Query 021178
Match_columns 316
No_of_seqs 187 out of 751
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 08:12:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021178.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021178hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.4 1.4E-13 3E-18 101.8 3.5 35 178-212 1-35 (54)
2 smart00401 ZnF_GATA zinc finge 99.4 3.6E-13 7.8E-18 98.6 2.7 39 175-213 2-40 (52)
3 PF00320 GATA: GATA zinc finge 99.3 1.9E-13 4.2E-18 93.3 1.1 34 179-212 1-34 (36)
4 KOG1601 GATA-4/5/6 transcripti 98.5 3.4E-08 7.4E-13 84.3 2.2 37 176-212 199-235 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.9 6.6E-06 1.4E-10 84.0 2.2 40 174-214 156-200 (498)
6 KOG3554 Histone deacetylase co 83.1 1.2 2.5E-05 46.7 3.5 40 174-213 384-425 (693)
7 PF14803 Nudix_N_2: Nudix N-te 65.6 1.8 4E-05 29.8 -0.2 30 177-206 1-30 (34)
8 COG5641 GAT1 GATA Zn-finger-co 60.5 4 8.6E-05 42.7 1.0 36 176-211 297-333 (498)
9 PRK03988 translation initiatio 60.0 2.8 6E-05 36.8 -0.2 30 176-206 102-131 (138)
10 smart00653 eIF2B_5 domain pres 57.1 3.4 7.5E-05 34.9 -0.1 29 177-206 81-109 (110)
11 TIGR00311 aIF-2beta translatio 56.9 3.4 7.4E-05 36.0 -0.1 29 177-206 98-126 (133)
12 PRK12336 translation initiatio 52.7 4.2 9.2E-05 37.2 -0.2 31 177-208 99-129 (201)
13 PF08271 TF_Zn_Ribbon: TFIIB z 50.1 4.9 0.00011 28.0 -0.2 27 178-207 2-28 (43)
14 KOG3740 Uncharacterized conser 49.1 7.6 0.00016 42.0 0.9 34 173-206 459-495 (706)
15 PF01873 eIF-5_eIF-2B: Domain 46.9 6.4 0.00014 33.9 -0.0 29 177-206 94-122 (125)
16 COG5347 GTPase-activating prot 45.4 8.9 0.00019 37.9 0.7 29 175-205 19-47 (319)
17 PF01412 ArfGap: Putative GTPa 37.7 22 0.00049 29.5 1.9 35 175-211 12-46 (116)
18 PRK12286 rpmF 50S ribosomal pr 34.3 13 0.00029 28.1 0.0 25 175-208 26-50 (57)
19 PF15396 FAM60A: Protein Famil 34.0 17 0.00037 34.4 0.7 15 199-213 50-64 (213)
20 PF11781 RRN7: RNA polymerase 34.0 19 0.00041 24.9 0.7 28 174-206 6-33 (36)
21 COG3529 Predicted nucleic-acid 33.6 12 0.00026 29.5 -0.3 38 175-212 9-46 (66)
22 PF06677 Auto_anti-p27: Sjogre 33.0 17 0.00036 26.0 0.3 27 174-205 15-41 (41)
23 KOG1598 Transcription initiati 32.8 23 0.0005 37.4 1.5 28 177-207 1-28 (521)
24 PRK00423 tfb transcription ini 31.2 21 0.00046 34.4 0.8 29 175-206 10-38 (310)
25 PF07282 OrfB_Zn_ribbon: Putat 31.1 23 0.0005 26.3 0.8 32 173-208 25-56 (69)
26 PF04161 Arv1: Arv1-like famil 29.5 21 0.00046 32.5 0.5 29 178-206 2-32 (208)
27 COG2816 NPY1 NTP pyrophosphohy 29.2 20 0.00044 35.1 0.3 31 174-208 109-139 (279)
28 PLN03114 ADP-ribosylation fact 28.2 29 0.00063 35.5 1.2 29 175-205 21-49 (395)
29 smart00105 ArfGap Putative GTP 26.6 46 0.001 27.5 2.0 33 176-210 3-35 (112)
30 PRK14892 putative transcriptio 25.9 21 0.00045 29.9 -0.2 34 176-210 21-54 (99)
31 COG4260 Membrane protease subu 25.7 35 0.00075 34.2 1.2 30 174-206 313-342 (345)
32 PF09526 DUF2387: Probable met 25.6 21 0.00046 28.2 -0.2 34 175-208 7-40 (71)
33 PF01096 TFIIS_C: Transcriptio 25.4 7.3 0.00016 27.1 -2.5 31 178-208 2-38 (39)
34 COG3952 Predicted membrane pro 24.8 19 0.00042 31.1 -0.6 18 189-208 76-93 (113)
