Query 017958
Match_columns 363
No_of_seqs 182 out of 671
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 04:55:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017958.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017958hhsearch_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 3.3E-15 7.1E-20 112.3 3.7 47 6-55 1-48 (54)
2 smart00401 ZnF_GATA zinc finge 99.5 1.1E-14 2.3E-19 108.4 4.2 50 2-53 1-50 (52)
3 PF00320 GATA: GATA zinc finge 99.4 4.4E-14 9.4E-19 98.1 0.7 36 7-42 1-36 (36)
4 PF13919 ASXH: Asx homology do 99.3 1.8E-12 3.8E-17 113.5 3.4 60 275-338 8-67 (138)
5 KOG1601 GATA-4/5/6 transcripti 98.7 7.8E-09 1.7E-13 89.8 3.6 49 4-55 199-247 (340)
6 COG5641 GAT1 GATA Zn-finger-co 98.4 7.4E-08 1.6E-12 99.5 2.3 47 5-55 159-211 (498)
7 KOG3554 Histone deacetylase co 91.2 0.14 3.1E-06 54.1 2.5 39 4-42 386-426 (693)
8 COG5641 GAT1 GATA Zn-finger-co 88.5 0.25 5.5E-06 52.1 2.0 48 5-55 298-346 (498)
9 PF14803 Nudix_N_2: Nudix N-te 63.5 2.3 4.9E-05 29.9 -0.1 30 5-34 1-30 (34)
10 PF15396 FAM60A: Protein Famil 55.4 13 0.00028 35.8 3.5 16 27-42 50-65 (213)
11 smart00778 Prim_Zn_Ribbon Zinc 51.7 13 0.00028 26.7 2.1 33 2-34 1-33 (37)
12 PF08271 TF_Zn_Ribbon: TFIIB z 50.4 4.2 9.2E-05 28.9 -0.5 30 5-37 1-30 (43)
13 PF09538 FYDLN_acid: Protein o 46.5 15 0.00032 31.6 2.2 34 1-39 6-39 (108)
14 TIGR02300 FYDLN_acid conserved 45.3 12 0.00026 33.6 1.5 34 1-39 6-39 (129)
15 PRK12336 translation initiatio 44.2 8.3 0.00018 36.0 0.3 29 5-34 99-127 (201)
16 PF01783 Ribosomal_L32p: Ribos 40.8 10 0.00022 28.8 0.3 23 6-38 28-50 (56)
17 TIGR00244 transcriptional regu 39.9 18 0.00038 33.1 1.7 51 5-55 1-57 (147)
18 KOG1598 Transcription initiati 39.5 17 0.00037 39.1 1.8 33 5-40 1-33 (521)
19 PRK12286 rpmF 50S ribosomal pr 39.3 13 0.00029 28.7 0.7 22 5-35 28-49 (57)
20 PF11781 RRN7: RNA polymerase 38.7 16 0.00034 25.8 0.9 28 2-34 6-33 (36)
21 smart00105 ArfGap Putative GTP 38.6 25 0.00054 29.6 2.3 46 4-51 3-49 (112)
22 PF01096 TFIIS_C: Transcriptio 38.0 7.1 0.00015 27.6 -0.9 32 6-37 2-39 (39)
23 PF01412 ArfGap: Putative GTPa 36.4 21 0.00045 30.3 1.5 38 3-42 12-49 (116)
24 COG5347 GTPase-activating prot 36.3 21 0.00046 36.0 1.8 37 3-41 19-55 (319)
25 COG2816 NPY1 NTP pyrophosphohy 35.9 18 0.00039 36.1 1.2 31 4-38 111-141 (279)
26 KOG0942 E3 ubiquitin protein l 35.5 22 0.00048 40.7 1.9 39 300-338 886-941 (1001)
27 PF06394 Pepsin-I3: Pepsin inh 35.3 11 0.00024 30.9 -0.3 18 312-329 34-51 (76)
28 PF09297 zf-NADH-PPase: NADH p 34.8 10 0.00023 25.4 -0.5 28 4-35 3-30 (32)
29 PRK00423 tfb transcription ini 34.3 20 0.00044 35.1 1.3 32 2-36 9-40 (310)
30 PRK14892 putative transcriptio 31.6 19 0.00042 30.7 0.6 45 5-55 22-66 (99)
31 TIGR03092 SASP_sspI small, aci 31.1 38 0.00082 27.4 2.1 22 310-331 40-61 (65)
32 PF09526 DUF2387: Probable met 30.6 17 0.00036 29.3 -0.0 33 5-37 9-41 (71)
33 PF13248 zf-ribbon_3: zinc-rib 29.5 35 0.00077 22.1 1.4 24 4-35 2-25 (26)
34 PF04161 Arv1: Arv1-like famil 29.4 22 0.00048 33.0 0.6 30 5-34 1-32 (208)
35 PF13080 DUF3926: Protein of u 29.3 34 0.00073 25.7 1.4 24 162-185 8-31 (44)
36 PF09723 Zn-ribbon_8: Zinc rib 28.6 21 0.00045 25.5 0.2 28 6-34 7-34 (42)
37 PF14156 AbbA_antirepres: Anti 28.5 37 0.00079 27.2 1.6 18 313-330 4-21 (63)
38 COG3529 Predicted nucleic-acid 28.2 15 0.00032 29.6 -0.6 34 5-38 11-44 (66)
39 smart00440 ZnF_C2C2 C2C2 Zinc 27.8 21 0.00046 25.4 0.2 32 6-37 2-39 (40)
40 PF02701 zf-Dof: Dof domain, z 27.8 60 0.0013 26.1 2.7 42 3-44 4-48 (63)
41 PF10080 DUF2318: Predicted me 27.8 16 0.00034 31.3 -0.6 29 6-39 37-65 (102)
42 PF12760 Zn_Tnp_IS1595: Transp 27.7 36 0.00078 24.5 1.3 28 3-33 17-44 (46)
43 smart00659 RPOLCX RNA polymera 27.1 21 0.00045 26.2 -0.0 31 6-41 4-34 (44)
44 KOG3740 Uncharacterized conser 26.1 26 0.00056 38.8 0.5 36 4-39 462-500 (706)
45 PF05313 Pox_P21: Poxvirus P21 25.5 26 0.00056 33.3 0.3 18 311-328 10-35 (189)
