Query 026465
Match_columns 238
No_of_seqs 250 out of 985
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:21:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026465.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026465hhsearch_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 1.4E-17 3.1E-22 107.6 5.2 35 66-100 2-36 (36)
2 PF00320 GATA: GATA zinc finge 99.6 8.3E-16 1.8E-20 99.4 1.0 35 201-237 1-35 (36)
3 cd00202 ZnF_GATA Zinc finger D 99.5 1.7E-15 3.8E-20 106.2 2.4 36 200-237 1-36 (54)
4 smart00401 ZnF_GATA zinc finge 99.5 3.1E-15 6.7E-20 104.1 2.6 39 198-238 3-41 (52)
5 PF06203 CCT: CCT motif; Inte 99.1 4.9E-11 1.1E-15 80.7 3.1 44 132-175 1-44 (45)
6 PF09425 CCT_2: Divergent CCT 98.8 1.9E-09 4E-14 65.4 1.5 25 130-155 2-26 (27)
7 KOG1601 GATA-4/5/6 transcripti 98.6 2.3E-08 5E-13 85.8 2.1 37 198-236 199-235 (340)
8 COG5641 GAT1 GATA Zn-finger-co 98.0 1.6E-06 3.5E-11 84.7 1.0 39 197-237 157-199 (498)
9 KOG3554 Histone deacetylase co 93.8 0.059 1.3E-06 52.8 3.5 39 198-238 386-426 (693)
10 PF14803 Nudix_N_2: Nudix N-te 81.1 0.46 9.9E-06 30.3 -0.1 30 199-230 1-30 (34)
11 PF01783 Ribosomal_L32p: Ribos 80.7 0.62 1.4E-05 32.7 0.4 29 197-237 25-53 (56)
12 COG5641 GAT1 GATA Zn-finger-co 79.5 0.91 2E-05 45.0 1.3 41 196-237 295-335 (498)
13 PF13619 KTSC: KTSC domain 78.3 4.1 9E-05 28.5 4.1 30 67-96 13-43 (60)
14 PF01412 ArfGap: Putative GTPa 71.0 3.4 7.4E-05 32.7 2.4 36 197-236 12-47 (116)
15 PRK12286 rpmF 50S ribosomal pr 70.3 1.7 3.6E-05 30.8 0.4 25 196-231 25-49 (57)
16 TIGR01031 rpmF_bact ribosomal 67.2 2.1 4.5E-05 30.1 0.3 28 196-235 24-51 (55)
17 PF09297 zf-NADH-PPase: NADH p 60.0 2.7 5.9E-05 25.9 -0.2 28 198-231 3-30 (32)
18 PRK03988 translation initiatio 59.6 3 6.5E-05 34.6 -0.0 31 198-231 102-132 (138)
19 TIGR00311 aIF-2beta translatio 58.5 3.2 7E-05 34.2 0.0 31 198-231 97-127 (133)
20 PF13717 zinc_ribbon_4: zinc-r 56.5 3.7 8E-05 26.2 0.0 33 199-232 3-35 (36)
21 PF06689 zf-C4_ClpX: ClpX C4-t 56.0 5.5 0.00012 26.1 0.8 32 199-231 2-33 (41)
22 smart00653 eIF2B_5 domain pres 54.8 4.1 8.9E-05 32.5 0.0 30 198-230 80-109 (110)
23 PRK12336 translation initiatio 50.7 5 0.00011 35.1 -0.1 31 198-231 98-128 (201)
24 COG3952 Predicted membrane pro 50.4 3.9 8.5E-05 32.7 -0.7 20 212-233 75-94 (113)
25 PF06677 Auto_anti-p27: Sjogre 49.8 7.4 0.00016 25.8 0.6 26 197-229 16-41 (41)
26 KOG3740 Uncharacterized conser 48.5 7 0.00015 39.9 0.5 36 196-233 460-498 (706)
27 TIGR02098 MJ0042_CXXC MJ0042 f 47.7 4.6 0.0001 25.4 -0.6 33 199-232 3-35 (38)
28 smart00105 ArfGap Putative GTP 44.9 17 0.00036 28.6 2.1 35 198-236 3-37 (112)
29 PRK14892 putative transcriptio 44.6 8.6 0.00019 30.2 0.4 36 197-235 20-55 (99)
30 PRK05978 hypothetical protein; 42.8 11 0.00025 31.6 0.9 33 198-235 33-65 (148)
31 smart00834 CxxC_CXXC_SSSS Puta 42.1 9.7 0.00021 24.0 0.3 30 199-231 6-35 (41)
32 PF01873 eIF-5_eIF-2B: Domain 41.9 8.9 0.00019 31.2 0.1 29 199-230 94-122 (125)
33 PF04810 zf-Sec23_Sec24: Sec23 40.9 13 0.00029 24.0 0.8 32 198-231 2-33 (40)
34 COG5349 Uncharacterized protei 40.5 11 0.00024 30.9 0.4 33 198-235 21-53 (126)
35 PF08271 TF_Zn_Ribbon: TFIIB z 40.5 11 0.00024 24.6 0.4 28 200-232 2-29 (43)
36 PF14122 YokU: YokU-like prote 38.8 7.9 0.00017 29.8 -0.6 37 200-236 1-49 (87)
37 KOG1601 GATA-4/5/6 transcripti 38.2 11 0.00025 31.9 0.2 40 130-169 291-330 (340)
38 COG2816 NPY1 NTP pyrophosphohy 37.8 13 0.00029 34.3 0.6 31 196-232 109-139 (279)
39 PF07282 OrfB_Zn_ribbon: Putat 37.6 15 0.00033 25.9 0.7 30 198-233 28-57 (69)
40 COG2331 Uncharacterized protei 37.1 11 0.00023 28.6 -0.1 34 199-235 13-46 (82)
41 PF13248 zf-ribbon_3: zinc-rib 35.7 23 0.00049 20.8 1.2 22 199-230 3-24 (26)
42 PF09723 Zn-ribbon_8: Zinc rib 35.3 13 0.00029 24.2 0.2 29 199-230 6-34 (42)
43 KOG0712 Molecular chaperone (D 32.9 30 0.00065 32.9 2.1 34 198-231 143-179 (337)
44 PRK01110 rpmF 50S ribosomal pr 32.5 20 0.00043 25.6 0.7 24 197-232 26-49 (60)
45 TIGR02605 CxxC_CxxC_SSSS putat 32.4 18 0.00039 24.2 0.4 29 199-230 6-34 (52)
46 PRK00420 hypothetical protein; 31.4 23 0.0005 28.4 0.9 30 197-233 22-51 (112)
47 PF09889 DUF2116: Uncharacteri 30.8 36 0.00077 24.3 1.7 29 197-235 2-31 (59)
48 PRK11788 tetratricopeptide rep 29.6 24 0.00052 32.0 0.9 23 197-229 353-375 (389)
49 smart00778 Prim_Zn_Ribbon Zinc 29.6 35 0.00076 22.1 1.4 30 199-230 4-33 (37)
50 TIGR00354 polC DNA polymerase, 29.3 21 0.00046 38.4 0.5 32 191-230 1005-1036(1095)
51 PF13240 zinc_ribbon_2: zinc-r 29.0 33 0.00071 19.8 1.1 8 223-230 14-21 (23)
52 PF12773 DZR: Double zinc ribb 28.5 37 0.00079 22.4 1.4 28 197-231 11-38 (50)
53 COG1645 Uncharacterized Zn-fin 28.2 24 0.00053 29.2 0.6 28 196-231 26-53 (131)
54 PF02994 Transposase_22: L1 tr 27.9 59 0.0013 31.0 3.2 25 69-95 318-342 (370)
