Query 021455
Match_columns 312
No_of_seqs 173 out of 735
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 03:05:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021455hhsearch_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 99.5 1.6E-14 3.5E-19 106.6 1.3 39 175-213 1-39 (54)
2 smart00401 ZnF_GATA zinc finge 99.4 2.4E-14 5.3E-19 104.6 1.5 40 172-211 2-41 (52)
3 PF00320 GATA: GATA zinc finge 99.4 2.3E-14 4.9E-19 97.7 1.2 35 176-210 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 98.7 7.5E-09 1.6E-13 88.1 2.1 37 173-209 199-235 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.9 1.6E-06 3.5E-11 88.2 -0.6 40 172-212 157-201 (498)
6 KOG3554 Histone deacetylase co 83.4 0.88 1.9E-05 47.6 2.8 39 171-209 384-424 (693)
7 PF14803 Nudix_N_2: Nudix N-te 70.0 1.1 2.5E-05 30.7 -0.5 30 174-203 1-30 (34)
8 COG5641 GAT1 GATA Zn-finger-co 69.0 1.2 2.7E-05 46.2 -0.7 41 173-213 297-338 (498)
9 PRK03988 translation initiatio 61.5 2.5 5.3E-05 37.0 -0.2 30 173-203 102-131 (138)
10 TIGR00311 aIF-2beta translatio 59.4 2.8 6.1E-05 36.4 -0.2 29 174-203 98-126 (133)
11 KOG3740 Uncharacterized conser 57.8 4.4 9.6E-05 43.6 0.9 35 170-204 459-496 (706)
12 smart00653 eIF2B_5 domain pres 57.4 3.3 7.1E-05 34.9 -0.1 29 174-203 81-109 (110)
13 COG5347 GTPase-activating prot 55.8 5.4 0.00012 39.3 1.0 32 173-206 20-51 (319)
14 PRK12336 translation initiatio 54.2 3.8 8.3E-05 37.5 -0.3 32 173-205 98-129 (201)
15 PF01412 ArfGap: Putative GTPa 54.2 12 0.00025 31.1 2.6 35 173-209 13-47 (116)
16 PF08271 TF_Zn_Ribbon: TFIIB z 48.1 4.7 0.0001 28.0 -0.5 26 175-203 2-27 (43)
17 COG3529 Predicted nucleic-acid 47.8 5.9 0.00013 31.2 -0.1 42 172-213 9-50 (66)
18 PF09889 DUF2116: Uncharacteri 46.4 23 0.0005 27.2 2.9 33 173-213 3-36 (59)
19 PF01873 eIF-5_eIF-2B: Domain 45.1 6.2 0.00014 33.9 -0.4 29 174-203 94-122 (125)
20 PF06677 Auto_anti-p27: Sjogre 44.9 8.5 0.00018 27.5 0.4 25 173-202 17-41 (41)
21 PF07282 OrfB_Zn_ribbon: Putat 44.2 10 0.00023 28.1 0.8 33 170-206 25-57 (69)
22 COG3952 Predicted membrane pro 41.6 6.8 0.00015 33.7 -0.6 19 186-206 76-94 (113)
23 PRK12286 rpmF 50S ribosomal pr 38.9 11 0.00024 28.5 0.2 25 171-204 25-49 (57)
24 PLN03114 ADP-ribosylation fact 38.1 18 0.00039 36.9 1.6 32 173-206 22-53 (395)
25 smart00105 ArfGap Putative GTP 37.0 28 0.0006 28.7 2.3 34 173-208 3-36 (112)
26 PRK00420 hypothetical protein; 33.6 18 0.0004 30.9 0.7 30 173-207 23-52 (112)
27 PF12760 Zn_Tnp_IS1595: Transp 32.8 19 0.0004 25.4 0.6 27 173-202 18-44 (46)
28 PRK14892 putative transcriptio 32.2 13 0.00028 31.1 -0.4 34 173-207 21-54 (99)
29 PF11781 RRN7: RNA polymerase 31.7 21 0.00045 24.7 0.6 28 171-203 6-33 (36)
30 COG0675 Transposase and inacti 28.1 28 0.0006 31.4 1.0 29 170-207 306-334 (364)
31 KOG1598 Transcription initiati 27.3 32 0.00069 36.4 1.3 30 174-206 1-30 (521)
32 PF09526 DUF2387: Probable met 27.2 18 0.00039 28.5 -0.3 36 172-207 7-42 (71)
33 KOG0703 Predicted GTPase-activ 26.3 26 0.00057 34.4 0.5 30 173-204 25-54 (287)
34 COG2816 NPY1 NTP pyrophosphohy 26.2 24 0.00052 34.5 0.2 30 173-206 111-140 (279)
35 PRK00423 tfb transcription ini 25.4 28 0.00061 33.5 0.6 29 173-204 11-39 (310)
