Query 023008
Match_columns 288
No_of_seqs 166 out of 606
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:47:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023008.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023008hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4367 Predicted Zn-finger pr 97.8 6.1E-06 1.3E-10 82.4 0.9 82 3-84 163-253 (699)
2 cd00021 BBOX B-Box-type zinc f 97.8 2E-05 4.3E-10 52.0 2.6 38 56-99 2-39 (39)
3 PF00643 zf-B_box: B-box zinc 97.7 2.4E-05 5.2E-10 53.0 2.6 40 54-99 3-42 (42)
4 cd00021 BBOX B-Box-type zinc f 97.6 5.6E-05 1.2E-09 49.8 2.4 39 3-47 1-39 (39)
5 smart00336 BBOX B-Box-type zin 97.3 0.00026 5.6E-09 47.3 2.9 39 55-99 4-42 (42)
6 PF00643 zf-B_box: B-box zinc 97.2 0.00032 7E-09 47.4 2.9 40 2-47 3-42 (42)
7 smart00336 BBOX B-Box-type zin 97.0 0.00054 1.2E-08 45.7 2.5 39 3-47 4-42 (42)
8 KOG2807 RNA polymerase II tran 78.1 0.94 2E-05 44.6 0.9 77 11-87 273-366 (378)
9 PF09416 UPF1_Zn_bind: RNA hel 72.5 2.8 6.1E-05 37.0 2.3 78 4-81 2-94 (152)
10 TIGR00622 ssl1 transcription f 72.5 2.5 5.5E-05 35.5 1.9 63 25-87 18-102 (112)
11 COG5151 SSL1 RNA polymerase II 69.1 2.2 4.7E-05 42.0 0.9 77 11-87 305-409 (421)
12 KOG4367 Predicted Zn-finger pr 67.1 1.8 4E-05 44.2 0.1 52 54-105 162-215 (699)
13 KOG0129 Predicted RNA-binding 65.7 2.2 4.8E-05 44.0 0.3 55 42-99 443-504 (520)
14 cd02342 ZZ_UBA_plant Zinc fing 61.8 7.8 0.00017 27.5 2.4 30 3-32 1-34 (43)
15 PF13248 zf-ribbon_3: zinc-rib 61.1 4.5 9.8E-05 25.1 1.0 24 1-30 1-24 (26)
16 cd02335 ZZ_ADA2 Zinc finger, Z 60.6 11 0.00024 26.6 3.0 40 56-95 2-45 (49)
17 PF04438 zf-HIT: HIT zinc fing 58.4 4.5 9.8E-05 26.3 0.7 25 1-26 1-25 (30)
18 KOG0129 Predicted RNA-binding 53.5 7.9 0.00017 40.1 1.8 44 3-49 456-506 (520)
19 PRK14559 putative protein seri 51.9 6.8 0.00015 41.6 1.1 22 1-23 1-24 (645)
20 PF15359 CDV3: Carnitine defic 50.4 22 0.00048 30.5 3.8 48 234-281 68-119 (129)
21 cd02341 ZZ_ZZZ3 Zinc finger, Z 49.7 16 0.00034 26.1 2.4 29 56-84 2-36 (48)
22 KOG2177 Predicted E3 ubiquitin 47.7 21 0.00045 30.8 3.3 40 56-102 88-128 (386)
23 PF07975 C1_4: TFIIH C1-like d 45.7 13 0.00029 27.1 1.5 23 13-35 20-42 (51)
24 KOG1280 Uncharacterized conser 43.1 14 0.00031 36.8 1.7 37 38-84 2-42 (381)
25 KOG4582 Uncharacterized conser 42.4 17 0.00036 34.7 2.0 30 3-32 153-186 (278)
26 PF01412 ArfGap: Putative GTPa 42.0 20 0.00044 29.4 2.2 37 3-43 14-50 (116)
27 PF10235 Cript: Microtubule-as 41.6 17 0.00037 29.5 1.7 48 34-84 27-79 (90)
28 PF07975 C1_4: TFIIH C1-like d 41.4 11 0.00023 27.6 0.5 24 64-87 19-42 (51)
29 KOG1428 Inhibitor of type V ad 39.8 15 0.00032 43.2 1.4 45 3-49 3323-3369(3738)
30 TIGR02098 MJ0042_CXXC MJ0042 f 36.4 28 0.00061 22.8 1.9 10 1-10 1-10 (38)
31 PRK14873 primosome assembly pr 36.2 18 0.00039 38.5 1.3 19 12-30 381-400 (665)
32 PLN02400 cellulose synthase 35.5 27 0.00058 39.4 2.5 30 53-82 35-71 (1085)
33 KOG0954 PHD finger protein [Ge 35.1 21 0.00045 38.9 1.6 30 3-35 272-301 (893)
34 PF08274 PhnA_Zn_Ribbon: PhnA 34.8 20 0.00042 23.5 0.8 25 54-81 2-26 (30)
35 PRK00415 rps27e 30S ribosomal 34.7 17 0.00037 27.4 0.6 31 1-32 10-40 (59)
36 KOG1428 Inhibitor of type V ad 33.8 15 0.00033 43.1 0.3 46 51-100 3319-3368(3738)
37 PF13842 Tnp_zf-ribbon_2: DDE_ 33.8 35 0.00075 22.4 1.9 24 56-79 2-29 (32)
38 PLN02436 cellulose synthase A 33.4 31 0.00067 39.0 2.6 31 53-83 35-72 (1094)
39 PLN02189 cellulose synthase 31.4 35 0.00075 38.4 2.6 31 53-83 33-70 (1040)
40 PF12773 DZR: Double zinc ribb 31.0 46 0.001 22.9 2.3 15 19-33 9-23 (50)
41 cd02334 ZZ_dystrophin Zinc fin 30.5 54 0.0012 23.5 2.6 32 56-87 2-37 (49)
42 cd02249 ZZ Zinc finger, ZZ typ 30.0 65 0.0014 22.2 2.9 30 56-85 2-34 (46)
43 PF00569 ZZ: Zinc finger, ZZ t 29.9 44 0.00095 23.2 2.0 30 2-31 4-37 (46)
44 smart00105 ArfGap Putative GTP 29.3 42 0.00092 27.3 2.2 35 4-42 5-39 (112)
45 PF07649 C1_3: C1-like domain; 29.2 27 0.00059 22.0 0.8 25 56-80 2-29 (30)
46 PRK14714 DNA polymerase II lar 28.8 32 0.0007 39.5 1.8 45 4-63 669-718 (1337)
47 PF13920 zf-C3HC4_3: Zinc fing 28.8 95 0.0021 21.3 3.6 32 3-34 3-35 (50)
48 COG1198 PriA Primosomal protei 28.4 31 0.00067 37.4 1.5 19 12-30 433-452 (730)
49 PF14569 zf-UDP: Zinc-binding 27.8 24 0.00052 28.1 0.5 30 53-82 8-44 (80)
50 PF01667 Ribosomal_S27e: Ribos 27.0 27 0.00058 25.9 0.6 28 1-29 6-33 (55)
51 KOG0016 Enoyl-CoA hydratase/is 26.4 18 0.0004 34.6 -0.5 55 227-281 142-201 (266)
52 cd02344 ZZ_HERC2 Zinc finger, 24.2 72 0.0016 22.6 2.3 28 3-30 1-32 (45)
53 PF14776 UNC-79: Cation-channe 23.5 41 0.00089 35.1 1.3 65 22-87 227-303 (525)
54 cd02335 ZZ_ADA2 Zinc finger, Z 23.4 87 0.0019 22.0 2.6 27 4-30 2-32 (49)
55 COG5141 PHD zinc finger-contai 21.6 55 0.0012 34.4 1.8 18 269-286 461-479 (669)
56 cd02338 ZZ_PCMF_like Zinc fing 21.5 1.2E+02 0.0025 21.5 2.9 31 56-86 2-36 (49)