46 PF06677 Auto_anti-p27: Sjogre 25.2 35 0.00076 24.9 0.9 24 5-33 18-41 (41)
47 PF07282 OrfB_Zn_ribbon: Putat 24.8 36 0.00077 25.8 0.9 29 4-36 28-56 (69)
48 PLN03114 ADP-ribosylation fact 24.6 50 0.0011 34.5 2.1 48 3-52 21-69 (395)
49 KOG0703 Predicted GTPase-activ 23.8 33 0.00072 34.4 0.7 28 4-33 25-52 (287)
50 PF14098 SSPI: Small, acid-sol 23.8 61 0.0013 26.1 2.0 21 311-331 42-62 (65)
51 PF10022 DUF2264: Uncharacteri 23.6 40 0.00088 34.3 1.3 56 289-344 97-155 (361)
52 TIGR02605 CxxC_CxxC_SSSS putat 23.1 36 0.00078 24.5 0.6 28 6-34 7-34 (52)
53 PRK02868 hypothetical protein; 22.7 58 0.0012 32.0 2.1 20 310-329 59-78 (245)
54 KOG0909 Peptide:N-glycanase [P 22.5 41 0.0009 35.9 1.1 34 4-37 161-205 (500)
55 PF09832 DUF2059: Uncharacteri 22.5 66 0.0014 24.0 2.0 20 311-330 10-29 (64)
56 PF08273 Prim_Zn_Ribbon: Zinc- 22.4 26 0.00057 25.4 -0.2 30 3-32 2-32 (40)
57 TIGR02443 conserved hypothetic 21.9 30 0.00066 27.4 0.0 33 5-37 10-42 (59)
58 smart00661 RPOL9 RNA polymeras 21.5 58 0.0012 23.2 1.4 30 5-37 1-31 (52)
59 KOG3507 DNA-directed RNA polym 21.4 43 0.00093 26.8 0.7 30 6-40 22-51 (62)
60 PF03604 DNA_RNApol_7kD: DNA d 21.3 38 0.00083 23.5 0.4 27 6-37 2-28 (32)
61 smart00834 CxxC_CXXC_SSSS Puta 21.1 38 0.00082 23.0 0.4 28 6-34 7-34 (41)
62 PRK00420 hypothetical protein; 20.5 56 0.0012 28.6 1.4 28 5-37 24-51 (112)
63 PF10083 DUF2321: Uncharacteri 20.4 54 0.0012 30.5 1.3 32 5-36 40-78 (158)
64 PF12773 DZR: Double zinc ribb 20.2 59 0.0013 23.2 1.2 27 4-35 12-38 (50)
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=99.54 E-value=3.3e-15 Score=112.27 Aligned_cols=47 Identities=47% Similarity=1.107 Sum_probs=42.7
Q ss_pred ccccCCCCCCCcccCCCCCCCcccchhhhhHHhcCCCCCCCCCcCCC-CCC
Q 017958 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARA-EPD 55 (363)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~~~~~RPl~~rk-d~i 55 (363)
.|+||++++||+||+||.|..+|||||||||++++.. ||+.++. +.+
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~---rp~~~~~~~~~ 48 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVM---RPLSKRKKDQI 48 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCCC---CCcccCccccc
Confidence 5999999999999999988899999999999999977 9998887 444
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.51 E-value=1.1e-14 Score=108.42 Aligned_cols=50 Identities=44% Similarity=0.998 Sum_probs=43.5
Q ss_pred CCCCccccCCCCCCCcccCCCCCCCcccchhhhhHHhcCCCCCCCCCcCCCC
Q 017958 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAE 53 (363)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~~~~~RPl~~rkd 53 (363)
+..+.|+||+++.||+||+||.|..+|||||||||++++.+ .||+.+.++
T Consensus 1 ~~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~--~rp~~~~~~ 50 (52)
T smart00401 1 GSGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL--KRPLSLKKD 50 (52)
T ss_pred CCCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC--CCccccccc
Confidence 45789999999999999999999889999999999999886 367666554
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=99.41 E-value=4.4e-14 Score=98.12 Aligned_cols=36 Identities=47% Similarity=1.127 Sum_probs=28.9
Q ss_pred cccCCCCCCCcccCCCCCCCcccchhhhhHHhcCCC
Q 017958 7 CYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTL 42 (363)
Q Consensus 7 CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~~ 42 (363)
|.||+++.||+||++|.|..+||||||+||++++++
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 899999999999999999988999999999999863
No 4
>PF13919 ASXH: Asx homology domain
Probab=99.28 E-value=1.8e-12 Score=113.52 Aligned_cols=60 Identities=43% Similarity=0.460 Sum_probs=53.7
Q ss_pred hhhhhhhhcchhhhhhhhcccCCCCceeccccccccHHHHHhhhCHHHHHHHHhcCCCCCCCCC
Q 017958 275 MQQDQLKRDKSQQEKLQILGSHTSPLCEIDLNDILNFKEFVGHLTHEEQQQLLKYLPLNDTTVF 338 (363)
Q Consensus 275 ~~~~~~k~~~~~~~~~~~l~~~~spl~~~dl~d~~nf~~f~~~~t~~eq~~l~~~l~~~d~~~~ 338 (363)
+...++|+++.. .+||+++.||||.+||++|+|+++| ..||+|||++||+|||.||....
