Query 018981
Match_columns 348
No_of_seqs 286 out of 930
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 05:42:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018981.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018981hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06200 tify: tify domain; I 99.7 1.2E-16 2.5E-21 110.5 4.9 36 70-105 1-36 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.6 1.2E-15 2.5E-20 114.0 3.9 44 206-251 1-44 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 9.8E-15 2.1E-19 108.1 2.8 45 204-250 3-48 (52)
4 PF00320 GATA: GATA zinc finge 99.5 9.3E-15 2E-19 100.7 1.4 36 207-244 1-36 (36)
5 PF06203 CCT: CCT motif; Inte 99.1 1.8E-11 3.9E-16 88.6 2.3 44 138-181 1-44 (45)
6 KOG1601 GATA-4/5/6 transcripti 98.6 2E-08 4.3E-13 90.3 2.8 46 204-251 199-244 (340)
7 COG5641 GAT1 GATA Zn-finger-co 98.3 3.2E-07 7E-12 95.0 2.8 59 198-258 152-215 (498)
8 PF09425 CCT_2: Divergent CCT 98.1 1E-06 2.2E-11 57.5 1.6 26 136-162 2-27 (27)
9 COG5641 GAT1 GATA Zn-finger-co 92.2 0.073 1.6E-06 55.9 1.8 51 204-255 297-347 (498)
10 KOG3554 Histone deacetylase co 82.2 5.2 0.00011 42.3 7.8 45 198-244 380-426 (693)
11 PF09889 DUF2116: Uncharacteri 63.1 3.7 8.1E-05 31.6 1.0 30 204-243 3-33 (59)
12 KOG1601 GATA-4/5/6 transcripti 60.5 3.3 7.1E-05 37.2 0.4 41 135-175 290-330 (340)
13 PF01783 Ribosomal_L32p: Ribos 59.7 1.7 3.8E-05 32.6 -1.3 24 204-239 26-49 (56)
14 PF13717 zinc_ribbon_4: zinc-r 58.7 2 4.4E-05 29.6 -1.0 33 205-238 3-35 (36)
15 PF14803 Nudix_N_2: Nudix N-te 56.5 3.4 7.4E-05 28.4 -0.1 30 205-236 1-30 (34)
16 PRK11823 DNA repair protein Ra 48.4 5.9 0.00013 41.0 -0.0 25 204-238 7-31 (446)
17 PF06677 Auto_anti-p27: Sjogre 48.0 6.3 0.00014 28.2 0.1 25 204-235 17-41 (41)
18 COG3952 Predicted membrane pro 47.7 5.7 0.00012 34.2 -0.2 20 219-240 76-95 (113)
19 smart00653 eIF2B_5 domain pres 45.1 7 0.00015 33.4 -0.0 28 205-236 81-109 (110)
20 TIGR00416 sms DNA repair prote 44.3 7.5 0.00016 40.4 0.0 24 204-237 7-30 (454)
21 PF01412 ArfGap: Putative GTPa 43.2 18 0.0004 30.5 2.2 36 204-243 13-48 (116)
22 PF04810 zf-Sec23_Sec24: Sec23 41.0 11 0.00024 26.3 0.4 31 204-236 2-32 (40)
23 TIGR02098 MJ0042_CXXC MJ0042 f 40.6 4.5 9.9E-05 27.4 -1.5 33 205-238 3-35 (38)
24 PF06689 zf-C4_ClpX: ClpX C4-t 40.5 14 0.0003 26.1 0.9 33 205-238 2-34 (41)
25 PRK05978 hypothetical protein; 39.2 10 0.00023 34.1 0.1 34 204-242 33-66 (148)
26 cd01121 Sms Sms (bacterial rad 39.1 10 0.00023 38.4 0.1 24 206-239 2-25 (372)
27 PRK12286 rpmF 50S ribosomal pr 37.3 9.5 0.00021 29.0 -0.4 23 204-237 27-49 (57)
28 PRK00420 hypothetical protein; 37.0 13 0.00028 32.1 0.4 31 204-241 23-53 (112)
29 PF13240 zinc_ribbon_2: zinc-r 35.8 18 0.0004 22.6 0.8 21 206-236 1-21 (23)
