Query 013454
Match_columns 442
No_of_seqs 179 out of 702
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 04:01:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013454.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013454hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13919 ASXH: Asx homology do 99.9 2.7E-23 6E-28 184.6 5.7 122 275-402 8-137 (138)
2 cd00202 ZnF_GATA Zinc finger D 99.5 6.8E-15 1.5E-19 112.9 4.0 47 6-55 1-48 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 2E-14 4.3E-19 109.3 4.1 50 2-53 1-50 (52)
4 PF00320 GATA: GATA zinc finge 99.4 6.7E-14 1.5E-18 99.3 1.1 35 7-41 1-35 (36)
5 KOG1601 GATA-4/5/6 transcripti 98.7 9E-09 2E-13 90.9 3.4 49 4-55 199-247 (340)
6 COG5641 GAT1 GATA Zn-finger-co 98.4 6.9E-08 1.5E-12 101.7 2.1 47 5-55 159-211 (498)
7 KOG3554 Histone deacetylase co 91.1 0.16 3.4E-06 54.9 2.8 39 4-42 386-426 (693)
8 COG5641 GAT1 GATA Zn-finger-co 88.2 0.25 5.5E-06 53.2 1.7 48 5-55 298-346 (498)
9 KOG3037 Cell membrane glycopro 76.8 3 6.5E-05 43.2 4.1 65 302-368 222-287 (330)
10 PF14803 Nudix_N_2: Nudix N-te 64.8 2.2 4.7E-05 30.8 0.1 30 5-34 1-30 (34)
11 smart00778 Prim_Zn_Ribbon Zinc 59.5 7.5 0.00016 28.6 2.0 33 2-34 1-33 (37)
12 PF15396 FAM60A: Protein Famil 57.5 13 0.00028 36.7 3.9 16 27-42 50-65 (213)
13 PF08271 TF_Zn_Ribbon: TFIIB z 48.7 4.6 0.0001 29.5 -0.5 28 5-35 1-28 (43)
14 PRK12336 translation initiatio 47.8 6.6 0.00014 37.5 0.2 28 6-34 100-127 (201)
15 KOG1598 Transcription initiati 42.4 14 0.0003 40.6 1.7 30 292-321 311-340 (521)
16 TIGR00244 transcriptional regu 42.0 15 0.00031 34.5 1.5 51 5-55 1-57 (147)
17 PRK12286 rpmF 50S ribosomal pr 39.9 12 0.00026 29.7 0.5 22 5-35 28-49 (57)
18 PF01783 Ribosomal_L32p: Ribos 37.4 10 0.00022 29.6 -0.2 23 6-38 28-50 (56)
19 PRK00423 tfb transcription ini 36.7 18 0.00039 36.3 1.3 30 2-34 9-38 (310)
20 PF09538 FYDLN_acid: Protein o 36.1 24 0.00052 31.2 1.9 34 1-39 6-39 (108)
21 TIGR02300 FYDLN_acid conserved 36.0 19 0.0004 33.3 1.2 34 1-39 6-39 (129)
22 PF01412 ArfGap: Putative GTPa 35.2 26 0.00056 30.4 1.9 37 3-41 12-48 (116)
23 PF02701 zf-Dof: Dof domain, z 34.9 42 0.00091 27.7 2.9 42 3-44 4-48 (63)
24 COG5347 GTPase-activating prot 34.9 22 0.00048 36.7 1.7 36 3-40 19-54 (319)
25 PF01096 TFIIS_C: Transcriptio 34.8 7.3 0.00016 28.4 -1.3 32 6-37 2-39 (39)
26 PF11781 RRN7: RNA polymerase 34.7 20 0.00043 26.0 0.9 27 3-34 7-33 (36)
27 COG2816 NPY1 NTP pyrophosphohy 34.0 19 0.00042 36.7 1.1 31 4-38 111-141 (279)
28 KOG3740 Uncharacterized conser 33.4 31 0.00067 39.0 2.6 36 4-39 462-500 (706)
29 PRK14892 putative transcriptio 32.2 17 0.00038 31.8 0.4 44 5-54 22-65 (99)
30 PF08273 Prim_Zn_Ribbon: Zinc- 30.0 17 0.00036 27.2 -0.1 30 3-32 2-32 (40)
31 PF04161 Arv1: Arv1-like famil 29.9 21 0.00046 34.0 0.5 30 5-34 1-32 (208)
32 smart00105 ArfGap Putative GTP 29.1 41 0.00088 29.1 2.1 36 4-41 3-38 (112)
33 PF12760 Zn_Tnp_IS1595: Transp 29.0 31 0.00067 25.5 1.2 28 3-33 17-44 (46)
34 smart00440 ZnF_C2C2 C2C2 Zinc 28.9 19 0.0004 26.4 -0.0 32 6-37 2-39 (40)
35 PF09526 DUF2387: Probable met 28.8 18 0.00039 29.9 -0.1 35 4-38 8-42 (71)
36 KOG0909 Peptide:N-glycanase [P 27.9 28 0.0006 38.0 1.1 20 381-400 424-443 (500)
37 PF06394 Pepsin-I3: Pepsin inh 26.7 19 0.00042 30.3 -0.3 18 312-329 34-51 (76)
38 PF13248 zf-ribbon_3: zinc-rib 26.5 43 0.00094 22.3 1.4 22 5-34 3-24 (26)
39 PF09297 zf-NADH-PPase: NADH p 26.4 20 0.00044 24.7 -0.2 28 4-35 3-30 (32)
40 COG1327 Predicted transcriptio 25.9 34 0.00073 32.5 1.1 51 5-55 1-57 (156)
41 PF07282 OrfB_Zn_ribbon: Putat 25.4 32 0.0007 26.7 0.8 29 4-36 28-56 (69)
42 KOG0703 Predicted GTPase-activ 24.9 29 0.00064 35.6 0.6 27 4-32 25-51 (287)
43 PF09723 Zn-ribbon_8: Zinc rib 24.8 24 0.00052 25.9 -0.1 28 6-34 7-34 (42)
44 PF10080 DUF2318: Predicted me 24.7 18 0.0004 31.7 -0.8 29 6-39 37-65 (102)