35 PF12760 Zn_Tnp_IS1595: Transp 24.5 33 0.00071 24.2 0.6 27 176-205 18-44 (46)
36 PF09297 zf-NADH-PPase: NADH p 24.2 17 0.00036 23.9 -0.9 28 176-207 3-30 (32)
37 PRK00085 recO DNA repair prote 24.1 35 0.00077 30.8 0.9 29 176-205 149-177 (247)
38 PF09723 Zn-ribbon_8: Zinc rib 24.0 25 0.00054 24.6 -0.1 28 178-206 7-34 (42)
39 PF09889 DUF2116: Uncharacteri 23.5 78 0.0017 24.4 2.5 31 176-214 3-34 (59)
40 PF01783 Ribosomal_L32p: Ribos 23.2 23 0.0005 26.3 -0.4 23 175-206 25-47 (56)
41 PRK00420 hypothetical protein; 23.1 37 0.0008 29.1 0.8 30 175-209 22-51 (112)
42 smart00440 ZnF_C2C2 C2C2 Zinc 23.1 20 0.00044 25.0 -0.7 31 178-208 2-38 (40)
43 TIGR01385 TFSII transcription 22.9 26 0.00055 34.3 -0.3 37 173-209 255-297 (299)
44 KOG0703 Predicted GTPase-activ 22.3 33 0.00071 33.8 0.3 27 176-204 25-51 (287)
45 COG1405 SUA7 Transcription ini 21.7 36 0.00077 33.1 0.5 28 177-207 2-29 (285)
46 PRK06556 vitamin B12-dependent 21.3 32 0.0007 38.8 0.1 27 174-206 922-948 (953)
47 PF13248 zf-ribbon_3: zinc-rib 21.1 62 0.0013 20.5 1.3 22 177-206 3-24 (26)
48 PHA02998 RNA polymerase subuni 20.0 33 0.00072 32.1 -0.1 36 175-210 142-183 (195)
No 1
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.41 E-value=1.4e-13 Score=101.82 Aligned_cols=35 Identities=60% Similarity=1.237 Sum_probs=32.8
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHhHHHHhhh
Q 021178 178 ICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 212 (316)
Q Consensus 178 ~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~rk~~ 212 (316)
.|++|++++||+||+||.|...|||||||||++..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999999999999999888999999999998875
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.35 E-value=3.6e-13 Score=98.61 Aligned_cols=39 Identities=56% Similarity=1.136 Sum_probs=35.6
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHhHHHHhhhh
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARK 213 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~rk~~k 213 (316)
..+.|++|++++||+||+||.|...|||||||||++...
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 468899999999999999999987999999999988754
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.35 E-value=1.9e-13 Score=93.29 Aligned_cols=34 Identities=56% Similarity=1.235 Sum_probs=27.2
Q ss_pred cccCCCCCCCccccCCCCCCccchhHhHHHHhhh
Q 021178 179 CSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 212 (316)
Q Consensus 179 CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~rk~~ 212 (316)
|++|++++||+||++|.|...|||||||+|++.+
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 8999999999999999997779999999998864
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.54 E-value=3.4e-08 Score=84.28 Aligned_cols=37 Identities=68% Similarity=1.399 Sum_probs=34.8
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHhHHHHhhh
Q 021178 176 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 212 (316)
Q Consensus 176 ~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~rk~~ 212 (316)
...|.+|+++.||+||+++.|+..+|||||++|++..
