Query 027800
Match_columns 218
No_of_seqs 166 out of 656
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 15:23:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027800.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027800hhsearch_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 3E-15 6.5E-20 105.4 1.9 35 170-204 1-35 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 4.7E-15 1E-19 103.4 1.7 39 167-205 2-40 (52)
3 PF00320 GATA: GATA zinc finge 99.5 2E-15 4.4E-20 98.2 -0.6 34 171-204 1-34 (36)
4 KOG1601 GATA-4/5/6 transcripti 98.9 9.1E-10 2E-14 88.1 1.8 37 168-204 199-235 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.9 5.9E-06 1.3E-10 80.2 2.3 38 165-202 155-196 (498)
6 KOG3554 Histone deacetylase co 87.9 0.37 7.9E-06 48.2 2.5 38 168-205 386-425 (693)
7 COG5347 GTPase-activating prot 83.7 0.56 1.2E-05 43.8 1.4 42 167-210 19-60 (319)
8 PF14803 Nudix_N_2: Nudix N-te 76.8 0.76 1.6E-05 30.1 -0.1 30 169-198 1-30 (34)
9 COG5641 GAT1 GATA Zn-finger-co 74.6 1.6 3.6E-05 43.1 1.5 38 168-205 297-335 (498)
10 smart00834 CxxC_CXXC_SSSS Puta 63.1 2.8 6.1E-05 26.5 0.3 35 169-204 6-40 (41)
11 KOG3740 Uncharacterized conser 61.9 5.1 0.00011 41.2 2.0 35 166-200 460-497 (706)
12 PF01412 ArfGap: Putative GTPa 59.4 4 8.7E-05 32.0 0.7 37 167-205 12-48 (116)
13 PF07282 OrfB_Zn_ribbon: Putat 50.2 10 0.00022 26.7 1.4 31 167-201 27-57 (69)
14 PF01096 TFIIS_C: Transcriptio 49.6 4.6 0.0001 26.6 -0.4 32 170-201 2-39 (39)
15 PF04810 zf-Sec23_Sec24: Sec23 49.4 6.9 0.00015 25.8 0.4 32 168-199 2-33 (40)
16 PF09297 zf-NADH-PPase: NADH p 48.1 4.8 0.00011 25.1 -0.4 29 168-200 3-31 (32)
17 smart00105 ArfGap Putative GTP 47.4 9.9 0.00022 29.7 1.1 37 167-205 2-38 (112)
18 PF09723 Zn-ribbon_8: Zinc rib 45.9 6.8 0.00015 26.0 0.0 35 169-204 6-41 (42)
19 PF09947 DUF2180: Uncharacteri 44.3 12 0.00026 28.2 1.1 37 162-198 10-64 (68)
20 PRK03988 translation initiatio 43.8 7.3 0.00016 32.4 -0.1 31 168-199 102-132 (138)
21 COG2816 NPY1 NTP pyrophosphohy 42.9 17 0.00038 33.7 2.2 35 167-205 110-144 (279)
22 TIGR00311 aIF-2beta translatio 42.9 7.8 0.00017 32.0 -0.1 30 169-199 98-127 (133)
23 PLN03114 ADP-ribosylation fact 42.7 16 0.00034 35.6 1.9 37 167-205 21-57 (395)
24 PF12773 DZR: Double zinc ribb 41.8 17 0.00036 24.1 1.4 32 166-202 10-41 (50)
25 PF12553 DUF3742: Protein of u 39.5 10 0.00022 27.2 0.1 10 180-189 34-43 (54)
26 PF13717 zinc_ribbon_4: zinc-r 39.2 12 0.00026 24.3 0.3 32 169-200 3-35 (36)
27 COG3952 Predicted membrane pro 38.6 8.8 0.00019 31.5 -0.4 18 181-200 76-93 (113)
28 smart00653 eIF2B_5 domain pres 38.5 9.8 0.00021 30.4 -0.1 29 169-198 81-109 (110)
29 COG5236 Uncharacterized conser 38.0 18 0.00038 35.5 1.4 64 144-209 37-100 (493)
30 PRK12286 rpmF 50S ribosomal pr 38.0 17 0.00036 26.1 1.0 30 165-203 24-53 (57)
31 PF08271 TF_Zn_Ribbon: TFIIB z 36.8 12 0.00026 24.7 0.1 30 170-202 2-31 (43)
32 PRK12336 translation initiatio 36.6 11 0.00023 32.7 -0.2 31 169-200 99-129 (201)
33 PF13248 zf-ribbon_3: zinc-rib 35.3 27 0.00059 21.0 1.5 23 169-199 3-25 (26)
34 PRK00241 nudC NADH pyrophospha 35.3 27 0.00058 31.2 2.1 32 167-202 98-129 (256)
35 TIGR02605 CxxC_CxxC_SSSS putat 35.2 14 0.0003 24.8 0.2 36 169-205 6-42 (52)
36 TIGR01385 TFSII transcription 34.2 23 0.0005 32.8 1.5 38 164-201 254-297 (299)
37 PF12760 Zn_Tnp_IS1595: Transp 33.5 21 0.00045 23.9 0.8 27 169-198 19-45 (46)
38 COG3529 Predicted nucleic-acid 33.0 8.4 0.00018 29.0 -1.2 37 166-202 8-44 (66)
39 PF06677 Auto_anti-p27: Sjogre 32.0 18 0.00038 24.6 0.3 25 168-197 17-41 (41)
40 PRK00420 hypothetical protein; 31.6 23 0.0005 28.8 1.0 29 168-201 23-51 (112)
41 KOG0703 Predicted GTPase-activ 31.0 18 0.00039 33.8 0.3 36 168-205 25-60 (287)
42 smart00659 RPOLCX RNA polymera 31.0 21 0.00045 24.4 0.5 27 169-200 3-29 (44)
43 PF01873 eIF-5_eIF-2B: Domain 30.9 16 0.00034 29.8 -0.1 30 169-199 94-123 (125)
44 COG0846 SIR2 NAD-dependent pro 29.6 29 0.00062 31.4 1.3 44 165-208 119-165 (250)
45 PF10083 DUF2321: Uncharacteri 29.4 32 0.00069 29.8 1.5 35 167-201 38-79 (158)
46 PRK14892 putative transcriptio 28.6 24 0.00052 28.0 0.6 40 166-206 19-58 (99)
47 smart00440 ZnF_C2C2 C2C2 Zinc 27.8 26 0.00055 23.2 0.5 32 170-201 2-39 (40)
48 PHA02998 RNA polymerase subuni 26.7 33 0.00072 30.6 1.2 39 167-205 142-186 (195)
49 smart00778 Prim_Zn_Ribbon Zinc 26.6 42 0.00091 22.4 1.4 31 168-198 3-33 (37)
50 smart00661 RPOL9 RNA polymeras 26.5 58 0.0013 21.4 2.1 31 169-202 1-32 (52)
51 PRK00085 recO DNA repair prote 25.5 30 0.00066 29.4 0.7 31 166-197 147-177 (247)
52 PF09698 GSu_C4xC__C2xCH: Geob 25.0 41 0.0009 21.8 1.1 18 176-196 18-35 (36)
53 PF11781 RRN7: RNA polymerase 25.0 37 0.0008 22.3 0.9 24 169-197 9-32 (36)
54 PF01783 Ribosomal_L32p: Ribos 24.9 31 0.00068 24.3 0.6 24 167-199 25-48 (56)
55 PF05876 Terminase_GpA: Phage 24.5 36 0.00077 33.7 1.1 37 165-201 197-240 (557)
56 TIGR02098 MJ0042_CXXC MJ0042 f 24.3 23 0.0005 22.4 -0.2 32 169-200 3-35 (38)
57 COG2331 Uncharacterized protei 24.1 16 0.00035 28.6 -1.1 36 168-206 12-49 (82)
58 COG4260 Membrane protease subu 23.6 64 0.0014 30.9 2.5 31 166-199 313-343 (345)
59 PRK00481 NAD-dependent deacety 23.1 59 0.0013 28.3 2.0 43 164-208 118-160 (242)
60 KOG0909 Peptide:N-glycanase [P 22.7 35 0.00076 34.1 0.6 32 168-199 161-203 (500)
61 COG0675 Transposase and inacti 22.7 45 0.00097 28.3 1.2 28 165-201 306-333 (364)
62 KOG0712 Molecular chaperone (D 21.6 75 0.0016 30.3 2.5 49 158-206 133-186 (337)