55 PF12553 DUF3742: Protein of u 27.9 22 0.00047 25.0 0.2 10 212-221 34-43 (54)
56 PRK04023 DNA polymerase II lar 27.4 25 0.00054 38.1 0.6 32 191-230 1030-1061(1121)
57 PRK00398 rpoP DNA-directed RNA 27.0 32 0.00069 22.6 0.9 28 198-231 3-30 (46)
58 PRK00241 nudC NADH pyrophospha 25.7 26 0.00056 31.6 0.4 31 196-232 97-127 (256)
59 PF11228 DUF3027: Protein of u 25.6 24 0.00053 31.0 0.1 26 212-237 127-160 (193)
60 PF08152 GUCT: GUCT (NUC152) d 25.4 44 0.00095 25.8 1.5 31 68-99 49-79 (97)
61 PRK14714 DNA polymerase II lar 25.3 28 0.00061 38.5 0.5 33 190-230 1245-1277(1337)
62 cd07168 NR_DBD_DHR4_like DNA-b 23.4 61 0.0013 24.7 2.0 32 197-235 5-36 (90)
63 PHA00626 hypothetical protein 22.8 37 0.00081 24.3 0.6 31 200-235 2-36 (59)
64 PF10083 DUF2321: Uncharacteri 22.7 43 0.00094 28.5 1.1 12 221-232 67-78 (158)
65 COG4260 Membrane protease subu 22.3 39 0.00084 31.8 0.8 31 197-232 314-344 (345)
66 COG1096 Predicted RNA-binding 21.8 37 0.00079 29.8 0.5 26 198-231 149-174 (188)
67 PF08114 PMP1_2: ATPase proteo 21.7 35 0.00077 22.9 0.3 10 130-139 34-43 (43)
68 TIGR03831 YgiT_finger YgiT-typ 21.6 1E+02 0.0023 19.4 2.6 20 70-89 14-33 (46)
69 PF11781 RRN7: RNA polymerase 21.5 40 0.00088 21.5 0.5 26 198-230 8-33 (36)
70 PF12172 DUF35_N: Rubredoxin-l 20.8 40 0.00088 21.1 0.4 23 197-229 10-32 (37)
71 PF15321 ATAD4: ATPase family 20.3 26 0.00056 26.9 -0.7 12 137-148 69-80 (84)
72 PF01096 TFIIS_C: Transcriptio 20.1 17 0.00036 23.5 -1.5 33 200-232 2-38 (39)
73 PF02701 zf-Dof: Dof domain, z 20.1 49 0.0011 24.1 0.7 40 197-238 4-46 (63)
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=99.71 E-value=1.4e-17 Score=107.58 Aligned_cols=35 Identities=46% Similarity=0.731 Sum_probs=32.5
Q ss_pred CCCCcceeEEeCCEEEEEcCCChHHHHHHHHHhcC
Q 026465 66 LSNSSQLTLSFRGQVYVFDSVTPDKVQAVLLLLGG 100 (238)
Q Consensus 66 ~~~~~qLTIfY~G~V~Vfd~vp~dKaqaim~la~~ 100 (238)
.+.++||||||+|+|+|||+||+|||++||+||+.
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 46789999999999999999999999999999963
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=99.55 E-value=8.3e-16 Score=99.38 Aligned_cols=35 Identities=51% Similarity=1.187 Sum_probs=28.7
Q ss_pred ccccccccCCCCccccCCCCCcccchhhhhhhhhhcC
Q 026465 201 CTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKVG 237 (238)
Q Consensus 201 C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~g~ 237 (238)
|+||+++ +||+||+||.|..+|||||||+|+++|+
T Consensus 1 C~~C~tt--~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTT--ETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--S--T-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCC--CCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 8999997 8999999999988899999999999986
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=99.55 E-value=1.7e-15 Score=106.24 Aligned_cols=36 Identities=53% Similarity=1.270 Sum_probs=33.9
Q ss_pred cccccccccCCCCccccCCCCCcccchhhhhhhhhhcC
Q 026465 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKVG 237 (238)
Q Consensus 200 ~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~g~ 237 (238)
.|+||+++ .||+||+||.|..+|||||||||+++|.
T Consensus 1 ~C~~C~~~--~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTT--TTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCC--CCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 59999997 9999999999889999999999999985
No 4
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.53 E-value=3.1e-15 Score=104.13 Aligned_cols=39 Identities=51% Similarity=1.206 Sum_probs=36.1
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhhhhhhcCC
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKVGV 238 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~g~l 238 (238)
...|+||+++ .||+||+||.|..+|||||||+|++++.+
T Consensus 3 ~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 3 GRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 5689999997 99999999999999999999999999853
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=99.11 E-value=4.9e-11 Score=80.75 Aligned_cols=44 Identities=45% Similarity=0.762 Sum_probs=41.6
Q ss_pred HHHHHHHHHHhhhhhhcccccchhhhHHHHHhhhcccccccccc
Q 026465 132 RAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKGQFTSAK 175 (238)
Q Consensus 132 RkaSL~RF~eKRK~R~~~kk~~Y~~rke~a~rm~Rekgqf~~~K 175 (238)
|.++|+||+|||+.|+|.++|+|++|+.+|+.++|.+|+|.+..
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 67899999999999999999999999999999999999999753
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=98.80 E-value=1.9e-09 Score=65.38 Aligned_cols=25 Identities=48% Similarity=0.612 Sum_probs=10.0
Q ss_pred hhHHHHHHHHHHhhhhhhcccccchh
Q 026465 130 PQRAASLDRFRQKRKERCFDKKVRYS 155 (238)
Q Consensus 130 paRkaSL~RF~eKRK~R~~~kk~~Y~ 155 (238)
.+|++||+||+||||+|+++ +.||.
