLSCDRNVHLANALSKRHSR----TLLCERCNSQPALVRCAEE 63 (289)
Q Consensus 10 ~a~A~vyC~aD----~A~LC~~CD~~vHsaN~La~RH~R----vpLCd~C~~~PA~v~C~~d 63 (289)
+.|-.+.|+-- -..||..||.+--- -.-|+| +.+|+.|.-..-.-+|..|
T Consensus 4 HhpDLi~CrkQPGi~~G~LCEkCDgkC~I----CDS~VRP~tlVRiC~eC~~Gs~q~~ciic 61 (110)
T KOG1705|consen 4 HHPDLIMCRKQPGIAIGRLCEKCDGKCVI----CDSYVRPCTLVRICDECNYGSYQGRCVIC 61 (110)
T ss_pred cCCcEEEEecCCCchhhhhHHhcCCcccc----cccccccceeeeeehhcCCccccCceEEe
Confidence 35666777644 35789999976533 233444 6778888765554444433
No 27
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=20.73 E-value=34 Score=35.66 Aligned_cols=33 Identities=33% Similarity=0.713 Sum_probs=29.0
Q ss_pred CCCCccCC-----CCeeEEecC--Cccccccccccccccc
Q 023005 3 YMCDFCGD-----QRSIVYCRS--DAACLCLSCDRNVHLA 35 (289)
Q Consensus 3 ~~Cd~C~~-----a~A~vyC~a--D~A~LC~~CD~~vHsa 35 (289)
.+||.|+. ..|.+||++ +--+.|..|=+.+|+-
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~ 495 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG 495 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC
Confidence 57999998 889999995 4689999999999986
Done!