63 PF13695 zf-3CxxC: Zinc-bindin 21.3 77 0.0017 24.3 2.1 14 116-129 13-26 (98)
64 KOG0706 Predicted GTPase-activ 20.7 42 0.00091 33.3 0.7 38 167-206 22-59 (454)
65 PRK00423 tfb transcription ini 20.7 52 0.0011 30.0 1.2 20 165-184 27-53 (310)
66 PRK05978 hypothetical protein; 20.6 49 0.0011 28.0 1.0 44 166-212 31-74 (148)
67 PF10080 DUF2318: Predicted me 20.6 30 0.00066 27.5 -0.2 40 166-210 33-75 (102)
68 PRK00432 30S ribosomal protein 20.6 46 0.001 23.2 0.7 29 167-200 19-47 (50)
69 TIGR00244 transcriptional regu 20.3 59 0.0013 27.8 1.4 33 170-202 2-40 (147)
70 PF03604 DNA_RNApol_7kD: DNA d 20.2 46 0.001 21.5 0.6 26 170-200 2-27 (32)
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=99.52 E-value=3e-15 Score=105.41 Aligned_cols=35 Identities=34% Similarity=0.601 Sum_probs=33.0
Q ss_pred ccccCCCCCCCCccCCCCCCchhhhhhhhcccccc
Q 027800 170 VCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPML 204 (218)
Q Consensus 170 ~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~ 204 (218)
.|++|++++||+||+||.|..+|||||||+|++..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999999999999999999999999999999864
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.51 E-value=4.7e-15 Score=103.35 Aligned_cols=39 Identities=36% Similarity=0.570 Sum_probs=35.7
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccc
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLV 205 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~ 205 (218)
..+.|++|+++.||+||+||.|+++|||||||+|+|...
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 468999999999999999999999999999999998543
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=99.50 E-value=2e-15 Score=98.21 Aligned_cols=34 Identities=32% Similarity=0.635 Sum_probs=27.4
Q ss_pred cccCCCCCCCCccCCCCCCchhhhhhhhcccccc
Q 027800 171 CADCNTTKTPLWRSGPRGPKVTKLILSIEKLPML 204 (218)
Q Consensus 171 C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~ 204 (218)
|++|++++||+||+||.|+.+|||||||+|+|..
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 8999999999999999999999999999999854
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.85 E-value=9.1e-10 Score=88.15 Aligned_cols=37 Identities=43% Similarity=0.776 Sum_probs=35.2
Q ss_pred CcccccCCCCCCCCccCCCCCCchhhhhhhhcccccc
Q 027800 168 IRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPML 204 (218)
Q Consensus 168 ~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~ 204 (218)
...|.+|+++.||+||++|.|++.+|||||++|++..
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGG 235 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcC
Confidence 6899999999999999999999999999999999973
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.88 E-value=5.9e-06 Score=80.15 Aligned_cols=38 Identities=29% Similarity=0.468 Sum_probs=32.1
Q ss_pred CCCCcccccCCCCCCCCccCCCCC----Cchhhhhhhhcccc
Q 027800 165 TNTIRVCADCNTTKTPLWRSGPRG----PKVTKLILSIEKLP 202 (218)
Q Consensus 165 ~~~~~~C~~Cgtt~TP~WR~GP~G----pktLCNACGLryrK 202 (218)
.....+|.+|.++.||+|||+..+ +-.|||||||++.=
T Consensus 155 s~~~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~kl 196 (498)
T COG5641 155 SNQPHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKL 196 (498)
T ss_pred ccccchhccccccCCccccccccccccCCccccccccccccc
Confidence 334459999999999999999994 37999999998864
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=87.94 E-value=0.37 Score=48.17 Aligned_cols=38 Identities=21% Similarity=0.113 Sum_probs=32.1
Q ss_pred CcccccCCCCCCCCc--cCCCCCCchhhhhhhhccccccc
Q 027800 168 IRVCADCNTTKTPLW--RSGPRGPKVTKLILSIEKLPMLV 205 (218)
Q Consensus 168 ~~~C~~Cgtt~TP~W--R~GP~GpktLCNACGLryrK~~~ 205 (218)
.+.|..|+||+.-+| .-+|.-.+.||-.|.++|+|...
T Consensus 386 g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygG 425 (693)
T KOG3554|consen 386 GRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGG 425 (693)
T ss_pred CCcccccccccccceeccCCCCccchhhHHHHHHHHHhcC
Confidence 679999999999999 44555577999999999999643
No 7
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=83.70 E-value=0.56 Score=43.76 Aligned_cols=42 Identities=24% Similarity=0.317 Sum_probs=37.6
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccceeeee
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLVFFFCV 210 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~~f~c~ 210 (218)
....|++|++.. |+|-.-.-| -.||--|.=.-|.+.+++.++
T Consensus 19 ~Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHRsLGvhiS~V 60 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHRSLGVHISKV 60 (319)
T ss_pred ccCccccCCCCC-CceEecccC-eEEEeecchhhhccccceeee
Confidence 467899999999 999999999 799999999999988887665
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=76.85 E-value=0.76 Score=30.08 Aligned_cols=30 Identities=10% Similarity=0.237 Sum_probs=15.9
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhh
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSI 198 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGL 198 (218)
+.|.+||..-+-.=-.|.+-++..|.+||-
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 469999987433333566667899999994
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=74.56 E-value=1.6 Score=43.10 Aligned_cols=38 Identities=21% Similarity=0.160 Sum_probs=30.5
Q ss_pred CcccccCCC-CCCCCccCCCCCCchhhhhhhhccccccc
Q 027800 168 IRVCADCNT-TKTPLWRSGPRGPKVTKLILSIEKLPMLV 205 (218)
Q Consensus 168 ~~~C~~Cgt-t~TP~WR~GP~GpktLCNACGLryrK~~~ 205 (218)
...|..|.+ +.||.||+...-.-.+|||||+.....+.
