Query 021461
Match_columns 312
No_of_seqs 280 out of 939
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 03:08:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021461.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021461hhsearch_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-21 108.7 4.9 35 71-105 2-36 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.6 1.3E-15 2.7E-20 112.1 3.7 44 206-251 1-44 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 6.3E-15 1.4E-19 107.5 3.2 45 204-250 3-48 (52)
4 PF00320 GATA: GATA zinc finge 99.5 5.9E-15 1.3E-19 100.0 1.3 36 207-244 1-36 (36)
5 PF06203 CCT: CCT motif; Inte 99.1 2.9E-11 6.2E-16 86.1 2.8 44 138-181 1-44 (45)
6 KOG1601 GATA-4/5/6 transcripti 98.6 2.4E-08 5.2E-13 88.5 3.2 45 204-250 199-243 (340)
7 COG5641 GAT1 GATA Zn-finger-co 98.2 5.5E-07 1.2E-11 91.9 3.1 53 197-251 151-208 (498)
8 PF09425 CCT_2: Divergent CCT 98.1 1.5E-06 3.3E-11 55.8 1.6 25 136-161 2-26 (27)
9 COG5641 GAT1 GATA Zn-finger-co 90.1 0.14 3E-06 53.0 1.5 48 204-252 297-344 (498)
10 PF09889 DUF2116: Uncharacteri 70.6 2.2 4.7E-05 32.3 1.0 30 204-243 3-33 (59)
11 KOG3554 Histone deacetylase co 69.9 4.5 9.7E-05 42.1 3.4 39 204-244 386-426 (693)
12 PF01783 Ribosomal_L32p: Ribos 69.5 1.2 2.5E-05 33.0 -0.6 24 204-239 26-49 (56)
13 PF14803 Nudix_N_2: Nudix N-te 67.4 1.8 3.9E-05 29.2 0.1 30 205-236 1-30 (34)
14 PF13717 zinc_ribbon_4: zinc-r 64.4 1.8 4E-05 29.2 -0.4 33 205-238 3-35 (36)
15 smart00653 eIF2B_5 domain pres 55.0 4.5 9.8E-05 33.9 0.3 28 205-236 81-109 (110)
16 PF06677 Auto_anti-p27: Sjogre 53.0 5.3 0.00012 28.0 0.4 25 204-235 17-41 (41)
17 PF09297 zf-NADH-PPase: NADH p 52.8 3.2 6.9E-05 27.0 -0.7 29 204-238 3-31 (32)
18 PRK11823 DNA repair protein Ra 50.6 5.5 0.00012 40.6 0.2 25 204-238 7-31 (446)
19 KOG1601 GATA-4/5/6 transcripti 50.5 6.1 0.00013 34.9 0.4 41 135-175 290-330 (340)
20 PRK12286 rpmF 50S ribosomal pr 49.3 5.7 0.00012 29.7 0.0 23 204-237 27-49 (57)
21 TIGR02098 MJ0042_CXXC MJ0042 f 47.3 3.9 8.5E-05 27.2 -1.0 33 205-238 3-35 (38)
22 TIGR00416 sms DNA repair prote 47.0 6.8 0.00015 40.0 0.2 25 204-238 7-31 (454)
23 PF01412 ArfGap: Putative GTPa 44.7 19 0.00041 29.9 2.5 36 204-243 13-48 (116)
24 PF06689 zf-C4_ClpX: ClpX C4-t 44.5 12 0.00026 25.9 1.1 33 205-238 2-34 (41)
25 COG3952 Predicted membrane pro 44.4 6.3 0.00014 33.3 -0.4 21 218-240 75-95 (113)
26 PF02701 zf-Dof: Dof domain, z 43.6 16 0.00035 28.1 1.7 48 204-251 5-53 (63)
27 PF13240 zinc_ribbon_2: zinc-r 43.1 14 0.0003 22.7 1.0 21 206-236 1-21 (23)
28 PRK00420 hypothetical protein; 43.0 11 0.00023 32.0 0.7 30 204-240 23-52 (112)
29 PRK05978 hypothetical protein; 42.7 9.8 0.00021 33.7 0.5 34 204-242 33-66 (148)
30 PF04810 zf-Sec23_Sec24: Sec23 42.5 10 0.00023 25.9 0.5 31 204-236 2-32 (40)
31 PF13248 zf-ribbon_3: zinc-rib 42.3 15 0.00033 22.9 1.2 22 205-236 3-24 (26)
32 cd01121 Sms Sms (bacterial rad 41.9 9.4 0.0002 38.1 0.3 24 205-238 1-24 (372)
33 TIGR00311 aIF-2beta translatio 40.5 9 0.00019 33.2 -0.1 30 205-237 98-127 (133)
34 PRK03988 translation initiatio 40.4 8.9 0.00019 33.4 -0.1 30 205-237 103-132 (138)
35 TIGR03573 WbuX N-acetyl sugar 37.3 22 0.00047 34.9 2.0 32 205-240 2-33 (343)
36 COG2816 NPY1 NTP pyrophosphohy 37.2 12 0.00026 36.4 0.2 31 204-240 111-141 (279)
37 KOG1598 Transcription initiati 37.1 16 0.00035 38.4 1.1 31 205-240 1-31 (521)
38 PF13619 KTSC: KTSC domain 36.8 64 0.0014 23.7 4.0 34 68-101 9-43 (60)
39 COG1645 Uncharacterized Zn-fin 36.5 12 0.00027 32.6 0.1 27 204-238 28-54 (131)
40 PRK12336 translation initiatio 34.8 12 0.00026 34.3 -0.2 32 205-239 99-130 (201)
41 PF07282 OrfB_Zn_ribbon: Putat 34.4 11 0.00024 28.0 -0.4 30 204-239 28-57 (69)
42 PF08271 TF_Zn_Ribbon: TFIIB z 34.1 15 0.00033 25.2 0.3 30 206-240 2-31 (43)
43 TIGR01031 rpmF_bact ribosomal 34.1 12 0.00027 27.6 -0.2 23 204-237 26-48 (55)