30 COG1645 Uncharacterized Zn-fin 35.6 12 0.00027 33.1 -0.0 27 204-238 28-54 (131)
31 KOG1598 Transcription initiati 34.7 17 0.00037 38.8 0.8 30 206-240 2-31 (521)
32 PF13248 zf-ribbon_3: zinc-rib 34.2 21 0.00045 22.7 0.9 23 204-236 2-24 (26)
33 PF08271 TF_Zn_Ribbon: TFIIB z 33.7 14 0.0003 25.9 0.0 30 206-240 2-31 (43)
34 TIGR00311 aIF-2beta translatio 32.9 13 0.00027 32.9 -0.3 30 205-237 98-127 (133)
35 PRK03988 translation initiatio 32.8 12 0.00027 33.1 -0.4 30 205-237 103-132 (138)
36 KOG3740 Uncharacterized conser 31.7 21 0.00046 39.0 1.0 36 204-241 462-500 (706)
37 PF02701 zf-Dof: Dof domain, z 31.2 34 0.00073 26.9 1.8 46 204-251 5-53 (63)
38 PF09297 zf-NADH-PPase: NADH p 31.0 15 0.00033 24.2 -0.1 28 204-237 3-30 (32)
39 TIGR03573 WbuX N-acetyl sugar 30.3 30 0.00064 34.5 1.7 32 205-240 2-33 (343)
40 PRK12496 hypothetical protein; 30.3 23 0.0005 32.0 0.9 32 204-243 127-158 (164)
41 COG5349 Uncharacterized protei 28.8 21 0.00045 31.5 0.3 34 204-242 21-54 (126)
42 smart00105 ArfGap Putative GTP 28.2 47 0.001 27.9 2.3 38 204-245 3-40 (112)
43 PRK12336 translation initiatio 27.9 17 0.00037 33.9 -0.5 31 205-238 99-129 (201)
44 PF07282 OrfB_Zn_ribbon: Putat 27.3 24 0.00052 26.6 0.4 29 204-238 28-56 (69)
45 PRK05342 clpX ATP-dependent pr 26.5 33 0.00071 35.4 1.3 29 204-234 9-37 (412)
46 COG2331 Uncharacterized protei 25.3 24 0.00051 28.9 0.0 37 204-243 12-48 (82)
47 PRK11788 tetratricopeptide rep 24.1 26 0.00057 33.7 0.0 21 205-235 355-375 (389)
48 COG2816 NPY1 NTP pyrophosphohy 23.8 26 0.00056 34.7 -0.0 31 204-240 111-141 (279)
49 TIGR01031 rpmF_bact ribosomal 23.7 20 0.00044 27.0 -0.6 22 204-236 26-47 (55)
50 TIGR00244 transcriptional regu 23.4 28 0.0006 31.5 0.1 37 206-242 2-42 (147)
51 COG5347 GTPase-activating prot 23.2 39 0.00084 34.0 1.1 36 204-243 20-55 (319)
52 smart00834 CxxC_CXXC_SSSS Puta 22.7 28 0.0006 23.5 -0.0 30 204-236 5-34 (41)
53 PF01873 eIF-5_eIF-2B: Domain 22.6 27 0.00059 30.4 -0.1 29 205-236 94-122 (125)
54 KOG0712 Molecular chaperone (D 22.5 47 0.001 33.8 1.5 36 204-239 143-181 (337)
55 PF11781 RRN7: RNA polymerase 22.4 33 0.00071 23.7 0.3 25 205-236 9-33 (36)
56 PRK14892 putative transcriptio 20.9 26 0.00057 29.5 -0.6 35 204-241 21-55 (99)
57 PRK01110 rpmF 50S ribosomal pr 20.6 29 0.00062 26.7 -0.4 22 204-237 27-48 (60)
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=99.65 E-value=1.2e-16 Score=110.46 Aligned_cols=36 Identities=42% Similarity=0.683 Sum_probs=33.2
Q ss_pred CCCCCccceEEeccEEEEeCCCChhHHHHHHHHhcC
Q 018981 70 TSTRTSELTVAYEGEVYVFPAVTPHKVQALLLLLGE 105 (348)
Q Consensus 70 ~~~~t~QLTIfY~G~V~VFDdVp~eKaqaImlLa~~ 105 (348)
+.+.++||||||+|+|+|||+||+|||++||+||+.
