Query 032401
Match_columns 141
No_of_seqs 137 out of 586
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 13:37:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032401hhsearch_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 98.3 7E-07 1.5E-11 51.9 2.6 38 70-113 2-39 (39)
2 PF00643 zf-B_box: B-box zinc 98.2 9.4E-07 2E-11 52.6 2.3 40 68-113 3-42 (42)
3 cd00021 BBOX B-Box-type zinc f 97.9 1.2E-05 2.7E-10 46.5 2.7 39 3-47 1-39 (39)
4 smart00336 BBOX B-Box-type zin 97.8 2.1E-05 4.7E-10 46.1 2.9 39 69-113 4-42 (42)
5 KOG4367 Predicted Zn-finger pr 97.7 8E-06 1.7E-10 71.4 0.2 91 4-101 164-256 (699)
6 PF00643 zf-B_box: B-box zinc 97.6 8.1E-05 1.8E-09 44.1 3.5 40 2-47 3-42 (42)
7 smart00336 BBOX B-Box-type zin 97.4 0.00017 3.7E-09 42.2 2.7 40 2-47 3-42 (42)
8 TIGR00622 ssl1 transcription f 79.6 1.3 2.8E-05 32.2 1.8 71 24-101 17-102 (112)
9 PF07975 C1_4: TFIIH C1-like d 79.5 0.82 1.8E-05 28.7 0.7 24 78-101 19-42 (51)
10 cd02335 ZZ_ADA2 Zinc finger, Z 79.3 2.5 5.4E-05 25.8 2.8 39 71-109 3-45 (49)
11 KOG4367 Predicted Zn-finger pr 76.6 0.86 1.9E-05 40.6 0.2 49 70-118 164-214 (699)
12 PF13248 zf-ribbon_3: zinc-rib 75.6 2.2 4.9E-05 22.7 1.6 25 1-31 1-25 (26)
13 KOG2807 RNA polymerase II tran 73.9 1.2 2.6E-05 38.1 0.4 84 11-101 273-366 (378)
14 KOG0129 Predicted RNA-binding 68.0 2.6 5.6E-05 37.9 1.1 45 67-114 454-505 (520)
15 COG5151 SSL1 RNA polymerase II 66.3 1.2 2.5E-05 38.2 -1.3 83 11-100 305-408 (421)
16 PF04438 zf-HIT: HIT zinc fing 64.8 2.8 6.1E-05 23.3 0.5 25 1-26 1-25 (30)
17 PF13842 Tnp_zf-ribbon_2: DDE_ 64.0 7.2 0.00016 21.9 2.1 23 71-93 3-29 (32)
18 cd02341 ZZ_ZZZ3 Zinc finger, Z 63.2 7.3 0.00016 23.9 2.2 28 71-98 3-36 (48)
19 PF07975 C1_4: TFIIH C1-like d 62.7 5.1 0.00011 25.1 1.4 23 13-35 20-42 (51)
20 KOG1280 Uncharacterized conser 57.2 9.8 0.00021 32.9 2.7 28 71-98 11-42 (381)
21 PF09416 UPF1_Zn_bind: RNA hel 51.7 14 0.00029 28.3 2.4 112 4-128 2-127 (152)
22 KOG4582 Uncharacterized conser 51.0 20 0.00043 29.7 3.5 38 3-40 153-196 (278)
23 KOG1428 Inhibitor of type V ad 49.1 6.6 0.00014 40.3 0.4 45 3-49 3323-3369(3738)
24 KOG2177 Predicted E3 ubiquitin 45.9 11 0.00024 28.7 1.2 40 70-116 88-128 (386)
25 KOG1428 Inhibitor of type V ad 42.8 10 0.00022 39.1 0.6 50 63-114 3317-3368(3738)
26 cd02338 ZZ_PCMF_like Zinc fing 41.3 35 0.00076 20.7 2.7 30 71-100 3-36 (49)
27 cd02334 ZZ_dystrophin Zinc fin 40.3 37 0.0008 20.9 2.7 32 70-101 2-37 (49)
28 PF00569 ZZ: Zinc finger, ZZ t 38.7 27 0.00058 20.8 1.9 30 2-31 4-37 (46)
29 PRK14559 putative protein seri 38.1 21 0.00045 33.1 1.9 23 1-30 1-23 (645)
30 cd02249 ZZ Zinc finger, ZZ typ 37.7 40 0.00088 19.9 2.6 29 71-99 3-34 (46)
31 PF08274 PhnA_Zn_Ribbon: PhnA 34.7 20 0.00044 20.0 0.8 25 68-95 2-26 (30)
32 cd02339 ZZ_Mind_bomb Zinc fing 34.7 29 0.00062 20.9 1.5 28 70-97 2-33 (45)
33 PF03107 C1_2: C1 domain; Int 33.0 21 0.00047 19.4 0.7 26 4-34 2-27 (30)
34 cd02342 ZZ_UBA_plant Zinc fing 32.6 41 0.00089 20.4 1.9 30 3-32 1-34 (43)
35 COG1594 RPB9 DNA-directed RNA 32.3 1.4E+02 0.0029 21.4 5.0 77 3-84 3-88 (113)
36 PF07649 C1_3: C1-like domain; 31.6 25 0.00054 18.9 0.8 22 71-92 3-27 (30)
37 KOG0129 Predicted RNA-binding 31.5 16 0.00035 33.0 0.0 43 3-48 456-505 (520)
38 KOG4317 Predicted Zn-finger pr 28.4 30 0.00064 29.8 1.1 34 65-98 4-38 (383)
39 cd02340 ZZ_NBR1_like Zinc fing 28.3 60 0.0013 19.2 2.2 28 71-98 3-33 (43)
40 PRK00415 rps27e 30S ribosomal 27.1 37 0.00079 22.0 1.1 31 1-32 10-40 (59)
41 PF14776 UNC-79: Cation-channe 27.0 47 0.001 30.1 2.2 67 22-101 227-303 (525)
42 PF14951 DUF4503: Domain of un 26.0 1E+02 0.0022 27.0 3.9 44 3-48 275-318 (389)
43 KOG2857 Predicted MYND Zn-fing 25.8 55 0.0012 25.0 2.1 34 70-103 7-40 (157)
44 PF15616 TerY-C: TerY-C metal 25.1 51 0.0011 24.5 1.8 25 68-93 77-101 (131)
45 smart00109 C1 Protein kinase C 24.8 32 0.00068 19.6 0.5 29 2-34 11-39 (49)
46 PRK14873 primosome assembly pr 24.6 36 0.00079 31.6 1.1 20 13-32 382-402 (665)
47 TIGR02098 MJ0042_CXXC MJ0042 f 24.4 60 0.0013 18.1 1.6 10 1-10 1-10 (38)
48 cd02344 ZZ_HERC2 Zinc finger, 23.9 51 0.0011 20.0 1.3 27 71-97 3-33 (45)
49 PF08271 TF_Zn_Ribbon: TFIIB z 23.4 73 0.0016 18.5 1.9 30 4-34 2-31 (43)
50 PF13920 zf-C3HC4_3: Zinc fing 22.0 38 0.00083 20.1 0.5 30 70-99 4-34 (50)
51 PF11781 RRN7: RNA polymerase 21.6 64 0.0014 18.5 1.3 24 4-30 10-33 (36)
52 PF14951 DUF4503: Domain of un 20.5 74 0.0016 27.8 2.1 49 64-114 270-318 (389)
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=98.26 E-value=7e-07 Score=51.91 Aligned_cols=38 Identities=42% Similarity=0.813 Sum_probs=34.4
Q ss_pred CccccCCcceEEEccCccccccccccccccCCCCCcCCCcceee
Q 032401 70 SCDICQERNGFFFCLEDRAILCRQCDVSIHMASPFLSSHQRFLI 113 (141)