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGG 235 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcC
Confidence 6899999999999999999998899999999998874
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.85 E-value=6.6e-06 Score=83.99 Aligned_cols=40 Identities=45% Similarity=1.004 Sum_probs=33.9
Q ss_pred CCCcccccCCCCCCCccccCCC-----CCCccchhHhHHHHhhhhh
Q 021178 174 NTVRICSDCNTTTTPLWRSGPR-----GPKSLCNACGIRQRKARKA 214 (316)
Q Consensus 174 ~~~~~CsnC~Tt~TPlWRrGP~-----G~~~LCNACGL~~rk~~k~ 214 (316)
....+|.||.|+.||+|||+.. | -+|||||||+++.+...
T Consensus 156 ~~~~vc~Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~ 200 (498)
T COG5641 156 NQPHVCSNCKTTSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSP 200 (498)
T ss_pred cccchhccccccCCccccccccccccCC-ccccccccccccccCCc
Confidence 3445999999999999999999 6 68999999999766543
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=83.05 E-value=1.2 Score=46.75 Aligned_cols=40 Identities=30% Similarity=0.530 Sum_probs=31.6
Q ss_pred CCCcccccCCCCCCCccc--cCCCCCCccchhHhHHHHhhhh
Q 021178 174 NTVRICSDCNTTTTPLWR--SGPRGPKSLCNACGIRQRKARK 213 (316)
Q Consensus 174 ~~~~~CsnC~Tt~TPlWR--rGP~G~~~LCNACGL~~rk~~k 213 (316)
..++.|.+|+|++.-+|- -+|+-...||-.|=+||+|...
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygG 425 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGG 425 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHHhcC
Confidence 347899999999999993 3444445699999999998743
No 7
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=65.57 E-value=1.8 Score=29.77 Aligned_cols=30 Identities=23% Similarity=0.656 Sum_probs=15.3
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 177 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 177 ~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
+.|.+|+..-+..--.|.+-.+.+|.+||.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 359999987543333456666679999984
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=60.46 E-value=4 Score=42.67 Aligned_cols=36 Identities=33% Similarity=0.477 Sum_probs=28.7
Q ss_pred CcccccCCC-CCCCccccCCCCCCccchhHhHHHHhh
Q 021178 176 VRICSDCNT-TTTPLWRSGPRGPKSLCNACGIRQRKA 211 (316)
Q Consensus 176 ~~~CsnC~T-t~TPlWRrGP~G~~~LCNACGL~~rk~ 211 (316)
...|.+|.+ +.||.||+...-.-++||+||++.+..
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~ 333 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPP 333 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCc
Confidence 567888887 789999998766578999999876444
No 9
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=59.99 E-value=2.8 Score=36.77 Aligned_cols=30 Identities=33% Similarity=0.684 Sum_probs=22.3
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 176 VRICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 176 ~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
--.|..|+...|-+=+.+..- -..|+|||-
T Consensus 102 yVlC~~C~spdT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeE-EEEcccCCC
Confidence 357999999999997753322 235999996
No 10
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=57.07 E-value=3.4 Score=34.86 Aligned_cols=29 Identities=28% Similarity=0.606 Sum_probs=21.7
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 177 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 177 ~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
..|..|+...|-+=+.+..- -..|+|||-
T Consensus 81 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeE-EEEccccCC
Confidence 57999999999998763222 224999994
No 11
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=56.85 E-value=3.4 Score=35.98 Aligned_cols=29 Identities=34% Similarity=0.766 Sum_probs=21.8
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 177 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 177 ~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
..|..|+...|-+-+.+.-- -..|+|||-
T Consensus 98 VlC~~C~sPdT~l~k~~r~~-~l~C~ACGa 126 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVS-LLKCEACGA 126 (133)
T ss_pred EECCCCCCCCcEEEEeCCeE-EEecccCCC
Confidence 57999999999998753321 235999996
No 12
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=52.74 E-value=4.2 Score=37.23 Aligned_cols=31 Identities=32% Similarity=0.620 Sum_probs=22.8
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHhHHH
Q 021178 177 RICSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 208 (316)
Q Consensus 177 ~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~ 208 (316)
-.|..|+...|-+-+.+..- -.-|+|||-..