T Consensus 1 ~~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~r 36 (36)
T PF06200_consen 1 PSPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLASR 36 (36)
T ss_pred CCCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhcC
Confidence 356789999999999999999999999999999973
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=99.58 E-value=1.2e-15 Score=113.99 Aligned_cols=44 Identities=52% Similarity=1.118 Sum_probs=40.7
Q ss_pred ccccccccccCCCccccCCCCCchhchHhhHHHHhcCCCCCCccCc
Q 018981 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGA 251 (348)
Q Consensus 206 ~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~r~~~k~~ 251 (348)
.|+||++ +.||+||+||.|..+|||||||||++++..||..+..
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 5999999 5799999999998999999999999999999988764
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.50 E-value=9.8e-15 Score=108.12 Aligned_cols=45 Identities=51% Similarity=1.029 Sum_probs=40.5
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcCCC-CCCccC
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL-RDLTKG 250 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~-r~~~k~ 250 (348)
...|+||++ +.||+||+||.|..+|||||||+|++++.+ |+..+.
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 579999999 579999999999889999999999999988 776654
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=99.48 E-value=9.3e-15 Score=100.66 Aligned_cols=36 Identities=56% Similarity=1.186 Sum_probs=28.2
Q ss_pred cccccccccCCCccccCCCCCchhchHhhHHHHhcCCC
Q 018981 207 CQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL 244 (348)
Q Consensus 207 C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~ 244 (348)
|+||++ +.||+||+||.|..+||||||++|++++++
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 469999999999889999999999999864
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=1.8e-11 Score=88.60 Aligned_cols=44 Identities=52% Similarity=0.819 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhhhhcccccceeeccchhhHHHHHhhcCcccccc
Q 018981 138 RIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNGQFTSSK 181 (348)
Q Consensus 138 R~aSL~Rf~eKRk~R~~~k~i~Y~~RK~~A~rrpR~KGqFas~k 181 (348)
|.++|+||++||+.|+|.|+|+|.+||.+|+.++|.+|+|++..
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 67899999999999999999999999999999999999998854
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.61 E-value=2e-08 Score=90.28 Aligned_cols=46 Identities=48% Similarity=0.988 Sum_probs=39.4
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcCCCCCCccCc
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGA 251 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~r~~~k~~ 251 (348)
...|.+|++ +.||+||++|.|...||||||++|++++..|.+....
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 479999999 5799999999999999999999999997555555443
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.29 E-value=3.2e-07 Score=94.98 Aligned_cols=59 Identities=27% Similarity=0.528 Sum_probs=47.0
Q ss_pred CCCcccccccccccccccCCCccccCCCC----CchhchHhhHHHHhcCCCC-CCccCcccccccc
Q 018981 198 APPESVSRICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKGTLR-DLTKGARNICFEQ 258 (348)
Q Consensus 198 ~~~~~~~~~C~~Cg~~~~~TP~WRrGP~G----~~tLCNACGl~~~~~~~~r-~~~k~~~~~~~~q 258 (348)
...+.+...|.||.+ +.||+|||+..+ .-.|||||||+|+.||++| |++.....++.+.
T Consensus 152 ~~~s~~~~vc~Nc~t--~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 152 SDNSNQPHVCSNCKT--TSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred cccccccchhccccc--cCCccccccccccccCCccccccccccccccCCcCCCcccccccccccc
Confidence 344445569999999 579999999993 3899999999999999999 8776655554443
No 8
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=98.14 E-value=1e-06 Score=57.54 Aligned_cols=26 Identities=50% Similarity=0.563 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHhhhhcccccceeecc
Q 018981 136 SQRIASLVRFREKRKERSFEKKIRYSC 162 (348)
Q Consensus 136 ~~R~aSL~Rf~eKRk~R~~~k~i~Y~~ 162 (348)
.+|++||+||+||||+|..+ +.+|..
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~-~~PY~~ 27 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA-KSPYQA 27 (27)
T ss_dssp ----HHHHHHHHHH-------------
T ss_pred chHHHHHHHHHHHHHHhhcc-CCCCCC
Confidence 47999999999999999988 489863
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=92.21 E-value=0.073 Score=55.94 Aligned_cols=51 Identities=24% Similarity=0.225 Sum_probs=43.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcCCCCCCccCccccc
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGARNIC 255 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~r~~~k~~~~~~ 255 (348)
...|.+|++. +.||.||+...-...+|||||++.+..+..+++.++..-..
