Query 030820
Match_columns 171
No_of_seqs 164 out of 550
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 05:03:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030820.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030820hhsearch_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 97.8 1.9E-05 4.1E-10 48.0 2.3 38 4-47 2-39 (39)
2 cd00021 BBOX B-Box-type zinc f 97.6 5.7E-05 1.2E-09 45.8 2.4 38 56-99 2-39 (39)
3 PF00643 zf-B_box: B-box zinc 97.3 0.00019 4.1E-09 44.7 2.4 40 2-47 3-42 (42)
4 smart00336 BBOX B-Box-type zin 97.2 0.00028 6E-09 43.3 2.4 39 3-47 4-42 (42)
5 PF00643 zf-B_box: B-box zinc 97.2 0.00017 3.6E-09 44.9 1.1 40 54-99 3-42 (42)
6 smart00336 BBOX B-Box-type zin 96.8 0.0011 2.4E-08 40.6 2.6 39 55-99 4-42 (42)
7 KOG4367 Predicted Zn-finger pr 96.4 0.00097 2.1E-08 61.9 0.2 82 3-84 163-253 (699)
8 PF13248 zf-ribbon_3: zinc-rib 79.6 1.3 2.8E-05 25.1 1.5 25 1-31 1-25 (26)
9 KOG0129 Predicted RNA-binding 75.2 0.88 1.9E-05 43.0 -0.1 47 41-87 442-495 (520)
10 PF12773 DZR: Double zinc ribb 67.6 5.8 0.00013 25.1 2.5 15 19-33 9-23 (50)
11 KOG4367 Predicted Zn-finger pr 64.3 2.3 5E-05 40.1 0.1 52 54-105 162-215 (699)
12 KOG2807 RNA polymerase II tran 58.3 3.3 7.2E-05 37.5 0.1 76 11-86 273-365 (378)
13 PF04438 zf-HIT: HIT zinc fing 57.3 4.1 8.9E-05 24.1 0.3 25 1-26 1-25 (30)
14 PF07975 C1_4: TFIIH C1-like d 54.5 7 0.00015 26.0 1.1 23 13-35 20-42 (51)
15 PRK14559 putative protein seri 53.8 7.3 0.00016 37.9 1.6 25 1-32 1-25 (645)
16 PF14776 UNC-79: Cation-channe 53.6 9.8 0.00021 36.3 2.3 66 22-88 227-304 (525)
17 PF09416 UPF1_Zn_bind: RNA hel 51.7 4.8 0.0001 32.5 -0.0 78 4-81 2-94 (152)
18 cd02342 ZZ_UBA_plant Zinc fing 50.2 14 0.0003 24.0 1.9 30 3-32 1-34 (43)
19 TIGR00622 ssl1 transcription f 41.7 15 0.00033 28.2 1.4 62 25-86 18-101 (112)
20 PF07649 C1_3: C1-like domain; 41.0 10 0.00022 21.8 0.3 26 4-34 2-27 (30)
21 KOG0129 Predicted RNA-binding 40.6 11 0.00023 36.0 0.4 42 3-47 456-504 (520)
22 PF08274 PhnA_Zn_Ribbon: PhnA 40.1 14 0.00031 21.9 0.8 25 54-81 2-26 (30)
23 PF03107 C1_2: C1 domain; Int 40.1 13 0.00028 21.6 0.6 26 4-34 2-27 (30)
24 PRK00415 rps27e 30S ribosomal 40.0 14 0.0003 25.4 0.8 31 1-32 10-40 (59)
25 PF13240 zinc_ribbon_2: zinc-r 39.0 19 0.00042 19.9 1.2 21 57-83 2-22 (23)
26 KOG3576 Ovo and related transc 37.5 6 0.00013 34.0 -1.6 57 3-63 118-182 (267)
27 cd02335 ZZ_ADA2 Zinc finger, Z 36.7 40 0.00087 21.6 2.6 30 56-85 2-35 (49)
28 KOG4582 Uncharacterized conser 36.1 26 0.00056 30.5 2.1 40 3-42 153-198 (278)
29 KOG1428 Inhibitor of type V ad 28.8 25 0.00055 38.4 0.9 45 3-49 3323-3369(3738)
30 smart00109 C1 Protein kinase C 27.3 30 0.00065 20.8 0.7 28 3-34 12-39 (49)
31 KOG2462 C2H2-type Zn-finger pr 26.4 25 0.00055 31.0 0.4 55 3-63 131-196 (279)
32 COG5151 SSL1 RNA polymerase II 26.3 15 0.00032 33.4 -1.0 80 7-86 299-408 (421)
33 TIGR02098 MJ0042_CXXC MJ0042 f 25.4 57 0.0012 19.3 1.7 10 1-10 1-10 (38)
34 KOG1428 Inhibitor of type V ad 25.1 16 0.00035 39.7 -1.2 57 53-111 3321-3383(3738)
35 PF13920 zf-C3HC4_3: Zinc fing 24.4 69 0.0015 20.0 2.1 32 3-34 3-35 (50)
36 PF01667 Ribosomal_S27e: Ribos 23.2 26 0.00056 23.7 -0.1 30 1-31 6-35 (55)
37 PF00569 ZZ: Zinc finger, ZZ t 23.1 55 0.0012 20.6 1.4 30 2-31 4-37 (46)
38 PF14354 Lar_restr_allev: Rest 23.1 78 0.0017 20.5 2.2 29 54-82 3-37 (61)
39 PF15616 TerY-C: TerY-C metal 21.9 56 0.0012 25.7 1.5 26 54-80 77-102 (131)
40 KOG2177 Predicted E3 ubiquitin 21.3 64 0.0014 25.4 1.8 38 56-100 88-126 (386)
41 PLN00209 ribosomal protein S27 20.9 42 0.00092 24.7 0.6 30 1-31 35-64 (86)
42 PF03660 PHF5: PHF5-like prote 20.3 25 0.00054 26.9 -0.7 23 53-80 54-76 (106)
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=97.76 E-value=1.9e-05 Score=47.96 Aligned_cols=38 Identities=42% Similarity=0.863 Sum_probs=33.7
