Query 021193
Match_columns 316
No_of_seqs 217 out of 803
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:19:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021193.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021193hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.5 9.4E-15 2E-19 108.0 3.3 44 234-280 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 2.2E-14 4.7E-19 105.2 2.8 45 231-277 2-46 (52)
3 PF00320 GATA: GATA zinc finge 99.4 2.6E-14 5.7E-19 97.5 -0.5 35 235-269 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.1 6.2E-11 1.3E-15 103.4 4.2 71 232-302 199-303 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.8 1E-05 2.2E-10 82.9 2.1 54 232-287 158-215 (498)
6 KOG3554 Histone deacetylase co 82.4 1.1 2.4E-05 46.8 3.0 36 231-266 385-422 (693)
7 PRK14892 putative transcriptio 68.8 2.2 4.9E-05 35.6 0.9 35 231-266 20-54 (99)
8 PF14803 Nudix_N_2: Nudix N-te 66.1 1.5 3.3E-05 29.9 -0.5 30 233-262 1-30 (34)
9 PRK12286 rpmF 50S ribosomal pr 63.9 4.2 9.1E-05 30.7 1.4 25 230-263 25-49 (57)
10 COG5641 GAT1 GATA Zn-finger-co 62.6 4.6 0.0001 42.3 1.9 37 232-268 297-334 (498)
11 PRK03988 translation initiatio 55.4 3.1 6.7E-05 36.5 -0.6 30 233-263 103-132 (138)
12 TIGR00311 aIF-2beta translatio 53.6 3.5 7.7E-05 35.9 -0.5 31 233-264 98-128 (133)
13 PF01783 Ribosomal_L32p: Ribos 52.4 4.9 0.00011 29.9 0.1 24 232-265 26-49 (56)
14 smart00653 eIF2B_5 domain pres 49.8 4.2 9.2E-05 34.3 -0.6 29 233-262 81-109 (110)
15 KOG0909 Peptide:N-glycanase [P 49.0 8.5 0.00019 40.0 1.3 50 232-299 161-221 (500)
16 KOG3740 Uncharacterized conser 48.2 6.6 0.00014 42.3 0.3 41 229-269 459-502 (706)
17 PRK12336 translation initiatio 46.6 5.2 0.00011 36.8 -0.7 32 233-265 99-130 (201)
18 COG5347 GTPase-activating prot 45.7 7.7 0.00017 38.4 0.3 30 231-262 19-48 (319)
19 PRK13130 H/ACA RNA-protein com 44.0 26 0.00056 26.6 2.9 49 232-299 5-53 (56)
20 COG2816 NPY1 NTP pyrophosphohy 43.3 11 0.00024 36.8 1.0 30 232-265 111-140 (279)
21 PF05077 DUF678: Protein of un 41.9 14 0.00029 29.7 1.1 51 215-265 7-68 (74)
22 PF08271 TF_Zn_Ribbon: TFIIB z 41.8 7.1 0.00015 27.1 -0.4 30 234-266 2-31 (43)
23 COG3529 Predicted nucleic-acid 41.6 4.7 0.0001 31.4 -1.4 33 233-265 11-43 (66)
24 PF01873 eIF-5_eIF-2B: Domain 37.8 8.1 0.00018 33.3 -0.8 29 233-262 94-122 (125)
25 PF01412 ArfGap: Putative GTPa 36.4 18 0.0004 30.1 1.2 34 231-266 12-45 (116)
26 PF13717 zinc_ribbon_4: zinc-r 36.4 10 0.00022 25.9 -0.3 31 234-264 4-35 (36)
27 PLN03114 ADP-ribosylation fact 35.8 17 0.00036 37.1 0.9 45 231-277 21-66 (395)
28 smart00105 ArfGap Putative GTP 35.5 17 0.00038 30.1 0.9 45 232-278 3-48 (112)
29 PF07282 OrfB_Zn_ribbon: Putat 35.5 13 0.00029 27.7 0.2 31 231-265 27-57 (69)
30 PF09538 FYDLN_acid: Protein o 34.3 20 0.00044 30.2 1.1 14 252-265 7-20 (108)
31 PF01096 TFIIS_C: Transcriptio 32.5 7.3 0.00016 26.9 -1.5 32 234-265 2-39 (39)
32 TIGR01385 TFSII transcription 32.0 19 0.00042 35.2 0.7 37 229-265 255-297 (299)
33 PF05361 PP1_inhibitor: PKC-ac 30.2 18 0.00038 32.4 0.1 16 38-53 71-86 (144)
34 PF09297 zf-NADH-PPase: NADH p 29.1 11 0.00023 24.8 -1.1 29 232-264 3-31 (32)
35 PF06677 Auto_anti-p27: Sjogre 29.0 20 0.00044 25.4 0.2 25 232-261 17-41 (41)
36 PF02701 zf-Dof: Dof domain, z 28.8 53 0.0011 25.7 2.4 44 231-274 4-50 (63)
37 TIGR01031 rpmF_bact ribosomal 28.5 28 0.00061 26.0 0.9 26 230-265 24-49 (55)
38 PF04810 zf-Sec23_Sec24: Sec23 28.1 21 0.00046 24.7 0.2 32 232-263 2-33 (40)
39 PRK00420 hypothetical protein; 28.0 23 0.0005 30.2 0.4 30 232-266 23-52 (112)
40 PF12760 Zn_Tnp_IS1595: Transp 28.0 23 0.0005 24.9 0.4 27 233-262 19-45 (46)
41 PF09526 DUF2387: Probable met 28.0 13 0.00029 29.2 -0.9 33 233-265 9-41 (71)
42 COG4888 Uncharacterized Zn rib 27.9 21 0.00045 30.3 0.1 35 232-266 22-58 (104)
43 PF12773 DZR: Double zinc ribb 27.5 33 0.00072 24.0 1.1 30 231-265 11-40 (50)
44 TIGR00244 transcriptional regu 25.9 29 0.00064 31.1 0.7 32 234-265 2-39 (147)