36 PF03991 Prion_octapep: Copper 24.6 36 0.00079 17.1 0.6 7 67-73 1-7 (8)
37 PF09723 Zn-ribbon_8: Zinc rib 24.6 22 0.00047 24.9 -0.3 28 175-203 7-34 (42)
38 PF01783 Ribosomal_L32p: Ribos 24.5 17 0.00036 27.1 -0.9 22 172-202 25-46 (56)
39 PRK00085 recO DNA repair prote 24.2 35 0.00075 30.8 0.9 29 173-202 149-177 (247)
40 COG4260 Membrane protease subu 24.0 43 0.00093 33.5 1.5 30 171-203 313-342 (345)
41 PF04810 zf-Sec23_Sec24: Sec23 23.1 33 0.00072 23.7 0.4 31 173-203 2-32 (40)
42 TIGR01385 TFSII transcription 22.7 23 0.0005 34.6 -0.6 35 172-206 257-297 (299)
43 PRK12496 hypothetical protein; 22.5 39 0.00085 30.0 0.8 37 170-212 124-160 (164)
44 COG1601 GCD7 Translation initi 20.9 30 0.00066 30.9 -0.2 33 172-205 104-136 (151)
45 PHA02998 RNA polymerase subuni 20.8 32 0.0007 32.1 -0.0 40 168-207 138-183 (195)
46 smart00778 Prim_Zn_Ribbon Zinc 20.8 66 0.0014 22.6 1.5 29 173-202 3-32 (37)
47 PLN03131 hypothetical protein; 20.7 49 0.0011 36.1 1.2 33 173-207 23-55 (705)
48 PLN03119 putative ADP-ribosyla 20.3 50 0.0011 35.7 1.2 33 173-207 23-55 (648)
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=99.45 E-value=1.6e-14 Score=106.56 Aligned_cols=39 Identities=56% Similarity=1.099 Sum_probs=35.0
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHHHHHHhhHHHH
Q 021455 175 ACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARRAMQ 213 (312)
Q Consensus 175 ~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk~~k~~~ 213 (312)
.|+||++++||+||+||.|..+|||||||||++....++
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp 39 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRP 39 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCCC
Confidence 599999999999999998889999999999999664444
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.44 E-value=2.4e-14 Score=104.59 Aligned_cols=40 Identities=55% Similarity=1.121 Sum_probs=36.6
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhHHHHHHHhhHH
Q 021455 172 TMRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARRA 211 (312)
Q Consensus 172 ~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk~~k~ 211 (312)
.++.|+||+++.||+||+||.|+..|||||||||+++.+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 4788999999999999999999889999999999996654
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=99.44 E-value=2.3e-14 Score=97.73 Aligned_cols=35 Identities=54% Similarity=1.225 Sum_probs=28.1
Q ss_pred cccCCCCCCCccccCCCCCcccchhHHHHHHHhhH
Q 021455 176 CSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARR 210 (312)
Q Consensus 176 CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk~~k 210 (312)
|++|++++||+||+||.|..+|||||||+|+++++
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999987799999999999764
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.68 E-value=7.5e-09 Score=88.14 Aligned_cols=37 Identities=68% Similarity=1.423 Sum_probs=35.1
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHHHhh
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 209 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk~~ 209 (312)
...|.+|+++.||+||+++.|++.+|||||++|++..