Q ss_pred cccccCCCCcEEEcccccccchhhhchhhhcCcccccCccccee
Q 030820 4 QCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (171)
Q Consensus 4 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (171)
.|+.++++++.+||..|.+.+|..|+...| +.|.|+||
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H------~~H~~~~i 39 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVH------SGHRRVPL 39 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhc------CCCCEeeC
Confidence 689999889999999999999999998877 38888875
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=97.56 E-value=5.7e-05 Score=45.79 Aligned_cols=38 Identities=42% Similarity=0.831 Sum_probs=33.4
Q ss_pred CCchhcccceEEEecCCccccccccCCCccCCCCCCCCCcceee
Q 030820 56 PCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (171)
Q Consensus 56 ~Cd~C~~~~A~v~C~~D~a~LC~~CD~~vH~an~ls~~HqR~~l 99 (171)
.|+.|+.+++.+||..|...+|..|+...| +.|.+++|
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H------~~H~~~~i 39 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVH------SGHRRVPL 39 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhc------CCCCEeeC
Confidence 499999989999999999999999998777 47888764
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=97.30 E-value=0.00019 Score=44.67 Aligned_cols=40 Identities=23% Similarity=0.571 Sum_probs=34.0
Q ss_pred CccccccCCCCcEEEcccccccchhhhchhhhcCcccccCccccee
Q 030820 2 KIQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (171)
Q Consensus 2 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (171)
...|+.+++.++.+||..+...+|..|....|.. |..++|
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 3579999998899999999999999999998853 887765
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.20 E-value=0.00028 Score=43.30 Aligned_cols=39 Identities=36% Similarity=0.642 Sum_probs=33.5
Q ss_pred ccccccCCCCcEEEcccccccchhhhchhhhcCcccccCccccee
Q 030820 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (171)
Q Consensus 3 ~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (171)
..|..++..++.+||..|.+.+|..|....| +.|.+++|
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 5689998889999999999999999997766 67877664
No 5
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=97.16 E-value=0.00017 Score=44.88 Aligned_cols=40 Identities=23% Similarity=0.494 Sum_probs=33.5
Q ss_pred CCCCchhcccceEEEecCCccccccccCCCccCCCCCCCCCcceee
Q 030820 54 LPPCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (171)
Q Consensus 54 ~p~Cd~C~~~~A~v~C~~D~a~LC~~CD~~vH~an~ls~~HqR~~l 99 (171)
...|+.|++..+.+||..+...+|..|....|. +|..++|
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 346999999999999999999999999988883 4877664
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.82 E-value=0.0011 Score=40.59 Aligned_cols=39 Identities=41% Similarity=0.782 Sum_probs=32.9
Q ss_pred CCCchhcccceEEEecCCccccccccCCCccCCCCCCCCCcceee
Q 030820 55 PPCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (171)
Q Consensus 55 p~Cd~C~~~~A~v~C~~D~a~LC~~CD~~vH~an~ls~~HqR~~l 99 (171)
..|+.|+..++.+||..|...+|..|....| ++|.+++|
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 3599999889999999999999999997766 56777654
No 7
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=96.35 E-value=0.00097 Score=61.94 Aligned_cols=82 Identities=27% Similarity=0.560 Sum_probs=68.9
Q ss_pred ccccccCCCC--cEEEcccccccchhhhchhhhcCcccccCcccceecc-------cCCCCCCCchhcccceEEEecCCc
Q 030820 3 IQCDVCEKAP--ATVICCADEAALCAKCDVEVHAANKLASKHQRLLLQC-------LSNKLPPCDICQEKAAFIFCVEDR 73 (171)
Q Consensus 3 ~~Cd~C~~~~--A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL~~-------~~~~~p~Cd~C~~~~A~v~C~~D~ 73 (171)
..|..|++++ |+|+|..++.+.|.-|..+.|-+-..+.||.-+|-.+ .+.+...|--|+.+.-.+||..+.
