Query 017834
Match_columns 365
No_of_seqs 286 out of 893
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:50:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017834.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017834hhsearch_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 99.6 1.5E-15 3.2E-20 105.8 4.8 35 70-104 1-35 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.6 1.5E-15 3.3E-20 114.2 3.7 44 206-251 1-44 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 7.8E-15 1.7E-19 109.4 2.7 45 204-250 3-48 (52)
4 PF00320 GATA: GATA zinc finge 99.5 6.8E-15 1.5E-19 102.0 1.2 36 207-244 1-36 (36)
5 PF06203 CCT: CCT motif; Inte 99.1 2E-11 4.3E-16 89.0 2.5 44 138-181 1-44 (45)
6 KOG1601 GATA-4/5/6 transcripti 98.6 1.8E-08 3.9E-13 90.9 2.8 45 204-250 199-243 (340)
7 COG5641 GAT1 GATA Zn-finger-co 98.3 4.2E-07 9E-12 94.8 3.1 53 198-252 152-209 (498)
8 PF09425 CCT_2: Divergent CCT 97.6 3.5E-05 7.6E-10 50.8 1.5 24 137-161 3-26 (27)
9 COG5641 GAT1 GATA Zn-finger-co 90.2 0.14 3.1E-06 54.2 1.6 52 204-256 297-348 (498)
10 KOG3554 Histone deacetylase co 74.3 3.6 7.8E-05 43.8 4.0 39 204-244 386-426 (693)
11 KOG1601 GATA-4/5/6 transcripti 70.6 1.8 3.9E-05 39.1 0.7 41 135-175 290-330 (340)
12 PF14803 Nudix_N_2: Nudix N-te 66.4 1.9 4.1E-05 29.9 -0.0 30 205-236 1-30 (34)
13 PF01783 Ribosomal_L32p: Ribos 64.5 1.8 3.9E-05 32.8 -0.4 25 204-240 26-50 (56)
14 PF09889 DUF2116: Uncharacteri 58.5 4.7 0.0001 31.3 0.9 30 204-243 3-33 (59)
15 PF13717 zinc_ribbon_4: zinc-r 58.2 2.4 5.1E-05 29.5 -0.7 33 205-238 3-35 (36)
16 PF01412 ArfGap: Putative GTPa 51.4 11 0.00024 32.1 2.1 36 204-243 13-48 (116)
17 PF06689 zf-C4_ClpX: ClpX C4-t 50.9 7.7 0.00017 27.6 0.9 32 205-237 2-33 (41)
18 PF06677 Auto_anti-p27: Sjogre 49.4 5.8 0.00012 28.6 0.1 25 204-235 17-41 (41)
19 smart00653 eIF2B_5 domain pres 49.3 5.6 0.00012 34.2 0.0 28 205-236 81-109 (110)
20 PRK11823 DNA repair protein Ra 48.3 6.1 0.00013 41.1 0.1 27 204-240 7-33 (446)
21 KOG1598 Transcription initiati 47.7 7.9 0.00017 41.5 0.8 31 205-240 1-31 (521)
22 TIGR00416 sms DNA repair prote 46.9 6.7 0.00014 41.0 0.1 26 204-239 7-32 (454)
23 COG3952 Predicted membrane pro 40.7 8.4 0.00018 33.4 -0.2 21 218-240 75-95 (113)
24 TIGR02098 MJ0042_CXXC MJ0042 f 40.2 5.5 0.00012 27.2 -1.2 34 205-239 3-36 (38)
25 cd01121 Sms Sms (bacterial rad 39.7 10 0.00022 38.7 0.2 25 206-240 2-26 (372)
26 PRK12286 rpmF 50S ribosomal pr 39.3 8.9 0.00019 29.4 -0.3 23 204-237 27-49 (57)
27 PF09297 zf-NADH-PPase: NADH p 38.7 7.2 0.00016 26.0 -0.7 29 204-238 3-31 (32)
28 PF08271 TF_Zn_Ribbon: TFIIB z 38.5 11 0.00024 26.7 0.1 31 206-241 2-32 (43)
29 PRK05978 hypothetical protein; 38.1 12 0.00027 33.9 0.4 34 204-242 33-66 (148)
30 PRK00420 hypothetical protein; 38.1 12 0.00026 32.5 0.4 31 204-241 23-53 (112)
31 PRK03988 translation initiatio 37.4 9.6 0.00021 34.1 -0.4 31 204-237 102-132 (138)
32 PF02701 zf-Dof: Dof domain, z 36.7 24 0.00052 27.9 1.7 46 204-251 5-53 (63)
33 TIGR00311 aIF-2beta translatio 36.5 10 0.00023 33.6 -0.3 31 204-237 97-127 (133)
34 smart00105 ArfGap Putative GTP 34.8 29 0.00064 29.3 2.2 38 204-245 3-40 (112)
35 COG1645 Uncharacterized Zn-fin 33.8 14 0.00031 33.0 0.1 27 204-238 28-54 (131)
36 PRK05342 clpX ATP-dependent pr 33.4 22 0.00047 36.9 1.4 29 204-234 9-37 (412)
37 PF04810 zf-Sec23_Sec24: Sec23 32.4 19 0.00042 25.3 0.6 32 204-237 2-33 (40)
38 PF13248 zf-ribbon_3: zinc-rib 31.8 24 0.00053 22.6 0.9 24 204-237 2-25 (26)
39 PF13240 zinc_ribbon_2: zinc-r 31.7 23 0.00051 22.3 0.8 21 206-236 1-21 (23)
40 PRK12336 translation initiatio 31.4 14 0.0003 34.8 -0.4 33 204-239 98-130 (201)
41 PRK11788 tetratricopeptide rep 31.4 17 0.00036 35.2 0.1 24 204-237 354-377 (389)
42 COG5525 Bacteriophage tail ass 31.3 15 0.00033 40.1 -0.2 45 283-327 330-381 (611)
43 KOG2691 RNA polymerase II subu 31.0 17 0.00038 31.6 0.2 86 150-239 17-112 (113)
44 TIGR03573 WbuX N-acetyl sugar 30.9 29 0.00062 34.8 1.7 32 205-240 2-33 (343)
45 smart00834 CxxC_CXXC_SSSS Puta 30.5 17 0.00036 24.8 -0.0 30 204-236 5-34 (41)
46 KOG0712 Molecular chaperone (D 30.1 29 0.00062 35.5 1.6 36 204-239 143-181 (337)
47 COG2816 NPY1 NTP pyrophosphohy 30.0 18 0.00039 36.1 0.1 31 204-240 111-141 (279)
48 PF07282 OrfB_Zn_ribbon: Putat 29.4 14 0.0003 28.2 -0.6 30 204-239 28-57 (69)
49 COG5349 Uncharacterized protei 28.8 22 0.00049 31.5 0.5 35 204-243 21-55 (126)
50 COG5347 GTPase-activating prot 28.7 27 0.00058 35.4 1.1 36 204-243 20-55 (319)
51 COG2331 Uncharacterized protei 28.0 20 0.00044 29.5 0.1 35 204-241 12-46 (82)
52 COG4683 Uncharacterized protei 27.2 41 0.0009 29.5 1.8 21 76-105 67-87 (120)
53 KOG3740 Uncharacterized conser 25.7 31 0.00066 38.1 0.9 36 204-241 462-500 (706)
