Query 023942
Match_columns 275
No_of_seqs 267 out of 1036
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 07:46:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023942.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023942hhsearch_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 1.7E-17 3.7E-22 110.7 5.2 35 66-100 2-36 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.6 6.8E-16 1.5E-20 111.5 3.7 44 200-245 1-44 (54)
3 smart00401 ZnF_GATA zinc finge 99.6 1.8E-15 3.9E-20 108.3 3.5 48 197-246 2-50 (52)
4 PF00320 GATA: GATA zinc finge 99.5 8.9E-15 1.9E-19 97.4 0.8 36 201-238 1-36 (36)
5 PF09425 CCT_2: Divergent CCT 99.1 5.4E-11 1.2E-15 74.6 1.5 24 131-155 3-26 (27)
6 PF06203 CCT: CCT motif; Inte 98.9 4.5E-10 9.8E-15 78.5 2.8 43 132-174 1-43 (45)
7 KOG1601 GATA-4/5/6 transcripti 98.7 9.6E-09 2.1E-13 89.5 3.7 47 198-246 199-245 (340)
8 COG5641 GAT1 GATA Zn-finger-co 98.4 1.8E-07 4E-12 93.6 2.5 52 196-250 156-213 (498)
9 COG5641 GAT1 GATA Zn-finger-co 90.8 0.12 2.6E-06 52.5 1.7 53 196-249 295-347 (498)
10 KOG3554 Histone deacetylase co 84.9 1.9 4.2E-05 43.9 5.9 39 198-238 386-426 (693)
11 PF14803 Nudix_N_2: Nudix N-te 78.5 0.54 1.2E-05 31.1 -0.4 30 199-230 1-30 (34)
12 PF13619 KTSC: KTSC domain 76.5 4.9 0.00011 29.1 4.1 30 67-96 13-43 (60)
13 PF01783 Ribosomal_L32p: Ribos 69.9 1.2 2.7E-05 32.2 -0.4 26 197-234 25-50 (56)
14 PRK03988 translation initiatio 59.4 3 6.4E-05 35.7 -0.1 32 196-230 100-131 (138)
15 TIGR00311 aIF-2beta translatio 57.2 3.5 7.5E-05 35.0 -0.0 31 197-230 96-126 (133)
16 smart00653 eIF2B_5 domain pres 54.6 4.1 8.9E-05 33.5 0.0 31 197-230 79-109 (110)
17 PRK12286 rpmF 50S ribosomal pr 54.5 4.8 0.0001 29.5 0.3 26 195-231 24-49 (57)
18 PRK12336 translation initiatio 51.7 4.7 0.0001 36.3 -0.1 31 197-230 97-127 (201)
19 PF01412 ArfGap: Putative GTPa 51.2 13 0.00028 30.3 2.4 38 196-237 11-48 (116)
20 PF13248 zf-ribbon_3: zinc-rib 49.6 10 0.00022 23.1 1.2 23 198-230 2-24 (26)
21 KOG3740 Uncharacterized conser 49.6 6.2 0.00013 41.5 0.4 39 195-235 459-500 (706)
22 KOG1598 Transcription initiati 46.9 8.8 0.00019 39.5 0.9 33 199-236 1-33 (521)
23 COG3952 Predicted membrane pro 45.8 5.2 0.00011 33.2 -0.7 20 213-234 76-95 (113)
24 PF06677 Auto_anti-p27: Sjogre 45.5 8.9 0.00019 26.3 0.5 25 198-229 17-41 (41)
25 PF04810 zf-Sec23_Sec24: Sec23 43.9 8 0.00017 26.0 0.1 31 198-230 2-32 (40)
26 PF01873 eIF-5_eIF-2B: Domain 43.4 8.1 0.00018 32.4 0.1 30 198-230 93-122 (125)
27 PF13240 zinc_ribbon_2: zinc-r 42.7 14 0.00031 22.2 1.0 20 201-230 2-21 (23)
28 PF13717 zinc_ribbon_4: zinc-r 42.1 5 0.00011 26.5 -1.1 33 199-232 3-35 (36)
29 PRK14892 putative transcriptio 39.5 9.8 0.00021 30.9 -0.0 37 196-235 19-55 (99)
30 TIGR01031 rpmF_bact ribosomal 39.2 10 0.00022 27.5 0.1 25 196-231 24-48 (55)
31 TIGR00416 sms DNA repair prote 39.2 12 0.00025 37.6 0.4 25 197-231 6-30 (454)
32 smart00105 ArfGap Putative GTP 38.8 26 0.00057 28.3 2.4 43 197-243 2-48 (112)
33 PF08271 TF_Zn_Ribbon: TFIIB z 38.6 11 0.00025 25.3 0.2 29 200-233 2-30 (43)
34 PF09297 zf-NADH-PPase: NADH p 38.4 7.2 0.00016 24.8 -0.8 28 198-231 3-30 (32)
35 PF09889 DUF2116: Uncharacteri 36.0 20 0.00043 26.6 1.2 30 197-236 2-32 (59)
36 COG4260 Membrane protease subu 34.7 21 0.00046 34.5 1.4 29 197-230 314-342 (345)
37 PF15396 FAM60A: Protein Famil 34.5 22 0.00047 32.7 1.4 25 223-247 50-74 (213)
38 TIGR03573 WbuX N-acetyl sugar 33.6 26 0.00057 33.6 1.9 32 199-234 2-33 (343)
39 PRK11823 DNA repair protein Ra 33.4 14 0.00031 36.8 0.1 25 197-231 6-30 (446)
40 smart00834 CxxC_CXXC_SSSS Puta 32.2 18 0.00039 23.4 0.4 28 200-230 7-34 (41)
41 PRK05342 clpX ATP-dependent pr 31.7 31 0.00068 34.3 2.1 31 197-229 8-38 (412)
42 PF02701 zf-Dof: Dof domain, z 31.4 31 0.00068 26.0 1.5 46 197-244 4-52 (63)
43 PRK11788 tetratricopeptide rep 31.3 18 0.0004 33.5 0.4 23 197-229 353-375 (389)
44 PRK00420 hypothetical protein; 31.2 23 0.00049 29.4 0.9 30 198-234 23-52 (112)
45 PF12773 DZR: Double zinc ribb 30.7 30 0.00064 23.6 1.3 29 196-231 10-38 (50)
46 COG2816 NPY1 NTP pyrophosphohy 30.7 19 0.0004 34.4 0.3 32 197-234 110-141 (279)
47 COG2331 Uncharacterized protei 30.6 17 0.00036 28.6 0.0 35 199-236 13-47 (82)
48 PF10083 DUF2321: Uncharacteri 29.7 25 0.00054 31.0 0.9 16 217-232 63-78 (158)
49 TIGR02098 MJ0042_CXXC MJ0042 f 29.6 8.5 0.00018 25.0 -1.5 33 199-232 3-35 (38)
50 PRK01110 rpmF 50S ribosomal pr 29.6 19 0.00042 26.5 0.2 24 197-232 26-49 (60)
51 KOG1007 WD repeat protein TSSC 28.5 46 0.001 32.5 2.6 53 41-95 317-369 (370)
52 PF09723 Zn-ribbon_8: Zinc rib 28.3 22 0.00048 24.0 0.3 28 200-230 7-34 (42)
53 PF07282 OrfB_Zn_ribbon: Putat 27.6 29 0.00062 25.2 0.8 29 198-232 28-56 (69)
54 cd01121 Sms Sms (bacterial rad 27.4 22 0.00047 34.8 0.2 22 200-231 2-23 (372)
55 KOG0706 Predicted GTPase-activ 27.2 31 0.00067 35.0 1.2 40 195-238 20-59 (454)
56 PF08114 PMP1_2: ATPase proteo 26.5 25 0.00054 24.5 0.3 10 130-139 34-43 (43)
57 smart00778 Prim_Zn_Ribbon Zinc 26.1 35 0.00077 22.9 1.0 30 198-229 3-32 (37)