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 3699999975 9999999999999999999999888888998766543 234577799999999999999999
Q ss_pred cccccccCCCc
Q 030820 74 ALFCKDCDEPI 84 (171)
Q Consensus 74 a~LC~~CD~~v 84 (171)
...|..|-...
T Consensus 243 ~pvc~~clee~ 253 (699)
T KOG4367|consen 243 MPVCYQCLEEG 253 (699)
T ss_pred ChHHHHHHHhh
Confidence 99999998553
No 8
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=79.61 E-value=1.3 Score=25.11 Aligned_cols=25 Identities=24% Similarity=0.706 Sum_probs=18.1
Q ss_pred CCccccccCCCCcEEEcccccccchhhhchh
Q 030820 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (171)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~ 31 (171)
|...|-.|+... .+++.+|..|.++
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 788899999732 5567778777654
No 9
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=75.23 E-value=0.88 Score=43.00 Aligned_cols=47 Identities=26% Similarity=0.445 Sum_probs=37.5
Q ss_pred CcccceecccCCCCCCCchhcc-----cceEEEec--CCccccccccCCCccCC
Q 030820 41 KHQRLLLQCLSNKLPPCDICQE-----KAAFIFCV--EDRALFCKDCDEPIHSP 87 (171)
Q Consensus 41 rH~RvpL~~~~~~~p~Cd~C~~-----~~A~v~C~--~D~a~LC~~CD~~vH~a 87 (171)
-++||-|.+---.-..|+.|+. +.|-+||. .|..+||..|-..+|+-
T Consensus 442 ~~KRVEIkPYv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~ 495 (520)
T KOG0129|consen 442 IDKRVEIKPYVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG 495 (520)
T ss_pred cceeeeecceeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC
Confidence 3458877655555677999999 88999995 67899999999999963
No 10
>PF12773 DZR: Double zinc ribbon
Probab=67.63 E-value=5.8 Score=25.06 Aligned_cols=15 Identities=27% Similarity=0.798 Sum_probs=9.6
Q ss_pred cccccchhhhchhhh
Q 030820 19 ADEAALCAKCDVEVH 33 (171)
Q Consensus 19 aD~A~LC~~CD~~vH 33 (171)
.+++.+|..|...+-
T Consensus 9 ~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP 23 (50)
T ss_pred CccccCChhhcCChh
Confidence 456777777775444
No 11
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=64.34 E-value=2.3 Score=40.15 Aligned_cols=52 Identities=23% Similarity=0.532 Sum_probs=42.3
Q ss_pred CCCCchhcccc--eEEEecCCccccccccCCCccCCCCCCCCCcceeeecceee
Q 030820 54 LPPCDICQEKA--AFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLATGIRVA 105 (171)
Q Consensus 54 ~p~Cd~C~~~~--A~v~C~~D~a~LC~~CD~~vH~an~ls~~HqR~~l~~~rv~ 105 (171)
...|..|...+ |.++|..+..++|.-|....|-+-...++|..++.+.=||.
T Consensus 162 a~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs 215 (699)
T KOG4367|consen 162 ALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVS 215 (699)
T ss_pred hhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCcee
Confidence 34577777665 88999999999999999999988877788998887744654
No 12
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=58.34 E-value=3.3 Score=37.52 Aligned_cols=76 Identities=25% Similarity=0.470 Sum_probs=52.1
Q ss_pred CCcEEEcccccccch------hhhchhhhcCccccc-Ccccceecc---cCC----CCCCCchhcccc---eEEEecCCc
Q 030820 11 APATVICCADEAALC------AKCDVEVHAANKLAS-KHQRLLLQC---LSN----KLPPCDICQEKA---AFIFCVEDR 73 (171)
Q Consensus 11 ~~A~vyC~aD~A~LC------~~CD~~vH~aN~la~-rH~RvpL~~---~~~----~~p~Cd~C~~~~---A~v~C~~D~ 73 (171)
.-+.++|..+.|..| .-|+...=++--|++ =|.-.||.+ ++. .+..|-.|+... ..+.|..+.
T Consensus 273 ~~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck 352 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCK 352 (378)
T ss_pred ccCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhcc
Confidence 347788998888865 467755544444554 566677753 332 244499994432 456799999
Q ss_pred cccccccCCCccC
Q 030820 74 ALFCKDCDEPIHS 86 (171)
Q Consensus 74 a~LC~~CD~~vH~ 86 (171)
..||.+||.=+|.