T Consensus 99 V~C~~C~~pdT~l~k~~~~~-~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVL-MLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCCcEEEEcCCeE-EEEcccCCCCc
Confidence 57999999999997764221 23499999743
No 13
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=50.11 E-value=4.9 Score=27.99 Aligned_cols=27 Identities=26% Similarity=0.829 Sum_probs=18.2
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHhHH
Q 021178 178 ICSDCNTTTTPLWRSGPRGPKSLCNACGIR 207 (316)
Q Consensus 178 ~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~ 207 (316)
.|.+|+.+. ..+- ...| ..+|..||+-
T Consensus 2 ~Cp~Cg~~~-~~~D-~~~g-~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFD-PERG-ELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEE-TTTT-EEEETTT-BB
T ss_pred CCcCCcCCc-eEEc-CCCC-eEECCCCCCE
Confidence 699999977 3333 3345 6799999973
No 14
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.09 E-value=7.6 Score=41.96 Aligned_cols=34 Identities=24% Similarity=0.634 Sum_probs=27.9
Q ss_pred CCCCcccccCCCCCCCccccCCCC---CCccchhHhH
Q 021178 173 NNTVRICSDCNTTTTPLWRSGPRG---PKSLCNACGI 206 (316)
Q Consensus 173 ~~~~~~CsnC~Tt~TPlWRrGP~G---~~~LCNACGL 206 (316)
.+..-.|..|.|.-||.|+.-+.+ ...+|.+|--
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvt 495 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVT 495 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhh
Confidence 456789999999999999987776 3368999954
No 15
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=46.89 E-value=6.4 Score=33.90 Aligned_cols=29 Identities=31% Similarity=0.684 Sum_probs=22.5
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 177 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 177 ~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
-.|..|+..+|-+=+.+..- -.-|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccCC
Confidence 57999999999998774433 345999994
No 16
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=45.40 E-value=8.9 Score=37.93 Aligned_cols=29 Identities=34% Similarity=0.833 Sum_probs=25.9
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHh
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACG 205 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACG 205 (316)
.-..|++|++.. |.|-.-.-| -.||-.|.
T Consensus 19 ~Nk~CaDCga~~-P~W~S~nlG-vfiCi~Ca 47 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVNLG-VFLCIDCA 47 (319)
T ss_pred ccCccccCCCCC-CceEecccC-eEEEeecc
Confidence 356799999999 999999999 79999993
No 17
>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=37.69 E-value=22 Score=29.46 Aligned_cols=35 Identities=31% Similarity=0.686 Sum_probs=22.9
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHhHHHHhh
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKA 211 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~rk~ 211 (316)
.-..|++|+.. -|.|-.-.-| -.||-.|.-..+..
T Consensus 12 ~N~~CaDCg~~-~p~w~s~~~G-iflC~~Cag~HR~l 46 (116)
T PF01412_consen 12 GNKVCADCGAP-NPTWASLNYG-IFLCLECAGIHRSL 46 (116)
T ss_dssp TCTB-TTT-SB-S--EEETTTT-EEE-HHHHHHHHHH
T ss_pred CcCcCCCCCCC-CCCEEEeecC-hhhhHHHHHHHHHh
Confidence 34779999955 4599999989 78999998665554
No 18
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=34.32 E-value=13 Score=28.09 Aligned_cols=25 Identities=24% Similarity=0.792 Sum_probs=19.2
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHhHHH
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 208 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~ 208 (316)
..-.|.+||...-| +.+|..||.|-
T Consensus 26 ~l~~C~~CG~~~~~---------H~vC~~CG~Y~ 50 (57)
T PRK12286 26 GLVECPNCGEPKLP---------HRVCPSCGYYK 50 (57)
T ss_pred cceECCCCCCccCC---------eEECCCCCcCC
Confidence 45679999987654 56999999753
No 19
>PF15396 FAM60A: Protein Family FAM60A
Probab=34.02 E-value=17 Score=34.43 Aligned_cols=15 Identities=33% Similarity=0.793 Sum_probs=11.2
Q ss_pred ccchhHhHHHHhhhh
Q 021178 199 SLCNACGIRQRKARK 213 (316)
Q Consensus 199 ~LCNACGL~~rk~~k 213 (316)
.+||||-|..++-++
T Consensus 50 eICNACVLLVKRwKK 64 (213)
T PF15396_consen 50 EICNACVLLVKRWKK 64 (213)
T ss_pred hhhHHHHHHHHHHhh
Confidence 499999997765443
No 20
>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=33.98 E-value=19 Score=24.94 Aligned_cols=28 Identities=25% Similarity=0.681 Sum_probs=20.9
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 174 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 174 ~~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
+....|..|+.. |-...+| ...|..||-
T Consensus 6 ~~~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 344569999987 5556678 689999984
No 21
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.65 E-value=12 Score=29.51 Aligned_cols=38 Identities=21% Similarity=0.367 Sum_probs=26.8
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHhHHHHhhh
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 212 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~rk~~ 212 (316)
.+..|-.|.+..|-.|.+-..-+..-|-+||...+...