45 COG3529 Predicted nucleic-acid 24.5 20 0.00043 29.7 -0.6 34 4-38 10-44 (66)
46 COG3952 Predicted membrane pro 24.3 21 0.00046 32.2 -0.5 20 17-38 76-95 (113)
47 PF10022 DUF2264: Uncharacteri 23.4 1.3E+02 0.0028 31.5 4.9 72 288-371 96-170 (361)
48 smart00659 RPOLCX RNA polymera 22.7 25 0.00054 26.5 -0.3 31 6-41 4-34 (44)
49 TIGR03092 SASP_sspI small, aci 22.4 66 0.0014 26.7 2.0 22 310-331 40-61 (65)
50 smart00027 EH Eps15 homology d 21.6 68 0.0015 26.2 2.0 37 304-344 56-92 (96)
51 PF05876 Terminase_GpA: Phage 21.2 45 0.00099 36.3 1.2 36 5-40 201-243 (557)
52 PF06677 Auto_anti-p27: Sjogre 20.8 43 0.00094 25.1 0.6 24 5-33 18-41 (41)
53 TIGR02605 CxxC_CxxC_SSSS putat 20.7 39 0.00084 25.1 0.4 28 6-34 7-34 (52)
54 PRK00420 hypothetical protein; 20.7 53 0.0011 29.5 1.3 29 5-38 24-52 (112)
55 KOG0942 E3 ubiquitin protein l 20.5 49 0.0011 38.9 1.3 37 300-336 886-939 (1001)
No 1
>PF13919 ASXH: Asx homology domain
Probab=99.88 E-value=2.7e-23 Score=184.64 Aligned_cols=122 Identities=35% Similarity=0.360 Sum_probs=111.9
Q ss_pred hhhhhhhhccchhhhhhhcccCCCCceeccccccccHHHHHhhhCHHHHHHHHhcCCCCCCCC----CChhHH---hhhc
Q 013454 275 MQQDQLKRDKSQQEKLQILGSHTSPLCEIDLNDILNFKEFVGHLTHEEQQQLLKYLPLNDTTV----FPDSLN---SMFD 347 (442)
Q Consensus 275 ~~~~~~k~~k~~~~~~~vl~~~~spl~~idl~dv~nf~ef~~~~t~eeq~~l~k~lp~~d~~~----~~~sl~---~mf~ 347 (442)
+...++|+++.. .+||+++.||||.+||++|+|+++| ..||+|||++||+|||.||... .+++++ +||+
T Consensus 8 ~~~~~~k~~~~~---~~~l~sp~SpL~~~dLr~L~N~~tw-~~L~~eeq~eLl~LLP~~D~~~~~~~~~~~~~l~~S~ln 83 (138)
T PF13919_consen 8 PSKAQLKRKWSE---EIDLTSPKSPLVNADLRALLNPETW-SCLPEEEQQELLKLLPEVDRQVGPDPPDDSLPLSESALN 83 (138)
T ss_pred CCcccccCCccc---ceeecCCCCcccccCHHHHhCHHHH-hcCCHHHHHHHHHhCCCCCcccccCCCcccccCCHHHhc
Confidence 455577777744 6799999999999999999999999 9999999999999999999966 688898 9999
Q ss_pred hhhhhhhHHHHHHHHhhcccccccCCCChhhHHHHHHHH-hccCCchhHHHHHHHh
Q 013454 348 SLQFKENISSFQQLLAEGVFDLSFLGVATEDCRTLKRLA-LSNLTTSNWVEHYQSL 402 (442)
Q Consensus 348 s~qfk~n~~~fqql~~~gvf~~s~~~~k~e~~~~~~~l~-l~~~~ks~~~e~y~~l 402 (442)
|.+|.+++..||+.|++|+|+..+. +.+...+.+|.+ ..|..|.++.|.|..-
T Consensus 84 n~~F~~a~~~fqe~L~~G~~~pe~~--~~~~~~~~~r~~g~~d~~K~~~fE~~wG~ 137 (138)
T PF13919_consen 84 NEFFRDACQEFQERLAEGEFDPEWQ--RQAWKAEEEREAGKFDPWKEEEFEEYWGQ 137 (138)
T ss_pred CHHHHHHHHHHHHHHHcCCCChHHH--HHHHHHHHHHHhccchhHHHHHHHHHhCC
Confidence 9999999999999999999999887 688899999999 9999999999999753
No 2
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.52 E-value=6.8e-15 Score=112.94 Aligned_cols=47 Identities=47% Similarity=1.107 Sum_probs=42.4
Q ss_pred ccccCCCCCCCcccCCCCCCcccchhhhhhHHhcCCCCCCCCCcCCC-CCC
Q 013454 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARA-EPD 55 (442)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~G~l~~~RPLs~rk-d~i 55 (442)
+|+||+++.||+||+||.|..+|||||||||++++.. ||+.++. +.+
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 5999999999999999988889999999999999976 8988887 443
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.49 E-value=2e-14 Score=109.29 Aligned_cols=50 Identities=44% Similarity=0.998 Sum_probs=43.3
Q ss_pred CCCCccccCCCCCCCcccCCCCCCcccchhhhhhHHhcCCCCCCCCCcCCCC
Q 013454 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAE 53 (442)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~G~l~~~RPLs~rkd 53 (442)
+..+.|+||+++.||+||+||.|..+|||||||||++++.+ .||+.+.++
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 366666554
No 4
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.39 E-value=6.7e-14 Score=99.33 Aligned_cols=35 Identities=49% Similarity=1.133 Sum_probs=28.9
Q ss_pred cccCCCCCCCcccCCCCCCcccchhhhhhHHhcCC
Q 013454 7 CYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (442)
Q Consensus 7 CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~G~ 41 (442)
|.||+++.||+||++|.|..+||||||+||+++++
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999999999988899999999999986
