Query 024594
Match_columns 265
No_of_seqs 256 out of 921
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 05:52:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024594.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024594hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06200 tify: tify domain; I 99.7 2.3E-17 5E-22 109.0 4.9 34 71-104 2-35 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.6 4E-16 8.7E-21 111.7 3.7 48 206-255 1-49 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 2.2E-15 4.9E-20 107.0 3.0 46 204-251 3-49 (52)
4 PF00320 GATA: GATA zinc finge 99.5 2.3E-15 5E-20 99.3 1.3 36 207-244 1-36 (36)
5 PF06203 CCT: CCT motif; Inte 99.3 3.2E-12 7E-17 88.4 3.1 44 138-181 1-44 (45)
6 KOG1601 GATA-4/5/6 transcripti 98.6 1.6E-08 3.5E-13 87.9 3.1 46 204-251 199-244 (340)
7 COG5641 GAT1 GATA Zn-finger-co 98.3 2.8E-07 6E-12 91.7 2.2 56 201-258 155-215 (498)
8 PF09425 CCT_2: Divergent CCT 98.3 4E-07 8.7E-12 56.6 1.6 25 136-161 2-26 (27)
9 COG5641 GAT1 GATA Zn-finger-co 91.1 0.11 2.3E-06 52.5 1.5 52 204-256 297-348 (498)
10 KOG3554 Histone deacetylase co 83.1 1.5 3.3E-05 44.2 4.3 47 195-243 377-425 (693)
11 PF14803 Nudix_N_2: Nudix N-te 75.8 0.87 1.9E-05 29.8 0.0 30 205-236 1-30 (34)
12 PF01783 Ribosomal_L32p: Ribos 71.4 1.3 2.8E-05 31.7 0.0 26 204-241 26-51 (56)
13 PF13717 zinc_ribbon_4: zinc-r 65.7 1.5 3.3E-05 28.7 -0.6 33 205-238 3-35 (36)
14 KOG1601 GATA-4/5/6 transcripti 65.2 2.4 5.1E-05 36.7 0.4 41 135-175 290-330 (340)
15 PF01412 ArfGap: Putative GTPa 64.0 5.3 0.00011 32.3 2.2 36 204-243 13-48 (116)
16 PF06689 zf-C4_ClpX: ClpX C4-t 62.3 4.2 9.1E-05 27.3 1.1 32 205-237 2-33 (41)
17 PF09297 zf-NADH-PPase: NADH p 57.5 2.5 5.5E-05 26.6 -0.6 29 204-238 3-31 (32)
18 PF09889 DUF2116: Uncharacteri 57.3 4.9 0.00011 29.5 0.8 30 204-243 3-33 (59)
19 smart00653 eIF2B_5 domain pres 55.4 4.1 8.9E-05 33.2 0.1 28 205-236 81-109 (110)
20 PF06677 Auto_anti-p27: Sjogre 54.3 5.1 0.00011 27.2 0.4 25 204-235 17-41 (41)
21 TIGR02098 MJ0042_CXXC MJ0042 f 52.3 2.9 6.3E-05 27.0 -1.0 34 205-239 3-36 (38)
22 COG5349 Uncharacterized protei 51.1 5.7 0.00012 33.3 0.3 36 202-242 19-54 (126)
23 PRK05978 hypothetical protein; 49.7 6.4 0.00014 33.8 0.4 34 204-242 33-66 (148)
24 PF02701 zf-Dof: Dof domain, z 48.5 17 0.00036 27.1 2.4 47 204-252 5-54 (63)
25 PF08271 TF_Zn_Ribbon: TFIIB z 47.0 6.3 0.00014 26.4 -0.0 30 206-240 2-31 (43)
26 TIGR00311 aIF-2beta translatio 44.1 7.2 0.00016 32.9 -0.1 30 205-237 98-127 (133)
27 PRK03988 translation initiatio 43.8 7.4 0.00016 33.0 -0.1 30 205-237 103-132 (138)
28 KOG2691 RNA polymerase II subu 43.5 6.4 0.00014 32.3 -0.5 88 150-239 17-112 (113)
29 PRK00420 hypothetical protein; 43.1 11 0.00023 31.0 0.8 31 204-241 23-53 (112)
30 PRK12286 rpmF 50S ribosomal pr 42.9 8.3 0.00018 27.9 0.1 23 204-237 27-49 (57)
31 smart00105 ArfGap Putative GTP 42.3 20 0.00044 28.7 2.2 37 204-244 3-39 (112)
32 smart00834 CxxC_CXXC_SSSS Puta 42.0 9.2 0.0002 24.7 0.2 30 204-236 5-34 (41)
33 KOG0706 Predicted GTPase-activ 41.2 11 0.00025 37.7 0.7 37 204-244 23-59 (454)
34 PRK14892 putative transcriptio 40.7 8.5 0.00018 31.0 -0.2 35 204-241 21-55 (99)
35 PRK11788 tetratricopeptide rep 40.2 11 0.00024 34.8 0.5 24 204-237 354-377 (389)
36 PF07282 OrfB_Zn_ribbon: Putat 39.6 7.8 0.00017 28.0 -0.5 28 205-238 29-56 (69)
37 PRK12336 translation initiatio 39.2 9.4 0.0002 34.1 -0.2 34 205-241 99-132 (201)
38 COG3952 Predicted membrane pro 38.8 8.5 0.00018 31.6 -0.5 19 219-239 76-94 (113)
39 KOG0712 Molecular chaperone (D 38.6 18 0.0004 35.0 1.7 36 204-239 143-181 (337)
40 COG1645 Uncharacterized Zn-fin 38.4 11 0.00025 31.8 0.2 27 204-238 28-54 (131)
41 COG5347 GTPase-activating prot 38.2 16 0.00035 35.1 1.2 36 204-243 20-55 (319)
42 PF04810 zf-Sec23_Sec24: Sec23 38.0 14 0.0003 24.6 0.5 31 204-236 2-32 (40)
43 COG2816 NPY1 NTP pyrophosphohy 37.6 12 0.00026 35.4 0.3 30 204-239 111-140 (279)
44 PRK05342 clpX ATP-dependent pr 37.5 18 0.00039 35.6 1.5 29 204-234 9-37 (412)
45 PF09723 Zn-ribbon_8: Zinc rib 36.2 12 0.00026 25.0 0.1 30 204-236 5-34 (42)
46 PF01096 TFIIS_C: Transcriptio 34.6 5.3 0.00012 26.5 -1.9 33 206-238 2-38 (39)
47 COG2331 Uncharacterized protei 34.2 14 0.00031 28.7 0.1 36 204-242 12-47 (82)
48 TIGR00244 transcriptional regu 34.1 15 0.00033 31.6 0.3 39 206-244 2-44 (147)
49 PF13248 zf-ribbon_3: zinc-rib 32.5 25 0.00054 21.1 1.0 22 205-236 3-24 (26)
50 TIGR02605 CxxC_CxxC_SSSS putat 32.1 17 0.00037 24.9 0.3 30 204-236 5-34 (52)
51 PF01873 eIF-5_eIF-2B: Domain 31.4 15 0.00033 30.5 -0.1 29 205-236 94-122 (125)
52 PF13240 zinc_ribbon_2: zinc-r 30.6 27 0.00059 20.7 0.9 9 228-236 13-21 (23)
53 PLN03114 ADP-ribosylation fact 30.4 30 0.00065 34.1 1.7 36 204-243 22-57 (395)
54 PF14122 YokU: YokU-like prote 29.7 16 0.00034 28.9 -0.3 38 206-243 1-50 (87)
55 COG4260 Membrane protease subu 28.5 34 0.00073 32.9 1.6 28 205-237 316-343 (345)
56 PRK12496 hypothetical protein; 27.5 30 0.00066 29.8 1.1 32 205-244 128-159 (164)
57 PHA00626 hypothetical protein 27.5 21 0.00045 26.2 0.0 31 206-241 2-36 (59)
58 PRK00398 rpoP DNA-directed RNA 26.3 28 0.0006 23.5 0.5 31 204-240 3-33 (46)
59 KOG3740 Uncharacterized conser 26.0 26 0.00056 36.7 0.4 36 204-241 462-500 (706)
60 PF08394 Arc_trans_TRASH: Arch 25.9 42 0.00091 22.4 1.3 35 207-241 1-36 (37)
61 TIGR03831 YgiT_finger YgiT-typ 25.6 69 0.0015 20.7 2.4 22 73-94 12-33 (46)