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGG 235 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcC
Confidence 6899999999999999999998899999999999975
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.93 E-value=1.6e-06 Score=88.20 Aligned_cols=40 Identities=43% Similarity=0.926 Sum_probs=35.6
Q ss_pred CCcccccCCCCCCCccccCCC-----CCcccchhHHHHHHHhhHHH
Q 021455 172 TMRACSDCNTTTTPLWRSGPR-----GPKSLCNACGIRQRKARRAM 212 (312)
Q Consensus 172 ~~r~CsnC~Tt~TP~WRrGP~-----G~~~LCNACGL~~rk~~k~~ 212 (312)
...+|.||.|+.||+|||+.. | -+|||||||+|+.+.+.+
T Consensus 157 ~~~vc~Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r 201 (498)
T COG5641 157 QPHVCSNCKTTSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSPR 201 (498)
T ss_pred ccchhccccccCCccccccccccccCC-ccccccccccccccCCcC
Confidence 445999999999999999999 6 599999999999977666
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=83.37 E-value=0.88 Score=47.57 Aligned_cols=39 Identities=36% Similarity=0.653 Sum_probs=31.5
Q ss_pred CCCcccccCCCCCCCcc-ccCCCC-CcccchhHHHHHHHhh
Q 021455 171 NTMRACSDCNTTTTPLW-RSGPRG-PKSLCNACGIRQRKAR 209 (312)
Q Consensus 171 ~~~r~CsnC~Tt~TP~W-RrGP~G-~~~LCNACGL~~rk~~ 209 (312)
..++.|-+|+|++.-+| .-||.| .+.||-.|=+||+|..
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 44889999999999999 345444 4679999999999853
No 7
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=70.04 E-value=1.1 Score=30.70 Aligned_cols=30 Identities=23% Similarity=0.619 Sum_probs=15.7
Q ss_pred cccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 174 RACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 174 r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
+-|.+|+..-+-.--.|.+-.+.+|.+||.
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 359999987533333566666889999983
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=69.00 E-value=1.2 Score=46.20 Aligned_cols=41 Identities=29% Similarity=0.404 Sum_probs=31.2
Q ss_pred CcccccCCC-CCCCccccCCCCCcccchhHHHHHHHhhHHHH
Q 021455 173 MRACSDCNT-TTTPLWRSGPRGPKSLCNACGIRQRKARRAMQ 213 (312)
Q Consensus 173 ~r~CsnC~T-t~TP~WRrGP~G~~~LCNACGL~~rk~~k~~~ 213 (312)
...|.+|.+ +.||.||+...-.-++|||||++.+..+..++
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p 338 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRP 338 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcccccc
Confidence 456788877 77999988876667999999998776544433
No 9
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=61.50 E-value=2.5 Score=37.02 Aligned_cols=30 Identities=30% Similarity=0.640 Sum_probs=23.3
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
-..|..|+...|-+=+.+..= -..|+|||-
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 367999999999998753322 468999995
No 10
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=59.40 E-value=2.8 Score=36.43 Aligned_cols=29 Identities=31% Similarity=0.711 Sum_probs=22.6
Q ss_pred cccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 174 RACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 174 r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
..|..|+...|-+-+.+.-= -..|+|||-
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 67999999999998754321 358999995
No 11
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.80 E-value=4.4 Score=43.57 Aligned_cols=35 Identities=26% Similarity=0.638 Sum_probs=29.3
Q ss_pred CCCCcccccCCCCCCCccccCCCC---CcccchhHHHH
Q 021455 170 NNTMRACSDCNTTTTPLWRSGPRG---PKSLCNACGIR 204 (312)
Q Consensus 170 ~~~~r~CsnC~Tt~TP~WRrGP~G---~~~LCNACGL~ 204 (312)
..++-.|..|.|.-||.|+.-+.+ ++.+|.+|-.-
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtS 496 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTS 496 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhhh
Confidence 455788999999999999988777 35899999763
No 12
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=57.42 E-value=3.3 Score=34.92 Aligned_cols=29 Identities=28% Similarity=0.560 Sum_probs=22.6