No 5
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.70 E-value=9e-09 Score=90.91 Aligned_cols=49 Identities=43% Similarity=0.938 Sum_probs=42.3
Q ss_pred CCccccCCCCCCCcccCCCCCCcccchhhhhhHHhcCCCCCCCCCcCCCCCC
Q 013454 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (442)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~G~l~~~RPLs~rkd~i 55 (442)
...|.+|+++.||+||+++.|...+|||||++++++++. |++.+....+
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 478999999999999999999788999999999999833 6777766655
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.45 E-value=6.9e-08 Score=101.72 Aligned_cols=47 Identities=36% Similarity=0.768 Sum_probs=43.9
Q ss_pred CccccCCCCCCCcccCCCC-----CCcccchhhhhhHHhcCCCCCCC-CCcCCCCCC
Q 013454 5 GPCYHCGVTSTPLWRNGPP-----EKPVLCNACGSRWRTKGTLANYT-PLHARAEPD 55 (442)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~-----G~~~LCNACGL~~k~~G~l~~~R-PLs~rkd~i 55 (442)
.+|.||.++.||+|||+.. | -++|||||||++.||++ | |+.++.+.+
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 5 56999999999999999 6 999999998
No 7
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=91.08 E-value=0.16 Score=54.90 Aligned_cols=39 Identities=28% Similarity=0.612 Sum_probs=32.2
Q ss_pred CCccccCCCCCCCccc--CCCCCCcccchhhhhhHHhcCCC
Q 013454 4 QGPCYHCGVTSTPLWR--NGPPEKPVLCNACGSRWRTKGTL 42 (442)
Q Consensus 4 ~r~CsnCgTt~TPlWR--rGp~G~~~LCNACGL~~k~~G~l 42 (442)
.+.|.+|+|+..-.|- -+|..+..||-.|.+|||+.|-+
T Consensus 386 g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccccccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 4699999999999993 34445667999999999998754
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=88.16 E-value=0.25 Score=53.22 Aligned_cols=48 Identities=31% Similarity=0.593 Sum_probs=39.8
Q ss_pred CccccCCC-CCCCcccCCCCCCcccchhhhhhHHhcCCCCCCCCCcCCCCCC
Q 013454 5 GPCYHCGV-TSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (442)
Q Consensus 5 r~CsnCgT-t~TPlWRrGp~G~~~LCNACGL~~k~~G~l~~~RPLs~rkd~i 55 (442)
..|.+|++ +.||.|||...-.-++|||||++.+.++.. +|+.-+.+++
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 45777876 789999988776678999999999999887 8888777776
No 9
>KOG3037 consensus Cell membrane glycoprotein [General function prediction only]
Probab=76.83 E-value=3 Score=43.23 Aligned_cols=65 Identities=25% Similarity=0.438 Sum_probs=57.6
Q ss_pred eccccccccHHHHHhhhCH-HHHHHHHhcCCCCCCCCCChhHHhhhchhhhhhhHHHHHHHHhhcccc
Q 013454 302 EIDLNDILNFKEFVGHLTH-EEQQQLLKYLPLNDTTVFPDSLNSMFDSLQFKENISSFQQLLAEGVFD 368 (442)
Q Consensus 302 ~idl~dv~nf~ef~~~~t~-eeq~~l~k~lp~~d~~~~~~sl~~mf~s~qfk~n~~~fqql~~~gvf~ 368 (442)
.|||-+||-=++-++.|++ .-|.+||-+||.=+... +-+.+..+|+||..-|..|-+-|+-|--+
T Consensus 222 ~vdLa~vL~~e~v~~vl~~~~v~erL~phlP~d~~~~--~~i~e~l~spqF~qal~sfs~aL~sgql~ 287 (330)
T KOG3037|consen 222 TVDLATVLKPEAVAPVLANPGVQERLMPHLPSDHDRA--EGILELLTSPQFRQALDSFSQALQSGQLG 287 (330)
T ss_pred ceehhhhcChHHHHHHhhCcchhhhhcccCCCCCcch--HHHHHhhcCHHHHHHHHHHHHHHhccccc
Confidence 7999999998888888887 46889999999876655 99999999999999999999999988655
No 10
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=64.79 E-value=2.2 Score=30.77 Aligned_cols=30 Identities=27% Similarity=0.560 Sum_probs=15.6
Q ss_pred CccccCCCCCCCcccCCCCCCcccchhhhh
Q 013454 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (442)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (442)
+-|.+||..-+..--.|..-.+.+|.+||.
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 359999987543333456667789999985
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=59.49 E-value=7.5 Score=28.63 Aligned_cols=33 Identities=27% Similarity=0.783 Sum_probs=24.4
Q ss_pred CCCCccccCCCCCCCcccCCCCCCcccchhhhh
Q 013454 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (442)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (442)
++..+|..|+.+..-.|.........+|+.||.
