Query 023724
Match_columns 278
No_of_seqs 175 out of 720
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 06:11:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023724.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023724hhsearch_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 2.3E-14 4.9E-19 104.3 2.2 38 140-177 1-38 (54)
2 PF00320 GATA: GATA zinc finge 99.4 2.1E-14 4.5E-19 96.5 1.4 35 141-175 1-35 (36)
3 smart00401 ZnF_GATA zinc finge 99.4 2.9E-14 6.3E-19 102.7 1.8 40 137-176 2-41 (52)
4 KOG1601 GATA-4/5/6 transcripti 98.7 6.7E-09 1.5E-13 86.8 1.7 37 138-174 199-235 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.8 4.1E-06 8.8E-11 84.1 -0.5 39 138-177 158-201 (498)
6 KOG3554 Histone deacetylase co 84.6 0.7 1.5E-05 47.6 2.6 41 136-176 384-426 (693)
7 PF14803 Nudix_N_2: Nudix N-te 76.0 0.69 1.5E-05 31.3 -0.4 30 139-168 1-30 (34)
8 KOG3740 Uncharacterized conser 63.7 3.1 6.7E-05 44.1 0.9 34 135-168 459-495 (706)
9 COG5641 GAT1 GATA Zn-finger-co 61.2 3.5 7.7E-05 42.3 0.8 36 138-173 297-333 (498)
10 COG5347 GTPase-activating prot 60.0 3.8 8.2E-05 39.7 0.8 28 137-166 19-46 (319)
11 PRK03988 translation initiatio 58.3 2.9 6.4E-05 36.0 -0.3 30 138-168 102-131 (138)
12 PF08271 TF_Zn_Ribbon: TFIIB z 56.6 2.8 6E-05 28.7 -0.6 27 140-169 2-28 (43)
13 TIGR00311 aIF-2beta translatio 56.5 3.3 7.2E-05 35.4 -0.3 30 138-168 97-126 (133)
14 smart00653 eIF2B_5 domain pres 55.3 3.6 7.9E-05 34.1 -0.2 30 138-168 80-109 (110)
15 PF01412 ArfGap: Putative GTPa 54.7 12 0.00025 30.6 2.6 36 137-174 12-47 (116)
16 PRK12336 translation initiatio 52.0 4.2 9.2E-05 36.5 -0.3 32 138-170 98-129 (201)
17 COG3529 Predicted nucleic-acid 47.5 5.7 0.00012 30.8 -0.2 37 138-174 10-46 (66)
18 PF01873 eIF-5_eIF-2B: Domain 44.3 6.4 0.00014 33.3 -0.4 28 139-167 94-121 (125)
19 PRK12286 rpmF 50S ribosomal pr 43.3 7.9 0.00017 28.8 -0.0 25 136-169 25-49 (57)
20 smart00105 ArfGap Putative GTP 42.9 18 0.0004 29.3 2.1 34 138-173 3-36 (112)
21 PF06677 Auto_anti-p27: Sjogre 41.5 9.5 0.00021 26.8 0.2 25 138-167 17-41 (41)
22 KOG0703 Predicted GTPase-activ 40.3 11 0.00023 36.4 0.4 27 138-166 25-51 (287)
23 PF09889 DUF2116: Uncharacteri 40.2 32 0.0007 26.0 2.8 33 138-178 3-36 (59)
24 PLN03114 ADP-ribosylation fact 39.8 17 0.00037 36.5 1.7 29 137-167 21-49 (395)
25 PRK14892 putative transcriptio 37.1 9.4 0.0002 31.4 -0.5 35 137-172 20-54 (99)
26 COG3952 Predicted membrane pro 36.2 9.3 0.0002 32.4 -0.6 19 151-171 76-94 (113)
27 PF15396 FAM60A: Protein Famil 33.4 16 0.00035 34.0 0.4 19 161-179 50-68 (213)
28 smart00778 Prim_Zn_Ribbon Zinc 33.3 24 0.00052 24.3 1.1 29 138-167 3-32 (37)
29 PF07282 OrfB_Zn_ribbon: Putat 32.3 20 0.00043 26.2 0.6 32 136-171 26-57 (69)
30 PF11781 RRN7: RNA polymerase 32.3 21 0.00045 24.3 0.7 28 136-168 6-33 (36)
31 PF09526 DUF2387: Probable met 31.9 13 0.00027 28.9 -0.5 35 138-172 8-42 (71)
32 PF12760 Zn_Tnp_IS1595: Transp 31.6 20 0.00043 24.9 0.5 27 138-167 18-44 (46)
33 PRK00423 tfb transcription ini 31.5 19 0.00042 34.0 0.6 28 138-168 11-38 (310)
34 PF04810 zf-Sec23_Sec24: Sec23 30.7 20 0.00044 24.4 0.4 31 138-168 2-32 (40)
35 PRK00420 hypothetical protein; 28.9 24 0.00052 29.7 0.7 30 138-172 23-52 (112)