T Consensus 353 ~~FCldCDv~iHe 365 (378)
T KOG2807|consen 353 NVFCLDCDVFIHE 365 (378)
T ss_pred ceeeccchHHHHh
Confidence 9999999988874
No 13
>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=57.29 E-value=4.1 Score=24.10 Aligned_cols=25 Identities=32% Similarity=0.644 Sum_probs=17.6
Q ss_pred CCccccccCCCCcEEEcccccccchh
Q 030820 1 MKIQCDVCEKAPATVICCADEAALCA 26 (171)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~ 26 (171)
+..+|.+|+. .+...|....+.+|.
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 999999999888885
No 14
>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=54.46 E-value=7 Score=26.04 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=15.7
Q ss_pred cEEEcccccccchhhhchhhhcC
Q 030820 13 ATVICCADEAALCAKCDVEVHAA 35 (171)
Q Consensus 13 A~vyC~aD~A~LC~~CD~~vH~a 35 (171)
..+.|..+...+|.+||.-||..
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 56789999999999999999963
No 15
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=53.80 E-value=7.3 Score=37.90 Aligned_cols=25 Identities=24% Similarity=0.671 Sum_probs=16.6
Q ss_pred CCccccccCCCCcEEEcccccccchhhhchhh
Q 030820 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (171)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 32 (171)
|+ .|-.|+.. ..+.+++|..|...+
T Consensus 1 M~-~Cp~Cg~~------n~~~akFC~~CG~~l 25 (645)
T PRK14559 1 ML-ICPQCQFE------NPNNNRFCQKCGTSL 25 (645)
T ss_pred CC-cCCCCCCc------CCCCCccccccCCCC
Confidence 54 69999875 245677777776443
No 16
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=53.60 E-value=9.8 Score=36.28 Aligned_cols=66 Identities=21% Similarity=0.393 Sum_probs=42.1
Q ss_pred ccchhhhchhhhcCcccccC-cccceecccCCC--CCCCchhcccceEEEecC---------CccccccccCCCccCCC
Q 030820 22 AALCAKCDVEVHAANKLASK-HQRLLLQCLSNK--LPPCDICQEKAAFIFCVE---------DRALFCKDCDEPIHSPG 88 (171)
Q Consensus 22 A~LC~~CD~~vH~aN~la~r-H~RvpL~~~~~~--~p~Cd~C~~~~A~v~C~~---------D~a~LC~~CD~~vH~an 88 (171)
.+||.+|...+|+.-+.... +.-.|+.+.+.. -..|... ++.|.+.|.. .-..||..|....|+.-
T Consensus 227 LylC~~Ca~~i~~e~~~~~~~~il~P~~~vS~~CenK~C~S~-~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~~~H~n~ 304 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSS-DKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNNR 304 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCC-CCCeEEEEechhhccccCCCcchhHHHHhhhhcccc
Confidence 46999999999985544333 344455444332 3344443 4458888742 24679999999998644
No 17
>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=51.73 E-value=4.8 Score=32.53 Aligned_cols=78 Identities=23% Similarity=0.555 Sum_probs=39.5
Q ss_pred cccccC--CCCcEEEcccccccchhhhch--hhhcCcc-cccCcccceecc---cCCCCCCCchhcccceEEE----ecC
Q 030820 4 QCDVCE--KAPATVICCADEAALCAKCDV--EVHAANK-LASKHQRLLLQC---LSNKLPPCDICQEKAAFIF----CVE 71 (171)
Q Consensus 4 ~Cd~C~--~~~A~vyC~aD~A~LC~~CD~--~vH~aN~-la~rH~RvpL~~---~~~~~p~Cd~C~~~~A~v~----C~~ 71 (171)
.|.+|| ....++.|..+.-.||-.=+. .-|--+- +.+||.-|-|-+ .+-....|..|+....+.. ...
T Consensus 2 aC~YCG~~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~NvF~LGFipak~ 81 (152)
T PF09416_consen 2 ACAYCGIHDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKS 81 (152)
T ss_dssp S-TTT----CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT----TTTEEEEEETT
T ss_pred CccccCCCCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCCceeeEEEEEecc
Confidence 589999 567888999999999985443 2232232 335888777743 3334667999999875543 344
Q ss_pred C--ccccccc-cC
Q 030820 72 D--RALFCKD-CD 81 (171)
Q Consensus 72 D--~a~LC~~-CD 81 (171)
| ..+||+. |.