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 48999999999999999987 88985
No 7
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.57 E-value=2.3e-08 Score=85.78 Aligned_cols=37 Identities=51% Similarity=1.134 Sum_probs=34.9
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhhhhhhc
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKV 236 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~g 236 (238)
...|.+|+++ .||+||++|.|+..|||||||+|++++
T Consensus 199 ~~~c~~~~~~--~t~~~r~~~~g~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 199 LRQCSNCGTT--KTPLWRRGPEGPKSLCNACGLRYKKGG 235 (340)
T ss_pred CcccCCCCCC--CCcceecCCCCCccccccchhhhhhcC
Confidence 5899999996 999999999999999999999999985
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.01 E-value=1.6e-06 Score=84.66 Aligned_cols=39 Identities=38% Similarity=0.784 Sum_probs=34.5
Q ss_pred ccccccccccccCCCCccccCCCC----CcccchhhhhhhhhhcC
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSG----PRSLCNACGLFWANKVG 237 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G----~~~lCNaCGl~~~~~g~ 237 (238)
...+|.||.++ .||+|||...+ .-.|||||||+|+.||+
T Consensus 157 ~~~vc~Nc~t~--stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~ 199 (498)
T COG5641 157 QPHVCSNCKTT--STPLWRRASSESSLPGNNLCNACGLYLKLHGS 199 (498)
T ss_pred ccchhcccccc--CCccccccccccccCCccccccccccccccCC
Confidence 34499999997 99999999993 37999999999999985
No 9
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=93.76 E-value=0.059 Score=52.82 Aligned_cols=39 Identities=21% Similarity=0.553 Sum_probs=31.9
Q ss_pred cccccccccccCCCCcc--ccCCCCCcccchhhhhhhhhhcCC
Q 026465 198 ETSCTHCGISSKSTPMM--RRGPSGPRSLCNACGLFWANKVGV 238 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~w--R~gp~G~~~lCNaCGl~~~~~g~l 238 (238)
.+.|-+|+++ ..-+| +-+|.-...||-.|.+||+|.|-|
T Consensus 386 g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 7799999997 66676 445555568999999999999865
No 10
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=81.07 E-value=0.46 Score=30.34 Aligned_cols=30 Identities=30% Similarity=0.708 Sum_probs=14.7
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
+.|.+||.+ .+..-=.|.+-.+..|.+||-
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 369999984 222222445556799999984
No 11
>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=80.69 E-value=0.62 Score=32.66 Aligned_cols=29 Identities=24% Similarity=0.795 Sum_probs=21.3
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhhhhhhhcC
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKVG 237 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~g~ 237 (238)
....|.+||.. .-+..+|..|| ||+.+-+
T Consensus 25 ~l~~c~~cg~~-----------~~~H~vc~~cG-~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEP-----------KLPHRVCPSCG-YYKGRQV 53 (56)
T ss_dssp SEEESSSSSSE-----------ESTTSBCTTTB-BSSSSSS
T ss_pred ceeeeccCCCE-----------ecccEeeCCCC-eECCEEE
Confidence 56799999984 33468999999 6655443
No 12
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=79.54 E-value=0.91 Score=45.01 Aligned_cols=41 Identities=27% Similarity=0.340 Sum_probs=34.1
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhhhhhhhcC
Q 026465 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKVG 237 (238)
Q Consensus 196 ~~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~g~ 237 (238)
.....|.+|.+. +.||.||+...-.-.+|||||++-+.+|.
T Consensus 295 ps~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~ 335 (498)
T COG5641 295 PSDKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGS 335 (498)
T ss_pred hhhcCccccccc-ccCcccccccccccccccccccccCCccc
Confidence 346689999975 58999999987778999999999888874
No 13
>PF13619 KTSC: KTSC domain
Probab=78.32 E-value=4.1 Score=28.54 Aligned_cols=30 Identities=30% Similarity=0.558 Sum_probs=26.2
Q ss_pred CCCcceeEEe-CCEEEEEcCCChHHHHHHHH
Q 026465 67 SNSSQLTLSF-RGQVYVFDSVTPDKVQAVLL 96 (238)
Q Consensus 67 ~~~~qLTIfY-~G~V~Vfd~vp~dKaqaim~ 96 (238)
+.+..|.|.| +|.++.|.+||++-.+++|.
T Consensus 13 ~~~~~L~V~F~~G~~Y~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 13 PETRTLEVEFKSGSVYRYFGVPPEVYEALLN 43 (60)
T ss_pred CCCCEEEEEEcCCCEEEECCCCHHHHHHHHc
Confidence 4677899999 99999999999998888774
No 14
>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=71.03 E-value=3.4 Score=32.69 Aligned_cols=36 Identities=22% Similarity=0.424 Sum_probs=27.0
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhhhhhhhc
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKV 236 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~g 236 (238)
....|+.|+. .-|.|-.=..| -.||-.|.-.++..|
T Consensus 12 ~N~~CaDCg~---~~p~w~s~~~G-iflC~~Cag~HR~lg 47 (116)
T PF01412_consen 12 GNKVCADCGA---PNPTWASLNYG-IFLCLECAGIHRSLG 47 (116)
T ss_dssp TCTB-TTT-S---BS--EEETTTT-EEE-HHHHHHHHHHT
T ss_pred CcCcCCCCCC---CCCCEEEeecC-hhhhHHHHHHHHHhc
Confidence 4679999997 68899999999 799999998888777
No 15
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=70.27 E-value=1.7 Score=30.83 Aligned_cols=25 Identities=32% Similarity=0.991 Sum_probs=18.8
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 196 ~~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
.....|.+||.. --+..+|..||.|
T Consensus 25 ~~l~~C~~CG~~-----------~~~H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEP-----------KLPHRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCc-----------cCCeEECCCCCcC
Confidence 356789999985 2236899999954
No 16
>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=67.23 E-value=2.1 Score=30.07 Aligned_cols=28 Identities=29% Similarity=0.927 Sum_probs=19.9
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhhhhhhh
Q 026465 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 235 (238)
Q Consensus 196 ~~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~ 235 (238)
.....|.+||.. --+..+|-.|| +|+-.
T Consensus 24 p~l~~C~~cG~~-----------~~~H~vc~~cG-~Y~gr 51 (55)
T TIGR01031 24 PTLVVCPNCGEF-----------KLPHRVCPSCG-YYKGR 51 (55)
T ss_pred CcceECCCCCCc-----------ccCeeECCccC-eECCE
Confidence 356689999984 23468999999 44433
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=60.01 E-value=2.7 Score=25.87 Aligned_cols=28 Identities=29% Similarity=0.695 Sum_probs=16.1
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
.+.|..||.. ....+.|....|.+||..