T Consensus 8 ~~~~~~k~~~~~---~~~l~sp~SpL~~~dLr~L~N~~tw-~~L~~eeq~eLl~LLP~~D~~~~ 67 (138)
T PF13919_consen 8 PSKAQLKRKWSE---EIDLTSPKSPLVNADLRALLNPETW-SCLPEEEQQELLKLLPEVDRQVG 67 (138)
T ss_pred CCcccccCCccc---ceeecCCCCcccccCHHHHhCHHHH-hcCCHHHHHHHHHhCCCCCcccc
Confidence 455677777744 6799999999999999999999999 99999999999999999999775
No 5
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.72 E-value=7.8e-09 Score=89.76 Aligned_cols=49 Identities=43% Similarity=0.938 Sum_probs=43.1
Q ss_pred CCccccCCCCCCCcccCCCCCCCcccchhhhhHHhcCCCCCCCCCcCCCCCC
Q 017958 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (363)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~~~~~RPl~~rkd~i 55 (363)
...|.+|+++.||+||+++.|...+|||||++++++++. |++.+....+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~---r~~~~~~~~~ 247 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVR---RPLPEKRPAS 247 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCcc---ccccccCccc
Confidence 478999999999999999999888999999999999833 7777777666
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.45 E-value=7.4e-08 Score=99.54 Aligned_cols=47 Identities=36% Similarity=0.768 Sum_probs=44.0
Q ss_pred CccccCCCCCCCcccCCCC-----CCCcccchhhhhHHhcCCCCCCC-CCcCCCCCC
Q 017958 5 GPCYHCGVTSTPLWRNGPP-----EKPVLCNACGSRWRTKGTLANYT-PLHARAEPD 55 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~-----G~~~LCNACGL~~k~~g~~~~~R-Pl~~rkd~i 55 (363)
.+|.||.|+.||+|||+.. | -+||||||||++.||++ | |+.++.+.+
T Consensus 159 ~vc~Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~---r~P~t~ks~~~ 211 (498)
T COG5641 159 HVCSNCKTTSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSP---RAPISLKSDSI 211 (498)
T ss_pred chhccccccCCccccccccccccCC-ccccccccccccccCCc---CCCcccccccc
Confidence 4899999999999999999 6 56999999999999999 6 999999999
No 7
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=91.16 E-value=0.14 Score=54.11 Aligned_cols=39 Identities=28% Similarity=0.614 Sum_probs=32.6
Q ss_pred CCccccCCCCCCCcc--cCCCCCCCcccchhhhhHHhcCCC
Q 017958 4 QGPCYHCGVTSTPLW--RNGPPEKPVLCNACGSRWRTKGTL 42 (363)
Q Consensus 4 ~r~CsnCgTt~TPlW--RrGp~G~~~LCNACGL~~k~~g~~ 42 (363)
.+.|.+|+|++.-.| .-+|+-+..||-.|-+|||+.|-+
T Consensus 386 g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccccccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 468999999999999 445555778999999999998754
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=88.52 E-value=0.25 Score=52.10 Aligned_cols=48 Identities=31% Similarity=0.593 Sum_probs=39.4
Q ss_pred CccccCCC-CCCCcccCCCCCCCcccchhhhhHHhcCCCCCCCCCcCCCCCC
Q 017958 5 GPCYHCGV-TSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (363)
Q Consensus 5 r~CsnCgT-t~TPlWRrGp~G~~~LCNACGL~~k~~g~~~~~RPl~~rkd~i 55 (363)
.-|.+|++ +.||.||+...-.-++|||||++.+..+.. +|+.-+.+.+
T Consensus 298 ~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~---~p~~pk~d~n 346 (498)
T COG5641 298 KKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSK---RPLLPKPDPN 346 (498)
T ss_pred cCcccccccccCcccccccccccccccccccccCCcccc---cccCCCCChh
Confidence 45677776 789999988776678999999999999988 8877777766
No 9
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=63.48 E-value=2.3 Score=29.89 Aligned_cols=30 Identities=27% Similarity=0.560 Sum_probs=15.6
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhh
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (363)
+-|.+||..-+..--.|..-...+|.+||.
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 369999988543333456667789999985
No 10
>PF15396 FAM60A: Protein Family FAM60A
Probab=55.37 E-value=13 Score=35.83 Aligned_cols=16 Identities=31% Similarity=0.457 Sum_probs=13.5
Q ss_pred cccchhhhhHHhcCCC
Q 017958 27 VLCNACGSRWRTKGTL 42 (363)
Q Consensus 27 ~LCNACGL~~k~~g~~ 42 (363)
.+||||-|..++...+
T Consensus 50 eICNACVLLVKRwKKL 65 (213)
T PF15396_consen 50 EICNACVLLVKRWKKL 65 (213)
T ss_pred hhhHHHHHHHHHHhhC
Confidence 3899999999987665
No 11
>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=51.75 E-value=13 Score=26.68 Aligned_cols=33 Identities=27% Similarity=0.783 Sum_probs=23.9
Q ss_pred CCCCccccCCCCCCCcccCCCCCCCcccchhhh
Q 017958 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (363)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (363)
++..+|..|+.+..=.|.........+|+.||.
T Consensus 1 ~~~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 1 GRHGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 356789999998877776533323569999973
No 12
>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=50.36 E-value=4.2 Score=28.89 Aligned_cols=30 Identities=20% Similarity=0.542 Sum_probs=19.7
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhhhHH
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k 37 (363)
+.|.+|+.+. .++- ...| .++|..||+-..
T Consensus 1 m~Cp~Cg~~~-~~~D-~~~g-~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFD-PERG-ELVCPNCGLVLE 30 (43)
T ss_dssp ESBTTTSSSE-EEEE-TTTT-EEEETTT-BBEE
T ss_pred CCCcCCcCCc-eEEc-CCCC-eEECCCCCCEee
Confidence 3799999987 4443 2334 459999998443
No 13
>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=46.53 E-value=15 Score=31.64 Aligned_cols=34 Identities=26% Similarity=0.799 Sum_probs=23.1
Q ss_pred CCCCCccccCCCCCCCcccCCCCCCCcccchhhhhHHhc
Q 017958 1 MGKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTK 39 (363)
Q Consensus 1 mGk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~ 39 (363)
+|.+|.|.+||+.-==|=| .|.+|--||--|..-
T Consensus 6 lGtKR~Cp~CG~kFYDLnk-----~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYDLNK-----DPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCcccCCCCcchhccCCC-----CCccCCCCCCccCcc
Confidence 4788888888887544412 345788888866554
No 14
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. 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=45.35 E-value=12 Score=33.60 Aligned_cols=34 Identities=21% Similarity=0.422 Sum_probs=25.0
Q ss_pred CCCCCccccCCCCCCCcccCCCCCCCcccchhhhhHHhc
Q 017958 1 MGKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTK 39 (363)
Q Consensus 1 mGk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~ 39 (363)
+|.+|.|.+||+.-==|=| .+.+|-.||--|...