44 PRK05342 clpX ATP-dependent pr 33.9 24 0.00051 35.8 1.7 30 204-235 9-38 (412)
45 COG2331 Uncharacterized protei 31.1 15 0.00033 29.4 -0.1 36 204-242 12-47 (82)
46 PRK11788 tetratricopeptide rep 30.9 19 0.00041 34.0 0.5 22 204-235 354-375 (389)
47 COG5349 Uncharacterized protei 29.7 22 0.00047 30.8 0.6 34 204-242 21-54 (126)
48 PRK01110 rpmF 50S ribosomal pr 29.6 18 0.00039 27.3 0.0 23 204-238 27-49 (60)
49 PF01873 eIF-5_eIF-2B: Domain 29.6 20 0.00043 30.7 0.3 29 205-236 94-122 (125)
50 PRK12496 hypothetical protein; 29.5 26 0.00055 31.2 1.0 32 204-243 127-158 (164)
51 TIGR00244 transcriptional regu 28.8 22 0.00048 31.6 0.4 58 206-263 2-68 (147)
52 smart00105 ArfGap Putative GTP 27.4 57 0.0012 26.9 2.7 38 204-245 3-40 (112)
53 KOG3740 Uncharacterized conser 27.2 25 0.00054 37.9 0.6 36 204-241 462-500 (706)
54 smart00834 CxxC_CXXC_SSSS Puta 26.4 24 0.00052 23.4 0.2 29 205-236 6-34 (41)
55 COG5347 GTPase-activating prot 25.3 37 0.0008 33.6 1.4 36 204-243 20-55 (319)
56 PRK14892 putative transcriptio 25.1 21 0.00046 29.5 -0.3 35 204-241 21-55 (99)
57 KOG0909 Peptide:N-glycanase [P 25.0 26 0.00057 36.3 0.3 32 204-236 161-202 (500)
58 PF11228 DUF3027: Protein of u 24.5 23 0.00049 32.8 -0.3 30 217-246 126-163 (193)
59 PF08394 Arc_trans_TRASH: Arch 24.3 52 0.0011 22.7 1.5 35 207-241 1-36 (37)
60 PF13719 zinc_ribbon_5: zinc-r 23.8 20 0.00043 24.2 -0.6 33 205-238 3-35 (37)
61 PF11781 RRN7: RNA polymerase 22.9 35 0.00076 23.1 0.5 25 205-236 9-33 (36)
62 PRK00398 rpoP DNA-directed RNA 22.6 37 0.00079 23.6 0.6 31 204-240 3-33 (46)
63 PRK00241 nudC NADH pyrophospha 22.3 25 0.00055 33.3 -0.4 31 204-240 99-129 (256)
64 PF14122 YokU: YokU-like prote 22.1 27 0.00058 28.5 -0.2 38 206-243 1-50 (87)
65 KOG0712 Molecular chaperone (D 22.1 58 0.0013 32.5 2.0 36 204-239 143-181 (337)
66 TIGR03831 YgiT_finger YgiT-typ 21.6 85 0.0018 20.9 2.2 23 72-94 11-33 (46)
67 PF12553 DUF3742: Protein of u 21.6 34 0.00074 25.4 0.3 11 218-228 34-44 (54)
68 PF09723 Zn-ribbon_8: Zinc rib 21.2 33 0.00072 23.6 0.1 29 205-236 6-34 (42)
69 COG1096 Predicted RNA-binding 20.9 35 0.00077 31.5 0.2 29 204-240 149-177 (188)
70 COG1631 RPL42A Ribosomal prote 20.2 41 0.00088 27.8 0.4 20 204-223 68-87 (94)
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=99.66 E-value=1.2e-16 Score=108.72 Aligned_cols=35 Identities=43% Similarity=0.701 Sum_probs=32.8
Q ss_pred CCCCccceEEecceEEEeCCCChhHHHHHHHHhcC
Q 021461 71 STRTSELTVAYEGEVYVFPAVTPHKVQALLLLLGE 105 (312)
Q Consensus 71 ~~~t~QLTIfY~G~V~VFDdVp~eKaq~Im~la~~ 105 (312)
.+.++||||||+|+|+|||+||+|||++||+||+.
T Consensus 2 ~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~r 36 (36)
T PF06200_consen 2 SPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLASR 36 (36)
T ss_pred CCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhcC
Confidence 57789999999999999999999999999999973
No 2
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.57 E-value=1.3e-15 Score=112.09 Aligned_cols=44 Identities=52% Similarity=1.118 Sum_probs=40.2
Q ss_pred ccccccccCCCCCccccCCCCCcccchHHHHHHHhcCCCCCCccCc
Q 021461 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGA 251 (312)
Q Consensus 206 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~r~~~~~~ 251 (312)
.|+||++ +.||+||+||+|..+|||||||||++++..|+.....
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 5799999999998999999999999999999987754
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.52 E-value=6.3e-15 Score=107.47 Aligned_cols=45 Identities=51% Similarity=1.039 Sum_probs=40.1
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcCCC-CCCccC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL-RDLTKG 250 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~-r~~~~~ 250 (312)
...|+||+++ .||+||+||.|.++|||||||+|++++.+ |+..+.