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 4689999985 344456777899999975
No 18
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=59.57 E-value=3 Score=34.60 Aligned_cols=31 Identities=29% Similarity=0.597 Sum_probs=22.8
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
--.|..|+.+ .|-+-+.+-. --.-|+|||-.
T Consensus 102 yVlC~~C~sp--dT~l~k~~r~-~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSP--DTKLIKEGRI-WVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCC--CcEEEEcCCe-EEEEcccCCCC
Confidence 4589999998 8888775321 14679999953
No 19
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=58.47 E-value=3.2 Score=34.17 Aligned_cols=31 Identities=26% Similarity=0.585 Sum_probs=22.4
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
--.|..|+.+ .|-+-+.+-. --.-|+|||-.
T Consensus 97 yVlC~~C~sP--dT~l~k~~r~-~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNRP--DTRIIKEGRV-SLLKCEACGAK 127 (133)
T ss_pred eEECCCCCCC--CcEEEEeCCe-EEEecccCCCC
Confidence 3589999998 8888775321 13579999954
No 20
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=56.50 E-value=3.7 Score=26.23 Aligned_cols=33 Identities=21% Similarity=0.594 Sum_probs=27.0
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~ 232 (238)
..|-+|++. -..+..+-.+.|.+.-|-.||-.|
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 478899986 777888888888888899998765
No 21
>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=56.04 E-value=5.5 Score=26.12 Aligned_cols=32 Identities=25% Similarity=0.675 Sum_probs=21.1
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
.+|+-||.+....-.+=.||.+ ...|+.|=..
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHH
Confidence 5899999986666666689977 6899999543
No 22
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=54.77 E-value=4.1 Score=32.49 Aligned_cols=30 Identities=27% Similarity=0.571 Sum_probs=21.8
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
--.|..|+.+ .|-+-+.+-.= -.-|+|||-
T Consensus 80 yVlC~~C~sp--dT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 80 YVLCPECGSP--DTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred cEECCCCCCC--CcEEEEeCCeE-EEEccccCC
Confidence 3589999998 88888872111 245999994
No 23
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=50.74 E-value=5 Score=35.06 Aligned_cols=31 Identities=26% Similarity=0.651 Sum_probs=22.4
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
--.|..|+.+ .|-+-+.+..= -.-|+|||-.
T Consensus 98 yV~C~~C~~p--dT~l~k~~~~~-~l~C~aCGa~ 128 (201)
T PRK12336 98 YVICSECGLP--DTRLVKEDRVL-MLRCDACGAH 128 (201)
T ss_pred eEECCCCCCC--CcEEEEcCCeE-EEEcccCCCC
Confidence 4589999997 88887763211 3579999954
No 24
>COG3952 Predicted membrane protein [Function unknown]
Probab=50.43 E-value=3.9 Score=32.70 Aligned_cols=20 Identities=40% Similarity=0.566 Sum_probs=15.6
Q ss_pred CccccCCCCCcccchhhhhhhh
Q 026465 212 PMMRRGPSGPRSLCNACGLFWA 233 (238)
Q Consensus 212 p~wR~gp~G~~~lCNaCGl~~~ 233 (238)
-+||..|-+ .||++||++-.
T Consensus 75 fi~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 75 FIRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHHhcchHH--HHHHhhhHHHH
Confidence 357888877 69999999743
No 25
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=49.84 E-value=7.4 Score=25.80 Aligned_cols=26 Identities=38% Similarity=1.091 Sum_probs=19.7
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCG 229 (238)
....|..|++ |++| ...| +.+|-+|+
T Consensus 16 L~~~Cp~C~~-----PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCGT-----PLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred hcCccCCCCC-----eeEE-ecCC-CEECCCCC
Confidence 4558999965 8999 3356 79999986
No 26
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.54 E-value=7 Score=39.90 Aligned_cols=36 Identities=19% Similarity=0.422 Sum_probs=28.9
Q ss_pred cccccccccccccCCCCccccCCCC---Ccccchhhhhhhh
Q 026465 196 PSETSCTHCGISSKSTPMMRRGPSG---PRSLCNACGLFWA 233 (238)
Q Consensus 196 ~~~~~C~~C~~t~~~Tp~wR~gp~G---~~~lCNaCGl~~~ 233 (238)
...-.|..|.+ +.||.|+.-+.+ +..+|.+|----.
T Consensus 460 ~~P~~caqckt--dftp~wk~ekstq~d~~i~cE~cvtSnq 498 (706)
T KOG3740|consen 460 TEPYACAQCKT--DFTPAWKKEKSTQADAAIVCENCVTSNQ 498 (706)
T ss_pred CCchhhhhccc--ccccccccccccCcchHHHHHhhhhhcc
Confidence 34679999999 599999999888 3589999964433
No 27
>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=47.71 E-value=4.6 Score=25.45 Aligned_cols=33 Identities=27% Similarity=0.690 Sum_probs=20.8
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~ 232 (238)
..|.+|++. -.-+..+.+..|....|-.||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 468888874 334444444556567788887654
No 28
>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=44.93 E-value=17 Score=28.60 Aligned_cols=35 Identities=23% Similarity=0.430 Sum_probs=29.9
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhhhhhhc
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKV 236 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~g 236 (238)
...|+.|+. .-|.|=.=..| ..||-.|.-..+..|
T Consensus 3 N~~CaDC~~---~~p~w~s~~~G-ifvC~~CsgiHR~lg 37 (112)
T smart00105 3 NKKCFDCGA---PNPTWASVNLG-VFLCIECSGIHRSLG 37 (112)
T ss_pred CCcccCCCC---CCCCcEEeccc-eeEhHHhHHHHHhcC
Confidence 579999998 56999888888 699999988877766
No 29
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=44.61 E-value=8.6 Score=30.22 Aligned_cols=36 Identities=22% Similarity=0.458 Sum_probs=23.6
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhhhhhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 235 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~ 235 (238)
....|.+|+.. ..+. ..+-..+...|..||.|+.+.