57 TIGR00622 ssl1 transcription f 21.2 60 0.0013 27.4 1.6 21 14-34 81-101 (112)
58 PF03107 C1_2: C1 domain; Int 20.9 33 0.00072 21.8 0.1 25 4-33 2-26 (30)
59 cd02339 ZZ_Mind_bomb Zinc fing 20.7 68 0.0015 22.5 1.6 28 56-83 2-33 (45)
60 PF11781 RRN7: RNA polymerase 20.3 67 0.0015 21.6 1.4 23 4-29 10-32 (36)
61 COG1198 PriA Primosomal protei 20.2 83 0.0018 34.2 2.8 18 4-24 437-454 (730)
No 1
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.80 E-value=6.1e-06 Score=82.41 Aligned_cols=82 Identities=26% Similarity=0.538 Sum_probs=71.6
Q ss_pred ccCccCCCC--CceEEecCCccccchhhhHhhhhccccccccccccCCC-------CCCCCCCCCcccCcceEEEccccc
Q 023008 3 IQCNVCEAA--EAKVLCCADEAALCWECDDKVHAANKLASKHQRVPLSS-------SSTQMPKCDICQETSGFFFCLQDR 73 (288)
Q Consensus 3 ~~Cd~Ce~a--~A~vyC~AD~A~LC~~CD~~VHsANkLa~rH~RvpL~~-------a~~~~p~CdiC~s~~A~ffC~~D~ 73 (288)
..|..|+++ .|.|+|..|..++|.-|..+.|-+-..+.||..+|-.+ .+.....|..|+-+.-..||.+|.
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 369999865 59999999999999999999999888889999887655 245667799999999999999999
Q ss_pred ccccccccccc
Q 023008 74 ALLCRKCDVAI 84 (288)
Q Consensus 74 a~LC~~CDv~i 84 (288)
+++|..|....
T Consensus 243 ~pvc~~clee~ 253 (699)
T KOG4367|consen 243 MPVCYQCLEEG 253 (699)
T ss_pred ChHHHHHHHhh
Confidence 99999999864
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=97.76 E-value=2e-05 Score=52.03 Aligned_cols=38 Identities=45% Similarity=0.855 Sum_probs=34.3
Q ss_pred CCCcccCcceEEEcccccccccccccccccCCCCCCCCCceeee
Q 023008 56 KCDICQETSGFFFCLQDRALLCRKCDVAIHTANSYVSAHQRFLL 99 (288)
Q Consensus 56 ~CdiC~s~~A~ffC~~D~a~LC~~CDv~iHsaN~l~s~H~RvpL 99 (288)
.|+.|+.+++.+||.+|...||..|+...|+ .|.+++|
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 5999998899999999999999999988775 8998875
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=97.72 E-value=2.4e-05 Score=53.03 Aligned_cols=40 Identities=30% Similarity=0.549 Sum_probs=34.9
Q ss_pred CCCCCcccCcceEEEcccccccccccccccccCCCCCCCCCceeee
Q 023008 54 MPKCDICQETSGFFFCLQDRALLCRKCDVAIHTANSYVSAHQRFLL 99 (288)
Q Consensus 54 ~p~CdiC~s~~A~ffC~~D~a~LC~~CDv~iHsaN~l~s~H~RvpL 99 (288)
...|+.|++..+.+||..|+.+||..|....|+. |..++|
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 4679999998899999999999999999998863 888876
No 4
>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=97.55 E-value=5.6e-05 Score=49.82 Aligned_cols=39 Identities=38% Similarity=0.750 Sum_probs=33.7
Q ss_pred ccCccCCCCCceEEecCCccccchhhhHhhhhccccccccccccC
Q 023008 3 IQCNVCEAAEAKVLCCADEAALCWECDDKVHAANKLASKHQRVPL 47 (288)
Q Consensus 3 ~~Cd~Ce~a~A~vyC~AD~A~LC~~CD~~VHsANkLa~rH~RvpL 47 (288)
..|+.++.+++.+||..|.+.+|..|+...|. .|.+++|
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 36889988899999999999999999977764 7888775
No 5
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.26 E-value=0.00026 Score=47.26 Aligned_cols=39 Identities=49% Similarity=0.870 Sum_probs=34.0
Q ss_pred CCCCcccCcceEEEcccccccccccccccccCCCCCCCCCceeee
Q 023008 55 PKCDICQETSGFFFCLQDRALLCRKCDVAIHTANSYVSAHQRFLL 99 (288)
Q Consensus 55 p~CdiC~s~~A~ffC~~D~a~LC~~CDv~iHsaN~l~s~H~RvpL 99 (288)
..|..|+.+++.+||..|...||..|....| +.|.+++|
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 4599999899999999999999999998867 47888765
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=97.20 E-value=0.00032 Score=47.43 Aligned_cols=40 Identities=25% Similarity=0.507 Sum_probs=33.9
Q ss_pred CccCccCCCCCceEEecCCccccchhhhHhhhhccccccccccccC
Q 023008 2 RIQCNVCEAAEAKVLCCADEAALCWECDDKVHAANKLASKHQRVPL 47 (288)
Q Consensus 2 k~~Cd~Ce~a~A~vyC~AD~A~LC~~CD~~VHsANkLa~rH~RvpL 47 (288)
...|+.|....+.+||..|...||..|....|.. |..++|
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 3579999998899999999999999999888864 887765
No 7
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.00 E-value=0.00054 Score=45.69 Aligned_cols=39 Identities=31% Similarity=0.550 Sum_probs=33.0
Q ss_pred ccCccCCCCCceEEecCCccccchhhhHhhhhccccccccccccC
Q 023008 3 IQCNVCEAAEAKVLCCADEAALCWECDDKVHAANKLASKHQRVPL 47 (288)
Q Consensus 3 ~~Cd~Ce~a~A~vyC~AD~A~LC~~CD~~VHsANkLa~rH~RvpL 47 (288)
..|..++..++.+||..|.+.+|..|....| +.|.+++|
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 5788998889999999999999999987655 56777664
No 8
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=78.06 E-value=0.94 Score=44.55 Aligned_cols=77 Identities=27% Similarity=0.505 Sum_probs=53.6
Q ss_pred CCceEEecCCccccc------hhhhHhhhhcccccc-ccccccCCC---CC----CCCCCCCcccC---cceEEEccccc
Q 023008 11 AEAKVLCCADEAALC------WECDDKVHAANKLAS-KHQRVPLSS---SS----TQMPKCDICQE---TSGFFFCLQDR 73 (288)
Q Consensus 11 a~A~vyC~AD~A~LC------~~CD~~VHsANkLa~-rH~RvpL~~---a~----~~~p~CdiC~s---~~A~ffC~~D~ 73 (288)
.-+.++|..|.|..| .-|+..+=++--|++ =|...||.. .+ .....|-.|+. ....|.|..|.