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~ 335 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGS 335 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCccc
Confidence 556777776 88999999887778999999998776443
No 10
>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=63.10 E-value=2.8 Score=26.52 Aligned_cols=35 Identities=17% Similarity=0.190 Sum_probs=23.9
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhhcccccc
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPML 204 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~ 204 (218)
-+|..||..-+ .|+.-.++....|-.||...+|++
T Consensus 6 y~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~~~~r~~ 40 (41)
T smart00834 6 YRCEDCGHTFE-VLQKISDDPLATCPECGGDVRRLI 40 (41)
T ss_pred EEcCCCCCEEE-EEEecCCCCCCCCCCCCCcceecc
Confidence 47899998655 344433356678999999766653
No 11
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=61.87 E-value=5.1 Score=41.19 Aligned_cols=35 Identities=20% Similarity=0.364 Sum_probs=28.6
Q ss_pred CCCcccccCCCCCCCCccCCCCC---Cchhhhhhhhcc
Q 027800 166 NTIRVCADCNTTKTPLWRSGPRG---PKVTKLILSIEK 200 (218)
Q Consensus 166 ~~~~~C~~Cgtt~TP~WR~GP~G---pktLCNACGLry 200 (218)
...-.|..|.|.-||.|+.-+.+ ++.+|.+|----
T Consensus 460 ~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSn 497 (706)
T KOG3740|consen 460 TEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSN 497 (706)
T ss_pred CCchhhhhcccccccccccccccCcchHHHHHhhhhhc
Confidence 34568999999999999988777 568999996543
No 12
>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=59.41 E-value=4 Score=32.04 Aligned_cols=37 Identities=30% Similarity=0.398 Sum_probs=26.1
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccc
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLV 205 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~ 205 (218)
..+.|++|+... |.|-.=..| -.||-.|.-..|.+..
T Consensus 12 ~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 12 GNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp TCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred CcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 458999999554 599998899 7999999988887653
No 13
>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=50.25 E-value=10 Score=26.66 Aligned_cols=31 Identities=19% Similarity=0.218 Sum_probs=23.0
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhccc
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKL 201 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryr 201 (218)
....|..||....- ...+....|..||..+-
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 56789999986544 44455689999998754
No 14
>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=49.60 E-value=4.6 Score=26.60 Aligned_cols=32 Identities=13% Similarity=0.155 Sum_probs=20.1
Q ss_pred ccccCCCCCCCCc----cCCCCCCc--hhhhhhhhccc
Q 027800 170 VCADCNTTKTPLW----RSGPRGPK--VTKLILSIEKL 201 (218)
Q Consensus 170 ~C~~Cgtt~TP~W----R~GP~Gpk--tLCNACGLryr 201 (218)
.|..|+-..+-.| |++.++.. ..|..||-+|+
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 5888888765444 66766633 47999998875
No 15
>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=49.38 E-value=6.9 Score=25.77 Aligned_cols=32 Identities=13% Similarity=0.171 Sum_probs=20.8
Q ss_pred CcccccCCCCCCCCccCCCCCCchhhhhhhhc
Q 027800 168 IRVCADCNTTKTPLWRSGPRGPKVTKLILSIE 199 (218)
Q Consensus 168 ~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLr 199 (218)
..+|.+|++=--|.=+=...|....||.|+..
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 46899999988887777777888999999863
No 16
>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=48.09 E-value=4.8 Score=25.12 Aligned_cols=29 Identities=24% Similarity=0.382 Sum_probs=16.8
Q ss_pred CcccccCCCCCCCCccCCCCCCchhhhhhhhcc
Q 027800 168 IRVCADCNTTKTPLWRSGPRGPKVTKLILSIEK 200 (218)
Q Consensus 168 ~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLry 200 (218)
.+.|..||....+. +.|....|.+||..+
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-EE
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcCEe
Confidence 47899999876543 336678999999764
No 17
>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=47.36 E-value=9.9 Score=29.71 Aligned_cols=37 Identities=24% Similarity=0.310 Sum_probs=30.5
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccc
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLV 205 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~ 205 (218)
...+|++|+. .-|.|=.=..| -.||-.|.-.-|.+..
T Consensus 2 ~N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~lg~ 38 (112)
T smart00105 2 GNKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSLGV 38 (112)
T ss_pred CCCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhcCC
Confidence 3578999998 55999988888 7999999888877643
No 18
>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=45.92 E-value=6.8 Score=26.00 Aligned_cols=35 Identities=14% Similarity=0.104 Sum_probs=23.2
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhh-cccccc
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSI-EKLPML 204 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGL-ryrK~~ 204 (218)
-+|..||.+-+-+..-.- .....|-+||- ..+|++
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~~~r~~ 41 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGSTEVRRVI 41 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCCCceEEec
Confidence 478999977654433333 55689999998 665543
No 19
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=44.32 E-value=12 Score=28.23 Aligned_cols=37 Identities=22% Similarity=0.532 Sum_probs=26.7
Q ss_pred CCCCCCCcccccCCC---------CCCCCccCCCCC---------Cchhhhhhhh
Q 027800 162 NNNTNTIRVCADCNT---------TKTPLWRSGPRG---------PKVTKLILSI 198 (218)
Q Consensus 162 ~~~~~~~~~C~~Cgt---------t~TP~WR~GP~G---------pktLCNACGL 198 (218)
++......+|..||. ..+|+|.-|... |+.||..|--
T Consensus 10 gkdt~AVavCivCG~GlC~~H~~~e~~~~~~g~yp~~~~~~~~~l~RilC~~C~~ 64 (68)
T PF09947_consen 10 GKDTDAVAVCIVCGAGLCMDHSKREEIPVWEGGYPFPSKKLKKPLPRILCPECHA 64 (68)
T ss_pred CCCccceehHHhcCchhhHHHHhhhheeeeccCCCCccccccCCCCeeecHHHHH
Confidence 456778899999995 368999666554 4567887753
No 20
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=43.77 E-value=7.3 Score=32.39 Aligned_cols=31 Identities=19% Similarity=0.298 Sum_probs=23.2
Q ss_pred CcccccCCCCCCCCccCCCCCCchhhhhhhhc
Q 027800 168 IRVCADCNTTKTPLWRSGPRGPKVTKLILSIE 199 (218)
Q Consensus 168 ~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLr 199 (218)
--.|..|+...|-+=+++- ---.-|+|||-.