T Consensus 20 t~f~CP~Cge~--~v~v-~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 20 KIFECPRCGKV--SISV-KIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred cEeECCCCCCe--Eeee-ecCCCcceEECCCCCCccCEE
Confidence 46789999952 2221 111135579999999998653
No 30
>PRK05978 hypothetical protein; Provisional
Probab=42.79 E-value=11 Score=31.62 Aligned_cols=33 Identities=27% Similarity=0.615 Sum_probs=24.6
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 235 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~ 235 (238)
..+|-+||. -.++| |-..-..-|.+||+.|..+
T Consensus 33 ~grCP~CG~----G~LF~-g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGE----GKLFR-AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCC----Ccccc-cccccCCCccccCCccccC
Confidence 458999996 35554 5556678999999988654
No 31
>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=42.07 E-value=9.7 Score=23.99 Aligned_cols=30 Identities=23% Similarity=0.606 Sum_probs=19.8
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
-+|..||. .-..|..-.++....|-.||.-
T Consensus 6 y~C~~Cg~---~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGH---TFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCC---EEEEEEecCCCCCCCCCCCCCc
Confidence 37888987 3444554434556789999873
No 32
>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=41.91 E-value=8.9 Score=31.22 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=22.5
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
-.|..|+.+ .|-+-+.+..= -.-|+|||-
T Consensus 94 VlC~~C~sp--dT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSP--DTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSS--SEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCC--ccEEEEcCCEE-EEEecccCC
Confidence 589999997 88887774333 478999994
No 33
>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=40.90 E-value=13 Score=24.03 Aligned_cols=32 Identities=25% Similarity=0.580 Sum_probs=20.8
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
..+|.+|++= .-|..+-...|..-.||-|+..
T Consensus 2 p~rC~~C~ay--lNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAY--LNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--B--S-TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCE--ECCcceEcCCCCEEECcCCCCc
Confidence 4689999985 8888888888878899999863
No 34
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.50 E-value=11 Score=30.87 Aligned_cols=33 Identities=30% Similarity=0.645 Sum_probs=22.1
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 235 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~ 235 (238)
.-+|-+||.- =+. +|=.....-|.|||+-|-.+
T Consensus 21 ~grCP~CGeG----rLF-~gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 21 RGRCPRCGEG----RLF-RGFLKVVPACEACGLDYGFA 53 (126)
T ss_pred cCCCCCCCCc----hhh-hhhcccCchhhhccccccCC
Confidence 4489999973 122 23334467899999988654
No 35
>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=40.49 E-value=11 Score=24.59 Aligned_cols=28 Identities=29% Similarity=0.789 Sum_probs=14.0
Q ss_pred cccccccccCCCCccccCCCCCcccchhhhhhh
Q 026465 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (238)
Q Consensus 200 ~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~ 232 (238)
+|.+|+.+ . .--.--.| ...|..||+-.
T Consensus 2 ~Cp~Cg~~--~--~~~D~~~g-~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSK--E--IVFDPERG-ELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSS--E--EEEETTTT-EEEETTT-BBE
T ss_pred CCcCCcCC--c--eEEcCCCC-eEECCCCCCEe
Confidence 57777764 2 11122223 56777777643
No 36
>PF14122 YokU: YokU-like protein
Probab=38.78 E-value=7.9 Score=29.83 Aligned_cols=37 Identities=24% Similarity=0.751 Sum_probs=23.7
Q ss_pred cccccccc---cCCCCccccCCCCCc---------ccchhhhhhhhhhc
Q 026465 200 SCTHCGIS---SKSTPMMRRGPSGPR---------SLCNACGLFWANKV 236 (238)
Q Consensus 200 ~C~~C~~t---~~~Tp~wR~gp~G~~---------~lCNaCGl~~~~~g 236 (238)
.|..|+.. +..+.-.+.=|+|.+ ..|+.||+-|....
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d~ 49 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDDE 49 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehhH
Confidence 37778763 123334555677754 67999999887654
No 37
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=38.21 E-value=11 Score=31.87 Aligned_cols=40 Identities=43% Similarity=0.651 Sum_probs=34.8
Q ss_pred hhHHHHHHHHHHhhhhhhcccccchhhhHHHHHhhhcccc
Q 026465 130 PQRAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKG 169 (238)
Q Consensus 130 paRkaSL~RF~eKRK~R~~~kk~~Y~~rke~a~rm~Rekg 169 (238)
-.|.+.+.|++++++.|.|.++++|..++..++.+++-++
T Consensus 291 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 291 HQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred chHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 3788889999999999999999999999988877776655
No 38
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=37.83 E-value=13 Score=34.31 Aligned_cols=31 Identities=32% Similarity=0.682 Sum_probs=21.3
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhhhh
Q 026465 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (238)
Q Consensus 196 ~~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~ 232 (238)
+..+.|..||+. +.| + ..|-+.+|+.||..+
T Consensus 109 ~~~RFCg~CG~~--~~~--~--~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCGRCGTK--TYP--R--EGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCCCCCCc--Ccc--c--cCceeeeCCCCCCcc
Confidence 346789999984 332 2 245678999999765
No 39
>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=37.55 E-value=15 Score=25.92 Aligned_cols=30 Identities=30% Similarity=0.655 Sum_probs=20.8
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 233 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~ 233 (238)
...|..||..... ...+....|..||..+.
T Consensus 28 Sq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRNKK------RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCccccccc------ccccceEEcCCCCCEEC
Confidence 4489999995222 44555689999998653
No 40
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.10 E-value=11 Score=28.63 Aligned_cols=34 Identities=26% Similarity=0.558 Sum_probs=23.1
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhhhhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 235 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~ 235 (238)
-+|.+||---.-...++.. |-+-|.+||-.+++.
T Consensus 13 Y~c~~cg~~~dvvq~~~dd---plt~ce~c~a~~kk~ 46 (82)
T COG2331 13 YECTECGNRFDVVQAMTDD---PLTTCEECGARLKKL 46 (82)
T ss_pred EeecccchHHHHHHhcccC---ccccChhhChHHHHh
Confidence 4799999742233445554 456899999887763
No 41
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.73 E-value=23 Score=20.80 Aligned_cols=22 Identities=27% Similarity=0.812 Sum_probs=13.7
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
+.|.+||.. . +.+ ...|..||.
T Consensus 3 ~~Cp~Cg~~--~-------~~~-~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAE--I-------DPD-AKFCPNCGA 24 (26)
T ss_pred CCCcccCCc--C-------Ccc-cccChhhCC
Confidence 578888873 2 223 467777774
No 42
>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=35.29 E-value=13 Score=24.23 Aligned_cols=29 Identities=21% Similarity=0.538 Sum_probs=17.9
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
-+|..||.. --.|+..-+.....|-+||-
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 368888862 33344443444678888886
No 43
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=32.85 E-value=30 Score=32.86 Aligned_cols=34 Identities=29% Similarity=0.620 Sum_probs=28.2
Q ss_pred cccccccccccCCCCccccCC---CCCcccchhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGP---SGPRSLCNACGLF 231 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp---~G~~~lCNaCGl~ 231 (238)
...|..|..++-.+..||-|| .-.++.|+.|+..