T Consensus 3 ~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~ 48 (52)
T smart00401 3 GRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLK 48 (52)
T ss_pred CCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCCCCccccc
Confidence 5799999994 69999999999889999999999999988 776554
No 4
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.49 E-value=5.9e-15 Score=100.04 Aligned_cols=36 Identities=56% Similarity=1.199 Sum_probs=28.1
Q ss_pred cccccccCCCCCccccCCCCCcccchHHHHHHHhcCCC
Q 021461 207 CQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL 244 (312)
Q Consensus 207 C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~ 244 (312)
|.||+++ .||+||+||.|..+||||||++|++++++
T Consensus 1 C~~C~tt--~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGTT--ETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT--S--T-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcCC--CCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 8999995 69999999999888999999999999864
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=99.13 E-value=2.9e-11 Score=86.12 Aligned_cols=44 Identities=52% Similarity=0.819 Sum_probs=41.9
Q ss_pred HHHHHHHHHHhhhhccccccccccchhhHHHHHhhhcccccccc
Q 021461 138 RIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNGQFTSSK 181 (312)
Q Consensus 138 R~aSL~Rf~eKRk~R~~~kki~Y~~rk~~A~r~~R~kGqFas~k 181 (312)
|.++|.||++||+.|+|.|+|+|.+|+.+|+.++|.+|+|++..
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 67899999999999999999999999999999999999999864
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.60 E-value=2.4e-08 Score=88.51 Aligned_cols=45 Identities=49% Similarity=1.015 Sum_probs=38.3
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcCCCCCCccC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKG 250 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~r~~~~~ 250 (312)
...|.+|++ +.||+||++|.|...||||||++|++++..|.+...
T Consensus 199 ~~~c~~~~~--~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~ 243 (340)
T KOG1601|consen 199 LRQCSNCGT--TKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEK 243 (340)
T ss_pred CcccCCCCC--CCCcceecCCCCCccccccchhhhhhcCcccccccc
Confidence 479999999 579999999999999999999999999744444443
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.24 E-value=5.5e-07 Score=91.87 Aligned_cols=53 Identities=28% Similarity=0.591 Sum_probs=43.6
Q ss_pred CCCCCCCCcccccccccCCCCCccccCCCC----CcccchHHHHHHHhcCCCC-CCccCc
Q 021461 197 SAPPESVSRICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKGTLR-DLTKGA 251 (312)
Q Consensus 197 ~~~~~~~~~~C~~Cg~~~~~Tp~wR~GP~G----~~~LCNACGl~~~~~~~~r-~~~~~~ 251 (312)
....+.+...|.||.+ +.||+|||+..+ .-.|||||||+|+.||++| +++-..
T Consensus 151 ~~~~s~~~~vc~Nc~t--~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks 208 (498)
T COG5641 151 QSDNSNQPHVCSNCKT--TSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKS 208 (498)
T ss_pred ccccccccchhccccc--cCCccccccccccccCCccccccccccccccCCcCCCccccc
Confidence 3445555669999999 579999999993 3899999999999999999 765443
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=98.09 E-value=1.5e-06 Score=55.76 Aligned_cols=25 Identities=52% Similarity=0.579 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHhhhhcccccccccc
Q 021461 136 SQRIASLVRFREKRKERSFEKKIRYS 161 (312)
Q Consensus 136 ~~R~aSL~Rf~eKRk~R~~~kki~Y~ 161 (312)
.+|++||+||+||||+|..+ +.+|.
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp ----HHHHHHHHHH------------
T ss_pred chHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 47999999999999999998 48886
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=90.12 E-value=0.14 Score=53.02 Aligned_cols=48 Identities=25% Similarity=0.264 Sum_probs=41.8
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcCCCCCCccCcc
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGAR 252 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~r~~~~~~~ 252 (312)
...|.+|++. +.||.||+...-.-.+|||||++-+..+..+++.+..-
T Consensus 297 ~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d 344 (498)
T COG5641 297 DKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPD 344 (498)
T ss_pred hcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCCC
Confidence 5789999976 57999999988879999999999999999999887443
No 10
>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=70.62 E-value=2.2 Score=32.30 Aligned_cols=30 Identities=20% Similarity=0.636 Sum_probs=24.2
Q ss_pred CcccccccccCCCCCccccCCCCCcccc-hHHHHHHHhcCC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLC-NACGLMWANKGT 243 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LC-NACGl~~~~~~~ 243 (312)
-++|-+||.+. |.+ +..| ..|+.-|.++++
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 47999999975 445 7899 599999998753
No 11
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=69.89 E-value=4.5 Score=42.12 Aligned_cols=39 Identities=26% Similarity=0.576 Sum_probs=31.3
Q ss_pred CcccccccccCCCCCccc--cCCCCCcccchHHHHHHHhcCCC
Q 021461 204 SRICQHCGISEKLTPAMR--RGPAGPRTLCNACGLMWANKGTL 244 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR--~GP~G~~~LCNACGl~~~~~~~~ 244 (312)
.+.|-+|+++ ..-+|= -+|.-...||-.|=+||++-|-+
T Consensus 386 g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 7899999994 577774 45666679999999999997753
No 12
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=69.50 E-value=1.2 Score=32.98 Aligned_cols=24 Identities=29% Similarity=0.838 Sum_probs=18.0
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~ 239 (312)
...|.+||.. .-+..+|..|| ||+
T Consensus 26 l~~c~~cg~~-----------~~~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 26 LVKCPNCGEP-----------KLPHRVCPSCG-YYK 49 (56)
T ss_dssp EEESSSSSSE-----------ESTTSBCTTTB-BSS
T ss_pred eeeeccCCCE-----------ecccEeeCCCC-eEC
Confidence 5799999973 23478999999 443
No 13
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=67.44 E-value=1.8 Score=29.19 Aligned_cols=30 Identities=33% Similarity=0.855 Sum_probs=14.6
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 236 (312)
+.|.+||.. .+..-=.|.+-.+..|.+||.