T Consensus 6 lGtKr~Cp~cg~kFYDLnk-----~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 6 LGTKRICPNTGSKFYDLNR-----RPAVSPYTGEQFPPE 39 (129)
T ss_pred hCccccCCCcCccccccCC-----CCccCCCcCCccCcc
Confidence 5889999999987655522 355899999877554
No 15
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=44.17 E-value=8.3 Score=36.01 Aligned_cols=29 Identities=31% Similarity=0.677 Sum_probs=22.3
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhh
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (363)
-.|..|+...|-+-+.+. ---.-|+|||-
T Consensus 99 V~C~~C~~pdT~l~k~~~-~~~l~C~aCGa 127 (201)
T PRK12336 99 VICSECGLPDTRLVKEDR-VLMLRCDACGA 127 (201)
T ss_pred EECCCCCCCCcEEEEcCC-eEEEEcccCCC
Confidence 369999999999977642 22347999997
No 16
>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=40.77 E-value=10 Score=28.80 Aligned_cols=23 Identities=26% Similarity=0.810 Sum_probs=13.9
Q ss_pred ccccCCCCCCCcccCCCCCCCcccchhhhhHHh
Q 017958 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRT 38 (363)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~ 38 (363)
.|.+||...- +..+|.+|| ||+-
T Consensus 28 ~c~~cg~~~~---------~H~vc~~cG-~y~~ 50 (56)
T PF01783_consen 28 KCPNCGEPKL---------PHRVCPSCG-YYKG 50 (56)
T ss_dssp ESSSSSSEES---------TTSBCTTTB-BSSS
T ss_pred eeccCCCEec---------ccEeeCCCC-eECC
Confidence 5777774322 245888888 4443
No 17
>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=39.89 E-value=18 Score=33.13 Aligned_cols=51 Identities=18% Similarity=0.225 Sum_probs=36.1
Q ss_pred CccccCCCCCCCcc--cCCCCC----CCcccchhhhhHHhcCCCCCCCCCcCCCCCC
Q 017958 5 GPCYHCGVTSTPLW--RNGPPE----KPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (363)
Q Consensus 5 r~CsnCgTt~TPlW--RrGp~G----~~~LCNACGL~~k~~g~~~~~RPl~~rkd~i 55 (363)
+.|..|+...|-+- |...+| ..-.|.+||-+|-..-+.....|+-.+++|.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l~ViKkdG~ 57 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGV 57 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccccEEEcCCCC
Confidence 57999999998876 444555 2247999999988876654445555566655
No 18
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=39.52 E-value=17 Score=39.07 Aligned_cols=33 Identities=21% Similarity=0.488 Sum_probs=21.9
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhhhHHhcC
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKG 40 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g 40 (363)
+.|.||+.+.--. +++..-..|.+||.-.....
T Consensus 1 ~~C~~C~~s~fe~---d~a~g~~~C~~CG~v~E~~~ 33 (521)
T KOG1598|consen 1 MVCKNCGGSNFER---DEATGNLYCTACGTVLEYNN 33 (521)
T ss_pred CcCCCCCCCCccc---ccccCCceeccccceeeccc
Confidence 5799999876332 33333459999998655443
No 19
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=39.33 E-value=13 Score=28.68 Aligned_cols=22 Identities=32% Similarity=0.807 Sum_probs=15.0
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhhh
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~ 35 (363)
-.|.+||...-| ..+|..||.|
T Consensus 28 ~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 28 VECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred eECCCCCCccCC---------eEECCCCCcC
Confidence 357788776554 4588888854
No 20
>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=38.66 E-value=16 Score=25.84 Aligned_cols=28 Identities=32% Similarity=0.841 Sum_probs=19.6
Q ss_pred CCCCccccCCCCCCCcccCCCCCCCcccchhhh
Q 017958 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (363)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (363)
|...+|..|+.. |-...+| .+.|..||-
T Consensus 6 ~~~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 334569999987 4445557 559999985
No 21
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=38.55 E-value=25 Score=29.64 Aligned_cols=46 Identities=24% Similarity=0.572 Sum_probs=33.2
Q ss_pred CCccccCCCCCCCcccCCCCCCCcccchhhhhHHhcCCCC-CCCCCcCC
Q 017958 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLA-NYTPLHAR 51 (363)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~~~-~~RPl~~r 51 (363)
...|+.|+. .-|.|-.-..| ..+|-.|.-..|.-|+.. ..+.+.|.
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~lg~his~VkSl~md 49 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSLGVHISKVRSLTLD 49 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhcCCCcCeeeecccC
Confidence 478999998 45889988888 569999988777666431 23444443
No 22
>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=38.02 E-value=7.1 Score=27.65 Aligned_cols=32 Identities=31% Similarity=0.837 Sum_probs=20.2
Q ss_pred ccccCCCCCCCcc----cCCCCCC--CcccchhhhhHH
Q 017958 6 PCYHCGVTSTPLW----RNGPPEK--PVLCNACGSRWR 37 (363)
Q Consensus 6 ~CsnCgTt~TPlW----RrGp~G~--~~LCNACGL~~k 37 (363)
.|.+|+-...-.| |.++++. -+.|..||-.|+
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 5899999886665 4555442 247999998774
No 23
>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=36.35 E-value=21 Score=30.25 Aligned_cols=38 Identities=26% Similarity=0.573 Sum_probs=26.0
Q ss_pred CCCccccCCCCCCCcccCCCCCCCcccchhhhhHHhcCCC
Q 017958 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTL 42 (363)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~~ 42 (363)
..+.|+.|+... |.|-.-..| -.||-.|.-..|.-|+.
T Consensus 12 ~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~lg~~ 49 (116)
T PF01412_consen 12 GNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRSLGVH 49 (116)
T ss_dssp TCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHHHTTT
T ss_pred CcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHHhccc
Confidence 347899999655 489988888 56999999888777753
No 24
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=36.31 E-value=21 Score=35.98 Aligned_cols=37 Identities=27% Similarity=0.654 Sum_probs=29.6
Q ss_pred CCCccccCCCCCCCcccCCCCCCCcccchhhhhHHhcCC
Q 017958 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (363)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~ 41 (363)
....|+.|++.. |.|-.-.-| ..||-.|.=-.|.=|+
T Consensus 19 ~Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHRsLGv 55 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHRSLGV 55 (319)
T ss_pred ccCccccCCCCC-CceEecccC-eEEEeecchhhhcccc
Confidence 357899999999 999999999 6799999554444343
No 25
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=35.88 E-value=18 Score=36.09 Aligned_cols=31 Identities=23% Similarity=0.495 Sum_probs=24.3
Q ss_pred CCccccCCCCCCCcccCCCCCCCcccchhhhhHHh
Q 017958 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRT 38 (363)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~ 38 (363)
.+.|..||+...+. ..|-..+|+.||.++..