T Consensus 102 yVlC~~C~spdT~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCCCcEEEEcCC-eEEEEcccCCCC
Confidence 3689999999998877532 124679999964
No 21
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=42.90 E-value=17 Score=33.70 Aligned_cols=35 Identities=23% Similarity=0.317 Sum_probs=26.9
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccc
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLV 205 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~ 205 (218)
..+.|..||+...|. ..|.+.+|+.||.++-..+.
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fPR~d 144 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEHFPRID 144 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCccCCCCC
Confidence 468999999988763 34667899999988765543
No 22
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=42.89 E-value=7.8 Score=32.02 Aligned_cols=30 Identities=17% Similarity=0.350 Sum_probs=22.7
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhhc
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSIE 199 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGLr 199 (218)
-.|..|+...|-+=+.+- ---.-|+|||-.
T Consensus 98 VlC~~C~sPdT~l~k~~r-~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGR-VSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCCcEEEEeCC-eEEEecccCCCC
Confidence 679999999998887532 213579999964
No 23
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=42.75 E-value=16 Score=35.57 Aligned_cols=37 Identities=27% Similarity=0.442 Sum_probs=30.3
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccc
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLV 205 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~ 205 (218)
..++|++|+... |.|-.-..| -.||-.|.=.-|.+..
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGv 57 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGV 57 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCC
Confidence 357899999865 999999999 7999999877766543
No 24
>PF12773 DZR: Double zinc ribbon
Probab=41.83 E-value=17 Score=24.10 Aligned_cols=32 Identities=22% Similarity=0.364 Sum_probs=22.6
Q ss_pred CCCcccccCCCCCCCCccCCCCCCchhhhhhhhcccc
Q 027800 166 NTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLP 202 (218)
Q Consensus 166 ~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK 202 (218)
...+.|.+||+.-. .+......|.+||-.+..
T Consensus 10 ~~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP-----PPDQSKKICPNCGAENPP 41 (50)
T ss_pred ccccCChhhcCChh-----hccCCCCCCcCCcCCCcC
Confidence 44788999998776 344446789999876544
No 25
>PF12553 DUF3742: Protein of unknown function (DUF3742); InterPro: IPR022213 This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Probab=39.51 E-value=10 Score=27.17 Aligned_cols=10 Identities=60% Similarity=1.341 Sum_probs=9.0
Q ss_pred CCccCCCCCC
Q 027800 180 PLWRSGPRGP 189 (218)
Q Consensus 180 P~WR~GP~Gp 189 (218)
|+||.||.|-
T Consensus 34 ~E~R~G~~Gf 43 (54)
T PF12553_consen 34 PEWREGPAGF 43 (54)
T ss_pred HhheecCCCc
Confidence 8999999984
No 26
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=39.16 E-value=12 Score=24.34 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=25.1
Q ss_pred cccccCCCC-CCCCccCCCCCCchhhhhhhhcc
Q 027800 169 RVCADCNTT-KTPLWRSGPRGPKVTKLILSIEK 200 (218)
Q Consensus 169 ~~C~~Cgtt-~TP~WR~GP~GpktLCNACGLry 200 (218)
..|-+|++. .-+..+=.+.|.+..|-.||-.|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 368889886 46777777888889999998665
No 27
>COG3952 Predicted membrane protein [Function unknown]
Probab=38.62 E-value=8.8 Score=31.55 Aligned_cols=18 Identities=17% Similarity=0.019 Sum_probs=14.2
Q ss_pred CccCCCCCCchhhhhhhhcc
Q 027800 181 LWRSGPRGPKVTKLILSIEK 200 (218)
Q Consensus 181 ~WR~GP~GpktLCNACGLry 200 (218)
.||.+|-+ .||+|||+.-
T Consensus 76 i~~~DpV~--Vl~~~~glF~ 93 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFI 93 (113)
T ss_pred HHhcchHH--HHHHhhhHHH
Confidence 46777777 7999999863
No 28
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=38.51 E-value=9.8 Score=30.45 Aligned_cols=29 Identities=14% Similarity=0.197 Sum_probs=22.0
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhh
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSI 198 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGL 198 (218)
-.|..|+...|-+=+.+- ---.-|+|||-
T Consensus 81 VlC~~C~spdT~l~k~~r-~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENR-LFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCC-eEEEEccccCC
Confidence 679999999998888731 11345999995
No 29
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=38.03 E-value=18 Score=35.53 Aligned_cols=64 Identities=13% Similarity=0.116 Sum_probs=39.6
Q ss_pred HhcCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccceeee
Q 027800 144 DHQKQPPSSSLEPDNGNNNNNTNTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLVFFFC 209 (218)
Q Consensus 144 ~kkk~~~~~~lg~~~s~s~~~~~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~~f~c 209 (218)
+++|..+++-...+.+++.........|.-|....|=.= .-|-| .-.|-+||+|+|.+-..-.|
T Consensus 37 kqkKNnlsaEPnlttsSaddtDEen~~C~ICA~~~TYs~-~~PC~-H~~CH~Ca~RlRALY~~K~C 100 (493)
T COG5236 37 KQKKNNLSAEPNLTTSSADDTDEENMNCQICAGSTTYSA-RYPCG-HQICHACAVRLRALYMQKGC 100 (493)
T ss_pred hccccccccCCccccccccccccccceeEEecCCceEEE-eccCC-chHHHHHHHHHHHHHhccCC
Confidence 345554442222333444455567789999987665332 34667 67899999999986544333
No 30
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=37.97 E-value=17 Score=26.13 Aligned_cols=30 Identities=17% Similarity=0.180 Sum_probs=22.5
Q ss_pred CCCCcccccCCCCCCCCccCCCCCCchhhhhhhhccccc
Q 027800 165 TNTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPM 203 (218)
Q Consensus 165 ~~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~ 203 (218)
...+-.|.+||...-| ..+|..||.+.-+.
