Query 018641
Match_columns 352
No_of_seqs 284 out of 766
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 02:48:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018641.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018641hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06203 CCT: CCT motif; Inte 99.4 4.4E-14 9.6E-19 102.4 3.2 44 153-196 1-44 (45)
2 cd00202 ZnF_GATA Zinc finger D 99.4 6.2E-14 1.3E-18 105.0 4.1 44 224-269 1-44 (54)
3 PF06200 tify: tify domain; I 99.4 1.2E-13 2.7E-18 95.8 4.8 34 86-119 2-35 (36)
4 smart00401 ZnF_GATA zinc finge 99.4 2.2E-13 4.7E-18 101.2 3.3 45 222-268 3-48 (52)
5 PF00320 GATA: GATA zinc finge 99.4 1.6E-13 3.6E-18 94.7 1.4 36 225-262 1-36 (36)
6 KOG1601 GATA-4/5/6 transcripti 98.4 1.6E-07 3.4E-12 84.3 3.3 46 222-269 199-244 (340)
7 COG5641 GAT1 GATA Zn-finger-co 97.8 7.6E-06 1.6E-10 85.1 1.5 52 219-272 155-211 (498)
8 PF09425 CCT_2: Divergent CCT 97.0 0.00039 8.5E-09 45.7 1.5 24 152-176 3-26 (27)
9 KOG1601 GATA-4/5/6 transcripti 82.1 0.5 1.1E-05 42.4 0.4 41 150-190 290-330 (340)
10 COG5641 GAT1 GATA Zn-finger-co 81.3 0.72 1.6E-05 48.8 1.3 52 222-274 297-348 (498)
11 KOG3554 Histone deacetylase co 69.8 8.2 0.00018 41.0 5.3 40 222-263 386-427 (693)
12 KOG1819 FYVE finger-containing 68.3 4.5 9.8E-05 43.3 3.1 43 2-48 393-446 (990)
13 PF14803 Nudix_N_2: Nudix N-te 59.6 3.1 6.7E-05 28.7 0.1 29 224-254 2-30 (34)
14 PF06689 zf-C4_ClpX: ClpX C4-t 49.5 9.1 0.0002 27.1 1.1 33 223-256 2-34 (41)
15 PF13717 zinc_ribbon_4: zinc-r 46.5 4.9 0.00011 27.8 -0.6 33 223-256 3-35 (36)
16 PF04810 zf-Sec23_Sec24: Sec23 46.5 8.2 0.00018 27.1 0.5 30 223-254 3-32 (40)
17 COG5349 Uncharacterized protei 38.6 12 0.00027 33.0 0.5 35 220-259 19-53 (126)
18 PRK11823 DNA repair protein Ra 37.0 12 0.00025 38.9 0.1 17 222-239 7-23 (446)
19 TIGR00416 sms DNA repair prote 36.5 13 0.00028 38.7 0.3 17 222-239 7-23 (454)
20 PF09889 DUF2116: Uncharacteri 36.0 19 0.00042 27.8 1.1 29 223-261 4-33 (59)
21 PF02701 zf-Dof: Dof domain, z 34.8 28 0.0006 27.5 1.8 46 222-269 5-53 (63)
22 COG1631 RPL42A Ribosomal prote 34.0 24 0.00051 29.8 1.4 21 221-241 67-87 (94)
23 PF01412 ArfGap: Putative GTPa 32.1 39 0.00084 28.6 2.5 36 222-261 13-48 (116)
24 TIGR02098 MJ0042_CXXC MJ0042 f 31.6 7.9 0.00017 26.3 -1.5 33 223-256 3-35 (38)
25 smart00653 eIF2B_5 domain pres 30.5 19 0.00041 30.8 0.3 27 224-254 82-109 (110)
26 PRK05342 clpX ATP-dependent pr 29.8 29 0.00063 35.8 1.6 32 222-255 9-40 (412)
27 PRK05978 hypothetical protein; 29.3 21 0.00045 32.3 0.4 33 222-259 33-65 (148)
28 cd01121 Sms Sms (bacterial rad 28.5 20 0.00044 36.4 0.2 8 224-231 2-9 (372)
29 PF08271 TF_Zn_Ribbon: TFIIB z 27.2 24 0.00052 24.8 0.3 30 224-258 2-31 (43)
30 KOG3740 Uncharacterized conser 26.9 26 0.00057 38.4 0.7 36 222-259 462-500 (706)
31 PF13619 KTSC: KTSC domain 26.2 76 0.0016 23.8 2.9 30 87-116 13-43 (60)
32 PF14812 PBP1_TM: Transmembran 25.8 23 0.00049 29.1 0.0 18 30-47 37-54 (81)
33 PF01783 Ribosomal_L32p: Ribos 24.8 19 0.0004 27.1 -0.6 21 222-253 26-46 (56)
34 KOG1598 Transcription initiati 24.8 35 0.00075 36.6 1.1 32 224-260 2-33 (521)