45 PF13248 zf-ribbon_3: zinc-rib 25.7 34 0.00075 21.5 0.8 23 233-263 3-25 (26)
46 PF10083 DUF2321: Uncharacteri 25.5 42 0.0009 30.5 1.6 34 232-265 39-79 (158)
47 TIGR02098 MJ0042_CXXC MJ0042 f 24.8 15 0.00033 24.5 -1.0 33 233-265 3-36 (38)
48 PRK01110 rpmF 50S ribosomal pr 23.4 34 0.00073 26.0 0.5 23 231-263 26-48 (60)
49 PRK00241 nudC NADH pyrophospha 23.2 28 0.0006 33.0 0.0 31 231-265 98-128 (256)
50 COG5349 Uncharacterized protei 23.0 37 0.00079 29.8 0.7 33 232-267 21-53 (126)
51 smart00440 ZnF_C2C2 C2C2 Zinc 22.8 24 0.00053 24.5 -0.3 32 234-265 2-39 (40)
52 PHA02893 hypothetical protein; 22.6 39 0.00085 27.9 0.8 15 251-265 66-80 (88)
53 smart00778 Prim_Zn_Ribbon Zinc 22.5 42 0.00092 23.4 0.8 30 233-262 4-33 (37)
54 TIGR02443 conserved hypothetic 22.3 21 0.00046 27.5 -0.7 33 233-265 10-42 (59)
55 COG3952 Predicted membrane pro 22.0 29 0.00062 29.8 -0.1 18 246-265 77-94 (113)
56 KOG1598 Transcription initiati 21.3 43 0.00093 35.5 0.9 33 233-268 1-33 (521)
57 PF11781 RRN7: RNA polymerase 21.0 34 0.00073 23.5 0.1 25 233-262 9-33 (36)
58 PRK00464 nrdR transcriptional 20.2 39 0.00084 30.2 0.3 32 234-265 2-39 (154)
59 PF14122 YokU: YokU-like prote 20.0 32 0.0007 28.4 -0.2 33 234-266 1-47 (87)
No 1
>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=99.50 E-value=9.4e-15 Score=108.05 Aligned_cols=44 Identities=48% Similarity=0.965 Sum_probs=39.6
Q ss_pred ccccccccCCCcccCCCCCChhhhhhhhhhhhcCCCCCCCCCCCCCC
Q 021193 234 RCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKSGRLFPEYRPACSPT 280 (316)
Q Consensus 234 ~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~~~~lp~yrp~~spt 280 (316)
.|+||++++||+||+||.|..+||||||+||++++ .+||...+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~---~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG---VMRPLSKRK 44 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC---CCCCcccCc
Confidence 49999999999999999888999999999999887 777876654
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.47 E-value=2.2e-14 Score=105.15 Aligned_cols=45 Identities=53% Similarity=1.004 Sum_probs=38.7
Q ss_pred CCCccccccccCCCcccCCCCCChhhhhhhhhhhhcCCCCCCCCCCC
Q 021193 231 FQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKSGRLFPEYRPAC 277 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~~~~lp~yrp~~ 277 (316)
..+.|+||++++||+||+||.|..+||||||++|++++.+ +||..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~--~rp~~ 46 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL--KRPLS 46 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC--CCccc
Confidence 3578999999999999999999889999999999987643 45543
No 3
>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=99.40 E-value=2.6e-14 Score=97.50 Aligned_cols=35 Identities=60% Similarity=1.203 Sum_probs=28.2
Q ss_pred cccccccCCCcccCCCCCChhhhhhhhhhhhcCCC
Q 021193 235 CSHCQTQKTPQWRTGPLGPKTLCNACGVRYKSGRL 269 (316)
Q Consensus 235 C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~~~~ 269 (316)
|.||++++||+||+||.|..+|||+||++|++++.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999988899999999998764
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.10 E-value=6.2e-11 Score=103.39 Aligned_cols=71 Identities=63% Similarity=1.185 Sum_probs=63.5
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhhhhhhcC---CCCCCCCCCCCCC--------------ccccccch------
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKSG---RLFPEYRPACSPT--------------FSVDMHSN------ 288 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~~---~~lp~yrp~~spt--------------~~~~~hsn------ 288 (316)
...|.||+++.||+||+++.|++.+|||||++|+++ +.++.++.+..++ +....|.+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRNVSPKGSGAVKGRTFTKSLHSNSAQLLL 278 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccccCCCccccccCCCCCcccccchhhhhh
Confidence 589999999999999999999999999999999998 8899999988887 56666666
Q ss_pred -----------hhHHHHHHHHhhcc
Q 021193 289 -----------SHRKVLEMRRKKES 302 (316)
Q Consensus 289 -----------~h~kvle~r~qk~~ 302 (316)
.+.++.++++.++.