62 TIGR01031 rpmF_bact ribosomal 25.2 22 0.00047 25.5 -0.2 24 204-239 26-49 (55)
63 PF13719 zinc_ribbon_5: zinc-r 24.6 19 0.00041 23.5 -0.6 33 205-238 3-35 (37)
64 PF15396 FAM60A: Protein Famil 24.5 41 0.0009 30.6 1.4 24 228-251 49-72 (213)
65 COG1096 Predicted RNA-binding 24.4 28 0.00061 31.2 0.3 27 204-238 149-175 (188)
66 PF12553 DUF3742: Protein of u 24.3 28 0.0006 25.1 0.2 10 218-227 34-43 (54)
67 PF12760 Zn_Tnp_IS1595: Transp 23.6 30 0.00065 23.4 0.3 27 205-236 19-45 (46)
68 PRK00241 nudC NADH pyrophospha 23.6 23 0.0005 32.6 -0.4 30 204-239 99-128 (256)
69 PRK01110 rpmF 50S ribosomal pr 23.5 29 0.00062 25.3 0.2 22 204-237 27-48 (60)
70 PF12773 DZR: Double zinc ribb 23.1 46 0.001 22.4 1.1 27 204-237 12-38 (50)
71 smart00661 RPOL9 RNA polymeras 22.7 40 0.00086 22.7 0.7 30 206-240 2-32 (52)
72 PF13619 KTSC: KTSC domain 21.8 97 0.0021 22.0 2.7 30 72-101 13-43 (60)
73 smart00778 Prim_Zn_Ribbon Zinc 21.7 51 0.0011 21.9 1.1 29 205-235 4-32 (37)
74 PF10083 DUF2321: Uncharacteri 21.5 40 0.00087 29.4 0.7 33 204-238 39-78 (158)
75 PF11781 RRN7: RNA polymerase 20.8 40 0.00086 22.1 0.4 25 205-236 9-33 (36)
76 TIGR03655 anti_R_Lar restricti 20.8 38 0.00083 23.6 0.3 31 205-238 2-36 (53)
77 COG1326 Uncharacterized archae 20.2 18 0.0004 32.5 -1.7 35 204-241 6-43 (201)
No 1
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=99.69 E-value=2.3e-17 Score=108.98 Aligned_cols=34 Identities=44% Similarity=0.718 Sum_probs=32.2
Q ss_pred CCCCcceeEEeccEEEEeCCCChhHHHHHHHHhc
Q 024594 71 STRTSELTVAYEGEVYVFPAVTPHKVQALLLLLG 104 (265)
Q Consensus 71 ~~~~aQLTIfY~G~V~Vfddvp~eKaq~Im~la~ 104 (265)
++.++||||||+|+|+|||+||+|||++||+||+
T Consensus 2 ~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~ 35 (36)
T PF06200_consen 2 SPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLAS 35 (36)
T ss_pred CCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhc
Confidence 5678999999999999999999999999999996
No 2
>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=99.61 E-value=4e-16 Score=111.72 Aligned_cols=48 Identities=50% Similarity=1.046 Sum_probs=42.6
Q ss_pred cccccccccCCCCccccCCCCCcccchhhhHHHHhcCCCCCCCCCC-CCcc
Q 024594 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGA-RNIC 255 (265)
Q Consensus 206 ~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~~r~~~~~~-~~~~ 255 (265)
.|+||+++ .||+||+||+|..+|||||||||++++.+|+..... ..+.
T Consensus 1 ~C~~C~~~--~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~~~~~~ 49 (54)
T cd00202 1 ACSNCGTT--TTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRKKDQIK 49 (54)
T ss_pred CCCCCCCC--CCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCcccccc
Confidence 49999998 599999999998999999999999999999988776 4443
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.55 E-value=2.2e-15 Score=106.98 Aligned_cols=46 Identities=50% Similarity=1.014 Sum_probs=40.6
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC-CCCCCCC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL-RDLTKGA 251 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~~-r~~~~~~ 251 (265)
...|+||+++ .||+||+||.|..+|||||||+|++++.+ ++.....
T Consensus 3 ~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~ 49 (52)
T smart00401 3 GRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKK 49 (52)
T ss_pred CCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCCCCcccccc
Confidence 4789999998 59999999999889999999999999988 7765443
No 4
>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=99.52 E-value=2.3e-15 Score=99.33 Aligned_cols=36 Identities=56% Similarity=1.199 Sum_probs=28.4
Q ss_pred ccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC
Q 024594 207 CQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL 244 (265)
Q Consensus 207 C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~~ 244 (265)
|.||+++ .||+||+||.|..+||||||++|++++++
T Consensus 1 C~~C~tt--~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGTT--ETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT--S--T-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcCC--CCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 8999998 59999999999889999999999999864
No 5
>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction. The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding
Probab=99.26 E-value=3.2e-12 Score=88.40 Aligned_cols=44 Identities=52% Similarity=0.819 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHhhhccccccccccchHHHHhhhhhccCCccccc
Q 024594 138 RIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNGQFTSSK 181 (265)
Q Consensus 138 R~~sl~r~~~Krk~r~~~k~i~Y~~RK~~A~~~~R~kGqFas~k 181 (265)
|.++|+||++||+.|.|.|+|+|.+||.+|+.++|.+|+|++..
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~~ 44 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKKS 44 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCCC
Confidence 67899999999999999999999999999999999999999764
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.64 E-value=1.6e-08 Score=87.95 Aligned_cols=46 Identities=48% Similarity=0.998 Sum_probs=38.5
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCCCCCCCCC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGA 251 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~~r~~~~~~ 251 (265)
...|.+|+++ .||+||++|.|...||||||++|+++...+.+....