36 PF06689 zf-C4_ClpX: ClpX C4-t 27.9 26 0.00057 24.1 0.6 32 139-171 2-35 (41)
37 COG2816 NPY1 NTP pyrophosphohy 27.8 21 0.00046 34.3 0.2 31 136-170 109-139 (279)
38 KOG1598 Transcription initiati 27.4 32 0.0007 35.8 1.4 31 139-172 1-31 (521)
39 PRK00085 recO DNA repair prote 27.4 27 0.00059 30.9 0.8 30 137-167 148-177 (247)
40 KOG0909 Peptide:N-glycanase [P 25.0 29 0.00062 35.8 0.5 31 138-168 161-202 (500)
41 TIGR01385 TFSII transcription 24.6 25 0.00054 33.8 0.0 35 137-171 257-297 (299)
42 COG4260 Membrane protease subu 24.4 43 0.00093 33.1 1.6 29 137-168 314-342 (345)
43 PF09723 Zn-ribbon_8: Zinc rib 24.3 21 0.00045 24.5 -0.4 28 140-168 7-34 (42)
44 PF03991 Prion_octapep: Copper 24.0 39 0.00084 16.8 0.6 7 36-42 1-7 (8)
45 PF14122 YokU: YokU-like prote 23.9 16 0.00035 29.8 -1.2 33 140-172 1-47 (87)
46 PF12773 DZR: Double zinc ribb 23.0 41 0.00089 23.0 0.9 27 137-168 11-37 (50)
47 PLN03119 putative ADP-ribosyla 22.8 39 0.00084 35.9 1.0 30 137-168 22-51 (648)
48 TIGR02443 conserved hypothetic 22.6 24 0.00052 26.9 -0.4 34 138-171 9-42 (59)
49 PF13248 zf-ribbon_3: zinc-rib 22.6 52 0.0011 20.5 1.2 22 139-168 3-24 (26)
50 PLN03131 hypothetical protein; 22.5 40 0.00087 36.2 1.0 30 137-168 22-51 (705)
51 COG1405 SUA7 Transcription ini 21.4 35 0.00076 32.6 0.3 22 257-278 113-136 (285)
52 PF04161 Arv1: Arv1-like famil 21.3 39 0.00084 30.3 0.6 34 139-172 1-36 (208)
53 PF01783 Ribosomal_L32p: Ribos 21.2 18 0.0004 26.4 -1.2 24 137-170 25-48 (56)
54 PF10083 DUF2321: Uncharacteri 21.1 45 0.00097 29.9 0.9 41 137-177 38-85 (158)
55 PF05876 Terminase_GpA: Phage 21.0 41 0.00089 34.6 0.7 39 137-175 199-244 (557)
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=99.46 E-value=2.3e-14 Score=104.25 Aligned_cols=38 Identities=55% Similarity=1.104 Sum_probs=34.4
Q ss_pred ccccCCCCCCCccccCCCCCcccchHHHHHHHHhhhhh
Q 023724 140 ICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARKAM 177 (278)
Q Consensus 140 ~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK~~k~~ 177 (278)
.|+||++++||+||+||.|..+|||||||||++....+
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~r 38 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMR 38 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCCC
Confidence 59999999999999999888999999999999887443
No 2
>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=99.45 E-value=2.1e-14 Score=96.49 Aligned_cols=35 Identities=57% Similarity=1.230 Sum_probs=27.9
Q ss_pred cccCCCCCCCccccCCCCCcccchHHHHHHHHhhh
Q 023724 141 CSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARK 175 (278)
Q Consensus 141 CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK~~k 175 (278)
|++|+|++||+||++|.|..+|||||||+|++.+.
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 89999999999999999988899999999998753
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.44 E-value=2.9e-14 Score=102.66 Aligned_cols=40 Identities=55% Similarity=1.098 Sum_probs=36.8
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHHHHHHHhhhh
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKARKA 176 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK~~k~ 176 (278)
..+.|++|++++||+||+||.|+.+|||||||+|++....