Q ss_pred cccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 174 RACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 174 r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
..|..|+...|-+=+.+..= -.-|+|||-
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 57999999999999873322 356999994
No 13
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=55.76 E-value=5.4 Score=39.33 Aligned_cols=32 Identities=34% Similarity=0.751 Sum_probs=28.0
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQR 206 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~r 206 (312)
.+.|++|++.. |+|-.-.-| -.||--|-=-.|
T Consensus 20 Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHR 51 (319)
T COG5347 20 NKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHR 51 (319)
T ss_pred cCccccCCCCC-CceEecccC-eEEEeecchhhh
Confidence 56799999999 999999999 699999976544
No 14
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=54.22 E-value=3.8 Score=37.46 Aligned_cols=32 Identities=28% Similarity=0.549 Sum_probs=24.4
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 205 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~ 205 (312)
-..|..|+...|-+-+.+..= -.-|+|||-..
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~-~l~C~aCGa~~ 129 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVL-MLRCDACGAHR 129 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeE-EEEcccCCCCc
Confidence 367999999999998764222 35899999754
No 15
>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=54.20 E-value=12 Score=31.08 Aligned_cols=35 Identities=31% Similarity=0.658 Sum_probs=24.5
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHHHhh
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 209 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk~~ 209 (312)
.+.|++|+.. -|.|-.=..| -.||-.|.-..|...
T Consensus 13 N~~CaDCg~~-~p~w~s~~~G-iflC~~Cag~HR~lg 47 (116)
T PF01412_consen 13 NKVCADCGAP-NPTWASLNYG-IFLCLECAGIHRSLG 47 (116)
T ss_dssp CTB-TTT-SB-S--EEETTTT-EEE-HHHHHHHHHHT
T ss_pred cCcCCCCCCC-CCCEEEeecC-hhhhHHHHHHHHHhc
Confidence 5789999955 4599999999 699999998877644
No 16
>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=48.13 E-value=4.7 Score=28.03 Aligned_cols=26 Identities=27% Similarity=0.919 Sum_probs=16.1
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 175 ACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 175 ~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
.|.+|+.+. -.+ ....| ..+|..||+
T Consensus 2 ~Cp~Cg~~~-~~~-D~~~g-~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE-IVF-DPERG-ELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE-EEE-ETTTT-EEEETTT-B
T ss_pred CCcCCcCCc-eEE-cCCCC-eEECCCCCC
Confidence 588888866 223 23445 578888886
No 17
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=47.77 E-value=5.9 Score=31.16 Aligned_cols=42 Identities=19% Similarity=0.353 Sum_probs=30.7
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhHHHHHHHhhHHHH
Q 021455 172 TMRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARRAMQ 213 (312)
Q Consensus 172 ~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk~~k~~~ 213 (312)
.+..|-.|.+..|-+|.+-..-+..-|-+||...+..-+...
T Consensus 9 AGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~~~k~v~ 50 (66)
T COG3529 9 AGAVCPACQAQDTLAMWRENNVEIVECVKCGHHMREADKEVR 50 (66)
T ss_pred ccCCCcccchhhHHHHHHhcCCceEehhhcchHhhhccHHHH
Confidence 456799999999887555444447899999998866544433
No 18
>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=46.42 E-value=23 Score=27.19 Aligned_cols=33 Identities=27% Similarity=0.684 Sum_probs=25.9
Q ss_pred CcccccCCCCCCCccccCCCCCcccc-hhHHHHHHHhhHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLC-NACGIRQRKARRAMQ 213 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LC-NACGL~~rk~~k~~~ 213 (312)
-+.|.+||...-| + +..| ..|+-.|.+.+++..