35 PRK11788 tetratricopeptide rep 23.8 30 0.00064 33.3 0.4 9 223-231 355-363 (389)
36 COG2331 Uncharacterized protei 23.8 23 0.00051 29.0 -0.3 36 222-260 12-47 (82)
37 PRK12286 rpmF 50S ribosomal pr 23.6 26 0.00056 26.7 -0.1 22 223-255 28-49 (57)
38 TIGR00311 aIF-2beta translatio 23.5 26 0.00057 31.0 -0.1 29 224-255 99-127 (133)
39 COG2816 NPY1 NTP pyrophosphohy 23.1 26 0.00056 34.8 -0.2 34 219-258 108-141 (279)
40 PRK03988 translation initiatio 22.9 27 0.00059 31.1 -0.1 29 224-255 104-132 (138)
41 TIGR00244 transcriptional regu 21.9 35 0.00075 31.0 0.4 38 224-261 2-43 (147)
42 COG3952 Predicted membrane pro 21.6 26 0.00056 30.4 -0.5 19 237-257 76-94 (113)
43 PF06677 Auto_anti-p27: Sjogre 21.3 36 0.00078 24.4 0.3 25 222-253 17-41 (41)
44 PRK12336 translation initiatio 20.6 32 0.00069 32.2 -0.1 31 224-257 100-130 (201)
45 PLN00162 transport protein sec 20.2 31 0.00068 38.3 -0.3 32 222-255 53-84 (761)
46 PRK14892 putative transcriptio 20.2 26 0.00055 29.7 -0.8 35 222-259 21-55 (99)
No 1
>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=99.45 E-value=4.4e-14 Score=102.39 Aligned_cols=44 Identities=50% Similarity=0.761 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhhhcccccccccchhhHHHHHHhhhccCCccccc
Q 018641 153 RIASLVRFREKRKERCFDKKIRYSVRKEVAQRMHRKNGQFASLK 196 (352)
Q Consensus 153 R~asL~RfREKRKeR~f~KkirYs~RK~~A~~r~R~KgrF~~~k 196 (352)
|.++|+||+|||+.|+|+|+|+|++||.+|+.|+|+||||++..
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 57899999999999999999999999999999999999998765
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=99.45 E-value=6.2e-14 Score=104.97 Aligned_cols=44 Identities=55% Similarity=1.141 Sum_probs=40.1
Q ss_pred ccccccCCCCCCCccccCCCCCcccchHHHHHHHhcCCCCCCCcCC
Q 018641 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTLRDLSKGG 269 (352)
Q Consensus 224 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~r~~~k~~ 269 (352)
.|++|++ +.||+||+||.|..+|||||||||++++..|+..+..
T Consensus 1 ~C~~C~~--~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGT--TTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCC--CCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 4999999 5799999999999999999999999999999887764
No 3
>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=99.44 E-value=1.2e-13 Score=95.77 Aligned_cols=34 Identities=38% Similarity=0.701 Sum_probs=32.1
Q ss_pred cCCcceeeeeecCeEEEecCCCHHHHHHHHHhhC
Q 018641 86 ASRTSELTLSFEGEVYVFPAVTPEKVQAVLLLLG 119 (352)
Q Consensus 86 ~~~tsqLTi~y~GeV~VFdsVspeKvqaVllL~g 119 (352)
++.++||||||+|+|+|||+||+|||++||+|++
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 4678999999999999999999999999999986
No 4
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.38 E-value=2.2e-13 Score=101.17 Aligned_cols=45 Identities=53% Similarity=1.053 Sum_probs=39.3
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHHHHHHhcCCC-CCCCcC
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTL-RDLSKG 268 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~-r~~~k~ 268 (352)
...|++|++ +.||+||+||.|+.+|||||||+|++++.+ |+..+.
