Query 025411
Match_columns 253
No_of_seqs 262 out of 1033
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 05:31:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025411.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025411hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06200 tify: tify domain; I 99.7 2.9E-17 6.4E-22 107.3 5.1 34 72-105 2-35 (36)
2 PF00320 GATA: GATA zinc finge 99.5 1.1E-14 2.5E-19 95.1 1.3 35 215-251 1-35 (36)
3 cd00202 ZnF_GATA Zinc finger D 99.5 2.6E-14 5.6E-19 101.4 2.5 36 214-251 1-36 (54)
4 smart00401 ZnF_GATA zinc finge 99.4 3.2E-14 7E-19 100.1 2.3 40 211-252 2-41 (52)
5 PF06203 CCT: CCT motif; Inte 99.4 1.1E-13 2.4E-18 94.7 2.6 44 139-182 1-44 (45)
6 PF09425 CCT_2: Divergent CCT 98.6 2.8E-08 6.1E-13 61.0 1.6 25 137-162 2-26 (27)
7 KOG1601 GATA-4/5/6 transcripti 98.4 9.8E-08 2.1E-12 82.7 1.9 36 212-249 199-234 (340)
8 COG5641 GAT1 GATA Zn-finger-co 97.6 1.4E-05 3.1E-10 79.0 0.2 35 211-248 157-196 (498)
9 KOG3554 Histone deacetylase co 91.6 0.35 7.6E-06 48.1 5.6 38 211-250 385-424 (693)
10 KOG1601 GATA-4/5/6 transcripti 74.1 0.99 2.1E-05 38.8 -0.1 41 136-176 290-330 (340)
11 PF14803 Nudix_N_2: Nudix N-te 71.3 1.2 2.5E-05 28.8 -0.2 29 213-243 1-29 (34)
12 COG5641 GAT1 GATA Zn-finger-co 70.7 1.6 3.4E-05 43.9 0.4 38 211-249 296-333 (498)
13 PF06677 Auto_anti-p27: Sjogre 55.8 4.4 9.4E-05 27.2 0.3 26 211-243 16-41 (41)
14 PF09889 DUF2116: Uncharacteri 51.8 11 0.00025 27.2 1.9 31 212-252 3-34 (59)
15 COG3952 Predicted membrane pro 50.4 4.6 9.9E-05 32.7 -0.3 19 227-247 76-94 (113)
16 COG2331 Uncharacterized protei 48.9 6.6 0.00014 30.1 0.3 37 212-251 12-48 (82)
17 PF13717 zinc_ribbon_4: zinc-r 48.9 3.9 8.5E-05 26.4 -0.8 33 213-246 3-35 (36)
18 PF04810 zf-Sec23_Sec24: Sec23 47.3 7.5 0.00016 25.5 0.4 31 212-244 2-32 (40)
19 PF01412 ArfGap: Putative GTPa 46.6 20 0.00044 28.6 2.9 37 210-250 11-47 (116)
20 PF06689 zf-C4_ClpX: ClpX C4-t 46.6 17 0.00037 24.1 2.0 38 213-251 2-39 (41)
21 KOG3740 Uncharacterized conser 46.4 8 0.00017 39.9 0.6 36 211-248 461-499 (706)
22 PF15396 FAM60A: Protein Famil 43.6 12 0.00026 33.7 1.2 16 237-253 50-65 (213)
23 PRK00420 hypothetical protein; 39.6 12 0.00027 30.4 0.6 30 211-247 22-51 (112)
24 PF08047 His_leader: Histidine 39.4 17 0.00036 19.6 0.9 11 21-31 4-14 (16)
25 COG5349 Uncharacterized protei 36.9 13 0.00028 30.9 0.3 32 211-247 20-51 (126)
26 PF14122 YokU: YokU-like prote 36.0 8 0.00017 30.1 -1.0 33 214-246 1-45 (87)
27 PRK14892 putative transcriptio 33.7 8.6 0.00019 30.6 -1.2 39 211-253 20-59 (99)
28 PRK05978 hypothetical protein; 33.7 14 0.00031 31.4 0.1 31 212-247 33-63 (148)
29 PRK09727 his operon leader pep 33.1 21 0.00047 21.3 0.7 11 21-31 4-14 (26)
30 PF08271 TF_Zn_Ribbon: TFIIB z 32.6 12 0.00026 24.7 -0.4 27 214-245 2-28 (43)
31 KOG1561 CCAAT-binding factor, 31.7 49 0.0011 31.4 3.3 31 158-188 216-249 (307)
32 PF09297 zf-NADH-PPase: NADH p 30.3 16 0.00035 22.6 -0.1 28 212-245 3-30 (32)
33 smart00834 CxxC_CXXC_SSSS Puta 30.0 9.5 0.00021 24.3 -1.3 32 213-247 6-37 (41)
34 PF12553 DUF3742: Protein of u 29.2 20 0.00043 25.5 0.2 11 226-236 34-44 (54)
35 PRK03988 translation initiatio 28.9 17 0.00037 30.5 -0.3 31 211-244 101-131 (138)
36 KOG0712 Molecular chaperone (D 27.9 29 0.00063 33.3 1.1 35 211-245 142-179 (337)
37 KOG3507 DNA-directed RNA polym 27.6 70 0.0015 23.4 2.7 38 209-253 17-56 (62)
38 PF08394 Arc_trans_TRASH: Arch 27.3 39 0.00084 22.3 1.3 36 215-250 1-37 (37)
39 PF12172 DUF35_N: Rubredoxin-l 27.0 20 0.00044 22.8 -0.1 23 211-243 10-32 (37)
40 TIGR00311 aIF-2beta translatio 27.0 19 0.00041 30.0 -0.3 31 211-244 96-126 (133)
41 TIGR02098 MJ0042_CXXC MJ0042 f 26.2 19 0.00041 22.8 -0.3 32 213-245 3-34 (38)
42 smart00653 eIF2B_5 domain pres 25.6 22 0.00048 28.6 -0.1 30 212-244 80-109 (110)
43 COG1645 Uncharacterized Zn-fin 25.5 25 0.00055 29.4 0.2 26 211-244 27-52 (131)
44 PF11781 RRN7: RNA polymerase 25.3 27 0.00059 22.6 0.3 27 211-244 7-33 (36)
45 PF13619 KTSC: KTSC domain 24.7 83 0.0018 22.1 2.8 31 72-102 12-43 (60)
46 smart00778 Prim_Zn_Ribbon Zinc 24.0 41 0.00088 22.1 0.9 28 213-243 4-32 (37)
47 COG1096 Predicted RNA-binding 22.9 29 0.00063 30.7 0.1 32 211-250 148-179 (188)
48 PRK12496 hypothetical protein; 22.8 33 0.00071 29.3 0.4 32 213-252 128-159 (164)
49 TIGR03655 anti_R_Lar restricti 22.7 31 0.00068 23.8 0.2 8 213-220 2-9 (53)
50 PRK12336 translation initiatio 22.7 25 0.00055 31.0 -0.3 31 212-245 98-128 (201)
51 KOG0706 Predicted GTPase-activ 22.3 33 0.00072 34.1 0.4 39 207-249 18-56 (454)