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 4689999999999999999999889999999999987765
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.67 E-value=6.7e-09 Score=86.82 Aligned_cols=37 Identities=68% Similarity=1.399 Sum_probs=35.2
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHHHHHHhh
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 174 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK~~ 174 (278)
...|.+|+++.||+||+++.|+..+|||||++|++..
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGG 235 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcC
Confidence 5899999999999999999999999999999999885
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.79 E-value=4.1e-06 Score=84.06 Aligned_cols=39 Identities=44% Similarity=0.983 Sum_probs=33.6
Q ss_pred CcccccCCCCCCCccccCCC-----CCcccchHHHHHHHHhhhhh
Q 023724 138 VRICSDCNTTTTPLWRSGPR-----GPKSLCNACGIRQRKARKAM 177 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~-----G~~~LCNACGL~yrK~~k~~ 177 (278)
..+|.||.|+.||+|||+.. | -+|||||||+|+-....+
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r 201 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSPR 201 (498)
T ss_pred cchhccccccCCccccccccccccCC-ccccccccccccccCCcC
Confidence 45999999999999999999 6 689999999996655444
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=84.60 E-value=0.7 Score=47.63 Aligned_cols=41 Identities=29% Similarity=0.509 Sum_probs=34.2
Q ss_pred CCCcccccCCCCCCCcc--ccCCCCCcccchHHHHHHHHhhhh
Q 023724 136 NTVRICSDCNTTTTPLW--RSGPRGPKSLCNACGIRQRKARKA 176 (278)
Q Consensus 136 ~~~~~CsnC~tt~TP~W--RrGP~G~~~LCNACGL~yrK~~k~ 176 (278)
...+.|-+|+|++.-+| ..+|+-...||-.|=++|+|...+
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 34789999999999999 556666678999999999997653
No 7
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=75.95 E-value=0.69 Score=31.27 Aligned_cols=30 Identities=23% Similarity=0.656 Sum_probs=16.1
Q ss_pred cccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 139 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 139 ~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
+.|.+|++.-+-.--.|.+-.+.+|.+||.
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 469999987544444667777889999983
No 8
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.74 E-value=3.1 Score=44.05 Aligned_cols=34 Identities=24% Similarity=0.634 Sum_probs=28.7
Q ss_pred CCCCcccccCCCCCCCccccCCCC---CcccchHHHH
Q 023724 135 NNTVRICSDCNTTTTPLWRSGPRG---PKSLCNACGI 168 (278)
Q Consensus 135 ~~~~~~CsnC~tt~TP~WRrGP~G---~~~LCNACGL 168 (278)
.+....|..|.|.-||.|+..+.+ .+++|.+|--
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 345789999999999999988877 4689999954
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=61.20 E-value=3.5 Score=42.28 Aligned_cols=36 Identities=33% Similarity=0.477 Sum_probs=28.8
Q ss_pred CcccccCCC-CCCCccccCCCCCcccchHHHHHHHHh
Q 023724 138 VRICSDCNT-TTTPLWRSGPRGPKSLCNACGIRQRKA 173 (278)
Q Consensus 138 ~~~CsnC~t-t~TP~WRrGP~G~~~LCNACGL~yrK~ 173 (278)
...|.+|.+ +.||.||+...-.-++|||||++-+..