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 457899999999875 467755544433433 466777754 11 23445999943 34568899999
Q ss_pred ccccccccccccCC
Q 023008 74 ALLCRKCDVAIHTA 87 (288)
Q Consensus 74 a~LC~~CDv~iHsa 87 (288)
-..|.+||+-+|..
T Consensus 353 ~~FCldCDv~iHes 366 (378)
T KOG2807|consen 353 NVFCLDCDVFIHES 366 (378)
T ss_pred ceeeccchHHHHhh
Confidence 99999999998863
No 9
>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=72.52 E-value=2.8 Score=36.96 Aligned_cols=78 Identities=27% Similarity=0.536 Sum_probs=40.9
Q ss_pred cCccCC--CCCceEEecCCccccchhhhH--hhhhccc-cccccccccCCCCC---CCCCCCCcccCcceE----EEccc
Q 023008 4 QCNVCE--AAEAKVLCCADEAALCWECDD--KVHAANK-LASKHQRVPLSSSS---TQMPKCDICQETSGF----FFCLQ 71 (288)
Q Consensus 4 ~Cd~Ce--~a~A~vyC~AD~A~LC~~CD~--~VHsANk-La~rH~RvpL~~a~---~~~p~CdiC~s~~A~----ffC~~ 71 (288)
.|.+|+ ...+++.|..|...+|..=+. .-|--+- +.+||.-|.|-+-. .....|..|+..+.+ +-...
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 599999 678999999999999985443 2222222 34688877775522 235569999987654 33445
Q ss_pred cc--cccccc-cc
Q 023008 72 DR--ALLCRK-CD 81 (288)
Q Consensus 72 D~--a~LC~~-CD 81 (288)
|. .+||+. |.
T Consensus 82 d~vvvllCR~pC~ 94 (152)
T PF09416_consen 82 DSVVVLLCRQPCA 94 (152)
T ss_dssp SCEEEEEETTTTT
T ss_pred CCeEEEEeCCchh
Confidence 54 689988 76
No 10
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.46 E-value=2.5 Score=35.52 Aligned_cols=63 Identities=27% Similarity=0.489 Sum_probs=39.9
Q ss_pred chhhhHhhhhcccccc-ccccccCCC---C----CCCCCCCCcccCc--------------ceEEEcccccccccccccc
Q 023008 25 CWECDDKVHAANKLAS-KHQRVPLSS---S----STQMPKCDICQET--------------SGFFFCLQDRALLCRKCDV 82 (288)
Q Consensus 25 C~~CD~~VHsANkLa~-rH~RvpL~~---a----~~~~p~CdiC~s~--------------~A~ffC~~D~a~LC~~CDv 82 (288)
|..|+..+=.+.-|++ =|.-.||.. . ......|-.|+.. ...+.|..|+...|.+||+
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 5566654433333433 355555532 1 1123459999763 2358899999999999999
Q ss_pred cccCC
Q 023008 83 AIHTA 87 (288)
Q Consensus 83 ~iHsa 87 (288)
-+|..
T Consensus 98 fiHe~ 102 (112)
T TIGR00622 98 FVHES 102 (112)
T ss_pred hhhhh
Confidence 99863
No 11
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=69.07 E-value=2.2 Score=42.04 Aligned_cols=77 Identities=27% Similarity=0.530 Sum_probs=53.6
Q ss_pred CCceEEecCCcccc------chhhhHhhhhccccc-cccccccCCC---C----CCCCCCCCcccC--------------
Q 023008 11 AEAKVLCCADEAAL------CWECDDKVHAANKLA-SKHQRVPLSS---S----STQMPKCDICQE-------------- 62 (288)
Q Consensus 11 a~A~vyC~AD~A~L------C~~CD~~VHsANkLa-~rH~RvpL~~---a----~~~~p~CdiC~s-------------- 62 (288)
..+.++|..|.+.. |..|+..+=...-|+ +-|...||.. . ......|-.|+.
T Consensus 305 ~~gGy~CP~CktkVCsLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~~~~~ 384 (421)
T COG5151 305 KGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPFDEST 384 (421)
T ss_pred ccCceeCCcccceeecCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCcccccc
Confidence 45788999998876 557875433322222 4577777755 1 123455888875
Q ss_pred cceEEEcccccccccccccccccCC
Q 023008 63 TSGFFFCLQDRALLCRKCDVAIHTA 87 (288)
Q Consensus 63 ~~A~ffC~~D~a~LC~~CDv~iHsa 87 (288)
....+.|+.|..-.|.+||+-+|..
T Consensus 385 ss~rY~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 385 SSGRYQCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred cccceechhhhhhhhhhhHHHHHHH
Confidence 2677899999999999999998853
No 12
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=67.12 E-value=1.8 Score=44.25 Aligned_cols=52 Identities=19% Similarity=0.471 Sum_probs=43.7
Q ss_pred CCCCCcccCc--ceEEEcccccccccccccccccCCCCCCCCCceeeeeCcccc
Q 023008 54 MPKCDICQET--SGFFFCLQDRALLCRKCDVAIHTANSYVSAHQRFLLTGVKVA 105 (288)
Q Consensus 54 ~p~CdiC~s~--~A~ffC~~D~a~LC~~CDv~iHsaN~l~s~H~RvpL~g~~~~ 105 (288)
..+|..|+.. .|.++|+.|.+..|.-|....|-+-...++|+.+|-...++.
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 4568888765 677999999999999999999999888899998887666654
No 13
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=65.75 E-value=2.2 Score=43.96 Aligned_cols=55 Identities=24% Similarity=0.419 Sum_probs=42.3
Q ss_pred cccccCCCCCCCCCCCCcccC-----cceEEEcc--cccccccccccccccCCCCCCCCCceeee
Q 023008 42 HQRVPLSSSSTQMPKCDICQE-----TSGFFFCL--QDRALLCRKCDVAIHTANSYVSAHQRFLL 99 (288)
Q Consensus 42 H~RvpL~~a~~~~p~CdiC~s-----~~A~ffC~--~D~a~LC~~CDv~iHsaN~l~s~H~RvpL 99 (288)
++||.|..--.+-..|++|+. +.|-|||. .|-...|..|-..+|+.- .++...||
T Consensus 443 ~KRVEIkPYv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~---~r~~HkPl 504 (520)
T KOG0129|consen 443 DKRVEIKPYVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGP---GREHHKPL 504 (520)
T ss_pred ceeeeecceeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCC---chhcCCce
Confidence 558887443346678999998 88999996 699999999999999864 34444454
No 14
>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=61.79 E-value=7.8 Score=27.52 Aligned_cols=30 Identities=27% Similarity=0.513 Sum_probs=23.4
Q ss_pred ccCccCCCCC---ceEEecCCccc-cchhhhHhh
Q 023008 3 IQCNVCEAAE---AKVLCCADEAA-LCWECDDKV 32 (288)
Q Consensus 3 ~~Cd~Ce~a~---A~vyC~AD~A~-LC~~CD~~V 32 (288)
+.||.|+..| ..+.|..|.-+ ||..|-.+.