Q Consensus 70 ~Cd~C~~~~a~~~C~~d~~~LC~~Cd~~~H~an~~~~~H~R~pl 113 (141)
.|+.|+.+++.+||.+|...||..|+...|. .|.++||
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 4999998899999999999999999998875 8888876
No 2
>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=98.20 E-value=9.4e-07 Score=52.58 Aligned_cols=40 Identities=33% Similarity=0.532 Sum_probs=34.7
Q ss_pred CCCccccCCcceEEEccCccccccccccccccCCCCCcCCCcceee
Q 032401 68 LPSCDICQERNGFFFCLEDRAILCRQCDVSIHMASPFLSSHQRFLI 113 (141)
Q Consensus 68 ~~~Cd~C~~~~a~~~C~~d~~~LC~~Cd~~~H~an~~~~~H~R~pl 113 (141)
...|+.|+..++.+||.+|..+||..|....|. +|..+||
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~------~H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHK------GHKIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTT------TSEEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCC------CCEEeEC
Confidence 456999999889999999999999999999986 4888876
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=97.88 E-value=1.2e-05 Score=46.53 Aligned_cols=39 Identities=33% Similarity=0.766 Sum_probs=33.8
Q ss_pred CcccccCCCceEEEeeCCCcccchhhhhccccCCCCCCCeeEEEe
Q 032401 3 LQCEVCEKAEAEVLCCADEAVLCSNCDVKVHTANKLSRKHQRFSL 47 (141)
Q Consensus 3 ~~C~~C~~~~A~~~C~~d~a~LC~~CD~~~H~an~l~~~H~Rv~l 47 (141)
..|+.++++++.+||..|...+|..|+...|. .|.++||
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 36889988899999999999999999977664 6888875
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.79 E-value=2.1e-05 Score=46.13 Aligned_cols=39 Identities=41% Similarity=0.819 Sum_probs=33.8
Q ss_pred CCccccCCcceEEEccCccccccccccccccCCCCCcCCCcceee
Q 032401 69 PSCDICQERNGFFFCLEDRAILCRQCDVSIHMASPFLSSHQRFLI 113 (141)
Q Consensus 69 ~~Cd~C~~~~a~~~C~~d~~~LC~~Cd~~~H~an~~~~~H~R~pl 113 (141)
..|+.|+..++.+||.+|...||..|....| .+|.+.||
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 3599999899999999999999999998866 37887765
No 5
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.71 E-value=8e-06 Score=71.44 Aligned_cols=91 Identities=24% Similarity=0.503 Sum_probs=75.6
Q ss_pred cccccCCC--ceEEEeeCCCcccchhhhhccccCCCCCCCeeEEEecccchhcccCCCCCCCCCCCCCCccccCCcceEE
Q 032401 4 QCEVCEKA--EAEVLCCADEAVLCSNCDVKVHTANKLSRKHQRFSLLKHNAAAASSSSSSSPSASQLPSCDICQERNGFF 81 (141)
Q Consensus 4 ~C~~C~~~--~A~~~C~~d~a~LC~~CD~~~H~an~l~~~H~Rv~l~~~~~~~~~~~~~~~~~~~~~~~Cd~C~~~~a~~ 81 (141)
.|.+|+++ .|+|+|..+..++|.-|..+.|-+-..+.+|.-+|-.+ +..+..-.+.+...|..|+-+...+
T Consensus 164 kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~-------grvs~~~s~r~~~~ct~h~~e~~sm 236 (699)
T KOG4367|consen 164 KCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQ-------GRVSRRLSPRKVSTCTDHELENHSM 236 (699)
T ss_pred hhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCccc-------CceeeccchhhhhhccCCCCCCceE
Confidence 58899885 58999999999999999999999888889998777522 2333445667778899999999999
Q ss_pred EccCccccccccccccccCC
Q 032401 82 FCLEDRAILCRQCDVSIHMA 101 (141)
Q Consensus 82 ~C~~d~~~LC~~Cd~~~H~a 101 (141)
||.+|.+++|..|-..+..+
T Consensus 237 yc~~ck~pvc~~clee~khs 256 (699)
T KOG4367|consen 237 YCVQCKMPVCYQCLEEGKHS 256 (699)
T ss_pred EEEecCChHHHHHHHhhccc
Confidence 99999999999998776333
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=97.61 E-value=8.1e-05 Score=44.09 Aligned_cols=40 Identities=23% Similarity=0.506 Sum_probs=34.6
Q ss_pred CCcccccCCCceEEEeeCCCcccchhhhhccccCCCCCCCeeEEEe
Q 032401 2 KLQCEVCEKAEAEVLCCADEAVLCSNCDVKVHTANKLSRKHQRFSL 47 (141)
Q Consensus 2 ~~~C~~C~~~~A~~~C~~d~a~LC~~CD~~~H~an~l~~~H~Rv~l 47 (141)
...|+.+.+.++.+||..|...+|..|....|.. |..+||
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 3679999998899999999999999999988864 888876
No 7
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.37 E-value=0.00017 Score=42.18 Aligned_cols=40 Identities=33% Similarity=0.583 Sum_probs=33.6
Q ss_pred CCcccccCCCceEEEeeCCCcccchhhhhccccCCCCCCCeeEEEe
Q 032401 2 KLQCEVCEKAEAEVLCCADEAVLCSNCDVKVHTANKLSRKHQRFSL 47 (141)
Q Consensus 2 ~~~C~~C~~~~A~~~C~~d~a~LC~~CD~~~H~an~l~~~H~Rv~l 47 (141)
...|..+++.++.+||..|...+|..|....| +.|.+++|
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 35789998889999999999999999997655 56877765
No 8
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.55 E-value=1.3 Score=32.23 Aligned_cols=71 Identities=23% Similarity=0.453 Sum_probs=42.7
Q ss_pred cchhhhhccccCCCCCC-CeeEEEecccchhcccCCCCCCCCCCCCCCccccCCc--------------ceEEEccCccc
Q 032401 24 LCSNCDVKVHTANKLSR-KHQRFSLLKHNAAAASSSSSSSPSASQLPSCDICQER--------------NGFFFCLEDRA 88 (141)
Q Consensus 24 LC~~CD~~~H~an~l~~-~H~Rv~l~~~~~~~~~~~~~~~~~~~~~~~Cd~C~~~--------------~a~~~C~~d~~ 88 (141)
-|.-|+..+=++.-|++ -|--+||....+- ++ ........|-.|+.. ...+.|..|..