T Consensus 82 d~vvvllCR~pC~ 94 (152)
T PF09416_consen 82 DSVVVLLCRQPCA 94 (152)
T ss_dssp SCEEEEEETTTTT
T ss_pred CCeEEEEeCCchh
Confidence 4 3788877 75
No 18
>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=50.24 E-value=14 Score=23.96 Aligned_cols=30 Identities=33% Similarity=0.588 Sum_probs=21.2
Q ss_pred ccccccCCCC---cEEEccccccc-chhhhchhh
Q 030820 3 IQCDVCEKAP---ATVICCADEAA-LCAKCDVEV 32 (171)
Q Consensus 3 ~~Cd~C~~~~---A~vyC~aD~A~-LC~~CD~~v 32 (171)
+.||.|+..| ..+.|..+.-+ ||..|-.+.
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 4699999865 55677766544 888886443
No 19
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.66 E-value=15 Score=28.20 Aligned_cols=62 Identities=27% Similarity=0.527 Sum_probs=38.6
Q ss_pred hhhhchhhhcCccccc-Ccccceecc---cC----CCCCCCchhcccc--------------eEEEecCCccccccccCC
Q 030820 25 CAKCDVEVHAANKLAS-KHQRLLLQC---LS----NKLPPCDICQEKA--------------AFIFCVEDRALFCKDCDE 82 (171)
Q Consensus 25 C~~CD~~vH~aN~la~-rH~RvpL~~---~~----~~~p~Cd~C~~~~--------------A~v~C~~D~a~LC~~CD~ 82 (171)
|.-|+..+=++.-|+| =|.-+||.. .+ .....|-.|+..- ..+.|..+...||.+||.
T Consensus 18 CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~ 97 (112)
T TIGR00622 18 CPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDV 97 (112)
T ss_pred CCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccch
Confidence 5566655444444554 355555542 21 1133588887742 235699999999999998
Q ss_pred CccC
Q 030820 83 PIHS 86 (171)
Q Consensus 83 ~vH~ 86 (171)
=+|.
T Consensus 98 fiHe 101 (112)
T TIGR00622 98 FVHE 101 (112)
T ss_pred hhhh
Confidence 8884
No 20
>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=41.05 E-value=10 Score=21.80 Aligned_cols=26 Identities=31% Similarity=0.740 Sum_probs=8.2
Q ss_pred cccccCCCCcEEEcccccccchhhhchhhhc
Q 030820 4 QCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (171)
Q Consensus 4 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~ 34 (171)
.|++|++.... +..+.|..||-.+|.
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 58888875432 234567788877773
No 21
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=40.64 E-value=11 Score=35.97 Aligned_cols=42 Identities=21% Similarity=0.432 Sum_probs=32.8
Q ss_pred ccccccCC-----CCcEEEcc--cccccchhhhchhhhcCcccccCccccee
Q 030820 3 IQCDVCEK-----APATVICC--ADEAALCAKCDVEVHAANKLASKHQRLLL 47 (171)
Q Consensus 3 ~~Cd~C~~-----~~A~vyC~--aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (171)
..||.|+. ..|.+||. .+--++|..|=+.+|+.- .++.=.||
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~---~r~~HkPl 504 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGP---GREHHKPL 504 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCC---chhcCCce
Confidence 46999998 88999999 467899999999999852 33333455
No 22
>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=40.13 E-value=14 Score=21.94 Aligned_cols=25 Identities=28% Similarity=0.925 Sum_probs=11.9
Q ss_pred CCCCchhcccceEEEecCCccccccccC
Q 030820 54 LPPCDICQEKAAFIFCVEDRALFCKDCD 81 (171)
Q Consensus 54 ~p~Cd~C~~~~A~v~C~~D~a~LC~~CD 81 (171)
+|.|+.|++.-.. .+...+.|..|.
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 5789999987654 556677888885
No 23
>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=40.12 E-value=13 Score=21.56 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=18.3
Q ss_pred cccccCCCCcEEEcccccccchhhhchhhhc
Q 030820 4 QCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (171)
Q Consensus 4 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~ 34 (171)
.|++|++.....+ .+-|..|+..+|.