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~r~~~~ 303 (340)
T KOG1601|consen 279 APSKSEPPLLSSHQRVAEVRRYRES 303 (340)
T ss_pred hhcccCccccccchHHHHHhhccCc
Confidence 78899999998875
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.77 E-value=1e-05 Score=82.92 Aligned_cols=54 Identities=33% Similarity=0.580 Sum_probs=41.5
Q ss_pred CCccccccccCCCcccCCCCC----ChhhhhhhhhhhhcCCCCCCCCCCCCCCccccccc
Q 021193 232 QRRCSHCQTQKTPQWRTGPLG----PKTLCNACGVRYKSGRLFPEYRPACSPTFSVDMHS 287 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G----~~~LCNACGl~yk~~~~lp~yrp~~spt~~~~~hs 287 (316)
...|.||.+..||+|||+..+ .-+|||||||+|+-++..-+ |...++.+...|.
T Consensus 158 ~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~--P~t~ks~~~ks~~ 215 (498)
T COG5641 158 PHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRA--PISLKSDSIKSRS 215 (498)
T ss_pred cchhccccccCCccccccccccccCCccccccccccccccCCcCC--Ccccccccccccc
Confidence 459999999999999999993 38999999999997774433 6655554444443
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=82.37 E-value=1.1 Score=46.78 Aligned_cols=36 Identities=31% Similarity=0.612 Sum_probs=30.6
Q ss_pred CCCccccccccCCCcc--cCCCCCChhhhhhhhhhhhc
Q 021193 231 FQRRCSHCQTQKTPQW--RTGPLGPKTLCNACGVRYKS 266 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~W--R~GP~G~~~LCNACGl~yk~ 266 (316)
..+.|-+|++++.-+| .-+|.-...||-.|=++||+
T Consensus 385 ~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKK 422 (693)
T KOG3554|consen 385 DGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKK 422 (693)
T ss_pred CCCcccccccccccceeccCCCCccchhhHHHHHHHHH
Confidence 3689999999999999 44555666799999999997
No 7
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=68.82 E-value=2.2 Score=35.55 Aligned_cols=35 Identities=14% Similarity=0.245 Sum_probs=23.0
Q ss_pred CCCccccccccCCCcccCCCCCChhhhhhhhhhhhc
Q 021193 231 FQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKS 266 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~ 266 (316)
..-.|.+|+.. +-.-..+-...+..|..||.||..
T Consensus 20 t~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKV-SISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCe-EeeeecCCCcceEECCCCCCccCE
Confidence 34679999953 322222223558899999999874
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=66.12 E-value=1.5 Score=29.92 Aligned_cols=30 Identities=23% Similarity=0.581 Sum_probs=15.8
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGV 262 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl 262 (316)
+.|.+||..-+-.--.|..-....|.+||.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 469999988543334566677789999984
No 9
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=63.86 E-value=4.2 Score=30.68 Aligned_cols=25 Identities=28% Similarity=0.683 Sum_probs=19.7
Q ss_pred CCCCccccccccCCCcccCCCCCChhhhhhhhhh
Q 021193 230 LFQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVR 263 (316)
Q Consensus 230 ~~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~ 263 (316)
...-.|.+||...-| +.+|..||.|
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcC
Confidence 345789999987655 7899999954
No 10
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=62.59 E-value=4.6 Score=42.26 Aligned_cols=37 Identities=30% Similarity=0.434 Sum_probs=30.5
Q ss_pred CCccccccc-cCCCcccCCCCCChhhhhhhhhhhhcCC
Q 021193 232 QRRCSHCQT-QKTPQWRTGPLGPKTLCNACGVRYKSGR 268 (316)
Q Consensus 232 ~r~C~~Cgt-~~TP~WR~GP~G~~~LCNACGl~yk~~~ 268 (316)
...|.+|++ +.||.||+...-..++||+||++.+..+
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~ 334 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPG 334 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcc
Confidence 467888887 6799999888777899999999988644
No 11
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=55.41 E-value=3.1 Score=36.49 Aligned_cols=30 Identities=27% Similarity=0.602 Sum_probs=23.2
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGVR 263 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~ 263 (316)
-.|..|+..+|-.=+.+-.= -.-|+|||-.
T Consensus 103 VlC~~C~spdT~l~k~~r~~-~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIW-VLKCEACGAE 132 (138)
T ss_pred EECCCCCCCCcEEEEcCCeE-EEEcccCCCC
Confidence 57999999999998753321 4589999964
No 12
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=53.65 E-value=3.5 Score=35.91 Aligned_cols=31 Identities=26% Similarity=0.603 Sum_probs=23.4
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGVRY 264 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~y 264 (316)
-.|..|+..+|-.-+.+.. --.-|+|||-..