T Consensus 17 ~CpiCgLtLVss~HLARSyHHLfPl~~f~ev--~~-----~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~ 89 (112)
T TIGR00622 17 ECPICGLTLILSTHLARSYHHLFPLKAFQEI--PL-----EEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKN 89 (112)
T ss_pred cCCcCCCEEeccchHHHhhhccCCCcccccc--cc-----cccCCCCcccCcCCCCCCcccccccccccccceeCCCCCC
Confidence 35566655544444444 4666777433211 00 111122348777652 23578999999
Q ss_pred cccccccccccCC
Q 032401 89 ILCRQCDVSIHMA 101 (141)
Q Consensus 89 ~LC~~Cd~~~H~a 101 (141)
.+|.+||+-+|..
T Consensus 90 ~FC~dCD~fiHe~ 102 (112)
T TIGR00622 90 VFCVDCDVFVHES 102 (112)
T ss_pred ccccccchhhhhh
Confidence 9999999999964
No 9
>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=79.49 E-value=0.82 Score=28.75 Aligned_cols=24 Identities=29% Similarity=0.623 Sum_probs=16.3
Q ss_pred ceEEEccCccccccccccccccCC
Q 032401 78 NGFFFCLEDRAILCRQCDVSIHMA 101 (141)
Q Consensus 78 ~a~~~C~~d~~~LC~~Cd~~~H~a 101 (141)
...+.|..|...+|.+||+-+|..
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTT
T ss_pred CCeEECCCCCCccccCcChhhhcc
Confidence 578999999999999999999964
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=79.31 E-value=2.5 Score=25.81 Aligned_cols=39 Identities=23% Similarity=0.348 Sum_probs=27.7
Q ss_pred ccccCCcceE---EEccCc-cccccccccccccCCCCCcCCCc
Q 032401 71 CDICQERNGF---FFCLED-RAILCRQCDVSIHMASPFLSSHQ 109 (141)
Q Consensus 71 Cd~C~~~~a~---~~C~~d-~~~LC~~Cd~~~H~an~~~~~H~ 109 (141)
|+.|...+.. +.|..| ..-||..|-..+...+.-...|.
T Consensus 3 Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~ 45 (49)
T cd02335 3 CDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHN 45 (49)
T ss_pred CCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCC
Confidence 7888766554 889999 89999999887754443333444
No 11
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=76.63 E-value=0.86 Score=40.64 Aligned_cols=49 Identities=18% Similarity=0.449 Sum_probs=41.3
Q ss_pred CccccCCc--ceEEEccCccccccccccccccCCCCCcCCCcceeeecccc
Q 032401 70 SCDICQER--NGFFFCLEDRAILCRQCDVSIHMASPFLSSHQRFLIGGIKV 118 (141)
Q Consensus 70 ~Cd~C~~~--~a~~~C~~d~~~LC~~Cd~~~H~an~~~~~H~R~pl~~~~~ 118 (141)
.|..|+.. .|.++|++|.++.|..|....|-+-.+.++|+.+|-+.-++
T Consensus 164 kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grv 214 (699)
T KOG4367|consen 164 KCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRV 214 (699)
T ss_pred hhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCce
Confidence 57777654 68999999999999999999999888889999888775554
No 12
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=75.58 E-value=2.2 Score=22.70 Aligned_cols=25 Identities=32% Similarity=0.761 Sum_probs=17.7
Q ss_pred CCCcccccCCCceEEEeeCCCcccchhhhhc
Q 032401 1 MKLQCEVCEKAEAEVLCCADEAVLCSNCDVK 31 (141)
Q Consensus 1 m~~~C~~C~~~~A~~~C~~d~a~LC~~CD~~ 31 (141)
|...|-.|+... .+.+.+|..|.++
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 788899998732 4567777777653
No 13
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=73.86 E-value=1.2 Score=38.13 Aligned_cols=84 Identities=24% Similarity=0.471 Sum_probs=53.4
Q ss_pred CceEEEeeCCCcccc------hhhhhccccCCCCCC-CeeEEEecccchhcccCCCCCCCCCCCCCCccccC---CcceE
Q 032401 11 AEAEVLCCADEAVLC------SNCDVKVHTANKLSR-KHQRFSLLKHNAAAASSSSSSSPSASQLPSCDICQ---ERNGF 80 (141)
Q Consensus 11 ~~A~~~C~~d~a~LC------~~CD~~~H~an~l~~-~H~Rv~l~~~~~~~~~~~~~~~~~~~~~~~Cd~C~---~~~a~ 80 (141)
.-+.++|..|.|..| .-|+..+=++.-|++ -|.-.||.+..+-. .........|-.|+ .....
T Consensus 273 ~~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip-------~~~~~~~~~Cf~C~~~~~~~~~ 345 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIP-------ETEYNGSRFCFACQGELLSSGR 345 (378)
T ss_pred ccCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhcc-------ccccCCCcceeeeccccCCCCc
Confidence 456788888888754 467765544433433 46667874332100 01112233488883 23567
Q ss_pred EEccCccccccccccccccCC
Q 032401 81 FFCLEDRAILCRQCDVSIHMA 101 (141)
Q Consensus 81 ~~C~~d~~~LC~~Cd~~~H~a 101 (141)
|.|..|...+|.+||+-+|..
T Consensus 346 y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred EEchhccceeeccchHHHHhh
Confidence 899999999999999999864
No 14
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=68.01 E-value=2.6 Score=37.87 Aligned_cols=45 Identities=22% Similarity=0.401 Sum_probs=35.5
Q ss_pred CCCCccccCC-----cceEEEcc--CccccccccccccccCCCCCcCCCcceeee
Q 032401 67 QLPSCDICQE-----RNGFFFCL--EDRAILCRQCDVSIHMASPFLSSHQRFLIG 114 (141)
Q Consensus 67 ~~~~Cd~C~~-----~~a~~~C~--~d~~~LC~~Cd~~~H~an~~~~~H~R~pl~ 114 (141)
+...|+.|+. +.|-|||. +|-...|..|-..+|+-- .++.-.||.