T Consensus 24 ~~~l~~C~~CG~~~~~---------H~vC~~CG~Y~gr~ 53 (57)
T PRK12286 24 APGLVECPNCGEPKLP---------HRVCPSCGYYKGRE 53 (57)
T ss_pred CCcceECCCCCCccCC---------eEECCCCCcCCCEE
Confidence 3456789999987655 67999999665544
No 31
>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=36.80 E-value=12 Score=24.67 Aligned_cols=30 Identities=13% Similarity=0.337 Sum_probs=17.5
Q ss_pred ccccCCCCCCCCccCCCCCCchhhhhhhhcccc
Q 027800 170 VCADCNTTKTPLWRSGPRGPKVTKLILSIEKLP 202 (218)
Q Consensus 170 ~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK 202 (218)
.|.+|+.+.+ .+- --.| ..+|..||+-+.-
T Consensus 2 ~Cp~Cg~~~~-~~D-~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKEI-VFD-PERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSEE-EEE-TTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCce-EEc-CCCC-eEECCCCCCEeec
Confidence 5888888662 332 1223 6788888876543
No 32
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=36.64 E-value=11 Score=32.75 Aligned_cols=31 Identities=13% Similarity=0.227 Sum_probs=22.7
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhhcc
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSIEK 200 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGLry 200 (218)
-.|..|+...|-+=+.+- ---.-|+|||-..
T Consensus 99 V~C~~C~~pdT~l~k~~~-~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPDTRLVKEDR-VLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCCcEEEEcCC-eEEEEcccCCCCc
Confidence 679999999998877631 1134799999653
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.33 E-value=27 Score=20.97 Aligned_cols=23 Identities=13% Similarity=0.196 Sum_probs=14.3
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhhc
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSIE 199 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGLr 199 (218)
+.|.+||....+. ...|-.||-.
T Consensus 3 ~~Cp~Cg~~~~~~--------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD--------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc--------cccChhhCCC
Confidence 5688888754332 3477777754
No 34
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=35.28 E-value=27 Score=31.21 Aligned_cols=32 Identities=16% Similarity=0.172 Sum_probs=23.2
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhcccc
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLP 202 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK 202 (218)
..+.|..||...... ..|.+..|.+||..+-.
T Consensus 98 ~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 98 SHRFCGYCGHPMHPS----KTEWAMLCPHCRERYYP 129 (256)
T ss_pred cCccccccCCCCeec----CCceeEECCCCCCEECC
Confidence 368999999875542 34667789999976654
No 35
>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=35.19 E-value=14 Score=24.78 Aligned_cols=36 Identities=14% Similarity=0.112 Sum_probs=24.3
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhh-ccccccc
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSI-EKLPMLV 205 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGL-ryrK~~~ 205 (218)
-+|.+|+..-+ .|+.--+.....|-.||- ..++++.
T Consensus 6 y~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~~~~~r~~s 42 (52)
T TIGR02605 6 YRCTACGHRFE-VLQKMSDDPLATCPECGGEKLRRLLS 42 (52)
T ss_pred EEeCCCCCEeE-EEEecCCCCCCCCCCCCCCceeEEec
Confidence 47999997665 566533344578999997 5556554
No 36
>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=34.20 E-value=23 Score=32.79 Aligned_cols=38 Identities=18% Similarity=0.206 Sum_probs=26.3
Q ss_pred CCCCCcccccCCCCCCCCc----cCCCCCCc--hhhhhhhhccc
Q 027800 164 NTNTIRVCADCNTTKTPLW----RSGPRGPK--VTKLILSIEKL 201 (218)
Q Consensus 164 ~~~~~~~C~~Cgtt~TP~W----R~GP~Gpk--tLCNACGLryr 201 (218)
.......|..|+-..+-.| |++.++-. ..|..||-+|+
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 3455789999998776555 44444422 38999999886
No 37
>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=33.49 E-value=21 Score=23.87 Aligned_cols=27 Identities=15% Similarity=0.148 Sum_probs=19.3
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhh
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSI 198 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGL 198 (218)
.+|.+|+.+ ..-|.++ .....|++|+-
T Consensus 19 ~~CP~Cg~~-~~~~~~~--~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT--RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeEEeCC--CCeEECCCCCC
Confidence 569999988 5556555 23678999874
No 38
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=32.98 E-value=8.4 Score=28.99 Aligned_cols=37 Identities=14% Similarity=0.029 Sum_probs=28.4
Q ss_pred CCCcccccCCCCCCCCccCCCCCCchhhhhhhhcccc
Q 027800 166 NTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLP 202 (218)
Q Consensus 166 ~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK 202 (218)
.....|..|.+..|-+|.+...-+-.-|-+||-.-+.
T Consensus 8 IAGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~ 44 (66)
T COG3529 8 IAGAVCPACQAQDTLAMWRENNVEIVECVKCGHHMRE 44 (66)
T ss_pred hccCCCcccchhhHHHHHHhcCCceEehhhcchHhhh
Confidence 3457899999999987666555667899999976543
No 39
>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=32.04 E-value=18 Score=24.59 Aligned_cols=25 Identities=36% Similarity=0.608 Sum_probs=18.7
Q ss_pred CcccccCCCCCCCCccCCCCCCchhhhhhh
Q 027800 168 IRVCADCNTTKTPLWRSGPRGPKVTKLILS 197 (218)
Q Consensus 168 ~~~C~~Cgtt~TP~WR~GP~GpktLCNACG 197 (218)
...|..| .||+.| ...| +.+|-+|+
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 4578888 589999 2345 68999986
No 40
>PRK00420 hypothetical protein; Validated
Probab=31.58 E-value=23 Score=28.75 Aligned_cols=29 Identities=21% Similarity=0.408 Sum_probs=21.6
Q ss_pred CcccccCCCCCCCCccCCCCCCchhhhhhhhccc
Q 027800 168 IRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKL 201 (218)
Q Consensus 168 ~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryr 201 (218)
...|..|| +|+.|- ..| +..|-+||-.+.
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 36788888 788874 335 789999998664
No 41
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=31.03 E-value=18 Score=33.82 Aligned_cols=36 Identities=31% Similarity=0.406 Sum_probs=29.4
Q ss_pred CcccccCCCCCCCCccCCCCCCchhhhhhhhccccccc
Q 027800 168 IRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLV 205 (218)
Q Consensus 168 ~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~ 205 (218)
.+.|++|++. .|.|-.---| .-+|-.|.=--|++.+
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C~giHR~lg~ 60 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRCAGIHRSLGV 60 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeecccccccccc
Confidence 6899999998 9999988888 6899888665666554
No 42
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=31.03 E-value=21 Score=24.37 Aligned_cols=27 Identities=11% Similarity=0.111 Sum_probs=19.9
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhhcc
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSIEK 200 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGLry 200 (218)
-.|..||...+..+ +...-|..||-+.
T Consensus 3 Y~C~~Cg~~~~~~~-----~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRENEIKS-----KDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCEeecCC-----CCceECCCCCceE
Confidence 36999999877652 2357899999765
No 43
>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=30.87 E-value=16 Score=29.84 Aligned_cols=30 Identities=17% Similarity=0.307 Sum_probs=23.4
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhhhc
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILSIE 199 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACGLr 199 (218)
-.|..|+...|-+=+.+.. --.-|+|||-.