T Consensus 3 HkHC~~CG~~Ip~-------~-~~fCS~~C~~~~~k~qk~~~ 36 (59)
T PF09889_consen 3 HKHCPVCGKPIPP-------D-ESFCSPKCREEYRKRQKRMR 36 (59)
T ss_pred CCcCCcCCCcCCc-------c-hhhhCHHHHHHHHHHHHHHH
Confidence 3679999987764 2 6899 599999988877655
No 19
>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=45.05 E-value=6.2 Score=33.90 Aligned_cols=29 Identities=31% Similarity=0.638 Sum_probs=23.5
Q ss_pred cccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 174 RACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 174 r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
..|..|+...|-+=+.+..= ..-|+|||-
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 56999999999998884443 478999993
No 20
>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=44.89 E-value=8.5 Score=27.49 Aligned_cols=25 Identities=48% Similarity=1.027 Sum_probs=19.2
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACG 202 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACG 202 (312)
...|..| .+|+.| ..+| +.+|-+|+
T Consensus 17 ~~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 4458889 499999 4456 68999985
No 21
>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=44.15 E-value=10 Score=28.12 Aligned_cols=33 Identities=21% Similarity=0.514 Sum_probs=24.0
Q ss_pred CCCCcccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 021455 170 NNTMRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQR 206 (312)
Q Consensus 170 ~~~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~r 206 (312)
.+....|..|+....- ...+....|..||..+.
T Consensus 25 ~~TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 25 AYTSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CCCccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 4457789999987655 34444689999998643
No 22
>COG3952 Predicted membrane protein [Function unknown]
Probab=41.57 E-value=6.8 Score=33.71 Aligned_cols=19 Identities=32% Similarity=0.434 Sum_probs=15.0
Q ss_pred ccccCCCCCcccchhHHHHHH
Q 021455 186 LWRSGPRGPKSLCNACGIRQR 206 (312)
Q Consensus 186 ~WRrGP~G~~~LCNACGL~~r 206 (312)
.||.+|-+ .+|++||++.-
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 36777777 79999999753
No 23
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=38.93 E-value=11 Score=28.48 Aligned_cols=25 Identities=24% Similarity=0.809 Sum_probs=19.7
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchhHHHH
Q 021455 171 NTMRACSDCNTTTTPLWRSGPRGPKSLCNACGIR 204 (312)
Q Consensus 171 ~~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~ 204 (312)
.....|.+||...-| +.+|..||.|
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcC
Confidence 346679999987755 6899999955
No 24
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=38.08 E-value=18 Score=36.90 Aligned_cols=32 Identities=38% Similarity=0.789 Sum_probs=26.3
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQR 206 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~r 206 (312)
.+.|.+|+... |.|-.-..| -.||-.|.=..|
T Consensus 22 Nk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHR 53 (395)
T PLN03114 22 NKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHR 53 (395)
T ss_pred CCcCccCCCCC-CCceeeccc-eeehhhhhHhhc
Confidence 56699999875 999999999 699999965443
No 25
>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=37.02 E-value=28 Score=28.74 Aligned_cols=34 Identities=32% Similarity=0.656 Sum_probs=29.1
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHHHh
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKA 208 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk~ 208 (312)
.+.|++|+. .-|.|-.-.-| -.||-.|.-..|..