54 PF01873 eIF-5_eIF-2B: Domain 25.2 24 0.00052 31.0 0.0 29 205-236 94-122 (125)
55 TIGR00244 transcriptional regu 25.1 26 0.00057 31.9 0.3 59 206-264 2-69 (147)
56 PF09723 Zn-ribbon_8: Zinc rib 24.6 24 0.00052 25.0 -0.1 29 205-236 6-34 (42)
57 PRK14892 putative transcriptio 24.4 23 0.0005 30.1 -0.2 35 204-241 21-55 (99)
58 TIGR01031 rpmF_bact ribosomal 23.4 22 0.00048 27.0 -0.5 22 204-236 26-47 (55)
59 PF14122 YokU: YokU-like prote 22.4 25 0.00053 29.5 -0.4 41 206-246 1-53 (87)
60 PF01096 TFIIS_C: Transcriptio 22.2 13 0.00028 26.1 -1.8 34 206-239 2-39 (39)
61 KOG0706 Predicted GTPase-activ 22.0 36 0.00077 36.1 0.6 36 204-243 23-58 (454)
62 PLN03114 ADP-ribosylation fact 21.9 51 0.0011 34.3 1.6 36 204-243 22-57 (395)
63 PRK01110 rpmF 50S ribosomal pr 21.9 28 0.00061 26.9 -0.2 23 204-238 27-49 (60)
64 TIGR02605 CxxC_CxxC_SSSS putat 21.5 32 0.00069 24.9 0.1 30 204-236 5-34 (52)
65 COG1326 Uncharacterized archae 21.3 22 0.00048 33.9 -1.0 40 204-246 6-48 (201)
66 PF11228 DUF3027: Protein of u 21.1 28 0.00062 33.0 -0.3 30 217-246 126-163 (193)
67 PRK12496 hypothetical protein; 20.9 43 0.00093 30.5 0.8 32 204-243 127-158 (164)
68 COG4260 Membrane protease subu 20.4 64 0.0014 32.8 1.9 29 204-237 315-343 (345)
69 COG1096 Predicted RNA-binding 20.4 34 0.00074 32.4 0.0 29 204-240 149-177 (188)
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=99.59 E-value=1.5e-15 Score=105.81 Aligned_cols=35 Identities=43% Similarity=0.698 Sum_probs=32.7
Q ss_pred CCCCCccceEEEccEEEEeCCCChHHHHHHHHHhc
Q 017834 70 TSTRTSELTVAYEGEVYVFPAVTPHKVQALLLLLG 104 (365)
Q Consensus 70 ~~~~t~QLTIfY~G~V~VFD~VppeKaqaImllag 104 (365)
+.+.++||||||+|+|+|||+||+|||++||+||+
T Consensus 1 ~~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~ 35 (36)
T PF06200_consen 1 PSPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLAS 35 (36)
T ss_pred CCCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhc
Confidence 35678899999999999999999999999999997
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=99.57 E-value=1.5e-15 Score=114.16 Aligned_cols=44 Identities=52% Similarity=1.129 Sum_probs=40.9
Q ss_pred ccccccccccCCCccccCCCCCchhchHhhhhHHhcCCCCCCCcCC
Q 017834 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGA 251 (365)
Q Consensus 206 ~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~r~~~k~~ 251 (365)
.|+||+++ .||+||+||.|..+|||||||||++++..|+.....
T Consensus 1 ~C~~C~~~--~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTT--TTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCC--CCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 59999998 799999999998999999999999999999988765
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.50 E-value=7.8e-15 Score=109.38 Aligned_cols=45 Identities=51% Similarity=1.039 Sum_probs=40.6
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCCC-CCCCcC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL-RDLTKG 250 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~-r~~~k~ 250 (365)
...|+||+++ .||+||+||.|..+|||||||+|++++.+ |+..+.
T Consensus 3 ~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~ 48 (52)
T smart00401 3 GRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLK 48 (52)
T ss_pred CCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCCCCccccc
Confidence 5799999998 69999999999889999999999999998 776554
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=99.49 E-value=6.8e-15 Score=102.03 Aligned_cols=36 Identities=56% Similarity=1.199 Sum_probs=28.6
Q ss_pred cccccccccCCCccccCCCCCchhchHhhhhHHhcCCC
Q 017834 207 CQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL 244 (365)
Q Consensus 207 C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~ 244 (365)
|+||+++ .||+||+||.|..+||||||++|++++++
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 69999999999889999999999999864
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=99.14 E-value=2e-11 Score=89.02 Aligned_cols=44 Identities=52% Similarity=0.819 Sum_probs=41.7
Q ss_pred HHHHHHHHHHhhccccCCceeeeccchhhHhhhhhccccccccc
Q 017834 138 RIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNGQFTSSK 181 (365)
Q Consensus 138 R~aSL~RfreKRk~R~f~KkirYs~RK~~A~r~~R~KGqFas~k 181 (365)
|.++|.||++||+.|+|.|+|+|.+|+.+|+.++|.+|+|++..
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 67899999999999999999999999999999999999999854
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.62 E-value=1.8e-08 Score=90.88 Aligned_cols=45 Identities=49% Similarity=1.025 Sum_probs=38.7
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCCCCCCCcC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKG 250 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~r~~~k~ 250 (365)
...|.+|+++ .||+||++|.|+..||||||++|++++..|.+...