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 469999973 122222445556799999995
No 14
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=64.42 E-value=1.8 Score=29.21 Aligned_cols=33 Identities=21% Similarity=0.569 Sum_probs=28.7
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
..|-+|++. ...+..+-.+.|....|-.||-.|
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 579999987 588999999999999999999766
No 15
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=54.98 E-value=4.5 Score=33.95 Aligned_cols=28 Identities=29% Similarity=0.712 Sum_probs=20.5
Q ss_pred cccccccccCCCCCccccCCCCC-cccchHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGP-RTLCNACGL 236 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~-~~LCNACGl 236 (312)
-.|..|+-+. |-+-+. .+. -.-|+|||-
T Consensus 81 VlC~~C~spd--T~l~k~--~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPD--TELIKE--NRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCC--cEEEEe--CCeEEEEccccCC
Confidence 5899999974 878876 232 244999994
No 16
>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=53.05 E-value=5.3 Score=28.03 Aligned_cols=25 Identities=44% Similarity=1.103 Sum_probs=19.6
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACG 235 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACG 235 (312)
...|..|+ +|++| .-+| +.+|-+|+
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 45899995 79999 3466 79999985
No 17
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=52.82 E-value=3.2 Score=27.02 Aligned_cols=29 Identities=31% Similarity=0.779 Sum_probs=16.5
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
.+.|..||.. ...-+.|....|.+||..+
T Consensus 3 ~rfC~~CG~~------t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAP------TKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--B------EEE-SSSS-EEESSSS-EE
T ss_pred CcccCcCCcc------ccCCCCcCEeECCCCcCEe
Confidence 4789999984 2334567788999999753
No 18
>PRK11823 DNA repair protein RadA; Provisional
Probab=50.64 E-value=5.5 Score=40.56 Aligned_cols=25 Identities=32% Similarity=0.795 Sum_probs=17.7
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
..+|.+||-. ++.|- -.|.+||-+=
T Consensus 7 ~y~C~~Cg~~---~~~~~-------g~Cp~C~~w~ 31 (446)
T PRK11823 7 AYVCQECGAE---SPKWL-------GRCPECGAWN 31 (446)
T ss_pred eEECCcCCCC---CcccC-------eeCcCCCCcc
Confidence 5899999985 45552 2599997653
No 19
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=50.53 E-value=6.1 Score=34.89 Aligned_cols=41 Identities=44% Similarity=0.678 Sum_probs=37.3
Q ss_pred hHHHHHHHHHHHHhhhhccccccccccchhhHHHHHhhhcc
Q 021461 135 LSQRIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNG 175 (312)
Q Consensus 135 l~~R~aSL~Rf~eKRk~R~~~kki~Y~~rk~~A~r~~R~kG 175 (312)
...|.+.+.|++++++.+.|.++++|..++..++.+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 34688899999999999999999999999999999998876
No 20
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=49.31 E-value=5.7 Score=29.68 Aligned_cols=23 Identities=30% Similarity=0.836 Sum_probs=17.4
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~ 237 (312)
.-.|.+||... =+..+|..||.|
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 237899999954
No 21
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=47.30 E-value=3.9 Score=27.21 Aligned_cols=33 Identities=27% Similarity=0.668 Sum_probs=23.6
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
..|.+|++. ..-+..+.+..|....|-.||..|
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 345555666667678898888765
No 22
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=47.05 E-value=6.8 Score=40.04 Aligned_cols=25 Identities=32% Similarity=0.566 Sum_probs=17.8
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
..+|.+||-. ...|+| .|.+||-+=
T Consensus 7 ~y~C~~Cg~~-~~~~~g---------~Cp~C~~w~ 31 (454)
T TIGR00416 7 KFVCQHCGAD-SPKWQG---------KCPACHAWN 31 (454)
T ss_pred eEECCcCCCC-CccccE---------ECcCCCCcc
Confidence 5899999985 244555 488887653
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=44.68 E-value=19 Score=29.88 Aligned_cols=36 Identities=25% Similarity=0.594 Sum_probs=26.9
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcCC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~ 243 (312)
...|..||.. -|.|-.=..| -.||-.|.-.++.-|+
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 8999999998888775
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=44.48 E-value=12 Score=25.90 Aligned_cols=33 Identities=27% Similarity=0.629 Sum_probs=22.0
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
.+|+=||.+++..-..=.||.| ..+|+.|=...
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 5899999987766666689978 79999996543
No 25
>COG3952 Predicted membrane protein [Function unknown]
Probab=44.40 E-value=6.3 Score=33.31 Aligned_cols=21 Identities=33% Similarity=0.387 Sum_probs=16.5
Q ss_pred CccccCCCCCcccchHHHHHHHh
Q 021461 218 PAMRRGPAGPRTLCNACGLMWAN 240 (312)
Q Consensus 218 p~wR~GP~G~~~LCNACGl~~~~ 240 (312)
-.||.+|-+ .||++||++-..