T Consensus 98 VlC~~C~sPdT~l~k~~r~-~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRV-SLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEEeCCe-EEEecccCCCCC
Confidence 5799999999998875332 134899999643
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=52.42 E-value=4.9 Score=29.86 Aligned_cols=24 Identities=38% Similarity=0.971 Sum_probs=17.5
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
.-.|.+||... -++.+|.+|| +|+
T Consensus 26 l~~c~~cg~~~---------~~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 26 LVKCPNCGEPK---------LPHRVCPSCG-YYK 49 (56)
T ss_dssp EEESSSSSSEE---------STTSBCTTTB-BSS
T ss_pred eeeeccCCCEe---------cccEeeCCCC-eEC
Confidence 36799999643 3378999999 554
No 14
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=49.82 E-value=4.2 Score=34.31 Aligned_cols=29 Identities=28% Similarity=0.532 Sum_probs=22.3
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGV 262 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl 262 (316)
-.|..|+..+|-.=+.+..= -.-|+|||-
T Consensus 81 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeE-EEEccccCC
Confidence 57999999999998873211 346999995
No 15
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=49.04 E-value=8.5 Score=40.02 Aligned_cols=50 Identities=28% Similarity=0.553 Sum_probs=33.7
Q ss_pred CCccccccccC-CCcccCCCCCCh----------hhhhhhhhhhhcCCCCCCCCCCCCCCccccccchhhHHHHHHHHh
Q 021193 232 QRRCSHCQTQK-TPQWRTGPLGPK----------TLCNACGVRYKSGRLFPEYRPACSPTFSVDMHSNSHRKVLEMRRK 299 (316)
Q Consensus 232 ~r~C~~Cgt~~-TP~WR~GP~G~~----------~LCNACGl~yk~~~~lp~yrp~~spt~~~~~hsn~h~kvle~r~q 299 (316)
.-.|.+||... ++.=+.+|.+.. +.||+||.--+ +|+ .|...|.|+.|+-
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R----FPR--------------YNdp~kLLeTRkG 221 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR----FPR--------------YNDPIKLLETRKG 221 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc----Ccc--------------cCCHHHHHhhccC
Confidence 36799999987 554444554433 68999997555 233 4667888887753
No 16
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.18 E-value=6.6 Score=42.32 Aligned_cols=41 Identities=22% Similarity=0.534 Sum_probs=32.8
Q ss_pred CCCCCccccccccCCCcccCCCCC---ChhhhhhhhhhhhcCCC
Q 021193 229 GLFQRRCSHCQTQKTPQWRTGPLG---PKTLCNACGVRYKSGRL 269 (316)
Q Consensus 229 ~~~~r~C~~Cgt~~TP~WR~GP~G---~~~LCNACGl~yk~~~~ 269 (316)
.++...|..|.+.-||.|+.-+.+ .+.+|.+|-.-..++.+
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqkkAl 502 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQKKAL 502 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhhhcccccc
Confidence 456789999999999999988777 46799999876555443
No 17
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=46.56 E-value=5.2 Score=36.80 Aligned_cols=32 Identities=25% Similarity=0.453 Sum_probs=24.5
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
-.|..|+..+|-.-+.+..= -.-|+|||-..-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~-~l~C~aCGa~~~ 130 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVL-MLRCDACGAHRP 130 (201)
T ss_pred EECCCCCCCCcEEEEcCCeE-EEEcccCCCCcc
Confidence 57999999999998764211 348999998654
No 18
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=45.73 E-value=7.7 Score=38.42 Aligned_cols=30 Identities=30% Similarity=0.825 Sum_probs=27.4
Q ss_pred CCCccccccccCCCcccCCCCCChhhhhhhhh
Q 021193 231 FQRRCSHCQTQKTPQWRTGPLGPKTLCNACGV 262 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl 262 (316)
+.+.|..||... |+|-.=..| -.||--|.-
T Consensus 19 ~Nk~CaDCga~~-P~W~S~nlG-vfiCi~Cag 48 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVNLG-VFLCIDCAG 48 (319)
T ss_pred ccCccccCCCCC-CceEecccC-eEEEeecch
Confidence 468999999999 999999999 999999954
No 19
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=43.96 E-value=26 Score=26.58 Aligned_cols=49 Identities=33% Similarity=0.646 Sum_probs=33.7
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhhhhhhcCCCCCCCCCCCCCCccccccchhhHHHHHHHHh
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKSGRLFPEYRPACSPTFSVDMHSNSHRKVLEMRRK 299 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~~~~lp~yrp~~spt~~~~~hsn~h~kvle~r~q 299 (316)
.+.|..||+-.- +..|-.||.... .+..|.|+.+-..-.+|-.|+.|..
T Consensus 5 mr~C~~CgvYTL----------k~~CP~CG~~t~---------~~~P~rfSp~D~y~~yR~~~kk~~~ 53 (56)
T PRK13130 5 IRKCPKCGVYTL----------KEICPVCGGKTK---------NPHPPRFSPEDKYGKYRRALKKRRK 53 (56)
T ss_pred ceECCCCCCEEc----------cccCcCCCCCCC---------CCCCCCCCCCCccHHHHHHHHHHhh
Confidence 467888887654 457888886543 4555678877777788877766543
No 20
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=43.31 E-value=11 Score=36.83 Aligned_cols=30 Identities=30% Similarity=0.624 Sum_probs=24.0
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
.|.|.+||+...+. ..|-+.+|+.||.++.
T Consensus 111 ~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 111 HRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred CcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 48999999988764 3456789999998765
No 21
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=41.89 E-value=14 Score=29.71 Aligned_cols=51 Identities=27% Similarity=0.532 Sum_probs=27.3
Q ss_pred hhhccCCCCccCCCC-CCCCcccccccc--------C--CCcccCCCCCChhhhhhhhhhhh
Q 021193 215 AKKLKKKPAVQSGGG-LFQRRCSHCQTQ--------K--TPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 215 ~Kk~kkk~~~~~~~~-~~~r~C~~Cgt~--------~--TP~WR~GP~G~~~LCNACGl~yk 265 (316)
.||+|||++-..... ..-..|+-|... + +-..+-.+.|...-|-|||--+.