T Consensus 454 eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~---~r~~HkPlv 505 (520)
T KOG0129|consen 454 EDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGP---GREHHKPLV 505 (520)
T ss_pred cccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCC---chhcCCcee
Confidence 4567999999 89999995 799999999999999863 344444544
No 15
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=66.31 E-value=1.2 Score=38.17 Aligned_cols=83 Identities=20% Similarity=0.464 Sum_probs=51.8
Q ss_pred CceEEEeeCCCccc------chhhhhccccCCCCC-CCeeEEEecccchhcccCCCCCCCCCCCCCCccccCC-------
Q 032401 11 AEAEVLCCADEAVL------CSNCDVKVHTANKLS-RKHQRFSLLKHNAAAASSSSSSSPSASQLPSCDICQE------- 76 (141)
Q Consensus 11 ~~A~~~C~~d~a~L------C~~CD~~~H~an~l~-~~H~Rv~l~~~~~~~~~~~~~~~~~~~~~~~Cd~C~~------- 76 (141)
.-+.++|..+.+.. |.-|+.++=...-|+ +-|.-+||.+..+-..+ ..+...-|-.|+.
T Consensus 305 ~~gGy~CP~CktkVCsLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~-------~~~ks~~Cf~CQ~~fp~~~~ 377 (421)
T COG5151 305 KGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEG-------TNPKSTHCFVCQGPFPKPPV 377 (421)
T ss_pred ccCceeCCcccceeecCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCC-------CCCCCccceeccCCCCCCCC
Confidence 34578888887774 557776543322222 25777888654321111 1122233555554
Q ss_pred -------cceEEEccCccccccccccccccC
Q 032401 77 -------RNGFFFCLEDRAILCRQCDVSIHM 100 (141)
Q Consensus 77 -------~~a~~~C~~d~~~LC~~Cd~~~H~ 100 (141)
....+.|+.|..-+|.+||+.+|.
T Consensus 378 ~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 378 SPFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred CcccccccccceechhhhhhhhhhhHHHHHH
Confidence 267889999999999999999985
No 16
>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=64.80 E-value=2.8 Score=23.32 Aligned_cols=25 Identities=32% Similarity=0.546 Sum_probs=17.9
Q ss_pred CCCcccccCCCceEEEeeCCCcccch
Q 032401 1 MKLQCEVCEKAEAEVLCCADEAVLCS 26 (141)
Q Consensus 1 m~~~C~~C~~~~A~~~C~~d~a~LC~ 26 (141)
+..+|.+|+. ++...|..+...+|.
T Consensus 1 ~~~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 1 PRKLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp --EEETSSSS-EESEE-TTT--EESS
T ss_pred CcCCCccCcC-CCEEECCCcCCceeC
Confidence 3568999998 999999999998885
No 17
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=64.03 E-value=7.2 Score=21.93 Aligned_cols=23 Identities=22% Similarity=0.798 Sum_probs=16.6
Q ss_pred ccccCCc----ceEEEccCcccccccc
Q 032401 71 CDICQER----NGFFFCLEDRAILCRQ 93 (141)
Q Consensus 71 Cd~C~~~----~a~~~C~~d~~~LC~~ 93 (141)
|.+|... ...|+|..|.+.||..
T Consensus 3 C~vC~~~k~rk~T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 3 CKVCSKKKRRKDTRYMCSKCDVPLCVE 29 (32)
T ss_pred CeECCcCCccceeEEEccCCCCcccCC
Confidence 4555433 3789999999999875
No 18
>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=63.20 E-value=7.3 Score=23.94 Aligned_cols=28 Identities=32% Similarity=0.611 Sum_probs=21.1
Q ss_pred ccccCCcc---eEEEccCcc---ccccccccccc
Q 032401 71 CDICQERN---GFFFCLEDR---AILCRQCDVSI 98 (141)
Q Consensus 71 Cd~C~~~~---a~~~C~~d~---~~LC~~Cd~~~ 98 (141)
|+.|+..| ..|.|..|. .-||..|-..+
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 77777644 457788776 89999997765
No 19
>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=62.71 E-value=5.1 Score=25.13 Aligned_cols=23 Identities=26% Similarity=0.605 Sum_probs=15.8
Q ss_pred eEEEeeCCCcccchhhhhccccC
Q 032401 13 AEVLCCADEAVLCSNCDVKVHTA 35 (141)
Q Consensus 13 A~~~C~~d~a~LC~~CD~~~H~a 35 (141)
..+.|..+...+|.+||.-+|..
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 57889999999999999999874
No 20
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=57.25 E-value=9.8 Score=32.91 Aligned_cols=28 Identities=25% Similarity=0.293 Sum_probs=23.5
Q ss_pred ccccCCcceEEEccCc----cccccccccccc
Q 032401 71 CDICQERNGFFFCLED----RAILCRQCDVSI 98 (141)
Q Consensus 71 Cd~C~~~~a~~~C~~d----~~~LC~~Cd~~~ 98 (141)
||.|.+..-.|+|..| ..-||..|..++
T Consensus 11 CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~ 42 (381)
T KOG1280|consen 11 CDGCGKTAFTFRRYKCLRCSDYDLCFSCYENG 42 (381)
T ss_pred eccccccceeeeeeEeeeecchhHHHHHhhcC
Confidence 8999999999887666 567999998776
No 21
>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=51.65 E-value=14 Score=28.31 Aligned_cols=112 Identities=23% Similarity=0.350 Sum_probs=50.6
Q ss_pred cccccC--CCceEEEeeCCCcccchhhhhc--cccCCC-CCCCeeEEEecccchhcccCCCCCCCCCCCCCCccccCCcc
Q 032401 4 QCEVCE--KAEAEVLCCADEAVLCSNCDVK--VHTANK-LSRKHQRFSLLKHNAAAASSSSSSSPSASQLPSCDICQERN 78 (141)
Q Consensus 4 ~C~~C~--~~~A~~~C~~d~a~LC~~CD~~--~H~an~-l~~~H~Rv~l~~~~~~~~~~~~~~~~~~~~~~~Cd~C~~~~ 78 (141)
.|.+|+ ....++.|..+...+|-.=+.. -|--+- +..+|.-|.|.+. +.-....-.|-.|+..+
T Consensus 2 aC~YCG~~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~-----------s~lgdt~leCy~Cg~~N 70 (152)
T PF09416_consen 2 ACAYCGIHDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPD-----------SPLGDTVLECYNCGSRN 70 (152)
T ss_dssp S-TTT----CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TT-----------STT-S-B---TTT----
T ss_pred CccccCCCCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCC-----------CCCCCcEEEEEecCCCc