T Consensus 297 ~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~ 347 (498)
T COG5641 297 DKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNS 347 (498)
T ss_pred hcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCCChhh
Confidence 6789999976 57999999988879999999999999999999887544333
No 10
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=82.19 E-value=5.2 Score=42.30 Aligned_cols=45 Identities=22% Similarity=0.451 Sum_probs=33.8
Q ss_pred CCCcccccccccccccccCCCccc--cCCCCCchhchHhhHHHHhcCCC
Q 018981 198 APPESVSRICQHCGISEKLTPAMR--RGPAGPRTLCNACGLMWANKGTL 244 (348)
Q Consensus 198 ~~~~~~~~~C~~Cg~~~~~TP~WR--rGP~G~~tLCNACGl~~~~~~~~ 244 (348)
..+....+.|-+|++ |..-+|= -+|.-...||-.|=+||++-|-+
T Consensus 380 t~~~~~g~~CEsC~t--tqs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 380 TFQNQDGRACESCYT--TQSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred cccCCCCCccccccc--ccccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 344344789999999 4676774 45666678999999999998754
No 11
>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=63.07 E-value=3.7 Score=31.60 Aligned_cols=30 Identities=20% Similarity=0.636 Sum_probs=23.9
Q ss_pred ccccccccccccCCCccccCCCCCchhc-hHhhHHHHhcCC
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLC-NACGLMWANKGT 243 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLC-NACGl~~~~~~~ 243 (348)
-+.|.+||.+. |.. +..| ..|+..|.++++
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 47899999975 334 7899 599999998764
No 12
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=60.48 E-value=3.3 Score=37.17 Aligned_cols=41 Identities=44% Similarity=0.678 Sum_probs=37.6
Q ss_pred hHHHHHHHHHHHHhhhhcccccceeeccchhhHHHHHhhcC
Q 018981 135 LSQRIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNG 175 (348)
Q Consensus 135 l~~R~aSL~Rf~eKRk~R~~~k~i~Y~~RK~~A~rrpR~KG 175 (348)
...|.+.+.|++++++.|.|.++++|..++..+..+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 34688999999999999999999999999999999999887
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=59.68 E-value=1.7 Score=32.60 Aligned_cols=24 Identities=29% Similarity=0.861 Sum_probs=18.0
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~ 239 (348)
...|.+||... -+..+|..|| +|+
T Consensus 26 l~~c~~cg~~~-----------~~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 26 LVKCPNCGEPK-----------LPHRVCPSCG-YYK 49 (56)
T ss_dssp EEESSSSSSEE-----------STTSBCTTTB-BSS
T ss_pred eeeeccCCCEe-----------cccEeeCCCC-eEC
Confidence 57999999742 2378999999 444
No 14
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=58.67 E-value=2 Score=29.56 Aligned_cols=33 Identities=21% Similarity=0.569 Sum_probs=28.5
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhHHH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~ 238 (348)
..|.+|++. ...+..+-.+.|...-|-.||-.|
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 588999999999999999998765
No 15
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=56.48 E-value=3.4 Score=28.38 Aligned_cols=30 Identities=33% Similarity=0.855 Sum_probs=13.9
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl 236 (348)
+-|.+||.. .+..-=.|.+-.+..|.+||.
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 369999973 111111344455689999984
No 16
>PRK11823 DNA repair protein RadA; Provisional
Probab=48.36 E-value=5.9 Score=40.97 Aligned_cols=25 Identities=36% Similarity=0.897 Sum_probs=18.2
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~ 238 (348)
..+|.+||-. ++.|- | .|.+||-|=
T Consensus 7 ~y~C~~Cg~~---~~~~~----g---~Cp~C~~w~ 31 (446)
T PRK11823 7 AYVCQECGAE---SPKWL----G---RCPECGAWN 31 (446)
T ss_pred eEECCcCCCC---CcccC----e---eCcCCCCcc
Confidence 6899999985 55552 2 599998653
No 17
>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=48.01 E-value=6.3 Score=28.20 Aligned_cols=25 Identities=44% Similarity=1.103 Sum_probs=19.6
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhh
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACG 235 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACG 235 (348)
...|..|+ +|++| .-+| +.+|-+|+
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 79999 3466 79999986
No 18
>COG3952 Predicted membrane protein [Function unknown]
Probab=47.74 E-value=5.7 Score=34.19 Aligned_cols=20 Identities=35% Similarity=0.469 Sum_probs=16.2
Q ss_pred ccccCCCCCchhchHhhHHHHh
Q 018981 219 AMRRGPAGPRTLCNACGLMWAN 240 (348)
Q Consensus 219 ~WRrGP~G~~tLCNACGl~~~~ 240 (348)
.||.+|-+ .||++||++-..