T Consensus 7 ~Krrkrk~~t~v~~~~d~c~tCSsC~SkLV~~Sdvtk~sl~~~~~~g~~~tLsCsACGS~L~ 68 (74)
T PF05077_consen 7 KKRRKRKPKTTVDDEEDDCTTCSSCQSKLVKFSDVTKVSLDEYKVAGKGNTLSCSACGSELR 68 (74)
T ss_pred chhcccCCCceeecCCCCccchhhhhhheeeeecccceehhhhcccCCCCeEeehhccccce
Confidence 345555665322111 223667777653 1 22344444465668999998665
No 22
>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=41.80 E-value=7.1 Score=27.15 Aligned_cols=30 Identities=20% Similarity=0.707 Sum_probs=17.8
Q ss_pred ccccccccCCCcccCCCCCChhhhhhhhhhhhc
Q 021193 234 RCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKS 266 (316)
Q Consensus 234 ~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~ 266 (316)
+|.+||... -.+ .--.| ...|..||+-..-
T Consensus 2 ~Cp~Cg~~~-~~~-D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE-IVF-DPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE-EEE-ETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCc-eEE-cCCCC-eEECCCCCCEeec
Confidence 588888866 222 22334 6789999876553
No 23
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=41.63 E-value=4.7 Score=31.41 Aligned_cols=33 Identities=24% Similarity=0.389 Sum_probs=26.9
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
-.|..|.+.+|-+|.+-..-...-|.+||-.-+
T Consensus 11 A~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 11 AVCPACQAQDTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred CCCcccchhhHHHHHHhcCCceEehhhcchHhh
Confidence 579999999998876655555889999998664
No 24
>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=37.77 E-value=8.1 Score=33.28 Aligned_cols=29 Identities=31% Similarity=0.610 Sum_probs=23.5
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGV 262 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl 262 (316)
-.|..|+..+|-.=+.+..- -.-|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccCC
Confidence 56999999999998874443 568999995
No 25
>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=36.43 E-value=18 Score=30.05 Aligned_cols=34 Identities=26% Similarity=0.609 Sum_probs=24.2
Q ss_pred CCCccccccccCCCcccCCCCCChhhhhhhhhhhhc
Q 021193 231 FQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKS 266 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~ 266 (316)
+.+.|..||... |.|-.=..| -.||-.|.-..+.
T Consensus 12 ~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~ 45 (116)
T PF01412_consen 12 GNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRS 45 (116)
T ss_dssp TCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHH
T ss_pred CcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHH
Confidence 458999999655 599999999 8999999987775
No 26
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=36.43 E-value=10 Score=25.92 Aligned_cols=31 Identities=29% Similarity=0.748 Sum_probs=22.9
Q ss_pred cccccccc-CCCcccCCCCCChhhhhhhhhhh
Q 021193 234 RCSHCQTQ-KTPQWRTGPLGPKTLCNACGVRY 264 (316)
Q Consensus 234 ~C~~Cgt~-~TP~WR~GP~G~~~LCNACGl~y 264 (316)
.|-+|++. .-+..+-.+.|....|-.||-.|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 57888877 46667777777777888888655
No 27
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=35.76 E-value=17 Score=37.11 Aligned_cols=45 Identities=24% Similarity=0.524 Sum_probs=32.4
Q ss_pred CCCccccccccCCCcccCCCCCChhhhhhhhhhhhc-CCCCCCCCCCC
Q 021193 231 FQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKS-GRLFPEYRPAC 277 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~-~~~lp~yrp~~ 277 (316)
++++|..|+... |+|-.=..| ..||..|.=.-+. |-.+...|...
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGvHISfVRSlt 66 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGVHISFVRSTN 66 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCCCCceeeccc
Confidence 358999999875 999999999 8999999655543 33334444443
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=35.54 E-value=17 Score=30.07 Aligned_cols=45 Identities=24% Similarity=0.508 Sum_probs=32.8
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhhhhhhcCC-CCCCCCCCCC
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKSGR-LFPEYRPACS 278 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~~~-~lp~yrp~~s 278 (316)
.+.|..|+. .-|+|-.=..| -.||-.|.-.-+.-+ .+...|....
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~lg~his~VkSl~m 48 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSLGVHISKVRSLTL 48 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhcCCCcCeeeeccc
Confidence 579999998 55999998899 899999987666532 2233444433
No 29
>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=35.48 E-value=13 Score=27.67 Aligned_cols=31 Identities=19% Similarity=0.533 Sum_probs=23.5
Q ss_pred CCCccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 231 FQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
....|..||....- ...+....|..||..+.