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 4799999654 67889988766 999996443
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=61.08 E-value=4.5 Score=25.09 Aligned_cols=24 Identities=29% Similarity=0.664 Sum_probs=15.5
Q ss_pred CCccCccCCCCCceEEecCCccccchhhhH
Q 023008 1 MRIQCNVCEAAEAKVLCCADEAALCWECDD 30 (288)
Q Consensus 1 Mk~~Cd~Ce~a~A~vyC~AD~A~LC~~CD~ 30 (288)
|...|-.|+... ..++.+|..|..
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~ 24 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGA 24 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCC
Confidence 788999998621 344555665543
No 16
>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=60.58 E-value=11 Score=26.60 Aligned_cols=40 Identities=23% Similarity=0.360 Sum_probs=27.6
Q ss_pred CCCcccCcce---EEEcccc-cccccccccccccCCCCCCCCCc
Q 023008 56 KCDICQETSG---FFFCLQD-RALLCRKCDVAIHTANSYVSAHQ 95 (288)
Q Consensus 56 ~CdiC~s~~A---~ffC~~D-~a~LC~~CDv~iHsaN~l~s~H~ 95 (288)
.|+.|..... .+.|..| ..-||..|-......+.....|.
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~ 45 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHN 45 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCC
Confidence 4888986644 4889998 77899999886544433333443
No 17
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=58.37 E-value=4.5 Score=26.25 Aligned_cols=25 Identities=36% Similarity=0.539 Sum_probs=18.4
Q ss_pred CCccCccCCCCCceEEecCCccccch
Q 023008 1 MRIQCNVCEAAEAKVLCCADEAALCW 26 (288)
Q Consensus 1 Mk~~Cd~Ce~a~A~vyC~AD~A~LC~ 26 (288)
++.+|.+|+. .+..-|..|.+.+|.
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 4568999999 999999999999986
No 18
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=53.52 E-value=7.9 Score=40.07 Aligned_cols=44 Identities=23% Similarity=0.459 Sum_probs=34.7
Q ss_pred ccCccCCC-----CCceEEecC--CccccchhhhHhhhhccccccccccccCCC
Q 023008 3 IQCNVCEA-----AEAKVLCCA--DEAALCWECDDKVHAANKLASKHQRVPLSS 49 (288)
Q Consensus 3 ~~Cd~Ce~-----a~A~vyC~A--D~A~LC~~CD~~VHsANkLa~rH~RvpL~~ 49 (288)
..||.|+. ..|-+||.+ |--++|..|=+.+|+. ..++.-.||..
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPlvr 506 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPLVR 506 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCceec
Confidence 46888887 889999997 8899999999999996 34444455533
No 19
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=51.92 E-value=6.8 Score=41.59 Aligned_cols=22 Identities=18% Similarity=0.425 Sum_probs=11.9
Q ss_pred CCccCccCCCC--CceEEecCCccc
Q 023008 1 MRIQCNVCEAA--EAKVLCCADEAA 23 (288)
Q Consensus 1 Mk~~Cd~Ce~a--~A~vyC~AD~A~ 23 (288)
|+ .|-.|+.. ....||..|++.
T Consensus 1 M~-~Cp~Cg~~n~~~akFC~~CG~~ 24 (645)
T PRK14559 1 ML-ICPQCQFENPNNNRFCQKCGTS 24 (645)
T ss_pred CC-cCCCCCCcCCCCCccccccCCC
Confidence 53 69999854 223344444433
No 20
>PF15359 CDV3: Carnitine deficiency-associated protein 3
Probab=50.36 E-value=22 Score=30.50 Aligned_cols=48 Identities=31% Similarity=0.481 Sum_probs=31.7
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCCCCC--C--CCCCceecccCCCCCCchh
Q 023008 234 QVPEASWAVPQIPSPPTASGLYWPKNPQ--N--QYDSAFVPDIHHHSQLNRT 281 (288)
Q Consensus 234 ~vpe~~~~vp~~pspptasgl~w~~~~~--~--~~~~~~vpdi~~~~~~~~~ 281 (288)
|+|...=.|.+.|.|.+++|+|.+-..- . ....---|||.+-.+||--
T Consensus 68 ~~~~~~~~v~~~~~p~~~~gvY~PP~~R~~~~~r~~~qgaPdI~Se~~FPSL 119 (129)
T PF15359_consen 68 QAPPAPAPVEEPPEPATTSGVYRPPAARNTTTKRKRPQGAPDIFSEEQFPSL 119 (129)
T ss_pred CCCCCCCccCCCCCCCCCCceecCcccccccccCCCCCCCCCccccccccch
Confidence 4554443488889999999999975531 0 0011125999999998863
No 21
>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=49.73 E-value=16 Score=26.13 Aligned_cols=29 Identities=31% Similarity=0.563 Sum_probs=22.0
Q ss_pred CCCcccCcce---EEEccccc---ccccccccccc
Q 023008 56 KCDICQETSG---FFFCLQDR---ALLCRKCDVAI 84 (288)
Q Consensus 56 ~CdiC~s~~A---~ffC~~D~---a~LC~~CDv~i 84 (288)
.|+.|+..+. .|.|..|. .-||..|-...
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 4888887443 38898887 78999997754
No 22
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.69 E-value=21 Score=30.77 Aligned_cols=40 Identities=30% Similarity=0.534 Sum_probs=29.7
Q ss_pred CCCcccCcceEEEccccccccccccc-ccccCCCCCCCCCceeeeeCc
Q 023008 56 KCDICQETSGFFFCLQDRALLCRKCD-VAIHTANSYVSAHQRFLLTGV 102 (288)
Q Consensus 56 ~CdiC~s~~A~ffC~~D~a~LC~~CD-v~iHsaN~l~s~H~RvpL~g~ 102 (288)
.|..|+.. ..+||..|...+|..|. ...|. .|.-.++..+
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 68888766 88999999999999999 44554 4555555433
No 23
>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=45.72 E-value=13 Score=27.06 Aligned_cols=23 Identities=22% Similarity=0.573 Sum_probs=15.9
Q ss_pred ceEEecCCccccchhhhHhhhhc
Q 023008 13 AKVLCCADEAALCWECDDKVHAA 35 (288)
Q Consensus 13 A~vyC~AD~A~LC~~CD~~VHsA 35 (288)
.++-|..|...+|..||.-||..