T Consensus 9 AGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~~~ 46 (66)
T COG3529 9 AGAVCPACQAQDTLAMWRENNVEIVECVKCGHHMREAD 46 (66)
T ss_pred ccCCCcccchhhHHHHHHhcCCceEehhhcchHhhhcc
Confidence 45679999999987754444343556999998765543
No 22
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=33.00 E-value=17 Score=26.03 Aligned_cols=27 Identities=44% Similarity=0.892 Sum_probs=20.1
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHh
Q 021178 174 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACG 205 (316)
Q Consensus 174 ~~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACG 205 (316)
.....|..| .+|+.| ..+| +.+|-+|+
T Consensus 15 ML~~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 15 MLDEHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred HhcCccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 345679999 589999 3456 67999985
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=32.81 E-value=23 Score=37.44 Aligned_cols=28 Identities=25% Similarity=0.692 Sum_probs=19.7
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHhHH
Q 021178 177 RICSDCNTTTTPLWRSGPRGPKSLCNACGIR 207 (316)
Q Consensus 177 ~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~ 207 (316)
+.|.||+.+.=-. +...| ...|.+||.-
T Consensus 1 ~~C~~C~~s~fe~--d~a~g-~~~C~~CG~v 28 (521)
T KOG1598|consen 1 MVCKNCGGSNFER--DEATG-NLYCTACGTV 28 (521)
T ss_pred CcCCCCCCCCccc--ccccC-Cceeccccce
Confidence 4699999876332 33446 5789999974
No 24
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=31.17 E-value=21 Score=34.37 Aligned_cols=29 Identities=24% Similarity=0.819 Sum_probs=17.4
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
....|.+|+.+ ..+.. -..| ..+|..||+
T Consensus 10 ~~~~Cp~Cg~~-~iv~d-~~~G-e~vC~~CG~ 38 (310)
T PRK00423 10 EKLVCPECGSD-KLIYD-YERG-EIVCADCGL 38 (310)
T ss_pred cCCcCcCCCCC-CeeEE-CCCC-eEeecccCC
Confidence 34568888852 23233 3456 577888887
No 25
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=31.10 E-value=23 Score=26.31 Aligned_cols=32 Identities=22% Similarity=0.525 Sum_probs=22.8
Q ss_pred CCCCcccccCCCCCCCccccCCCCCCccchhHhHHH
Q 021178 173 NNTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 208 (316)
Q Consensus 173 ~~~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~ 208 (316)
.+....|..|+..... ...+....|..||..+
T Consensus 25 ~~TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKK----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred CCCccCccCccccccc----ccccceEEcCCCCCEE
Confidence 3456779999987755 3344456899999864
No 26
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=29.54 E-value=21 Score=32.54 Aligned_cols=29 Identities=31% Similarity=0.763 Sum_probs=23.1
Q ss_pred ccccCCCCCCCccccCCCCCC--ccchhHhH
Q 021178 178 ICSDCNTTTTPLWRSGPRGPK--SLCNACGI 206 (316)
Q Consensus 178 ~CsnC~Tt~TPlWRrGP~G~~--~LCNACGL 206 (316)
+|.+|+.....++|.-..|.- +.|..||-
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 699999999999998665533 35999983
No 27
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.24 E-value=20 Score=35.06 Aligned_cols=31 Identities=32% Similarity=0.716 Sum_probs=24.3
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHhHHH
Q 021178 174 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 208 (316)
Q Consensus 174 ~~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~ 208 (316)
..-+.|..||+...+. ..|-..+|+.||.++
T Consensus 109 ~~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCGRCGTKTYPR----EGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCCCCCCcCccc----cCceeeeCCCCCCcc
Confidence 4578899999998875 445567999999865
No 28
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=28.17 E-value=29 Score=35.53 Aligned_cols=29 Identities=41% Similarity=0.890 Sum_probs=24.5
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHh
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACG 205 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACG 205 (316)
.-..|.+|+... |.|-.-.-| -.||..|.