52 PRK11788 tetratricopeptide rep 21.8 36 0.00078 31.1 0.5 11 210-220 352-362 (389)
53 COG1631 RPL42A Ribosomal prote 21.5 37 0.00081 26.8 0.4 22 210-231 66-87 (94)
54 COG4260 Membrane protease subu 21.5 48 0.001 31.6 1.2 30 210-244 313-342 (345)
55 COG4683 Uncharacterized protei 21.0 1.3E+02 0.0028 24.7 3.4 25 73-106 63-87 (120)
56 COG2816 NPY1 NTP pyrophosphohy 20.3 33 0.00071 32.2 -0.1 30 211-246 110-139 (279)
57 TIGR03831 YgiT_finger YgiT-typ 20.1 1.1E+02 0.0024 19.5 2.4 20 76-95 14-33 (46)
58 PF11685 DUF3281: Protein of u 20.0 1.1E+02 0.0024 28.4 3.3 71 6-89 59-134 (268)
No 1
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=99.69 E-value=2.9e-17 Score=107.34 Aligned_cols=34 Identities=47% Similarity=0.705 Sum_probs=32.2
Q ss_pred CCCCCceeEEEccEEEeeCCCCHHHHHHHHHHhC
Q 025411 72 SEIGDQLTLSFQGQVYVFDSVSPEKVQAVLLLLG 105 (253)
Q Consensus 72 ~~~~~QLTIfY~G~V~VfD~v~~eKaq~Im~lA~ 105 (253)
++.++||||||+|+|+|||+||+|||++||+||+
T Consensus 2 ~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~ 35 (36)
T PF06200_consen 2 SPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLAS 35 (36)
T ss_pred CCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhc
Confidence 4678999999999999999999999999999997
No 2
>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=99.47 E-value=1.1e-14 Score=95.08 Aligned_cols=35 Identities=54% Similarity=1.153 Sum_probs=27.9
Q ss_pred ccccccccCCCCccccCCCCCcccchHHHHHHHhhhc
Q 025411 215 CRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKVR 251 (253)
Q Consensus 215 C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~~~ 251 (253)
|.+|++ +.||+||+||.|..+|||||||+|+|..+
T Consensus 1 C~~C~t--t~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGT--TETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT----ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcC--CCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 899999 78999999999998899999999999764
No 3
>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=99.46 E-value=2.6e-14 Score=101.41 Aligned_cols=36 Identities=53% Similarity=1.186 Sum_probs=33.1
Q ss_pred cccccccccCCCCccccCCCCCcccchHHHHHHHhhhc
Q 025411 214 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKVR 251 (253)
Q Consensus 214 ~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~~~ 251 (253)
.|++|++ +.||+||+||+|..+|||||||+|+|...
T Consensus 1 ~C~~C~~--~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGT--TTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCC--CCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 4999999 78999999999989999999999998753
No 4
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.45 E-value=3.2e-14 Score=100.09 Aligned_cols=40 Identities=45% Similarity=0.961 Sum_probs=35.8
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHHHHHhhhcc
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKVRE 252 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~~~~ 252 (253)
....|++|++ +.||+||+||.|+++|||||||+|+|..+.
T Consensus 2 ~~~~C~~C~~--~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGT--TETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCC--CCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 3568999999 789999999999989999999999987653
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=99.40 E-value=1.1e-13 Score=94.68 Aligned_cols=44 Identities=57% Similarity=0.801 Sum_probs=42.1
Q ss_pred HHHHHHHHHHhhhhcccccccchhhhHHHHHHhHhhcCccccCC
Q 025411 139 RLASLIRFREKRKERNFEKKIRYTVRKEVALRMQRNKGQFTSAK 182 (253)
Q Consensus 139 R~asl~Rf~eKRk~R~~~k~~~Y~~Rk~~A~~r~R~KGrf~ssk 182 (253)
|+++|+||+|||+.|.|.|+|+|++||.+|+.++|++|+|++.+
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 68999999999999999999999999999999999999999864
No 6
>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=98.55 E-value=2.8e-08 Score=60.98 Aligned_cols=25 Identities=52% Similarity=0.549 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHhhhhcccccccchh
Q 025411 137 PQRLASLIRFREKRKERNFEKKIRYT 162 (253)
Q Consensus 137 ~~R~asl~Rf~eKRk~R~~~k~~~Y~ 162 (253)
++|++||+||+||||+|+.. +.+|.
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 58999999999999999988 57885
No 7
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.41 E-value=9.8e-08 Score=82.66 Aligned_cols=36 Identities=53% Similarity=1.159 Sum_probs=34.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchHHHHHHHhh
Q 025411 212 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 249 (253)
Q Consensus 212 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~ 249 (253)
...|.+|++ +.||+||++|.|+..|||||||+|++.