T Consensus 3 ~~~C~~C~~--~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~ 48 (52)
T smart00401 3 GRSCSNCGT--TETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLK 48 (52)
T ss_pred CCCcCCCCC--CCCCccccCCCCCCcEeecccHHHHHcCCCCCccccc
Confidence 357999999 569999999999999999999999999988 665443
No 5
>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=99.36 E-value=1.6e-13 Score=94.69 Aligned_cols=36 Identities=56% Similarity=1.230 Sum_probs=28.0
Q ss_pred cccccCCCCCCCccccCCCCCcccchHHHHHHHhcCCC
Q 018641 225 CQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTL 262 (352)
Q Consensus 225 C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~ 262 (352)
|.+|++ +.||+||+||.|+.+|||+||++|++++++
T Consensus 1 C~~C~t--t~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGT--TETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT----ST-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcC--CCCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 899999 469999999999989999999999998764
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.41 E-value=1.6e-07 Score=84.27 Aligned_cols=46 Identities=48% Similarity=1.068 Sum_probs=38.3
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHHHHHHhcCCCCCCCcCC
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTLRDLSKGG 269 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~r~~~k~~ 269 (352)
...|.+|++ +.||+||++|.|+..+|||||++|+++...|.+....
T Consensus 199 ~~~c~~~~~--~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~ 244 (340)
T KOG1601|consen 199 LRQCSNCGT--TKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKR 244 (340)
T ss_pred CcccCCCCC--CCCcceecCCCCCccccccchhhhhhcCccccccccC
Confidence 468999999 5799999999999999999999999997444444443
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.79 E-value=7.6e-06 Score=85.09 Aligned_cols=52 Identities=33% Similarity=0.611 Sum_probs=42.3
Q ss_pred cccccccccccCCCCCCCccccCCCC----CcccchHHHHHHHhcCCCC-CCCcCCCCC
Q 018641 219 ETVVRRCQHCGVSENNTPAMRRGPAG----PRTLCNACGLMWANKGTLR-DLSKGGRSL 272 (352)
Q Consensus 219 e~~~~~C~~Cg~~~~~Tp~wR~GP~G----~~~LCNACGl~~~~~~~~r-~~~k~~~~~ 272 (352)
+.+...|.+|.+ +.||+|||+..+ .-.|||||||+|+-|+++| +++.+...+
T Consensus 155 s~~~~vc~Nc~t--~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ 211 (498)
T COG5641 155 SNQPHVCSNCKT--TSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSI 211 (498)
T ss_pred ccccchhccccc--cCCccccccccccccCCccccccccccccccCCcCCCcccccccc
Confidence 333448999999 579999999994 3799999999999999999 776654433
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=96.97 E-value=0.00039 Score=45.72 Aligned_cols=24 Identities=54% Similarity=0.627 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHhhhcccccccccch
Q 018641 152 RRIASLVRFREKRKERCFDKKIRYS 176 (352)
Q Consensus 152 ~R~asL~RfREKRKeR~f~KkirYs 176 (352)
.|.+||+||.||||+|... +..|.
T Consensus 3 aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 3 ARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp ---HHHHHHHHHH------------
T ss_pred hHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 6899999999999999988 66664
No 9
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=82.11 E-value=0.5 Score=42.42 Aligned_cols=41 Identities=44% Similarity=0.680 Sum_probs=38.2
Q ss_pred hHHHHHHHHHHHHhhhcccccccccchhhHHHHHHhhhccC
Q 018641 150 LSRRIASLVRFREKRKERCFDKKIRYSVRKEVAQRMHRKNG 190 (352)
Q Consensus 150 ls~R~asL~RfREKRKeR~f~KkirYs~RK~~A~~r~R~Kg 190 (352)
...|.+.+.|++++++.|.|.++++|..|+..++.++|.|+
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 45789999999999999999999999999999999999887
No 10
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=81.29 E-value=0.72 Score=48.77 Aligned_cols=52 Identities=25% Similarity=0.236 Sum_probs=42.6
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHHHHHHhcCCCCCCCcCCCCCcc
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTLRDLSKGGRSLSM 274 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~r~~~k~~~~~~~ 274 (352)
...|.+|++. +.||.||+...---.+||+||++-+..+..+++.++......
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 4568999875 579999999877789999999999999999988886554444
No 11
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=69.83 E-value=8.2 Score=41.00 Aligned_cols=40 Identities=25% Similarity=0.577 Sum_probs=31.4
Q ss_pred ccccccccCCCCCCCcccc--CCCCCcccchHHHHHHHhcCCCC
Q 018641 222 VRRCQHCGVSENNTPAMRR--GPAGPRTLCNACGLMWANKGTLR 263 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~--GP~G~~~LCNACGl~~~~~~~~r 263 (352)
.+.|-.|++ +..-+|-. +|.-...||..|=++|+|.+-|.