T Consensus 75 fi~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 75 FIRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHHhcchHH--HHHHhhhHHHHH
Confidence 357888877 899999997544
No 26
>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=43.58 E-value=16 Score=28.10 Aligned_cols=48 Identities=25% Similarity=0.576 Sum_probs=32.3
Q ss_pred CcccccccccCCCCCccc-cCCCCCcccchHHHHHHHhcCCCCCCccCc
Q 021461 204 SRICQHCGISEKLTPAMR-RGPAGPRTLCNACGLMWANKGTLRDLTKGA 251 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR-~GP~G~~~LCNACGl~~~~~~~~r~~~~~~ 251 (312)
...|..|..+.|+-=-.= -...-|+..|-+|..+|-..|++|.+--++
T Consensus 5 ~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvgg 53 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGG 53 (63)
T ss_pred CCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCC
Confidence 578888887532110011 112345789999999999999999986554
No 27
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=43.13 E-value=14 Score=22.73 Aligned_cols=21 Identities=29% Similarity=0.865 Sum_probs=11.5
Q ss_pred ccccccccCCCCCccccCCCCCcccchHHHH
Q 021461 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (312)
Q Consensus 206 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 236 (312)
.|.+||... +++ ...|.-||.
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 366676643 333 445666664
No 28
>PRK00420 hypothetical protein; Validated
Probab=43.03 E-value=11 Score=32.04 Aligned_cols=30 Identities=27% Similarity=0.661 Sum_probs=23.9
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHh
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 240 (312)
...|..|| +|+.|. -+| ...|-.||..+..
T Consensus 23 ~~~CP~Cg-----~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCG-----LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCC-----Ccceec-CCC-ceECCCCCCeeee
Confidence 46899998 678875 456 8999999987765
No 29
>PRK05978 hypothetical protein; Provisional
Probab=42.69 E-value=9.8 Score=33.69 Aligned_cols=34 Identities=26% Similarity=0.537 Sum_probs=26.4
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~ 242 (312)
..+|-+||. -.++| |-..-..-|.+||+.|..+.
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 578999997 44665 56666789999999997764
No 30
>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=42.52 E-value=10 Score=25.94 Aligned_cols=31 Identities=29% Similarity=0.639 Sum_probs=20.4
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 236 (312)
..+|.+|++= --|..+-...|..-.||-|+.
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 3689999984 588888888888889999986
No 31
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=42.28 E-value=15 Score=22.87 Aligned_cols=22 Identities=27% Similarity=0.833 Sum_probs=14.5
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 236 (312)
+.|.+||... +.+ ...|-.||.
T Consensus 3 ~~Cp~Cg~~~---------~~~-~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEI---------DPD-AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcC---------Ccc-cccChhhCC
Confidence 5788888742 333 467888875
No 32
>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=41.90 E-value=9.4 Score=38.09 Aligned_cols=24 Identities=33% Similarity=0.848 Sum_probs=16.5
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
..|.+||-. ++.|- | -|.+||-+=
T Consensus 1 ~~c~~cg~~---~~~~~----g---~cp~c~~w~ 24 (372)
T cd01121 1 YVCSECGYV---SPKWL----G---KCPECGEWN 24 (372)
T ss_pred CCCCCCCCC---CCCcc----E---ECcCCCCce
Confidence 379999974 55553 2 588887653
No 33
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=40.53 E-value=9 Score=33.23 Aligned_cols=30 Identities=30% Similarity=0.688 Sum_probs=20.8
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~ 237 (312)
-.|..|+-+. |-+-+.+- -.-.-|+|||-.
T Consensus 98 VlC~~C~sPd--T~l~k~~r-~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPD--TRIIKEGR-VSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCC--cEEEEeCC-eEEEecccCCCC
Confidence 5799999975 77777531 112579999954
No 34
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=40.37 E-value=8.9 Score=33.43 Aligned_cols=30 Identities=33% Similarity=0.666 Sum_probs=20.9
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~ 237 (312)
-.|..|+.+. |-+-+.+= ---.-|+|||-.
T Consensus 103 VlC~~C~spd--T~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGSPD--TKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred EECCCCCCCC--cEEEEcCC-eEEEEcccCCCC
Confidence 5899999974 77777521 113679999954
No 35
>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=37.27 E-value=22 Score=34.87 Aligned_cols=32 Identities=22% Similarity=0.649 Sum_probs=26.2
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHHHHh
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 240 (312)
+.|..|..+ ++.|.-.-..+| +||+|--+-.+
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 477877778888 99999987643
No 36
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=37.18 E-value=12 Score=36.37 Aligned_cols=31 Identities=29% Similarity=0.652 Sum_probs=22.2
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHh
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 240 (312)
.+.|.+||+. ..+ ...|.+.+|+.||.++--
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 5799999983 222 245667899999987754
No 37
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=37.07 E-value=16 Score=38.38 Aligned_cols=31 Identities=29% Similarity=0.685 Sum_probs=22.5
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHHHHh
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 240 (312)
..|.|||.+ ++.-+- -+| -..|++||.....
T Consensus 1 ~~C~~C~~s---~fe~d~-a~g-~~~C~~CG~v~E~ 31 (521)
T KOG1598|consen 1 MVCKNCGGS---NFERDE-ATG-NLYCTACGTVLEY 31 (521)
T ss_pred CcCCCCCCC---Cccccc-ccC-Cceeccccceeec
Confidence 369999984 555443 556 7999999986654
No 38
>PF13619 KTSC: KTSC domain
Probab=36.75 E-value=64 Score=23.69 Aligned_cols=34 Identities=32% Similarity=0.480 Sum_probs=27.0
Q ss_pred cCCCCCCccceEEe-cceEEEeCCCChhHHHHHHH
Q 021461 68 SSTSTRTSELTVAY-EGEVYVFPAVTPHKVQALLL 101 (312)
Q Consensus 68 ~~~~~~t~QLTIfY-~G~V~VFDdVp~eKaq~Im~ 101 (312)
+.=.+.+..|.|.| +|.++.|.+||++-.+++|.