T Consensus 199 ~~~c~~~~~--~~t~~~r~~~~g~~~~cnacgl~~k~~ 234 (340)
T KOG1601|consen 199 LRQCSNCGT--TKTPLWRRGPEGPKSLCNACGLRYKKG 234 (340)
T ss_pred CcccCCCCC--CCCcceecCCCCCccccccchhhhhhc
Confidence 589999999 789999999999999999999999986
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.60 E-value=1.4e-05 Score=78.97 Aligned_cols=35 Identities=49% Similarity=0.924 Sum_probs=30.7
Q ss_pred ccccccccccccCCCCccccCCC-----CCcccchHHHHHHHh
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPE-----GPRTLCNACGLMWAN 248 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~-----G~~~LCNaCGl~~~k 248 (253)
....|.+|.+ +.||+|||+.. | -.|||||||+++-
T Consensus 157 ~~~vc~Nc~t--~stPlwrR~~~~~s~~~-n~lcnaCgl~~kl 196 (498)
T COG5641 157 QPHVCSNCKT--TSTPLWRRASSESSLPG-NNLCNACGLYLKL 196 (498)
T ss_pred ccchhccccc--cCCccccccccccccCC-ccccccccccccc
Confidence 4449999999 89999999999 6 5999999999863
No 9
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=91.57 E-value=0.35 Score=48.09 Aligned_cols=38 Identities=21% Similarity=0.526 Sum_probs=30.5
Q ss_pred ccccccccccccCCCCcccc-CCCC-CcccchHHHHHHHhhh
Q 025411 211 QDIVCRHCGISEKSTPMMRR-GPEG-PRTLCNACGLMWANKV 250 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~-Gp~G-~~~LCNaCGl~~~k~~ 250 (253)
..+.|.+|++ |+.-+|-. ||-+ ...||--|=++|+|..
T Consensus 385 ~g~~CEsC~t--tqs~qWYsWGppnmqcrLCasCWiyWKKyg 424 (693)
T KOG3554|consen 385 DGRACESCYT--TQSLQWYSWGPPNMQCRLCASCWIYWKKYG 424 (693)
T ss_pred CCCccccccc--ccccceeccCCCCccchhhHHHHHHHHHhc
Confidence 3679999999 78888876 5544 4489999999999864
No 10
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=74.08 E-value=0.99 Score=38.84 Aligned_cols=41 Identities=46% Similarity=0.633 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHhhhhcccccccchhhhHHHHHHhHhhcC
Q 025411 136 VPQRLASLIRFREKRKERNFEKKIRYTVRKEVALRMQRNKG 176 (253)
Q Consensus 136 ~~~R~asl~Rf~eKRk~R~~~k~~~Y~~Rk~~A~~r~R~KG 176 (253)
...|.+.+.|++++++.|.|.+.++|..|+..|+.+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 45889999999999999999999999999999999999988
No 11
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=71.29 E-value=1.2 Score=28.82 Aligned_cols=29 Identities=31% Similarity=0.740 Sum_probs=13.7
Q ss_pred ccccccccccCCCCccccCCCCCcccchHHH
Q 025411 213 IVCRHCGISEKSTPMMRRGPEGPRTLCNACG 243 (253)
Q Consensus 213 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCG 243 (253)
+.|.+||.. -+..-=.|.+-.+..|.+||
T Consensus 1 kfC~~CG~~--l~~~ip~gd~r~R~vC~~Cg 29 (34)
T PF14803_consen 1 KFCPQCGGP--LERRIPEGDDRERLVCPACG 29 (34)
T ss_dssp -B-TTT--B---EEE--TT-SS-EEEETTTT
T ss_pred CccccccCh--hhhhcCCCCCccceECCCCC
Confidence 369999962 12122235566679999998
No 12
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=70.70 E-value=1.6 Score=43.87 Aligned_cols=38 Identities=26% Similarity=0.315 Sum_probs=31.4
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHHHHHhh
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 249 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~ 249 (253)
....|.+|.+. +.||.||+...-.-.+|||||+..+..
T Consensus 296 s~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~ 333 (498)
T COG5641 296 SDKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPP 333 (498)
T ss_pred hhcCccccccc-ccCcccccccccccccccccccccCCc
Confidence 47789999976 689999998777789999999876543
No 13
>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=55.79 E-value=4.4 Score=27.24 Aligned_cols=26 Identities=46% Similarity=1.137 Sum_probs=19.9
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACG 243 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCG 243 (253)
....|..|+ +|++| ..+| +.+|-+|+
T Consensus 16 L~~~Cp~C~-----~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCG-----TPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred hcCccCCCC-----CeeEE-ecCC-CEECCCCC
Confidence 345899996 79999 3366 68999985
No 14
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=51.79 E-value=11 Score=27.20 Aligned_cols=31 Identities=23% Similarity=0.670 Sum_probs=23.9
Q ss_pred cccccccccccCCCCccccCCCCCcccc-hHHHHHHHhhhcc
Q 025411 212 DIVCRHCGISEKSTPMMRRGPEGPRTLC-NACGLMWANKVRE 252 (253)
Q Consensus 212 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LC-NaCGl~~~k~~~~ 252 (253)
-+.|.+||.+. | | . +..| ..|+..|.|+-||
T Consensus 3 HkHC~~CG~~I---p-----~-~-~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 3 HKHCPVCGKPI---P-----P-D-ESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CCcCCcCCCcC---C-----c-c-hhhhCHHHHHHHHHHHHH
Confidence 46899999753 3 2 2 6899 5999999998775
No 15
>COG3952 Predicted membrane protein [Function unknown]
Probab=50.36 E-value=4.6 Score=32.73 Aligned_cols=19 Identities=37% Similarity=0.569 Sum_probs=15.6
Q ss_pred ccccCCCCCcccchHHHHHHH
Q 025411 227 MMRRGPEGPRTLCNACGLMWA 247 (253)
Q Consensus 227 ~wR~Gp~G~~~LCNaCGl~~~ 247 (253)
.||.+|-+ -||++|||+-.