T Consensus 94 VlC~~C~spdT~l~k~~r~-~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRL-IFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEETTC-CEEEETTTSCE
T ss_pred EEcCCCCCCccEEEEcCCE-EEEEecccCCc
Confidence 6799999999988877433 25789999953
No 44
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=29.64 E-value=29 Score=31.40 Aligned_cols=44 Identities=14% Similarity=-0.046 Sum_probs=29.2
Q ss_pred CCCCcccccCCCCCCCC-ccCCC-CCCchhhhhhhh-ccccccceee
Q 027800 165 TNTIRVCADCNTTKTPL-WRSGP-RGPKVTKLILSI-EKLPMLVFFF 208 (218)
Q Consensus 165 ~~~~~~C~~Cgtt~TP~-WR~GP-~GpktLCNACGL-ryrK~~~~f~ 208 (218)
.-...+|..|+...... +.+.. .+--..|..||- .+|+.++.|.
T Consensus 119 sl~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~lrP~VV~fG 165 (250)
T COG0846 119 SLKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVLRPDVVWFG 165 (250)
T ss_pred ceeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCccccCCEEEeC
Confidence 44457899998765532 22222 222358999999 8888888774
No 45
>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=29.42 E-value=32 Score=29.80 Aligned_cols=35 Identities=17% Similarity=0.137 Sum_probs=23.6
Q ss_pred CCcccccCCCCCCCCccC-------CCCCCchhhhhhhhccc
Q 027800 167 TIRVCADCNTTKTPLWRS-------GPRGPKVTKLILSIEKL 201 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~-------GP~GpktLCNACGLryr 201 (218)
.+..|.+|++..--.|-- ++.-....|+.||..|-
T Consensus 38 tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 38 TITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 356777777766555522 44556689999998873
No 46
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.57 E-value=24 Score=28.04 Aligned_cols=40 Identities=10% Similarity=-0.050 Sum_probs=25.7
Q ss_pred CCCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccce
Q 027800 166 NTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLVF 206 (218)
Q Consensus 166 ~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~~ 206 (218)
...-.|.+|+...-+.=+.- ..+...|..||.++.+.+..
T Consensus 19 pt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y~~~~V~~ 58 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKK-NIAIITCGNCGLYTEFEVPS 58 (99)
T ss_pred CcEeECCCCCCeEeeeecCC-CcceEECCCCCCccCEECCc
Confidence 34678999995332211111 35578999999998775543
No 47
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=27.81 E-value=26 Score=23.21 Aligned_cols=32 Identities=13% Similarity=0.184 Sum_probs=20.5
Q ss_pred ccccCCCCCCCCc----cCCCCCCc--hhhhhhhhccc
Q 027800 170 VCADCNTTKTPLW----RSGPRGPK--VTKLILSIEKL 201 (218)
Q Consensus 170 ~C~~Cgtt~TP~W----R~GP~Gpk--tLCNACGLryr 201 (218)
.|..|+-...--| |++.+|.. ..|-.||-+|+
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 5778886654433 56555532 46888887775
No 48
>PHA02998 RNA polymerase subunit; Provisional
Probab=26.66 E-value=33 Score=30.56 Aligned_cols=39 Identities=15% Similarity=0.136 Sum_probs=30.5
Q ss_pred CCcccccCCCCCCCCc----cCCCCCCc--hhhhhhhhccccccc
Q 027800 167 TIRVCADCNTTKTPLW----RSGPRGPK--VTKLILSIEKLPMLV 205 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~W----R~GP~Gpk--tLCNACGLryrK~~~ 205 (218)
....|..|+-..+--| |++.++.. ..|-.||-+|+.-..
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkppkf 186 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPPKF 186 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCccc
Confidence 5689999998887655 88877743 389999999987543
No 49
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=26.59 E-value=42 Score=22.38 Aligned_cols=31 Identities=6% Similarity=0.063 Sum_probs=20.9
Q ss_pred CcccccCCCCCCCCccCCCCCCchhhhhhhh
Q 027800 168 IRVCADCNTTKTPLWRSGPRGPKVTKLILSI 198 (218)
Q Consensus 168 ~~~C~~Cgtt~TP~WR~GP~GpktLCNACGL 198 (218)
...|-.|+.+..=.|.+-...-...|+.||.
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 4578889887766675532222578999874
No 50
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=26.53 E-value=58 Score=21.41 Aligned_cols=31 Identities=13% Similarity=0.221 Sum_probs=20.1
Q ss_pred cccccCCCCCCCC-ccCCCCCCchhhhhhhhcccc
Q 027800 169 RVCADCNTTKTPL-WRSGPRGPKVTKLILSIEKLP 202 (218)
Q Consensus 169 ~~C~~Cgtt~TP~-WR~GP~GpktLCNACGLryrK 202 (218)
+.|..||.--.+. +.. .....|.+||-.++.
T Consensus 1 ~FCp~Cg~~l~~~~~~~---~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 1 KFCPKCGNMLIPKEGKE---KRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCCccccccCCC---CCEEECCcCCCeEEC
Confidence 3689998855443 322 247889999966544
No 51
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=25.46 E-value=30 Score=29.42 Aligned_cols=31 Identities=16% Similarity=0.162 Sum_probs=24.8
Q ss_pred CCCcccccCCCCCCCCccCCCCCCchhhhhhh
Q 027800 166 NTIRVCADCNTTKTPLWRSGPRGPKVTKLILS 197 (218)
Q Consensus 166 ~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACG 197 (218)
.....|..||......|-.-+.| ..+|..|+
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccC-Cccccccc
Confidence 34568999998877677776677 79999997
No 52
>PF09698 GSu_C4xC__C2xCH: Geobacter CxxxxCH...CXXCH motif (GSu_C4xC__C2xCH); InterPro: IPR010176 This motif occurs from three to eight times in eight different proteins of Geobacter sulfurreducens. The final CXXCH motif matches the cytochrome c family haem-binding site signature, suggesting that the sequence may be involved in haem-binding.