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CS 49 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCS 49 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhh
Confidence 356699999875 999999999 78999993
No 29
>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=26.64 E-value=46 Score=27.49 Aligned_cols=33 Identities=33% Similarity=0.671 Sum_probs=26.7
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHhHHHHh
Q 021178 176 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 210 (316)
Q Consensus 176 ~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~rk 210 (316)
-..|++|+. .-|.|-.-.-| -.||-.|.-..+.
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~ 35 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRS 35 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHh
Confidence 467999998 55999998889 6899999765544
No 30
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.93 E-value=21 Score=29.91 Aligned_cols=34 Identities=15% Similarity=0.411 Sum_probs=21.1
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHhHHHHh
Q 021178 176 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 210 (316)
Q Consensus 176 ~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~rk 210 (316)
.-.|.+|+...-+. ..+....+..|-.||.|+..
T Consensus 21 ~f~CP~Cge~~v~v-~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 21 IFECPRCGKVSISV-KIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred EeECCCCCCeEeee-ecCCCcceEECCCCCCccCE
Confidence 56699999532221 11223446789999998744
No 31
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=25.72 E-value=35 Score=34.23 Aligned_cols=30 Identities=27% Similarity=0.720 Sum_probs=21.9
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 174 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 174 ~~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
.....|.+|+...|+-.-.|. --+|-+||-
T Consensus 313 ~k~nfc~ncG~~~t~~~~ng~---a~fcp~cgq 342 (345)
T COG4260 313 AKLNFCLNCGCGTTADFDNGK---AKFCPECGQ 342 (345)
T ss_pred cccccccccCcccccCCccch---hhhChhhcC
Confidence 345589999988888644444 349999984
No 32
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=25.56 E-value=21 Score=28.16 Aligned_cols=34 Identities=18% Similarity=0.394 Sum_probs=25.8
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHhHHH
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 208 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~ 208 (316)
.+-.|-.|.+..|.+|.+.......-|-+||...
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred cCccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 4668999999999886555445344599999865
No 33
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=25.39 E-value=7.3 Score=27.05 Aligned_cols=31 Identities=26% Similarity=0.614 Sum_probs=18.3
Q ss_pred ccccCCCCCCCcc----ccCCCCCC--ccchhHhHHH
Q 021178 178 ICSDCNTTTTPLW----RSGPRGPK--SLCNACGIRQ 208 (316)
Q Consensus 178 ~CsnC~Tt~TPlW----RrGP~G~~--~LCNACGL~~ 208 (316)
.|.+|+-.+.-.| |++.++.- +.|..||-.|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 5888988776555 55665522 2599998654
No 34
>COG3952 Predicted membrane protein [Function unknown]
Probab=24.83 E-value=19 Score=31.07 Aligned_cols=18 Identities=33% Similarity=0.492 Sum_probs=13.7
Q ss_pred ccccCCCCCCccchhHhHHH
Q 021178 189 LWRSGPRGPKSLCNACGIRQ 208 (316)
Q Consensus 189 lWRrGP~G~~~LCNACGL~~ 208 (316)
+||.+|-+ .+|++||++.