58 TIGR02605 CxxC_CxxC_SSSS putat 25.9 28 0.00061 24.0 0.5 29 199-230 6-34 (52)
59 PF06689 zf-C4_ClpX: ClpX C4-t 25.9 29 0.00064 23.4 0.6 32 199-231 2-33 (41)
60 PRK05978 hypothetical protein; 25.3 29 0.00063 30.1 0.5 35 197-236 32-66 (148)
61 PRK12496 hypothetical protein; 25.3 36 0.00078 29.6 1.2 34 197-238 126-159 (164)
62 COG1645 Uncharacterized Zn-fin 25.3 27 0.00059 29.8 0.4 26 197-230 27-52 (131)
63 COG5349 Uncharacterized protei 24.8 26 0.00057 29.7 0.2 35 197-236 20-54 (126)
64 PRK00398 rpoP DNA-directed RNA 24.4 33 0.00072 23.3 0.6 29 199-233 4-32 (46)
65 COG5347 GTPase-activating prot 24.4 42 0.00092 32.5 1.5 37 197-237 19-55 (319)
66 PF14122 YokU: YokU-like prote 23.7 28 0.0006 27.8 0.1 37 201-237 2-50 (87)
67 PHA00626 hypothetical protein 23.1 31 0.00068 25.6 0.3 31 200-235 2-36 (59)
68 PRK00423 tfb transcription ini 22.6 43 0.00092 31.8 1.2 30 198-232 11-40 (310)
69 KOG0712 Molecular chaperone (D 22.4 56 0.0012 32.0 1.9 36 198-233 143-181 (337)
70 TIGR03831 YgiT_finger YgiT-typ 21.9 95 0.0021 20.2 2.5 22 69-90 13-34 (46)
71 KOG1601 GATA-4/5/6 transcripti 21.4 27 0.00058 30.2 -0.4 39 131-169 292-330 (340)
72 PLN03114 ADP-ribosylation fact 20.7 66 0.0014 32.1 2.0 37 197-237 21-57 (395)
73 COG3529 Predicted nucleic-acid 20.2 22 0.00047 26.8 -1.1 33 199-233 11-43 (66)
74 PF00641 zf-RanBP: Zn-finger i 20.0 29 0.00062 21.5 -0.4 24 197-230 3-26 (30)
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=99.70 E-value=1.7e-17 Score=110.72 Aligned_cols=35 Identities=46% Similarity=0.731 Sum_probs=32.6
Q ss_pred CCCCcceeEEeCCEEEEecCCChHHHHHHHHHhcC
Q 023942 66 LSNSSQLTLSFRGQVYVFDSVTPDKVQAVLLLLGG 100 (275)
Q Consensus 66 ~~~~~QLTIfY~G~V~Vfd~V~~dKaq~Im~lA~~ 100 (275)
.+.++||||||+|+|+|||+||+|||++||+||+.
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 36789999999999999999999999999999973
No 2
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.59 E-value=6.8e-16 Score=111.47 Aligned_cols=44 Identities=52% Similarity=1.258 Sum_probs=41.9
Q ss_pred cceeecccCCCCCceecCCCCCCccchhhhhHHHhcCCCCCCCCCC
Q 023942 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKM 245 (275)
Q Consensus 200 ~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~~r~~~~k~ 245 (275)
.|+||+++ .||+||+||.+..+|||||||||++++..||..+..
T Consensus 1 ~C~~C~~~--~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTT--TTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCC--CCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 59999998 999999999888999999999999999999999877
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.56 E-value=1.8e-15 Score=108.32 Aligned_cols=48 Identities=52% Similarity=1.112 Sum_probs=43.8
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcCCC-CCCCCCCC
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL-RDLGKKME 246 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~~-r~~~~k~~ 246 (275)
....|+||+++ .||+||+||.|..+|||||||||++++.+ ||..+.++
T Consensus 2 ~~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~~ 50 (52)
T smart00401 2 SGRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKKD 50 (52)
T ss_pred CCCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCCCCccccccc
Confidence 35789999998 99999999999889999999999999998 88887765
No 4
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.47 E-value=8.9e-15 Score=97.38 Aligned_cols=36 Identities=53% Similarity=1.278 Sum_probs=28.6
Q ss_pred ceeecccCCCCCceecCCCCCCccchhhhhHHHhcCCC
Q 023942 201 CTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL 238 (275)
Q Consensus 201 C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~~ 238 (275)
|+||+++ .||+||+||.|..+|||||||+|++++++
T Consensus 1 C~~C~tt--~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGTT--ETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT--S--T-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcCC--CCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 8999999 99999999999888999999999999863
No 5
>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=99.06 E-value=5.4e-11 Score=74.61 Aligned_cols=24 Identities=50% Similarity=0.674 Sum_probs=10.0
Q ss_pred hHHHHHHHHHhhhhhhhcccchhhh
Q 023942 131 QRAASLDRFRQKRKERCFDKKVRYS 155 (275)
Q Consensus 131 aRkASLqRFlEKRKeR~f~kk~pY~ 155 (275)
+|++||||||||||+|+++ ++||.
T Consensus 3 aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 3 ARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp ---HHHHHHHHHH------------
T ss_pred hHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 8999999999999999987 78996
No 6
>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=98.95 E-value=4.5e-10 Score=78.53 Aligned_cols=43 Identities=47% Similarity=0.779 Sum_probs=41.2
Q ss_pred HHHHHHHHHhhhhhhhcccchhhhhHHHHHHHhhhhccccccc
Q 023942 132 RAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKGQFTSA 174 (275)
Q Consensus 132 RkASLqRFlEKRKeR~f~kk~pY~~rkeva~Rm~RekGQF~ss 174 (275)
|.++|+||+|||+.|+|.+++.|.+|+.+|+.++|.+|+|+..