Confidence 589998 5677999999999999864431 122122 3458888888321 11222334699998876
Q ss_pred eE----EEccCcc--cccccc-ccccc--cCCCCCcCCCcceeeecccccccccCCCCC
Q 032401 79 GF----FFCLEDR--AILCRQ-CDVSI--HMASPFLSSHQRFLIGGIKVALESSADNNS 128 (141)
Q Consensus 79 a~----~~C~~d~--~~LC~~-Cd~~~--H~an~~~~~H~R~pl~~~~~~~~~~~~~~~ 128 (141)
++ +--.++. +.||+. |-... +..| -...+-.||-+-+..|.-+.+.++
T Consensus 71 vF~LGFipak~d~vvvllCR~pC~~~~~~kd~~--wD~~~W~PLI~dr~fl~wlv~~Ps 127 (152)
T PF09416_consen 71 VFLLGFIPAKSDSVVVLLCRQPCANQPSLKDMN--WDTSQWQPLIEDRQFLPWLVKIPS 127 (152)
T ss_dssp TTTEEEEEETTSCEEEEEETTTTTSTTTCTTTT--S-GGG-EESEETTCE-TTTS----
T ss_pred eeeEEEEEeccCCeEEEEeCCchhccchhcccc--CCHhhCccccccccchHhhcCCCC
Confidence 54 2234444 788987 75222 2222 224455666655656666665544
No 22
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=51.05 E-value=20 Score=29.67 Aligned_cols=38 Identities=29% Similarity=0.656 Sum_probs=29.6
Q ss_pred CcccccCC---CceEEEeeCCCcc-cchhhhhc--cccCCCCCC
Q 032401 3 LQCEVCEK---AEAEVLCCADEAV-LCSNCDVK--VHTANKLSR 40 (141)
Q Consensus 3 ~~C~~C~~---~~A~~~C~~d~a~-LC~~CD~~--~H~an~l~~ 40 (141)
..||.|.. .-..+.|..|..+ ||..|.+. +|.+.++++
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR 196 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNEHHAAHAMLR 196 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCCCCCcccceee
Confidence 57999998 3468999999776 99999988 455555555
No 23
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=49.07 E-value=6.6 Score=40.30 Aligned_cols=45 Identities=27% Similarity=0.547 Sum_probs=34.7
Q ss_pred CcccccC--CCceEEEeeCCCcccchhhhhccccCCCCCCCeeEEEecc
Q 032401 3 LQCEVCE--KAEAEVLCCADEAVLCSNCDVKVHTANKLSRKHQRFSLLK 49 (141)
Q Consensus 3 ~~C~~C~--~~~A~~~C~~d~a~LC~~CD~~~H~an~l~~~H~Rv~l~~ 49 (141)
++||+-. +..|.++|..|. .||.+||.-+|-. +-.+.|+|--+.+
T Consensus 3323 PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLH-rrtktH~~q~f~e 3369 (3738)
T KOG1428|consen 3323 PMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLH-RRTKTHQRQVFKE 3369 (3738)
T ss_pred CcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHH-hhccchhhhhhhh
Confidence 4788774 467899999998 9999999877763 3357899877743
No 24
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.85 E-value=11 Score=28.66 Aligned_cols=40 Identities=28% Similarity=0.511 Sum_probs=29.5
Q ss_pred CccccCCcceEEEccCcccccccccc-ccccCCCCCcCCCcceeeecc
Q 032401 70 SCDICQERNGFFFCLEDRAILCRQCD-VSIHMASPFLSSHQRFLIGGI 116 (141)
Q Consensus 70 ~Cd~C~~~~a~~~C~~d~~~LC~~Cd-~~~H~an~~~~~H~R~pl~~~ 116 (141)
.|..|... ..+||..|...+|..|. ...|. .|.-.++..+
T Consensus 88 ~c~~~~~~-~~~~c~~~~~~~c~~c~~~~~h~------~h~~~~~~~~ 128 (386)
T KOG2177|consen 88 LCEKHGEE-LKLFCEEDEKLLCVLCRESGEHR------GHPVLPLEEA 128 (386)
T ss_pred hhhhcCCc-ceEEecccccccCCCCCCccccc------CCccccHHHH
Confidence 68888765 89999999999999998 33343 5555555543
No 25
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=42.80 E-value=10 Score=39.12 Aligned_cols=50 Identities=26% Similarity=0.506 Sum_probs=37.2
Q ss_pred CCCCCCCCccccCCc--ceEEEccCccccccccccccccCCCCCcCCCcceeee
Q 032401 63 PSASQLPSCDICQER--NGFFFCLEDRAILCRQCDVSIHMASPFLSSHQRFLIG 114 (141)
Q Consensus 63 ~~~~~~~~Cd~C~~~--~a~~~C~~d~~~LC~~Cd~~~H~an~~~~~H~R~pl~ 114 (141)
.-..+.++|++|.+. .|.++|-.|. .||.+||...|-. .-..+|+|.-+.
T Consensus 3317 ~qqkQ~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLH-rrtktH~~q~f~ 3368 (3738)
T KOG1428|consen 3317 GQQKQMPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLH-RRTKTHQRQVFK 3368 (3738)
T ss_pred cchhcCCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHH-hhccchhhhhhh
Confidence 455677899999754 6889999999 9999999887522 123588886554
No 26
>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=41.26 E-value=35 Score=20.71 Aligned_cols=30 Identities=33% Similarity=0.496 Sum_probs=21.5
Q ss_pred ccccCCcc---eEEEccCc-cccccccccccccC
Q 032401 71 CDICQERN---GFFFCLED-RAILCRQCDVSIHM 100 (141)
Q Consensus 71 Cd~C~~~~---a~~~C~~d-~~~LC~~Cd~~~H~ 100 (141)
|+.|...+ ..|.|..| ..-||..|-.....
T Consensus 3 C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~ 36 (49)
T cd02338 3 CDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVT 36 (49)
T ss_pred CCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCc
Confidence 78887544 34778777 67899999776643
No 27
>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=40.32 E-value=37 Score=20.86 Aligned_cols=32 Identities=31% Similarity=0.570 Sum_probs=23.2
Q ss_pred CccccCCcc---eEEEccCc-cccccccccccccCC
Q 032401 70 SCDICQERN---GFFFCLED-RAILCRQCDVSIHMA 101 (141)
Q Consensus 70 ~Cd~C~~~~---a~~~C~~d-~~~LC~~Cd~~~H~a 101 (141)
.|+.|...| ..|.|..| +.-||..|-..+...
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 388887654 56678766 678999998877544
No 28
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=38.74 E-value=27 Score=20.85 Aligned_cols=30 Identities=23% Similarity=0.505 Sum_probs=21.2
Q ss_pred CCcccccCCC---ceEEEeeCCC-cccchhhhhc
Q 032401 2 KLQCEVCEKA---EAEVLCCADE-AVLCSNCDVK 31 (141)
Q Consensus 2 ~~~C~~C~~~---~A~~~C~~d~-a~LC~~CD~~ 31 (141)
...|+.|+.. ...+.|..+. -.||..|=..