T Consensus 111 ~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 111 HRFCGRCGTKTYPR----EGGWARVCPKCGHEHFP 141 (279)
T ss_pred CcCCCCCCCcCccc----cCceeeeCCCCCCccCC
Confidence 57899999998885 34556799999986654
No 26
>KOG0942 consensus E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.50 E-value=22 Score=40.72 Aligned_cols=39 Identities=21% Similarity=0.422 Sum_probs=29.9
Q ss_pred ceeccccccccHHHH-----------------HhhhCHHHHHHHHhcCCCCCCCCC
Q 017958 300 LCEIDLNDILNFKEF-----------------VGHLTHEEQQQLLKYLPLNDTTVF 338 (363)
Q Consensus 300 l~~~dl~d~~nf~~f-----------------~~~~t~~eq~~l~~~l~~~d~~~~ 338 (363)
=..|||+|+=+|-|| ++.|++||+.+||||.-++--+.+
T Consensus 886 ~~pidldDLr~~teY~Ggy~~~hp~Iv~FWeVl~~F~~edKr~fLKFVTscsRpPl 941 (1001)
T KOG0942|consen 886 EDPIDLDDLRKNTEYAGGYSPDHPTIVMFWEVLEEFSDEDKRKFLKFVTSCSRPPL 941 (1001)
T ss_pred cCcccHHHHHhhccccCCCCCCCCchhHHHHHHHhcchHHHHHHHHHHhcCCCccc
Confidence 356888887666555 788999999999999866655444
No 27
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=35.31 E-value=11 Score=30.91 Aligned_cols=18 Identities=39% Similarity=0.617 Sum_probs=13.7
Q ss_pred HHHHhhhCHHHHHHHHhc
Q 017958 312 KEFVGHLTHEEQQQLLKY 329 (363)
Q Consensus 312 ~~f~~~~t~~eq~~l~~~ 329 (363)
..|+|.||.+||++|-.|
T Consensus 34 g~~~R~Lt~~E~~eL~~y 51 (76)
T PF06394_consen 34 GKYARDLTPDEQQELKTY 51 (76)
T ss_dssp TCEEEE--HHHHHHHHHH
T ss_pred CEeeccCCHHHHHHHHHH
Confidence 468999999999999766
No 28
>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=34.78 E-value=10 Score=25.44 Aligned_cols=28 Identities=29% Similarity=0.698 Sum_probs=16.6
Q ss_pred CCccccCCCCCCCcccCCCCCCCcccchhhhh
Q 017958 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (363)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~ 35 (363)
.+.|..||....+. +.|-...|.+||..
T Consensus 3 ~rfC~~CG~~t~~~----~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----PGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-----SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCC----CCcCEeECCCCcCE
Confidence 46799999887775 34556799999974
No 29
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=34.27 E-value=20 Score=35.13 Aligned_cols=32 Identities=19% Similarity=0.494 Sum_probs=22.2
Q ss_pred CCCCccccCCCCCCCcccCCCCCCCcccchhhhhH
Q 017958 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRW 36 (363)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~ 36 (363)
++...|.+||.+ ..+.. -..| .++|..||+-.
T Consensus 9 ~~~~~Cp~Cg~~-~iv~d-~~~G-e~vC~~CG~Vl 40 (310)
T PRK00423 9 EEKLVCPECGSD-KLIYD-YERG-EIVCADCGLVI 40 (310)
T ss_pred ccCCcCcCCCCC-CeeEE-CCCC-eEeecccCCcc
Confidence 566789999963 33344 3457 45999999933
No 30
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=31.61 E-value=19 Score=30.68 Aligned_cols=45 Identities=16% Similarity=0.276 Sum_probs=27.0
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhhhHHhcCCCCCCCCCcCCCCCC
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~~~~~RPl~~rkd~i 55 (363)
-.|.+|+...-++ ..+.......|-.||.|+-.. + ++|..+-|..
T Consensus 22 f~CP~Cge~~v~v-~~~k~~~h~~C~~CG~y~~~~-V----~~l~epIDVY 66 (99)
T PRK14892 22 FECPRCGKVSISV-KIKKNIAIITCGNCGLYTEFE-V----PSVYDEVDVY 66 (99)
T ss_pred eECCCCCCeEeee-ecCCCcceEECCCCCCccCEE-C----CccccchhhH
Confidence 3599999533222 112234467999999987652 2 5666665544
No 31
>TIGR03092 SASP_sspI small, acid-soluble spore protein I. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspI. The gene in Bacillus subtilis previously was designated ysfA.
Probab=31.10 E-value=38 Score=27.35 Aligned_cols=22 Identities=23% Similarity=0.413 Sum_probs=19.7
Q ss_pred cHHHHHhhhCHHHHHHHHhcCC
Q 017958 310 NFKEFVGHLTHEEQQQLLKYLP 331 (363)
Q Consensus 310 nf~~f~~~~t~~eq~~l~~~l~ 331 (363)
=||.+-.+.+++||..+|..|-
T Consensus 40 lFE~~W~~~~~~ek~~m~~~l~ 61 (65)
T TIGR03092 40 LFEAIWKHANEQEKDEMLETLE 61 (65)
T ss_pred HHHHHHHhcCHHHHHHHHHHHH
Confidence 3999999999999999998763
No 32
>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=30.61 E-value=17 Score=29.34 Aligned_cols=33 Identities=24% Similarity=0.383 Sum_probs=26.2
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhhhHH
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k 37 (363)
-.|-.|+...|.+|.+...-...-|-+||..-.
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 479999999999876555566779999998544
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=29.45 E-value=35 Score=22.08 Aligned_cols=24 Identities=29% Similarity=0.886 Sum_probs=16.5
Q ss_pred CCccccCCCCCCCcccCCCCCCCcccchhhhh
Q 017958 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (363)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~ 35 (363)
.+.|.+||+... .+.. +|-.||-.