T Consensus 1 ~~~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 1 GRHGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 356789999999888886643333569999973
No 12
>PF15396 FAM60A: Protein Family FAM60A
Probab=57.54 E-value=13 Score=36.70 Aligned_cols=16 Identities=31% Similarity=0.457 Sum_probs=13.3
Q ss_pred ccchhhhhhHHhcCCC
Q 013454 27 VLCNACGSRWRTKGTL 42 (442)
Q Consensus 27 ~LCNACGL~~k~~G~l 42 (442)
.+||||-|..++..++
T Consensus 50 eICNACVLLVKRwKKL 65 (213)
T PF15396_consen 50 EICNACVLLVKRWKKL 65 (213)
T ss_pred hhhHHHHHHHHHHhhC
Confidence 3899999998887665
No 13
>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=48.74 E-value=4.6 Score=29.45 Aligned_cols=28 Identities=21% Similarity=0.584 Sum_probs=18.8
Q ss_pred CccccCCCCCCCcccCCCCCCcccchhhhhh
Q 013454 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (442)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~ 35 (442)
..|.+|+.+. .++- ...| .++|..||+-
T Consensus 1 m~Cp~Cg~~~-~~~D-~~~g-~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFD-PERG-ELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSE-EEEE-TTTT-EEEETTT-BB
T ss_pred CCCcCCcCCc-eEEc-CCCC-eEECCCCCCE
Confidence 3799999977 4443 2334 4699999983
No 14
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=47.76 E-value=6.6 Score=37.51 Aligned_cols=28 Identities=32% Similarity=0.740 Sum_probs=21.8
Q ss_pred ccccCCCCCCCcccCCCCCCcccchhhhh
Q 013454 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (442)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (442)
.|..|+...|-+-+.+. ---.-|+|||-
T Consensus 100 ~C~~C~~pdT~l~k~~~-~~~l~C~aCGa 127 (201)
T PRK12336 100 ICSECGLPDTRLVKEDR-VLMLRCDACGA 127 (201)
T ss_pred ECCCCCCCCcEEEEcCC-eEEEEcccCCC
Confidence 69999999999977642 11347999997
No 15
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=42.37 E-value=14 Score=40.60 Aligned_cols=30 Identities=13% Similarity=-0.030 Sum_probs=20.8
Q ss_pred hcccCCCCceeccccccccHHHHHhhhCHH
Q 013454 292 ILGSHTSPLCEIDLNDILNFKEFVGHLTHE 321 (442)
Q Consensus 292 vl~~~~spl~~idl~dv~nf~ef~~~~t~e 321 (442)
|-.-|+.|-+.--|.+.-++-+|...+|+-
T Consensus 311 ~~~~~~~~~~~~~l~~~~q~~~~~~~~~e~ 340 (521)
T KOG1598|consen 311 VTLRHSLPVITGGLFLAWQDLQPRDRLVES 340 (521)
T ss_pred hccccCCcccchhhhcccccchhhhhhhhh
Confidence 445677777776677777777777777764
No 16
>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=41.98 E-value=15 Score=34.51 Aligned_cols=51 Identities=18% Similarity=0.225 Sum_probs=37.0
Q ss_pred CccccCCCCCCCcc--cCCCCC----CcccchhhhhhHHhcCCCCCCCCCcCCCCCC
Q 013454 5 GPCYHCGVTSTPLW--RNGPPE----KPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (442)
Q Consensus 5 r~CsnCgTt~TPlW--RrGp~G----~~~LCNACGL~~k~~G~l~~~RPLs~rkd~i 55 (442)
+.|..|+...|-+- |...+| ..--|.+||-+|-+.-+.....|+-.+++|.
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 57999999998875 444555 2237999999998877665555666666664
No 17
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=39.86 E-value=12 Score=29.71 Aligned_cols=22 Identities=32% Similarity=0.807 Sum_probs=14.9
Q ss_pred CccccCCCCCCCcccCCCCCCcccchhhhhh
Q 013454 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (442)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~ 35 (442)
-.|.+||...-| ..+|..||.|
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 18
>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=37.43 E-value=10 Score=29.56 Aligned_cols=23 Identities=26% Similarity=0.810 Sum_probs=13.9
Q ss_pred ccccCCCCCCCcccCCCCCCcccchhhhhhHHh
Q 013454 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRT 38 (442)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~ 38 (442)
.|.+||...- +..+|.+|| ||+-
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 19
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=36.74 E-value=18 Score=36.35 Aligned_cols=30 Identities=20% Similarity=0.568 Sum_probs=21.5
Q ss_pred CCCCccccCCCCCCCcccCCCCCCcccchhhhh
Q 013454 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (442)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (442)
++...|.+||.+ ..+.. -..| .++|..||+
T Consensus 9 ~~~~~Cp~Cg~~-~iv~d-~~~G-e~vC~~CG~ 38 (310)
T PRK00423 9 EEKLVCPECGSD-KLIYD-YERG-EIVCADCGL 38 (310)
T ss_pred ccCCcCcCCCCC-CeeEE-CCCC-eEeecccCC
Confidence 566789999963 33344 3456 469999999
No 20
>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=36.12 E-value=24 Score=31.18 Aligned_cols=34 Identities=26% Similarity=0.799 Sum_probs=23.0
Q ss_pred CCCCCccccCCCCCCCcccCCCCCCcccchhhhhhHHhc
Q 013454 1 MGKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTK 39 (442)
Q Consensus 1 mGk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~ 39 (442)
+|.+|.|.+||+.===|=| .|.+|--||--|..-
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 4778889988886544412 244788888866553
No 21
>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=36.02 E-value=19 Score=33.26 Aligned_cols=34 Identities=21% Similarity=0.422 Sum_probs=24.6
Q ss_pred CCCCCccccCCCCCCCcccCCCCCCcccchhhhhhHHhc
Q 013454 1 MGKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTK 39 (442)
Q Consensus 1 mGk~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~ 39 (442)
+|.+|.|.+||+.-==|=| .+.+|-.||--|...