T Consensus 386 g~~CEsC~t--tqs~qWYsWGppnmqcrLCasCWiyWKKygGLk 427 (693)
T KOG3554|consen 386 GRACESCYT--TQSLQWYSWGPPNMQCRLCASCWIYWKKYGGLK 427 (693)
T ss_pred CCccccccc--ccccceeccCCCCccchhhHHHHHHHHHhcCcC
Confidence 467999999 56777754 55566689999999999987654
No 12
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=68.25 E-value=4.5 Score=43.29 Aligned_cols=43 Identities=44% Similarity=0.701 Sum_probs=27.7
Q ss_pred CCCCCCCCCCCCCccc-----------cCCCCceecCCCCCCCCCCCccccccCCccc
Q 018641 2 AAANPQPLQARPFEEH-----------ARAPPIQIEDEDGDYEDGEGMDDIDEGNINS 48 (352)
Q Consensus 2 ~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 48 (352)
+.+-|.|- +.|+| .+.||++.+|.|++.+|||+.| ++|.+|+|
T Consensus 393 ~~aspaps---~s~~hsiastssaatsstnppad~~dgdde~eddddid-vdeedies 446 (990)
T KOG1819|consen 393 ALASPAPS---GSEEHSIASTSSAATSSTNPPADNEDGDDEAEDDDDID-VDEEDIES 446 (990)
T ss_pred cccCCCCC---CCccccccccccccccCCCCccccccCcccccCccccc-cccccccc
Confidence 34556665 78888 3578899888887666655543 34445555
No 13
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=59.62 E-value=3.1 Score=28.71 Aligned_cols=29 Identities=31% Similarity=0.739 Sum_probs=15.2
Q ss_pred ccccccCCCCCCCccccCCCCCcccchHHHH
Q 018641 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGL 254 (352)
Q Consensus 224 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 254 (352)
.|.+||.. .+..-=.|..-.+..|.+||.
T Consensus 2 fC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGP--LERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred ccccccCh--hhhhcCCCCCccceECCCCCC
Confidence 59999973 232223566777899999985
No 14
>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=49.45 E-value=9.1 Score=27.11 Aligned_cols=33 Identities=30% Similarity=0.749 Sum_probs=21.8
Q ss_pred cccccccCCCCCCCccccCCCCCcccchHHHHHH
Q 018641 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (352)
Q Consensus 223 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 256 (352)
.+|+.||.+...+-..=.||.+ -..|+.|=...
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~~ 34 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQA 34 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHHH
Confidence 4799999987666666688977 79999996543
No 15
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=46.55 E-value=4.9 Score=27.77 Aligned_cols=33 Identities=21% Similarity=0.627 Sum_probs=27.9
Q ss_pred cccccccCCCCCCCccccCCCCCcccchHHHHHH
Q 018641 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (352)
Q Consensus 223 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 256 (352)
..|-+|++. ...+..+-.+.|...-|-.||-.|
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 369999987 478888888999899999999776
No 16
>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=46.51 E-value=8.2 Score=27.07 Aligned_cols=30 Identities=30% Similarity=0.672 Sum_probs=20.5
Q ss_pred cccccccCCCCCCCccccCCCCCcccchHHHH
Q 018641 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGL 254 (352)
Q Consensus 223 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 254 (352)
.+|.+|++ -.-|..+-...|....|+.|+.