T Consensus 9 v~Yd~~~~~L~V~F~~G~~Y~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 9 VGYDPETRTLEVEFKSGSVYRYFGVPPEVYEALLN 43 (60)
T ss_pred EeECCCCCEEEEEEcCCCEEEECCCCHHHHHHHHc
Confidence 33456677888866 68999999999999988875
No 39
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=36.46 E-value=12 Score=32.56 Aligned_cols=27 Identities=37% Similarity=0.959 Sum_probs=22.7
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
..+|.-|| ||++| =+| ...|-.||...
T Consensus 28 ~~hCp~Cg-----~PLF~--KdG-~v~CPvC~~~~ 54 (131)
T COG1645 28 AKHCPKCG-----TPLFR--KDG-EVFCPVCGYRE 54 (131)
T ss_pred HhhCcccC-----Cccee--eCC-eEECCCCCceE
Confidence 57899998 68999 678 89999999643
No 40
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=34.84 E-value=12 Score=34.29 Aligned_cols=32 Identities=28% Similarity=0.649 Sum_probs=22.3
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~ 239 (312)
-.|..|+-+. |-+-+.+ .---.-|+|||-..-
T Consensus 99 V~C~~C~~pd--T~l~k~~-~~~~l~C~aCGa~~~ 130 (201)
T PRK12336 99 VICSECGLPD--TRLVKED-RVLMLRCDACGAHRP 130 (201)
T ss_pred EECCCCCCCC--cEEEEcC-CeEEEEcccCCCCcc
Confidence 5899999974 7777763 111257999996543
No 41
>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=34.44 E-value=11 Score=28.04 Aligned_cols=30 Identities=27% Similarity=0.624 Sum_probs=21.8
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~ 239 (312)
...|..||... .. ...+....|..||..+.
T Consensus 28 Sq~C~~CG~~~-~~-----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRN-KK-----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCccccc-cc-----ccccceEEcCCCCCEEC
Confidence 57899999863 22 45555789999998753
No 42
>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=34.15 E-value=15 Score=25.24 Aligned_cols=30 Identities=27% Similarity=0.700 Sum_probs=17.3
Q ss_pred ccccccccCCCCCccccCCCCCcccchHHHHHHHh
Q 021461 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (312)
Q Consensus 206 ~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 240 (312)
.|.+||.+ . .--+--.| ..+|..||+-...
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 58888874 1 22233334 6789888876543
No 43
>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=34.06 E-value=12 Score=27.60 Aligned_cols=23 Identities=30% Similarity=0.850 Sum_probs=16.9
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~ 237 (312)
...|.+||.. -=+..+|-.||.|
T Consensus 26 l~~C~~cG~~-----------~~~H~vc~~cG~Y 48 (55)
T TIGR01031 26 LVVCPNCGEF-----------KLPHRVCPSCGYY 48 (55)
T ss_pred ceECCCCCCc-----------ccCeeECCccCeE
Confidence 4679999973 2337899999943
No 44
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=33.91 E-value=24 Score=35.83 Aligned_cols=30 Identities=27% Similarity=0.620 Sum_probs=25.5
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACG 235 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACG 235 (312)
..+|+.||.+...+...-.||.. .+|+.|=
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~Ci 38 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDECI 38 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchHH
Confidence 46999999998888888889854 6999993
No 45
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.14 E-value=15 Score=29.42 Aligned_cols=36 Identities=31% Similarity=0.525 Sum_probs=26.0
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~ 242 (312)
...|.+||-.-+-...++..| -+.|.+||-++++.-
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 578999997533345566655 569999999887743
No 46
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=30.86 E-value=19 Score=34.04 Aligned_cols=22 Identities=23% Similarity=0.733 Sum_probs=0.0
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACG 235 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACG 235 (312)
.+.|.|||.+ +..| ..+|-.||
T Consensus 354 ~~~c~~cg~~---~~~~-------~~~c~~c~ 375 (389)
T PRK11788 354 RYRCRNCGFT---ARTL-------YWHCPSCK 375 (389)
T ss_pred CEECCCCCCC---Cccc-------eeECcCCC
No 47
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.75 E-value=22 Score=30.82 Aligned_cols=34 Identities=29% Similarity=0.579 Sum_probs=24.1
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~ 242 (312)
..+|-+||-- -+.| |=.-...-|.|||+-|..+.
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 5799999963 2333 33444678999999997764
No 48
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=29.59 E-value=18 Score=27.25 Aligned_cols=23 Identities=13% Similarity=0.079 Sum_probs=16.5
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
...|.+||... =+..+|- ||.|.
T Consensus 27 ~~~c~~cg~~~-----------~pH~vc~-cG~Y~ 49 (60)
T PRK01110 27 LSVDKTTGEYH-----------LPHHVSP-KGYYK 49 (60)
T ss_pred eeEcCCCCcee-----------ccceecC-CcccC
Confidence 46899999842 2367899 99554
No 49
>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=29.55 E-value=20 Score=30.75 Aligned_cols=29 Identities=31% Similarity=0.728 Sum_probs=20.7
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 236 (312)
-.|..|+.++ |-+-+.+-.= -.-|+|||-
T Consensus 94 VlC~~C~spd--T~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPD--TELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSS--EEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCCc--cEEEEcCCEE-EEEecccCC
Confidence 5799999864 7777773222 477999984
No 50
>PRK12496 hypothetical protein; Provisional
Probab=29.47 E-value=26 Score=31.17 Aligned_cols=32 Identities=22% Similarity=0.550 Sum_probs=22.0
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcCC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~ 243 (312)
..+|..||.. .+ .++. ...|--||...+++..