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 5679999873 4688899886 5699999865
No 29
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=38.11 E-value=21 Score=33.09 Aligned_cols=23 Identities=22% Similarity=0.654 Sum_probs=12.9
Q ss_pred CCCcccccCCCceEEEeeCCCcccchhhhh
Q 032401 1 MKLQCEVCEKAEAEVLCCADEAVLCSNCDV 30 (141)
Q Consensus 1 m~~~C~~C~~~~A~~~C~~d~a~LC~~CD~ 30 (141)
|. .|-.|+.. ..+.+.+|..|..
T Consensus 1 M~-~Cp~Cg~~------n~~~akFC~~CG~ 23 (645)
T PRK14559 1 ML-ICPQCQFE------NPNNNRFCQKCGT 23 (645)
T ss_pred CC-cCCCCCCc------CCCCCccccccCC
Confidence 53 58888764 2344555555544
No 30
>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=37.74 E-value=40 Score=19.93 Aligned_cols=29 Identities=28% Similarity=0.517 Sum_probs=21.3
Q ss_pred ccccCC--cceEEEccCcc-cccccccccccc
Q 032401 71 CDICQE--RNGFFFCLEDR-AILCRQCDVSIH 99 (141)
Q Consensus 71 Cd~C~~--~~a~~~C~~d~-~~LC~~Cd~~~H 99 (141)
|+.|.. ....|.|..|. .-||..|-...+
T Consensus 3 C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 3 CDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 666654 23677898886 899999977664
No 31
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=34.72 E-value=20 Score=19.97 Aligned_cols=25 Identities=24% Similarity=0.889 Sum_probs=11.6
Q ss_pred CCCccccCCcceEEEccCcccccccccc
Q 032401 68 LPSCDICQERNGFFFCLEDRAILCRQCD 95 (141)
Q Consensus 68 ~~~Cd~C~~~~a~~~C~~d~~~LC~~Cd 95 (141)
.+.|+.|...... .....++|..|.
T Consensus 2 ~p~Cp~C~se~~y---~D~~~~vCp~C~ 26 (30)
T PF08274_consen 2 LPKCPLCGSEYTY---EDGELLVCPECG 26 (30)
T ss_dssp S---TTT-----E---E-SSSEEETTTT
T ss_pred CCCCCCCCCccee---ccCCEEeCCccc
Confidence 3568998875554 556778888884
No 32
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=34.71 E-value=29 Score=20.94 Aligned_cols=28 Identities=29% Similarity=0.594 Sum_probs=21.5
Q ss_pred CccccCCc---ceEEEccCc-ccccccccccc
Q 032401 70 SCDICQER---NGFFFCLED-RAILCRQCDVS 97 (141)
Q Consensus 70 ~Cd~C~~~---~a~~~C~~d-~~~LC~~Cd~~ 97 (141)
.|+.|+.. ...+.|..| ..-||..|-..
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~ 33 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHG 33 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCC
Confidence 37888754 457889988 78999999664
No 33
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=32.98 E-value=21 Score=19.37 Aligned_cols=26 Identities=27% Similarity=0.654 Sum_probs=17.6
Q ss_pred cccccCCCceEEEeeCCCcccchhhhhcccc
Q 032401 4 QCEVCEKAEAEVLCCADEAVLCSNCDVKVHT 34 (141)
Q Consensus 4 ~C~~C~~~~A~~~C~~d~a~LC~~CD~~~H~ 34 (141)
.|+.|++.....+ .+-|..|+..+|.
T Consensus 2 ~C~~C~~~~~~~~-----~Y~C~~c~f~lh~ 27 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-----FYHCSECCFTLHV 27 (30)
T ss_pred CCCCCCCCcCCCE-----eEEeCCCCCeEcC
Confidence 5888887555443 5777777766664
No 34
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=32.61 E-value=41 Score=20.41 Aligned_cols=30 Identities=23% Similarity=0.510 Sum_probs=22.7
Q ss_pred CcccccCCCc---eEEEeeCCCcc-cchhhhhcc
Q 032401 3 LQCEVCEKAE---AEVLCCADEAV-LCSNCDVKV 32 (141)
Q Consensus 3 ~~C~~C~~~~---A~~~C~~d~a~-LC~~CD~~~ 32 (141)
+.||.|+..| ..+.|..+..+ ||..|-.+.
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 3699998755 46888888766 999997544
No 35
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=32.35 E-value=1.4e+02 Score=21.41 Aligned_cols=77 Identities=12% Similarity=0.324 Sum_probs=40.5
Q ss_pred CcccccCCCceEEEee---CCCcccchhhhhccccCCCCCCCeeEEEecccchh--cccCCCCCCCC----CCCCCCccc
Q 032401 3 LQCEVCEKAEAEVLCC---ADEAVLCSNCDVKVHTANKLSRKHQRFSLLKHNAA--AASSSSSSSPS----ASQLPSCDI 73 (141)
Q Consensus 3 ~~C~~C~~~~A~~~C~---~d~a~LC~~CD~~~H~an~l~~~H~Rv~l~~~~~~--~~~~~~~~~~~----~~~~~~Cd~ 73 (141)
..|..|+. .++=+ .+...-|..|.......++.+-++.+..=.+.... ..+. +.... +.....|+.
T Consensus 3 ~FCp~Cgs---ll~p~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~Cpk 77 (113)
T COG1594 3 RFCPKCGS---LLYPKKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVE--DETQGAKTLPTAKEKCPK 77 (113)
T ss_pred cccCCccC---eeEEeEcCCCcEEECCCCCcchhccccceeEEEEeeccCCcceeeeeec--ccccCccccccccccCCC
Confidence 34666664 33333 45678899999877777655444443332211100 0000 01111 111346999
Q ss_pred cCCcceEEEcc
Q 032401 74 CQERNGFFFCL 84 (141)
Q Consensus 74 C~~~~a~~~C~ 84 (141)
|++..+.||=.
T Consensus 78 Cg~~ea~y~~~ 88 (113)
T COG1594 78 CGNKEAYYWQL 88 (113)
T ss_pred CCCceeEEEee
Confidence 99999988843
No 36
>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=31.63 E-value=25 Score=18.95 Aligned_cols=22 Identities=32% Similarity=0.528 Sum_probs=6.5
Q ss_pred ccccCCcc---eEEEccCccccccc
Q 032401 71 CDICQERN---GFFFCLEDRAILCR 92 (141)
Q Consensus 71 Cd~C~~~~---a~~~C~~d~~~LC~ 92 (141)
|+.|+... ..++|..|...|-.