T Consensus 199 ~~~c~~~~~~--~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~ 244 (340)
T KOG1601|consen 199 LRQCSNCGTT--KTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKR 244 (340)
T ss_pred CcccCCCCCC--CCcceecCCCCCccccccchhhhhhcCccccccccC
Confidence 4799999997 599999999999999999999999997444444333
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.29 E-value=2.8e-07 Score=91.67 Aligned_cols=56 Identities=29% Similarity=0.567 Sum_probs=46.1
Q ss_pred ccccccccccccccCCCCccccCCCC----CcccchhhhHHHHhcCCCC-CCCCCCCCccccc
Q 024594 201 ESVSRICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKGTLR-DLTKGARNICFEQ 258 (265)
Q Consensus 201 ~~~~~~C~~C~~t~~~Tp~wR~Gp~g----~~~LCNaCGl~~~~~~~~r-~~~~~~~~~~~~~ 258 (265)
+.+...|.||.++ .||+|||+..+ .-.|||||||+|+.|+++| |++.+...|+...
T Consensus 155 s~~~~vc~Nc~t~--stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 155 SNQPHVCSNCKTT--STPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred ccccchhcccccc--CCccccccccccccCCccccccccccccccCCcCCCcccccccccccc
Confidence 3345599999998 69999999993 3899999999999999999 8777766555543
No 8
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=98.26 E-value=4e-07 Score=56.58 Aligned_cols=25 Identities=52% Similarity=0.579 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHhhhcccccccccc
Q 024594 136 SQRIASLVRFREKRKERSFEKKIRYS 161 (265)
Q Consensus 136 ~~R~~sl~r~~~Krk~r~~~k~i~Y~ 161 (265)
.+|++||+||+||||+|..+ +.+|.
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp ----HHHHHHHHHH------------
T ss_pred chHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 37999999999999999888 68885
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=91.07 E-value=0.11 Score=52.49 Aligned_cols=52 Identities=23% Similarity=0.200 Sum_probs=44.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCCCCCCCCCCCccc
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGARNICF 256 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~~r~~~~~~~~~~~ 256 (265)
...|.+|++. +.||.||+...-.-.+|||||++-+..+.++++.++.....+
T Consensus 297 ~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~~ 348 (498)
T COG5641 297 DKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNSK 348 (498)
T ss_pred hcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCCChhhh
Confidence 4578888875 469999999888899999999999999999998887665554
No 10
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=83.12 E-value=1.5 Score=44.15 Aligned_cols=47 Identities=23% Similarity=0.503 Sum_probs=34.2
Q ss_pred CCCCCCccccccccccccccCCCCcccc--CCCCCcccchhhhHHHHhcCC
Q 024594 195 NGSAPPESVSRICQHCGISEKLTPAMRR--GPAGPRTLCNACGLMWANKGT 243 (265)
Q Consensus 195 ~~~~~~~~~~~~C~~C~~t~~~Tp~wR~--Gp~g~~~LCNaCGl~~~~~~~ 243 (265)
+|........+.|-+|+++ +.-+|=. +|.-...||..|=+||+|.+-
T Consensus 377 ~gtt~~~~~g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygG 425 (693)
T KOG3554|consen 377 NGTTFQNQDGRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGG 425 (693)
T ss_pred ccccccCCCCCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcC
Confidence 3433433336799999998 4667754 455556999999999999874
No 11
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=75.84 E-value=0.87 Score=29.76 Aligned_cols=30 Identities=30% Similarity=0.780 Sum_probs=14.8
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl 236 (265)
+.|.+||..- +..-=.|.+-.+..|.+||-
T Consensus 1 kfC~~CG~~l--~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPL--ERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChh--hhhcCCCCCccceECCCCCC
Confidence 3699999752 21222455666789999994
No 12
>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=71.40 E-value=1.3 Score=31.73 Aligned_cols=26 Identities=27% Similarity=0.834 Sum_probs=19.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhc
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~ 241 (265)
...|.+||... -++.+|..|| +|+.+
T Consensus 26 l~~c~~cg~~~-----------~~H~vc~~cG-~y~~r 51 (56)
T PF01783_consen 26 LVKCPNCGEPK-----------LPHRVCPSCG-YYKGR 51 (56)
T ss_dssp EEESSSSSSEE-----------STTSBCTTTB-BSSSS
T ss_pred eeeeccCCCEe-----------cccEeeCCCC-eECCE
Confidence 46899999752 3478999999 55443
No 13
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=65.68 E-value=1.5 Score=28.69 Aligned_cols=33 Identities=21% Similarity=0.569 Sum_probs=28.2
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~ 238 (265)
..|.+|++. ...+..+-.+.|...-|-.||-.|
T Consensus 3 i~Cp~C~~~-y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAK-YEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCE-EeCCHHHCCCCCcEEECCCCCCEe
Confidence 479999987 588889889999889999998765
No 14
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=65.25 E-value=2.4 Score=36.67 Aligned_cols=41 Identities=44% Similarity=0.678 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHHHhhhccccccccccchHHHHhhhhhccC
Q 024594 135 LSQRIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNG 175 (265)
Q Consensus 135 l~~R~~sl~r~~~Krk~r~~~k~i~Y~~RK~~A~~~~R~kG 175 (265)
...|...+.|++++++.+.|.++++|..++..++.+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 45788999999999999999999999999999999999887
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=64.01 E-value=5.3 Score=32.30 Aligned_cols=36 Identities=25% Similarity=0.594 Sum_probs=27.4
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~ 243 (265)
+..|..||.. -|.|-.=..| ..||-.|.-.++.-++
T Consensus 13 N~~CaDCg~~---~p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 13 NKVCADCGAP---NPTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp CTB-TTT-SB---S--EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred cCcCCCCCCC---CCCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 5799999976 7899999999 8999999998888775
No 16
>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=62.31 E-value=4.2 Score=27.34 Aligned_cols=32 Identities=28% Similarity=0.686 Sum_probs=21.3
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~ 237 (265)
.+|+-||.+...+-..=.||.| ...|+.|=..
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHH
Confidence 5899999997666566689977 7999999544
No 17
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=57.54 E-value=2.5 Score=26.64 Aligned_cols=29 Identities=31% Similarity=0.785 Sum_probs=16.9
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~ 238 (265)
.+.|..||... ...+.|....|.+||..+
T Consensus 3 ~rfC~~CG~~t------~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPT------KPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BE------EE-SSSS-EEESSSS-EE
T ss_pred CcccCcCCccc------cCCCCcCEeECCCCcCEe
Confidence 46899999852 345667889999999753
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=57.32 E-value=4.9 Score=29.47 Aligned_cols=30 Identities=20% Similarity=0.636 Sum_probs=23.2
Q ss_pred cccccccccccCCCCccccCCCCCcccc-hhhhHHHHhcCC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLC-NACGLMWANKGT 243 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LC-NaCGl~~~~~~~ 243 (265)
-+.|.+||... | .. +..| ..|+.-|.++++
T Consensus 3 HkHC~~CG~~I---p------~~-~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 3 HKHCPVCGKPI---P------PD-ESFCSPKCREEYRKRQK 33 (59)
T ss_pred CCcCCcCCCcC---C------cc-hhhhCHHHHHHHHHHHH
Confidence 36899999874 2 23 7899 599999998764
No 19
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=55.38 E-value=4.1 Score=33.19 Aligned_cols=28 Identities=29% Similarity=0.633 Sum_probs=20.3
Q ss_pred ccccccccccCCCCccccCCCCC-cccchhhhH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGP-RTLCNACGL 236 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~-~~LCNaCGl 236 (265)
-.|..|+-. .|-+-+. .+. -.-|+|||-
T Consensus 81 VlC~~C~sp--dT~l~k~--~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSP--DTELIKE--NRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCC--CcEEEEe--CCeEEEEccccCC
Confidence 479999998 4877776 222 245999994
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=54.28 E-value=5.1 Score=27.21 Aligned_cols=25 Identities=44% Similarity=1.103 Sum_probs=19.3
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhh
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACG 235 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCG 235 (265)
...|..|+ +|++| .-+| +.+|-+|+
T Consensus 17 ~~~Cp~C~-----~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCG-----TPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCCC-----CeeEE-ecCC-CEECCCCC
Confidence 45799996 78999 3355 78999986
No 21
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=52.30 E-value=2.9 Score=27.02 Aligned_cols=34 Identities=26% Similarity=0.621 Sum_probs=24.0
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHHH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~ 239 (265)
..|.+|++.- ..+....+..|....|-.||..|.