T Consensus 3 ~rC~~C~a--ylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRA--YLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp -B-TTT----BS-TTSEEETTTTEEEETTT--
T ss_pred cccCCCCC--EECCcceEcCCCCEEECcCCCC
Confidence 57999998 5689999888998999999986
No 17
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.57 E-value=12 Score=32.98 Aligned_cols=35 Identities=31% Similarity=0.621 Sum_probs=26.6
Q ss_pred ccccccccccCCCCCCCccccCCCCCcccchHHHHHHHhc
Q 018641 220 TVVRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (352)
Q Consensus 220 ~~~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~ 259 (352)
.+..+|-+||.- .-.+|.--...-|.|||+-|-.+
T Consensus 19 Gl~grCP~CGeG-----rLF~gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 19 GLRGRCPRCGEG-----RLFRGFLKVVPACEACGLDYGFA 53 (126)
T ss_pred HhcCCCCCCCCc-----hhhhhhcccCchhhhccccccCC
Confidence 335679999973 35567777788999999998665
No 18
>PRK11823 DNA repair protein RadA; Provisional
Probab=37.02 E-value=12 Score=38.86 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=11.1
Q ss_pred ccccccccCCCCCCCccc
Q 018641 222 VRRCQHCGVSENNTPAMR 239 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR 239 (352)
...|.+||.. +..|.||
T Consensus 7 ~y~C~~Cg~~-~~~~~g~ 23 (446)
T PRK11823 7 AYVCQECGAE-SPKWLGR 23 (446)
T ss_pred eEECCcCCCC-CcccCee
Confidence 4679999985 2444443
No 19
>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=36.49 E-value=13 Score=38.72 Aligned_cols=17 Identities=29% Similarity=0.512 Sum_probs=11.8
Q ss_pred ccccccccCCCCCCCccc
Q 018641 222 VRRCQHCGVSENNTPAMR 239 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR 239 (352)
..+|.+||.. ...|+||
T Consensus 7 ~y~C~~Cg~~-~~~~~g~ 23 (454)
T TIGR00416 7 KFVCQHCGAD-SPKWQGK 23 (454)
T ss_pred eEECCcCCCC-CccccEE
Confidence 4689999986 3555554
No 20
>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=36.02 E-value=19 Score=27.80 Aligned_cols=29 Identities=21% Similarity=0.697 Sum_probs=22.0
Q ss_pred cccccccCCCCCCCccccCCCCCcccc-hHHHHHHHhcCC
Q 018641 223 RRCQHCGVSENNTPAMRRGPAGPRTLC-NACGLMWANKGT 261 (352)
Q Consensus 223 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LC-NACGl~~~~~~~ 261 (352)
+.|.+||.+. | .. +..| ..|+.-|.++++
T Consensus 4 kHC~~CG~~I---p------~~-~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 4 KHCPVCGKPI---P------PD-ESFCSPKCREEYRKRQK 33 (59)
T ss_pred CcCCcCCCcC---C------cc-hhhhCHHHHHHHHHHHH
Confidence 4699999863 3 22 7899 599999998753
No 21
>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=34.76 E-value=28 Score=27.45 Aligned_cols=46 Identities=33% Similarity=0.715 Sum_probs=32.9
Q ss_pred ccccccccCCCCCCCccc---cCCCCCcccchHHHHHHHhcCCCCCCCcCC
Q 018641 222 VRRCQHCGVSENNTPAMR---RGPAGPRTLCNACGLMWANKGTLRDLSKGG 269 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR---~GP~G~~~LCNACGl~~~~~~~~r~~~k~~ 269 (352)
...|..|... .|-+.= --..-|+..|-+|..+|-..|+||.+-.++
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 4578888863 343321 124457899999999999999999885543
No 22
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=33.97 E-value=24 Score=29.82 Aligned_cols=21 Identities=33% Similarity=0.767 Sum_probs=16.7
Q ss_pred cccccccccCCCCCCCccccC
Q 018641 221 VVRRCQHCGVSENNTPAMRRG 241 (352)
Q Consensus 221 ~~~~C~~Cg~~~~~Tp~wR~G 241 (352)
+..+|.-|+...+.+|.||-+
T Consensus 67 Lr~~Ct~Cgkah~~~~~~Rak 87 (94)
T COG1631 67 LRLRCTECGKAHQRTPGFRAK 87 (94)
T ss_pred EEEEehhhccccccCcceeee
Confidence 356799999987667899965
No 23
>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=32.06 E-value=39 Score=28.58 Aligned_cols=36 Identities=25% Similarity=0.527 Sum_probs=26.4
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHHHHHHhcCC
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGT 261 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~ 261 (352)
...|..|+.. -|.|-.=..| -.||-.|.-..+.-++
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 4689999974 6899999999 8999999998888764
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=31.65 E-value=7.9 Score=26.26 Aligned_cols=33 Identities=27% Similarity=0.735 Sum_probs=23.1
Q ss_pred cccccccCCCCCCCccccCCCCCcccchHHHHHH
Q 018641 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (352)
Q Consensus 223 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 256 (352)
..|.+|++. ...+..+-+..|....|-.||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 468899885 245555556666678898888765
No 25
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=30.50 E-value=19 Score=30.84 Aligned_cols=27 Identities=30% Similarity=0.720 Sum_probs=19.7
Q ss_pred ccccccCCCCCCCccccCCCCC-cccchHHHH
Q 018641 224 RCQHCGVSENNTPAMRRGPAGP-RTLCNACGL 254 (352)
Q Consensus 224 ~C~~Cg~~~~~Tp~wR~GP~G~-~~LCNACGl 254 (352)
.|..|+-+. |-+-+.+ +- -.-|+|||-
T Consensus 82 lC~~C~spd--T~l~k~~--r~~~l~C~aCGa 109 (110)
T smart00653 82 LCPECGSPD--TELIKEN--RLFFLKCEACGA 109 (110)
T ss_pred ECCCCCCCC--cEEEEeC--CeEEEEccccCC
Confidence 599999974 8888872 21 245999994
No 26
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=29.83 E-value=29 Score=35.79 Aligned_cols=32 Identities=25% Similarity=0.660 Sum_probs=25.3
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHHHH
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~ 255 (352)
..+|+.||.+...+...-.||.. ..|+.|=-.