T Consensus 2 ~~~Cp~Cg~~~~-------~~~~-fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEID-------PDAK-FCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCC-------cccc-cChhhCCC
Confidence 367999998542 2333 89999863
No 34
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=29.37 E-value=22 Score=33.04 Aligned_cols=30 Identities=30% Similarity=0.714 Sum_probs=24.0
Q ss_pred CccccCCCCCCCcccCCCCC--CCcccchhhh
Q 017958 5 GPCYHCGVTSTPLWRNGPPE--KPVLCNACGS 34 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G--~~~LCNACGL 34 (363)
++|.+||.....++|.-..| +-+.|..||-
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 47999999999999876554 3367999974
No 35
>PF13080 DUF3926: Protein of unknown function (DUF3926)
Probab=29.30 E-value=34 Score=25.73 Aligned_cols=24 Identities=33% Similarity=0.592 Sum_probs=21.7
Q ss_pred CChhhhhhHHHHHhhhhccccccC
Q 017958 162 QSPVEKLTKDLYTILHEQQSSYFS 185 (363)
Q Consensus 162 ~spvekL~kdl~~Il~~qq~s~~s 185 (363)
++|+-+-+|+..+||+|+-++|.-
T Consensus 8 P~PiqQsAkqmlnILQEELssy~~ 31 (44)
T PF13080_consen 8 PTPIQQSAKQMLNILQEELSSYPQ 31 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHhchh
Confidence 689999999999999999888765
No 36
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=28.56 E-value=21 Score=25.51 Aligned_cols=28 Identities=36% Similarity=0.722 Sum_probs=20.2
Q ss_pred ccccCCCCCCCcccCCCCCCCcccchhhh
Q 017958 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (363)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (363)
+|..||..-+-+..-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 68899977766554444 45668999986
No 37
>PF14156 AbbA_antirepres: Antirepressor AbbA
Probab=28.48 E-value=37 Score=27.25 Aligned_cols=18 Identities=44% Similarity=0.663 Sum_probs=15.5
Q ss_pred HHHhhhCHHHHHHHHhcC
Q 017958 313 EFVGHLTHEEQQQLLKYL 330 (363)
Q Consensus 313 ~f~~~~t~~eq~~l~~~l 330 (363)
+++..||+|||.-||..|
T Consensus 4 ~~~~rlt~EE~~LLLdiL 21 (63)
T PF14156_consen 4 ELIERLTEEEKKLLLDIL 21 (63)
T ss_pred HHHHHhhHHHHHHHHHHH
Confidence 677889999999998765
No 38
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.20 E-value=15 Score=29.56 Aligned_cols=34 Identities=24% Similarity=0.391 Sum_probs=25.3
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhhhHHh
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRT 38 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~ 38 (363)
-.|..|.+..|-.|.+-..-...-|-+||...+.
T Consensus 11 A~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~ 44 (66)
T COG3529 11 AVCPACQAQDTLAMWRENNVEIVECVKCGHHMRE 44 (66)
T ss_pred CCCcccchhhHHHHHHhcCCceEehhhcchHhhh
Confidence 4799999999987544444446689999986643
No 39
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=27.85 E-value=21 Score=25.41 Aligned_cols=32 Identities=34% Similarity=0.955 Sum_probs=22.4
Q ss_pred ccccCCCCCCCcc----cCCCCCC--CcccchhhhhHH
Q 017958 6 PCYHCGVTSTPLW----RNGPPEK--PVLCNACGSRWR 37 (363)
Q Consensus 6 ~CsnCgTt~TPlW----RrGp~G~--~~LCNACGL~~k 37 (363)
.|.+|+-...-.| |.+.++. -+.|-.||-.|+
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 6899997776655 5555442 247999998775
No 40
>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=27.81 E-value=60 Score=26.10 Aligned_cols=42 Identities=31% Similarity=0.691 Sum_probs=30.3
Q ss_pred CCCccccCCCCCCCc--ccCCC-CCCCcccchhhhhHHhcCCCCC
Q 017958 3 KQGPCYHCGVTSTPL--WRNGP-PEKPVLCNACGSRWRTKGTLAN 44 (363)
Q Consensus 3 k~r~CsnCgTt~TPl--WRrGp-~G~~~LCNACGL~~k~~g~~~~ 44 (363)
....|..|..+.|=- .-+.. .-+...|-+|..||-..|.++.
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRn 48 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRN 48 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecC
Confidence 357899999988754 12222 2345799999999999999853
No 41
>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=27.78 E-value=16 Score=31.32 Aligned_cols=29 Identities=24% Similarity=0.691 Sum_probs=19.2
Q ss_pred ccccCCCCCCCcccCCCCCCCcccchhhhhHHhc
Q 017958 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTK 39 (363)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~ 39 (363)
.|.-|+-.. - . ..|..++|++||.+|.+-
T Consensus 37 aCeiC~~~G--Y-~--q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 37 ACEICGPKG--Y-Y--QEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred eccccCCCc--e-E--EECCEEEEecCCCEEehh
Confidence 477773322 1 1 346678999999998764
No 42
>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=27.71 E-value=36 Score=24.53 Aligned_cols=28 Identities=29% Similarity=0.482 Sum_probs=18.5
Q ss_pred CCCccccCCCCCCCcccCCCCCCCcccchhh
Q 017958 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACG 33 (363)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGp~G~~~LCNACG 33 (363)
....|.+||.+ ...|.++ . ...-|++|+
T Consensus 17 ~g~~CP~Cg~~-~~~~~~~-~-~~~~C~~C~ 44 (46)
T PF12760_consen 17 DGFVCPHCGST-KHYRLKT-R-GRYRCKACR 44 (46)
T ss_pred CCCCCCCCCCe-eeEEeCC-C-CeEECCCCC
Confidence 34678888887 5555454 2 356788886
No 43
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=27.13 E-value=21 Score=26.22 Aligned_cols=31 Identities=29% Similarity=0.513 Sum_probs=22.6
Q ss_pred ccccCCCCCCCcccCCCCCCCcccchhhhhHHhcCC
Q 017958 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (363)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~ 41 (363)
.|.+||...+.. .+.+.-|..||-+.-.+.+
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~rIlyK~R 34 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYRILYKKR 34 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCceEEEEeC
Confidence 699999987765 2335589999987665544
No 44
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.08 E-value=26 Score=38.76 Aligned_cols=36 Identities=22% Similarity=0.624 Sum_probs=28.4
Q ss_pred CCccccCCCCCCCcccCCCCC---CCcccchhhhhHHhc