T Consensus 199 ~~~c~~~~~~--~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~ 243 (340)
T KOG1601|consen 199 LRQCSNCGTT--KTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEK 243 (340)
T ss_pred CcccCCCCCC--CCcceecCCCCCccccccchhhhhhcCcccccccc
Confidence 4799999997 79999999999999999999999999744444444
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.27 E-value=4.2e-07 Score=94.76 Aligned_cols=53 Identities=28% Similarity=0.597 Sum_probs=43.6
Q ss_pred CCCcccccccccccccccCCCccccCCCC----CchhchHhhhhHHhcCCCC-CCCcCCC
Q 017834 198 APPESVSRICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKGTLR-DLTKGAR 252 (365)
Q Consensus 198 ~~~~~~~~~C~~Cg~t~~~TP~WRrGP~G----~~tLCNACGl~~~~~~~~r-~~~k~~~ 252 (365)
...+.+...|.||.++ .||+|||+..+ .-.|||||||+|+.|+++| +++-...
T Consensus 152 ~~~s~~~~vc~Nc~t~--stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~ 209 (498)
T COG5641 152 SDNSNQPHVCSNCKTT--STPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSD 209 (498)
T ss_pred cccccccchhcccccc--CCccccccccccccCCccccccccccccccCCcCCCcccccc
Confidence 3344456699999998 79999999993 3899999999999999999 7665543
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=97.56 E-value=3.5e-05 Score=50.81 Aligned_cols=24 Identities=54% Similarity=0.628 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHhhccccCCceeeec
Q 017834 137 QRIASLVRFREKRKERSFEKKIRYS 161 (365)
Q Consensus 137 ~R~aSL~RfreKRk~R~f~KkirYs 161 (365)
+|++||+||+||||+|.+.+ .+|.
T Consensus 3 aRK~SLqRFLeKRK~R~~~~-~PY~ 26 (27)
T PF09425_consen 3 ARKASLQRFLEKRKDRLAAK-SPYQ 26 (27)
T ss_dssp ---HHHHHHHHHH------------
T ss_pred hHHHHHHHHHHHHHHhhccC-CCCC
Confidence 68999999999999999984 7885
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=90.21 E-value=0.14 Score=54.17 Aligned_cols=52 Identities=23% Similarity=0.200 Sum_probs=43.2
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCCCCCCCcCCCcccc
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGARNICF 256 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~r~~~k~~~~i~~ 256 (365)
...|.+|++. +.||.||+...-.-.+|||||++-+.++..+++.++......
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 5688999875 469999999888789999999999999999998886543333
No 10
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=74.29 E-value=3.6 Score=43.77 Aligned_cols=39 Identities=26% Similarity=0.576 Sum_probs=31.5
Q ss_pred ccccccccccccCCCccc--cCCCCCchhchHhhhhHHhcCCC
Q 017834 204 SRICQHCGISEKLTPAMR--RGPAGPRTLCNACGLMWANKGTL 244 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WR--rGP~G~~tLCNACGl~~~~~~~~ 244 (365)
.+.|.+|+++ ..-+|= -+|.-...||--|=+||+|.|-+
T Consensus 386 g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 7899999998 577774 34555668999999999998754
No 11
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=70.57 E-value=1.8 Score=39.08 Aligned_cols=41 Identities=44% Similarity=0.678 Sum_probs=38.2
Q ss_pred hhHHHHHHHHHHHhhccccCCceeeeccchhhHhhhhhccc
Q 017834 135 LSQRIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNG 175 (365)
Q Consensus 135 l~~R~aSL~RfreKRk~R~f~KkirYs~RK~~A~r~~R~KG 175 (365)
...|.+.+.|++++++.+.|.++++|..++..+..+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 45799999999999999999999999999999999999887
No 12
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=66.38 E-value=1.9 Score=29.92 Aligned_cols=30 Identities=33% Similarity=0.855 Sum_probs=14.1
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhh
Q 017834 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (365)
Q Consensus 205 ~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl 236 (365)
+.|.+||.. .+..-=.|.+-.+..|.+||.
T Consensus 1 kfC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGP--LERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred CccccccCh--hhhhcCCCCCccceECCCCCC
Confidence 369999964 121112344455689999995
No 13
>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=64.52 E-value=1.8 Score=32.77 Aligned_cols=25 Identities=28% Similarity=0.810 Sum_probs=18.7
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (365)
...|.+||.. .-+..+|..|| +|+.
T Consensus 26 l~~c~~cg~~-----------~~~H~vc~~cG-~y~~ 50 (56)
T PF01783_consen 26 LVKCPNCGEP-----------KLPHRVCPSCG-YYKG 50 (56)
T ss_dssp EEESSSSSSE-----------ESTTSBCTTTB-BSSS
T ss_pred eeeeccCCCE-----------ecccEeeCCCC-eECC
Confidence 5799999975 23478999999 4443
No 14
>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=58.48 E-value=4.7 Score=31.30 Aligned_cols=30 Identities=20% Similarity=0.636 Sum_probs=23.9
Q ss_pred ccccccccccccCCCccccCCCCCchhc-hHhhhhHHhcCC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLC-NACGLMWANKGT 243 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLC-NACGl~~~~~~~ 243 (365)
.+.|.+||... |.+ +..| ..|+.-|.++++
T Consensus 3 HkHC~~CG~~I---------p~~-~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 3 HKHCPVCGKPI---------PPD-ESFCSPKCREEYRKRQK 33 (59)
T ss_pred CCcCCcCCCcC---------Ccc-hhhhCHHHHHHHHHHHH
Confidence 57899999875 344 7899 599999998654
No 15
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=58.25 E-value=2.4 Score=29.48 Aligned_cols=33 Identities=21% Similarity=0.569 Sum_probs=28.8
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhhhH
Q 017834 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (365)
Q Consensus 205 ~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~ 238 (365)
..|.+|++. ...+..+-.+.|...-|-.||-.|
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 579999997 589999999999899999999766
No 16
>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=51.38 E-value=11 Score=32.08 Aligned_cols=36 Identities=25% Similarity=0.594 Sum_probs=27.2
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (365)
+..|..||.. -|.|-.=.-| -.||-.|.-.++.-|+
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 6899999975 7899999999 8999999988888775
No 17
>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=50.88 E-value=7.7 Score=27.63 Aligned_cols=32 Identities=28% Similarity=0.686 Sum_probs=21.4
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhhh
Q 017834 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (365)
Q Consensus 205 ~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~ 237 (365)
++|+-||.++...-..=.||.| ..+|+.|=..