T Consensus 27 TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 45789999988655 44555789999998754
No 30
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=34.35 E-value=20 Score=30.22 Aligned_cols=14 Identities=36% Similarity=1.047 Sum_probs=6.6
Q ss_pred CChhhhhhhhhhhh
Q 021193 252 GPKTLCNACGVRYK 265 (316)
Q Consensus 252 G~~~LCNACGl~yk 265 (316)
|.|-+|..||.+|-
T Consensus 7 GtKR~Cp~CG~kFY 20 (108)
T PF09538_consen 7 GTKRTCPSCGAKFY 20 (108)
T ss_pred CCcccCCCCcchhc
Confidence 44445555554443
No 31
>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=32.51 E-value=7.3 Score=26.94 Aligned_cols=32 Identities=25% Similarity=0.641 Sum_probs=19.4
Q ss_pred ccccccccCCC----cccCCCCCCh--hhhhhhhhhhh
Q 021193 234 RCSHCQTQKTP----QWRTGPLGPK--TLCNACGVRYK 265 (316)
Q Consensus 234 ~C~~Cgt~~TP----~WR~GP~G~~--~LCNACGl~yk 265 (316)
.|..||..++- |=|.+.++.. +.|..||-+|+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 47888887643 3366666633 38999998774
No 32
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=32.02 E-value=19 Score=35.24 Aligned_cols=37 Identities=24% Similarity=0.478 Sum_probs=25.9
Q ss_pred CCCCCccccccccCCCcc----cCCCCCC--hhhhhhhhhhhh
Q 021193 229 GLFQRRCSHCQTQKTPQW----RTGPLGP--KTLCNACGVRYK 265 (316)
Q Consensus 229 ~~~~r~C~~Cgt~~TP~W----R~GP~G~--~~LCNACGl~yk 265 (316)
.+....|.+|+-.+.-.| |.+.++- -+.|..||-+|+
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 345689999998876555 4443331 238999999997
No 33
>PF05361 PP1_inhibitor: PKC-activated protein phosphatase-1 inhibitor; InterPro: IPR008025 Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction [].; GO: 0042325 regulation of phosphorylation, 0005737 cytoplasm; PDB: 2RLT_A 1J2M_A 1K5O_A 1J2N_A.
Probab=30.19 E-value=18 Score=32.38 Aligned_cols=16 Identities=31% Similarity=0.750 Sum_probs=13.4
Q ss_pred CCCcccccccCCCCCC
Q 021193 38 NEDFSVDDLLDFSNGD 53 (316)
Q Consensus 38 ~ddF~VDDLLDfsn~~ 53 (316)
.+++-||||||+++++
T Consensus 71 p~EIDIDeLLDl~sde 86 (144)
T PF05361_consen 71 PEEIDIDELLDLESDE 86 (144)
T ss_dssp -SSSHHHHHHCTSSTT
T ss_pred CCcccHHHHhcCCchH
Confidence 4578999999999987
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=29.14 E-value=11 Score=24.80 Aligned_cols=29 Identities=28% Similarity=0.565 Sum_probs=16.0
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhhhhh
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRY 264 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~y 264 (316)
.+.|..||....+.. .|....|.+||..+
T Consensus 3 ~rfC~~CG~~t~~~~----~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAP----GGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-S----SSS-EEESSSS-EE
T ss_pred CcccCcCCccccCCC----CcCEeECCCCcCEe
Confidence 378999998765442 35567899998753
No 35
>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=28.99 E-value=20 Score=25.42 Aligned_cols=25 Identities=40% Similarity=0.933 Sum_probs=19.3
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhh
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACG 261 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACG 261 (316)
...|..| .+|+.| ...| +..|-+|+
T Consensus 17 ~~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 4678889 589999 3456 78999996
No 36
>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=28.76 E-value=53 Score=25.68 Aligned_cols=44 Identities=16% Similarity=0.394 Sum_probs=33.4
Q ss_pred CCCccccccccCCCcc---cCCCCCChhhhhhhhhhhhcCCCCCCCC
Q 021193 231 FQRRCSHCQTQKTPQW---RTGPLGPKTLCNACGVRYKSGRLFPEYR 274 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~W---R~GP~G~~~LCNACGl~yk~~~~lp~yr 274 (316)
+...|..|.+.+|--= --...-|.+.|-+|..+|-.|+.|....
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVP 50 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVP 50 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCc
Confidence 3578999999988652 2233456789999999999999776663
No 37
>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=28.48 E-value=28 Score=26.01 Aligned_cols=26 Identities=35% Similarity=0.788 Sum_probs=18.8
Q ss_pred CCCCccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 230 LFQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 230 ~~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
...-.|.+||...- ++.+|-.|| +|+
T Consensus 24 p~l~~C~~cG~~~~---------~H~vc~~cG-~Y~ 49 (55)
T TIGR01031 24 PTLVVCPNCGEFKL---------PHRVCPSCG-YYK 49 (55)
T ss_pred CcceECCCCCCccc---------CeeECCccC-eEC
Confidence 34567999997543 478999999 444
No 38
>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=28.11 E-value=21 Score=24.68 Aligned_cols=32 Identities=28% Similarity=0.648 Sum_probs=20.6
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhhhh
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACGVR 263 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~ 263 (316)
..+|.+|++---|.-+-...|..-.||-|+..
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 46899999998888777778877799999874
No 39
>PRK00420 hypothetical protein; Validated
Probab=28.04 E-value=23 Score=30.25 Aligned_cols=30 Identities=23% Similarity=0.593 Sum_probs=23.5
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhhhhhhc
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKS 266 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~ 266 (316)
...|..|| +|..|- ..| +..|-+||..+..