Q 017958 4 QGPCYHCGVTSTPLWRNGPPE---KPVLCNACGSRWRTK 39 (363)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G---~~~LCNACGL~~k~~ 39 (363)
.-.|..|.|.-||.|+.-+.+ ..++|.+|-.--.++
T Consensus 462 P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqkk 500 (706)
T KOG3740|consen 462 PYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQKK 500 (706)
T ss_pred chhhhhcccccccccccccccCcchHHHHHhhhhhcccc
Confidence 457999999999999877666 356999997754444
No 45
>PF05313 Pox_P21: Poxvirus P21 membrane protein; InterPro: IPR007977 The p21 membrane protein of vaccinia virus, encoded by the A17L (or A18L) gene, has been reported to localise on the inner of the two membranes of the intracellular mature virus (IMV). It has also been shown that p21 acts as a membrane anchor for the externally located fusion protein P14 (A27L gene) [].; GO: 0016021 integral to membrane
Probab=25.51 E-value=26 Score=33.33 Aligned_cols=18 Identities=39% Similarity=0.659 Sum_probs=13.9
Q ss_pred HHHHH--------hhhCHHHHHHHHh
Q 017958 311 FKEFV--------GHLTHEEQQQLLK 328 (363)
Q Consensus 311 f~~f~--------~~~t~~eq~~l~~ 328 (363)
||||. |.||+|||.+.|-
T Consensus 10 ~ddF~AGAGV~D~ELFT~EEq~sFlP 35 (189)
T PF05313_consen 10 FDDFSAGAGVSDEELFTEEEQESFLP 35 (189)
T ss_pred hhhcccCCCCChhhhcCHHHHHccCC
Confidence 67774 6799999997543
No 46
>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=25.19 E-value=35 Score=24.91 Aligned_cols=24 Identities=38% Similarity=0.910 Sum_probs=17.6
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhh
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACG 33 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACG 33 (363)
..|..| .+|+.| ...| ..+|-+|+
T Consensus 18 ~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred CccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 468888 589999 3345 46999995
No 47
>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=24.80 E-value=36 Score=25.79 Aligned_cols=29 Identities=21% Similarity=0.541 Sum_probs=20.4
Q ss_pred CCccccCCCCCCCcccCCCCCCCcccchhhhhH
Q 017958 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRW 36 (363)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~ 36 (363)
...|..||....- ...+....|..||..+
T Consensus 28 Sq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc----ccccceEEcCCCCCEE
Confidence 3579999887655 3344567899999853
No 48
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=24.57 E-value=50 Score=34.53 Aligned_cols=48 Identities=19% Similarity=0.451 Sum_probs=34.4
Q ss_pred CCCccccCCCCCCCcccCCCCCCCcccchhhhhHHhcCCCC-CCCCCcCCC
Q 017958 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLA-NYTPLHARA 52 (363)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g~~~-~~RPl~~rk 52 (363)
....|+.|+... |.|-.-..| ..||-.|.=..|--|+.. ..|.+.|..
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRsLGvHISfVRSltLD~ 69 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRSLGVHISFVRSTNLDS 69 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhhHhhccCCCCCceeecccCCC
Confidence 357899999875 889999989 569999966555555432 346666543
No 49
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=23.81 E-value=33 Score=34.41 Aligned_cols=28 Identities=25% Similarity=0.686 Sum_probs=24.8
Q ss_pred CCccccCCCCCCCcccCCCCCCCcccchhh
Q 017958 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACG 33 (363)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACG 33 (363)
.+.|+.|++. .|.|-.-.-| ..+|-.|.
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C~ 52 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRCA 52 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeecc
Confidence 4789999999 9999999889 67999984
No 50
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=23.80 E-value=61 Score=26.14 Aligned_cols=21 Identities=19% Similarity=0.316 Sum_probs=19.2
Q ss_pred HHHHHhhhCHHHHHHHHhcCC
Q 017958 311 FKEFVGHLTHEEQQQLLKYLP 331 (363)
Q Consensus 311 f~~f~~~~t~~eq~~l~~~l~ 331 (363)
||.+-.+.+++||+++|..|-
T Consensus 42 FE~~W~~~~~~ek~~m~~~l~ 62 (65)
T PF14098_consen 42 FEVIWKNSDESEKQEMVNTLE 62 (65)
T ss_pred HHHHHHhCCHHHHHHHHHHHH
Confidence 999999999999999998763
No 51
>PF10022 DUF2264: Uncharacterized protein conserved in bacteria (DUF2264); InterPro: IPR016624 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.56 E-value=40 Score=34.33 Aligned_cols=56 Identities=21% Similarity=0.239 Sum_probs=46.9
Q ss_pred hhhhcccCCCCce---eccccccccHHHHHhhhCHHHHHHHHhcCCCCCCCCCCCcccc
Q 017958 289 KLQILGSHTSPLC---EIDLNDILNFKEFVGHLTHEEQQQLLKYLPLNDTTVFPDSNCL 344 (363)
Q Consensus 289 ~~~~l~~~~spl~---~~dl~d~~nf~~f~~~~t~~eq~~l~~~l~~~d~~~~~~~~~~ 344 (363)
-..-++.++-+|| +|-+-=++.=+.|-+.||++||++|.+.|-++-..+.|+.|=+
T Consensus 97 yw~~~~~~dQ~~VEaa~la~aL~~a~~~lW~~L~~~~k~~l~~wL~~~~~~~~~~nNW~ 155 (361)
T PF10022_consen 97 YWGFIGDYDQRLVEAASLALALLRAPEWLWDPLDEEEKENLVDWLKQIRGIKPPDNNWL 155 (361)
T ss_pred ccCCcccchhhHhHHHHHHHHHHHCHHHHHhhCCHHHHHHHHHHHHhcCcCCCccchhH
Confidence 3445566667777 6667777888999999999999999999999999999999954
No 52
>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=23.13 E-value=36 Score=24.55 Aligned_cols=28 Identities=21% Similarity=0.574 Sum_probs=19.7
Q ss_pred ccccCCCCCCCcccCCCCCCCcccchhhh
Q 017958 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (363)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (363)
+|.+|+..-+ +|+.-.+.....|-.||-
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 6999997665 466533344567999997
No 53
>PRK02868 hypothetical protein; Provisional
Probab=22.75 E-value=58 Score=31.95 Aligned_cols=20 Identities=40% Similarity=0.489 Sum_probs=17.8
Q ss_pred cHHHHHhhhCHHHHHHHHhc
Q 017958 310 NFKEFVGHLTHEEQQQLLKY 329 (363)
Q Consensus 310 nf~~f~~~~t~~eq~~l~~~ 329 (363)
..-|++.++|+|||+-|||.