T Consensus 3 C~~C~~~~~~~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSECDFDLHE 27 (30)
T ss_dssp -TTTS----S--EEE-TTT-----H
T ss_pred CCcCCCcCCCCceEECccCCCccCh
Confidence 77776554 34555555544433
No 37
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=31.52 E-value=16 Score=33.00 Aligned_cols=43 Identities=21% Similarity=0.471 Sum_probs=34.3
Q ss_pred CcccccCC-----CceEEEee--CCCcccchhhhhccccCCCCCCCeeEEEec
Q 032401 3 LQCEVCEK-----AEAEVLCC--ADEAVLCSNCDVKVHTANKLSRKHQRFSLL 48 (141)
Q Consensus 3 ~~C~~C~~-----~~A~~~C~--~d~a~LC~~CD~~~H~an~l~~~H~Rv~l~ 48 (141)
..||.|+. ..|-+||. .|--++|..|=+.+|+. ..++.=.||.
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPlv 505 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPLV 505 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCcee
Confidence 47999988 88999999 46789999999999986 3445555663
No 38
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=28.42 E-value=30 Score=29.78 Aligned_cols=34 Identities=21% Similarity=0.538 Sum_probs=28.3
Q ss_pred CCCCCCccccCCcceEEEccCccccccc-cccccc
Q 032401 65 ASQLPSCDICQERNGFFFCLEDRAILCR-QCDVSI 98 (141)
Q Consensus 65 ~~~~~~Cd~C~~~~a~~~C~~d~~~LC~-~Cd~~~ 98 (141)
...+..|.+|+.+++.|-|.-|+.+.|. .|..++
T Consensus 4 ts~~~~C~ic~vq~~~YtCPRCn~~YCsl~CYr~h 38 (383)
T KOG4317|consen 4 TSSFLACGICGVQKREYTCPRCNLLYCSLKCYRNH 38 (383)
T ss_pred CCceeeccccccccccccCCCCCccceeeeeecCC
Confidence 4566779999999999999999999996 576553
No 39
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=28.28 E-value=60 Score=19.20 Aligned_cols=28 Identities=32% Similarity=0.583 Sum_probs=20.5
Q ss_pred ccccCC--cceEEEccCc-cccccccccccc
Q 032401 71 CDICQE--RNGFFFCLED-RAILCRQCDVSI 98 (141)
Q Consensus 71 Cd~C~~--~~a~~~C~~d-~~~LC~~Cd~~~ 98 (141)
|+.|+. ....|.|..| +.-||..|-...
T Consensus 3 Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~~ 33 (43)
T cd02340 3 CDGCQGPIVGVRYKCLVCPDYDLCESCEAKG 33 (43)
T ss_pred CCCCCCcCcCCeEECCCCCCccchHHhhCcC
Confidence 666665 2467789988 789999996553
No 40
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=27.14 E-value=37 Score=21.97 Aligned_cols=31 Identities=29% Similarity=0.621 Sum_probs=25.6
Q ss_pred CCCcccccCCCceEEEeeCCCcccchhhhhcc
Q 032401 1 MKLQCEVCEKAEAEVLCCADEAVLCSNCDVKV 32 (141)
Q Consensus 1 m~~~C~~C~~~~A~~~C~~d~a~LC~~CD~~~ 32 (141)
|++.|..|+. .-++|=++.....|..|...+
T Consensus 10 ~~VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCGN-EQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEEECCCCCC-eEEEEecCCcEEECcccCCCc
Confidence 6778999986 678888899999999998655
No 41
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=26.96 E-value=47 Score=30.15 Aligned_cols=67 Identities=18% Similarity=0.376 Sum_probs=41.6
Q ss_pred cccchhhhhccccCCCCCCC-eeEEEecccchhcccCCCCCCCCCCCCCCccccCCcceEEEccC--c-------ccccc
Q 032401 22 AVLCSNCDVKVHTANKLSRK-HQRFSLLKHNAAAASSSSSSSPSASQLPSCDICQERNGFFFCLE--D-------RAILC 91 (141)
Q Consensus 22 a~LC~~CD~~~H~an~l~~~-H~Rv~l~~~~~~~~~~~~~~~~~~~~~~~Cd~C~~~~a~~~C~~--d-------~~~LC 91 (141)
.+||.+|...+|+.-+.... +.--|+.+ ....-+...|... +..|.+.|.. | -+.+|
T Consensus 227 LylC~~Ca~~i~~e~~~~~~~~il~P~~~------------vS~~CenK~C~S~-~k~AvvtCFS~eCt~~~gn~PiRlC 293 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQMFVDILQPMQQ------------VSMTCENKNCRSS-DKSAVVTCFSTECTSYNGNRPIRLC 293 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccc------------cccccCCCCCcCC-CCCeEEEEechhhccccCCCcchhH
Confidence 45999999999986543322 22233311 1222334556665 4678888843 3 56799
Q ss_pred ccccccccCC
Q 032401 92 RQCDVSIHMA 101 (141)
Q Consensus 92 ~~Cd~~~H~a 101 (141)
.+|....|..
T Consensus 294 ~~Ch~~~H~n 303 (525)
T PF14776_consen 294 QQCHSNRHNN 303 (525)
T ss_pred HHHhhhhccc
Confidence 9999988854
No 42
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=25.98 E-value=1e+02 Score=26.99 Aligned_cols=44 Identities=23% Similarity=0.330 Sum_probs=33.8
Q ss_pred CcccccCCCceEEEeeCCCcccchhhhhccccCCCCCCCeeEEEec
Q 032401 3 LQCEVCEKAEAEVLCCADEAVLCSNCDVKVHTANKLSRKHQRFSLL 48 (141)
Q Consensus 3 ~~C~~C~~~~A~~~C~~d~a~LC~~CD~~~H~an~l~~~H~Rv~l~ 48 (141)
+.|+.|+...=...=..-.++.|..|+.-+- ++++++|.-|-|.