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~ 333 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPP 333 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCc
Confidence 567888877 789999888776579999999976543
No 10
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=60.03 E-value=3.8 Score=39.73 Aligned_cols=28 Identities=36% Similarity=0.857 Sum_probs=26.2
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHH
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNAC 166 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNAC 166 (278)
.-..|.+|++.. |+|-.-.-| ..||--|
T Consensus 19 ~Nk~CaDCga~~-P~W~S~nlG-vfiCi~C 46 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVNLG-VFLCIDC 46 (319)
T ss_pred ccCccccCCCCC-CceEecccC-eEEEeec
Confidence 467899999999 999999999 7999999
No 11
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=58.34 E-value=2.9 Score=35.96 Aligned_cols=30 Identities=33% Similarity=0.684 Sum_probs=23.0
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
--.|..|+...|-+=+.+..= -.-|+|||-
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 468999999999998753321 358999994
No 12
>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=56.57 E-value=2.8 Score=28.71 Aligned_cols=27 Identities=26% Similarity=0.839 Sum_probs=16.1
Q ss_pred ccccCCCCCCCccccCCCCCcccchHHHHH
Q 023724 140 ICSDCNTTTTPLWRSGPRGPKSLCNACGIR 169 (278)
Q Consensus 140 ~CsnC~tt~TP~WRrGP~G~~~LCNACGL~ 169 (278)
.|.+|+.+. -.+ ....| ..+|..||+-
T Consensus 2 ~Cp~Cg~~~-~~~-D~~~g-~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVF-DPERG-ELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEE-ETTTT-EEEETTT-BB
T ss_pred CCcCCcCCc-eEE-cCCCC-eEECCCCCCE
Confidence 588888866 222 23345 5688888853
No 13
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=56.53 E-value=3.3 Score=35.44 Aligned_cols=30 Identities=33% Similarity=0.728 Sum_probs=22.7
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
--.|..|+..+|-+-+.+.- --.-|+|||-
T Consensus 97 yVlC~~C~sPdT~l~k~~r~-~~l~C~ACGa 126 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGRV-SLLKCEACGA 126 (133)
T ss_pred eEECCCCCCCCcEEEEeCCe-EEEecccCCC
Confidence 36899999999999875322 1247999994
No 14
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=55.35 E-value=3.6 Score=34.09 Aligned_cols=30 Identities=27% Similarity=0.574 Sum_probs=22.6
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
--.|..|+..+|-+=+.+..= -.-|+|||-
T Consensus 80 yVlC~~C~spdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSPDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred cEECCCCCCCCcEEEEeCCeE-EEEccccCC
Confidence 368999999999998873221 246999994
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=54.70 E-value=12 Score=30.58 Aligned_cols=36 Identities=31% Similarity=0.658 Sum_probs=24.9
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHHHHHHHhh
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 174 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK~~ 174 (278)
.-+.|++|+.. -|.|-.-..| ..||-.|.-..|...
T Consensus 12 ~N~~CaDCg~~-~p~w~s~~~G-iflC~~Cag~HR~lg 47 (116)
T PF01412_consen 12 GNKVCADCGAP-NPTWASLNYG-IFLCLECAGIHRSLG 47 (116)
T ss_dssp TCTB-TTT-SB-S--EEETTTT-EEE-HHHHHHHHHHT
T ss_pred CcCcCCCCCCC-CCCEEEeecC-hhhhHHHHHHHHHhc
Confidence 45899999854 5699999999 789999987776554
No 16
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=51.99 E-value=4.2 Score=36.55 Aligned_cols=32 Identities=31% Similarity=0.589 Sum_probs=24.0
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 170 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~y 170 (278)
--.|..|+..+|-+-+.+..= -.-|+|||-..
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 368999999999998764221 34799999654
No 17
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=47.47 E-value=5.7 Score=30.79 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=29.4
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHHHHHHhh
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKAR 174 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK~~ 174 (278)
+..|..|.+..|-+|.+...=+..-|-+||...+..-
T Consensus 10 GA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~~~ 46 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENNVEIVECVKCGHHMREAD 46 (66)
T ss_pred cCCCcccchhhHHHHHHhcCCceEehhhcchHhhhcc
Confidence 5689999999998876666655789999998875443
No 18
>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=44.35 E-value=6.4 Score=33.29 Aligned_cols=28 Identities=32% Similarity=0.718 Sum_probs=22.9
Q ss_pred cccccCCCCCCCccccCCCCCcccchHHH
Q 023724 139 RICSDCNTTTTPLWRSGPRGPKSLCNACG 167 (278)
Q Consensus 139 ~~CsnC~tt~TP~WRrGP~G~~~LCNACG 167 (278)
-.|..|+..+|-+=+.+..= -.-|+|||
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCG 121 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACG 121 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTS
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccC
Confidence 57999999999998874433 46899998
No 19
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=43.28 E-value=7.9 Score=28.81 Aligned_cols=25 Identities=24% Similarity=0.760 Sum_probs=19.9
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchHHHHH
Q 023724 136 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIR 169 (278)
Q Consensus 136 ~~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~ 169 (278)
...-.|.+||...-| +.+|..||.|
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 456789999987755 6899999954
No 20
>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=42.90 E-value=18 Score=29.29 Aligned_cols=34 Identities=32% Similarity=0.640 Sum_probs=28.7
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHHHHHHh
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRKA 173 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK~ 173 (278)
-..|.+|+. .-|.|-.-..| ..||-.|.-..|..