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~Ci~~ 40 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDECIEL 40 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchHHHH
Confidence 34899999988778888888844 699999433
No 27
>PRK05978 hypothetical protein; Provisional
Probab=29.31 E-value=21 Score=32.27 Aligned_cols=33 Identities=30% Similarity=0.625 Sum_probs=24.8
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHHHHHHhc
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~ 259 (352)
..+|-+||. -.++ +|...-..-|.+||+.|..+
T Consensus 33 ~grCP~CG~----G~LF-~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGE----GKLF-RAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCC----Cccc-ccccccCCCccccCCccccC
Confidence 456999997 3344 46666688999999999765
No 28
>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=28.53 E-value=20 Score=36.39 Aligned_cols=8 Identities=38% Similarity=1.086 Sum_probs=6.3
Q ss_pred ccccccCC
Q 018641 224 RCQHCGVS 231 (352)
Q Consensus 224 ~C~~Cg~~ 231 (352)
.|.+||..
T Consensus 2 ~c~~cg~~ 9 (372)
T cd01121 2 VCSECGYV 9 (372)
T ss_pred CCCCCCCC
Confidence 58888875
No 29
>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=27.18 E-value=24 Score=24.79 Aligned_cols=30 Identities=27% Similarity=0.773 Sum_probs=17.7
Q ss_pred ccccccCCCCCCCccccCCCCCcccchHHHHHHHh
Q 018641 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWAN 258 (352)
Q Consensus 224 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 258 (352)
+|.+|+.. . .--+--.| ...|..||+...-
T Consensus 2 ~Cp~Cg~~--~--~~~D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSK--E--IVFDPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSS--E--EEEETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCC--c--eEEcCCCC-eEECCCCCCEeec
Confidence 58888873 1 33333334 7789999876543
No 30
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.91 E-value=26 Score=38.42 Aligned_cols=36 Identities=22% Similarity=0.482 Sum_probs=28.7
Q ss_pred ccccccccCCCCCCCccccCCCC---CcccchHHHHHHHhc
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAG---PRTLCNACGLMWANK 259 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G---~~~LCNACGl~~~~~ 259 (352)
...|..|.+ ..||.|+.-+.+ ...+|.+|----.|+
T Consensus 462 P~~caqckt--dftp~wk~ekstq~d~~i~cE~cvtSnqkk 500 (706)
T KOG3740|consen 462 PYACAQCKT--DFTPAWKKEKSTQADAAIVCENCVTSNQKK 500 (706)
T ss_pred chhhhhccc--ccccccccccccCcchHHHHHhhhhhcccc
Confidence 457999999 579999998888 458999997655544
No 31
>PF13619 KTSC: KTSC domain
Probab=26.21 E-value=76 Score=23.78 Aligned_cols=30 Identities=37% Similarity=0.586 Sum_probs=25.0
Q ss_pred CCcceeeeee-cCeEEEecCCCHHHHHHHHH
Q 018641 87 SRTSELTLSF-EGEVYVFPAVTPEKVQAVLL 116 (352)
Q Consensus 87 ~~tsqLTi~y-~GeV~VFdsVspeKvqaVll 116 (352)
..+..|.|.| .|.+|.|..||++.++++|.
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 4566787766 68899999999999999885
No 32
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=25.80 E-value=23 Score=29.15 Aligned_cols=18 Identities=39% Similarity=0.625 Sum_probs=0.0
Q ss_pred CCCCCCCCccccccCCcc
Q 018641 30 GDYEDGEGMDDIDEGNIN 47 (352)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~ 47 (352)
+||.|||..|+.|+.+|.