T Consensus 143 ~~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G~ 179 (337)
T KOG0712|consen 143 APKCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNGS 179 (337)
T ss_pred CCCCCCCCCCCceeEEEeccccccccceeEeccCCCc
Confidence 338999999989999999999 4557899999753
No 44
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=32.49 E-value=20 Score=25.55 Aligned_cols=24 Identities=13% Similarity=0.101 Sum_probs=17.3
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~ 232 (238)
....|.+||.. --+..+|. ||.|-
T Consensus 26 ~~~~c~~cg~~-----------~~pH~vc~-cG~Y~ 49 (60)
T PRK01110 26 TLSVDKTTGEY-----------HLPHHVSP-KGYYK 49 (60)
T ss_pred ceeEcCCCCce-----------eccceecC-CcccC
Confidence 35689999984 23467899 99654
No 45
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=32.40 E-value=18 Score=24.18 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=16.9
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
-+|..||. .--.|+.--+.....|-.||-
T Consensus 6 y~C~~Cg~---~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGH---RFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCC---EeEEEEecCCCCCCCCCCCCC
Confidence 36777776 344565432333456777775
No 46
>PRK00420 hypothetical protein; Validated
Probab=31.36 E-value=23 Score=28.44 Aligned_cols=30 Identities=23% Similarity=0.708 Sum_probs=22.6
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhhhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 233 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~ 233 (238)
....|..||+ |..|- ..| ...|-.||-.+.
T Consensus 22 l~~~CP~Cg~-----pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 22 LSKHCPVCGL-----PLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred ccCCCCCCCC-----cceec-CCC-ceECCCCCCeee
Confidence 3458999986 68874 356 799999997653
No 47
>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=30.80 E-value=36 Score=24.35 Aligned_cols=29 Identities=24% Similarity=0.687 Sum_probs=21.4
Q ss_pred ccccccccccccCCCCccccCCCCCcccc-hhhhhhhhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLC-NACGLFWANK 235 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lC-NaCGl~~~~~ 235 (238)
+-+.|-+||.+ -| .. +..| ..|+.-|.++
T Consensus 2 ~HkHC~~CG~~---Ip------~~-~~fCS~~C~~~~~k~ 31 (59)
T PF09889_consen 2 PHKHCPVCGKP---IP------PD-ESFCSPKCREEYRKR 31 (59)
T ss_pred CCCcCCcCCCc---CC------cc-hhhhCHHHHHHHHHH
Confidence 35689999985 22 22 6899 5999988765
No 48
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=29.64 E-value=24 Score=31.97 Aligned_cols=23 Identities=22% Similarity=0.707 Sum_probs=0.0
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCG 229 (238)
+.+.|.+||. .+..| ..+|..||
T Consensus 353 p~~~c~~cg~---~~~~~-------~~~c~~c~ 375 (389)
T PRK11788 353 PRYRCRNCGF---TARTL-------YWHCPSCK 375 (389)
T ss_pred CCEECCCCCC---CCccc-------eeECcCCC
No 49
>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=29.56 E-value=35 Score=22.12 Aligned_cols=30 Identities=23% Similarity=0.530 Sum_probs=18.7
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 199 ~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
..|-.|+-+ ..-.|..-.....-.|+.||.
T Consensus 4 ~pCP~CGG~--DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGS--DRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCc--cccccccCCCCcCEEeCCCCC
Confidence 468888875 444455432222578998873
No 50
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=29.30 E-value=21 Score=38.38 Aligned_cols=32 Identities=34% Similarity=0.517 Sum_probs=25.8
Q ss_pred CCCCCcccccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 191 GQDDSPSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 191 ~~~~~~~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
.+..+++..+|..|++. .||-|... -|.-||=
T Consensus 1005 LRaFsrQ~fRC~kC~~k------YRR~PL~G--~C~kCGg 1036 (1095)
T TIGR00354 1005 LRAFSRQEVRCTKCNTK------YRRIPLVG--KCLKCGN 1036 (1095)
T ss_pred HhhhhccceeecccCCc------cccCCCCC--cccccCC
Confidence 44566789999999995 89988874 7988984
No 51
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=28.97 E-value=33 Score=19.77 Aligned_cols=8 Identities=38% Similarity=1.215 Sum_probs=4.5
Q ss_pred ccchhhhh
Q 026465 223 SLCNACGL 230 (238)
Q Consensus 223 ~lCNaCGl 230 (238)
..|.-||-
T Consensus 14 ~fC~~CG~ 21 (23)
T PF13240_consen 14 KFCPNCGT 21 (23)
T ss_pred cchhhhCC
Confidence 45666663
No 52
>PF12773 DZR: Double zinc ribbon
Probab=28.47 E-value=37 Score=22.38 Aligned_cols=28 Identities=29% Similarity=0.787 Sum_probs=15.6
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
....|.+||+. .. .+......|..||-.
T Consensus 11 ~~~fC~~CG~~--l~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 11 DAKFCPHCGTP--LP-----PPDQSKKICPNCGAE 38 (50)
T ss_pred cccCChhhcCC--hh-----hccCCCCCCcCCcCC
Confidence 35677777774 22 223334567777654
No 53
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=28.22 E-value=24 Score=29.15 Aligned_cols=28 Identities=32% Similarity=0.896 Sum_probs=22.7
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 196 ~~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
.....|.-||+ |++| -+| ...|--||..
T Consensus 26 ML~~hCp~Cg~-----PLF~--KdG-~v~CPvC~~~ 53 (131)
T COG1645 26 MLAKHCPKCGT-----PLFR--KDG-EVFCPVCGYR 53 (131)
T ss_pred HHHhhCcccCC-----ccee--eCC-eEECCCCCce
Confidence 45668999987 8999 478 7999999943
No 54
>PF02994 Transposase_22: L1 transposable element; InterPro: IPR004244 Many human L1 elements are capable of retrotransposition. Some of these have been shown to exhibit reverse transcriptase (RT) activity [] although the function of many are, as yet, unknown. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 2LDY_A 3SOO_A 2YKQ_A 2YKO_C 2YKP_B 2W7A_B 2JRB_A.