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 57889999999999999999973
No 24
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=43.11 E-value=14 Score=36.77 Aligned_cols=37 Identities=32% Similarity=0.411 Sum_probs=29.4
Q ss_pred cccccccccCCCCCCCCCCCCcccCcceEEEccccc----ccccccccccc
Q 023008 38 LASKHQRVPLSSSSTQMPKCDICQETSGFFFCLQDR----ALLCRKCDVAI 84 (288)
Q Consensus 38 La~rH~RvpL~~a~~~~p~CdiC~s~~A~ffC~~D~----a~LC~~CDv~i 84 (288)
++++|++|. ||.|.+..-.|+|..|- .-||.+|....
T Consensus 2 ~~~rHe~v~----------CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~ 42 (381)
T KOG1280|consen 2 LTSRHEGVS----------CDGCGKTAFTFRRYKCLRCSDYDLCFSCYENG 42 (381)
T ss_pred CCCCcCCce----------eccccccceeeeeeEeeeecchhHHHHHhhcC
Confidence 578999987 99999988887766553 36999998753
No 25
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=42.44 E-value=17 Score=34.66 Aligned_cols=30 Identities=23% Similarity=0.589 Sum_probs=25.3
Q ss_pred ccCccCCC---CCceEEecCCccc-cchhhhHhh
Q 023008 3 IQCNVCEA---AEAKVLCCADEAA-LCWECDDKV 32 (288)
Q Consensus 3 ~~Cd~Ce~---a~A~vyC~AD~A~-LC~~CD~~V 32 (288)
+.||.|.. .-..+-|.-|..| ||..|.++.
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~ 186 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN 186 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC
Confidence 68999987 4588999999765 999999874
No 26
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=41.99 E-value=20 Score=29.39 Aligned_cols=37 Identities=24% Similarity=0.424 Sum_probs=24.9
Q ss_pred ccCccCCCCCceEEecCCccccchhhhHhhhhccccccccc
Q 023008 3 IQCNVCEAAEAKVLCCADEAALCWECDDKVHAANKLASKHQ 43 (288)
Q Consensus 3 ~~Cd~Ce~a~A~vyC~AD~A~LC~~CD~~VHsANkLa~rH~ 43 (288)
..|--|+.....+-+..=..+||..| +.+|+. ++.|.
T Consensus 14 ~~CaDCg~~~p~w~s~~~GiflC~~C-ag~HR~---lg~~i 50 (116)
T PF01412_consen 14 KVCADCGAPNPTWASLNYGIFLCLEC-AGIHRS---LGVHI 50 (116)
T ss_dssp TB-TTT-SBS--EEETTTTEEE-HHH-HHHHHH---HTTTT
T ss_pred CcCCCCCCCCCCEEEeecChhhhHHH-HHHHHH---hcccc
Confidence 36889998777777777799999999 799985 45444
No 27
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=41.60 E-value=17 Score=29.51 Aligned_cols=48 Identities=31% Similarity=0.617 Sum_probs=35.2
Q ss_pred hccccccccccccCCCCCCCCCCCCcccCcc---eEEEccccc--ccccccccccc
Q 023008 34 AANKLASKHQRVPLSSSSTQMPKCDICQETS---GFFFCLQDR--ALLCRKCDVAI 84 (288)
Q Consensus 34 sANkLa~rH~RvpL~~a~~~~p~CdiC~s~~---A~ffC~~D~--a~LC~~CDv~i 84 (288)
.-|+|+++-.+-|+. ..+..|.+|.... ...||..|. ..+|.-|-..+
T Consensus 27 ~eNKlLs~~~~nPy~---~~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 27 GENKLLSKKKKNPYA---PYSSKCKICKTKVHQPGAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred cceeeecccccCccc---ccCccccccccccccCCCccChhhhcccCcccccCCee
Confidence 458888877776663 2356799997653 458999994 57999998764
No 28
>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=41.38 E-value=11 Score=27.57 Aligned_cols=24 Identities=33% Similarity=0.676 Sum_probs=16.0
Q ss_pred ceEEEcccccccccccccccccCC
Q 023008 64 SGFFFCLQDRALLCRKCDVAIHTA 87 (288)
Q Consensus 64 ~A~ffC~~D~a~LC~~CDv~iHsa 87 (288)
...+.|..|+...|.+||+-+|..
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 467899999999999999999864
No 29
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=39.79 E-value=15 Score=43.20 Aligned_cols=45 Identities=27% Similarity=0.516 Sum_probs=32.9
Q ss_pred ccCccCC--CCCceEEecCCccccchhhhHhhhhccccccccccccCCC
Q 023008 3 IQCNVCE--AAEAKVLCCADEAALCWECDDKVHAANKLASKHQRVPLSS 49 (288)
Q Consensus 3 ~~Cd~Ce--~a~A~vyC~AD~A~LC~~CD~~VHsANkLa~rH~RvpL~~ 49 (288)
++||+=. ...|.++|..|. .||..||+-.|-. +-.+.|+|--+.+
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 4677765 456999999999 9999999866542 2346788766554
No 30
>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=36.44 E-value=28 Score=22.78 Aligned_cols=10 Identities=60% Similarity=1.245 Sum_probs=7.8
Q ss_pred CCccCccCCC
Q 023008 1 MRIQCNVCEA 10 (288)
Q Consensus 1 Mk~~Cd~Ce~ 10 (288)
|++.|..|+.
T Consensus 1 M~~~CP~C~~ 10 (38)
T TIGR02098 1 MRIQCPNCKT 10 (38)
T ss_pred CEEECCCCCC
Confidence 7788888875
No 31
>PRK14873 primosome assembly protein PriA; Provisional
Probab=36.19 E-value=18 Score=38.55 Aligned_cols=19 Identities=21% Similarity=0.529 Sum_probs=14.5
Q ss_pred CceEEecCCc-cccchhhhH
Q 023008 12 EAKVLCCADE-AALCWECDD 30 (288)
Q Consensus 12 ~A~vyC~AD~-A~LC~~CD~ 30 (288)
...++|..|. ..-|..||.
T Consensus 381 ap~l~C~~Cg~~~~C~~C~~ 400 (665)
T PRK14873 381 VPSLACARCRTPARCRHCTG 400 (665)
T ss_pred CCeeEhhhCcCeeECCCCCC
Confidence 3567899995 667999973
No 32
>PLN02400 cellulose synthase
Probab=35.53 E-value=27 Score=39.44 Aligned_cols=30 Identities=27% Similarity=0.584 Sum_probs=24.8
Q ss_pred CCCCCCcccCc-------ceEEEcccccccccccccc
Q 023008 53 QMPKCDICQET-------SGFFFCLQDRALLCRKCDV 82 (288)
Q Consensus 53 ~~p~CdiC~s~-------~A~ffC~~D~a~LC~~CDv 82 (288)
....|.+|++. ..++-|.+|.-++|+.|-.