T Consensus 3 ~~CP~C~~~~-~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSF-RVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEE-EeCHHHcCCCCCEEECCCCCCEEE
Confidence 4688999862 555566666676788988887653
No 22
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.08 E-value=5.7 Score=33.28 Aligned_cols=36 Identities=28% Similarity=0.563 Sum_probs=25.7
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhHHHHhcC
Q 024594 202 SVSRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (265)
Q Consensus 202 ~~~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~ 242 (265)
..--+|.+||-- .-=+|=-....-|.|||+-|-.+.
T Consensus 19 Gl~grCP~CGeG-----rLF~gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 19 GLRGRCPRCGEG-----RLFRGFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred HhcCCCCCCCCc-----hhhhhhcccCchhhhccccccCCc
Confidence 345689999974 233444555679999999997765
No 23
>PRK05978 hypothetical protein; Provisional
Probab=49.73 E-value=6.4 Score=33.82 Aligned_cols=34 Identities=26% Similarity=0.552 Sum_probs=26.9
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~ 242 (265)
..+|-+||.- .+++ |-.....-|.+||+.|..+.
T Consensus 33 ~grCP~CG~G----~LF~-g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 33 RGRCPACGEG----KLFR-AFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cCcCCCCCCC----cccc-cccccCCCccccCCccccCC
Confidence 4689999974 3554 67777889999999998764
No 24
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=48.46 E-value=17 Score=27.10 Aligned_cols=47 Identities=28% Similarity=0.645 Sum_probs=33.6
Q ss_pred cccccccccccCCCCc--cc-cCCCCCcccchhhhHHHHhcCCCCCCCCCCC
Q 024594 204 SRICQHCGISEKLTPA--MR-RGPAGPRTLCNACGLMWANKGTLRDLTKGAR 252 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~--wR-~Gp~g~~~LCNaCGl~~~~~~~~r~~~~~~~ 252 (265)
...|..|..+. |-- .- --..-++..|-+|-.+|-..|++|.++.+..
T Consensus 5 ~~~CPRC~S~n--TKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg 54 (63)
T PF02701_consen 5 PLPCPRCDSTN--TKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGG 54 (63)
T ss_pred CCCCCCcCCCC--CEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCC
Confidence 56899998763 311 11 1234467899999999999999999877654
No 25
>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=46.98 E-value=6.3 Score=26.36 Aligned_cols=30 Identities=30% Similarity=0.741 Sum_probs=16.7
Q ss_pred cccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 024594 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (265)
Q Consensus 206 ~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~ 240 (265)
.|.+||.+. .--.--.| ..+|..||+-...
T Consensus 2 ~Cp~Cg~~~----~~~D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE----IVFDPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE----EEEETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCc----eEEcCCCC-eEECCCCCCEeec
Confidence 588888752 22222334 6788888876543
No 26
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=44.10 E-value=7.2 Score=32.86 Aligned_cols=30 Identities=30% Similarity=0.688 Sum_probs=20.8
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~ 237 (265)
-.|..|+-.. |-+-+.+- -.-.-|+|||-.
T Consensus 98 VlC~~C~sPd--T~l~k~~r-~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPD--TRIIKEGR-VSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCC--cEEEEeCC-eEEEecccCCCC
Confidence 4799999984 77776521 213589999954
No 27
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=43.82 E-value=7.4 Score=32.98 Aligned_cols=30 Identities=33% Similarity=0.592 Sum_probs=20.8
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~ 237 (265)
-.|..|+-. .|-+-+++= ---.-|+|||-.
T Consensus 103 VlC~~C~sp--dT~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGSP--DTKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred EECCCCCCC--CcEEEEcCC-eEEEEcccCCCC
Confidence 479999997 477776421 123679999953
No 28
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=43.46 E-value=6.4 Score=32.32 Aligned_cols=88 Identities=19% Similarity=0.398 Sum_probs=46.4
Q ss_pred hhccccccccccchHHHHhhhhhccCCcccccccccccc----CCCCCCCCCCCCccccccccccccccCC--CCccccC
Q 024594 150 KERSFEKKIRYSCRKEVAQRMQRKNGQFTSSKATFNIAS----ANSNPSNGSAPPESVSRICQHCGISEKL--TPAMRRG 223 (265)
Q Consensus 150 k~r~~~k~i~Y~~RK~~A~~~~R~kGqFas~k~Ssn~dS----aqSs~~~~~~~~~~~~~~C~~C~~t~~~--Tp~wR~G 223 (265)
|+..+++++.|+||.-.-... -.+.+|...+-+.+.+. .....+|.. .|.+....|..||-.+.- -++-|++
T Consensus 17 kEDked~~L~laCrnCd~ve~-A~s~~vY~~~~~~e~dE~t~ii~Dl~~DPT-LPrts~~~C~~C~~~eavffQ~~~~r~ 94 (113)
T KOG2691|consen 17 KEDKEDRILLLACRNCDYVEE-ADSSRVYVNELSHEHDELTQIIMDLASDPT-LPRTSDKHCPKCGHREAVFFQAQTRRA 94 (113)
T ss_pred cccccccEEEEEecCCcceEe-cCCcceEcCCcccchhhHHHHHHhhccCCC-cCccccccCCccCCcceEEEecccccc
Confidence 344678899999995311000 01222332222222221 111122322 222236899999986411 3456777
Q ss_pred CCCCc--ccchhhhHHHH
Q 024594 224 PAGPR--TLCNACGLMWA 239 (265)
Q Consensus 224 p~g~~--~LCNaCGl~~~ 239 (265)
..+.. .+|-.||-+|.
T Consensus 95 d~~m~l~yvC~~C~h~wt 112 (113)
T KOG2691|consen 95 DEAMRLFYVCCSCGHRWT 112 (113)
T ss_pred cceEEEEEEecccccccc
Confidence 77755 57888998884
No 29
>PRK00420 hypothetical protein; Validated
Probab=43.12 E-value=11 Score=31.04 Aligned_cols=31 Identities=29% Similarity=0.674 Sum_probs=24.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhc
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~ 241 (265)
...|..|| +|+.|- -+| ...|-.||..+...