T Consensus 76 i~~~DpV~--Vl~~~~glF~ 93 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFI 93 (113)
T ss_pred HHhcchHH--HHHHhhhHHH
Confidence 46667766 5999999975
No 35
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=24.51 E-value=33 Score=24.23 Aligned_cols=27 Identities=30% Similarity=0.668 Sum_probs=19.4
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHh
Q 021178 176 VRICSDCNTTTTPLWRSGPRGPKSLCNACG 205 (316)
Q Consensus 176 ~~~CsnC~Tt~TPlWRrGP~G~~~LCNACG 205 (316)
+.+|.+|+.+ ...|.++ .+ ..-|++|+
T Consensus 18 g~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~ 44 (46)
T PF12760_consen 18 GFVCPHCGST-KHYRLKT-RG-RYRCKACR 44 (46)
T ss_pred CCCCCCCCCe-eeEEeCC-CC-eEECCCCC
Confidence 3679999998 5555555 34 56799996
No 36
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=24.19 E-value=17 Score=23.93 Aligned_cols=28 Identities=36% Similarity=0.837 Sum_probs=15.3
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHhHH
Q 021178 176 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIR 207 (316)
Q Consensus 176 ~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~ 207 (316)
-+.|..|+....+. +.|...+|.+||..
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcCE
Confidence 36788999877665 33545689999864
No 37
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=24.07 E-value=35 Score=30.81 Aligned_cols=29 Identities=24% Similarity=0.660 Sum_probs=24.0
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhHh
Q 021178 176 VRICSDCNTTTTPLWRSGPRGPKSLCNACG 205 (316)
Q Consensus 176 ~~~CsnC~Tt~TPlWRrGP~G~~~LCNACG 205 (316)
...|..|+......|-.-..| +.+|..|+
T Consensus 149 l~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 149 LDHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred hhhHhcCCCCCCceEEecccC-Cccccccc
Confidence 457999998877777777777 78999997
No 38
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=24.04 E-value=25 Score=24.63 Aligned_cols=28 Identities=21% Similarity=0.489 Sum_probs=18.8
Q ss_pred ccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 178 ICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 178 ~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
.|..|+..-+-+..-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 58888876665554444 43567888875
No 39
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=23.49 E-value=78 Score=24.38 Aligned_cols=31 Identities=29% Similarity=0.649 Sum_probs=22.7
Q ss_pred CcccccCCCCCCCccccCCCCCCccc-hhHhHHHHhhhhh
Q 021178 176 VRICSDCNTTTTPLWRSGPRGPKSLC-NACGIRQRKARKA 214 (316)
Q Consensus 176 ~~~CsnC~Tt~TPlWRrGP~G~~~LC-NACGL~~rk~~k~ 214 (316)
-+-|.+||...-| . +.+| ..|+-.|.+.++.
T Consensus 3 HkHC~~CG~~Ip~-------~-~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 3 HKHCPVCGKPIPP-------D-ESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CCcCCcCCCcCCc-------c-hhhhCHHHHHHHHHHHHH
Confidence 3569999966543 2 5699 6999988777654
No 40
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=23.19 E-value=23 Score=26.34 Aligned_cols=23 Identities=26% Similarity=0.852 Sum_probs=16.8
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
....|.+||... -++.+|.+||.
T Consensus 25 ~l~~c~~cg~~~---------~~H~vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------LPHRVCPSCGY 47 (56)
T ss_dssp SEEESSSSSSEE---------STTSBCTTTBB
T ss_pred ceeeeccCCCEe---------cccEeeCCCCe
Confidence 467899999533 23579999994
No 41
>PRK00420 hypothetical protein; Validated
Probab=23.13 E-value=37 Score=29.13 Aligned_cols=30 Identities=23% Similarity=0.521 Sum_probs=22.0
Q ss_pred CCcccccCCCCCCCccccCCCCCCccchhHhHHHH
Q 021178 175 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQR 209 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~~r 209 (316)
....|..|+ +|+.|- ..| +.+|-.||-.+.