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 4888999999987554422 345899999876554
No 22
>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=35.21 E-value=26 Score=30.39 Aligned_cols=37 Identities=27% Similarity=0.605 Sum_probs=25.6
Q ss_pred CCCccccCCCCCCCcccCCCCCCcccchhhhhhHHhcCC
Q 013454 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (442)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~G~ 41 (442)
..+.|+.|+... |.|-.-..| ..||-.|.-..|.-|+
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 357899999655 589998888 6799999887777774
No 23
>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=34.92 E-value=42 Score=27.72 Aligned_cols=42 Identities=31% Similarity=0.650 Sum_probs=30.9
Q ss_pred CCCccccCCCCCCCcc--cCCC-CCCcccchhhhhhHHhcCCCCC
Q 013454 3 KQGPCYHCGVTSTPLW--RNGP-PEKPVLCNACGSRWRTKGTLAN 44 (442)
Q Consensus 3 k~r~CsnCgTt~TPlW--RrGp-~G~~~LCNACGL~~k~~G~l~~ 44 (442)
....|..|..+.|-.= -... .-+.+.|-+|.-||-..|.+++
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 3578999999887542 2222 2356799999999999999864
No 24
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=34.87 E-value=22 Score=36.67 Aligned_cols=36 Identities=28% Similarity=0.672 Sum_probs=28.7
Q ss_pred CCCccccCCCCCCCcccCCCCCCcccchhhhhhHHhcC
Q 013454 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKG 40 (442)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~G 40 (442)
....|+.|++.. |.|-.-.-| ..||-.|.--.|.=|
T Consensus 19 ~Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHRsLG 54 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHRSLG 54 (319)
T ss_pred ccCccccCCCCC-CceEecccC-eEEEeecchhhhccc
Confidence 457899999999 999999999 789999944333333
No 25
>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=34.78 E-value=7.3 Score=28.35 Aligned_cols=32 Identities=31% Similarity=0.878 Sum_probs=20.1
Q ss_pred ccccCCCCCCCcc----cCCCCCCc--ccchhhhhhHH
Q 013454 6 PCYHCGVTSTPLW----RNGPPEKP--VLCNACGSRWR 37 (442)
Q Consensus 6 ~CsnCgTt~TPlW----RrGp~G~~--~LCNACGL~~k 37 (442)
.|.+||...+-.| |.++++.- +.|..||-.|+
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 5899999876655 55554422 48999998774
No 26
>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=34.71 E-value=20 Score=26.04 Aligned_cols=27 Identities=30% Similarity=0.791 Sum_probs=18.9
Q ss_pred CCCccccCCCCCCCcccCCCCCCcccchhhhh
Q 013454 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (442)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (442)
...+|..|+.. |-...+| .+.|..||-
T Consensus 7 ~~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 7 PNEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 34569999987 4444457 569999984
No 27
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=34.03 E-value=19 Score=36.73 Aligned_cols=31 Identities=23% Similarity=0.495 Sum_probs=23.9
Q ss_pred CCccccCCCCCCCcccCCCCCCcccchhhhhhHHh
Q 013454 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRT 38 (442)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~ 38 (442)
.|.|..||+...|. ..|-..+|+.||.++..
T Consensus 111 ~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 111 HRFCGRCGTKTYPR----EGGWARVCPKCGHEHFP 141 (279)
T ss_pred CcCCCCCCCcCccc----cCceeeeCCCCCCccCC
Confidence 58899999998885 33455699999986654
No 28
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.37 E-value=31 Score=39.02 Aligned_cols=36 Identities=22% Similarity=0.624 Sum_probs=28.4
Q ss_pred CCccccCCCCCCCcccCCCCC---CcccchhhhhhHHhc
Q 013454 4 QGPCYHCGVTSTPLWRNGPPE---KPVLCNACGSRWRTK 39 (442)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G---~~~LCNACGL~~k~~ 39 (442)
.-.|..|.|.-||.|+.-+.+ ..++|.+|----.++
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 457999999999999987776 346999997754443
No 29
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=32.16 E-value=17 Score=31.75 Aligned_cols=44 Identities=16% Similarity=0.317 Sum_probs=26.3
Q ss_pred CccccCCCCCCCcccCCCCCCcccchhhhhhHHhcCCCCCCCCCcCCCCC
Q 013454 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAEP 54 (442)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~G~l~~~RPLs~rkd~ 54 (442)
-.|.+|+...-++ ..+.......|-.||.|+-.. . ++|..+-|.