Probab=27.93 E-value=59 Score=30.97 Aligned_cols=25 Identities=20% Similarity=0.616 Sum_probs=21.5
Q ss_pred CcceeEEeCCEEEEEcCCChHHHHHHH
Q 026465 69 SSQLTLSFRGQVYVFDSVTPDKVQAVL 95 (238)
Q Consensus 69 ~~qLTIfY~G~V~Vfd~vp~dKaqaim 95 (238)
++-|.|+|+|++.+|.+ +++|++.+
T Consensus 318 PakL~i~~~G~~~~F~~--~~~~~~fl 342 (370)
T PF02994_consen 318 PAKLRITYNGKTKSFTD--PEEAKEFL 342 (370)
T ss_dssp TTEEEEESSSSEEEESS--HHHHHHHH
T ss_pred cchhcceeCCceecCCC--HHHHHHHH
Confidence 68899999999999985 77777765
No 55
>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=27.87 E-value=22 Score=24.99 Aligned_cols=10 Identities=50% Similarity=0.926 Sum_probs=9.1
Q ss_pred CccccCCCCC
Q 026465 212 PMMRRGPSGP 221 (238)
Q Consensus 212 p~wR~gp~G~ 221 (238)
|+||.||.|-
T Consensus 34 ~E~R~G~~Gf 43 (54)
T PF12553_consen 34 PEWREGPAGF 43 (54)
T ss_pred HhheecCCCc
Confidence 8999999985
No 56
>PRK04023 DNA polymerase II large subunit; Validated
Probab=27.41 E-value=25 Score=38.05 Aligned_cols=32 Identities=38% Similarity=0.633 Sum_probs=25.8
Q ss_pred CCCCCcccccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 191 GQDDSPSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 191 ~~~~~~~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
.+..+++..+|..|++. .||-|... -|.-||=
T Consensus 1030 LRaFsrQ~fRC~kC~~k------YRR~PL~G--~C~kCGg 1061 (1121)
T PRK04023 1030 LRAFSRQEFRCTKCGAK------YRRPPLSG--KCPKCGG 1061 (1121)
T ss_pred hhhhcccceeecccCcc------cccCCCCC--cCccCCC
Confidence 44567789999999995 89999874 7988984
No 57
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=27.00 E-value=32 Score=22.65 Aligned_cols=28 Identities=29% Similarity=0.640 Sum_probs=15.7
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
.-+|.+||.. ....+......|.-||-.
T Consensus 3 ~y~C~~CG~~------~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGRE------VELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCE------EEECCCCCceECCCCCCe
Confidence 3468888873 112222225678888753
No 58
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.74 E-value=26 Score=31.59 Aligned_cols=31 Identities=26% Similarity=0.485 Sum_probs=21.1
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhhhh
Q 026465 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (238)
Q Consensus 196 ~~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~ 232 (238)
...+.|..||.. ... ...|.+..|.+||..+
T Consensus 97 ~~~~fC~~CG~~--~~~----~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 97 RSHRFCGYCGHP--MHP----SKTEWAMLCPHCRERY 127 (256)
T ss_pred hcCccccccCCC--Cee----cCCceeEECCCCCCEE
Confidence 346689999984 222 2356677899999654
No 59
>PF11228 DUF3027: Protein of unknown function (DUF3027); InterPro: IPR021391 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=25.59 E-value=24 Score=30.97 Aligned_cols=26 Identities=23% Similarity=0.539 Sum_probs=15.9
Q ss_pred CccccCCCCCc--------ccchhhhhhhhhhcC
Q 026465 212 PMMRRGPSGPR--------SLCNACGLFWANKVG 237 (238)
Q Consensus 212 p~wR~gp~G~~--------~lCNaCGl~~~~~g~ 237 (238)
..|++|+.||+ ..|.-||-|...-|.
T Consensus 127 ~RW~~g~~GP~s~~a~~a~~~C~tCgF~~plaG~ 160 (193)
T PF11228_consen 127 QRWYEGEFGPDSEMARAAPAQCSTCGFYVPLAGS 160 (193)
T ss_pred HHHHcCCCCCCCHHHHhcccCCCcCccceEcCCc
Confidence 34666666665 357777766655553
No 60
>PF08152 GUCT: GUCT (NUC152) domain; InterPro: IPR012562 This is the C-terminal domain found in the RNA helicase II / Gu protein family [].; GO: 0003723 RNA binding, 0004386 helicase activity, 0005524 ATP binding, 0005634 nucleus; PDB: 2E29_A.
Probab=25.40 E-value=44 Score=25.80 Aligned_cols=31 Identities=23% Similarity=0.170 Sum_probs=23.7
Q ss_pred CCcceeEEeCCEEEEEcCCChHHHHHHHHHhc
Q 026465 68 NSSQLTLSFRGQVYVFDSVTPDKVQAVLLLLG 99 (238)
Q Consensus 68 ~~~qLTIfY~G~V~Vfd~vp~dKaqaim~la~ 99 (238)
.-..|||.=++.=.||| ||.+.++.++....
T Consensus 49 ~v~~m~l~~d~~GavFD-vP~~~~~~~~~~~~ 79 (97)
T PF08152_consen 49 KVKGMTLLKDKMGAVFD-VPSEIAEEFLAKWE 79 (97)
T ss_dssp T-EEEEE-TTSSEEEEE-EEHHHHHHHHHH--
T ss_pred hhCcEEEecCCCEEEEE-ChHHHHHHHHHhCc
Confidence 45679998888999998 99999999987654
No 61
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.29 E-value=28 Score=38.47 Aligned_cols=33 Identities=33% Similarity=0.562 Sum_probs=26.6
Q ss_pred CCCCCCcccccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 190 PGQDDSPSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 190 ~~~~~~~~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
.++..+++..+|..|++. .||-|... -|.-||=
T Consensus 1245 NLraFsrQ~~RC~kC~~k------yRR~PL~G--~C~kCGg 1277 (1337)
T PRK14714 1245 NLRAFSRQEFRCLKCGTK------YRRMPLAG--KCRKCGG 1277 (1337)
T ss_pred hhhhhhccceeecccCcc------cccCCCCC--cccccCC
Confidence 345567889999999995 89988864 7988984
No 62
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=23.43 E-value=61 Score=24.67 Aligned_cols=32 Identities=22% Similarity=0.489 Sum_probs=22.7
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhhhhhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 235 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~~~~ 235 (238)
....|.-|+.. +-...- | ...|+||..+|++.
T Consensus 5 ~~~~C~VCg~~---~~g~hy---G-v~sC~aCk~FFRR~ 36 (90)
T cd07168 5 SPKLCSICEDK---ATGLHY---G-IITCEGCKGFFKRT 36 (90)
T ss_pred cCCCCcccCCc---CcceEE---C-ceehhhhhHhhhhh
Confidence 34579999973 334444 3 47899999999875
No 63
>PHA00626 hypothetical protein
Probab=22.81 E-value=37 Score=24.27 Aligned_cols=31 Identities=32% Similarity=0.694 Sum_probs=20.1
Q ss_pred cccccccccCCCCccc----cCCCCCcccchhhhhhhhhh
Q 026465 200 SCTHCGISSKSTPMMR----RGPSGPRSLCNACGLFWANK 235 (238)
Q Consensus 200 ~C~~C~~t~~~Tp~wR----~gp~G~~~lCNaCGl~~~~~ 235 (238)
.|-+||.. -..| +++.. ...|.-||-+|-+.