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 5899988665554 6677777776664
No 24
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=39.97 E-value=14 Score=25.40 Aligned_cols=31 Identities=23% Similarity=0.564 Sum_probs=26.2
Q ss_pred CCccccccCCCCcEEEcccccccchhhhchhh
Q 030820 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (171)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 32 (171)
|+..|..|+ +.-++|=.+.....|..|...+
T Consensus 10 ~~VkCp~C~-n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCG-NEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEEECCCCC-CeEEEEecCCcEEECcccCCCc
Confidence 678899999 5788899999999999998544
No 25
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=38.97 E-value=19 Score=19.89 Aligned_cols=21 Identities=43% Similarity=1.053 Sum_probs=13.5
Q ss_pred CchhcccceEEEecCCccccccccCCC
Q 030820 57 CDICQEKAAFIFCVEDRALFCKDCDEP 83 (171)
Q Consensus 57 Cd~C~~~~A~v~C~~D~a~LC~~CD~~ 83 (171)
|+.|+... .+.+.||..|..+
T Consensus 2 Cp~CG~~~------~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEI------EDDAKFCPNCGTP 22 (23)
T ss_pred CcccCCCC------CCcCcchhhhCCc
Confidence 66666654 4567778777654
No 26
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=37.46 E-value=6 Score=34.04 Aligned_cols=57 Identities=23% Similarity=0.531 Sum_probs=40.8
Q ss_pred ccccccCCC-------CcEEEcccc-cccchhhhchhhhcCcccccCcccceecccCCCCCCCchhccc
Q 030820 3 IQCDVCEKA-------PATVICCAD-EAALCAKCDVEVHAANKLASKHQRLLLQCLSNKLPPCDICQEK 63 (171)
Q Consensus 3 ~~Cd~C~~~-------~A~vyC~aD-~A~LC~~CD~~vH~aN~la~rH~RvpL~~~~~~~p~Cd~C~~~ 63 (171)
..|++|++. .--+-|.+| ...||..|.+..|-+- -+.||.|..- +.....|..|...
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtf-dlkrh~rtht---gvrpykc~~c~ka 182 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTF-DLKRHTRTHT---GVRPYKCSLCEKA 182 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchh-hhhhhhcccc---CccccchhhhhHH
Confidence 468888875 234678888 6889999999988654 4589999753 3334457777654
No 27
>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=36.71 E-value=40 Score=21.57 Aligned_cols=30 Identities=27% Similarity=0.498 Sum_probs=18.2
Q ss_pred CCchhcccceE---EEecCC-ccccccccCCCcc
Q 030820 56 PCDICQEKAAF---IFCVED-RALFCKDCDEPIH 85 (171)
Q Consensus 56 ~Cd~C~~~~A~---v~C~~D-~a~LC~~CD~~vH 85 (171)
.|+.|...... +.|..+ .--||..|-....
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 36666665533 556655 4558888875443
No 28
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=36.15 E-value=26 Score=30.53 Aligned_cols=40 Identities=33% Similarity=0.681 Sum_probs=28.9
Q ss_pred ccccccCCCC---cEEEcccccc-cchhhhchhh--hcCcccccCc
Q 030820 3 IQCDVCEKAP---ATVICCADEA-ALCAKCDVEV--HAANKLASKH 42 (171)
Q Consensus 3 ~~Cd~C~~~~---A~vyC~aD~A-~LC~~CD~~v--H~aN~la~rH 42 (171)
..||.|++++ ..+-|..+.. -||.+|.+.. |.+-++++-|
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~ 198 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNEHHAAHAMLRLH 198 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCCCCCcccceeecc
Confidence 5799999843 7788998864 5999999884 4444444433
No 29
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=28.78 E-value=25 Score=38.39 Aligned_cols=45 Identities=27% Similarity=0.558 Sum_probs=32.8
Q ss_pred ccccccC--CCCcEEEcccccccchhhhchhhhcCcccccCcccceecc
Q 030820 3 IQCDVCE--KAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLLQC 49 (171)
Q Consensus 3 ~~Cd~C~--~~~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL~~ 49 (171)
++||.-. +..|.++|..+. +||.+||+-.|-. +-.+.|+|--+.+
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 4677654 356889999888 9999999887742 3357888866543
No 30
>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=27.26 E-value=30 Score=20.83 Aligned_cols=28 Identities=29% Similarity=0.615 Sum_probs=21.0
Q ss_pred ccccccCCCCcEEEcccccccchhhhchhhhc
Q 030820 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (171)
Q Consensus 3 ~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~ 34 (171)
..|+.|++.-..+. .+.-|..|...+|.