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 468999998 56999999999 78999997776654
No 21
>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=41.48 E-value=9.5 Score=26.79 Aligned_cols=25 Identities=48% Similarity=1.010 Sum_probs=19.5
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACG 167 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACG 167 (278)
...|..| .+|+.| ..+| ..+|-+|+
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 4678888 589999 4466 68999985
No 22
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=40.27 E-value=11 Score=36.44 Aligned_cols=27 Identities=33% Similarity=0.874 Sum_probs=25.1
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNAC 166 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNAC 166 (278)
-+.|++|++. .|.|-.---| .-+|--|
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 6789999999 9999999999 7899999
No 23
>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=40.21 E-value=32 Score=25.98 Aligned_cols=33 Identities=30% Similarity=0.668 Sum_probs=25.3
Q ss_pred CcccccCCCCCCCccccCCCCCcccc-hHHHHHHHHhhhhhH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLC-NACGIRQRKARKAMQ 178 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LC-NACGL~yrK~~k~~~ 178 (278)
-+-|.+||...-| + ...| ..|+--|.+.+++.+
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 3679999976654 3 6799 599999998877654
No 24
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=39.83 E-value=17 Score=36.48 Aligned_cols=29 Identities=41% Similarity=0.890 Sum_probs=25.3
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHH
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACG 167 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACG 167 (278)
.-+.|.+|+... |.|-.-..| ..||..|.
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 457899999865 999999999 78999993
No 25
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=37.13 E-value=9.4 Score=31.39 Aligned_cols=35 Identities=14% Similarity=0.336 Sum_probs=22.7
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHHHHHHH
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 172 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK 172 (278)
..-.|.+|+...-+.=+ +...++..|..||.|+..
T Consensus 20 t~f~CP~Cge~~v~v~~-~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKVSISVKI-KKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCeEeeeec-CCCcceEECCCCCCccCE
Confidence 35679999953222211 223457899999999754
No 26
>COG3952 Predicted membrane protein [Function unknown]
Probab=36.24 E-value=9.3 Score=32.42 Aligned_cols=19 Identities=32% Similarity=0.434 Sum_probs=14.9
Q ss_pred ccccCCCCCcccchHHHHHHH
Q 023724 151 LWRSGPRGPKSLCNACGIRQR 171 (278)
Q Consensus 151 ~WRrGP~G~~~LCNACGL~yr 171 (278)
.||.+|-+ .||++||++-.
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 36777777 69999999763
No 27
>PF15396 FAM60A: Protein Family FAM60A
Probab=33.44 E-value=16 Score=34.03 Aligned_cols=19 Identities=26% Similarity=0.569 Sum_probs=15.2
Q ss_pred ccchHHHHHHHHhhhhhHH
Q 023724 161 SLCNACGIRQRKARKAMQA 179 (278)
Q Consensus 161 ~LCNACGL~yrK~~k~~~~ 179 (278)
-+||||-|..++-.+++..
T Consensus 50 eICNACVLLVKRwKKLP~G 68 (213)
T PF15396_consen 50 EICNACVLLVKRWKKLPPG 68 (213)
T ss_pred hhhHHHHHHHHHHhhCCCC
Confidence 5999999998887766653
No 28
>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=33.32 E-value=24 Score=24.35 Aligned_cols=29 Identities=24% Similarity=0.649 Sum_probs=21.6
Q ss_pred CcccccCCCCCCCccccC-CCCCcccchHHH
Q 023724 138 VRICSDCNTTTTPLWRSG-PRGPKSLCNACG 167 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrG-P~G~~~LCNACG 167 (278)
...|..|+.+..=.|... ..| ..+|+.||
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 457999999887777553 335 67999996
No 29
>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=32.27 E-value=20 Score=26.16 Aligned_cols=32 Identities=22% Similarity=0.525 Sum_probs=23.6
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchHHHHHHH
Q 023724 136 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQR 171 (278)
Q Consensus 136 ~~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yr 171 (278)
+....|+.|+..... ...+....|..||..+.
T Consensus 26 ~TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CCccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 457889999987655 34444679999998754
No 30
>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=32.26 E-value=21 Score=24.27 Aligned_cols=28 Identities=25% Similarity=0.681 Sum_probs=21.3
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 136 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 136 ~~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
+....|..|+.. |-...+| ...|..||-
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 6666778 789999984
No 31
>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=31.91 E-value=13 Score=28.91 Aligned_cols=35 Identities=20% Similarity=0.436 Sum_probs=28.4
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHHHHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 172 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK 172 (278)
+-.|..|.+..|-.|.+..+-...-|-+||.....