T Consensus 2 ~CP~CGS~----~Ivrcg~cr~~sn-rYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSG----NIAKEKTMRGWSD-DYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCc----eeeeeceecccCc-ceEcCCCCCeechh
Confidence 57777762 1123 24445 68999999888764
No 64
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.65 E-value=43 Score=28.54 Aligned_cols=12 Identities=33% Similarity=0.841 Sum_probs=8.1
Q ss_pred Ccccchhhhhhh
Q 026465 221 PRSLCNACGLFW 232 (238)
Q Consensus 221 ~~~lCNaCGl~~ 232 (238)
.-+.|+.||..|
T Consensus 67 ~PsYC~~CGkpy 78 (158)
T PF10083_consen 67 APSYCHNCGKPY 78 (158)
T ss_pred CChhHHhCCCCC
Confidence 346788888765
No 65
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=22.35 E-value=39 Score=31.76 Aligned_cols=31 Identities=26% Similarity=0.644 Sum_probs=22.0
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~~ 232 (238)
....|.+||+. .|+-. |+|..-.|-+||..+
T Consensus 314 k~nfc~ncG~~--~t~~~---~ng~a~fcp~cgq~~ 344 (345)
T COG4260 314 KLNFCLNCGCG--TTADF---DNGKAKFCPECGQGF 344 (345)
T ss_pred ccccccccCcc--cccCC---ccchhhhChhhcCCC
Confidence 34588999975 66643 456667999999654
No 66
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=21.78 E-value=37 Score=29.76 Aligned_cols=26 Identities=27% Similarity=0.754 Sum_probs=20.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl~ 231 (238)
...|++|+. ++.+ .|...-|..||--
T Consensus 149 ~A~CsrC~~-----~L~~---~~~~l~Cp~Cg~t 174 (188)
T COG1096 149 YARCSRCRA-----PLVK---KGNMLKCPNCGNT 174 (188)
T ss_pred EEEccCCCc-----ceEE---cCcEEECCCCCCE
Confidence 458999987 5777 4667889999854
No 67
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=21.75 E-value=35 Score=22.85 Aligned_cols=10 Identities=40% Similarity=0.700 Sum_probs=8.6
Q ss_pred hhHHHHHHHH
Q 026465 130 PQRAASLDRF 139 (238)
Q Consensus 130 paRkaSL~RF 139 (238)
.+|+++|+||
T Consensus 34 ~aRkr~l~rf 43 (43)
T PF08114_consen 34 QARKRALQRF 43 (43)
T ss_pred HHHHHHHhcC
Confidence 5899999987
No 68
>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=21.61 E-value=1e+02 Score=19.36 Aligned_cols=20 Identities=20% Similarity=0.380 Sum_probs=16.9
Q ss_pred cceeEEeCCEEEEEcCCChH
Q 026465 70 SQLTLSFRGQVYVFDSVTPD 89 (238)
Q Consensus 70 ~qLTIfY~G~V~Vfd~vp~d 89 (238)
..+++-|+|...++.+||+.
T Consensus 14 ~~~~~~~~~~~~~i~~vp~~ 33 (46)
T TIGR03831 14 TTETYEYGGELIVIENVPAL 33 (46)
T ss_pred EEEEEEeCCEEEEEeCCCcc
Confidence 36778889999999999975
No 69
>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=21.51 E-value=40 Score=21.52 Aligned_cols=26 Identities=27% Similarity=0.666 Sum_probs=19.5
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhh
Q 026465 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (238)
Q Consensus 198 ~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCGl 230 (238)
...|..|+. . |-...+| ...|..||-
T Consensus 8 ~~~C~~C~~---~---~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGS---R---WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCcCCCCCC---e---EeEccCC-EEEhhhCce
Confidence 446999997 2 6666678 799999983
No 70
>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=20.76 E-value=40 Score=21.05 Aligned_cols=23 Identities=35% Similarity=0.904 Sum_probs=11.9
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhh
Q 026465 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~wR~gp~G~~~lCNaCG 229 (238)
...+|..||.. .-- |+..|..||
T Consensus 10 ~~~rC~~Cg~~-------~~p---Pr~~Cp~C~ 32 (37)
T PF12172_consen 10 LGQRCRDCGRV-------QFP---PRPVCPHCG 32 (37)
T ss_dssp EEEE-TTT--E-------EES-----SEETTTT
T ss_pred EEEEcCCCCCE-------ecC---CCcCCCCcC
Confidence 45688888883 332 345888887
No 71
>PF15321 ATAD4: ATPase family AAA domain containing 4
Probab=20.34 E-value=26 Score=26.89 Aligned_cols=12 Identities=50% Similarity=0.789 Sum_probs=9.8
Q ss_pred HHHHHhhhhhhc
Q 026465 137 DRFRQKRKERCF 148 (238)
Q Consensus 137 ~RF~eKRK~R~~ 148 (238)
=||.||||-|..
T Consensus 69 GRFKEKrKvRat 80 (84)
T PF15321_consen 69 GRFKEKRKVRAT 80 (84)
T ss_pred cccccccccccc
Confidence 389999999853
No 72
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=20.11 E-value=17 Score=23.53 Aligned_cols=33 Identities=24% Similarity=0.612 Sum_probs=14.8
Q ss_pred cccccccccCC--CCccccCCCCCc--ccchhhhhhh
Q 026465 200 SCTHCGISSKS--TPMMRRGPSGPR--SLCNACGLFW 232 (238)
Q Consensus 200 ~C~~C~~t~~~--Tp~wR~gp~G~~--~lCNaCGl~~ 232 (238)
.|..||-.... .-+-|.+.++.. ..|..||-.|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 46667664111 113455544421 4577777666
No 73
>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=20.07 E-value=49 Score=24.07 Aligned_cols=40 Identities=23% Similarity=0.626 Sum_probs=27.1
Q ss_pred ccccccccccccCCCCcc---ccCCCCCcccchhhhhhhhhhcCC
Q 026465 197 SETSCTHCGISSKSTPMM---RRGPSGPRSLCNACGLFWANKVGV 238 (238)
Q Consensus 197 ~~~~C~~C~~t~~~Tp~w---R~gp~G~~~lCNaCGl~~~~~g~l 238 (238)
....|..|..+ .|-.- =-...-|+..|-+|-.+|-..|+|
T Consensus 4 ~~~~CPRC~S~--nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~l 46 (63)
T PF02701_consen 4 QPLPCPRCDST--NTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTL 46 (63)
T ss_pred cCCCCCCcCCC--CCEEEeecCCCCCCcchhhHHHHHHHHhccee
Confidence 45678888875 44321 112235678999999999988875
Done!