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 47888888 69999999753
No 16
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.92 E-value=6.6 Score=30.10 Aligned_cols=37 Identities=24% Similarity=0.516 Sum_probs=25.9
Q ss_pred cccccccccccCCCCccccCCCCCcccchHHHHHHHhhhc
Q 025411 212 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKVR 251 (253)
Q Consensus 212 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~~~ 251 (253)
.-+|.+|+-.-+--..++..| -+.|.+||-.++|.+-
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 358999996322234556555 6799999999888763
No 17
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.89 E-value=3.9 Score=26.44 Aligned_cols=33 Identities=24% Similarity=0.652 Sum_probs=26.0
Q ss_pred ccccccccccCCCCccccCCCCCcccchHHHHHH
Q 025411 213 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 246 (253)
Q Consensus 213 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~ 246 (253)
..|.+|++. -..+..+-.|.|....|-.||-.|
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 478889885 577788888888888898888655
No 18
>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=47.29 E-value=7.5 Score=25.54 Aligned_cols=31 Identities=29% Similarity=0.681 Sum_probs=19.8
Q ss_pred cccccccccccCCCCccccCCCCCcccchHHHH
Q 025411 212 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 244 (253)
Q Consensus 212 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 244 (253)
+.+|.+|++ ---|..+-...|..-.||-|+.
T Consensus 2 p~rC~~C~a--ylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRA--YLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT----BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCC--EECCcceEcCCCCEEECcCCCC
Confidence 468999998 5688888888887789999985
No 19
>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=46.64 E-value=20 Score=28.56 Aligned_cols=37 Identities=24% Similarity=0.424 Sum_probs=26.3
Q ss_pred cccccccccccccCCCCccccCCCCCcccchHHHHHHHhhh
Q 025411 210 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKV 250 (253)
Q Consensus 210 ~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~~ 250 (253)
+....|.+|+. .-|.|-.=..| -.||-.|.-.++...
T Consensus 11 ~~N~~CaDCg~---~~p~w~s~~~G-iflC~~Cag~HR~lg 47 (116)
T PF01412_consen 11 PGNKVCADCGA---PNPTWASLNYG-IFLCLECAGIHRSLG 47 (116)
T ss_dssp TTCTB-TTT-S---BS--EEETTTT-EEE-HHHHHHHHHHT
T ss_pred cCcCcCCCCCC---CCCCEEEeecC-hhhhHHHHHHHHHhc
Confidence 46689999996 57899998899 699999998877654
No 20
>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=46.55 E-value=17 Score=24.05 Aligned_cols=38 Identities=24% Similarity=0.541 Sum_probs=25.6
Q ss_pred ccccccccccCCCCccccCCCCCcccchHHHHHHHhhhc
Q 025411 213 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKVR 251 (253)
Q Consensus 213 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~~~ 251 (253)
..|+-||.++...-..=.||.| -..|+.|=......++
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~~~~il~ 39 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQAYEILK 39 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHHHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHHHHHHHh
Confidence 5899999977666666689977 5899999877766654
No 21
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.38 E-value=8 Score=39.94 Aligned_cols=36 Identities=17% Similarity=0.436 Sum_probs=29.0
Q ss_pred ccccccccccccCCCCccccCCCC---CcccchHHHHHHHh
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEG---PRTLCNACGLMWAN 248 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G---~~~LCNaCGl~~~k 248 (253)
++-.|..|.+ .-||.|+.-+.+ +..+|.+|----.|
T Consensus 461 ~P~~caqckt--dftp~wk~ekstq~d~~i~cE~cvtSnqk 499 (706)
T KOG3740|consen 461 EPYACAQCKT--DFTPAWKKEKSTQADAAIVCENCVTSNQK 499 (706)
T ss_pred Cchhhhhccc--ccccccccccccCcchHHHHHhhhhhccc
Confidence 5779999999 889999998877 34899999654443
No 22
>PF15396 FAM60A: Protein Family FAM60A
Probab=43.61 E-value=12 Score=33.66 Aligned_cols=16 Identities=38% Similarity=0.866 Sum_probs=11.1
Q ss_pred ccchHHHHHHHhhhccC
Q 025411 237 TLCNACGLMWANKVREL 253 (253)
Q Consensus 237 ~LCNaCGl~~~k~~~~~ 253 (253)
.+||||=|+. |+.|||
T Consensus 50 eICNACVLLV-KRwKKL 65 (213)
T PF15396_consen 50 EICNACVLLV-KRWKKL 65 (213)
T ss_pred hhhHHHHHHH-HHHhhC
Confidence 6999997765 444554
No 23
>PRK00420 hypothetical protein; Validated
Probab=39.57 E-value=12 Score=30.37 Aligned_cols=30 Identities=23% Similarity=0.668 Sum_probs=23.1
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHHHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWA 247 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~ 247 (253)
....|..|| +|+.|. .+| +.+|-.||-.+.