T Consensus 23 ~~~CP~Cg-----~pLf~l-k~g-~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 23 SKHCPVCG-----LPLFEL-KDG-EVVCPVHGKVYIVK 53 (112)
T ss_pred cCCCCCCC-----Ccceec-CCC-ceECCCCCCeeeec
Confidence 36899999 568875 556 78999999877643
No 30
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=42.86 E-value=8.3 Score=27.93 Aligned_cols=23 Identities=30% Similarity=0.836 Sum_probs=17.3
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~ 237 (265)
...|.+||... -+..+|..||.|
T Consensus 27 l~~C~~CG~~~-----------~~H~vC~~CG~Y 49 (57)
T PRK12286 27 LVECPNCGEPK-----------LPHRVCPSCGYY 49 (57)
T ss_pred ceECCCCCCcc-----------CCeEECCCCCcC
Confidence 35799999863 237899999944
No 31
>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=42.25 E-value=20 Score=28.74 Aligned_cols=37 Identities=24% Similarity=0.516 Sum_probs=32.1
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL 244 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~~ 244 (265)
+..|..|+.. -|.|=.=.-| ..||-.|.-..+..+.+
T Consensus 3 N~~CaDC~~~---~p~w~s~~~G-ifvC~~CsgiHR~lg~h 39 (112)
T smart00105 3 NKKCFDCGAP---NPTWASVNLG-VFLCIECSGIHRSLGVH 39 (112)
T ss_pred CCcccCCCCC---CCCcEEeccc-eeEhHHhHHHHHhcCCC
Confidence 5799999985 7999998889 89999999888887754
No 32
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS 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=42.03 E-value=9.2 Score=24.66 Aligned_cols=30 Identities=23% Similarity=0.624 Sum_probs=21.2
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl 236 (265)
.-+|..||.. -..|..-.++....|-.||.
T Consensus 5 ~y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 3579999985 33555544466778999997
No 33
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=41.20 E-value=11 Score=37.67 Aligned_cols=37 Identities=27% Similarity=0.601 Sum_probs=32.9
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL 244 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~~ 244 (265)
+++|+.|+.. -|-|=.-+.| -.||--|---.+.-|++
T Consensus 23 NKvCFDCgAk---nPtWaSVTYG-IFLCiDCSAvHRnLGVH 59 (454)
T KOG0706|consen 23 NKVCFDCGAK---NPTWASVTYG-IFLCIDCSAVHRNLGVH 59 (454)
T ss_pred CceecccCCC---CCCceeecce-EEEEEecchhhhccccc
Confidence 6899999985 8999999999 89999998887777764
No 34
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=40.68 E-value=8.5 Score=30.95 Aligned_cols=35 Identities=20% Similarity=0.329 Sum_probs=22.7
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhc
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~ 241 (265)
.-.|.+|+.....-+.=| ......|..||.||.+.
T Consensus 21 ~f~CP~Cge~~v~v~~~k---~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 21 IFECPRCGKVSISVKIKK---NIAIITCGNCGLYTEFE 55 (99)
T ss_pred EeECCCCCCeEeeeecCC---CcceEECCCCCCccCEE
Confidence 457999994321112222 35579999999998764
No 35
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=40.17 E-value=11 Score=34.77 Aligned_cols=24 Identities=21% Similarity=0.642 Sum_probs=15.1
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~ 237 (265)
.+.|.|||.+ +..| ..+|-.||-+
T Consensus 354 ~~~c~~cg~~---~~~~-------~~~c~~c~~~ 377 (389)
T PRK11788 354 RYRCRNCGFT---ARTL-------YWHCPSCKAW 377 (389)
T ss_pred CEECCCCCCC---Cccc-------eeECcCCCCc
Confidence 4678888876 3333 3467777643
No 36
>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=39.60 E-value=7.8 Score=28.00 Aligned_cols=28 Identities=29% Similarity=0.739 Sum_probs=20.4
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~ 238 (265)
..|+.||.... +...+....|..||..+
T Consensus 29 q~C~~CG~~~~------~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 29 QTCPRCGHRNK------KRRSGRVFTCPNCGFEM 56 (69)
T ss_pred cCccCcccccc------cccccceEEcCCCCCEE
Confidence 57999998631 15556678999999764
No 37
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=39.16 E-value=9.4 Score=34.06 Aligned_cols=34 Identities=29% Similarity=0.621 Sum_probs=23.3
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHHHhc
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~ 241 (265)
-.|..|+-.. |-+-+.+ .---.-|+|||-..-..
T Consensus 99 V~C~~C~~pd--T~l~k~~-~~~~l~C~aCGa~~~v~ 132 (201)
T PRK12336 99 VICSECGLPD--TRLVKED-RVLMLRCDACGAHRPVK 132 (201)
T ss_pred EECCCCCCCC--cEEEEcC-CeEEEEcccCCCCcccc
Confidence 4799999984 7777663 12135799999765443
No 38
>COG3952 Predicted membrane protein [Function unknown]
Probab=38.78 E-value=8.5 Score=31.58 Aligned_cols=19 Identities=37% Similarity=0.546 Sum_probs=14.6
Q ss_pred ccccCCCCCcccchhhhHHHH
Q 024594 219 AMRRGPAGPRTLCNACGLMWA 239 (265)
Q Consensus 219 ~wR~Gp~g~~~LCNaCGl~~~ 239 (265)
.||.+|-+ .||++||++-.
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 56677766 79999998743
No 39
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=38.56 E-value=18 Score=35.02 Aligned_cols=36 Identities=25% Similarity=0.506 Sum_probs=29.5
Q ss_pred cccccccccccCCCCccccCC---CCCcccchhhhHHHH
Q 024594 204 SRICQHCGISEKLTPAMRRGP---AGPRTLCNACGLMWA 239 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp---~g~~~LCNaCGl~~~ 239 (265)
...|..|.-+.-.+..|+-|| .-.++.|+.|+..-.
T Consensus 143 ~~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G~G~ 181 (337)
T KOG0712|consen 143 APKCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNGSGE 181 (337)
T ss_pred CCCCCCCCCCCceeEEEeccccccccceeEeccCCCccc
Confidence 458999999988999999999 556789999976543
No 40
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=38.36 E-value=11 Score=31.79 Aligned_cols=27 Identities=37% Similarity=0.959 Sum_probs=22.4
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~ 238 (265)
...|.-|| ||++| =+| ...|-.||...
T Consensus 28 ~~hCp~Cg-----~PLF~--KdG-~v~CPvC~~~~ 54 (131)
T COG1645 28 AKHCPKCG-----TPLFR--KDG-EVFCPVCGYRE 54 (131)
T ss_pred HhhCcccC-----Cccee--eCC-eEECCCCCceE
Confidence 46899999 68999 677 89999999543
No 41
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=38.20 E-value=16 Score=35.09 Aligned_cols=36 Identities=25% Similarity=0.528 Sum_probs=31.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~ 243 (265)
..+|..||.. . |.|=.-.-| ..||=-|-=..|.-|+
T Consensus 20 Nk~CaDCga~--~-P~W~S~nlG-vfiCi~CagvHRsLGv 55 (319)
T COG5347 20 NKKCADCGAP--N-PTWASVNLG-VFLCIDCAGVHRSLGV 55 (319)
T ss_pred cCccccCCCC--C-CceEecccC-eEEEeecchhhhcccc
Confidence 5799999997 4 999999999 8999999877666664
No 42
>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=38.05 E-value=14 Score=24.55 Aligned_cols=31 Identities=29% Similarity=0.639 Sum_probs=20.2
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl 236 (265)
..+|.+|++- --|...-...|..-.||-|+.