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 5899999997666566688978 8899999554
No 18
>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=49.43 E-value=5.8 Score=28.63 Aligned_cols=25 Identities=44% Similarity=1.103 Sum_probs=19.8
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACG 235 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACG 235 (365)
...|..|+ +|++| .-+| +.+|-+|+
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 45799995 89999 3466 78999986
No 19
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=49.27 E-value=5.6 Score=34.21 Aligned_cols=28 Identities=29% Similarity=0.633 Sum_probs=20.9
Q ss_pred cccccccccccCCCccccCCCCC-chhchHhhh
Q 017834 205 RICQHCGISEKLTPAMRRGPAGP-RTLCNACGL 236 (365)
Q Consensus 205 ~~C~~Cg~t~~~TP~WRrGP~G~-~tLCNACGl 236 (365)
-.|..|+.. .|-+-+. .+- -.-|+|||-
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 689999998 5888876 232 245999995
No 20
>PRK11823 DNA repair protein RadA; Provisional
Probab=48.29 E-value=6.1 Score=41.14 Aligned_cols=27 Identities=33% Similarity=0.801 Sum_probs=19.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (365)
..+|.+||-+ ++.|- | .|.+||-+--.
T Consensus 7 ~y~C~~Cg~~---~~~~~----g---~Cp~C~~w~t~ 33 (446)
T PRK11823 7 AYVCQECGAE---SPKWL----G---RCPECGAWNTL 33 (446)
T ss_pred eEECCcCCCC---CcccC----e---eCcCCCCccce
Confidence 6899999986 55552 2 59999865433
No 21
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=47.74 E-value=7.9 Score=41.55 Aligned_cols=31 Identities=29% Similarity=0.685 Sum_probs=21.8
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhhhHHh
Q 017834 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (365)
Q Consensus 205 ~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (365)
..|.|||.+ ++.-+- -.| -..|++||.-...
T Consensus 1 ~~C~~C~~s---~fe~d~-a~g-~~~C~~CG~v~E~ 31 (521)
T KOG1598|consen 1 MVCKNCGGS---NFERDE-ATG-NLYCTACGTVLEY 31 (521)
T ss_pred CcCCCCCCC---Cccccc-ccC-Cceeccccceeec
Confidence 369999985 555443 455 7899999976543
No 22
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=46.88 E-value=6.7 Score=41.02 Aligned_cols=26 Identities=31% Similarity=0.553 Sum_probs=18.0
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHH
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~ 239 (365)
..+|.+||-+. ..|+| -|.+||-+--
T Consensus 7 ~y~C~~Cg~~~-~~~~g---------~Cp~C~~w~t 32 (454)
T TIGR00416 7 KFVCQHCGADS-PKWQG---------KCPACHAWNT 32 (454)
T ss_pred eEECCcCCCCC-ccccE---------ECcCCCCccc
Confidence 68999999862 44444 4888876543
No 23
>COG3952 Predicted membrane protein [Function unknown]
Probab=40.74 E-value=8.4 Score=33.43 Aligned_cols=21 Identities=33% Similarity=0.387 Sum_probs=16.0
Q ss_pred CccccCCCCCchhchHhhhhHHh
Q 017834 218 PAMRRGPAGPRTLCNACGLMWAN 240 (365)
Q Consensus 218 P~WRrGP~G~~tLCNACGl~~~~ 240 (365)
-+||.+|-+ .||++||++-..
T Consensus 75 fi~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 75 FIRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHHhcchHH--HHHHhhhHHHHH
Confidence 356777776 799999998654
No 24
>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=40.19 E-value=5.5 Score=27.19 Aligned_cols=34 Identities=26% Similarity=0.621 Sum_probs=24.6
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhhhHH
Q 017834 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (365)
Q Consensus 205 ~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~ 239 (365)
..|.+|++.- .-+..+.+..|....|-.||..|.
T Consensus 3 ~~CP~C~~~~-~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSF-RVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEE-EeCHHHcCCCCCEEECCCCCCEEE
Confidence 5788999863 566666666676788988887653
No 25
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=39.71 E-value=10 Score=38.72 Aligned_cols=25 Identities=32% Similarity=0.806 Sum_probs=17.3
Q ss_pred ccccccccccCCCccccCCCCCchhchHhhhhHHh
Q 017834 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (365)
Q Consensus 206 ~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (365)
+|.+||-. +|.|- | -|.+||-+--.
T Consensus 2 ~c~~cg~~---~~~~~----g---~cp~c~~w~~~ 26 (372)
T cd01121 2 VCSECGYV---SPKWL----G---KCPECGEWNTL 26 (372)
T ss_pred CCCCCCCC---CCCcc----E---ECcCCCCceee
Confidence 69999986 66663 3 58888765433
No 26
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=39.33 E-value=8.9 Score=29.42 Aligned_cols=23 Identities=30% Similarity=0.836 Sum_probs=17.5
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~ 237 (365)
.-.|.+||... =+..+|..||.|
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 56899999862 237899999954
No 27
>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=38.70 E-value=7.2 Score=26.02 Aligned_cols=29 Identities=34% Similarity=0.815 Sum_probs=16.4
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhH
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~ 238 (365)
.+.|..||.. | ...+.|....|.+||..+
T Consensus 3 ~rfC~~CG~~---t---~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAP---T---KPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--B---E---EE-SSSS-EEESSSS-EE
T ss_pred CcccCcCCcc---c---cCCCCcCEeECCCCcCEe
Confidence 5789999975 2 234567788999999753
No 28
>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=38.53 E-value=11 Score=26.69 Aligned_cols=31 Identities=26% Similarity=0.686 Sum_probs=18.3
Q ss_pred ccccccccccCCCccccCCCCCchhchHhhhhHHhc
Q 017834 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (365)
Q Consensus 206 ~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~ 241 (365)
+|.+||.+ . .--.--.| ..+|..||+-...+
T Consensus 2 ~Cp~Cg~~---~-~~~D~~~g-~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 2 KCPNCGSK---E-IVFDPERG-ELVCPNCGLVLEEN 32 (43)
T ss_dssp SBTTTSSS---E-EEEETTTT-EEEETTT-BBEE-T
T ss_pred CCcCCcCC---c-eEEcCCCC-eEECCCCCCEeecc
Confidence 68888875 2 22333345 67899998766543
No 29
>PRK05978 hypothetical protein; Provisional
Probab=38.14 E-value=12 Score=33.88 Aligned_cols=34 Identities=26% Similarity=0.537 Sum_probs=26.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~ 242 (365)
..+|-+||. -.++| |-..-..-|.+||+.|..+.