T Consensus 22 l~~~CP~Cg-----~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCG-----LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCC-----Ccceec-CCC-ceECCCCCCeee
Confidence 346899998 688885 456 799999997654
No 24
>PF08047 His_leader: Histidine operon leader peptide; InterPro: IPR012565 This family consists of the leader peptide of the histidine (his) operon. The his operon contains all the genes necessary for histidine biosynthesis. The region corresponding to the untranslated 5'-end of the transcript, named the his leader region, displays the typical features of the T box transcriptional attenuation mechanism which is involved in the regulation of many amino acid biosynthetic operons [].; GO: 0000105 histidine biosynthetic process
Probab=39.37 E-value=17 Score=19.61 Aligned_cols=11 Identities=36% Similarity=0.706 Sum_probs=4.9
Q ss_pred ccccCCCccCC
Q 025411 21 VNYVPEHELHH 31 (253)
Q Consensus 21 ~~~~~~h~~h~ 31 (253)
||+-++|+.||
T Consensus 4 vqfk~hhhhhh 14 (16)
T PF08047_consen 4 VQFKHHHHHHH 14 (16)
T ss_pred eEecccccccC
Confidence 55544444443
No 25
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.90 E-value=13 Score=30.86 Aligned_cols=32 Identities=31% Similarity=0.618 Sum_probs=21.0
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHHHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWA 247 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~ 247 (253)
-..+|.+||.- =+.| |=--...-|.|||+-|-
T Consensus 20 l~grCP~CGeG----rLF~-gFLK~~p~C~aCG~dyg 51 (126)
T COG5349 20 LRGRCPRCGEG----RLFR-GFLKVVPACEACGLDYG 51 (126)
T ss_pred hcCCCCCCCCc----hhhh-hhcccCchhhhcccccc
Confidence 34589999962 2333 33334578999999874
No 26
>PF14122 YokU: YokU-like protein
Probab=35.96 E-value=8 Score=30.15 Aligned_cols=33 Identities=30% Similarity=0.907 Sum_probs=20.0
Q ss_pred cccccccc---cCCCCccccCCCCCc---------ccchHHHHHH
Q 025411 214 VCRHCGIS---EKSTPMMRRGPEGPR---------TLCNACGLMW 246 (253)
Q Consensus 214 ~C~~C~~~---~~~Tp~wR~Gp~G~~---------~LCNaCGl~~ 246 (253)
.|.+|+.- +..+...+.=|+|.+ ..|+-||+-|
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvY 45 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVY 45 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEE
Confidence 37777652 223444445577754 5788888765
No 27
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=33.70 E-value=8.6 Score=30.57 Aligned_cols=39 Identities=23% Similarity=0.478 Sum_probs=25.9
Q ss_pred ccccccccccccCCCC-ccccCCCCCcccchHHHHHHHhhhccC
Q 025411 211 QDIVCRHCGISEKSTP-MMRRGPEGPRTLCNACGLMWANKVREL 253 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp-~wR~Gp~G~~~LCNaCGl~~~k~~~~~ 253 (253)
....|.+|+. ..-+ ..-+ .-+...|..||.++.+.+..|
T Consensus 20 t~f~CP~Cge--~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l 59 (99)
T PRK14892 20 KIFECPRCGK--VSISVKIKK--NIAIITCGNCGLYTEFEVPSV 59 (99)
T ss_pred cEeECCCCCC--eEeeeecCC--CcceEECCCCCCccCEECCcc
Confidence 4568999994 2222 1112 344689999999988877654
No 28
>PRK05978 hypothetical protein; Provisional
Probab=33.66 E-value=14 Score=31.37 Aligned_cols=31 Identities=29% Similarity=0.564 Sum_probs=23.1
Q ss_pred cccccccccccCCCCccccCCCCCcccchHHHHHHH
Q 025411 212 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWA 247 (253)
Q Consensus 212 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~ 247 (253)
..+|-+||. -.+++ |-..-..-|.+||+.|.
T Consensus 33 ~grCP~CG~----G~LF~-g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 33 RGRCPACGE----GKLFR-AFLKPVDHCAACGEDFT 63 (148)
T ss_pred cCcCCCCCC----Ccccc-cccccCCCccccCCccc
Confidence 468999996 45555 55555688999999775
No 29
>PRK09727 his operon leader peptide; Provisional
Probab=33.05 E-value=21 Score=21.31 Aligned_cols=11 Identities=36% Similarity=0.706 Sum_probs=5.3
Q ss_pred ccccCCCccCC
Q 025411 21 VNYVPEHELHH 31 (253)
Q Consensus 21 ~~~~~~h~~h~ 31 (253)
||+-|||+.||
T Consensus 4 vqfkhhhhhhh 14 (26)
T PRK09727 4 VQFKHHHHHHH 14 (26)
T ss_pred eeeeccccccC
Confidence 55544444444
No 30
>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=32.64 E-value=12 Score=24.67 Aligned_cols=27 Identities=30% Similarity=0.828 Sum_probs=13.7
Q ss_pred cccccccccCCCCccccCCCCCcccchHHHHH
Q 025411 214 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 245 (253)
Q Consensus 214 ~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 245 (253)
.|.+|+.. . .--.--.| ..+|..||+.
T Consensus 2 ~Cp~Cg~~--~--~~~D~~~g-~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSK--E--IVFDPERG-ELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSS--E--EEEETTTT-EEEETTT-BB
T ss_pred CCcCCcCC--c--eEEcCCCC-eEECCCCCCE
Confidence 57777762 1 22222234 5677777753
No 31
>KOG1561 consensus CCAAT-binding factor, subunit B (HAP2) [Transcription]
Probab=31.75 E-value=49 Score=31.38 Aligned_cols=31 Identities=29% Similarity=0.490 Sum_probs=25.1
Q ss_pred ccch--hhhHHHHHHhHh-hcCccccCCCcCccc
Q 025411 158 KIRY--TVRKEVALRMQR-NKGQFTSAKSNNEDS 188 (253)
Q Consensus 158 ~~~Y--~~Rk~~A~~r~R-~KGrf~ssk~s~ddS 188 (253)
+.+| ++|..+|++|+| .-|||-..+...+++
T Consensus 216 RkpYLHESRH~HAmkR~RG~GGRFln~k~~~~~s 249 (307)
T KOG1561|consen 216 RKPYLHESRHLHAMKRARGEGGRFLNTKEYHDDS 249 (307)
T ss_pred cCccccchhhHHHhhcccCCCCCCCchhhhhhhc
Confidence 3455 899999999999 788999988766554
No 32
>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=30.34 E-value=16 Score=22.62 Aligned_cols=28 Identities=29% Similarity=0.713 Sum_probs=14.8
Q ss_pred cccccccccccCCCCccccCCCCCcccchHHHHH
Q 025411 212 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 245 (253)
Q Consensus 212 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 245 (253)
.+.|..||.. ...-+.|-...|.+||+.
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 4579999973 233345667899999864
No 33
>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=29.95 E-value=9.5 Score=24.31 Aligned_cols=32 Identities=22% Similarity=0.567 Sum_probs=20.6
Q ss_pred ccccccccccCCCCccccCCCCCcccchHHHHHHH
Q 025411 213 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWA 247 (253)
Q Consensus 213 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~ 247 (253)
-+|..|+. .-..|..-.++....|-.||-...
T Consensus 6 y~C~~Cg~---~fe~~~~~~~~~~~~CP~Cg~~~~ 37 (41)
T smart00834 6 YRCEDCGH---TFEVLQKISDDPLATCPECGGDVR 37 (41)
T ss_pred EEcCCCCC---EEEEEEecCCCCCCCCCCCCCcce
Confidence 47999986 233455433355678999997433
No 34
>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=29.23 E-value=20 Score=25.47 Aligned_cols=11 Identities=45% Similarity=0.779 Sum_probs=9.6
Q ss_pred CccccCCCCCc
Q 025411 226 PMMRRGPEGPR 236 (253)
Q Consensus 226 p~wR~Gp~G~~ 236 (253)
|.||.||.|-.