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 3589999999888765
No 51
>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=28.82 E-value=22 Score=31.58 Aligned_cols=58 Identities=16% Similarity=0.217 Sum_probs=37.3
Q ss_pred ccccccccCCCCCccccCCCC----CcccchHHHHHHHhcCCC-----CCCccCcccccccccccCC
Q 021461 206 ICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKGTL-----RDLTKGARNICFEQHELET 263 (312)
Q Consensus 206 ~C~~Cg~~~~~Tp~wR~GP~G----~~~LCNACGl~~~~~~~~-----r~~~~~~~~~~~~~~~~~~ 263 (312)
+|-.||...|..--=|...+| .+--|.+||.+|-..-+. .=+++.|..-.+...++-.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l~ViKkdG~re~Fdr~Kl~~ 68 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLR 68 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccccEEEcCCCCCCCCCHHHHHH
Confidence 688898876555556666666 347899999998664332 2246666655555554443
No 52
>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=27.38 E-value=57 Score=26.89 Aligned_cols=38 Identities=24% Similarity=0.482 Sum_probs=31.9
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcCCCC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLR 245 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~~r 245 (312)
...|..|+.. -|.|=.=..| -.||-.|.-..+.-|+..
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 5799999984 6999888888 899999999888877543
No 53
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.24 E-value=25 Score=37.90 Aligned_cols=36 Identities=22% Similarity=0.527 Sum_probs=28.9
Q ss_pred CcccccccccCCCCCccccCCCC---CcccchHHHHHHHhc
Q 021461 204 SRICQHCGISEKLTPAMRRGPAG---PRTLCNACGLMWANK 241 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G---~~~LCNACGl~~~~~ 241 (312)
...|..|.+ .-||.|+.-+.| ..++|.+|----.++
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 578999999 579999998888 458999997654443
No 54
>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=26.38 E-value=24 Score=23.35 Aligned_cols=29 Identities=24% Similarity=0.643 Sum_probs=20.1
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 236 (312)
-+|..||.. -..|..--++....|-.||.
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 579999973 33455444466778999997
No 55
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=25.32 E-value=37 Score=33.58 Aligned_cols=36 Identities=25% Similarity=0.528 Sum_probs=31.1
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhcCC
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~~~ 243 (312)
...|..||.. . |.|=.-..| -.||--|-=..|.-|+
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 5899999994 5 999999999 8999999877776664
No 56
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.07 E-value=21 Score=29.54 Aligned_cols=35 Identities=20% Similarity=0.329 Sum_probs=22.5
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHhc
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~~ 241 (312)
.-.|.+||.....-++=| .-....|..||.|+.+.
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 578999994211112222 34479999999998663
No 57
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=25.03 E-value=26 Score=36.32 Aligned_cols=32 Identities=25% Similarity=0.535 Sum_probs=21.2
Q ss_pred CcccccccccCCCCCccccCCCCCc----------ccchHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPR----------TLCNACGL 236 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~----------~LCNACGl 236 (312)
...|.+||-- |.+++-+-+|.+.. ..||+||-
T Consensus 161 ~PpC~~CG~e-t~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~ 202 (500)
T KOG0909|consen 161 NPPCNKCGGE-TSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGT 202 (500)
T ss_pred CCCccccccc-ccccccCCCCchhHhhcCCceEEEEEecCCCC
Confidence 3579999874 34555555565533 68999985
No 58
>PF11228 DUF3027: Protein of unknown function (DUF3027); InterPro: IPR021391 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=24.51 E-value=23 Score=32.81 Aligned_cols=30 Identities=27% Similarity=0.593 Sum_probs=24.7
Q ss_pred CCccccCCCCCc--------ccchHHHHHHHhcCCCCC
Q 021461 217 TPAMRRGPAGPR--------TLCNACGLMWANKGTLRD 246 (312)
Q Consensus 217 Tp~wR~GP~G~~--------~LCNACGl~~~~~~~~r~ 246 (312)
-..|++|+.||+ ..|.-||.|+...|.|+.
T Consensus 126 a~RW~~g~~GP~s~~a~~a~~~C~tCgF~~plaG~L~~ 163 (193)
T PF11228_consen 126 AQRWYEGEFGPDSEMARAAPAQCSTCGFYVPLAGSLGQ 163 (193)
T ss_pred HHHHHcCCCCCCCHHHHhcccCCCcCccceEcCCchhc
Confidence 457888888877 479999999998888775
No 59
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=24.25 E-value=52 Score=22.73 Aligned_cols=35 Identities=20% Similarity=0.357 Sum_probs=23.6
Q ss_pred cccccccCCCCCccccCCCCCccc-chHHHHHHHhc
Q 021461 207 CQHCGISEKLTPAMRRGPAGPRTL-CNACGLMWANK 241 (312)
Q Consensus 207 C~~Cg~~~~~Tp~wR~GP~G~~~L-CNACGl~~~~~ 241 (312)
|..||..++..|.--+--.-...+ |+.|-..|+++
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~fk~k 36 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQFKKK 36 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHHHHhh
Confidence 788998877777655542222334 59998888765
No 60
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.79 E-value=20 Score=24.20 Aligned_cols=33 Identities=21% Similarity=0.561 Sum_probs=23.1
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~ 238 (312)
..|-+|++. -.-|.=+-+..|.+.-|-.||-.|
T Consensus 3 i~CP~C~~~-f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTR-FRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCce-EEcCHHHcccCCcEEECCCCCcEe
Confidence 468888876 355665666777778888887655
No 61
>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=22.92 E-value=35 Score=23.13 Aligned_cols=25 Identities=28% Similarity=0.632 Sum_probs=19.1
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 236 (312)
..|..|+. . |=..-+| ...|..||-
T Consensus 9 ~~C~~C~~----~--~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGS----R--WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CcCCCCCC----e--EeEccCC-EEEhhhCce
Confidence 46999986 3 5566677 899999983
No 62
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.58 E-value=37 Score=23.62 Aligned_cols=31 Identities=23% Similarity=0.431 Sum_probs=19.5
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHh
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 240 (312)
..+|.+||..- .-.+......|.-||-.+-.