Probab=25.01 E-value=41 Score=21.83 Aligned_cols=18 Identities=28% Similarity=0.359 Sum_probs=14.1
Q ss_pred CCCCCCccCCCCCCchhhhhh
Q 027800 176 TTKTPLWRSGPRGPKVTKLIL 196 (218)
Q Consensus 176 tt~TP~WR~GP~GpktLCNAC 196 (218)
...||.|-.++.+. |++|
T Consensus 18 ~~~~p~W~~~~~~~---C~~C 35 (36)
T PF09698_consen 18 SYTTPTWGSGATTA---CGSC 35 (36)
T ss_pred cccCceeCCCCCCc---cccc
Confidence 45689999988773 8887
No 53
>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=24.97 E-value=37 Score=22.27 Aligned_cols=24 Identities=17% Similarity=0.268 Sum_probs=12.7
Q ss_pred cccccCCCCCCCCccCCCCCCchhhhhhh
Q 027800 169 RVCADCNTTKTPLWRSGPRGPKVTKLILS 197 (218)
Q Consensus 169 ~~C~~Cgtt~TP~WR~GP~GpktLCNACG 197 (218)
..|..|+.. |-...+| ...|..||
T Consensus 9 ~~C~~C~~~----~~~~~dG-~~yC~~cG 32 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDG-FYYCDRCG 32 (36)
T ss_pred CcCCCCCCe----EeEccCC-EEEhhhCc
Confidence 346666655 3333344 56666665
No 54
>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=24.93 E-value=31 Score=24.27 Aligned_cols=24 Identities=17% Similarity=0.267 Sum_probs=17.8
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhc
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIE 199 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLr 199 (218)
....|.+||... -+..+|.+||.+
T Consensus 25 ~l~~c~~cg~~~---------~~H~vc~~cG~y 48 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------LPHRVCPSCGYY 48 (56)
T ss_dssp SEEESSSSSSEE---------STTSBCTTTBBS
T ss_pred ceeeeccCCCEe---------cccEeeCCCCeE
Confidence 568899999633 236899999943
No 55
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=24.52 E-value=36 Score=33.69 Aligned_cols=37 Identities=14% Similarity=0.254 Sum_probs=28.9
Q ss_pred CCCCcccccCCCCCCCCccC-------CCCCCchhhhhhhhccc
Q 027800 165 TNTIRVCADCNTTKTPLWRS-------GPRGPKVTKLILSIEKL 201 (218)
Q Consensus 165 ~~~~~~C~~Cgtt~TP~WR~-------GP~GpktLCNACGLryr 201 (218)
..-..+|-||+....+.|.. .|......|-.||-.+.
T Consensus 197 r~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 197 RRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred eEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 35568999999999998853 25556789999998765
No 56
>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=24.32 E-value=23 Score=22.35 Aligned_cols=32 Identities=22% Similarity=0.148 Sum_probs=21.0
Q ss_pred cccccCCCCC-CCCccCCCCCCchhhhhhhhcc
Q 027800 169 RVCADCNTTK-TPLWRSGPRGPKVTKLILSIEK 200 (218)
Q Consensus 169 ~~C~~Cgtt~-TP~WR~GP~GpktLCNACGLry 200 (218)
..|.+|++.. -+..+-+..|....|-.||..+
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 4688888753 3344445556678888888755
No 57
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.10 E-value=16 Score=28.59 Aligned_cols=36 Identities=14% Similarity=0.112 Sum_probs=25.9
Q ss_pred CcccccCCCCCC--CCccCCCCCCchhhhhhhhccccccce
Q 027800 168 IRVCADCNTTKT--PLWRSGPRGPKVTKLILSIEKLPMLVF 206 (218)
Q Consensus 168 ~~~C~~Cgtt~T--P~WR~GP~GpktLCNACGLryrK~~~~ 206 (218)
.-+|..|+-..+ .-.++.| -+.|.+||-+++|++..
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~l~~ 49 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDP---LTTCEECGARLKKLLNA 49 (82)
T ss_pred EEeecccchHHHHHHhcccCc---cccChhhChHHHHhhcc
Confidence 457999987554 3345555 46899999999997643
No 58
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=23.63 E-value=64 Score=30.92 Aligned_cols=31 Identities=13% Similarity=0.195 Sum_probs=23.5
Q ss_pred CCCcccccCCCCCCCCccCCCCCCchhhhhhhhc
Q 027800 166 NTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIE 199 (218)
Q Consensus 166 ~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLr 199 (218)
.....|.+||...|+-. |.|....|-+||-.
T Consensus 313 ~k~nfc~ncG~~~t~~~---~ng~a~fcp~cgq~ 343 (345)
T COG4260 313 AKLNFCLNCGCGTTADF---DNGKAKFCPECGQG 343 (345)
T ss_pred cccccccccCcccccCC---ccchhhhChhhcCC
Confidence 34458999999988855 44666799999964
No 59
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=23.07 E-value=59 Score=28.26 Aligned_cols=43 Identities=14% Similarity=0.019 Sum_probs=24.5
Q ss_pred CCCCCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccceee
Q 027800 164 NTNTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLVFFF 208 (218)
Q Consensus 164 ~~~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~~f~ 208 (218)
..-...+|..|+.... |..--......|..||-.++..+..|.
T Consensus 118 G~~~~~~C~~C~~~~~--~~~~~~~~~p~C~~Cgg~lrP~Vv~fg 160 (242)
T PRK00481 118 GSLLRARCTKCGQTYD--LDEYLKPEPPRCPKCGGILRPDVVLFG 160 (242)
T ss_pred CCcCceeeCCCCCCcC--hhhhccCCCCCCCCCCCccCCCeEECC
Confidence 3444578999975421 111001112349999988888777543
No 60
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=22.65 E-value=35 Score=34.13 Aligned_cols=32 Identities=16% Similarity=0.172 Sum_probs=20.9
Q ss_pred CcccccCCCCC-CCCccCCCCCCc----------hhhhhhhhc
Q 027800 168 IRVCADCNTTK-TPLWRSGPRGPK----------VTKLILSIE 199 (218)
Q Consensus 168 ~~~C~~Cgtt~-TP~WR~GP~Gpk----------tLCNACGLr 199 (218)
...|.+||... +++-+-+|.+.. ..||+||--
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~ 203 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTE 203 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCc
Confidence 35688888765 666565665432 578888853
No 61
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.65 E-value=45 Score=28.26 Aligned_cols=28 Identities=14% Similarity=0.106 Sum_probs=20.9
Q ss_pred CCCCcccccCCCCCCCCccCCCCCCchhhhhhhhccc
Q 027800 165 TNTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKL 201 (218)
Q Consensus 165 ~~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryr 201 (218)
......|..||. ..+....|..||...-