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~ 43 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKK 43 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCC
Confidence 6789999999999999999999999999999999999999874
No 7
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.71 E-value=9.6e-09 Score=89.48 Aligned_cols=47 Identities=49% Similarity=1.009 Sum_probs=42.5
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhhhHHHhcCCCCCCCCCCC
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKME 246 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~~r~~~~k~~ 246 (275)
...|.+|+++ .||+||++|.|+..+|||||++|++++..|++.+++.
T Consensus 199 ~~~c~~~~~~--~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~ 245 (340)
T KOG1601|consen 199 LRQCSNCGTT--KTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRP 245 (340)
T ss_pred CcccCCCCCC--CCcceecCCCCCccccccchhhhhhcCccccccccCc
Confidence 5899999998 9999999999999999999999999987777777665
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.35 E-value=1.8e-07 Score=93.58 Aligned_cols=52 Identities=37% Similarity=0.729 Sum_probs=45.5
Q ss_pred CCCccceeecccCCCCCceecCCC-----CCCccchhhhhHHHhcCCCC-CCCCCCCCCCC
Q 023942 196 PSETSCTHCGISSKSTPMMRRGPS-----GPRSLCNACGLFWANKGALR-DLGKKMEDQPL 250 (275)
Q Consensus 196 ~~~~~C~~Cgtt~~~Tp~WRrGp~-----G~~~LCNACGl~~~~~~~~r-~~~~k~~~~~~ 250 (275)
.....|.||.++ .||+|||+.. | -.|||||||+++.|+++| |+++|..-+..
T Consensus 156 ~~~~vc~Nc~t~--stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r~P~t~ks~~~ks 213 (498)
T COG5641 156 NQPHVCSNCKTT--STPLWRRASSESSLPG-NNLCNACGLYLKLHGSPRAPISLKSDSIKS 213 (498)
T ss_pred cccchhcccccc--CCccccccccccccCC-ccccccccccccccCCcCCCcccccccccc
Confidence 344599999998 9999999999 6 699999999999999999 99998874443
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=90.85 E-value=0.12 Score=52.52 Aligned_cols=53 Identities=28% Similarity=0.360 Sum_probs=44.6
Q ss_pred CCCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcCCCCCCCCCCCCCC
Q 023942 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKMEDQP 249 (275)
Q Consensus 196 ~~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~~r~~~~k~~~~~ 249 (275)
+....|.+|++. +.||.||+...-.-++||+||++.+..+..+|+..|.+...
T Consensus 295 ps~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~ 347 (498)
T COG5641 295 PSDKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNS 347 (498)
T ss_pred hhhcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCCChhh
Confidence 446689999985 58999999887778999999999999999999988766443
No 10
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=84.93 E-value=1.9 Score=43.86 Aligned_cols=39 Identities=23% Similarity=0.609 Sum_probs=31.3
Q ss_pred CccceeecccCCCCCceec--CCCCCCccchhhhhHHHhcCCC
Q 023942 198 ETSCTHCGISSKSTPMMRR--GPSGPRSLCNACGLFWANKGAL 238 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRr--Gp~G~~~LCNACGl~~~~~~~~ 238 (275)
.+.|.+|+|+ ..-+|=. +|.-...||--|=+||++.|-+
T Consensus 386 g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 7799999998 7777744 5555558999999999998853
No 11
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=78.49 E-value=0.54 Score=31.07 Aligned_cols=30 Identities=30% Similarity=0.708 Sum_probs=15.5
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
+.|.+||.. .+..-=.|.+-.+.+|.+||.
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 359999986 333333466667789999985
No 12
>PF13619 KTSC: KTSC domain
Probab=76.49 E-value=4.9 Score=29.06 Aligned_cols=30 Identities=30% Similarity=0.558 Sum_probs=26.8
Q ss_pred CCCcceeEEe-CCEEEEecCCChHHHHHHHH
Q 023942 67 SNSSQLTLSF-RGQVYVFDSVTPDKVQAVLL 96 (275)
Q Consensus 67 ~~~~QLTIfY-~G~V~Vfd~V~~dKaq~Im~ 96 (275)
+.+..|.|.| +|.+|.|.+||++-.+++|.
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 4678999998 89999999999999998876
No 13
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=69.91 E-value=1.2 Score=32.18 Aligned_cols=26 Identities=27% Similarity=0.913 Sum_probs=19.1
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHHHh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 234 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~ 234 (275)
....|.+||.. .-++.+|.+|| ||+.
T Consensus 25 ~l~~c~~cg~~-----------~~~H~vc~~cG-~y~~ 50 (56)
T PF01783_consen 25 NLVKCPNCGEP-----------KLPHRVCPSCG-YYKG 50 (56)
T ss_dssp SEEESSSSSSE-----------ESTTSBCTTTB-BSSS
T ss_pred ceeeeccCCCE-----------ecccEeeCCCC-eECC
Confidence 56789999974 22368999999 4543
No 14
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=59.40 E-value=3 Score=35.67 Aligned_cols=32 Identities=28% Similarity=0.625 Sum_probs=24.1
Q ss_pred CCCccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 196 ~~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
..--.|..|+.+ .|-+-+.+-.- -.-|+|||-
T Consensus 100 ~~yVlC~~C~sp--dT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 100 KEYVICPECGSP--DTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred HhcEECCCCCCC--CcEEEEcCCeE-EEEcccCCC
Confidence 345689999998 88888764322 368999996
No 15
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=57.17 E-value=3.5 Score=35.04 Aligned_cols=31 Identities=26% Similarity=0.622 Sum_probs=23.1
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
.--.|..|+.+ .|-+-+.+--- -.-|+|||-
T Consensus 96 ~yVlC~~C~sP--dT~l~k~~r~~-~l~C~ACGa 126 (133)
T TIGR00311 96 KYVICRECNRP--DTRIIKEGRVS-LLKCEACGA 126 (133)
T ss_pred heEECCCCCCC--CcEEEEeCCeE-EEecccCCC
Confidence 44679999998 88888764221 257999996
No 16
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=54.61 E-value=4.1 Score=33.50 Aligned_cols=31 Identities=26% Similarity=0.554 Sum_probs=22.8
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
.--.|..|+.+ .|-+-+.+-.- -.-|+|||-
T Consensus 79 ~yVlC~~C~sp--dT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 79 EYVLCPECGSP--DTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred hcEECCCCCCC--CcEEEEeCCeE-EEEccccCC
Confidence 34679999999 89888873222 245999994
No 17
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=54.47 E-value=4.8 Score=29.46 Aligned_cols=26 Identities=31% Similarity=1.007 Sum_probs=19.4
Q ss_pred CCCCccceeecccCCCCCceecCCCCCCccchhhhhH
Q 023942 195 SPSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (275)
Q Consensus 195 ~~~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~ 231 (275)
......|.+||.. .- +..+|..||.|
T Consensus 24 ~~~l~~C~~CG~~--~~---------~H~vC~~CG~Y 49 (57)
T PRK12286 24 APGLVECPNCGEP--KL---------PHRVCPSCGYY 49 (57)
T ss_pred CCcceECCCCCCc--cC---------CeEECCCCCcC
Confidence 3456789999985 22 26899999964
No 18
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=51.68 E-value=4.7 Score=36.25 Aligned_cols=31 Identities=26% Similarity=0.654 Sum_probs=23.6
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
.--.|..|+.+ .|-+-+.+..- -.-|+|||-
T Consensus 97 ~yV~C~~C~~p--dT~l~k~~~~~-~l~C~aCGa 127 (201)
T PRK12336 97 EYVICSECGLP--DTRLVKEDRVL-MLRCDACGA 127 (201)
T ss_pred heEECCCCCCC--CcEEEEcCCeE-EEEcccCCC
Confidence 45679999998 89888764222 357999997
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=51.16 E-value=13 Score=30.27 Aligned_cols=38 Identities=26% Similarity=0.556 Sum_probs=27.7
Q ss_pred CCCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcCC
Q 023942 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 237 (275)
Q Consensus 196 ~~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~ 237 (275)
+....|+.|+. .-|.|-.=.-| -.||-.|.-..+.-|+
T Consensus 11 ~~N~~CaDCg~---~~p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 11 PGNKVCADCGA---PNPTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp TTCTB-TTT-S---BS--EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred cCcCcCCCCCC---CCCCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 45788999997 57899998888 6999999998888774
No 20
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.58 E-value=10 Score=23.14 Aligned_cols=23 Identities=30% Similarity=0.790 Sum_probs=15.7
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
.+.|.+||.. -+.+ ...|-.||.