T Consensus 12 ~~C~~C~~~i~~~~----~~~~C~~C~~~~H~ 39 (49)
T smart00109 12 TKCCVCRKSIWGSF----QGLRCSWCKVKCHK 39 (49)
T ss_pred CCccccccccCcCC----CCcCCCCCCchHHH
Confidence 45888887654433 57889999999995
No 31
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=26.40 E-value=25 Score=31.02 Aligned_cols=55 Identities=24% Similarity=0.333 Sum_probs=33.8
Q ss_pred ccccccCCCCcEE---------Ecccc--cccchhhhchhhhcCcccccCcccceecccCCCCCCCchhccc
Q 030820 3 IQCDVCEKAPATV---------ICCAD--EAALCAKCDVEVHAANKLASKHQRLLLQCLSNKLPPCDICQEK 63 (171)
Q Consensus 3 ~~Cd~C~~~~A~v---------yC~aD--~A~LC~~CD~~vH~aN~la~rH~RvpL~~~~~~~p~Cd~C~~~ 63 (171)
..|+.|++.-|+. .|..| .|+-|..||+.-= .=+.+++|.|+--- .-.|.+|+.+
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~Yv-SmpALkMHirTH~l-----~c~C~iCGKa 196 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYV-SMPALKMHIRTHTL-----PCECGICGKA 196 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceee-ehHHHhhHhhccCC-----Cccccccccc
Confidence 4688888866665 47766 4888999995433 33445677775421 1136666654
No 32
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=26.33 E-value=15 Score=33.43 Aligned_cols=80 Identities=26% Similarity=0.497 Sum_probs=52.1
Q ss_pred ccCC--CCcEEEcccccccch------hhhchhhhcCcccc-cCcccceecc---cCC----CCCCCchhccc-------
Q 030820 7 VCEK--APATVICCADEAALC------AKCDVEVHAANKLA-SKHQRLLLQC---LSN----KLPPCDICQEK------- 63 (171)
Q Consensus 7 ~C~~--~~A~vyC~aD~A~LC------~~CD~~vH~aN~la-~rH~RvpL~~---~~~----~~p~Cd~C~~~------- 63 (171)
+|.. .-+.++|..+.+..| .-|+...=...-|+ +-|.-.||.+ ++. +...|-.|+..
T Consensus 299 aCHs~~~~gGy~CP~CktkVCsLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~ 378 (421)
T COG5151 299 ACHSEVKGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVS 378 (421)
T ss_pred eeeeeeccCceeCCcccceeecCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCC
Confidence 4444 347788888888754 57775543322244 3677777754 222 35558888872
Q ss_pred -------ceEEEecCCccccccccCCCccC
Q 030820 64 -------AAFIFCVEDRALFCKDCDEPIHS 86 (171)
Q Consensus 64 -------~A~v~C~~D~a~LC~~CD~~vH~ 86 (171)
...+.|..+..-||.+||.=+|.
T Consensus 379 ~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 379 PFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred cccccccccceechhhhhhhhhhhHHHHHH
Confidence 24466999999999999987773
No 33
>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=25.44 E-value=57 Score=19.33 Aligned_cols=10 Identities=50% Similarity=1.168 Sum_probs=7.4
Q ss_pred CCccccccCC
Q 030820 1 MKIQCDVCEK 10 (171)
Q Consensus 1 m~~~Cd~C~~ 10 (171)
|+..|..|+.
T Consensus 1 M~~~CP~C~~ 10 (38)
T TIGR02098 1 MRIQCPNCKT 10 (38)
T ss_pred CEEECCCCCC
Confidence 6777777775
No 34
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=25.11 E-value=16 Score=39.71 Aligned_cols=57 Identities=33% Similarity=0.633 Sum_probs=42.9
Q ss_pred CCCCCchhccc--ceEEEecCCccccccccCCCccCCCCCCCCCcceeee----cceeecccccc
Q 030820 53 KLPPCDICQEK--AAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLAT----GIRVALSSSCS 111 (171)
Q Consensus 53 ~~p~Cd~C~~~--~A~v~C~~D~a~LC~~CD~~vH~an~ls~~HqR~~l~----~~rv~~~s~c~ 111 (171)
+.|.|+.|-+- .|.++|..+. -||.+||.-.|-.- -.++|+|..+. .|.|-+...|.
T Consensus 3321 Q~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHr-rtktH~~q~f~eeeea~kvdlHeGC~ 3383 (3738)
T KOG1428|consen 3321 QMPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHR-RTKTHQRQVFKEEEEAIKVDLHEGCG 3383 (3738)
T ss_pred cCCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHh-hccchhhhhhhhhhhhcccchhhcch
Confidence 57889998654 5889999887 89999996655322 23689996653 58898888884
No 35
>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=24.39 E-value=69 Score=20.02 Aligned_cols=32 Identities=19% Similarity=0.536 Sum_probs=22.4
Q ss_pred ccccccCCCCcEEEccccc-ccchhhhchhhhc
Q 030820 3 IQCDVCEKAPATVICCADE-AALCAKCDVEVHA 34 (171)
Q Consensus 3 ~~Cd~C~~~~A~vyC~aD~-A~LC~~CD~~vH~ 34 (171)
..|.+|.++++.+.-.... ..+|..|-.+...
T Consensus 3 ~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 3 EECPICFENPRDVVLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp SB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHH
T ss_pred CCCccCCccCCceEEeCCCChHHHHHHhHHhcc
Confidence 4688999877666555554 5599999877664
No 36
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=23.16 E-value=26 Score=23.72 Aligned_cols=30 Identities=27% Similarity=0.547 Sum_probs=19.2
Q ss_pred CCccccccCCCCcEEEcccccccchhhhchh
Q 030820 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (171)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~ 31 (171)
|+..|..|+ +.-+||=.+-...+|..|...