T Consensus 59 ~l~~~v~~ms~eqq~~ll~~ 78 (245)
T PRK02868 59 GLFELVQNMSPEQQQILLKA 78 (245)
T ss_pred cHHHHHHhCCHHHHHHHHHH
Confidence 56789999999999999985
No 54
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=22.52 E-value=41 Score=35.91 Aligned_cols=34 Identities=35% Similarity=0.730 Sum_probs=22.3
Q ss_pred CCccccCCCCC-CCcccCCCCCC----------CcccchhhhhHH
Q 017958 4 QGPCYHCGVTS-TPLWRNGPPEK----------PVLCNACGSRWR 37 (363)
Q Consensus 4 ~r~CsnCgTt~-TPlWRrGp~G~----------~~LCNACGL~~k 37 (363)
.+.|.+||... +++=+-+|.+. -+.||+||---|
T Consensus 161 ~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~R 205 (500)
T KOG0909|consen 161 NPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETR 205 (500)
T ss_pred CCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCccc
Confidence 57899999888 55433233322 268999987443
No 55
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=22.50 E-value=66 Score=24.04 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=16.4
Q ss_pred HHHHHhhhCHHHHHHHHhcC
Q 017958 311 FKEFVGHLTHEEQQQLLKYL 330 (363)
Q Consensus 311 f~~f~~~~t~~eq~~l~~~l 330 (363)
.+.|.++||++|-++|+.|.
T Consensus 10 ~~~y~~~ft~~El~~i~~FY 29 (64)
T PF09832_consen 10 APIYAEHFTEEELDAILAFY 29 (64)
T ss_dssp HHHHHHHS-HHHHHHHHHHH
T ss_pred HHHHHHHCCHHHHHHHHHHH
Confidence 35789999999999999885
No 56
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=22.42 E-value=26 Score=25.44 Aligned_cols=30 Identities=27% Similarity=0.654 Sum_probs=17.0
Q ss_pred CCCccccCCCCCCCc-ccCCCCCCCcccchh
Q 017958 3 KQGPCYHCGVTSTPL-WRNGPPEKPVLCNAC 32 (363)
Q Consensus 3 k~r~CsnCgTt~TPl-WRrGp~G~~~LCNAC 32 (363)
+..+|..|+.+.-=. |.........+|+.|
T Consensus 2 ~h~pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 2 KHGPCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp EEE--TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCCCCcCccccccCcCcccCCCEECCCC
Confidence 456899999987766 765333336699999
No 57
>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=21.87 E-value=30 Score=27.37 Aligned_cols=33 Identities=21% Similarity=0.349 Sum_probs=25.0
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhhhHH
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k 37 (363)
-.|..|+...|-+|.+...-...-|-+||..-+
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~ 42 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQEQ 42 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCccc
Confidence 479999999998865444445678999998554
No 58
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.52 E-value=58 Score=23.22 Aligned_cols=30 Identities=23% Similarity=0.522 Sum_probs=19.3
Q ss_pred CccccCCCCCCCcccCCCC-CCCcccchhhhhHH
Q 017958 5 GPCYHCGVTSTPLWRNGPP-EKPVLCNACGSRWR 37 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~-G~~~LCNACGL~~k 37 (363)
+.|..||..-.+. ... .....|..||-.++
T Consensus 1 ~FCp~Cg~~l~~~---~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 1 KFCPKCGNMLIPK---EGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCCccccc---cCCCCCEEECCcCCCeEE
Confidence 3699998855443 222 23679999996443
No 59
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=21.35 E-value=43 Score=26.82 Aligned_cols=30 Identities=30% Similarity=0.530 Sum_probs=22.4
Q ss_pred ccccCCCCCCCcccCCCCCCCcccchhhhhHHhcC
Q 017958 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKG 40 (363)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~g 40 (363)
.|..|+...|.. .|...-|-.||-+.-.+.
T Consensus 22 iCgdC~~en~lk-----~~D~irCReCG~RIlyKk 51 (62)
T KOG3507|consen 22 ICGDCGQENTLK-----RGDVIRCRECGYRILYKK 51 (62)
T ss_pred Eecccccccccc-----CCCcEehhhcchHHHHHH
Confidence 599999988875 455667999997665543
No 60
>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=21.28 E-value=38 Score=23.51 Aligned_cols=27 Identities=33% Similarity=0.776 Sum_probs=17.6
Q ss_pred ccccCCCCCCCcccCCCCCCCcccchhhhhHH
Q 017958 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (363)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k 37 (363)
.|..||....-. .+.+.-|..||-+.-
T Consensus 2 ~C~~Cg~~~~~~-----~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 2 ICGECGAEVELK-----PGDPIRCPECGHRIL 28 (32)
T ss_dssp BESSSSSSE-BS-----TSSTSSBSSSS-SEE
T ss_pred CCCcCCCeeEcC-----CCCcEECCcCCCeEE
Confidence 589999998832 233567999997543
No 61
>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=21.08 E-value=38 Score=22.97 Aligned_cols=28 Identities=25% Similarity=0.557 Sum_probs=19.0
Q ss_pred ccccCCCCCCCcccCCCCCCCcccchhhh
Q 017958 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (363)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (363)
+|..||..-+. |..-..+....|-.||-
T Consensus 7 ~C~~Cg~~fe~-~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEV-LQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEE-EEecCCCCCCCCCCCCC
Confidence 68899986554 33332255668999998
No 62
>PRK00420 hypothetical protein; Validated
Probab=20.50 E-value=56 Score=28.57 Aligned_cols=28 Identities=29% Similarity=0.619 Sum_probs=20.1
Q ss_pred CccccCCCCCCCcccCCCCCCCcccchhhhhHH
Q 017958 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (363)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k 37 (363)
..|..|| +|+.|- ..| ..+|-+||-.+.
T Consensus 24 ~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 5788888 778773 234 459999998554
No 63
>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=20.42 E-value=54 Score=30.46 Aligned_cols=32 Identities=25% Similarity=0.644 Sum_probs=22.3
Q ss_pred CccccCCCCCCCcccC-------CCCCCCcccchhhhhH
Q 017958 5 GPCYHCGVTSTPLWRN-------GPPEKPVLCNACGSRW 36 (363)
Q Consensus 5 r~CsnCgTt~TPlWRr-------Gp~G~~~LCNACGL~~ 36 (363)
..|.+|++..---|-- ++...|..|..||-.|
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 4688888876554532 4445778999999855
No 64
>PF12773 DZR: Double zinc ribbon
Probab=20.22 E-value=59 Score=23.18 Aligned_cols=27 Identities=30% Similarity=0.778 Sum_probs=15.7
Q ss_pred CCccccCCCCCCCcccCCCCCCCcccchhhhh
Q 017958 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (363)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~ 35 (363)
...|.+||+.-. .+......|..||-.
T Consensus 12 ~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLP-----PPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChh-----hccCCCCCCcCCcCC
Confidence 356777777666 222334467777763
Done!