T Consensus 2 ~~~Cp~Cg~~---------~~~~-~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAE---------IDPD-AKFCPNCGA 24 (26)
T ss_pred cCCCcccCCc---------CCcc-cccChhhCC
Confidence 3578889885 2333 468888885
No 21
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.56 E-value=6.2 Score=41.47 Aligned_cols=39 Identities=21% Similarity=0.433 Sum_probs=30.9
Q ss_pred CCCCccceeecccCCCCCceecCCCC---CCccchhhhhHHHhc
Q 023942 195 SPSETSCTHCGISSKSTPMMRRGPSG---PRSLCNACGLFWANK 235 (275)
Q Consensus 195 ~~~~~~C~~Cgtt~~~Tp~WRrGp~G---~~~LCNACGl~~~~~ 235 (275)
..+.-.|..|.|. .||.|+.-+.+ ..++|.+|----.++
T Consensus 459 a~~P~~caqcktd--ftp~wk~ekstq~d~~i~cE~cvtSnqkk 500 (706)
T KOG3740|consen 459 ATEPYACAQCKTD--FTPAWKKEKSTQADAAIVCENCVTSNQKK 500 (706)
T ss_pred cCCchhhhhcccc--cccccccccccCcchHHHHHhhhhhcccc
Confidence 3457789999997 99999998877 348999997654443
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=46.87 E-value=8.8 Score=39.49 Aligned_cols=33 Identities=24% Similarity=0.472 Sum_probs=22.6
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhhHHHhcC
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 236 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~ 236 (275)
..|.||+.+ ++.- .++..-..|++||.-.-...
T Consensus 1 ~~C~~C~~s---~fe~--d~a~g~~~C~~CG~v~E~~~ 33 (521)
T KOG1598|consen 1 MVCKNCGGS---NFER--DEATGNLYCTACGTVLEYNN 33 (521)
T ss_pred CcCCCCCCC---Cccc--ccccCCceeccccceeeccc
Confidence 369999984 5553 33443699999998655443
No 23
>COG3952 Predicted membrane protein [Function unknown]
Probab=45.81 E-value=5.2 Score=33.15 Aligned_cols=20 Identities=40% Similarity=0.579 Sum_probs=15.6
Q ss_pred ceecCCCCCCccchhhhhHHHh
Q 023942 213 MMRRGPSGPRSLCNACGLFWAN 234 (275)
Q Consensus 213 ~WRrGp~G~~~LCNACGl~~~~ 234 (275)
+||.+|-+ .||++||++-..
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 46777777 799999997543
No 24
>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=45.45 E-value=8.9 Score=26.34 Aligned_cols=25 Identities=44% Similarity=1.204 Sum_probs=18.5
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhh
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACG 229 (275)
...|..|+ +|++| ...| +.+|-+|+
T Consensus 17 ~~~Cp~C~-----~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCG-----TPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCCC-----CeeEE-ecCC-CEECCCCC
Confidence 45688886 48999 3356 68999985
No 25
>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=43.85 E-value=8 Score=25.97 Aligned_cols=31 Identities=26% Similarity=0.634 Sum_probs=21.0
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
..+|.+|++- .-|...-...|....||-|+.
T Consensus 2 p~rC~~C~ay--lNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAY--LNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--B--S-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCE--ECCcceEcCCCCEEECcCCCC
Confidence 4689999997 888888888888889999986
No 26
>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=43.40 E-value=8.1 Score=32.42 Aligned_cols=30 Identities=30% Similarity=0.646 Sum_probs=23.6
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
--.|..|+.+ .|-+-+.+..- -.-|+|||-
T Consensus 93 yVlC~~C~sp--dT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 93 YVLCPECGSP--DTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp HSSCTSTSSS--SEEEEEETTCC-EEEETTTSC
T ss_pred EEEcCCCCCC--ccEEEEcCCEE-EEEecccCC
Confidence 3579999998 88888885444 478999994
No 27
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=42.68 E-value=14 Score=22.16 Aligned_cols=20 Identities=30% Similarity=0.908 Sum_probs=12.4
Q ss_pred ceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 201 CTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 201 C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
|.+||.. -+++ ..+|..||.
T Consensus 2 Cp~CG~~---------~~~~-~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAE---------IEDD-AKFCPNCGT 21 (23)
T ss_pred CcccCCC---------CCCc-CcchhhhCC
Confidence 7777775 2333 357777774
No 28
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=42.09 E-value=5 Score=26.54 Aligned_cols=33 Identities=21% Similarity=0.594 Sum_probs=25.9
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhhHH
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~ 232 (275)
..|.+|++. ...+..+-.+.|...-|-.||-.|
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 468889886 677777778888888898888654
No 29
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.48 E-value=9.8 Score=30.89 Aligned_cols=37 Identities=24% Similarity=0.514 Sum_probs=24.4
Q ss_pred CCCccceeecccCCCCCceecCCCCCCccchhhhhHHHhc
Q 023942 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 235 (275)
Q Consensus 196 ~~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~ 235 (275)
+....|.+|+.. .-+. ..+-..+...|..||.|+-+.