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE 71 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE 71 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchhh
Confidence 45589999865 4667799999999999985
No 33
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=35.08 E-value=21 Score=38.87 Aligned_cols=30 Identities=33% Similarity=0.771 Sum_probs=21.7
Q ss_pred ccCccCCCCCceEEecCCccccchhhhHhhhhc
Q 023008 3 IQCNVCEAAEAKVLCCADEAALCWECDDKVHAA 35 (288)
Q Consensus 3 ~~Cd~Ce~a~A~vyC~AD~A~LC~~CD~~VHsA 35 (288)
++||+|...-.- .++++.+|+.|..-||.+
T Consensus 272 viCDvCrspD~e---~~neMVfCd~Cn~cVHqa 301 (893)
T KOG0954|consen 272 VICDVCRSPDSE---EANEMVFCDKCNICVHQA 301 (893)
T ss_pred ceeceecCCCcc---ccceeEEeccchhHHHHh
Confidence 579999753221 246788899999999986
No 34
>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=34.79 E-value=20 Score=23.50 Aligned_cols=25 Identities=28% Similarity=0.886 Sum_probs=12.4
Q ss_pred CCCCCcccCcceEEEccccccccccccc
Q 023008 54 MPKCDICQETSGFFFCLQDRALLCRKCD 81 (288)
Q Consensus 54 ~p~CdiC~s~~A~ffC~~D~a~LC~~CD 81 (288)
.++|+.|+....+ .+...++|..|.
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 4679999877665 466778898885
No 35
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=34.74 E-value=17 Score=27.44 Aligned_cols=31 Identities=23% Similarity=0.622 Sum_probs=24.6
Q ss_pred CCccCccCCCCCceEEecCCccccchhhhHhh
Q 023008 1 MRIQCNVCEAAEAKVLCCADEAALCWECDDKV 32 (288)
Q Consensus 1 Mk~~Cd~Ce~a~A~vyC~AD~A~LC~~CD~~V 32 (288)
|++.|..|++ .-+||=++.....|..|...+
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 7889999995 677888888888888886433
No 36
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=33.80 E-value=15 Score=43.14 Aligned_cols=46 Identities=35% Similarity=0.650 Sum_probs=35.7
Q ss_pred CCCCCCCCccc--CcceEEEccccccccccccccc--ccCCCCCCCCCceeeee
Q 023008 51 STQMPKCDICQ--ETSGFFFCLQDRALLCRKCDVA--IHTANSYVSAHQRFLLT 100 (288)
Q Consensus 51 ~~~~p~CdiC~--s~~A~ffC~~D~a~LC~~CDv~--iHsaN~l~s~H~RvpL~ 100 (288)
..+.|.||.|. +..|.++|..|. .||.+||.- .|..| ++|+|.-+.
T Consensus 3319 qkQ~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHrrt---ktH~~q~f~ 3368 (3738)
T KOG1428|consen 3319 QKQMPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHRRT---KTHQRQVFK 3368 (3738)
T ss_pred hhcCCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHhhc---cchhhhhhh
Confidence 35678899995 457789999999 999999986 45554 588887553
No 37
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=33.80 E-value=35 Score=22.37 Aligned_cols=24 Identities=21% Similarity=0.744 Sum_probs=17.4
Q ss_pred CCCcccCc----ceEEEccccccccccc
Q 023008 56 KCDICQET----SGFFFCLQDRALLCRK 79 (288)
Q Consensus 56 ~CdiC~s~----~A~ffC~~D~a~LC~~ 79 (288)
.|.+|... ...|+|..|...||..
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLCVE 29 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCcccCC
Confidence 36666543 3679999999999875
No 38
>PLN02436 cellulose synthase A
Probab=33.39 E-value=31 Score=38.96 Aligned_cols=31 Identities=26% Similarity=0.552 Sum_probs=25.1
Q ss_pred CCCCCCcccCcc-------eEEEccccccccccccccc
Q 023008 53 QMPKCDICQETS-------GFFFCLQDRALLCRKCDVA 83 (288)
Q Consensus 53 ~~p~CdiC~s~~-------A~ffC~~D~a~LC~~CDv~ 83 (288)
....|.+|++.. .++-|.+|..++|+.|-.-
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyey 72 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEY 72 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchhhh
Confidence 455899998663 6678999999999999853
No 39
>PLN02189 cellulose synthase
Probab=31.44 E-value=35 Score=38.40 Aligned_cols=31 Identities=26% Similarity=0.550 Sum_probs=24.7
Q ss_pred CCCCCCcccCc-------ceEEEccccccccccccccc
Q 023008 53 QMPKCDICQET-------SGFFFCLQDRALLCRKCDVA 83 (288)
Q Consensus 53 ~~p~CdiC~s~-------~A~ffC~~D~a~LC~~CDv~ 83 (288)
....|.+|++. ..++-|.+|.-++|+.|-.-
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyey 70 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEY 70 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhhh
Confidence 34579999865 35677999999999999863
No 40
>PF12773 DZR: Double zinc ribbon
Probab=30.98 E-value=46 Score=22.86 Aligned_cols=15 Identities=27% Similarity=0.674 Sum_probs=9.2
Q ss_pred CCccccchhhhHhhh
Q 023008 19 ADEAALCWECDDKVH 33 (288)
Q Consensus 19 AD~A~LC~~CD~~VH 33 (288)
.+++.+|..|...+-
T Consensus 9 ~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP 23 (50)
T ss_pred CccccCChhhcCChh
Confidence 455777777764443
No 41
>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=30.49 E-value=54 Score=23.50 Aligned_cols=32 Identities=34% Similarity=0.647 Sum_probs=22.8
Q ss_pred CCCcccCcc---eEEEcccc-cccccccccccccCC
Q 023008 56 KCDICQETS---GFFFCLQD-RALLCRKCDVAIHTA 87 (288)
Q Consensus 56 ~CdiC~s~~---A~ffC~~D-~a~LC~~CDv~iHsa 87 (288)
.|+.|+..+ ..|.|..| ..-||..|-...+..