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 57888877 799999998654
No 19
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=45.10 E-value=7 Score=33.37 Aligned_cols=28 Identities=29% Similarity=0.633 Sum_probs=20.2
Q ss_pred cccccccccccCCCccccCCCCC-chhchHhhH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGP-RTLCNACGL 236 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~-~tLCNACGl 236 (348)
-.|..|+.. .|-+-+. .+- -.-|+|||-
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 589999996 4878776 222 235999994
No 20
>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=44.31 E-value=7.5 Score=40.38 Aligned_cols=24 Identities=33% Similarity=0.639 Sum_probs=17.4
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~ 237 (348)
..+|.+||-. ...|.| -|.+||-|
T Consensus 7 ~y~C~~Cg~~-~~~~~g---------~Cp~C~~w 30 (454)
T TIGR00416 7 KFVCQHCGAD-SPKWQG---------KCPACHAW 30 (454)
T ss_pred eEECCcCCCC-CccccE---------ECcCCCCc
Confidence 5899999985 244444 49999865
No 21
>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=43.22 E-value=18 Score=30.48 Aligned_cols=36 Identities=25% Similarity=0.594 Sum_probs=26.8
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcCC
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (348)
...|..||.. -|.|-.=.-| -.||-.|.-.++.-|+
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 5899999974 7899999999 8999999988887775
No 22
>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=41.02 E-value=11 Score=26.34 Aligned_cols=31 Identities=29% Similarity=0.639 Sum_probs=20.5
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl 236 (348)
..+|.+|++- --|..+-...|..-.||-||.
T Consensus 2 p~rC~~C~ay--lNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAY--LNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--B--S-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCE--ECCcceEcCCCCEEECcCCCC
Confidence 3689999994 588888888988889999986
No 23
>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=40.55 E-value=4.5 Score=27.39 Aligned_cols=33 Identities=27% Similarity=0.668 Sum_probs=23.1
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhHHH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~ 238 (348)
..|.+|++. ..-+..+.+..|....|-.||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 578899885 345555555667678888888655
No 24
>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=40.52 E-value=14 Score=26.10 Aligned_cols=33 Identities=27% Similarity=0.629 Sum_probs=21.4
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhHHH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~ 238 (348)
++|+-||.++...-..=.||.| .-+|+.|=...
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 5899999987666555588977 78999996543
No 25
>PRK05978 hypothetical protein; Provisional
Probab=39.24 E-value=10 Score=34.10 Aligned_cols=34 Identities=26% Similarity=0.537 Sum_probs=26.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcC
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~ 242 (348)
..+|-+||. -.++| |-..-..-|.+||+.|..+.
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 568999997 34665 55566788999999998764
No 26
>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=39.05 E-value=10 Score=38.42 Aligned_cols=24 Identities=33% Similarity=0.881 Sum_probs=17.0
Q ss_pred ccccccccccCCCccccCCCCCchhchHhhHHHH
Q 018981 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (348)
Q Consensus 206 ~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~ 239 (348)
+|.+||-. +|.|- | -|.+||-|=-
T Consensus 2 ~c~~cg~~---~~~~~----g---~cp~c~~w~~ 25 (372)
T cd01121 2 VCSECGYV---SPKWL----G---KCPECGEWNT 25 (372)
T ss_pred CCCCCCCC---CCCcc----E---ECcCCCCcee
Confidence 79999984 66663 3 5999987633
No 27
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=37.28 E-value=9.5 Score=29.01 Aligned_cols=23 Identities=30% Similarity=0.836 Sum_probs=17.3
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~ 237 (348)
.-.|.+||... =+..+|..||.|
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 46899999842 127899999954
No 28
>PRK00420 hypothetical protein; Validated
Probab=36.99 E-value=13 Score=32.07 Aligned_cols=31 Identities=29% Similarity=0.674 Sum_probs=24.2
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhc
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~ 241 (348)
...|..|| +|+.|- -+| ...|-.||-.+...
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 46899999 578885 466 89999999877643
No 29
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=35.82 E-value=18 Score=22.61 Aligned_cols=21 Identities=29% Similarity=0.865 Sum_probs=12.6
Q ss_pred ccccccccccCCCccccCCCCCchhchHhhH
Q 018981 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (348)
Q Consensus 206 ~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl 236 (348)
.|.+||... +++ ...|.-||.