T Consensus 22 f~CP~Cge~~v~v-~~~k~~~h~~C~~CG~y~~~~--V---~~l~epIDV 65 (99)
T PRK14892 22 FECPRCGKVSISV-KIKKNIAIITCGNCGLYTEFE--V---PSVYDEVDV 65 (99)
T ss_pred eECCCCCCeEeee-ecCCCcceEECCCCCCccCEE--C---Cccccchhh
Confidence 3599999533222 112233467999999987662 2 556555443
No 30
>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=30.02 E-value=17 Score=27.20 Aligned_cols=30 Identities=27% Similarity=0.654 Sum_probs=17.5
Q ss_pred CCCccccCCCCCCCc-ccCCCCCCcccchhh
Q 013454 3 KQGPCYHCGVTSTPL-WRNGPPEKPVLCNAC 32 (442)
Q Consensus 3 k~r~CsnCgTt~TPl-WRrGp~G~~~LCNAC 32 (442)
+..+|..|+.+.--. |.........+|+.|
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 456899999988777 865433335699999
No 31
>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=29.88 E-value=21 Score=33.99 Aligned_cols=30 Identities=30% Similarity=0.714 Sum_probs=24.0
Q ss_pred CccccCCCCCCCcccCCCCC--Ccccchhhhh
Q 013454 5 GPCYHCGVTSTPLWRNGPPE--KPVLCNACGS 34 (442)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G--~~~LCNACGL 34 (442)
++|.+||.....++|+-.+| +-+.|..||-
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 47999999999999886655 3357999975
No 32
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=29.09 E-value=41 Score=29.09 Aligned_cols=36 Identities=28% Similarity=0.735 Sum_probs=29.2
Q ss_pred CCccccCCCCCCCcccCCCCCCcccchhhhhhHHhcCC
Q 013454 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (442)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~G~ 41 (442)
...|+.|+. .-|.|-.-..| ..+|-.|.-..|.-|+
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~lg~ 38 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSLGV 38 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhcCC
Confidence 578999998 45889988888 6799999877776554
No 33
>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=29.05 E-value=31 Score=25.55 Aligned_cols=28 Identities=29% Similarity=0.482 Sum_probs=18.8
Q ss_pred CCCccccCCCCCCCcccCCCCCCcccchhhh
Q 013454 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACG 33 (442)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGp~G~~~LCNACG 33 (442)
....|.+||.+ ..-|-++ . ..+-|++|+
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 34679999988 5545444 2 356888886
No 34
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=28.88 E-value=19 Score=26.44 Aligned_cols=32 Identities=34% Similarity=0.955 Sum_probs=22.3
Q ss_pred ccccCCCCCCCcc----cCCCCCC--cccchhhhhhHH
Q 013454 6 PCYHCGVTSTPLW----RNGPPEK--PVLCNACGSRWR 37 (442)
Q Consensus 6 ~CsnCgTt~TPlW----RrGp~G~--~~LCNACGL~~k 37 (442)
.|.+|+-...-.| |.+.++. -+.|-.||-.|+
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 6999997776555 5555442 248999998775
No 35
>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=28.82 E-value=18 Score=29.87 Aligned_cols=35 Identities=23% Similarity=0.352 Sum_probs=26.6
Q ss_pred CCccccCCCCCCCcccCCCCCCcccchhhhhhHHh
Q 013454 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRT 38 (442)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~ 38 (442)
.-.|..|+...|-+|.+...-...-|-+||.....
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred CccCCCCcCccEEEEEEeCCceEEEecCCCCeecc
Confidence 35799999999988655544556799999985443
No 36
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=27.95 E-value=28 Score=38.00 Aligned_cols=20 Identities=20% Similarity=0.316 Sum_probs=17.0
Q ss_pred HHHHHHhccCCchhHHHHHH
Q 013454 381 TLKRLALSNLTTSNWVEHYQ 400 (442)
Q Consensus 381 ~~~~l~l~~~~ks~~~e~y~ 400 (442)
-|.||..+++..+-|-+.|.
T Consensus 424 ylaR~~~~s~~~isw~fd~~ 443 (500)
T KOG0909|consen 424 YLARLEGDSPGNISWHFDFK 443 (500)
T ss_pred HHHHhcCCCCccccchhhhh
Confidence 47788889999999988887
No 37
>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=26.68 E-value=19 Score=30.34 Aligned_cols=18 Identities=39% Similarity=0.617 Sum_probs=13.0
Q ss_pred HHHHhhhCHHHHHHHHhc
Q 013454 312 KEFVGHLTHEEQQQLLKY 329 (442)
Q Consensus 312 ~ef~~~~t~eeq~~l~k~ 329 (442)
..|+|.||.+||++|=.|
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 468999999999999543
No 38
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.49 E-value=43 Score=22.31 Aligned_cols=22 Identities=32% Similarity=0.899 Sum_probs=15.7
Q ss_pred CccccCCCCCCCcccCCCCCCcccchhhhh
Q 013454 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (442)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (442)
+.|.+||+... .+.. .|-.||-
T Consensus 3 ~~Cp~Cg~~~~-------~~~~-fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEID-------PDAK-FCPNCGA 24 (26)
T ss_pred CCCcccCCcCC-------cccc-cChhhCC
Confidence 67999998542 2333 8999985
No 39
>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=26.45 E-value=20 Score=24.69 Aligned_cols=28 Identities=29% Similarity=0.698 Sum_probs=16.4
Q ss_pred CCccccCCCCCCCcccCCCCCCcccchhhhhh
Q 013454 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (442)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~ 35 (442)
.+-|..||....+. +.|-...|.+||..
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 47899999987765 33556689999974
No 40
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=25.90 E-value=34 Score=32.51 Aligned_cols=51 Identities=20% Similarity=0.322 Sum_probs=36.8
Q ss_pred CccccCCCCCCCcc--cCCCCCC----cccchhhhhhHHhcCCCCCCCCCcCCCCCC
Q 013454 5 GPCYHCGVTSTPLW--RNGPPEK----PVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (442)
Q Consensus 5 r~CsnCgTt~TPlW--RrGp~G~----~~LCNACGL~~k~~G~l~~~RPLs~rkd~i 55 (442)
+.|..|+...|-+- |...+|. .--|..||-++-+.-+..-..|+-.+++|.