T Consensus 275 PvCd~CGn~rLe~~pe~rg~~~C~~Cs~~V~--sP~~r~~LeVfl~ 318 (389)
T PF14951_consen 275 PVCDRCGNGRLEQSPEDRGAFSCGDCSRVVT--SPVLRMHLEVFLD 318 (389)
T ss_pred ccccccCCccceeCccCCCceeccchhhhcc--CcceeeeEEEEEe
Confidence 5799998765554444556899999998664 6789999999984
No 43
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=25.75 E-value=55 Score=24.97 Aligned_cols=34 Identities=26% Similarity=0.483 Sum_probs=30.7
Q ss_pred CccccCCcceEEEccCccccccccccccccCCCC
Q 032401 70 SCDICQERNGFFFCLEDRAILCRQCDVSIHMASP 103 (141)
Q Consensus 70 ~Cd~C~~~~a~~~C~~d~~~LC~~Cd~~~H~an~ 103 (141)
.|.+|...+..+.|..|.++.|.-==+.+|..++
T Consensus 7 tC~ic~e~~~KYKCpkC~vPYCSl~CfKiHk~tP 40 (157)
T KOG2857|consen 7 TCVICLESEIKYKCPKCSVPYCSLPCFKIHKSTP 40 (157)
T ss_pred eehhhhcchhhccCCCCCCccccchhhhhccCCc
Confidence 4999999999999999999999987788898866
No 44
>PF15616 TerY-C: TerY-C metal binding domain
Probab=25.13 E-value=51 Score=24.53 Aligned_cols=25 Identities=24% Similarity=0.708 Sum_probs=21.3
Q ss_pred CCCccccCCcceEEEccCcccccccc
Q 032401 68 LPSCDICQERNGFFFCLEDRAILCRQ 93 (141)
Q Consensus 68 ~~~Cd~C~~~~a~~~C~~d~~~LC~~ 93 (141)
.|.|+.|++.-+...| .|..++|.+
T Consensus 77 ~PgCP~CGn~~~fa~C-~CGkl~Ci~ 101 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVC-GCGKLFCID 101 (131)
T ss_pred CCCCCCCcChhcEEEe-cCCCEEEeC
Confidence 4789999999999999 698888843
No 45
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=24.76 E-value=32 Score=19.65 Aligned_cols=29 Identities=34% Similarity=0.669 Sum_probs=20.5
Q ss_pred CCcccccCCCceEEEeeCCCcccchhhhhcccc
Q 032401 2 KLQCEVCEKAEAEVLCCADEAVLCSNCDVKVHT 34 (141)
Q Consensus 2 ~~~C~~C~~~~A~~~C~~d~a~LC~~CD~~~H~ 34 (141)
...|+.|++.-..+. .+.-|..|...+|.
T Consensus 11 ~~~C~~C~~~i~~~~----~~~~C~~C~~~~H~ 39 (49)
T smart00109 11 PTKCCVCRKSIWGSF----QGLRCSWCKVKCHK 39 (49)
T ss_pred CCCccccccccCcCC----CCcCCCCCCchHHH
Confidence 346888887543332 57889999988886
No 46
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.56 E-value=36 Score=31.57 Aligned_cols=20 Identities=15% Similarity=0.497 Sum_probs=14.7
Q ss_pred eEEEeeCCC-cccchhhhhcc
Q 032401 13 AEVLCCADE-AVLCSNCDVKV 32 (141)
Q Consensus 13 A~~~C~~d~-a~LC~~CD~~~ 32 (141)
..++|..|. ..-|..||..+
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L 402 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPL 402 (665)
T ss_pred CeeEhhhCcCeeECCCCCCce
Confidence 467888885 67899998543
No 47
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=24.37 E-value=60 Score=18.11 Aligned_cols=10 Identities=40% Similarity=1.135 Sum_probs=7.9
Q ss_pred CCCcccccCC
Q 032401 1 MKLQCEVCEK 10 (141)
Q Consensus 1 m~~~C~~C~~ 10 (141)
|...|..|+.
T Consensus 1 M~~~CP~C~~ 10 (38)
T TIGR02098 1 MRIQCPNCKT 10 (38)
T ss_pred CEEECCCCCC
Confidence 7778888875
No 48
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=23.93 E-value=51 Score=19.95 Aligned_cols=27 Identities=30% Similarity=0.503 Sum_probs=20.5
Q ss_pred ccccCCcc---eEEEccCc-ccccccccccc
Q 032401 71 CDICQERN---GFFFCLED-RAILCRQCDVS 97 (141)
Q Consensus 71 Cd~C~~~~---a~~~C~~d-~~~LC~~Cd~~ 97 (141)
|+.|+..| ..|.|..| ..-||..|-..
T Consensus 3 Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 3 CDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 78887655 45888877 48899999665
No 49
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=23.40 E-value=73 Score=18.48 Aligned_cols=30 Identities=23% Similarity=0.586 Sum_probs=23.0
Q ss_pred cccccCCCceEEEeeCCCcccchhhhhcccc
Q 032401 4 QCEVCEKAEAEVLCCADEAVLCSNCDVKVHT 34 (141)
Q Consensus 4 ~C~~C~~~~A~~~C~~d~a~LC~~CD~~~H~ 34 (141)
.|..|++.. +++-.......|..|..-+..
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BBEE-
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCEeec
Confidence 588999866 888888888899999876654
No 50
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=22.05 E-value=38 Score=20.07 Aligned_cols=30 Identities=23% Similarity=0.523 Sum_probs=23.7
Q ss_pred CccccCCcceEEEccCcccc-cccccccccc
Q 032401 70 SCDICQERNGFFFCLEDRAI-LCRQCDVSIH 99 (141)
Q Consensus 70 ~Cd~C~~~~a~~~C~~d~~~-LC~~Cd~~~H 99 (141)
.|.+|.+++..+.-..|... +|..|.....
T Consensus 4 ~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~ 34 (50)
T PF13920_consen 4 ECPICFENPRDVVLLPCGHLCFCEECAERLL 34 (50)
T ss_dssp B-TTTSSSBSSEEEETTCEEEEEHHHHHHHH
T ss_pred CCccCCccCCceEEeCCCChHHHHHHhHHhc
Confidence 48899988888887788888 9999977653
No 51
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=21.56 E-value=64 Score=18.51 Aligned_cols=24 Identities=25% Similarity=0.632 Sum_probs=19.7
Q ss_pred cccccCCCceEEEeeCCCcccchhhhh
Q 032401 4 QCEVCEKAEAEVLCCADEAVLCSNCDV 30 (141)
Q Consensus 4 ~C~~C~~~~A~~~C~~d~a~LC~~CD~ 30 (141)
.|+.|+.. +|=..|.-+.|..|..
T Consensus 10 ~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe---EeEccCCEEEhhhCce
Confidence 48998864 8888999999998864
No 52
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=20.53 E-value=74 Score=27.80 Aligned_cols=49 Identities=24% Similarity=0.416 Sum_probs=35.9
Q ss_pred CCCCCCCccccCCcceEEEccCccccccccccccccCCCCCcCCCcceeee
Q 032401 64 SASQLPSCDICQERNGFFFCLEDRAILCRQCDVSIHMASPFLSSHQRFLIG 114 (141)
Q Consensus 64 ~~~~~~~Cd~C~~~~a~~~C~~d~~~LC~~Cd~~~H~an~~~~~H~R~pl~ 114 (141)
-+..-+.|+.|++...+..=+.-..+.|.+|..-+ .+|+.++|--+-|.
T Consensus 270 TAfSWPvCd~CGn~rLe~~pe~rg~~~C~~Cs~~V--~sP~~r~~LeVfl~ 318 (389)
T PF14951_consen 270 TAFSWPVCDRCGNGRLEQSPEDRGAFSCGDCSRVV--TSPVLRMHLEVFLD 318 (389)
T ss_pred ccccCccccccCCccceeCccCCCceeccchhhhc--cCcceeeeEEEEEe
Confidence 34445679999999999877777778888997766 56777777655443
Done!