T Consensus 34 ~E~R~G~~GfG 44 (54)
T PF12553_consen 34 PEWREGPAGFG 44 (54)
T ss_pred HhheecCCCcc
Confidence 89999999854
No 35
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=28.87 E-value=17 Score=30.49 Aligned_cols=31 Identities=29% Similarity=0.711 Sum_probs=21.1
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 244 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 244 (253)
.-..|..|+-+ .|-+-+.+- ---.-|+|||-
T Consensus 101 ~yVlC~~C~sp--dT~l~k~~r-~~~l~C~ACGa 131 (138)
T PRK03988 101 EYVICPECGSP--DTKLIKEGR-IWVLKCEACGA 131 (138)
T ss_pred hcEECCCCCCC--CcEEEEcCC-eEEEEcccCCC
Confidence 35689999985 577766532 11367999994
No 36
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=27.91 E-value=29 Score=33.33 Aligned_cols=35 Identities=26% Similarity=0.557 Sum_probs=28.7
Q ss_pred ccccccccccccCCCCccccCC---CCCcccchHHHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGP---EGPRTLCNACGLM 245 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp---~G~~~LCNaCGl~ 245 (253)
....|..|..+.-.+..|+.|| .-.++.|+.|+..
T Consensus 142 ~~~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G~ 179 (337)
T KOG0712|consen 142 SAPKCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNGS 179 (337)
T ss_pred CCCCCCCCCCCCceeEEEeccccccccceeEeccCCCc
Confidence 3447999999888999999999 5567889999754
No 37
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=27.56 E-value=70 Score=23.40 Aligned_cols=38 Identities=24% Similarity=0.631 Sum_probs=24.3
Q ss_pred CcccccccccccccCCCCccccCCCCCcccchHHHH--HHHhhhccC
Q 025411 209 QNQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL--MWANKVREL 253 (253)
Q Consensus 209 ~~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl--~~~k~~~~~ 253 (253)
+.-.-.|..|+. ..|-. |.. ---|--||- +|+|+.|+|
T Consensus 17 ~~miYiCgdC~~--en~lk-~~D----~irCReCG~RIlyKkRtkrl 56 (62)
T KOG3507|consen 17 ATMIYICGDCGQ--ENTLK-RGD----VIRCRECGYRILYKKRTKRL 56 (62)
T ss_pred ccEEEEeccccc--ccccc-CCC----cEehhhcchHHHHHHHHhhh
Confidence 445668999997 34433 322 367999995 566666653
No 38
>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=27.32 E-value=39 Score=22.28 Aligned_cols=36 Identities=22% Similarity=0.483 Sum_probs=23.6
Q ss_pred ccccccccCCCCcccc-CCCCCcccchHHHHHHHhhh
Q 025411 215 CRHCGISEKSTPMMRR-GPEGPRTLCNACGLMWANKV 250 (253)
Q Consensus 215 C~~C~~~~~~Tp~wR~-Gp~G~~~LCNaCGl~~~k~~ 250 (253)
|..||..++..|.--+ +-.=.-.=|+.|--.+++++
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~fk~k~ 37 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQFKKKL 37 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHHHHhhC
Confidence 7889988777885444 22221134699988888764
No 39
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=27.03 E-value=20 Score=22.77 Aligned_cols=23 Identities=39% Similarity=0.975 Sum_probs=12.5
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACG 243 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCG 243 (253)
...+|..|+. |.--| +..|..||
T Consensus 10 ~~~rC~~Cg~-------~~~pP---r~~Cp~C~ 32 (37)
T PF12172_consen 10 LGQRCRDCGR-------VQFPP---RPVCPHCG 32 (37)
T ss_dssp EEEE-TTT---------EEES-----SEETTTT
T ss_pred EEEEcCCCCC-------EecCC---CcCCCCcC
Confidence 4568999987 44444 45888887
No 40
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=26.99 E-value=19 Score=29.99 Aligned_cols=31 Identities=29% Similarity=0.758 Sum_probs=20.8
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 244 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 244 (253)
.-..|..|+-+ .|-+-+.+- ---.-|+|||-
T Consensus 96 ~yVlC~~C~sP--dT~l~k~~r-~~~l~C~ACGa 126 (133)
T TIGR00311 96 KYVICRECNRP--DTRIIKEGR-VSLLKCEACGA 126 (133)
T ss_pred heEECCCCCCC--CcEEEEeCC-eEEEecccCCC
Confidence 34689999985 477776532 11257999994
No 41
>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=26.19 E-value=19 Score=22.85 Aligned_cols=32 Identities=28% Similarity=0.610 Sum_probs=18.2
Q ss_pred ccccccccccCCCCccccCCCCCcccchHHHHH
Q 025411 213 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 245 (253)
Q Consensus 213 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 245 (253)
..|.+|++. -.-+....+..|....|-.||..
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCE
Confidence 467777763 23344444445556677777653
No 42
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=25.60 E-value=22 Score=28.65 Aligned_cols=30 Identities=27% Similarity=0.635 Sum_probs=20.4
Q ss_pred cccccccccccCCCCccccCCCCCcccchHHHH
Q 025411 212 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 244 (253)
Q Consensus 212 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 244 (253)
-..|..|+-+ .|-+-+.+- ---.-|+|||-
T Consensus 80 yVlC~~C~sp--dT~l~k~~r-~~~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSP--DTELIKENR-LFFLKCEACGA 109 (110)
T ss_pred cEECCCCCCC--CcEEEEeCC-eEEEEccccCC
Confidence 4689999985 577777621 11245999993
No 43
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=25.46 E-value=25 Score=29.38 Aligned_cols=26 Identities=38% Similarity=1.055 Sum_probs=21.8
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 244 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 244 (253)
....|.-|| ||++| -+| ...|--||.