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~~VvKkdg~ 57 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRPLIVVKKDGR 57 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeeccceEECcCCC
Confidence 57999999999886 5555552 237999999988876654445666666664
No 41
>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=25.35 E-value=32 Score=26.69 Aligned_cols=29 Identities=21% Similarity=0.541 Sum_probs=20.3
Q ss_pred CCccccCCCCCCCcccCCCCCCcccchhhhhhH
Q 013454 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRW 36 (442)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~ 36 (442)
...|..||..... ...+....|..||..+
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 3679999987655 3344567899999853
No 42
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=24.93 E-value=29 Score=35.59 Aligned_cols=27 Identities=26% Similarity=0.705 Sum_probs=24.5
Q ss_pred CCccccCCCCCCCcccCCCCCCcccchhh
Q 013454 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNAC 32 (442)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGp~G~~~LCNAC 32 (442)
.+.|+.|++. .|.|-.-..| ..+|-.|
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C 51 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRC 51 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeec
Confidence 4789999999 9999999889 7799998
No 43
>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=24.78 E-value=24 Score=25.90 Aligned_cols=28 Identities=36% Similarity=0.722 Sum_probs=19.7
Q ss_pred ccccCCCCCCCcccCCCCCCcccchhhhh
Q 013454 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (442)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (442)
+|..||..-+-+..-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 68899977665544444 44568999986
No 44
>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=24.69 E-value=18 Score=31.70 Aligned_cols=29 Identities=24% Similarity=0.654 Sum_probs=18.9
Q ss_pred ccccCCCCCCCcccCCCCCCcccchhhhhhHHhc
Q 013454 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTK 39 (442)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~ 39 (442)
.|.-|+-..=- ..|..++|++||.+|.+-
T Consensus 37 aCeiC~~~GY~-----q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 37 ACEICGPKGYY-----QEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred eccccCCCceE-----EECCEEEEecCCCEEehh
Confidence 47777332211 245678999999998764
No 45
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.47 E-value=20 Score=29.67 Aligned_cols=34 Identities=26% Similarity=0.470 Sum_probs=25.0
Q ss_pred CCccccCCCCCCCcc-cCCCCCCcccchhhhhhHHh
Q 013454 4 QGPCYHCGVTSTPLW-RNGPPEKPVLCNACGSRWRT 38 (442)
Q Consensus 4 ~r~CsnCgTt~TPlW-RrGp~G~~~LCNACGL~~k~ 38 (442)
.-.|..|.+..|-.| |.+. -...-|-+||...+.
T Consensus 10 GA~CP~C~~~Dtl~mW~En~-ve~vECV~CG~~~~~ 44 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENN-VEIVECVKCGHHMRE 44 (66)
T ss_pred cCCCcccchhhHHHHHHhcC-CceEehhhcchHhhh
Confidence 357999999988765 5544 346689999986644
No 46
>COG3952 Predicted membrane protein [Function unknown]
Probab=24.28 E-value=21 Score=32.24 Aligned_cols=20 Identities=35% Similarity=0.418 Sum_probs=15.0
Q ss_pred cccCCCCCCcccchhhhhhHHh
Q 013454 17 LWRNGPPEKPVLCNACGSRWRT 38 (442)
Q Consensus 17 lWRrGp~G~~~LCNACGL~~k~ 38 (442)
+||.+|-+ .+|++||++--.
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 46777766 499999997654
No 47
>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=23.40 E-value=1.3e+02 Score=31.55 Aligned_cols=72 Identities=17% Similarity=0.174 Sum_probs=58.6
Q ss_pred hhhhhcccCCCCce---eccccccccHHHHHhhhCHHHHHHHHhcCCCCCCCCCChhHHhhhchhhhhhhHHHHHHHHhh
Q 013454 288 EKLQILGSHTSPLC---EIDLNDILNFKEFVGHLTHEEQQQLLKYLPLNDTTVFPDSLNSMFDSLQFKENISSFQQLLAE 364 (442)
Q Consensus 288 ~~~~vl~~~~spl~---~idl~dv~nf~ef~~~~t~eeq~~l~k~lp~~d~~~~~~sl~~mf~s~qfk~n~~~fqql~~~ 364 (442)
+-..-.+.++-++| +|-+-=++.=+.+-+.||++||++|.+.|-++-..+.|+. |--+|+-|++.
T Consensus 96 dyw~~~~~~dQ~~VEaa~la~aL~~a~~~lW~~L~~~~k~~l~~wL~~~~~~~~~~n------------NW~lF~v~v~~ 163 (361)
T PF10022_consen 96 DYWGFIGDYDQRLVEAASLALALLRAPEWLWDPLDEEEKENLVDWLKQIRGIKPPDN------------NWLLFRVMVEA 163 (361)
T ss_pred cccCCcccchhhHhHHHHHHHHHHHCHHHHHhhCCHHHHHHHHHHHHhcCcCCCccc------------hhHHHHHHHHH
Confidence 34445666677777 6666677888999999999999999999999999998874 88889999988
Q ss_pred ccccccc
Q 013454 365 GVFDLSF 371 (442)
Q Consensus 365 gvf~~s~ 371 (442)
+...+..