T Consensus 3 ~y~C~~CG~~~------~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREV------ELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEE------EECCCCCceECCCCCCeEEE
Confidence 35799999842 12233336789999965543
No 63
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=22.32 E-value=25 Score=33.26 Aligned_cols=31 Identities=23% Similarity=0.462 Sum_probs=22.0
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHh
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 240 (312)
.+.|.+||.. |-. ...|.+..|.+||..+.-
T Consensus 99 ~~fC~~CG~~---~~~---~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 99 HRFCGYCGHP---MHP---SKTEWAMLCPHCRERYYP 129 (256)
T ss_pred CccccccCCC---Cee---cCCceeEECCCCCCEECC
Confidence 6799999984 222 246777889999976654
No 64
>PF14122 YokU: YokU-like protein
Probab=22.09 E-value=27 Score=28.50 Aligned_cols=38 Identities=26% Similarity=0.745 Sum_probs=24.4
Q ss_pred ccccccccC---CCCCccccCCCCCc---------ccchHHHHHHHhcCC
Q 021461 206 ICQHCGISE---KLTPAMRRGPAGPR---------TLCNACGLMWANKGT 243 (312)
Q Consensus 206 ~C~~Cg~~~---~~Tp~wR~GP~G~~---------~LCNACGl~~~~~~~ 243 (312)
.|..|+... ..+.....=|+|.+ ..|+.||+-|....+
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d~v 50 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDDEV 50 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehhHH
Confidence 377787631 12333344577754 679999999987654
No 65
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=22.08 E-value=58 Score=32.54 Aligned_cols=36 Identities=25% Similarity=0.506 Sum_probs=30.1
Q ss_pred CcccccccccCCCCCccccCC---CCCcccchHHHHHHH
Q 021461 204 SRICQHCGISEKLTPAMRRGP---AGPRTLCNACGLMWA 239 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP---~G~~~LCNACGl~~~ 239 (312)
...|..|..++-.+..||-|| .-.++.|..|+..-.
T Consensus 143 ~~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G~G~ 181 (337)
T KOG0712|consen 143 APKCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNGSGE 181 (337)
T ss_pred CCCCCCCCCCCceeEEEeccccccccceeEeccCCCccc
Confidence 458999999988999999999 556789999976544
No 66
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=21.65 E-value=85 Score=20.93 Aligned_cols=23 Identities=30% Similarity=0.405 Sum_probs=18.6
Q ss_pred CCCccceEEecceEEEeCCCChh
Q 021461 72 TRTSELTVAYEGEVYVFPAVTPH 94 (312)
Q Consensus 72 ~~t~QLTIfY~G~V~VFDdVp~e 94 (312)
.....+++-|+|+++++.+||+.
T Consensus 11 ~~~~~~~~~~~~~~~~i~~vp~~ 33 (46)
T TIGR03831 11 GKTTTETYEYGGELIVIENVPAL 33 (46)
T ss_pred ceEEEEEEEeCCEEEEEeCCCcc
Confidence 34447788899999999999974
No 67
>PF12553 DUF3742: Protein of unknown function (DUF3742); InterPro: IPR022213 This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Probab=21.65 E-value=34 Score=25.39 Aligned_cols=11 Identities=55% Similarity=0.912 Sum_probs=9.5
Q ss_pred CccccCCCCCc
Q 021461 218 PAMRRGPAGPR 228 (312)
Q Consensus 218 p~wR~GP~G~~ 228 (312)
|.||.||.|-.
T Consensus 34 ~E~R~G~~GfG 44 (54)
T PF12553_consen 34 PEWREGPAGFG 44 (54)
T ss_pred HhheecCCCcc
Confidence 89999999943
No 68
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.22 E-value=33 Score=23.64 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=18.7
Q ss_pred cccccccccCCCCCccccCCCCCcccchHHHH
Q 021461 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (312)
Q Consensus 205 ~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl 236 (312)
-+|..||.. --.|+..-+.....|-+||-
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHE---FEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCE---EEEEEEcCCCCCCcCCCCCC
Confidence 578889853 23444444455688988886
No 69
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=20.85 E-value=35 Score=31.45 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=22.2
Q ss_pred CcccccccccCCCCCccccCCCCCcccchHHHHHHHh
Q 021461 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~GP~G~~~LCNACGl~~~~ 240 (312)
--+|++|+ +++.+ .|...-|-.||.-=++
T Consensus 149 ~A~CsrC~-----~~L~~---~~~~l~Cp~Cg~tEkR 177 (188)
T COG1096 149 YARCSRCR-----APLVK---KGNMLKCPNCGNTEKR 177 (188)
T ss_pred EEEccCCC-----cceEE---cCcEEECCCCCCEEee
Confidence 56899998 56888 6667889999965433
No 70
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=20.21 E-value=41 Score=27.82 Aligned_cols=20 Identities=30% Similarity=0.652 Sum_probs=17.4
Q ss_pred CcccccccccCCCCCccccC
Q 021461 204 SRICQHCGISEKLTPAMRRG 223 (312)
Q Consensus 204 ~~~C~~Cg~~~~~Tp~wR~G 223 (312)
..+|+-||..++.+|.||-+
T Consensus 68 r~~Ct~Cgkah~~~~~~Rak 87 (94)
T COG1631 68 RLRCTECGKAHQRTPGFRAK 87 (94)
T ss_pred EEEehhhccccccCcceeee
Confidence 57999999998778899965
Done!