T Consensus 33 ~grCP~CG~----G~LF~-g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 33 RGRCPACGE----GKLFR-AFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cCcCCCCCC----Ccccc-cccccCCCccccCCccccCC
Confidence 678999996 45665 55556788999999998764
No 30
>PRK00420 hypothetical protein; Validated
Probab=38.07 E-value=12 Score=32.48 Aligned_cols=31 Identities=29% Similarity=0.674 Sum_probs=24.8
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhc
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~ 241 (365)
...|..|| +|+.|- -+| ...|-.||-.+...
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 46899998 678885 567 89999999977643
No 31
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=37.44 E-value=9.6 Score=34.07 Aligned_cols=31 Identities=32% Similarity=0.552 Sum_probs=21.9
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~ 237 (365)
--.|..|+.. .|-+-+.+- ---.-|+|||-.
T Consensus 102 yVlC~~C~sp--dT~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSP--DTKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCC--CcEEEEcCC-eEEEEcccCCCC
Confidence 4689999998 587877521 113679999954
No 32
>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=36.68 E-value=24 Score=27.92 Aligned_cols=46 Identities=28% Similarity=0.633 Sum_probs=32.5
Q ss_pred ccccccccccccCCCcc--c-cCCCCCchhchHhhhhHHhcCCCCCCCcCC
Q 017834 204 SRICQHCGISEKLTPAM--R-RGPAGPRTLCNACGLMWANKGTLRDLTKGA 251 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~W--R-rGP~G~~tLCNACGl~~~~~~~~r~~~k~~ 251 (365)
...|..|..+ +|--- = -...-|+..|-+|..+|-..|++|.+.-++
T Consensus 5 ~~~CPRC~S~--nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvgg 53 (63)
T PF02701_consen 5 PLPCPRCDST--NTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGG 53 (63)
T ss_pred CCCCCCcCCC--CCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCC
Confidence 5788888876 33111 0 012345789999999999999999986654
No 33
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=36.47 E-value=10 Score=33.65 Aligned_cols=31 Identities=29% Similarity=0.574 Sum_probs=21.7
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~ 237 (365)
--.|..|+.. .|-+-+.+- -.-.-|+|||-.
T Consensus 97 yVlC~~C~sP--dT~l~k~~r-~~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNRP--DTRIIKEGR-VSLLKCEACGAK 127 (133)
T ss_pred eEECCCCCCC--CcEEEEeCC-eEEEecccCCCC
Confidence 3689999998 477777521 112579999964
No 34
>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=34.82 E-value=29 Score=29.33 Aligned_cols=38 Identities=24% Similarity=0.482 Sum_probs=32.3
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCCCC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLR 245 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~r 245 (365)
+..|..|+.. -|.|=.=.-| ..||-.|.-..+.-|++.
T Consensus 3 N~~CaDC~~~---~p~w~s~~~G-ifvC~~CsgiHR~lg~hi 40 (112)
T smart00105 3 NKKCFDCGAP---NPTWASVNLG-VFLCIECSGIHRSLGVHI 40 (112)
T ss_pred CCcccCCCCC---CCCcEEeccc-eeEhHHhHHHHHhcCCCc
Confidence 5799999985 7999988889 899999998888877543
No 35
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=33.77 E-value=14 Score=32.98 Aligned_cols=27 Identities=37% Similarity=0.959 Sum_probs=23.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhH
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~ 238 (365)
...|.-|| ||++| -+| ...|-.||.+.
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 57899998 78999 588 89999999643
No 36
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=33.43 E-value=22 Score=36.95 Aligned_cols=29 Identities=28% Similarity=0.693 Sum_probs=24.9
Q ss_pred ccccccccccccCCCccccCCCCCchhchHh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNAC 234 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNAC 234 (365)
..+|+.||.+...+...-.||.. .+|+.|
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~C 37 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDEC 37 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchH
Confidence 56999999998788888889844 699999
No 37
>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=32.35 E-value=19 Score=25.32 Aligned_cols=32 Identities=28% Similarity=0.605 Sum_probs=20.7
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~ 237 (365)
..+|.+|++- --|..+-...|..-.||-||..
T Consensus 2 p~rC~~C~ay--lNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAY--LNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--B--S-TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCE--ECCcceEcCCCCEEECcCCCCc
Confidence 3689999986 5888888888888899999863
No 38
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=31.77 E-value=24 Score=22.58 Aligned_cols=24 Identities=25% Similarity=0.747 Sum_probs=15.5
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~ 237 (365)
.+.|.+||... +.+ ...|..||..
T Consensus 2 ~~~Cp~Cg~~~---------~~~-~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEI---------DPD-AKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcC---------Ccc-cccChhhCCC
Confidence 35788888752 233 4678888853
No 39
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=31.74 E-value=23 Score=22.33 Aligned_cols=21 Identities=29% Similarity=0.865 Sum_probs=12.0
Q ss_pred ccccccccccCCCccccCCCCCchhchHhhh
Q 017834 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (365)
Q Consensus 206 ~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl 236 (365)
.|.+||... +++ ...|.-||.