T Consensus 164 ~L~~~G~ 170 (361)
T PF10022_consen 164 FLKKVGE 170 (361)
T ss_pred HHHHcCC
Confidence 8877743
No 48
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.66 E-value=25 Score=26.53 Aligned_cols=31 Identities=29% Similarity=0.513 Sum_probs=22.2
Q ss_pred ccccCCCCCCCcccCCCCCCcccchhhhhhHHhcCC
Q 013454 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (442)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~~G~ 41 (442)
.|.+||...+.. .+.+.-|..||-+.-.+.+
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~rIlyK~R 34 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYRILYKKR 34 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCceEEEEeC
Confidence 699999987764 2234579999986665543
No 49
>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=22.41 E-value=66 Score=26.73 Aligned_cols=22 Identities=23% Similarity=0.413 Sum_probs=19.6
Q ss_pred cHHHHHhhhCHHHHHHHHhcCC
Q 013454 310 NFKEFVGHLTHEEQQQLLKYLP 331 (442)
Q Consensus 310 nf~ef~~~~t~eeq~~l~k~lp 331 (442)
=||.+..+.+++||..+|..|-
T Consensus 40 lFE~~W~~~~~~ek~~m~~~l~ 61 (65)
T TIGR03092 40 LFEAIWKHANEQEKDEMLETLE 61 (65)
T ss_pred HHHHHHHhcCHHHHHHHHHHHH
Confidence 3999999999999999998763
No 50
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=21.58 E-value=68 Score=26.25 Aligned_cols=37 Identities=22% Similarity=0.154 Sum_probs=28.4
Q ss_pred cccccccHHHHHhhhCHHHHHHHHhcCCCCCCCCCChhHHh
Q 013454 304 DLNDILNFKEFVGHLTHEEQQQLLKYLPLNDTTVFPDSLNS 344 (442)
Q Consensus 304 dl~dv~nf~ef~~~~t~eeq~~l~k~lp~~d~~~~~~sl~~ 344 (442)
+-+..++|+||+..+....|-+.-+=|| +++|..|+.
T Consensus 56 ~~~g~I~~~eF~~~~~~~~~~~~g~~~~----~~~~~~~~~ 92 (96)
T smart00027 56 DNDGELDKDEFALAMHLIYRKLNGYPIP----ASLPPSLIP 92 (96)
T ss_pred CCCCCcCHHHHHHHHHHHHHHHcCCCCC----ccCCHhhcC
Confidence 4567899999999999888877766665 467777653
No 51
>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=21.18 E-value=45 Score=36.34 Aligned_cols=36 Identities=31% Similarity=0.767 Sum_probs=27.4
Q ss_pred CccccCCCCCCCcccC-------CCCCCcccchhhhhhHHhcC
Q 013454 5 GPCYHCGVTSTPLWRN-------GPPEKPVLCNACGSRWRTKG 40 (442)
Q Consensus 5 r~CsnCgTt~TPlWRr-------Gp~G~~~LCNACGL~~k~~G 40 (442)
-+|.|||....+.|.. .+....+.|-.||-.+.-+.
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~ 243 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHD 243 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHH
Confidence 4799999999988752 24556789999998766543
No 52
>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=20.84 E-value=43 Score=25.12 Aligned_cols=24 Identities=38% Similarity=0.910 Sum_probs=17.6
Q ss_pred CccccCCCCCCCcccCCCCCCcccchhhh
Q 013454 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACG 33 (442)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACG 33 (442)
..|..| .||+.| ...| ..+|-+|+
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 53
>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=20.75 E-value=39 Score=25.05 Aligned_cols=28 Identities=21% Similarity=0.574 Sum_probs=19.6
Q ss_pred ccccCCCCCCCcccCCCCCCcccchhhhh
Q 013454 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (442)
Q Consensus 6 ~CsnCgTt~TPlWRrGp~G~~~LCNACGL 34 (442)
+|.+|+..-+ .|+.-.+.....|-.||-
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFE-VLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeE-EEEecCCCCCCCCCCCCC
Confidence 6999997655 466533344557999997
No 54
>PRK00420 hypothetical protein; Validated
Probab=20.67 E-value=53 Score=29.49 Aligned_cols=29 Identities=28% Similarity=0.598 Sum_probs=20.4
Q ss_pred CccccCCCCCCCcccCCCCCCcccchhhhhhHHh
Q 013454 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRT 38 (442)
Q Consensus 5 r~CsnCgTt~TPlWRrGp~G~~~LCNACGL~~k~ 38 (442)
..|..|| +|+.|- ..| ..+|-+||-.+..
T Consensus 24 ~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCG---LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCC---Ccceec-CCC-ceECCCCCCeeee
Confidence 5788888 778773 234 4599999985443
No 55
>KOG0942 consensus E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.46 E-value=49 Score=38.90 Aligned_cols=37 Identities=22% Similarity=0.442 Sum_probs=28.0
Q ss_pred ceeccccccccHHHH-----------------HhhhCHHHHHHHHhcCCCCCCC
Q 013454 300 LCEIDLNDILNFKEF-----------------VGHLTHEEQQQLLKYLPLNDTT 336 (442)
Q Consensus 300 l~~idl~dv~nf~ef-----------------~~~~t~eeq~~l~k~lp~~d~~ 336 (442)
=..|||+|+=+|-|| ++.|++||+.+||||.-++--+
T Consensus 886 ~~pidldDLr~~teY~Ggy~~~hp~Iv~FWeVl~~F~~edKr~fLKFVTscsRp 939 (1001)
T KOG0942|consen 886 EDPIDLDDLRKNTEYAGGYSPDHPTIVMFWEVLEEFSDEDKRKFLKFVTSCSRP 939 (1001)
T ss_pred cCcccHHHHHhhccccCCCCCCCCchhHHHHHHHhcchHHHHHHHHHHhcCCCc
Confidence 356888876665555 7889999999999998655433
Done!