T Consensus 19 pt~f~CP~Cge~--~v~v-~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 19 PKIFECPRCGKV--SISV-KIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred CcEeECCCCCCe--Eeee-ecCCCcceEECCCCCCccCEE
Confidence 356779999953 2222 222245579999999997764
No 30
>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=39.21 E-value=10 Score=27.45 Aligned_cols=25 Identities=32% Similarity=0.947 Sum_probs=18.6
Q ss_pred CCCccceeecccCCCCCceecCCCCCCccchhhhhH
Q 023942 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (275)
Q Consensus 196 ~~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~ 231 (275)
.....|.+||.. --+..+|-.||.|
T Consensus 24 p~l~~C~~cG~~-----------~~~H~vc~~cG~Y 48 (55)
T TIGR01031 24 PTLVVCPNCGEF-----------KLPHRVCPSCGYY 48 (55)
T ss_pred CcceECCCCCCc-----------ccCeeECCccCeE
Confidence 456789999985 2236899999943
No 31
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=39.17 E-value=12 Score=37.64 Aligned_cols=25 Identities=36% Similarity=0.899 Sum_probs=16.6
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhH
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~ 231 (275)
....|.+||.+ ++.|- --|.+||-+
T Consensus 6 ~~y~C~~Cg~~---~~~~~-------g~Cp~C~~w 30 (454)
T TIGR00416 6 SKFVCQHCGAD---SPKWQ-------GKCPACHAW 30 (454)
T ss_pred CeEECCcCCCC---Ccccc-------EECcCCCCc
Confidence 35689999984 55552 258888763
No 32
>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=38.84 E-value=26 Score=28.30 Aligned_cols=43 Identities=26% Similarity=0.491 Sum_probs=33.7
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcCC----CCCCCC
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA----LRDLGK 243 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~----~r~~~~ 243 (275)
....|+.|+. .-|.|=.=.-| -.||-.|.-..+..|. .+.++|
T Consensus 2 ~N~~CaDC~~---~~p~w~s~~~G-ifvC~~CsgiHR~lg~his~VkSl~m 48 (112)
T smart00105 2 GNKKCFDCGA---PNPTWASVNLG-VFLCIECSGIHRSLGVHISKVRSLTL 48 (112)
T ss_pred CCCcccCCCC---CCCCcEEeccc-eeEhHHhHHHHHhcCCCcCeeeeccc
Confidence 3678999998 46999888888 6999999988887764 444444
No 33
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=38.56 E-value=11 Score=25.34 Aligned_cols=29 Identities=28% Similarity=0.762 Sum_probs=17.9
Q ss_pred cceeecccCCCCCceecCCCCCCccchhhhhHHH
Q 023942 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 233 (275)
Q Consensus 200 ~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~ 233 (275)
.|.+|+.+ . .--.--.| ..+|..||+-..
T Consensus 2 ~Cp~Cg~~--~--~~~D~~~g-~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSK--E--IVFDPERG-ELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSS--E--EEEETTTT-EEEETTT-BBEE
T ss_pred CCcCCcCC--c--eEEcCCCC-eEECCCCCCEee
Confidence 69999985 3 22222234 689999998543
No 34
>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=38.36 E-value=7.2 Score=24.78 Aligned_cols=28 Identities=29% Similarity=0.689 Sum_probs=15.3
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhhhH
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~ 231 (275)
.+.|..||.. +. ..+.|-...|.+||..
T Consensus 3 ~rfC~~CG~~--t~----~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAP--TK----PAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--B--EE----E-SSSS-EEESSSS-E
T ss_pred CcccCcCCcc--cc----CCCCcCEeECCCCcCE
Confidence 4679999986 22 2445667899999874
No 35
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=36.00 E-value=20 Score=26.55 Aligned_cols=30 Identities=23% Similarity=0.610 Sum_probs=22.4
Q ss_pred CCccceeecccCCCCCceecCCCCCCccc-hhhhhHHHhcC
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLC-NACGLFWANKG 236 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LC-NACGl~~~~~~ 236 (275)
+-+.|.+||.+ =|.. +..| ..|+.-|.++.
T Consensus 2 ~HkHC~~CG~~---------Ip~~-~~fCS~~C~~~~~k~q 32 (59)
T PF09889_consen 2 PHKHCPVCGKP---------IPPD-ESFCSPKCREEYRKRQ 32 (59)
T ss_pred CCCcCCcCCCc---------CCcc-hhhhCHHHHHHHHHHH
Confidence 34679999986 2233 6899 59999888764
No 36
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=34.73 E-value=21 Score=34.51 Aligned_cols=29 Identities=28% Similarity=0.629 Sum_probs=21.3
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
....|.+||+. .|+- -+.|..-+|-+||-
T Consensus 314 k~nfc~ncG~~--~t~~---~~ng~a~fcp~cgq 342 (345)
T COG4260 314 KLNFCLNCGCG--TTAD---FDNGKAKFCPECGQ 342 (345)
T ss_pred ccccccccCcc--cccC---CccchhhhChhhcC
Confidence 44578999976 6775 35566679999985
No 37
>PF15396 FAM60A: Protein Family FAM60A
Probab=34.46 E-value=22 Score=32.74 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=20.5
Q ss_pred ccchhhhhHHHhcCCCCCCCCCCCC
Q 023942 223 SLCNACGLFWANKGALRDLGKKMED 247 (275)
Q Consensus 223 ~LCNACGl~~~~~~~~r~~~~k~~~ 247 (275)
.+||||=|..++..+|++=+++.=.
T Consensus 50 eICNACVLLVKRwKKLP~Gs~rnW~ 74 (213)
T PF15396_consen 50 EICNACVLLVKRWKKLPPGSKRNWN 74 (213)
T ss_pred hhhHHHHHHHHHHhhCCCCcccchh
Confidence 6999999999998888777766543
No 38
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=33.55 E-value=26 Score=33.63 Aligned_cols=32 Identities=25% Similarity=0.620 Sum_probs=25.5
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhhHHHh
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 234 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~ 234 (275)
..|..|..+ .+.|--.-..+| +||+|--+-.+
T Consensus 2 ~~C~~C~~~-~t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMP-TTRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCC-CCCCCeeECCCC---CchhhhhHHhh
Confidence 479999998 567777777777 99999987643
No 39
>PRK11823 DNA repair protein RadA; Provisional
Probab=33.42 E-value=14 Score=36.80 Aligned_cols=25 Identities=28% Similarity=0.824 Sum_probs=16.8
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhH
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~ 231 (275)
...+|.+||. +++.|- --|.+||-+
T Consensus 6 ~~y~C~~Cg~---~~~~~~-------g~Cp~C~~w 30 (446)
T PRK11823 6 TAYVCQECGA---ESPKWL-------GRCPECGAW 30 (446)
T ss_pred CeEECCcCCC---CCcccC-------eeCcCCCCc
Confidence 4567999998 456652 258888764
No 40
>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=32.25 E-value=18 Score=23.44 Aligned_cols=28 Identities=25% Similarity=0.725 Sum_probs=18.7
Q ss_pred cceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 200 ~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
+|..||.. -..|..-.++....|-.||.