T Consensus 1 ~Cp~CG~~~---------~~~-~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEI---------EDD-AKFCPNCGT 21 (23)
T ss_pred CCcccCCCC---------CCc-CcchhhhCC
Confidence 367777652 233 456777764
No 40
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=31.40 E-value=14 Score=34.77 Aligned_cols=33 Identities=27% Similarity=0.543 Sum_probs=23.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHH
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~ 239 (365)
--.|..|+.. .|-+-+.+ .---.-|+|||-..-
T Consensus 98 yV~C~~C~~p--dT~l~k~~-~~~~l~C~aCGa~~~ 130 (201)
T PRK12336 98 YVICSECGLP--DTRLVKED-RVLMLRCDACGAHRP 130 (201)
T ss_pred eEECCCCCCC--CcEEEEcC-CeEEEEcccCCCCcc
Confidence 3689999998 58887763 111357999996543
No 41
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=31.37 E-value=17 Score=35.23 Aligned_cols=24 Identities=21% Similarity=0.642 Sum_probs=15.8
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~ 237 (365)
.+.|.|||.+ +..| ..+|-.||-+
T Consensus 354 ~~~c~~cg~~---~~~~-------~~~c~~c~~~ 377 (389)
T PRK11788 354 RYRCRNCGFT---ARTL-------YWHCPSCKAW 377 (389)
T ss_pred CEECCCCCCC---Cccc-------eeECcCCCCc
Confidence 4778888886 3344 3467777754
No 42
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=31.27 E-value=15 Score=40.08 Aligned_cols=45 Identities=16% Similarity=0.173 Sum_probs=31.7
Q ss_pred CCCCCCCCCCCCC-CC----CC-CCCCCchhhhhhcccCCCC-CcCceeccC
Q 017834 283 EQGSPHETKPAPL-DP----QN-HSMRSNEQYLLESDDGFAC-PLPIQEDNS 327 (365)
Q Consensus 283 ~~~s~~~sk~v~~-d~----~~-~~~~~~eq~l~Ea~e~~t~-~Lp~~v~~s 327 (365)
...+++-.|++.. +- .+ ...+++.+.|++=+|+++. ..|.+|.-.
T Consensus 330 ~~~~~e~lktf~Nttlg~~~~~~~~E~~~~e~ll~R~e~y~a~~VPdgv~~L 381 (611)
T COG5525 330 ATGSPEKLKTFVNTTLGRPWEEKWGEQADHEALLARAEVYPARSVPDGVLVL 381 (611)
T ss_pred ccCChhhceeeeecccCccchhhhhhhcchHHHHhccccCccccccCceeEE
Confidence 4556666665332 11 33 6889999999999999998 788877544
No 43
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=30.96 E-value=17 Score=31.62 Aligned_cols=86 Identities=21% Similarity=0.431 Sum_probs=45.4
Q ss_pred ccccCCceeeeccch----hhHhhh--hhccccccccccccccccCCCCCCCCCCCCcccccccccccccccC--CCccc
Q 017834 150 KERSFEKKIRYSCRK----EVAQRM--QRKNGQFTSSKATFNIASANSNPSNGSAPPESVSRICQHCGISEKL--TPAMR 221 (365)
Q Consensus 150 k~R~f~KkirYs~RK----~~A~r~--~R~KGqFas~k~~~~~~s~~~~s~~~~~~~~~~~~~C~~Cg~t~~~--TP~WR 221 (365)
|+..+++++.|++|. ..|..+ .+.+++-.-..- . .-..+-+...-.|....+.|..||-.+.- -++=|
T Consensus 17 kEDked~~L~laCrnCd~ve~A~s~~vY~~~~~~e~dE~---t-~ii~Dl~~DPTLPrts~~~C~~C~~~eavffQ~~~~ 92 (113)
T KOG2691|consen 17 KEDKEDRILLLACRNCDYVEEADSSRVYVNELSHEHDEL---T-QIIMDLASDPTLPRTSDKHCPKCGHREAVFFQAQTR 92 (113)
T ss_pred cccccccEEEEEecCCcceEecCCcceEcCCcccchhhH---H-HHHHhhccCCCcCccccccCCccCCcceEEEecccc
Confidence 456788899999985 333322 234332110000 0 00001112222233347899999986411 34556
Q ss_pred cCCCCCc--hhchHhhhhHH
Q 017834 222 RGPAGPR--TLCNACGLMWA 239 (365)
Q Consensus 222 rGP~G~~--tLCNACGl~~~ 239 (365)
|+..+-. .+|-.||-+|.
T Consensus 93 r~d~~m~l~yvC~~C~h~wt 112 (113)
T KOG2691|consen 93 RADEAMRLFYVCCSCGHRWT 112 (113)
T ss_pred cccceEEEEEEecccccccc
Confidence 6666633 47888998884
No 44
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=30.89 E-value=29 Score=34.84 Aligned_cols=32 Identities=22% Similarity=0.647 Sum_probs=25.8
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhhhHHh
Q 017834 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (365)
Q Consensus 205 ~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (365)
+.|..|.... +.|--.-..+| +||+|--+-.+
T Consensus 2 ~~C~~C~~~~-t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMPT-TRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCCC-CCCCeeECCCC---CchhhhhHHhh
Confidence 5799999985 77777777788 99999987643
No 45
>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=30.53 E-value=17 Score=24.79 Aligned_cols=30 Identities=23% Similarity=0.624 Sum_probs=21.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl 236 (365)
.-+|..||.. -..|+.--++....|-.||.
T Consensus 5 ~y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 3479999974 44555444466778999997
No 46
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=30.14 E-value=29 Score=35.51 Aligned_cols=36 Identities=25% Similarity=0.506 Sum_probs=30.2
Q ss_pred ccccccccccccCCCccccCC---CCCchhchHhhhhHH
Q 017834 204 SRICQHCGISEKLTPAMRRGP---AGPRTLCNACGLMWA 239 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP---~G~~tLCNACGl~~~ 239 (365)
...|..|..+.-.+..||-|| .-.++.|+.|+..-.
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 458999999988899999999 556789999986554
No 47
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=30.04 E-value=18 Score=36.09 Aligned_cols=31 Identities=29% Similarity=0.652 Sum_probs=22.5
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (365)
.+.|.+||+. +.+ ...|.+.+|+.||.++--
T Consensus 111 ~RFCg~CG~~--~~~----~~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 111 HRFCGRCGTK--TYP----REGGWARVCPKCGHEHFP 141 (279)
T ss_pred CcCCCCCCCc--Ccc----ccCceeeeCCCCCCccCC
Confidence 6899999985 222 245667899999987764
No 48
>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=29.44 E-value=14 Score=28.18 Aligned_cols=30 Identities=30% Similarity=0.683 Sum_probs=21.2
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHH
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~ 239 (365)
...|..||.... . ...+....|..||..+.