T Consensus 2 p~rC~~C~ay--lNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAY--LNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--B--S-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCE--ECCcceEcCCCCEEECcCCCC
Confidence 3589999986 478888888888889999986
No 43
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=37.59 E-value=12 Score=35.37 Aligned_cols=30 Identities=27% Similarity=0.603 Sum_probs=22.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~ 239 (265)
.+.|..||+.. . -...|.+.+|+.||..+-
T Consensus 111 ~RFCg~CG~~~--~----~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 111 HRFCGRCGTKT--Y----PREGGWARVCPKCGHEHF 140 (279)
T ss_pred CcCCCCCCCcC--c----cccCceeeeCCCCCCccC
Confidence 57999999862 2 234566789999998764
No 44
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=37.46 E-value=18 Score=35.64 Aligned_cols=29 Identities=28% Similarity=0.693 Sum_probs=24.7
Q ss_pred cccccccccccCCCCccccCCCCCcccchhh
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNAC 234 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaC 234 (265)
..+|+.||.+...+...-.||.. .+|+.|
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~C 37 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDEC 37 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchH
Confidence 46999999998788888889844 699999
No 45
>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=36.22 E-value=12 Score=25.04 Aligned_cols=30 Identities=20% Similarity=0.511 Sum_probs=20.4
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl 236 (265)
.-+|..||.. --.|+..-+.....|-+||-
T Consensus 5 ey~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHE---FEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCE---EEEEEEcCCCCCCcCCCCCC
Confidence 3578999954 33555555555788999986
No 46
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=34.63 E-value=5.3 Score=26.50 Aligned_cols=33 Identities=27% Similarity=0.670 Sum_probs=15.7
Q ss_pred cccccccccCC--CCccccCCCCCc--ccchhhhHHH
Q 024594 206 ICQHCGISEKL--TPAMRRGPAGPR--TLCNACGLMW 238 (265)
Q Consensus 206 ~C~~C~~t~~~--Tp~wR~Gp~g~~--~LCNaCGl~~ 238 (265)
.|..||-.+.. .-+-|.+.++.. ..|..||-.|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 46667654311 123455555533 3577777665
No 47
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.19 E-value=14 Score=28.66 Aligned_cols=36 Identities=31% Similarity=0.525 Sum_probs=25.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~ 242 (265)
.-+|.+||-...-...++.. +-+.|.+||-.+++.-
T Consensus 12 ~Y~c~~cg~~~dvvq~~~dd---plt~ce~c~a~~kk~l 47 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDD---PLTTCEECGARLKKLL 47 (82)
T ss_pred EEeecccchHHHHHHhcccC---ccccChhhChHHHHhh
Confidence 35899999763233445544 4569999999888754
No 48
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=34.05 E-value=15 Score=31.59 Aligned_cols=39 Identities=18% Similarity=0.267 Sum_probs=26.8
Q ss_pred cccccccccCCCCccccCCCC----CcccchhhhHHHHhcCCC
Q 024594 206 ICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKGTL 244 (265)
Q Consensus 206 ~C~~C~~t~~~Tp~wR~Gp~g----~~~LCNaCGl~~~~~~~~ 244 (265)
+|..|+...+..=-=|...+| .+.-|.+||.+|-...+.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERA 44 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeec
Confidence 688998875444445556666 336899999988766543
No 49
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=32.50 E-value=25 Score=21.14 Aligned_cols=22 Identities=27% Similarity=0.833 Sum_probs=14.1
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl 236 (265)
+.|.+||... +.+ ...|..||.
T Consensus 3 ~~Cp~Cg~~~---------~~~-~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEI---------DPD-AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcC---------Ccc-cccChhhCC
Confidence 5788888742 222 467888874
No 50
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=32.11 E-value=17 Score=24.85 Aligned_cols=30 Identities=23% Similarity=0.584 Sum_probs=21.1
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl 236 (265)
.-+|..||.. .-.|+.--+.....|-.||-
T Consensus 5 ey~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHR---FEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCE---eEEEEecCCCCCCCCCCCCC
Confidence 3579999985 44676543444678999997
No 51
>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=31.38 E-value=15 Score=30.53 Aligned_cols=29 Identities=31% Similarity=0.673 Sum_probs=20.8
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl 236 (265)
-.|..|+.. .|-+-+.+-. -..-|+|||-
T Consensus 94 VlC~~C~sp--dT~l~k~~r~-~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSP--DTELIKEGRL-IFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSS--SEEEEEETTC-CEEEETTTSC
T ss_pred EEcCCCCCC--ccEEEEcCCE-EEEEecccCC
Confidence 479999987 4777777332 2478999984
No 52
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=30.61 E-value=27 Score=20.66 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=5.1
Q ss_pred cccchhhhH
Q 024594 228 RTLCNACGL 236 (265)
Q Consensus 228 ~~LCNaCGl 236 (265)
...|.-||-
T Consensus 13 ~~fC~~CG~ 21 (23)
T PF13240_consen 13 AKFCPNCGT 21 (23)
T ss_pred CcchhhhCC
Confidence 345666663
No 53
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=30.41 E-value=30 Score=34.09 Aligned_cols=36 Identities=25% Similarity=0.559 Sum_probs=30.7
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCC
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~ 243 (265)
+..|..|+.. -|.|=.-..| ..||-.|.=..+..|.
T Consensus 22 Nk~CaDCga~---nPtWASvn~G-IFLCl~CSGVHRsLGv 57 (395)
T PLN03114 22 NKICFDCNAK---NPTWASVTYG-IFLCIDCSAVHRSLGV 57 (395)
T ss_pred CCcCccCCCC---CCCceeeccc-eeehhhhhHhhccCCC
Confidence 5799999986 7999999999 8999999877666654
No 54
>PF14122 YokU: YokU-like protein
Probab=29.73 E-value=16 Score=28.90 Aligned_cols=38 Identities=26% Similarity=0.745 Sum_probs=24.1
Q ss_pred ccccccccc---CCCCccccCCCCCc---------ccchhhhHHHHhcCC
Q 024594 206 ICQHCGISE---KLTPAMRRGPAGPR---------TLCNACGLMWANKGT 243 (265)
Q Consensus 206 ~C~~C~~t~---~~Tp~wR~Gp~g~~---------~LCNaCGl~~~~~~~ 243 (265)
.|..|+... ..+.....=|+|.+ ..|+-||+-|.....
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d~v 50 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDDEV 50 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehhHH
Confidence 377777641 11333444577754 689999999877654
No 55
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=28.46 E-value=34 Score=32.87 Aligned_cols=28 Identities=29% Similarity=0.666 Sum_probs=20.5
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~ 237 (265)
..|.+||+. .|+- =|+|.--.|-+||..
T Consensus 316 nfc~ncG~~--~t~~---~~ng~a~fcp~cgq~ 343 (345)
T COG4260 316 NFCLNCGCG--TTAD---FDNGKAKFCPECGQG 343 (345)
T ss_pred ccccccCcc--cccC---CccchhhhChhhcCC
Confidence 489999976 3553 356666799999964
No 56
>PRK12496 hypothetical protein; Provisional
Probab=27.53 E-value=30 Score=29.84 Aligned_cols=32 Identities=22% Similarity=0.530 Sum_probs=22.3
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL 244 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~~~~~ 244 (265)
.+|..|+.. .+ .++. ...|--||...+++...