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 377777643 333 456777774
No 30
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=35.55 E-value=12 Score=33.12 Aligned_cols=27 Identities=37% Similarity=0.959 Sum_probs=22.8
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~ 238 (348)
..+|.-|| ||++| =+| .+.|-.||...
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 57899999 68999 588 89999999633
No 31
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=34.69 E-value=17 Score=38.82 Aligned_cols=30 Identities=30% Similarity=0.727 Sum_probs=21.9
Q ss_pred ccccccccccCCCccccCCCCCchhchHhhHHHHh
Q 018981 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (348)
Q Consensus 206 ~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (348)
.|.|||.+ ++.-+- -+| -..|++||.....
T Consensus 2 ~C~~C~~s---~fe~d~-a~g-~~~C~~CG~v~E~ 31 (521)
T KOG1598|consen 2 VCKNCGGS---NFERDE-ATG-NLYCTACGTVLEY 31 (521)
T ss_pred cCCCCCCC---Cccccc-ccC-Cceeccccceeec
Confidence 79999984 454443 456 7999999976554
No 32
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=34.18 E-value=21 Score=22.68 Aligned_cols=23 Identities=26% Similarity=0.800 Sum_probs=15.3
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl 236 (348)
.+.|.+||... +.+ ...|..||.
T Consensus 2 ~~~Cp~Cg~~~---------~~~-~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEI---------DPD-AKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcC---------Ccc-cccChhhCC
Confidence 35788888742 233 568888885
No 33
>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=33.73 E-value=14 Score=25.91 Aligned_cols=30 Identities=30% Similarity=0.741 Sum_probs=17.0
Q ss_pred ccccccccccCCCccccCCCCCchhchHhhHHHHh
Q 018981 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (348)
Q Consensus 206 ~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (348)
+|.+||... .--.--.| ..+|..||+-..-
T Consensus 2 ~Cp~Cg~~~----~~~D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE----IVFDPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE----EEEETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCc----eEEcCCCC-eEECCCCCCEeec
Confidence 588888731 22222344 6788888875543
No 34
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=32.94 E-value=13 Score=32.87 Aligned_cols=30 Identities=30% Similarity=0.691 Sum_probs=20.6
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhHH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~ 237 (348)
-.|..|+... |-+-+.+ .---.-|+|||-.
T Consensus 98 VlC~~C~sPd--T~l~k~~-r~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPD--TRIIKEG-RVSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCC--cEEEEeC-CeEEEecccCCCC
Confidence 5799999964 7777752 1112479999954
No 35
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=32.84 E-value=12 Score=33.11 Aligned_cols=30 Identities=33% Similarity=0.592 Sum_probs=20.6
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhHH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~ 237 (348)
-.|..|+.. .|-+-+.+= ---.-|+|||-.
T Consensus 103 VlC~~C~sp--dT~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGSP--DTKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred EECCCCCCC--CcEEEEcCC-eEEEEcccCCCC
Confidence 579999996 477776421 113579999953
No 36
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.66 E-value=21 Score=39.02 Aligned_cols=36 Identities=22% Similarity=0.527 Sum_probs=29.0
Q ss_pred ccccccccccccCCCccccCCCC---CchhchHhhHHHHhc
Q 018981 204 SRICQHCGISEKLTPAMRRGPAG---PRTLCNACGLMWANK 241 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G---~~tLCNACGl~~~~~ 241 (348)
...|..|.+ .-||.|+.-+.| ..++|.+|----.++
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 579999999 579999998887 458999997655443
No 37
>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=31.24 E-value=34 Score=26.86 Aligned_cols=46 Identities=28% Similarity=0.633 Sum_probs=32.4
Q ss_pred ccccccccccccCCCcc--c-cCCCCCchhchHhhHHHHhcCCCCCCccCc
Q 018981 204 SRICQHCGISEKLTPAM--R-RGPAGPRTLCNACGLMWANKGTLRDLTKGA 251 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~W--R-rGP~G~~tLCNACGl~~~~~~~~r~~~k~~ 251 (348)
...|..|..+ +|--- = -...-|+..|-+|..+|-..|++|.+.-++
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 5789999875 33110 0 012335689999999999999999987664
No 38
>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=31.00 E-value=15 Score=24.24 Aligned_cols=28 Identities=32% Similarity=0.816 Sum_probs=15.6
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~ 237 (348)
.+.|..||.. ....+.|....|.+||..