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 56899999999988766666667899999987653
No 32
>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=31.56 E-value=20 Score=24.89 Aligned_cols=27 Identities=30% Similarity=0.668 Sum_probs=19.9
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACG 167 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACG 167 (278)
+..|.+|+.+ ..-|.++ .+ ..-|++|+
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 4679999998 5555555 34 67899996
No 33
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=31.45 E-value=19 Score=33.98 Aligned_cols=28 Identities=29% Similarity=0.801 Sum_probs=14.6
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
...|.+|+. ++.--.-..| .++|..||+
T Consensus 11 ~~~Cp~Cg~--~~iv~d~~~G-e~vC~~CG~ 38 (310)
T PRK00423 11 KLVCPECGS--DKLIYDYERG-EIVCADCGL 38 (310)
T ss_pred CCcCcCCCC--CCeeEECCCC-eEeecccCC
Confidence 445666664 2232223445 466666666
No 34
>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=30.66 E-value=20 Score=24.41 Aligned_cols=31 Identities=26% Similarity=0.606 Sum_probs=19.7
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
+.+|.+|++---|--+=...|..-.||-|+.
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 5689999998888877777776779999985
No 35
>PRK00420 hypothetical protein; Validated
Probab=28.94 E-value=24 Score=29.67 Aligned_cols=30 Identities=23% Similarity=0.516 Sum_probs=23.0
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHHHHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 172 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK 172 (278)
...|..|+ +|+.|- ..| ...|-+||-.+.-
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 47798898 677774 456 6899999987653
No 36
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=27.92 E-value=26 Score=24.14 Aligned_cols=32 Identities=28% Similarity=0.661 Sum_probs=19.9
Q ss_pred cccccCCCCCCCc--cccCCCCCcccchHHHHHHH
Q 023724 139 RICSDCNTTTTPL--WRSGPRGPKSLCNACGIRQR 171 (278)
Q Consensus 139 ~~CsnC~tt~TP~--WRrGP~G~~~LCNACGL~yr 171 (278)
+.|+-|+.+.+.. .=.||.| ..+|+.|-....
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~~~ 35 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQAY 35 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHHHH
Confidence 5799999987644 2368877 689999976543
No 37
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=27.79 E-value=21 Score=34.32 Aligned_cols=31 Identities=32% Similarity=0.716 Sum_probs=24.4
Q ss_pred CCCcccccCCCCCCCccccCCCCCcccchHHHHHH
Q 023724 136 NTVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 170 (278)
Q Consensus 136 ~~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~y 170 (278)
...+.|..||+...|. ..|-+.+|+.||.++
T Consensus 109 ~~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCGRCGTKTYPR----EGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCCCCCCcCccc----cCceeeeCCCCCCcc
Confidence 3578999999988774 345568999999876
No 38
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=27.42 E-value=32 Score=35.81 Aligned_cols=31 Identities=26% Similarity=0.664 Sum_probs=21.3
Q ss_pred cccccCCCCCCCccccCCCCCcccchHHHHHHHH
Q 023724 139 RICSDCNTTTTPLWRSGPRGPKSLCNACGIRQRK 172 (278)
Q Consensus 139 ~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yrK 172 (278)
+.|.||+.+.-- |+...| ...|.+||.-...
T Consensus 1 ~~C~~C~~s~fe--~d~a~g-~~~C~~CG~v~E~ 31 (521)
T KOG1598|consen 1 MVCKNCGGSNFE--RDEATG-NLYCTACGTVLEY 31 (521)
T ss_pred CcCCCCCCCCcc--cccccC-Cceeccccceeec
Confidence 479999986522 233556 5899999985543
No 39
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=27.37 E-value=27 Score=30.92 Aligned_cols=30 Identities=23% Similarity=0.638 Sum_probs=25.3
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHH
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACG 167 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACG 167 (278)
....|..|++.....|-.-.+| +.+|..|+
T Consensus 148 ~l~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 148 DLDHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred chhhHhcCCCCCCceEEecccC-Cccccccc
Confidence 4578999999887778877888 78999997
No 40
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=24.99 E-value=29 Score=35.82 Aligned_cols=31 Identities=29% Similarity=0.594 Sum_probs=22.2
Q ss_pred CcccccCCCCC-CCccccCCCCCc----------ccchHHHH
Q 023724 138 VRICSDCNTTT-TPLWRSGPRGPK----------SLCNACGI 168 (278)
Q Consensus 138 ~~~CsnC~tt~-TP~WRrGP~G~~----------~LCNACGL 168 (278)
...|.+|+... +++-+-+|.+.. +.||+||.