T Consensus 306 ~~tS~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 306 YYTSKTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred CCCcccccccCC---------ccceeEECCCCCCeeh
Confidence 455689999999 3355679999998643
No 62
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=21.63 E-value=75 Score=30.32 Aligned_cols=49 Identities=12% Similarity=0.238 Sum_probs=36.5
Q ss_pred CCCCCCCCCCCcccccCCCC--CCCCccCCC---CCCchhhhhhhhccccccce
Q 027800 158 NGNNNNNTNTIRVCADCNTT--KTPLWRSGP---RGPKVTKLILSIEKLPMLVF 206 (218)
Q Consensus 158 ~s~s~~~~~~~~~C~~Cgtt--~TP~WR~GP---~GpktLCNACGLryrK~~~~ 206 (218)
.+.++........|..|..+ .|..||-|| .-.++.|..|+..-..+..+
T Consensus 133 C~GsGgksg~~~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G~G~~~~~k 186 (337)
T KOG0712|consen 133 CSGSGGKSGSAPKCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNGSGETISLK 186 (337)
T ss_pred CCCCCCCCCCCCCCCCCCCCCceeEEEeccccccccceeEeccCCCcccccccc
Confidence 34555666677799999976 599999999 45678999998766654333
No 63
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=21.28 E-value=77 Score=24.33 Aligned_cols=14 Identities=29% Similarity=0.577 Sum_probs=8.5
Q ss_pred ccchhhhHHHHHHh
Q 027800 116 VKWMSSKMRLMKKM 129 (218)
Q Consensus 116 ~kWm~sKmRlmrKm 129 (218)
..|.|.|..++-.|
T Consensus 13 ~~W~S~~v~i~f~~ 26 (98)
T PF13695_consen 13 RGWTSAKVWILFHM 26 (98)
T ss_pred CCCccCEEEEEEEE
Confidence 45777766666444
No 64
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=20.66 E-value=42 Score=33.32 Aligned_cols=38 Identities=29% Similarity=0.414 Sum_probs=32.1
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccce
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLVF 206 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~~ 206 (218)
..++|++|+. +.|-|-.-+.| -.||--|.---|-+.++
T Consensus 22 ~NKvCFDCgA-knPtWaSVTYG-IFLCiDCSAvHRnLGVH 59 (454)
T KOG0706|consen 22 ENKVCFDCGA-KNPTWASVTYG-IFLCIDCSAVHRNLGVH 59 (454)
T ss_pred CCceecccCC-CCCCceeecce-EEEEEecchhhhccccc
Confidence 4689999997 56999999999 79999998877776655
No 65
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.65 E-value=52 Score=29.98 Aligned_cols=20 Identities=40% Similarity=0.863 Sum_probs=15.4
Q ss_pred CCCCcccccCCC-------CCCCCccC
Q 027800 165 TNTIRVCADCNT-------TKTPLWRS 184 (218)
Q Consensus 165 ~~~~~~C~~Cgt-------t~TP~WR~ 184 (218)
..+..+|.+||+ ...|+||.
T Consensus 27 ~~Ge~vC~~CG~Vl~e~~iD~g~EWR~ 53 (310)
T PRK00423 27 ERGEIVCADCGLVIEENIIDQGPEWRA 53 (310)
T ss_pred CCCeEeecccCCcccccccccCCCccC
Confidence 456789999996 35789985
No 66
>PRK05978 hypothetical protein; Provisional
Probab=20.63 E-value=49 Score=28.03 Aligned_cols=44 Identities=16% Similarity=0.095 Sum_probs=30.0
Q ss_pred CCCcccccCCCCCCCCccCCCCCCchhhhhhhhccccccceeeeeec
Q 027800 166 NTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPMLVFFFCVYI 212 (218)
Q Consensus 166 ~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~~~f~c~yi 212 (218)
+...+|-+||.-+ ++| |-..-..-|.+||+.|.......+=-|+
T Consensus 31 Gl~grCP~CG~G~--LF~-g~Lkv~~~C~~CG~~~~~~~a~DgpAy~ 74 (148)
T PRK05978 31 GFRGRCPACGEGK--LFR-AFLKPVDHCAACGEDFTHHRADDLPAYL 74 (148)
T ss_pred HHcCcCCCCCCCc--ccc-cccccCCCccccCCccccCCccccCcch
Confidence 4567899998653 444 4445567899999999887655443343
No 67
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=20.63 E-value=30 Score=27.50 Aligned_cols=40 Identities=10% Similarity=0.085 Sum_probs=25.6
Q ss_pred CCCcccccCCCCCCCCccCCCCCCchhhhhhhhcccccc---ceeeee
Q 027800 166 NTIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEKLPML---VFFFCV 210 (218)
Q Consensus 166 ~~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLryrK~~---~~f~c~ 210 (218)
...-.|.-|+-+. --. .|...+|++||.++..-. ....|+
T Consensus 33 va~daCeiC~~~G--Y~q---~g~~lvC~~C~~~~~~~~ig~~~GGCN 75 (102)
T PF10080_consen 33 VAFDACEICGPKG--YYQ---EGDQLVCKNCGVRFNLPTIGGKSGGCN 75 (102)
T ss_pred EEEEeccccCCCc--eEE---ECCEEEEecCCCEEehhhcccccCCCC
Confidence 3456788894322 112 356799999999998733 336665
No 68
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.56 E-value=46 Score=23.20 Aligned_cols=29 Identities=7% Similarity=0.051 Sum_probs=21.0
Q ss_pred CCcccccCCCCCCCCccCCCCCCchhhhhhhhcc
Q 027800 167 TIRVCADCNTTKTPLWRSGPRGPKVTKLILSIEK 200 (218)
Q Consensus 167 ~~~~C~~Cgtt~TP~WR~GP~GpktLCNACGLry 200 (218)
..+.|..|+.. -++... .+..|..||..+
T Consensus 19 ~~~fCP~Cg~~--~m~~~~---~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSG--FMAEHL---DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcc--hheccC---CcEECCCcCCEE
Confidence 45689999975 444443 478999999865
No 69
>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=20.27 E-value=59 Score=27.80 Aligned_cols=33 Identities=18% Similarity=0.156 Sum_probs=21.5
Q ss_pred ccccCCCCCCCCc--cCCCCC----Cchhhhhhhhcccc
Q 027800 170 VCADCNTTKTPLW--RSGPRG----PKVTKLILSIEKLP 202 (218)
Q Consensus 170 ~C~~Cgtt~TP~W--R~GP~G----pktLCNACGLryrK 202 (218)
.|..|+...|-.= |...+| .+--|.+||-|+-.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 5888887777655 444455 33578888877643
No 70
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=20.21 E-value=46 Score=21.48 Aligned_cols=26 Identities=12% Similarity=0.187 Sum_probs=16.3
Q ss_pred ccccCCCCCCCCccCCCCCCchhhhhhhhcc
Q 027800 170 VCADCNTTKTPLWRSGPRGPKVTKLILSIEK 200 (218)
Q Consensus 170 ~C~~Cgtt~TP~WR~GP~GpktLCNACGLry 200 (218)
.|..|+....-.. +...-|..||-|.
T Consensus 2 ~C~~Cg~~~~~~~-----~~~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVELKP-----GDPIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE-BST-----SSTSSBSSSS-SE
T ss_pred CCCcCCCeeEcCC-----CCcEECCcCCCeE
Confidence 5889998877222 2246899998764
Done!