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~l 36 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSL 36 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhc
Confidence 567999998 55999999999 69999998887764
No 26
>PRK00420 hypothetical protein; Validated
Probab=33.60 E-value=18 Score=30.90 Aligned_cols=30 Identities=23% Similarity=0.527 Sum_probs=23.1
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 207 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk 207 (312)
...|..|+ +|+.|- ..| +..|-+||-.+.-
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeeee
Confidence 35699999 788875 456 6899999987653
No 27
>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=32.84 E-value=19 Score=25.44 Aligned_cols=27 Identities=30% Similarity=0.629 Sum_probs=20.1
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACG 202 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACG 202 (312)
+.+|.+|+.+ ...|.++ .+ ..-|++|+
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 3669999998 5555555 34 58999997
No 28
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=32.19 E-value=13 Score=31.11 Aligned_cols=34 Identities=15% Similarity=0.431 Sum_probs=21.9
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 207 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk 207 (312)
.-.|.+|+...-+. ..+-..++..|-.||.|+-.
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 55699999532222 11223457999999998754
No 29
>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=31.65 E-value=21 Score=24.68 Aligned_cols=28 Identities=25% Similarity=0.716 Sum_probs=21.1
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 171 NTMRACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 171 ~~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
+....|..|+.. |-...+| ...|..||-
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 6666678 699999984
No 30
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.10 E-value=28 Score=31.39 Aligned_cols=29 Identities=24% Similarity=0.562 Sum_probs=22.0
Q ss_pred CCCCcccccCCCCCCCccccCCCCCcccchhHHHHHHH
Q 021455 170 NNTMRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 207 (312)
Q Consensus 170 ~~~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk 207 (312)
......|..||. ..+....|..||..+..
T Consensus 306 ~~tS~~C~~cg~---------~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 306 YYTSKTCPCCGH---------LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred CCCcccccccCC---------ccceeEECCCCCCeehh
Confidence 456788999999 33546799999986544
No 31
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=27.26 E-value=32 Score=36.40 Aligned_cols=30 Identities=27% Similarity=0.650 Sum_probs=20.9
Q ss_pred cccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 021455 174 RACSDCNTTTTPLWRSGPRGPKSLCNACGIRQR 206 (312)
Q Consensus 174 r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~r 206 (312)
+.|.||+.+.- . |+--.| -..|.+||.-..
T Consensus 1 ~~C~~C~~s~f-e-~d~a~g-~~~C~~CG~v~E 30 (521)
T KOG1598|consen 1 MVCKNCGGSNF-E-RDEATG-NLYCTACGTVLE 30 (521)
T ss_pred CcCCCCCCCCc-c-cccccC-Cceeccccceee
Confidence 47999998652 2 333556 489999998543
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=27.20 E-value=18 Score=28.49 Aligned_cols=36 Identities=19% Similarity=0.400 Sum_probs=28.4
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhHHHHHHH
Q 021455 172 TMRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 207 (312)
Q Consensus 172 ~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk 207 (312)
.+..|-.|.+..|-.|.+...-...-|-+||...+.
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred cCccCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 467899999999888655444557899999987765
No 33
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=26.35 E-value=26 Score=34.42 Aligned_cols=30 Identities=30% Similarity=0.682 Sum_probs=25.4
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIR 204 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~ 204 (312)
.+.|++|++. .|.|-.---| -.+|=.|-=-
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C~gi 54 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRCAGI 54 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeecccc
Confidence 5679999999 9999998999 6899888443
No 34
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=26.22 E-value=24 Score=34.55 Aligned_cols=30 Identities=33% Similarity=0.656 Sum_probs=22.4
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQR 206 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~r 206 (312)
-|-|..||+...|. ..|-..+|+.||.++-
T Consensus 111 ~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 111 HRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred CcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 56799999988763 3344689999998753
No 35
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=25.39 E-value=28 Score=33.46 Aligned_cols=29 Identities=28% Similarity=0.720 Sum_probs=16.5
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIR 204 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~ 204 (312)
...|.+|+. ++.--.-..| ..+|..||+-
T Consensus 11 ~~~Cp~Cg~--~~iv~d~~~G-e~vC~~CG~V 39 (310)
T PRK00423 11 KLVCPECGS--DKLIYDYERG-EIVCADCGLV 39 (310)
T ss_pred CCcCcCCCC--CCeeEECCCC-eEeecccCCc
Confidence 445777775 2332223456 5777777773
No 36
>PF03991 Prion_octapep: Copper binding octapeptide repeat; InterPro: IPR020949 Prion protein (PrP-c) [, , ] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) []. The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process. This repeat is found at the amino terminus of mammalian prion proteins. It has been shown to bind to copper [].