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~ 202 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGT 202 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCC
Confidence 57899999977 555554454422 68999987
No 41
>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=24.55 E-value=25 Score=33.78 Aligned_cols=35 Identities=23% Similarity=0.539 Sum_probs=25.2
Q ss_pred CCcccccCCCCCCCcc----ccCCCCC--cccchHHHHHHH
Q 023724 137 TVRICSDCNTTTTPLW----RSGPRGP--KSLCNACGIRQR 171 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~W----RrGP~G~--~~LCNACGL~yr 171 (278)
....|..|+-...--| |+..++- -+.|..||-+|+
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 4689999998877665 4455442 238999998874
No 42
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=24.35 E-value=43 Score=33.06 Aligned_cols=29 Identities=28% Similarity=0.748 Sum_probs=21.9
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
....|.+|+...|+-.-. |..-.|-+||-
T Consensus 314 k~nfc~ncG~~~t~~~~n---g~a~fcp~cgq 342 (345)
T COG4260 314 KLNFCLNCGCGTTADFDN---GKAKFCPECGQ 342 (345)
T ss_pred ccccccccCcccccCCcc---chhhhChhhcC
Confidence 456999999988886544 44459999984
No 43
>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=24.32 E-value=21 Score=24.53 Aligned_cols=28 Identities=21% Similarity=0.489 Sum_probs=15.4
Q ss_pred ccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 140 ICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 140 ~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
.|..|+..-+-+..-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 57777765544433333 33456777764
No 44
>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=24.03 E-value=39 Score=16.77 Aligned_cols=7 Identities=29% Similarity=0.444 Sum_probs=5.2
Q ss_pred cCCCCCc
Q 023724 36 AGGGSSD 42 (278)
Q Consensus 36 ~~~gs~~ 42 (278)
||||.|.
T Consensus 1 phgG~Wg 7 (8)
T PF03991_consen 1 PHGGGWG 7 (8)
T ss_pred CCCCcCC
Confidence 6888874
No 45
>PF14122 YokU: YokU-like protein
Probab=23.92 E-value=16 Score=29.81 Aligned_cols=33 Identities=24% Similarity=0.731 Sum_probs=21.4
Q ss_pred ccccCCCCC-----CCccccCCCC---------CcccchHHHHHHHH
Q 023724 140 ICSDCNTTT-----TPLWRSGPRG---------PKSLCNACGIRQRK 172 (278)
Q Consensus 140 ~CsnC~tt~-----TP~WRrGP~G---------~~~LCNACGL~yrK 172 (278)
.|..|+..+ +.....-|+| |...|+.||+-|-.
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~ 47 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQD 47 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEeh
Confidence 388888753 3333344555 44689999998754
No 46
>PF12773 DZR: Double zinc ribbon
Probab=22.96 E-value=41 Score=23.05 Aligned_cols=27 Identities=30% Similarity=0.842 Sum_probs=15.3
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
....|.+|++.-. .+.....+|..||-
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcC
Confidence 3567777777665 22232456666664
No 47
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=22.76 E-value=39 Score=35.95 Aligned_cols=30 Identities=27% Similarity=0.497 Sum_probs=25.6
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
.-+.|.+|+... |.|-.-..| ..||-.|.=
T Consensus 22 gNk~CADCgs~~-P~WASiNlG-IFICi~CSG 51 (648)
T PLN03119 22 PNRRCINCNSLG-PQYVCTTFW-TFVCMACSG 51 (648)
T ss_pred CCCccccCCCCC-CCceeeccc-eEEeccchh
Confidence 458999999866 999999999 789999943
No 48
>TIGR02443 conserved hypothetical metal-binding protein. 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=22.64 E-value=24 Score=26.92 Aligned_cols=34 Identities=18% Similarity=0.388 Sum_probs=26.3
Q ss_pred CcccccCCCCCCCccccCCCCCcccchHHHHHHH
Q 023724 138 VRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQR 171 (278)
Q Consensus 138 ~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~yr 171 (278)
+-.|..|.+..|-.|.+...-...-|-.||....