T Consensus 27 L~~hCp~Cg-----~PLF~--KdG-~v~CPvC~~ 52 (131)
T COG1645 27 LAKHCPKCG-----TPLFR--KDG-EVFCPVCGY 52 (131)
T ss_pred HHhhCcccC-----Cccee--eCC-eEECCCCCc
Confidence 456899998 69999 478 799999994
No 44
>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=25.29 E-value=27 Score=22.62 Aligned_cols=27 Identities=26% Similarity=0.610 Sum_probs=20.0
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 244 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 244 (253)
....|..|+. . |-...+| ...|..||-
T Consensus 7 ~~~~C~~C~~----~--~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 7 PNEPCPVCGS----R--WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCCcCCCCCC----e--EeEccCC-EEEhhhCce
Confidence 3456999986 3 5566678 799999983
No 45
>PF13619 KTSC: KTSC domain
Probab=24.73 E-value=83 Score=22.10 Aligned_cols=31 Identities=32% Similarity=0.486 Sum_probs=24.7
Q ss_pred CCCCCceeEEE-ccEEEeeCCCCHHHHHHHHH
Q 025411 72 SEIGDQLTLSF-QGQVYVFDSVSPEKVQAVLL 102 (253)
Q Consensus 72 ~~~~~QLTIfY-~G~V~VfD~v~~eKaq~Im~ 102 (253)
.+.+..|.|.| +|.++.|.+||++-.+++|.
T Consensus 12 d~~~~~L~V~F~~G~~Y~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 12 DPETRTLEVEFKSGSVYRYFGVPPEVYEALLN 43 (60)
T ss_pred CCCCCEEEEEEcCCCEEEECCCCHHHHHHHHc
Confidence 35577888755 68899999999999998643
No 46
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=24.03 E-value=41 Score=22.10 Aligned_cols=28 Identities=25% Similarity=0.574 Sum_probs=18.2
Q ss_pred ccccccccccCCCCccccC-CCCCcccchHHH
Q 025411 213 IVCRHCGISEKSTPMMRRG-PEGPRTLCNACG 243 (253)
Q Consensus 213 ~~C~~C~~~~~~Tp~wR~G-p~G~~~LCNaCG 243 (253)
..|..|+- +..-.|..- -.| ...|+.||
T Consensus 4 ~pCP~CGG--~DrFr~~d~~g~G-~~~C~~Cg 32 (37)
T smart00778 4 GPCPNCGG--SDRFRFDDKDGRG-TWFCSVCG 32 (37)
T ss_pred cCCCCCCC--ccccccccCCCCc-CEEeCCCC
Confidence 47888987 455555542 234 57899887
No 47
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=22.89 E-value=29 Score=30.72 Aligned_cols=32 Identities=25% Similarity=0.612 Sum_probs=23.8
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHHHHHhhh
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKV 250 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~~ 250 (253)
-...|++|+ +++.+ .|....|..||--=++|+
T Consensus 148 I~A~CsrC~-----~~L~~---~~~~l~Cp~Cg~tEkRKi 179 (188)
T COG1096 148 IYARCSRCR-----APLVK---KGNMLKCPNCGNTEKRKI 179 (188)
T ss_pred EEEEccCCC-----cceEE---cCcEEECCCCCCEEeeee
Confidence 356899998 58888 566789999996554443
No 48
>PRK12496 hypothetical protein; Provisional
Probab=22.80 E-value=33 Score=29.33 Aligned_cols=32 Identities=25% Similarity=0.558 Sum_probs=22.3
Q ss_pred ccccccccccCCCCccccCCCCCcccchHHHHHHHhhhcc
Q 025411 213 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKVRE 252 (253)
Q Consensus 213 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~~~~ 252 (253)
.+|.-|+.. .+ .++.+ ..|.-||...+++..|
T Consensus 128 ~~C~gC~~~---~~---~~~~~--~~C~~CG~~~~r~~~~ 159 (164)
T PRK12496 128 KVCKGCKKK---YP---EDYPD--DVCEICGSPVKRKMVK 159 (164)
T ss_pred EECCCCCcc---cc---CCCCC--CcCCCCCChhhhcchh
Confidence 579999962 22 23333 5899999998877654
No 49
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=22.75 E-value=31 Score=23.75 Aligned_cols=8 Identities=38% Similarity=0.841 Sum_probs=5.4
Q ss_pred cccccccc
Q 025411 213 IVCRHCGI 220 (253)
Q Consensus 213 ~~C~~C~~ 220 (253)
+.|..||.
T Consensus 2 kPCPfCGg 9 (53)
T TIGR03655 2 KPCPFCGG 9 (53)
T ss_pred CCCCCCCC
Confidence 46777775
No 50
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=22.69 E-value=25 Score=31.00 Aligned_cols=31 Identities=26% Similarity=0.711 Sum_probs=20.5
Q ss_pred cccccccccccCCCCccccCCCCCcccchHHHHH
Q 025411 212 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 245 (253)
Q Consensus 212 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 245 (253)
-..|..|+-+ .|-+-+.+- ---.-|+|||-.
T Consensus 98 yV~C~~C~~p--dT~l~k~~~-~~~l~C~aCGa~ 128 (201)
T PRK12336 98 YVICSECGLP--DTRLVKEDR-VLMLRCDACGAH 128 (201)
T ss_pred eEECCCCCCC--CcEEEEcCC-eEEEEcccCCCC
Confidence 4689999984 577766531 112479999843
No 51
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=22.30 E-value=33 Score=34.12 Aligned_cols=39 Identities=31% Similarity=0.538 Sum_probs=32.1
Q ss_pred CCCcccccccccccccCCCCccccCCCCCcccchHHHHHHHhh
Q 025411 207 GSQNQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 249 (253)
Q Consensus 207 ~~~~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~k~ 249 (253)
...+..+.|..|+. .-|-|-.=+.| -.||--|--..+..
T Consensus 18 Rs~~~NKvCFDCgA---knPtWaSVTYG-IFLCiDCSAvHRnL 56 (454)
T KOG0706|consen 18 RSQSENKVCFDCGA---KNPTWASVTYG-IFLCIDCSAVHRNL 56 (454)
T ss_pred hcCCCCceecccCC---CCCCceeecce-EEEEEecchhhhcc
Confidence 34568899999997 68999999999 69999997665543
No 52
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=21.84 E-value=36 Score=31.13 Aligned_cols=11 Identities=36% Similarity=1.032 Sum_probs=7.5
Q ss_pred ccccccccccc
Q 025411 210 NQDIVCRHCGI 220 (253)
Q Consensus 210 ~~~~~C~~C~~ 220 (253)
.+.+.|.+||.