Probab=24.62 E-value=36 Score=17.12 Aligned_cols=7 Identities=29% Similarity=0.468 Sum_probs=5.4
Q ss_pred cCCCCCc
Q 021455 67 DHSGSSN 73 (312)
Q Consensus 67 ~~~gss~ 73 (312)
+|||+|.
T Consensus 1 phgG~Wg 7 (8)
T PF03991_consen 1 PHGGGWG 7 (8)
T ss_pred CCCCcCC
Confidence 6888884
No 37
>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=24.61 E-value=22 Score=24.88 Aligned_cols=28 Identities=21% Similarity=0.510 Sum_probs=17.6
Q ss_pred ccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 175 ACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 175 ~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
.|..|+..-+-+..-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 57788866655544333 44578888875
No 38
>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=24.50 E-value=17 Score=27.06 Aligned_cols=22 Identities=27% Similarity=0.942 Sum_probs=16.9
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhHH
Q 021455 172 TMRACSDCNTTTTPLWRSGPRGPKSLCNACG 202 (312)
Q Consensus 172 ~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACG 202 (312)
....|.+||... -++.+|.+||
T Consensus 25 ~l~~c~~cg~~~---------~~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------LPHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEE---------STTSBCTTTB
T ss_pred ceeeeccCCCEe---------cccEeeCCCC
Confidence 467899999643 3468999999
No 39
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=24.21 E-value=35 Score=30.81 Aligned_cols=29 Identities=24% Similarity=0.687 Sum_probs=24.2
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACG 202 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACG 202 (312)
...|..|+......|-.-..| ..+|..|+
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 557999998887777777777 69999997
No 40
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=24.03 E-value=43 Score=33.54 Aligned_cols=30 Identities=27% Similarity=0.695 Sum_probs=22.3
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 171 NTMRACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 171 ~~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
.....|.||+...|+-.-.|. --+|-+||-
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 345589999988888665444 459999984
No 41
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=23.08 E-value=33 Score=23.74 Aligned_cols=31 Identities=26% Similarity=0.619 Sum_probs=19.9
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGI 203 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL 203 (312)
+.+|.+|++---|.-+-...|..-.||-|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 4679999999888877777776789999986
No 42
>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=22.70 E-value=23 Score=34.56 Aligned_cols=35 Identities=23% Similarity=0.560 Sum_probs=25.3
Q ss_pred CCcccccCCCCCCCcc----ccCCCCC--cccchhHHHHHH
Q 021455 172 TMRACSDCNTTTTPLW----RSGPRGP--KSLCNACGIRQR 206 (312)
Q Consensus 172 ~~r~CsnC~Tt~TP~W----RrGP~G~--~~LCNACGL~~r 206 (312)
....|..|+-...-.| |...++- -+.|..||.+|+
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 4678999998887776 4444442 248999998875
No 43
>PRK12496 hypothetical protein; Provisional
Probab=22.47 E-value=39 Score=30.02 Aligned_cols=37 Identities=14% Similarity=0.419 Sum_probs=24.3
Q ss_pred CCCCcccccCCCCCCCccccCCCCCcccchhHHHHHHHhhHHH
Q 021455 170 NNTMRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARRAM 212 (312)
Q Consensus 170 ~~~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk~~k~~ 212 (312)
.....+|..|+.. +-.++.+ ..|.-||...++++.+.