T Consensus 7 ~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 68889884 33444433355678999997
No 41
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=31.65 E-value=31 Score=34.26 Aligned_cols=31 Identities=26% Similarity=0.609 Sum_probs=25.3
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACG 229 (275)
....|+-||.+...+...-.||.. ..|+.|-
T Consensus 8 ~~~~CSFCGr~~~ev~~li~g~~~--~IC~~Ci 38 (412)
T PRK05342 8 KLLYCSFCGKSQHEVRKLIAGPGV--YICDECI 38 (412)
T ss_pred CccccCCCCCChhhccccccCCCC--cccchHH
Confidence 355899999997788888888854 7999994
No 42
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=31.38 E-value=31 Score=25.99 Aligned_cols=46 Identities=26% Similarity=0.676 Sum_probs=32.3
Q ss_pred CCccceeecccCCCCCce--e-cCCCCCCccchhhhhHHHhcCCCCCCCCC
Q 023942 197 SETSCTHCGISSKSTPMM--R-RGPSGPRSLCNACGLFWANKGALRDLGKK 244 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~W--R-rGp~G~~~LCNACGl~~~~~~~~r~~~~k 244 (275)
+...|..|..+ .|--- = -...-|+.+|-+|-.||-..|.+|.+...
T Consensus 4 ~~~~CPRC~S~--nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvg 52 (63)
T PF02701_consen 4 QPLPCPRCDST--NTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVG 52 (63)
T ss_pred cCCCCCCcCCC--CCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccC
Confidence 46678888876 33220 0 02234568999999999999999988653
No 43
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=31.28 E-value=18 Score=33.48 Aligned_cols=23 Identities=22% Similarity=0.707 Sum_probs=0.0
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACG 229 (275)
+.+.|.|||. .+..| ..+|..||
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 44
>PRK00420 hypothetical protein; Validated
Probab=31.17 E-value=23 Score=29.44 Aligned_cols=30 Identities=23% Similarity=0.707 Sum_probs=22.2
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhhhHHHh
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 234 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~ 234 (275)
...|..||+ |+.|- ..| +.+|-.||-.+..
T Consensus 23 ~~~CP~Cg~-----pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCGL-----PLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCCC-----cceec-CCC-ceECCCCCCeeee
Confidence 456999986 67774 345 6999999986553
No 45
>PF12773 DZR: Double zinc ribbon
Probab=30.71 E-value=30 Score=23.59 Aligned_cols=29 Identities=28% Similarity=0.752 Sum_probs=17.2
Q ss_pred CCCccceeecccCCCCCceecCCCCCCccchhhhhH
Q 023942 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (275)
Q Consensus 196 ~~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~ 231 (275)
.....|.+||+. .. .+......|..||-.
T Consensus 10 ~~~~fC~~CG~~--l~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 10 DDAKFCPHCGTP--LP-----PPDQSKKICPNCGAE 38 (50)
T ss_pred ccccCChhhcCC--hh-----hccCCCCCCcCCcCC
Confidence 346678888875 32 223334677777763
No 46
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=30.66 E-value=19 Score=34.41 Aligned_cols=32 Identities=28% Similarity=0.570 Sum_probs=22.3
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHHHh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 234 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~ 234 (275)
..+.|..||+. +.+. ..|-..+|+.||..+..
T Consensus 110 ~~RFCg~CG~~--~~~~----~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 110 SHRFCGRCGTK--TYPR----EGGWARVCPKCGHEHFP 141 (279)
T ss_pred hCcCCCCCCCc--Cccc----cCceeeeCCCCCCccCC
Confidence 46679999996 4332 34556899999986653
No 47
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.61 E-value=17 Score=28.60 Aligned_cols=35 Identities=26% Similarity=0.500 Sum_probs=23.8
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhhHHHhcC
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 236 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~ 236 (275)
-.|.+|+-.-..-..++..| -+-|.+||-.+++--
T Consensus 13 Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~l 47 (82)
T COG2331 13 YECTECGNRFDVVQAMTDDP---LTTCEECGARLKKLL 47 (82)
T ss_pred EeecccchHHHHHHhcccCc---cccChhhChHHHHhh
Confidence 47999998533334456555 458999999777653
No 48
>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=29.67 E-value=25 Score=30.96 Aligned_cols=16 Identities=31% Similarity=0.690 Sum_probs=11.1
Q ss_pred CCCCCCccchhhhhHH
Q 023942 217 GPSGPRSLCNACGLFW 232 (275)
Q Consensus 217 Gp~G~~~LCNACGl~~ 232 (275)
++.-....|+.||..|
T Consensus 63 ~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 63 GHYEAPSYCHNCGKPY 78 (158)
T ss_pred CCCCCChhHHhCCCCC
Confidence 4444567899999754
No 49
>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=29.60 E-value=8.5 Score=25.01 Aligned_cols=33 Identities=27% Similarity=0.690 Sum_probs=19.5
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhhHH
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~ 232 (275)
..|.+|++. -.-+....+..|....|-.||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 458888875 223333334455567888887643
No 50
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=29.56 E-value=19 Score=26.53 Aligned_cols=24 Identities=13% Similarity=0.101 Sum_probs=17.1
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHH
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~ 232 (275)
....|.+||.. . -++.+|. ||.|.