T Consensus 352 ~p~~~c~~cg~ 362 (389)
T PRK11788 352 KPRYRCRNCGF 362 (389)
T ss_pred CCCEECCCCCC
Confidence 35567888875
No 53
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=21.52 E-value=37 Score=26.83 Aligned_cols=22 Identities=27% Similarity=0.649 Sum_probs=18.3
Q ss_pred cccccccccccccCCCCccccC
Q 025411 210 NQDIVCRHCGISEKSTPMMRRG 231 (253)
Q Consensus 210 ~~~~~C~~C~~~~~~Tp~wR~G 231 (253)
..-.+|+-|+.+.+.+|.||.+
T Consensus 66 ~Lr~~Ct~Cgkah~~~~~~Rak 87 (94)
T COG1631 66 DLRLRCTECGKAHQRTPGFRAK 87 (94)
T ss_pred EEEEEehhhccccccCcceeee
Confidence 3567999999998888899974
No 54
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=21.47 E-value=48 Score=31.55 Aligned_cols=30 Identities=27% Similarity=0.651 Sum_probs=21.1
Q ss_pred cccccccccccccCCCCccccCCCCCcccchHHHH
Q 025411 210 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 244 (253)
Q Consensus 210 ~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 244 (253)
.....|.+||+ ..|+-. |+|.--+|-+||.
T Consensus 313 ~k~nfc~ncG~--~~t~~~---~ng~a~fcp~cgq 342 (345)
T COG4260 313 AKLNFCLNCGC--GTTADF---DNGKAKFCPECGQ 342 (345)
T ss_pred cccccccccCc--ccccCC---ccchhhhChhhcC
Confidence 34558899997 566644 4454569999985
No 55
>COG4683 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.99 E-value=1.3e+02 Score=24.67 Aligned_cols=25 Identities=40% Similarity=0.627 Sum_probs=18.0
Q ss_pred CCCCceeEEEccEEEeeCCCCHHHHHHHHHHhCC
Q 025411 73 EIGDQLTLSFQGQVYVFDSVSPEKVQAVLLLLGG 106 (253)
Q Consensus 73 ~~~~QLTIfY~G~V~VfD~v~~eKaq~Im~lA~~ 106 (253)
..+.+.-|+|+ || |+ -|+||+++|.
T Consensus 63 ~~G~piRilfA-----FD--P~--R~AIlL~~Gn 87 (120)
T COG4683 63 GQGTPIRILFA-----FD--PA--RQAILLLGGN 87 (120)
T ss_pred CCCCeEEEEEe-----cC--hH--hHHHhhhccC
Confidence 34588889987 77 22 5789888873
No 56
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=20.32 E-value=33 Score=32.16 Aligned_cols=30 Identities=30% Similarity=0.643 Sum_probs=20.5
Q ss_pred ccccccccccccCCCCccccCCCCCcccchHHHHHH
Q 025411 211 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 246 (253)
Q Consensus 211 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~ 246 (253)
..+.|..||+ +.. -+. .|-..+|+.||..+
T Consensus 110 ~~RFCg~CG~--~~~--~~~--~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGT--KTY--PRE--GGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCC--cCc--ccc--CceeeeCCCCCCcc
Confidence 5568999997 222 233 35568999999765
No 57
>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=20.06 E-value=1.1e+02 Score=19.52 Aligned_cols=20 Identities=20% Similarity=0.380 Sum_probs=16.8
Q ss_pred CceeEEEccEEEeeCCCCHH
Q 025411 76 DQLTLSFQGQVYVFDSVSPE 95 (253)
Q Consensus 76 ~QLTIfY~G~V~VfD~v~~e 95 (253)
..+++-|+|..+++.+||+.
T Consensus 14 ~~~~~~~~~~~~~i~~vp~~ 33 (46)
T TIGR03831 14 TTETYEYGGELIVIENVPAL 33 (46)
T ss_pred EEEEEEeCCEEEEEeCCCcc
Confidence 36778899999999999874
No 58
>PF11685 DUF3281: Protein of unknown function (DUF3281); InterPro: IPR021699 This family of bacterial proteins has no known function.
Probab=20.05 E-value=1.1e+02 Score=28.38 Aligned_cols=71 Identities=20% Similarity=0.316 Sum_probs=39.3
Q ss_pred CCccccCCCCCccccccccCCCccC-CCCCCCCCCCCCc----CCCCCCCCccCCCCCCCCCCccCCCCCCCCCCCceeE
Q 025411 6 NPQMQMSDEQHAIHHVNYVPEHELH-HISNGDVMDDEHD----EGNGVGESEAMEGDAPSDPGSLSDNRAVSEIGDQLTL 80 (253)
Q Consensus 6 ~~~~~~~~~~~~~hh~~~~~~h~~h-~~~~~~~~~~~~~----~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~QLTI 80 (253)
.+.|.+.+.|+|+|-+|.- .- +...+-...|-.+ =|.+|++++. ...+|+..+... ..|-+|
T Consensus 59 gktiervesqtpl~diqgt----i~W~~p~ga~~adn~~v~~elg~~Cqdd~C---t~nsNPtAy~l~------~Gsn~I 125 (268)
T PF11685_consen 59 GKTIERVESQTPLRDIQGT----ITWNAPAGATLADNSDVVTELGSGCQDDNC---TANSNPTAYNLP------VGSNTI 125 (268)
T ss_pred hceEEEEeccCchHHhCee----EEEecCCCccccchHHHHHHhcCCCcCCcc---cCCCCCeeEEcc------CCceEE
Confidence 3568889999998855543 11 1111111111000 1557877762 334555555442 356789
Q ss_pred EEccEEEee
Q 025411 81 SFQGQVYVF 89 (253)
Q Consensus 81 fY~G~V~Vf 89 (253)
+-.|.|.|-
T Consensus 126 sVSG~vtv~ 134 (268)
T PF11685_consen 126 SVSGTVTVN 134 (268)
T ss_pred EEEEEEEEC
Confidence 999999883
Done!