T Consensus 37 dd~~DDD~dDdeeee~m~ 54 (81)
T PF14812_consen 37 DDYEDDDDDDDEEEEPMP 54 (81)
T ss_dssp ------------------
T ss_pred cccccccccchhhccccc
Confidence 455555555544554444
No 33
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=24.81 E-value=19 Score=27.13 Aligned_cols=21 Identities=33% Similarity=1.053 Sum_probs=16.0
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHH
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACG 253 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACG 253 (352)
...|.+||.. .-+..+|..||
T Consensus 26 l~~c~~cg~~-----------~~~H~vc~~cG 46 (56)
T PF01783_consen 26 LVKCPNCGEP-----------KLPHRVCPSCG 46 (56)
T ss_dssp EEESSSSSSE-----------ESTTSBCTTTB
T ss_pred eeeeccCCCE-----------ecccEeeCCCC
Confidence 4579999973 23468999999
No 34
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=24.80 E-value=35 Score=36.65 Aligned_cols=32 Identities=31% Similarity=0.687 Sum_probs=23.1
Q ss_pred ccccccCCCCCCCccccCCCCCcccchHHHHHHHhcC
Q 018641 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKG 260 (352)
Q Consensus 224 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~ 260 (352)
+|.||+.+ ++ =|+--.| -..|.+||.......
T Consensus 2 ~C~~C~~s---~f-e~d~a~g-~~~C~~CG~v~E~~~ 33 (521)
T KOG1598|consen 2 VCKNCGGS---NF-ERDEATG-NLYCTACGTVLEYNN 33 (521)
T ss_pred cCCCCCCC---Cc-ccccccC-Cceeccccceeeccc
Confidence 69999983 34 3444566 799999998776543
No 35
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=23.83 E-value=30 Score=33.28 Aligned_cols=9 Identities=44% Similarity=1.361 Sum_probs=6.1
Q ss_pred cccccccCC
Q 018641 223 RRCQHCGVS 231 (352)
Q Consensus 223 ~~C~~Cg~~ 231 (352)
+.|.|||..
T Consensus 355 ~~c~~cg~~ 363 (389)
T PRK11788 355 YRCRNCGFT 363 (389)
T ss_pred EECCCCCCC
Confidence 567777764
No 36
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.83 E-value=23 Score=29.03 Aligned_cols=36 Identities=28% Similarity=0.508 Sum_probs=25.1
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHHHHHHhcC
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKG 260 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~ 260 (352)
.-+|..|+-.-+-...+++.| -+.|.+||-++++.-
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~l 47 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDP---LTTCEECGARLKKLL 47 (82)
T ss_pred EEeecccchHHHHHHhcccCc---cccChhhChHHHHhh
Confidence 356999986423345556554 579999999888754
No 37
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=23.63 E-value=26 Score=26.75 Aligned_cols=22 Identities=32% Similarity=0.964 Sum_probs=16.3
Q ss_pred cccccccCCCCCCCccccCCCCCcccchHHHHH
Q 018641 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (352)
Q Consensus 223 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~ 255 (352)
..|.+||... -+..+|..||.|
T Consensus 28 ~~C~~CG~~~-----------~~H~vC~~CG~Y 49 (57)
T PRK12286 28 VECPNCGEPK-----------LPHRVCPSCGYY 49 (57)
T ss_pred eECCCCCCcc-----------CCeEECCCCCcC
Confidence 4699999842 236899999954
No 38
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=23.53 E-value=26 Score=30.98 Aligned_cols=29 Identities=28% Similarity=0.666 Sum_probs=20.3
Q ss_pred ccccccCCCCCCCccccCCCCCcccchHHHHH
Q 018641 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (352)
Q Consensus 224 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~ 255 (352)
.|..|+-+. |-+-+++- ---.-|+|||-.