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeeee
Confidence 46799998 678774 456 8899999998774
No 40
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=28.00 E-value=23 Score=24.94 Aligned_cols=27 Identities=26% Similarity=0.540 Sum_probs=19.6
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGV 262 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl 262 (316)
-.|.+||.+ ..-|.++ .+ ...|++|+-
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RG-RYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CC-eEECCCCCC
Confidence 569999998 5555554 33 789999974
No 41
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=27.97 E-value=13 Score=29.19 Aligned_cols=33 Identities=21% Similarity=0.321 Sum_probs=27.1
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
-.|-.|+..+|-+|.+...-...-|-+||-.-.
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 579999999998876655566789999997665
No 42
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=27.86 E-value=21 Score=30.33 Aligned_cols=35 Identities=17% Similarity=0.507 Sum_probs=24.7
Q ss_pred CCccccccccCCCc--ccCCCCCChhhhhhhhhhhhc
Q 021193 232 QRRCSHCQTQKTPQ--WRTGPLGPKTLCNACGVRYKS 266 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~--WR~GP~G~~~LCNACGl~yk~ 266 (316)
.-.|.+|+..+..+ -.++-.+.-..|-.||++|.-
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceEEE
Confidence 35799999876442 344444446799999999873
No 43
>PF12773 DZR: Double zinc ribbon
Probab=27.50 E-value=33 Score=24.00 Aligned_cols=30 Identities=30% Similarity=0.644 Sum_probs=21.0
Q ss_pred CCCccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 231 FQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
..+.|.+||+.-. ........|..||-.+.
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENP 40 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCc
Confidence 3578999988876 33444568888887644
No 44
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=25.89 E-value=29 Score=31.06 Aligned_cols=32 Identities=28% Similarity=0.557 Sum_probs=23.6
Q ss_pred ccccccccCCCcc--cCCCCCCh----hhhhhhhhhhh
Q 021193 234 RCSHCQTQKTPQW--RTGPLGPK----TLCNACGVRYK 265 (316)
Q Consensus 234 ~C~~Cgt~~TP~W--R~GP~G~~----~LCNACGl~yk 265 (316)
+|..|+..+|-.- |...+|.. -.|.+||-+|-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 5888998888775 55555532 48999998886
No 45
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=25.74 E-value=34 Score=21.53 Aligned_cols=23 Identities=26% Similarity=0.873 Sum_probs=13.3
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGVR 263 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~ 263 (316)
+.|.+||....+. ...|-.||..
T Consensus 3 ~~Cp~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc--------cccChhhCCC
Confidence 4677777754322 4466667653
No 46
>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=25.52 E-value=42 Score=30.49 Aligned_cols=34 Identities=24% Similarity=0.662 Sum_probs=23.8
Q ss_pred CCccccccccCCCcccC-------CCCCChhhhhhhhhhhh
Q 021193 232 QRRCSHCQTQKTPQWRT-------GPLGPKTLCNACGVRYK 265 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~-------GP~G~~~LCNACGl~yk 265 (316)
...|.+|++..--.|-- ++.-...-|+.||..|-
T Consensus 39 I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 39 ITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 36788888876555533 44445679999999874
No 47
>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=24.84 E-value=15 Score=24.50 Aligned_cols=33 Identities=27% Similarity=0.587 Sum_probs=19.9
Q ss_pred CccccccccC-CCcccCCCCCChhhhhhhhhhhh
Q 021193 233 RRCSHCQTQK-TPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 233 r~C~~Cgt~~-TP~WR~GP~G~~~LCNACGl~yk 265 (316)
..|.||++.. -+..+-+..|....|-.||..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 3578888753 23344444555677888876553
No 48
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=23.36 E-value=34 Score=26.03 Aligned_cols=23 Identities=9% Similarity=-0.050 Sum_probs=16.7
Q ss_pred CCCccccccccCCCcccCCCCCChhhhhhhhhh
Q 021193 231 FQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVR 263 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~ 263 (316)
..-.|.+||...-| +.+|. ||.|
T Consensus 26 ~~~~c~~cg~~~~p---------H~vc~-cG~Y 48 (60)
T PRK01110 26 TLSVDKTTGEYHLP---------HHVSP-KGYY 48 (60)
T ss_pred ceeEcCCCCceecc---------ceecC-Cccc
Confidence 35689999986644 56799 9954
No 49
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=23.19 E-value=28 Score=33.05 Aligned_cols=31 Identities=29% Similarity=0.536 Sum_probs=22.0
Q ss_pred CCCccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 231 FQRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 231 ~~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
..+.|.+||...... ..|....|.+||..+-
T Consensus 98 ~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 98 SHRFCGYCGHPMHPS----KTEWAMLCPHCRERYY 128 (256)
T ss_pred cCccccccCCCCeec----CCceeEECCCCCCEEC
Confidence 348999999975442 3455678999996543
No 50
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.03 E-value=37 Score=29.79 Aligned_cols=33 Identities=30% Similarity=0.663 Sum_probs=22.3
Q ss_pred CCccccccccCCCcccCCCCCChhhhhhhhhhhhcC
Q 021193 232 QRRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKSG 267 (316)
Q Consensus 232 ~r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~~ 267 (316)
..+|-|||--+ -=+|=.-...-|.|||+.|-.+
T Consensus 21 ~grCP~CGeGr---LF~gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 21 RGRCPRCGEGR---LFRGFLKVVPACEACGLDYGFA 53 (126)
T ss_pred cCCCCCCCCch---hhhhhcccCchhhhccccccCC
Confidence 36899999643 1223333456899999999853
No 51
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=22.77 E-value=24 Score=24.49 Aligned_cols=32 Identities=22% Similarity=0.608 Sum_probs=20.8
Q ss_pred ccccccccCCCc----ccCCCCCCh--hhhhhhhhhhh
Q 021193 234 RCSHCQTQKTPQ----WRTGPLGPK--TLCNACGVRYK 265 (316)
Q Consensus 234 ~C~~Cgt~~TP~----WR~GP~G~~--~LCNACGl~yk 265 (316)
.|.+||-.+.-- =|.+.+|.. +.|..||-+|+
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 588888665333 355555532 48999998775
No 52
>PHA02893 hypothetical protein; Provisional
Probab=22.61 E-value=39 Score=27.88 Aligned_cols=15 Identities=27% Similarity=0.490 Sum_probs=11.1
Q ss_pred CCChhhhhhhhhhhh
Q 021193 251 LGPKTLCNACGVRYK 265 (316)
Q Consensus 251 ~G~~~LCNACGl~yk 265 (316)
.|...-|-|||--+.