T Consensus 26 ~~~~c~~cg~~--~---------~pH~vc~-cG~Y~ 49 (60)
T PRK01110 26 TLSVDKTTGEY--H---------LPHHVSP-KGYYK 49 (60)
T ss_pred ceeEcCCCCce--e---------ccceecC-CcccC
Confidence 46679999985 2 2357899 99643
No 51
>KOG1007 consensus WD repeat protein TSSC1, WD repeat superfamily [Function unknown]
Probab=28.49 E-value=46 Score=32.50 Aligned_cols=53 Identities=21% Similarity=0.171 Sum_probs=30.6
Q ss_pred ccccCCccccccccCCCCCCCCCCCCCCCcceeEEeCCEEEEecCCChHHHHHHH
Q 023942 41 SALENGIVVVEDVAHDSGYATGGNELSNSSQLTLSFRGQVYVFDSVTPDKVQAVL 95 (275)
Q Consensus 41 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~QLTIfY~G~V~Vfd~V~~dKaq~Im 95 (275)
+|+||-... =+-.-|+||...=|..+.=-=-.++|+|+|.| ..||+.--..||
T Consensus 317 pL~dg~l~t-ydehEDSVY~~aWSsadPWiFASLSYDGRviI-s~V~r~~ky~i~ 369 (370)
T KOG1007|consen 317 PLQDGQLET-YDEHEDSVYALAWSSADPWIFASLSYDGRVII-SSVPRFLKYRIM 369 (370)
T ss_pred ccccccccc-ccccccceEEEeeccCCCeeEEEeccCceEEe-ecCChhhhhhhc
Confidence 455543222 24455677765422222222346899999999 678876655555
No 52
>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=28.34 E-value=22 Score=24.00 Aligned_cols=28 Identities=21% Similarity=0.579 Sum_probs=17.4
Q ss_pred cceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 200 ~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
+|..||.. --.++..-+.....|-+||-
T Consensus 7 ~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHE---FEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCE---EEEEEEcCCCCCCcCCCCCC
Confidence 68888863 33334433345678888886
No 53
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.59 E-value=29 Score=25.20 Aligned_cols=29 Identities=31% Similarity=0.681 Sum_probs=19.9
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhhhHH
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~ 232 (275)
...|..||..... ...+....|..||..+
T Consensus 28 Sq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc------ccccceEEcCCCCCEE
Confidence 4569999997222 3344458999999853
No 54
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=27.36 E-value=22 Score=34.84 Aligned_cols=22 Identities=36% Similarity=1.019 Sum_probs=13.9
Q ss_pred cceeecccCCCCCceecCCCCCCccchhhhhH
Q 023942 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (275)
Q Consensus 200 ~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~ 231 (275)
.|.+||. .+|.|- | -|.+||-+
T Consensus 2 ~c~~cg~---~~~~~~----g---~cp~c~~w 23 (372)
T cd01121 2 VCSECGY---VSPKWL----G---KCPECGEW 23 (372)
T ss_pred CCCCCCC---CCCCcc----E---ECcCCCCc
Confidence 5888887 455552 2 57777653
No 55
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=27.24 E-value=31 Score=34.98 Aligned_cols=40 Identities=25% Similarity=0.486 Sum_probs=33.7
Q ss_pred CCCCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcCCC
Q 023942 195 SPSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL 238 (275)
Q Consensus 195 ~~~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~~ 238 (275)
.+..++|+.|+. .-|-|-.=+.| -.||--|---.+.-|++
T Consensus 20 ~~~NKvCFDCgA---knPtWaSVTYG-IFLCiDCSAvHRnLGVH 59 (454)
T KOG0706|consen 20 QSENKVCFDCGA---KNPTWASVTYG-IFLCIDCSAVHRNLGVH 59 (454)
T ss_pred CCCCceecccCC---CCCCceeecce-EEEEEecchhhhccccc
Confidence 357889999999 69999999999 69999998866666654
No 56
>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=26.51 E-value=25 Score=24.53 Aligned_cols=10 Identities=40% Similarity=0.700 Sum_probs=8.7
Q ss_pred hhHHHHHHHH
Q 023942 130 PQRAASLDRF 139 (275)
Q Consensus 130 paRkASLqRF 139 (275)
-+|+++||||
T Consensus 34 ~aRkr~l~rf 43 (43)
T PF08114_consen 34 QARKRALQRF 43 (43)
T ss_pred HHHHHHHhcC
Confidence 4899999998
No 57
>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=26.13 E-value=35 Score=22.94 Aligned_cols=30 Identities=23% Similarity=0.547 Sum_probs=18.4
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhh
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACG 229 (275)
...|..|+-+ ..-.|..-.......|+.||
T Consensus 3 ~~pCP~CGG~--DrFr~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 3 HGPCPNCGGS--DRFRFDDKDGRGTWFCSVCG 32 (37)
T ss_pred ccCCCCCCCc--cccccccCCCCcCEEeCCCC
Confidence 3468888876 44445442222258899886
No 58
>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=25.87 E-value=28 Score=23.96 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=19.3
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
-+|..||.. --.|+.--+.....|-.||-
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHR---FEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCE---eEEEEecCCCCCCCCCCCCC
Confidence 368889873 44676533344567999986
No 59
>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=25.87 E-value=29 Score=23.45 Aligned_cols=32 Identities=25% Similarity=0.675 Sum_probs=20.7
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhhH
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~ 231 (275)
..|+=||.+....-..=.||.+ ...|+.|-..
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 5799999986666555588877 6899999764
No 60
>PRK05978 hypothetical protein; Provisional
Probab=25.34 E-value=29 Score=30.13 Aligned_cols=35 Identities=26% Similarity=0.544 Sum_probs=24.4
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcC
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 236 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~ 236 (275)
...+|-+||. -.+++ |--.-..-|.+||+.|..+.
T Consensus 32 l~grCP~CG~----G~LF~-g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 32 FRGRCPACGE----GKLFR-AFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred HcCcCCCCCC----Ccccc-cccccCCCccccCCccccCC
Confidence 3558999996 35555 33344678999999887653
No 61
>PRK12496 hypothetical protein; Provisional
Probab=25.31 E-value=36 Score=29.60 Aligned_cols=34 Identities=21% Similarity=0.365 Sum_probs=23.7
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcCCC
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL 238 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~~ 238 (275)
...+|..|+.. .+. ++.+ ..|.-||...+++...
T Consensus 126 w~~~C~gC~~~---~~~---~~~~--~~C~~CG~~~~r~~~~ 159 (164)
T PRK12496 126 WRKVCKGCKKK---YPE---DYPD--DVCEICGSPVKRKMVK 159 (164)
T ss_pred eeEECCCCCcc---ccC---CCCC--CcCCCCCChhhhcchh
Confidence 45789999974 332 3333 5899999988777553
No 62
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=25.31 E-value=27 Score=29.82 Aligned_cols=26 Identities=35% Similarity=1.036 Sum_probs=21.3
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
....|.-||+ |++| -+| ..+|--||.
T Consensus 27 L~~hCp~Cg~-----PLF~--KdG-~v~CPvC~~ 52 (131)
T COG1645 27 LAKHCPKCGT-----PLFR--KDG-EVFCPVCGY 52 (131)
T ss_pred HHhhCcccCC-----ccee--eCC-eEECCCCCc
Confidence 4557999986 7999 578 699999995
No 63
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.76 E-value=26 Score=29.71 Aligned_cols=35 Identities=26% Similarity=0.504 Sum_probs=23.0
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcC
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 236 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~ 236 (275)
...+|.+||-- =+.|.= --...-|.|||+-|-.+.