T Consensus 128 ~~C~gC~~~---~~---~~~~--~~~C~~CG~~~~r~~~~ 159 (164)
T PRK12496 128 KVCKGCKKK---YP---EDYP--DDVCEICGSPVKRKMVK 159 (164)
T ss_pred EECCCCCcc---cc---CCCC--CCcCCCCCChhhhcchh
Confidence 579999975 22 2222 35899999998877653
No 57
>PHA00626 hypothetical protein
Probab=27.46 E-value=21 Score=26.20 Aligned_cols=31 Identities=26% Similarity=0.630 Sum_probs=21.8
Q ss_pred cccccccccCCCCccc----cCCCCCcccchhhhHHHHhc
Q 024594 206 ICQHCGISEKLTPAMR----RGPAGPRTLCNACGLMWANK 241 (265)
Q Consensus 206 ~C~~C~~t~~~Tp~wR----~Gp~g~~~LCNaCGl~~~~~ 241 (265)
.|.+||... ..| +++.. ...|.-||..|-+.
T Consensus 2 ~CP~CGS~~----Ivrcg~cr~~sn-rYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGN----IAKEKTMRGWSD-DYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCce----eeeeceecccCc-ceEcCCCCCeechh
Confidence 588888742 334 24455 68999999998764
No 58
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=26.27 E-value=28 Score=23.47 Aligned_cols=31 Identities=23% Similarity=0.431 Sum_probs=19.9
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~~ 240 (265)
.-+|.+||..- .-.+......|.-||-.+-.
T Consensus 3 ~y~C~~CG~~~------~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREV------ELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEE------EECCCCCceECCCCCCeEEE
Confidence 45899999852 22333336789999965543
No 59
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.04 E-value=26 Score=36.74 Aligned_cols=36 Identities=22% Similarity=0.527 Sum_probs=28.4
Q ss_pred cccccccccccCCCCccccCCCC---CcccchhhhHHHHhc
Q 024594 204 SRICQHCGISEKLTPAMRRGPAG---PRTLCNACGLMWANK 241 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g---~~~LCNaCGl~~~~~ 241 (265)
.-.|..|.+- -||.|+.-+.+ ..++|.+|----.|+
T Consensus 462 P~~caqcktd--ftp~wk~ekstq~d~~i~cE~cvtSnqkk 500 (706)
T KOG3740|consen 462 PYACAQCKTD--FTPAWKKEKSTQADAAIVCENCVTSNQKK 500 (706)
T ss_pred chhhhhcccc--cccccccccccCcchHHHHHhhhhhcccc
Confidence 4689999996 59999998777 458999997655444
No 60
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=25.88 E-value=42 Score=22.41 Aligned_cols=35 Identities=20% Similarity=0.321 Sum_probs=24.2
Q ss_pred ccccccccCCCCccccCCCCCc-ccchhhhHHHHhc
Q 024594 207 CQHCGISEKLTPAMRRGPAGPR-TLCNACGLMWANK 241 (265)
Q Consensus 207 C~~C~~t~~~Tp~wR~Gp~g~~-~LCNaCGl~~~~~ 241 (265)
|..||......|.--+--.-.. .=|+.|--.|+++
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~fk~k 36 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQFKKK 36 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHHHHhh
Confidence 7889988877777665433323 3459998888775
No 61
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=25.56 E-value=69 Score=20.72 Aligned_cols=22 Identities=32% Similarity=0.440 Sum_probs=18.1
Q ss_pred CCcceeEEeccEEEEeCCCChh
Q 024594 73 RTSELTVAYEGEVYVFPAVTPH 94 (265)
Q Consensus 73 ~~aQLTIfY~G~V~Vfddvp~e 94 (265)
....+++-|+|+.+++.+||+.
T Consensus 12 ~~~~~~~~~~~~~~~i~~vp~~ 33 (46)
T TIGR03831 12 KTTTETYEYGGELIVIENVPAL 33 (46)
T ss_pred eEEEEEEEeCCEEEEEeCCCcc
Confidence 3447788899999999999974
No 62
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=25.23 E-value=22 Score=25.49 Aligned_cols=24 Identities=29% Similarity=0.888 Sum_probs=17.5
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~ 239 (265)
...|.+||... -+..+|-.|| +|+
T Consensus 26 l~~C~~cG~~~-----------~~H~vc~~cG-~Y~ 49 (55)
T TIGR01031 26 LVVCPNCGEFK-----------LPHRVCPSCG-YYK 49 (55)
T ss_pred ceECCCCCCcc-----------cCeeECCccC-eEC
Confidence 35799999752 2478999999 444
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.56 E-value=19 Score=23.53 Aligned_cols=33 Identities=21% Similarity=0.561 Sum_probs=22.1
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~ 238 (265)
..|.+|++. ..-|.=+-+..|...-|-.||-.|
T Consensus 3 i~CP~C~~~-f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTR-FRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCce-EEcCHHHcccCCcEEECCCCCcEe
Confidence 468888876 355555556667677788777554
No 64
>PF15396 FAM60A: Protein Family FAM60A
Probab=24.51 E-value=41 Score=30.64 Aligned_cols=24 Identities=29% Similarity=0.399 Sum_probs=18.4
Q ss_pred cccchhhhHHHHhcCCCCCCCCCC
Q 024594 228 RTLCNACGLMWANKGTLRDLTKGA 251 (265)
Q Consensus 228 ~~LCNaCGl~~~~~~~~r~~~~~~ 251 (265)
..+||||=|..++-.+|++-++..
T Consensus 49 GeICNACVLLVKRwKKLP~Gs~rn 72 (213)
T PF15396_consen 49 GEICNACVLLVKRWKKLPPGSKRN 72 (213)
T ss_pred chhhHHHHHHHHHHhhCCCCcccc
Confidence 369999999999887777655443
No 65
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=24.40 E-value=28 Score=31.16 Aligned_cols=27 Identities=26% Similarity=0.616 Sum_probs=20.8
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~ 238 (265)
--+|++|+ +++.+ .|...-|-.||--=
T Consensus 149 ~A~CsrC~-----~~L~~---~~~~l~Cp~Cg~tE 175 (188)
T COG1096 149 YARCSRCR-----APLVK---KGNMLKCPNCGNTE 175 (188)
T ss_pred EEEccCCC-----cceEE---cCcEEECCCCCCEE
Confidence 45899999 45888 66678999999643
No 66
>PF12553 DUF3742: Protein of unknown function (DUF3742); InterPro: IPR022213 This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Probab=24.26 E-value=28 Score=25.05 Aligned_cols=10 Identities=60% Similarity=1.036 Sum_probs=9.0
Q ss_pred CccccCCCCC
Q 024594 218 PAMRRGPAGP 227 (265)
Q Consensus 218 p~wR~Gp~g~ 227 (265)
|.||.||.|-
T Consensus 34 ~E~R~G~~Gf 43 (54)
T PF12553_consen 34 PEWREGPAGF 43 (54)
T ss_pred HhheecCCCc
Confidence 8999999984
No 67
>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=23.61 E-value=30 Score=23.40 Aligned_cols=27 Identities=33% Similarity=0.731 Sum_probs=18.0
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl 236 (265)
..|.+||.+ ...|.++ .+ ..-|++|+.