T Consensus 6 m~VkCp~C~-~~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 6 MDVKCPGCY-NIQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp EEEE-TTT--SEEEEETT-SS-EE-SSSTSE
T ss_pred EEEECCCCC-CeeEEEecCCeEEEcccCCCE
Confidence 677888898 567778888888888888643
No 37
>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=23.12 E-value=55 Score=20.62 Aligned_cols=30 Identities=23% Similarity=0.486 Sum_probs=20.4
Q ss_pred CccccccCCC---CcEEEccccc-ccchhhhchh
Q 030820 2 KIQCDVCEKA---PATVICCADE-AALCAKCDVE 31 (171)
Q Consensus 2 ~~~Cd~C~~~---~A~vyC~aD~-A~LC~~CD~~ 31 (171)
...|+.|+.. ...+.|..+. --||..|=..
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 5689999983 4677888664 7799999765
No 38
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=23.08 E-value=78 Score=20.53 Aligned_cols=29 Identities=31% Similarity=0.643 Sum_probs=16.8
Q ss_pred CCCCchhcccceEEEecCC------ccccccccCC
Q 030820 54 LPPCDICQEKAAFIFCVED------RALFCKDCDE 82 (171)
Q Consensus 54 ~p~Cd~C~~~~A~v~C~~D------~a~LC~~CD~ 82 (171)
+..|++|+.....+.-... ....|..|..
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4569999655444332221 3456888865
No 39
>PF15616 TerY-C: TerY-C metal binding domain
Probab=21.92 E-value=56 Score=25.73 Aligned_cols=26 Identities=38% Similarity=0.795 Sum_probs=20.8
Q ss_pred CCCCchhcccceEEEecCCcccccccc
Q 030820 54 LPPCDICQEKAAFIFCVEDRALFCKDC 80 (171)
Q Consensus 54 ~p~Cd~C~~~~A~v~C~~D~a~LC~~C 80 (171)
.|-|+.|+.+.+++.| .+..++|.+=
T Consensus 77 ~PgCP~CGn~~~fa~C-~CGkl~Ci~g 102 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVC-GCGKLFCIDG 102 (131)
T ss_pred CCCCCCCcChhcEEEe-cCCCEEEeCC
Confidence 3889999999999988 6777777443
No 40
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.29 E-value=64 Score=25.37 Aligned_cols=38 Identities=29% Similarity=0.548 Sum_probs=28.6
Q ss_pred CCchhcccceEEEecCCccccccccC-CCccCCCCCCCCCcceeee
Q 030820 56 PCDICQEKAAFIFCVEDRALFCKDCD-EPIHSPGSLSANHQRFLAT 100 (171)
Q Consensus 56 ~Cd~C~~~~A~v~C~~D~a~LC~~CD-~~vH~an~ls~~HqR~~l~ 100 (171)
.|..|... ..+||..|...+|..|. ...| ..|.-.++.
T Consensus 88 ~c~~~~~~-~~~~c~~~~~~~c~~c~~~~~h------~~h~~~~~~ 126 (386)
T KOG2177|consen 88 LCEKHGEE-LKLFCEEDEKLLCVLCRESGEH------RGHPVLPLE 126 (386)
T ss_pred hhhhcCCc-ceEEecccccccCCCCCCcccc------cCCccccHH
Confidence 68888777 78899999999999998 4455 345555554
No 41
>PLN00209 ribosomal protein S27; Provisional
Probab=20.91 E-value=42 Score=24.74 Aligned_cols=30 Identities=23% Similarity=0.623 Sum_probs=24.5
Q ss_pred CCccccccCCCCcEEEcccccccchhhhchh
Q 030820 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (171)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~ 31 (171)
|++.|-.|+ +.-+||=.+-...+|..|...
T Consensus 35 m~VkCp~C~-n~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 35 MDVKCQGCF-NITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred EEEECCCCC-CeeEEEecCceEEEccccCCE
Confidence 678899998 577888888888999999743
No 42
>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=20.29 E-value=25 Score=26.87 Aligned_cols=23 Identities=26% Similarity=0.666 Sum_probs=11.4
Q ss_pred CCCCCchhcccceEEEecCCcccccccc
Q 030820 53 KLPPCDICQEKAAFIFCVEDRALFCKDC 80 (171)
Q Consensus 53 ~~p~Cd~C~~~~A~v~C~~D~a~LC~~C 80 (171)
....|-+|+..++. ..|++|..|
T Consensus 54 ~~~rCIiCg~~~g~-----sdAYYC~eC 76 (106)
T PF03660_consen 54 LQGRCIICGSGPGV-----SDAYYCWEC 76 (106)
T ss_dssp TTSB-TTTSSSB-------EE-EE-HHH
T ss_pred cCceEEEecCCCCc-----ccceehhhh
Confidence 34567777755433 257888877
Done!