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 488998653 34778877 457999998765443
No 42
>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=30.04 E-value=65 Score=22.19 Aligned_cols=30 Identities=27% Similarity=0.520 Sum_probs=22.6
Q ss_pred CCCcccCc--ceEEEccccc-cccccccccccc
Q 023008 56 KCDICQET--SGFFFCLQDR-ALLCRKCDVAIH 85 (288)
Q Consensus 56 ~CdiC~s~--~A~ffC~~D~-a~LC~~CDv~iH 85 (288)
.|+.|... ...|.|..|. .-||..|-...+
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 48888763 3568899887 789999987654
No 43
>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=29.86 E-value=44 Score=23.19 Aligned_cols=30 Identities=23% Similarity=0.520 Sum_probs=21.8
Q ss_pred CccCccCCC---CCceEEecCCc-cccchhhhHh
Q 023008 2 RIQCNVCEA---AEAKVLCCADE-AALCWECDDK 31 (288)
Q Consensus 2 k~~Cd~Ce~---a~A~vyC~AD~-A~LC~~CD~~ 31 (288)
...|+.|+. ....+-|..|. --||..|-.+
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 578999997 35789999985 6799999755
No 44
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=29.28 E-value=42 Score=27.35 Aligned_cols=35 Identities=26% Similarity=0.496 Sum_probs=28.3
Q ss_pred cCccCCCCCceEEecCCccccchhhhHhhhhcccccccc
Q 023008 4 QCNVCEAAEAKVLCCADEAALCWECDDKVHAANKLASKH 42 (288)
Q Consensus 4 ~Cd~Ce~a~A~vyC~AD~A~LC~~CD~~VHsANkLa~rH 42 (288)
.|--|+.....+-+..=+.+||..| ..+|+. ++.|
T Consensus 5 ~CaDC~~~~p~w~s~~~GifvC~~C-sgiHR~---lg~h 39 (112)
T smart00105 5 KCFDCGAPNPTWASVNLGVFLCIEC-SGIHRS---LGVH 39 (112)
T ss_pred cccCCCCCCCCcEEeccceeEhHHh-HHHHHh---cCCC
Confidence 5888998777777777799999999 899985 4555
No 45
>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=29.19 E-value=27 Score=22.01 Aligned_cols=25 Identities=28% Similarity=0.668 Sum_probs=8.1
Q ss_pred CCCcccCcc---eEEEcccccccccccc
Q 023008 56 KCDICQETS---GFFFCLQDRALLCRKC 80 (288)
Q Consensus 56 ~CdiC~s~~---A~ffC~~D~a~LC~~C 80 (288)
.|+.|+... ..++|..|...|...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 488887654 3455666555554444
No 46
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.84 E-value=32 Score=39.48 Aligned_cols=45 Identities=20% Similarity=0.472 Sum_probs=0.0
Q ss_pred cCccCCCCCceEEecCCcccc-----chhhhHhhhhccccccccccccCCCCCCCCCCCCcccCc
Q 023008 4 QCNVCEAAEAKVLCCADEAAL-----CWECDDKVHAANKLASKHQRVPLSSSSTQMPKCDICQET 63 (288)
Q Consensus 4 ~Cd~Ce~a~A~vyC~AD~A~L-----C~~CD~~VHsANkLa~rH~RvpL~~a~~~~p~CdiC~s~ 63 (288)
.|..|+...-..||..|.+.+ |..|...+.. .+.. ...|+.|+..
T Consensus 669 kCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~-------------des~--a~~CP~CGtp 718 (1337)
T PRK14714 669 RCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPP-------------DESG--RVECPRCDVE 718 (1337)
T ss_pred ECCCCCCccccccCcccCCcCCCceeCccCCCccCC-------------Cccc--cccCCCCCCc
No 47
>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=28.80 E-value=95 Score=21.30 Aligned_cols=32 Identities=19% Similarity=0.468 Sum_probs=25.2
Q ss_pred ccCccCCCCCceEEecCCccc-cchhhhHhhhh
Q 023008 3 IQCNVCEAAEAKVLCCADEAA-LCWECDDKVHA 34 (288)
Q Consensus 3 ~~Cd~Ce~a~A~vyC~AD~A~-LC~~CD~~VHs 34 (288)
..|..|..+.+.+.-.-|+-. +|..|-.+...
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 468999988888888889888 99999766554
No 48
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.41 E-value=31 Score=37.39 Aligned_cols=19 Identities=32% Similarity=0.560 Sum_probs=14.0
Q ss_pred CceEEecCCc-cccchhhhH
Q 023008 12 EAKVLCCADE-AALCWECDD 30 (288)
Q Consensus 12 ~A~vyC~AD~-A~LC~~CD~ 30 (288)
...+.|..|+ .+=|..||.
T Consensus 433 s~~l~C~~Cg~v~~Cp~Cd~ 452 (730)
T COG1198 433 APLLLCRDCGYIAECPNCDS 452 (730)
T ss_pred cceeecccCCCcccCCCCCc
Confidence 3578899986 455999984
No 49
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=27.83 E-value=24 Score=28.14 Aligned_cols=30 Identities=27% Similarity=0.593 Sum_probs=13.5
Q ss_pred CCCCCCcccCc-------ceEEEcccccccccccccc
Q 023008 53 QMPKCDICQET-------SGFFFCLQDRALLCRKCDV 82 (288)
Q Consensus 53 ~~p~CdiC~s~-------~A~ffC~~D~a~LC~~CDv 82 (288)
....|.+|++. ..++-|.+|..++|+.|-.
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE 44 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYE 44 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHH
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHH
Confidence 45669999754 4556799999999999975
No 50
>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=27.04 E-value=27 Score=25.94 Aligned_cols=28 Identities=25% Similarity=0.545 Sum_probs=14.8
Q ss_pred CCccCccCCCCCceEEecCCccccchhhh
Q 023008 1 MRIQCNVCEAAEAKVLCCADEAALCWECD 29 (288)
Q Consensus 1 Mk~~Cd~Ce~a~A~vyC~AD~A~LC~~CD 29 (288)
|++.|..|++ .-+||=++-...+|..|.
T Consensus 6 m~VkCp~C~~-~q~vFSha~t~V~C~~Cg 33 (55)
T PF01667_consen 6 MDVKCPGCYN-IQTVFSHAQTVVKCVVCG 33 (55)
T ss_dssp EEEE-TTT-S-EEEEETT-SS-EE-SSST
T ss_pred EEEECCCCCC-eeEEEecCCeEEEcccCC
Confidence 7788999974 445555555555555553
No 51
>KOG0016 consensus Enoyl-CoA hydratase/isomerase [Lipid transport and metabolism]
Probab=26.38 E-value=18 Score=34.61 Aligned_cols=55 Identities=22% Similarity=0.285 Sum_probs=34.9
Q ss_pred cccccccCCCc--ccccCCCCCCCCCCCCCCCCCCCCCCC---CCceecccCCCCCCchh
Q 023008 227 DDDECLGQVPE--ASWAVPQIPSPPTASGLYWPKNPQNQY---DSAFVPDIHHHSQLNRT 281 (288)
Q Consensus 227 ~~~~~~g~vpe--~~~~vp~~pspptasgl~w~~~~~~~~---~~~~vpdi~~~~~~~~~ 281 (288)
....-|||+|| ++|+.|+|=+...|+=+..=+.+=... ..-||-.|.-...|+.-
T Consensus 142 TPfa~lGq~PEG~Ss~t~p~imG~~~A~E~ll~~~kltA~Ea~~~glVskif~~~tf~~~ 201 (266)
T KOG0016|consen 142 TPFAKLGQSPEGCSSVTLPKIMGSASANEMLLFGEKLTAQEACEKGLVSKIFPAETFNEE 201 (266)
T ss_pred ccchhcCCCCCcceeeeehHhhchhhHHHHHHhCCcccHHHHHhcCchhhhcChHHHHHH
Confidence 44466999999 899999998888887765544431100 12266666555445543
No 52
>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=24.22 E-value=72 Score=22.59 Aligned_cols=28 Identities=18% Similarity=0.568 Sum_probs=22.1
Q ss_pred ccCccCCCCC---ceEEecCCc-cccchhhhH
Q 023008 3 IQCNVCEAAE---AKVLCCADE-AALCWECDD 30 (288)
Q Consensus 3 ~~Cd~Ce~a~---A~vyC~AD~-A~LC~~CD~ 30 (288)
+.||.|+..+ ..+.|..|. --||..|-.