T Consensus 124 ~~w~~~C~gC~~~----~~~~~~~--~~C~~CG~~~~r~~~~~ 160 (164)
T PRK12496 124 IKWRKVCKGCKKK----YPEDYPD--DVCEICGSPVKRKMVKR 160 (164)
T ss_pred eeeeEECCCCCcc----ccCCCCC--CcCCCCCChhhhcchhh
Confidence 3456789999943 2223333 58999999987765443
No 44
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=20.89 E-value=30 Score=30.94 Aligned_cols=33 Identities=24% Similarity=0.482 Sum_probs=26.1
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchhHHHHH
Q 021455 172 TMRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 205 (312)
Q Consensus 172 ~~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~ 205 (312)
.-..|.-|+...|++-+.+-.= ...|-|||-..
T Consensus 104 ~yv~C~~c~s~dt~l~~~~R~~-~l~c~acGa~~ 136 (151)
T COG1601 104 EYVKCKECGSPDTELIKEERLL-FLKCEACGAIR 136 (151)
T ss_pred heeEeccCCCCchhhhhhhhhH-hhHHHHhCCcc
Confidence 4577999999999999884433 47899999654
No 45
>PHA02998 RNA polymerase subunit; Provisional
Probab=20.82 E-value=32 Score=32.14 Aligned_cols=40 Identities=18% Similarity=0.469 Sum_probs=30.7
Q ss_pred CCCCCCcccccCCCCCCCcc----ccCCCCC--cccchhHHHHHHH
Q 021455 168 NSNNTMRACSDCNTTTTPLW----RSGPRGP--KSLCNACGIRQRK 207 (312)
Q Consensus 168 ~s~~~~r~CsnC~Tt~TP~W----RrGP~G~--~~LCNACGL~~rk 207 (312)
.+......|..|+-..+-.| |.+.++. -..|-.||-+|+-
T Consensus 138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 34446789999999988777 7777774 2489999998864
No 46
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=20.79 E-value=66 Score=22.57 Aligned_cols=29 Identities=24% Similarity=0.690 Sum_probs=20.8
Q ss_pred CcccccCCCCCCCccccC-CCCCcccchhHH
Q 021455 173 MRACSDCNTTTTPLWRSG-PRGPKSLCNACG 202 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrG-P~G~~~LCNACG 202 (312)
...|-.|+.+..=.|..- ..| ...|+.||
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G-~~~C~~Cg 32 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRG-TWFCSVCG 32 (37)
T ss_pred ccCCCCCCCccccccccCCCCc-CEEeCCCC
Confidence 356999998877667542 345 58999996
No 47
>PLN03131 hypothetical protein; Provisional
Probab=20.73 E-value=49 Score=36.07 Aligned_cols=33 Identities=24% Similarity=0.494 Sum_probs=26.6
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 207 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk 207 (312)
.+.|.+|+... |.|-.-.-| ..+|-.|.=..|.
T Consensus 23 Nk~CADCga~~-P~WASiNlG-IFICi~CSGIHRs 55 (705)
T PLN03131 23 NRRCINCNSLG-PQFVCTNFW-TFICMTCSGIHRE 55 (705)
T ss_pred CCccccCCCCC-CCeeEeccc-eEEchhchhhhcc
Confidence 56799999754 999998999 6999999765443
No 48
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=20.28 E-value=50 Score=35.69 Aligned_cols=33 Identities=27% Similarity=0.517 Sum_probs=26.9
Q ss_pred CcccccCCCCCCCccccCCCCCcccchhHHHHHHH
Q 021455 173 MRACSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 207 (312)
Q Consensus 173 ~r~CsnC~Tt~TP~WRrGP~G~~~LCNACGL~~rk 207 (312)
.+.|.+|+... |.|-.-.-| -.+|-.|.=..|.
T Consensus 23 Nk~CADCgs~~-P~WASiNlG-IFICi~CSGIHRs 55 (648)
T PLN03119 23 NRRCINCNSLG-PQYVCTTFW-TFVCMACSGIHRE 55 (648)
T ss_pred CCccccCCCCC-CCceeeccc-eEEeccchhhhcc
Confidence 46799999866 999999999 6999999755443
Done!