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~ 42 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNIELVECVECGYQEQ 42 (59)
T ss_pred cccCCCCcCccEEEEEEeCCceEEEeccCCCccc
Confidence 5689999999988865544444679999997664
No 49
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.59 E-value=52 Score=20.47 Aligned_cols=22 Identities=23% Similarity=0.813 Sum_probs=13.6
Q ss_pred cccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 139 RICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 139 ~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
+.|.+|++... .+ ...|..||-
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 56888887432 23 347777774
No 50
>PLN03131 hypothetical protein; Provisional
Probab=22.48 E-value=40 Score=36.15 Aligned_cols=30 Identities=23% Similarity=0.472 Sum_probs=25.3
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHHH
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGI 168 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL 168 (278)
.-+.|.+|+.. -|.|-.-..| ..||-.|.=
T Consensus 22 gNk~CADCga~-~P~WASiNlG-IFICi~CSG 51 (705)
T PLN03131 22 PNRRCINCNSL-GPQFVCTNFW-TFICMTCSG 51 (705)
T ss_pred CCCccccCCCC-CCCeeEeccc-eEEchhchh
Confidence 45799999975 5999999999 789999943
No 51
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=21.41 E-value=35 Score=32.61 Aligned_cols=22 Identities=23% Similarity=0.335 Sum_probs=14.6
Q ss_pred CcccHHHHHH--HHHHhhcccccC
Q 023724 257 FPRDVEEAAI--LLMELSCGFSHT 278 (278)
Q Consensus 257 fp~d~~eAA~--LLM~LScGlv~~ 278 (278)
.|..+.|.|. ...++.-||++|
T Consensus 113 LP~~v~e~A~~iyr~a~~~~l~rG 136 (285)
T COG1405 113 LPESVRETAARIYRKAVDKGLLRG 136 (285)
T ss_pred CCchHHHHHHHHHHHHhhcCCCcC
Confidence 6777655554 446688888775
No 52
>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=21.27 E-value=39 Score=30.28 Aligned_cols=34 Identities=29% Similarity=0.642 Sum_probs=25.8
Q ss_pred cccccCCCCCCCccccCCCCC--cccchHHHHHHHH
Q 023724 139 RICSDCNTTTTPLWRSGPRGP--KSLCNACGIRQRK 172 (278)
Q Consensus 139 ~~CsnC~tt~TP~WRrGP~G~--~~LCNACGL~yrK 172 (278)
.+|.+|+..-..++|.-..|. -+.|..||-.-.|
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDk 36 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADK 36 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCcccc
Confidence 479999999888898876553 2689999864443
No 53
>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=21.22 E-value=18 Score=26.38 Aligned_cols=24 Identities=25% Similarity=0.778 Sum_probs=18.0
Q ss_pred CCcccccCCCCCCCccccCCCCCcccchHHHHHH
Q 023724 137 TVRICSDCNTTTTPLWRSGPRGPKSLCNACGIRQ 170 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRrGP~G~~~LCNACGL~y 170 (278)
....|.+||... -++.+|.+|| +|
T Consensus 25 ~l~~c~~cg~~~---------~~H~vc~~cG-~y 48 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------LPHRVCPSCG-YY 48 (56)
T ss_dssp SEEESSSSSSEE---------STTSBCTTTB-BS
T ss_pred ceeeeccCCCEe---------cccEeeCCCC-eE
Confidence 467899999643 3478999999 44
No 54
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.15 E-value=45 Score=29.91 Aligned_cols=41 Identities=24% Similarity=0.515 Sum_probs=27.2
Q ss_pred CCcccccCCCCCCCcccc-------CCCCCcccchHHHHHHHHhhhhh
Q 023724 137 TVRICSDCNTTTTPLWRS-------GPRGPKSLCNACGIRQRKARKAM 177 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRr-------GP~G~~~LCNACGL~yrK~~k~~ 177 (278)
.+..|.+|.+..--.|-- ++.-.-..|+.||..|=-.....
T Consensus 38 tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~~L 85 (158)
T PF10083_consen 38 TITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTENAL 85 (158)
T ss_pred HHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHHHHH
Confidence 467889998876555533 33334579999999875444333
No 55
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=20.96 E-value=41 Score=34.56 Aligned_cols=39 Identities=21% Similarity=0.566 Sum_probs=29.1
Q ss_pred CCcccccCCCCCCCcccc-------CCCCCcccchHHHHHHHHhhh
Q 023724 137 TVRICSDCNTTTTPLWRS-------GPRGPKSLCNACGIRQRKARK 175 (278)
Q Consensus 137 ~~~~CsnC~tt~TP~WRr-------GP~G~~~LCNACGL~yrK~~k 175 (278)
--..|.||+....+.|.. .|....+.|-.||-.+.-..+
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k 244 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDK 244 (557)
T ss_pred EEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHH
Confidence 457899999999998753 245567899999987654443
Done!