T Consensus 28 Sq~C~~CG~~~~-~-----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRNK-K-----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCcccccc-c-----ccccceEEcCCCCCEEC
Confidence 468999998732 2 44555789999998643
No 49
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.81 E-value=22 Score=31.54 Aligned_cols=35 Identities=29% Similarity=0.568 Sum_probs=23.5
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (365)
-.+|-+||-- -+.| |=--...-|.|||+-|-.+..
T Consensus 21 ~grCP~CGeG----rLF~-gFLK~~p~C~aCG~dyg~~~a 55 (126)
T COG5349 21 RGRCPRCGEG----RLFR-GFLKVVPACEACGLDYGFADA 55 (126)
T ss_pred cCCCCCCCCc----hhhh-hhcccCchhhhccccccCCcc
Confidence 6799999953 2333 222335689999999987653
No 50
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=28.72 E-value=27 Score=35.41 Aligned_cols=36 Identities=25% Similarity=0.528 Sum_probs=30.7
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (365)
...|..||.. + |.|=.-.-| -.||--|-=..|.=|+
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 6899999997 4 999999999 8999999766665544
No 51
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.01 E-value=20 Score=29.52 Aligned_cols=35 Identities=31% Similarity=0.582 Sum_probs=24.5
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhc
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~ 241 (365)
.-.|.+||-.-.--..++. .+-+.|.+||-++++.
T Consensus 12 ~Y~c~~cg~~~dvvq~~~d---dplt~ce~c~a~~kk~ 46 (82)
T COG2331 12 SYECTECGNRFDVVQAMTD---DPLTTCEECGARLKKL 46 (82)
T ss_pred EEeecccchHHHHHHhccc---CccccChhhChHHHHh
Confidence 4689999975323445554 4467999999988764
No 52
>COG4683 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.16 E-value=41 Score=29.46 Aligned_cols=21 Identities=38% Similarity=0.762 Sum_probs=14.7
Q ss_pred cceEEEccEEEEeCCCChHHHHHHHHHhcC
Q 017834 76 ELTVAYEGEVYVFPAVTPHKVQALLLLLGE 105 (365)
Q Consensus 76 QLTIfY~G~V~VFD~VppeKaqaImllagg 105 (365)
+.-|+| -|| |-. |+|||++|.
T Consensus 67 piRilf-----AFD---P~R-~AIlL~~Gn 87 (120)
T COG4683 67 PIRILF-----AFD---PAR-QAILLLGGN 87 (120)
T ss_pred eEEEEE-----ecC---hHh-HHHhhhccC
Confidence 667765 477 544 789999884
No 53
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.71 E-value=31 Score=38.10 Aligned_cols=36 Identities=22% Similarity=0.527 Sum_probs=29.4
Q ss_pred ccccccccccccCCCccccCCCC---CchhchHhhhhHHhc
Q 017834 204 SRICQHCGISEKLTPAMRRGPAG---PRTLCNACGLMWANK 241 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G---~~tLCNACGl~~~~~ 241 (365)
.-.|..|.+- -||.|+.-+.| ..++|.+|----.++
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 5789999996 79999998888 458999997665554
No 54
>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=25.18 E-value=24 Score=31.02 Aligned_cols=29 Identities=31% Similarity=0.673 Sum_probs=21.5
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhh
Q 017834 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (365)
Q Consensus 205 ~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl 236 (365)
-.|..|+.. .|-+-+.+-. --.-|+|||-
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 579999988 4877777322 2468999994
No 55
>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=25.09 E-value=26 Score=31.89 Aligned_cols=59 Identities=15% Similarity=0.219 Sum_probs=37.7
Q ss_pred ccccccccccCCCccccCCCC----CchhchHhhhhHHhcCCCC-----CCCcCCCcccccccccCCC
Q 017834 206 ICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKGTLR-----DLTKGARNICFEQHELETS 264 (365)
Q Consensus 206 ~C~~Cg~t~~~TP~WRrGP~G----~~tLCNACGl~~~~~~~~r-----~~~k~~~~i~~~q~~~~~~ 264 (365)
+|..|+...+..=-=|...+| .+--|.+||.+|-..-+.. =+++.+..-.|....+...
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l~ViKkdG~re~Fdr~Kl~~g 69 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRG 69 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccccEEEcCCCCCCCCCHHHHHHH
Confidence 688999875444444555566 2468999999987654432 2455666666666665543
No 56
>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=24.59 E-value=24 Score=25.02 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=19.2
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhh
Q 017834 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (365)
Q Consensus 205 ~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl 236 (365)
-+|..||.. --.|+..-+.....|-+||-
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHE---FEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCE---EEEEEEcCCCCCCcCCCCCC
Confidence 478899954 33444444455678999986
No 57
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.39 E-value=23 Score=30.13 Aligned_cols=35 Identities=20% Similarity=0.329 Sum_probs=22.6
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhc
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~ 241 (365)
.-.|.+|+.....-++=| .-....|..||.|+.+.
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 578999994311112222 34478999999998763
No 58
>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=23.36 E-value=22 Score=26.98 Aligned_cols=22 Identities=32% Similarity=0.892 Sum_probs=16.6
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl 236 (365)
...|.+||.. -=+..+|-.||.