T Consensus 22 l~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 446799998 677764 445 679999998653
No 42
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.09 E-value=20 Score=25.04 Aligned_cols=31 Identities=26% Similarity=0.654 Sum_probs=20.5
Q ss_pred ccccCCCCCCCcc----ccCCCCCC--ccchhHhHHH
Q 021178 178 ICSDCNTTTTPLW----RSGPRGPK--SLCNACGIRQ 208 (316)
Q Consensus 178 ~CsnC~Tt~TPlW----RrGP~G~~--~LCNACGL~~ 208 (316)
.|.+|+-.+.-.| |++.++.- +.|-.||-.|
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 5888887665555 55665522 2588898766
No 43
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=22.93 E-value=26 Score=34.34 Aligned_cols=37 Identities=22% Similarity=0.525 Sum_probs=25.7
Q ss_pred CCCCcccccCCCCCCCcc----ccCCCCCC--ccchhHhHHHH
Q 021178 173 NNTVRICSDCNTTTTPLW----RSGPRGPK--SLCNACGIRQR 209 (316)
Q Consensus 173 ~~~~~~CsnC~Tt~TPlW----RrGP~G~~--~LCNACGL~~r 209 (316)
......|..|+-.....| |.+.++-- +.|..||-+|+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 345688999998887766 44444421 26999998874
No 44
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=22.26 E-value=33 Score=33.82 Aligned_cols=27 Identities=33% Similarity=0.874 Sum_probs=24.2
Q ss_pred CcccccCCCCCCCccccCCCCCCccchhH
Q 021178 176 VRICSDCNTTTTPLWRSGPRGPKSLCNAC 204 (316)
Q Consensus 176 ~~~CsnC~Tt~TPlWRrGP~G~~~LCNAC 204 (316)
-+.|++|++. .|.|-.---| .-+|-.|
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C 51 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRC 51 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeec
Confidence 5679999999 9999998889 6789999
No 45
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=21.74 E-value=36 Score=33.15 Aligned_cols=28 Identities=29% Similarity=0.776 Sum_probs=18.5
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHhHH
Q 021178 177 RICSDCNTTTTPLWRSGPRGPKSLCNACGIR 207 (316)
Q Consensus 177 ~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL~ 207 (316)
..|.+|+.+ -.=+.-..| ..+|-.||+-
T Consensus 2 ~~CpeCg~~--~~~~d~~~g-e~VC~~CG~V 29 (285)
T COG1405 2 MSCPECGST--NIITDYERG-EIVCADCGLV 29 (285)
T ss_pred CCCCCCCCc--cceeeccCC-eEEeccCCEE
Confidence 469999988 222222356 6889999873
No 46
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=21.26 E-value=32 Score=38.76 Aligned_cols=27 Identities=26% Similarity=0.703 Sum_probs=19.6
Q ss_pred CCCcccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 174 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 174 ~~~~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
...+.|.+|++.- -++|..++|..||.
T Consensus 922 ~~~~~c~~c~~~~------~~~g~c~~c~~cg~ 948 (953)
T PRK06556 922 ADAPLCPTCGTKM------VRNGSCYVCEGCGS 948 (953)
T ss_pred ccCCcCCCccCee------eECCceEeccCCCC
Confidence 3456699997533 24577889999995
No 47
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.05 E-value=62 Score=20.52 Aligned_cols=22 Identities=23% Similarity=0.813 Sum_probs=14.9
Q ss_pred cccccCCCCCCCccccCCCCCCccchhHhH
Q 021178 177 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 206 (316)
Q Consensus 177 ~~CsnC~Tt~TPlWRrGP~G~~~LCNACGL 206 (316)
..|.+|++... .+ ..+|-.||-
T Consensus 3 ~~Cp~Cg~~~~-------~~-~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEID-------PD-AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCC-------cc-cccChhhCC
Confidence 57889988432 23 358888885
No 48
>PHA02998 RNA polymerase subunit; Provisional
Probab=20.02 E-value=33 Score=32.10 Aligned_cols=36 Identities=19% Similarity=0.457 Sum_probs=27.9
Q ss_pred CCcccccCCCCCCCcc----ccCCCCCC--ccchhHhHHHHh
Q 021178 175 TVRICSDCNTTTTPLW----RSGPRGPK--SLCNACGIRQRK 210 (316)
Q Consensus 175 ~~~~CsnC~Tt~TPlW----RrGP~G~~--~LCNACGL~~rk 210 (316)
....|..|+-..+-.| |++.++.- ..|-.||-.|+.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 6788999999887766 77777632 259999998844
Done!