T Consensus 3 ~rfC~~CG~~------t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAP------TKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--B------EEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCcc------ccCCCCcCEeECCCCcCE
Confidence 4689999984 233456777899999864
No 39
>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=30.32 E-value=30 Score=34.50 Aligned_cols=32 Identities=22% Similarity=0.649 Sum_probs=25.7
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhHHHHh
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (348)
+.|..|... ++.|--.-..+| +||+|--+-.+
T Consensus 2 ~~C~~C~~~-~t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMP-TTRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCC-CCCCCeeECCCC---CchhhhhHHhh
Confidence 589999998 477777777778 99999987643
No 40
>PRK12496 hypothetical protein; Provisional
Probab=30.32 E-value=23 Score=32.01 Aligned_cols=32 Identities=22% Similarity=0.550 Sum_probs=22.2
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcCC
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (348)
..+|..|+.. .+ .++. ...|--||...+++..
T Consensus 127 ~~~C~gC~~~---~~---~~~~--~~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 127 RKVCKGCKKK---YP---EDYP--DDVCEICGSPVKRKMV 158 (164)
T ss_pred eEECCCCCcc---cc---CCCC--CCcCCCCCChhhhcch
Confidence 3679999973 22 1122 3589999999887765
No 41
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.85 E-value=21 Score=31.48 Aligned_cols=34 Identities=29% Similarity=0.579 Sum_probs=23.6
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcC
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~ 242 (348)
..+|-+||-- -+.| |=--...-|.|||+-|-.+.
T Consensus 21 ~grCP~CGeG----rLF~-gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 21 RGRCPRCGEG----RLFR-GFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred cCCCCCCCCc----hhhh-hhcccCchhhhccccccCCc
Confidence 5689999973 1333 33334578999999987665
No 42
>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=28.20 E-value=47 Score=27.90 Aligned_cols=38 Identities=24% Similarity=0.482 Sum_probs=31.9
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcCCCC
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLR 245 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~~r 245 (348)
...|+.|+.. -|.|=.=.-| -.||-.|.-..+.-|.+.
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 5799999983 6999988889 899999998888777543
No 43
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=27.92 E-value=17 Score=33.93 Aligned_cols=31 Identities=29% Similarity=0.595 Sum_probs=21.5
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhHHH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~ 238 (348)
-.|..|+.. .|-+-+.+ .---.-|+|||-..
T Consensus 99 V~C~~C~~p--dT~l~k~~-~~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLP--DTRLVKED-RVLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCC--CcEEEEcC-CeEEEEcccCCCCc
Confidence 589999996 47777753 11124799998643
No 44
>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=27.26 E-value=24 Score=26.65 Aligned_cols=29 Identities=28% Similarity=0.649 Sum_probs=20.8
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~ 238 (348)
...|..||... .. ...+....|..||..+
T Consensus 28 Sq~C~~CG~~~-~~-----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRN-KK-----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccc-cc-----ccccceEEcCCCCCEE
Confidence 56899999853 22 4455578999999764
No 45
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=26.49 E-value=33 Score=35.40 Aligned_cols=29 Identities=28% Similarity=0.693 Sum_probs=24.7
Q ss_pred ccccccccccccCCCccccCCCCCchhchHh
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNAC 234 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNAC 234 (348)
..+|+.||.+...+...-.||.. .+|+.|
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~C 37 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDEC 37 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchH
Confidence 46999999988788888889844 699999
No 46
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.34 E-value=24 Score=28.90 Aligned_cols=37 Identities=30% Similarity=0.515 Sum_probs=26.1
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcCC
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (348)
...|.+||-.-+--..++..| -+.|.+||-++++.-.