T Consensus 1 V~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~ 32 (45)
T cd02344 1 VTCDGCQMFPINGPRFKCRNCDDFDFCENCFK 32 (45)
T ss_pred CCCCCCCCCCCccCeEECCCCCCccchHHhhC
Confidence 4799998544 678999986 669999964
No 53
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=23.47 E-value=41 Score=35.14 Aligned_cols=65 Identities=22% Similarity=0.451 Sum_probs=42.0
Q ss_pred cccchhhhHhhhhccccccc-cccccCCCCC--CCCCCCCcccCcceEEEcc--cc-------cccccccccccccCC
Q 023008 22 AALCWECDDKVHAANKLASK-HQRVPLSSSS--TQMPKCDICQETSGFFFCL--QD-------RALLCRKCDVAIHTA 87 (288)
Q Consensus 22 A~LC~~CD~~VHsANkLa~r-H~RvpL~~a~--~~~p~CdiC~s~~A~ffC~--~D-------~a~LC~~CDv~iHsa 87 (288)
.+||..|...||+.-+.... +.--|+.+.+ .+...|... +..|.+.|- +| .+.+|..|....|..
T Consensus 227 LylC~~Ca~~i~~e~~~~~~~~il~P~~~vS~~CenK~C~S~-~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~~~H~n 303 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSS-DKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNN 303 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCC-CCCeEEEEechhhccccCCCcchhHHHHhhhhccc
Confidence 47999999999986544333 4445554422 233445444 467777773 33 457999999998864
No 54
>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=23.38 E-value=87 Score=21.98 Aligned_cols=27 Identities=26% Similarity=0.738 Sum_probs=21.6
Q ss_pred cCccCCCCC---ceEEecCC-ccccchhhhH
Q 023008 4 QCNVCEAAE---AKVLCCAD-EAALCWECDD 30 (288)
Q Consensus 4 ~Cd~Ce~a~---A~vyC~AD-~A~LC~~CD~ 30 (288)
.|+.|.... -.+.|..| .--||..|=.
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~ 32 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFS 32 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhh
Confidence 599998644 45999999 6779999954
No 55
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=21.63 E-value=55 Score=34.40 Aligned_cols=18 Identities=33% Similarity=0.516 Sum_probs=9.7
Q ss_pred ecccCCC-CCCchhhhhhh
Q 023008 269 VPDIHHH-SQLNRTATRRR 286 (288)
Q Consensus 269 vpdi~~~-~~~~~~~~~~~ 286 (288)
.|||-.+ .+.+--.||||
T Consensus 461 ~~~~~~sl~tl~~~~sk~R 479 (669)
T COG5141 461 LPDIVYSLKTLEDWMSKRR 479 (669)
T ss_pred chhhhhcccccHHHHHHHH
Confidence 4555444 22555567776
No 56
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=21.49 E-value=1.2e+02 Score=21.47 Aligned_cols=31 Identities=29% Similarity=0.492 Sum_probs=21.8
Q ss_pred CCCcccCcc---eEEEcccc-cccccccccccccC
Q 023008 56 KCDICQETS---GFFFCLQD-RALLCRKCDVAIHT 86 (288)
Q Consensus 56 ~CdiC~s~~---A~ffC~~D-~a~LC~~CDv~iHs 86 (288)
.|+.|...+ ..|.|..| ..-||..|-...+.
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~ 36 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVT 36 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCc
Confidence 488888443 33788877 55899999875443
No 57
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.19 E-value=60 Score=27.36 Aligned_cols=21 Identities=29% Similarity=0.735 Sum_probs=19.2
Q ss_pred eEEecCCccccchhhhHhhhh
Q 023008 14 KVLCCADEAALCWECDDKVHA 34 (288)
Q Consensus 14 ~vyC~AD~A~LC~~CD~~VHs 34 (288)
..-|..|.-.+|.+||.-||.
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred ceeCCCCCCccccccchhhhh
Confidence 567999999999999999997
No 58
>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=20.92 E-value=33 Score=21.78 Aligned_cols=25 Identities=28% Similarity=0.513 Sum_probs=14.5
Q ss_pred cCccCCCCCceEEecCCccccchhhhHhhh
Q 023008 4 QCNVCEAAEAKVLCCADEAALCWECDDKVH 33 (288)
Q Consensus 4 ~Cd~Ce~a~A~vyC~AD~A~LC~~CD~~VH 33 (288)
.|++|++.....+ .+-|..|+..+|
T Consensus 2 ~C~~C~~~~~~~~-----~Y~C~~c~f~lh 26 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-----FYHCSECCFTLH 26 (30)
T ss_pred CCCCCCCCcCCCE-----eEEeCCCCCeEc
Confidence 5899986544432 455555554444
No 59
>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=20.66 E-value=68 Score=22.53 Aligned_cols=28 Identities=25% Similarity=0.551 Sum_probs=21.9
Q ss_pred CCCcccCcc---eEEEcccc-ccccccccccc
Q 023008 56 KCDICQETS---GFFFCLQD-RALLCRKCDVA 83 (288)
Q Consensus 56 ~CdiC~s~~---A~ffC~~D-~a~LC~~CDv~ 83 (288)
.|+.|+..+ ..+.|..| ..-||..|-..
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~ 33 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHG 33 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCC
Confidence 489998653 45889988 67899999763
No 60
>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=20.29 E-value=67 Score=21.60 Aligned_cols=23 Identities=26% Similarity=0.601 Sum_probs=19.2
Q ss_pred cCccCCCCCceEEecCCccccchhhh
Q 023008 4 QCNVCEAAEAKVLCCADEAALCWECD 29 (288)
Q Consensus 4 ~Cd~Ce~a~A~vyC~AD~A~LC~~CD 29 (288)
.|++|+.. +|=..|.-+.|..|.
T Consensus 10 ~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 10 PCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCCCCe---EeEccCCEEEhhhCc
Confidence 49999864 888889999999885
No 61
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.16 E-value=83 Score=34.20 Aligned_cols=18 Identities=22% Similarity=0.445 Sum_probs=9.6
Q ss_pred cCccCCCCCceEEecCCcccc
Q 023008 4 QCNVCEAAEAKVLCCADEAAL 24 (288)
Q Consensus 4 ~Cd~Ce~a~A~vyC~AD~A~L 24 (288)
.|..|+. ++-|..|+..|
T Consensus 437 ~C~~Cg~---v~~Cp~Cd~~l 454 (730)
T COG1198 437 LCRDCGY---IAECPNCDSPL 454 (730)
T ss_pred ecccCCC---cccCCCCCcce
Confidence 4555553 44566665554
Done!