T Consensus 19 ~~CP~Cg~~---~~~~~~~-~~-~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST---KHYRLKT-RG-RYRCKACRK 45 (46)
T ss_pred CCCCCCCCe---eeEEeCC-CC-eEECCCCCC
Confidence 469999986 3334444 33 678999974
No 68
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=23.60 E-value=23 Score=32.58 Aligned_cols=30 Identities=23% Similarity=0.487 Sum_probs=20.8
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~~~ 239 (265)
.+.|.+||.. |-. ...|....|.+||..+.
T Consensus 99 ~~fC~~CG~~---~~~---~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 99 HRFCGYCGHP---MHP---SKTEWAMLCPHCRERYY 128 (256)
T ss_pred CccccccCCC---Cee---cCCceeEECCCCCCEEC
Confidence 4689999985 212 24566788999996554
No 69
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=23.53 E-value=29 Score=25.34 Aligned_cols=22 Identities=14% Similarity=0.135 Sum_probs=16.2
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~ 237 (265)
...|.+||... -++.+|. ||.|
T Consensus 27 ~~~c~~cg~~~-----------~pH~vc~-cG~Y 48 (60)
T PRK01110 27 LSVDKTTGEYH-----------LPHHVSP-KGYY 48 (60)
T ss_pred eeEcCCCCcee-----------ccceecC-Cccc
Confidence 35799999863 2467899 9954
No 70
>PF12773 DZR: Double zinc ribbon
Probab=23.07 E-value=46 Score=22.40 Aligned_cols=27 Identities=33% Similarity=0.995 Sum_probs=18.2
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHH
Q 024594 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl~ 237 (265)
...|.+||+.- + .+......|..||-.
T Consensus 12 ~~fC~~CG~~l---~----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPL---P----PPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCCh---h----hccCCCCCCcCCcCC
Confidence 56888888862 2 444445788888864
No 71
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.67 E-value=40 Score=22.75 Aligned_cols=30 Identities=23% Similarity=0.557 Sum_probs=18.9
Q ss_pred cccccccccCCCCccccCCC-CCcccchhhhHHHHh
Q 024594 206 ICQHCGISEKLTPAMRRGPA-GPRTLCNACGLMWAN 240 (265)
Q Consensus 206 ~C~~C~~t~~~Tp~wR~Gp~-g~~~LCNaCGl~~~~ 240 (265)
.|..||.- +-.+... .....|..||..+..
T Consensus 2 FCp~Cg~~-----l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNM-----LIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCc-----cccccCCCCCEEECCcCCCeEEC
Confidence 68999875 2233222 247889999965543
No 72
>PF13619 KTSC: KTSC domain
Probab=21.84 E-value=97 Score=22.00 Aligned_cols=30 Identities=37% Similarity=0.566 Sum_probs=24.7
Q ss_pred CCCcceeEEe-ccEEEEeCCCChhHHHHHHH
Q 024594 72 TRTSELTVAY-EGEVYVFPAVTPHKVQALLL 101 (265)
Q Consensus 72 ~~~aQLTIfY-~G~V~Vfddvp~eKaq~Im~ 101 (265)
+.+..|.|.| .|.++.|.+||++-.+++|.
T Consensus 13 ~~~~~L~V~F~~G~~Y~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 13 PETRTLEVEFKSGSVYRYFGVPPEVYEALLN 43 (60)
T ss_pred CCCCEEEEEEcCCCEEEECCCCHHHHHHHHc
Confidence 3456787755 68999999999999999885
No 73
>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=21.70 E-value=51 Score=21.90 Aligned_cols=29 Identities=24% Similarity=0.562 Sum_probs=17.3
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhh
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACG 235 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCG 235 (265)
..|..||-+- .-.|..-...-...|+.||
T Consensus 4 ~pCP~CGG~D--rFr~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 4 GPCPNCGGSD--RFRFDDKDGRGTWFCSVCG 32 (37)
T ss_pred cCCCCCCCcc--ccccccCCCCcCEEeCCCC
Confidence 4788898753 3334432222257899886
No 74
>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=21.52 E-value=40 Score=29.40 Aligned_cols=33 Identities=18% Similarity=0.482 Sum_probs=18.3
Q ss_pred cccccccccccCCCCcccc-------CCCCCcccchhhhHHH
Q 024594 204 SRICQHCGISEKLTPAMRR-------GPAGPRTLCNACGLMW 238 (265)
Q Consensus 204 ~~~C~~C~~t~~~Tp~wR~-------Gp~g~~~LCNaCGl~~ 238 (265)
...|.+|++.+.. .|-- ++.-...-|+.||..|
T Consensus 39 I~~Cp~C~~~IrG--~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 39 ITSCPNCSTPIRG--DYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHHCcCCCCCCCC--ceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 3467777665421 1111 3333456799998766
No 75
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=20.80 E-value=40 Score=22.11 Aligned_cols=25 Identities=28% Similarity=0.632 Sum_probs=19.4
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 024594 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~g~~~LCNaCGl 236 (265)
..|..|+. . |-...+| ...|..||-
T Consensus 9 ~~C~~C~~----~--~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGS----R--WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CcCCCCCC----e--EeEccCC-EEEhhhCce
Confidence 46999986 3 6667788 889999983
No 76
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=20.77 E-value=38 Score=23.58 Aligned_cols=31 Identities=29% Similarity=0.568 Sum_probs=17.6
Q ss_pred ccccccccccCCCCccccCCC---CCc-ccchhhhHHH
Q 024594 205 RICQHCGISEKLTPAMRRGPA---GPR-TLCNACGLMW 238 (265)
Q Consensus 205 ~~C~~C~~t~~~Tp~wR~Gp~---g~~-~LCNaCGl~~ 238 (265)
+.|..||.. .=.||++.+ +.. ..|..||-..
T Consensus 2 kPCPfCGg~---~~~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGA---DVYLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCCc---ceeeEeccCCCCCEEEEECCCCCCCc
Confidence 478999874 222664322 211 2588888653
No 77
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=20.16 E-value=18 Score=32.55 Aligned_cols=35 Identities=29% Similarity=0.640 Sum_probs=23.6
Q ss_pred cccccccccccCCC--Ccccc-CCCCCcccchhhhHHHHhc
Q 024594 204 SRICQHCGISEKLT--PAMRR-GPAGPRTLCNACGLMWANK 241 (265)
Q Consensus 204 ~~~C~~C~~t~~~T--p~wR~-Gp~g~~~LCNaCGl~~~~~ 241 (265)
...|.+|+ .+ .+ -.-+. |++ +-.-|+.||..|.-.
T Consensus 6 y~~Cp~Cg-~e-ev~hEVik~~g~~-~lvrC~eCG~V~~~~ 43 (201)
T COG1326 6 YIECPSCG-SE-EVSHEVIKERGRE-PLVRCEECGTVHPAI 43 (201)
T ss_pred EEECCCCC-cc-hhhHHHHHhcCCc-eEEEccCCCcEeece
Confidence 56899999 43 34 23444 444 467899999999543
Done!