T Consensus 20 l~grCP~CGeG----rLF~gF-LK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 20 LRGRCPRCGEG----RLFRGF-LKVVPACEACGLDYGFAD 54 (126)
T ss_pred hcCCCCCCCCc----hhhhhh-cccCchhhhccccccCCc
Confidence 45689999963 233322 223478999999887664
No 64
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=24.39 E-value=33 Score=23.33 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=18.2
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhhHHH
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 233 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~ 233 (275)
-.|.+||.. . ...+......|..||-..-
T Consensus 4 y~C~~CG~~--~----~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGRE--V----ELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCE--E----EECCCCCceECCCCCCeEE
Confidence 469999985 2 1233332578999997444
No 65
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=24.38 E-value=42 Score=32.51 Aligned_cols=37 Identities=27% Similarity=0.535 Sum_probs=30.7
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcCC
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 237 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~ 237 (275)
....|..|+.+ . |.|=.=.-| -.||--|-=..|.-|+
T Consensus 19 ~Nk~CaDCga~--~-P~W~S~nlG-vfiCi~CagvHRsLGv 55 (319)
T COG5347 19 SNKKCADCGAP--N-PTWASVNLG-VFLCIDCAGVHRSLGV 55 (319)
T ss_pred ccCccccCCCC--C-CceEecccC-eEEEeecchhhhcccc
Confidence 46789999997 5 999999999 6999999876665553
No 66
>PF14122 YokU: YokU-like protein
Probab=23.70 E-value=28 Score=27.83 Aligned_cols=37 Identities=22% Similarity=0.714 Sum_probs=22.3
Q ss_pred ceeeccc---CCCCCceecCCCCC---------CccchhhhhHHHhcCC
Q 023942 201 CTHCGIS---SKSTPMMRRGPSGP---------RSLCNACGLFWANKGA 237 (275)
Q Consensus 201 C~~Cgtt---~~~Tp~WRrGp~G~---------~~LCNACGl~~~~~~~ 237 (275)
|..|+.. ...+.....=|+|. ...|+.||+-|....+
T Consensus 2 C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~d~v 50 (87)
T PF14122_consen 2 CEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQDDEV 50 (87)
T ss_pred cccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEehhHH
Confidence 7777763 11233333345554 3689999998876553
No 67
>PHA00626 hypothetical protein
Probab=23.13 E-value=31 Score=25.60 Aligned_cols=31 Identities=32% Similarity=0.694 Sum_probs=21.3
Q ss_pred cceeecccCCCCCcee----cCCCCCCccchhhhhHHHhc
Q 023942 200 SCTHCGISSKSTPMMR----RGPSGPRSLCNACGLFWANK 235 (275)
Q Consensus 200 ~C~~Cgtt~~~Tp~WR----rGp~G~~~LCNACGl~~~~~ 235 (275)
.|.+||.. -..| +++.. .+.|.-||.++-+.
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 58888873 1224 34555 69999999987654
No 68
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=22.57 E-value=43 Score=31.80 Aligned_cols=30 Identities=27% Similarity=0.679 Sum_probs=14.3
Q ss_pred CccceeecccCCCCCceecCCCCCCccchhhhhHH
Q 023942 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~ 232 (275)
...|.+||.+ ....- --.| .++|..||+-.
T Consensus 11 ~~~Cp~Cg~~---~iv~d-~~~G-e~vC~~CG~Vl 40 (310)
T PRK00423 11 KLVCPECGSD---KLIYD-YERG-EIVCADCGLVI 40 (310)
T ss_pred CCcCcCCCCC---CeeEE-CCCC-eEeecccCCcc
Confidence 3456666642 11122 2234 46666666643
No 69
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=22.39 E-value=56 Score=32.02 Aligned_cols=36 Identities=28% Similarity=0.549 Sum_probs=29.2
Q ss_pred CccceeecccCCCCCceecCC---CCCCccchhhhhHHH
Q 023942 198 ETSCTHCGISSKSTPMMRRGP---SGPRSLCNACGLFWA 233 (275)
Q Consensus 198 ~~~C~~Cgtt~~~Tp~WRrGp---~G~~~LCNACGl~~~ 233 (275)
...|..|..++-.|..|+-|| .-.++.|+.|+..-.
T Consensus 143 ~~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G~G~ 181 (337)
T KOG0712|consen 143 APKCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNGSGE 181 (337)
T ss_pred CCCCCCCCCCCceeEEEeccccccccceeEeccCCCccc
Confidence 347999999999999999999 455688999977433
No 70
>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=21.94 E-value=95 Score=20.24 Aligned_cols=22 Identities=18% Similarity=0.342 Sum_probs=18.0
Q ss_pred CcceeEEeCCEEEEecCCChHH
Q 023942 69 SSQLTLSFRGQVYVFDSVTPDK 90 (275)
Q Consensus 69 ~~QLTIfY~G~V~Vfd~V~~dK 90 (275)
...+++-|+|...++.+||+..
T Consensus 13 ~~~~~~~~~~~~~~i~~vp~~~ 34 (46)
T TIGR03831 13 TTTETYEYGGELIVIENVPALV 34 (46)
T ss_pred EEEEEEEeCCEEEEEeCCCccc
Confidence 3467888999999999999743
No 71
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=21.38 E-value=27 Score=30.17 Aligned_cols=39 Identities=44% Similarity=0.677 Sum_probs=34.0
Q ss_pred hHHHHHHHHHhhhhhhhcccchhhhhHHHHHHHhhhhcc
Q 023942 131 QRAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKG 169 (275)
Q Consensus 131 aRkASLqRFlEKRKeR~f~kk~pY~~rkeva~Rm~RekG 169 (275)
.|.+.+.|..++|+.|.|.++++|..++..++.+.+-++
T Consensus 292 ~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 292 QRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred hHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 889999999999999999999999999987777766554
No 72
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=20.70 E-value=66 Score=32.08 Aligned_cols=37 Identities=22% Similarity=0.451 Sum_probs=30.1
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhhHHHhcCC
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 237 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~~~~~ 237 (275)
....|..|+.. -|.|=.=..| -.||-.|.=..+.-|+
T Consensus 21 gNk~CaDCga~---nPtWASvn~G-IFLCl~CSGVHRsLGv 57 (395)
T PLN03114 21 DNKICFDCNAK---NPTWASVTYG-IFLCIDCSAVHRSLGV 57 (395)
T ss_pred CCCcCccCCCC---CCCceeeccc-eeehhhhhHhhccCCC
Confidence 46789999984 6999999999 6999999876665553
No 73
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.18 E-value=22 Score=26.85 Aligned_cols=33 Identities=24% Similarity=0.408 Sum_probs=23.2
Q ss_pred ccceeecccCCCCCceecCCCCCCccchhhhhHHH
Q 023942 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 233 (275)
Q Consensus 199 ~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl~~~ 233 (275)
..|..|.+. .|-+|.+-..-+..-|-+||-.-+
T Consensus 11 A~CP~C~~~--Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 11 AVCPACQAQ--DTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred CCCcccchh--hHHHHHHhcCCceEehhhcchHhh
Confidence 359999997 565544444444789999998553
No 74
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=20.03 E-value=29 Score=21.53 Aligned_cols=24 Identities=38% Similarity=0.888 Sum_probs=14.9
Q ss_pred CCccceeecccCCCCCceecCCCCCCccchhhhh
Q 023942 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (275)
Q Consensus 197 ~~~~C~~Cgtt~~~Tp~WRrGp~G~~~LCNACGl 230 (275)
..|.|..|... .+.. ..-|.+||-
T Consensus 3 g~W~C~~C~~~---------N~~~-~~~C~~C~~ 26 (30)
T PF00641_consen 3 GDWKCPSCTFM---------NPAS-RSKCVACGA 26 (30)
T ss_dssp SSEEETTTTEE---------EESS-SSB-TTT--
T ss_pred cCccCCCCcCC---------chHH-hhhhhCcCC
Confidence 36888888886 3333 478999885
Done!