T Consensus 26 l~~C~~cG~~-----------~~~H~vc~~cG~ 47 (55)
T TIGR01031 26 LVVCPNCGEF-----------KLPHRVCPSCGY 47 (55)
T ss_pred ceECCCCCCc-----------ccCeeECCccCe
Confidence 4679999974 223789999993
No 59
>PF14122 YokU: YokU-like protein
Probab=22.39 E-value=25 Score=29.48 Aligned_cols=41 Identities=24% Similarity=0.757 Sum_probs=26.0
Q ss_pred ccccccccc---cCCCccccCCCCCc---------hhchHhhhhHHhcCCCCC
Q 017834 206 ICQHCGISE---KLTPAMRRGPAGPR---------TLCNACGLMWANKGTLRD 246 (365)
Q Consensus 206 ~C~~Cg~t~---~~TP~WRrGP~G~~---------tLCNACGl~~~~~~~~r~ 246 (365)
.|..|+... ..+.....=|+|.+ ..|+.||+-|.......+
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d~vi~E 53 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDDEVIKE 53 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehhHHHHH
Confidence 477887641 11333334478864 589999999987665443
No 60
>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=22.16 E-value=13 Score=26.11 Aligned_cols=34 Identities=26% Similarity=0.644 Sum_probs=16.2
Q ss_pred ccccccccccC--CCccccCCCCCc--hhchHhhhhHH
Q 017834 206 ICQHCGISEKL--TPAMRRGPAGPR--TLCNACGLMWA 239 (365)
Q Consensus 206 ~C~~Cg~t~~~--TP~WRrGP~G~~--tLCNACGl~~~ 239 (365)
.|..||-.+.. .-+-|.+.++.. ..|..||-.|+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 46677765211 123455555522 35777777663
No 61
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=22.02 E-value=36 Score=36.08 Aligned_cols=36 Identities=28% Similarity=0.635 Sum_probs=31.8
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (365)
++.|+.|+.. -|-|=.=+.| -.||--|---.+.-|+
T Consensus 23 NKvCFDCgAk---nPtWaSVTYG-IFLCiDCSAvHRnLGV 58 (454)
T KOG0706|consen 23 NKVCFDCGAK---NPTWASVTYG-IFLCIDCSAVHRNLGV 58 (454)
T ss_pred CceecccCCC---CCCceeecce-EEEEEecchhhhcccc
Confidence 6899999984 9999999999 8999999877777655
No 62
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=21.90 E-value=51 Score=34.31 Aligned_cols=36 Identities=25% Similarity=0.559 Sum_probs=29.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (365)
+..|..|+.. -|.|=.-..| ..||-.|.=..+.-|+
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 6799999985 6999998899 8999999766665443
No 63
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=21.86 E-value=28 Score=26.94 Aligned_cols=23 Identities=13% Similarity=0.062 Sum_probs=16.5
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhH
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~ 238 (365)
...|.+||.. -=+..+|- ||.|.
T Consensus 27 ~~~c~~cg~~-----------~~pH~vc~-cG~Y~ 49 (60)
T PRK01110 27 LSVDKTTGEY-----------HLPHHVSP-KGYYK 49 (60)
T ss_pred eeEcCCCCce-----------eccceecC-CcccC
Confidence 4689999985 22367899 99543
No 64
>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=21.54 E-value=32 Score=24.86 Aligned_cols=30 Identities=23% Similarity=0.584 Sum_probs=20.9
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl 236 (365)
.-+|..||.. --.|+.--+.....|-.||-
T Consensus 5 ey~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHR---FEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCE---eEEEEecCCCCCCCCCCCCC
Confidence 3579999975 44676533444677999997
No 65
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=21.28 E-value=22 Score=33.85 Aligned_cols=40 Identities=25% Similarity=0.510 Sum_probs=25.9
Q ss_pred ccccccccccccCC--Ccccc-CCCCCchhchHhhhhHHhcCCCCC
Q 017834 204 SRICQHCGISEKLT--PAMRR-GPAGPRTLCNACGLMWANKGTLRD 246 (365)
Q Consensus 204 ~~~C~~Cg~t~~~T--P~WRr-GP~G~~tLCNACGl~~~~~~~~r~ 246 (365)
...|-.|+ .+ .+ -.-+. |++ +-.-|+.||..|...-+.+.
T Consensus 6 y~~Cp~Cg-~e-ev~hEVik~~g~~-~lvrC~eCG~V~~~~i~~~k 48 (201)
T COG1326 6 YIECPSCG-SE-EVSHEVIKERGRE-PLVRCEECGTVHPAIIKTPK 48 (201)
T ss_pred EEECCCCC-cc-hhhHHHHHhcCCc-eEEEccCCCcEeeceeeccc
Confidence 57899999 43 34 33344 443 46679999999965444444
No 66
>PF11228 DUF3027: Protein of unknown function (DUF3027); InterPro: IPR021391 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.09 E-value=28 Score=32.99 Aligned_cols=30 Identities=27% Similarity=0.593 Sum_probs=25.0
Q ss_pred CCccccCCCCCc--------hhchHhhhhHHhcCCCCC
Q 017834 217 TPAMRRGPAGPR--------TLCNACGLMWANKGTLRD 246 (365)
Q Consensus 217 TP~WRrGP~G~~--------tLCNACGl~~~~~~~~r~ 246 (365)
-..|++|+.||+ ..|.-||.|+...|.|+.
T Consensus 126 a~RW~~g~~GP~s~~a~~a~~~C~tCgF~~plaG~L~~ 163 (193)
T PF11228_consen 126 AQRWYEGEFGPDSEMARAAPAQCSTCGFYVPLAGSLGQ 163 (193)
T ss_pred HHHHHcCCCCCCCHHHHhcccCCCcCccceEcCCchhc
Confidence 457888888887 479999999999888875
No 67
>PRK12496 hypothetical protein; Provisional
Probab=20.95 E-value=43 Score=30.48 Aligned_cols=32 Identities=25% Similarity=0.621 Sum_probs=22.2
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHhcCC
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (365)
..+|..|+.. .+. ++ ....|--||...+++..
T Consensus 127 ~~~C~gC~~~---~~~---~~--~~~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 127 RKVCKGCKKK---YPE---DY--PDDVCEICGSPVKRKMV 158 (164)
T ss_pred eEECCCCCcc---ccC---CC--CCCcCCCCCChhhhcch
Confidence 4689999975 221 11 13589999999887765
No 68
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=20.41 E-value=64 Score=32.76 Aligned_cols=29 Identities=28% Similarity=0.697 Sum_probs=21.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~ 237 (365)
...|.+||+. .|+-. +.|.--.|-+||..
T Consensus 315 ~nfc~ncG~~--~t~~~---~ng~a~fcp~cgq~ 343 (345)
T COG4260 315 LNFCLNCGCG--TTADF---DNGKAKFCPECGQG 343 (345)
T ss_pred cccccccCcc--cccCC---ccchhhhChhhcCC
Confidence 4589999975 46533 56666799999964
No 69
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=20.40 E-value=34 Score=32.35 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=22.5
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhhhHHh
Q 017834 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (365)
Q Consensus 204 ~~~C~~Cg~t~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (365)
--+|++|+ +++.| .|....|-.||.-=++
T Consensus 149 ~A~CsrC~-----~~L~~---~~~~l~Cp~Cg~tEkR 177 (188)
T COG1096 149 YARCSRCR-----APLVK---KGNMLKCPNCGNTEKR 177 (188)
T ss_pred EEEccCCC-----cceEE---cCcEEECCCCCCEEee
Confidence 56899998 56888 6777899999965443
Done!