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~l~ 48 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDP---LTTCEECGARLKKLLN 48 (82)
T ss_pred EEeecccchHHHHHHhcccCc---cccChhhChHHHHhhc
Confidence 578999997532345555554 5799999998887543
No 47
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=24.06 E-value=26 Score=33.66 Aligned_cols=21 Identities=24% Similarity=0.771 Sum_probs=0.0
Q ss_pred cccccccccccCCCccccCCCCCchhchHhh
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACG 235 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACG 235 (348)
+.|.|||.. +..| ..+|-.||
T Consensus 355 ~~c~~cg~~---~~~~-------~~~c~~c~ 375 (389)
T PRK11788 355 YRCRNCGFT---ARTL-------YWHCPSCK 375 (389)
T ss_pred EECCCCCCC---Cccc-------eeECcCCC
No 48
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=23.77 E-value=26 Score=34.72 Aligned_cols=31 Identities=29% Similarity=0.652 Sum_probs=21.2
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHh
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~ 240 (348)
.+-|.+||+. +.+ ...|-+.+|+.||..+--
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 5789999973 222 235667899999987654
No 49
>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=23.71 E-value=20 Score=26.96 Aligned_cols=22 Identities=32% Similarity=0.892 Sum_probs=16.4
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl 236 (348)
...|.+||.. -=+..+|-.||.
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 123789999993
No 50
>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=23.42 E-value=28 Score=31.51 Aligned_cols=37 Identities=19% Similarity=0.293 Sum_probs=25.6
Q ss_pred ccccccccccCCCccccCCCC----CchhchHhhHHHHhcC
Q 018981 206 ICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKG 242 (348)
Q Consensus 206 ~C~~Cg~~~~~TP~WRrGP~G----~~tLCNACGl~~~~~~ 242 (348)
+|..|+...|..=-=|...+| .+--|.+||.+|-..-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyE 42 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFE 42 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceee
Confidence 688998865444444555666 3468999999887644
No 51
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=23.18 E-value=39 Score=34.01 Aligned_cols=36 Identities=25% Similarity=0.528 Sum_probs=30.9
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhcCC
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~~~ 243 (348)
...|+.||.. . |.|=.=.-| -.||--|.=..+.-|+
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 6899999994 5 999999999 8999999877776664
No 52
>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=22.71 E-value=28 Score=23.46 Aligned_cols=30 Identities=23% Similarity=0.624 Sum_probs=20.6
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl 236 (348)
.-+|..||.. -..|..--++....|-.||.
T Consensus 5 ~y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 3579999973 33455444466778999997
No 53
>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=22.61 E-value=27 Score=30.44 Aligned_cols=29 Identities=31% Similarity=0.673 Sum_probs=20.5
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl 236 (348)
-.|..|+.. .|-+-+.+-. --.-|+|||-
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 579999986 4777776322 2467999984
No 54
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=22.48 E-value=47 Score=33.76 Aligned_cols=36 Identities=25% Similarity=0.506 Sum_probs=29.8
Q ss_pred ccccccccccccCCCccccCC---CCCchhchHhhHHHH
Q 018981 204 SRICQHCGISEKLTPAMRRGP---AGPRTLCNACGLMWA 239 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP---~G~~tLCNACGl~~~ 239 (348)
...|..|..++-.+..||-|| .=.++.|..|+..-.
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 555789999976544
No 55
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=22.39 E-value=33 Score=23.74 Aligned_cols=25 Identities=28% Similarity=0.632 Sum_probs=19.2
Q ss_pred cccccccccccCCCccccCCCCCchhchHhhH
Q 018981 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (348)
Q Consensus 205 ~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl 236 (348)
..|..|+. . |-..-+| ...|..||-
T Consensus 9 ~~C~~C~~----~--~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGS----R--WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CcCCCCCC----e--EeEccCC-EEEhhhCce
Confidence 46999997 3 5556688 899999983
No 56
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=20.90 E-value=26 Score=29.54 Aligned_cols=35 Identities=20% Similarity=0.329 Sum_probs=22.7
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHHHHhc
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~~~~~ 241 (348)
.-.|.+|+.....-++=| .-....|..||.|+.+.
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 568999995311112222 34478999999998764
No 57
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=20.60 E-value=29 Score=26.65 Aligned_cols=22 Identities=14% Similarity=0.135 Sum_probs=15.9
Q ss_pred ccccccccccccCCCccccCCCCCchhchHhhHH
Q 018981 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (348)
Q Consensus 204 ~~~C~~Cg~~~~~TP~WRrGP~G~~tLCNACGl~ 237 (348)
...|.+||... =+..+|- ||.|
T Consensus 27 ~~~c~~cg~~~-----------~pH~vc~-cG~Y 48 (60)
T PRK01110 27 LSVDKTTGEYH-----------LPHHVSP-KGYY 48 (60)
T ss_pred eeEcCCCCcee-----------ccceecC-Cccc
Confidence 46899999842 2367899 9954
Done!