T Consensus 99 lC~~C~sPd--T~l~k~~r-~~~l~C~ACGa~ 127 (133)
T TIGR00311 99 ICRECNRPD--TRIIKEGR-VSLLKCEACGAK 127 (133)
T ss_pred ECCCCCCCC--cEEEEeCC-eEEEecccCCCC
Confidence 499999975 77777531 112479999964
No 39
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=23.09 E-value=26 Score=34.82 Aligned_cols=34 Identities=29% Similarity=0.496 Sum_probs=21.3
Q ss_pred cccccccccccCCCCCCCccccCCCCCcccchHHHHHHHh
Q 018641 219 ETVVRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWAN 258 (352)
Q Consensus 219 e~~~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 258 (352)
.+..+.|..||+. |- -+. .|-+..|+.||.++--
T Consensus 108 ~~~~RFCg~CG~~---~~-~~~--~g~~~~C~~cg~~~fP 141 (279)
T COG2816 108 YRSHRFCGRCGTK---TY-PRE--GGWARVCPKCGHEHFP 141 (279)
T ss_pred HhhCcCCCCCCCc---Cc-ccc--CceeeeCCCCCCccCC
Confidence 3334569999883 22 223 3556899999987743
No 40
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=22.88 E-value=27 Score=31.07 Aligned_cols=29 Identities=31% Similarity=0.647 Sum_probs=20.2
Q ss_pred ccccccCCCCCCCccccCCCCCcccchHHHHH
Q 018641 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (352)
Q Consensus 224 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~ 255 (352)
.|..|+-+. |-+-+++= ---.-|+|||-.
T Consensus 104 lC~~C~spd--T~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 104 ICPECGSPD--TKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred ECCCCCCCC--cEEEEcCC-eEEEEcccCCCC
Confidence 499999974 77777531 113579999954
No 41
>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=21.89 E-value=35 Score=30.98 Aligned_cols=38 Identities=18% Similarity=0.336 Sum_probs=26.0
Q ss_pred ccccccCCCCCCCccccCCCC----CcccchHHHHHHHhcCC
Q 018641 224 RCQHCGVSENNTPAMRRGPAG----PRTLCNACGLMWANKGT 261 (352)
Q Consensus 224 ~C~~Cg~~~~~Tp~wR~GP~G----~~~LCNACGl~~~~~~~ 261 (352)
+|-.|+...|..=-=|...+| .+.-|.+||.+|-..-+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyEr 43 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFER 43 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeee
Confidence 588888765555555555555 34789999999876543
No 42
>COG3952 Predicted membrane protein [Function unknown]
Probab=21.56 E-value=26 Score=30.40 Aligned_cols=19 Identities=37% Similarity=0.546 Sum_probs=14.7
Q ss_pred ccccCCCCCcccchHHHHHHH
Q 018641 237 AMRRGPAGPRTLCNACGLMWA 257 (352)
Q Consensus 237 ~wR~GP~G~~~LCNACGl~~~ 257 (352)
.||..|-+ .||++||+.-.
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 35677777 89999998754
No 43
>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=21.29 E-value=36 Score=24.42 Aligned_cols=25 Identities=44% Similarity=1.095 Sum_probs=18.3
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHH
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACG 253 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACG 253 (352)
...|..|+ +|++| .-.| +.+|-+|+
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 34688885 69999 2345 78998885
No 44
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=20.58 E-value=32 Score=32.18 Aligned_cols=31 Identities=26% Similarity=0.609 Sum_probs=21.5
Q ss_pred ccccccCCCCCCCccccCCCCCcccchHHHHHHH
Q 018641 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWA 257 (352)
Q Consensus 224 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~ 257 (352)
.|..|+-+. |-+-+.+- ---.-|+|||-..-
T Consensus 100 ~C~~C~~pd--T~l~k~~~-~~~l~C~aCGa~~~ 130 (201)
T PRK12336 100 ICSECGLPD--TRLVKEDR-VLMLRCDACGAHRP 130 (201)
T ss_pred ECCCCCCCC--cEEEEcCC-eEEEEcccCCCCcc
Confidence 499999975 77777641 11247999997543
No 45
>PLN00162 transport protein sec23; Provisional
Probab=20.19 E-value=31 Score=38.33 Aligned_cols=32 Identities=22% Similarity=0.321 Sum_probs=28.0
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHHHH
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~ 255 (352)
..+|..|++ -.-|..+-.+.|.+..||.|+.+
T Consensus 53 pvRC~~Cra--ylNPf~~~d~~~~~W~C~~C~~~ 84 (761)
T PLN00162 53 PLRCRTCRA--VLNPYCRVDFQAKIWICPFCFQR 84 (761)
T ss_pred CCccCCCcC--EECCceEEecCCCEEEccCCCCC
Confidence 468999998 57999999999999999999854
No 46
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.16 E-value=26 Score=29.69 Aligned_cols=35 Identities=20% Similarity=0.431 Sum_probs=23.1
Q ss_pred ccccccccCCCCCCCccccCCCCCcccchHHHHHHHhc
Q 018641 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (352)
Q Consensus 222 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~ 259 (352)
...|.+|+...-..+.-| ..+...|-.||.|+.+.
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 357999995321223333 35578999999998653
Done!