T Consensus 66 ~~~tL~CaACGS~L~ 80 (88)
T PHA02893 66 SNSNIKCIACGSSLC 80 (88)
T ss_pred CCCceeehhhchhhh
Confidence 355668999998665
No 53
>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=22.47 E-value=42 Score=23.37 Aligned_cols=30 Identities=17% Similarity=0.474 Sum_probs=20.6
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGV 262 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl 262 (316)
..|-.|+....=.|......-...||.||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 468999988776675432222679999974
No 54
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=22.29 E-value=21 Score=27.47 Aligned_cols=33 Identities=21% Similarity=0.340 Sum_probs=25.4
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk 265 (316)
-.|-.|+..+|-+|.+...-...-|-.||-.-.
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~ 42 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQEQ 42 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCccc
Confidence 579999999988765544444789999997654
No 55
>COG3952 Predicted membrane protein [Function unknown]
Probab=21.97 E-value=29 Score=29.85 Aligned_cols=18 Identities=33% Similarity=0.490 Sum_probs=13.6
Q ss_pred ccCCCCCChhhhhhhhhhhh
Q 021193 246 WRTGPLGPKTLCNACGVRYK 265 (316)
Q Consensus 246 WR~GP~G~~~LCNACGl~yk 265 (316)
||.+|-+ .||++||++-.
T Consensus 77 ~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 77 RRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HhcchHH--HHHHhhhHHHH
Confidence 5666655 79999999754
No 56
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=21.27 E-value=43 Score=35.54 Aligned_cols=33 Identities=24% Similarity=0.591 Sum_probs=22.0
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhhhhhcCC
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGVRYKSGR 268 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl~yk~~~ 268 (316)
..|.|||.+.= . |+--.| ...|++||.-.-...
T Consensus 1 ~~C~~C~~s~f-e-~d~a~g-~~~C~~CG~v~E~~~ 33 (521)
T KOG1598|consen 1 MVCKNCGGSNF-E-RDEATG-NLYCTACGTVLEYNN 33 (521)
T ss_pred CcCCCCCCCCc-c-cccccC-Cceeccccceeeccc
Confidence 36999998642 1 222345 789999998765433
No 57
>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=21.04 E-value=34 Score=23.52 Aligned_cols=25 Identities=28% Similarity=0.777 Sum_probs=19.5
Q ss_pred CccccccccCCCcccCCCCCChhhhhhhhh
Q 021193 233 RRCSHCQTQKTPQWRTGPLGPKTLCNACGV 262 (316)
Q Consensus 233 r~C~~Cgt~~TP~WR~GP~G~~~LCNACGl 262 (316)
..|..|+.. |-...+| ...|..||-
T Consensus 9 ~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 459999877 6666678 889999985
No 58
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=20.16 E-value=39 Score=30.19 Aligned_cols=32 Identities=31% Similarity=0.663 Sum_probs=21.5
Q ss_pred ccccccccCCCcccCC--CCC----Chhhhhhhhhhhh
Q 021193 234 RCSHCQTQKTPQWRTG--PLG----PKTLCNACGVRYK 265 (316)
Q Consensus 234 ~C~~Cgt~~TP~WR~G--P~G----~~~LCNACGl~yk 265 (316)
.|.+||...|-.--.- +.| ...-|.+||-+|.
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence 5999998877653221 123 1268999999886
No 59
>PF14122 YokU: YokU-like protein
Probab=20.03 E-value=32 Score=28.38 Aligned_cols=33 Identities=24% Similarity=0.791 Sum_probs=21.9
Q ss_pred ccccccccC-----CCcccCCCCCC---------hhhhhhhhhhhhc
Q 021193 234 RCSHCQTQK-----TPQWRTGPLGP---------KTLCNACGVRYKS 266 (316)
Q Consensus 234 ~C~~Cgt~~-----TP~WR~GP~G~---------~~LCNACGl~yk~ 266 (316)
.|..|+..+ +.....-|+|. ...|+.||+-|..
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvYq~ 47 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVYQD 47 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEEeh
Confidence 388898864 23333345554 3589999998874
Done!