Query 009221
Match_columns 540
No_of_seqs 207 out of 690
Neff 3.1
Searched_HMMs 46136
Date Thu Mar 28 21:54:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009221.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009221hhsearch_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 1.7E-22 3.8E-27 183.5 5.5 123 272-400 7-137 (138)
2 cd00202 ZnF_GATA Zinc finger D 99.5 1.3E-14 2.8E-19 113.9 4.0 47 6-55 1-48 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 5.6E-14 1.2E-18 109.3 4.2 49 2-52 1-49 (52)
4 PF00320 GATA: GATA zinc finge 99.4 1.2E-13 2.7E-18 100.2 0.8 36 7-42 1-36 (36)
5 KOG1601 GATA-4/5/6 transcripti 98.6 1.8E-08 3.9E-13 91.3 3.5 49 4-55 199-247 (340)
6 COG5641 GAT1 GATA Zn-finger-co 98.3 2E-07 4.4E-12 100.4 2.3 48 5-55 159-211 (498)
7 KOG3554 Histone deacetylase co 92.2 0.095 2.1E-06 57.6 2.7 39 4-42 386-426 (693)
8 COG5641 GAT1 GATA Zn-finger-co 86.0 0.43 9.3E-06 52.7 2.0 48 5-55 298-346 (498)
9 KOG3037 Cell membrane glycopro 64.1 6.1 0.00013 42.0 3.1 65 300-366 222-287 (330)
10 smart00778 Prim_Zn_Ribbon Zinc 58.3 8.4 0.00018 29.1 2.1 33 2-34 1-33 (37)
11 PF14803 Nudix_N_2: Nudix N-te 57.4 3.6 7.7E-05 30.5 0.1 30 5-34 1-30 (34)
12 PRK12336 translation initiatio 44.5 8.1 0.00018 37.9 0.3 29 5-34 99-127 (201)
13 PF08271 TF_Zn_Ribbon: TFIIB z 40.8 7.2 0.00016 29.2 -0.5 30 5-37 1-30 (43)
14 COG5347 GTPase-activating prot 39.3 17 0.00038 38.4 1.8 37 3-41 19-55 (319)
15 KOG3740 Uncharacterized conser 38.3 13 0.00029 42.7 0.7 37 4-40 462-501 (706)
16 PF15396 FAM60A: Protein Famil 38.2 29 0.00062 35.2 3.0 17 27-43 50-66 (213)
17 KOG1598 Transcription initiati 37.9 18 0.0004 40.7 1.7 30 5-37 1-30 (521)
18 COG2816 NPY1 NTP pyrophosphohy 34.8 19 0.0004 37.7 1.1 32 3-38 110-141 (279)
19 PRK12286 rpmF 50S ribosomal pr 34.7 17 0.00037 29.6 0.7 22 5-35 28-49 (57)
20 PF01783 Ribosomal_L32p: Ribos 34.6 13 0.00028 29.8 -0.0 22 6-37 28-49 (56)
21 TIGR00244 transcriptional regu 34.5 22 0.00047 34.2 1.4 51 5-55 1-57 (147)
22 PF01096 TFIIS_C: Transcriptio 33.9 7.9 0.00017 28.9 -1.2 32 6-37 2-39 (39)
23 COG3529 Predicted nucleic-acid 33.6 9.4 0.0002 32.3 -1.0 33 5-37 11-43 (66)
24 PF01412 ArfGap: Putative GTPa 31.8 31 0.00067 30.7 1.9 37 3-41 12-48 (116)
25 PF09538 FYDLN_acid: Protein o 31.5 26 0.00056 31.8 1.3 34 1-39 6-39 (108)
26 PF09526 DUF2387: Probable met 31.3 16 0.00034 31.0 -0.0 33 5-37 9-41 (71)
27 TIGR02300 FYDLN_acid conserved 31.2 25 0.00055 33.2 1.3 34 1-39 6-39 (129)
28 PF08273 Prim_Zn_Ribbon: Zinc- 30.1 17 0.00036 27.9 -0.1 30 3-32 2-32 (40)
29 PRK00423 tfb transcription ini 29.9 27 0.00059 36.0 1.4 30 2-34 9-38 (310)
30 PF12760 Zn_Tnp_IS1595: Transp 28.6 32 0.0007 26.1 1.3 28 3-33 17-44 (46)
31 PF02701 zf-Dof: Dof domain, z 28.5 57 0.0012 27.7 2.8 42 4-45 5-49 (63)
32 PF11781 RRN7: RNA polymerase 27.9 30 0.00065 25.8 0.9 27 3-34 7-33 (36)
33 smart00440 ZnF_C2C2 C2C2 Zinc 27.8 21 0.00046 26.8 0.1 32 6-37 2-39 (40)
34 PF06394 Pepsin-I3: Pepsin inh 27.4 25 0.00055 30.4 0.5 18 310-327 34-51 (76)
35 PRK14892 putative transcriptio 26.2 27 0.00058 31.4 0.5 44 5-54 22-65 (99)
36 PF09297 zf-NADH-PPase: NADH p 25.6 22 0.00049 25.2 -0.1 28 4-35 3-30 (32)
37 PF13248 zf-ribbon_3: zinc-rib 23.8 52 0.0011 22.5 1.5 24 4-35 2-25 (26)
38 KOG0909 Peptide:N-glycanase [P 23.8 38 0.00082 37.9 1.2 25 374-398 417-443 (500)
39 PF09723 Zn-ribbon_8: Zinc rib 23.1 29 0.00063 26.2 0.1 29 5-34 6-34 (42)
40 PF07282 OrfB_Zn_ribbon: Putat 23.0 40 0.00086 26.9 0.9 29 4-36 28-56 (69)
41 smart00105 ArfGap Putative GTP 22.8 64 0.0014 28.7 2.2 36 4-41 3-38 (112)
42 TIGR02443 conserved hypothetic 22.1 30 0.00065 28.9 0.0 33 5-37 10-42 (59)
43 PF10022 DUF2264: Uncharacteri 21.8 1.3E+02 0.0029 32.2 4.7 76 286-373 96-174 (361)
44 PF04161 Arv1: Arv1-like famil 20.9 40 0.00086 33.0 0.6 30 5-34 1-32 (208)
45 smart00659 RPOLCX RNA polymera 20.9 31 0.00067 26.7 -0.1 32 5-41 3-34 (44)
46 COG3952 Predicted membrane pro 20.4 27 0.00058 32.4 -0.6 20 17-38 76-95 (113)
47 KOG0703 Predicted GTPase-activ 20.1 43 0.00094 35.3 0.7 28 4-33 25-52 (287)
No 1
>PF13919 ASXH: Asx homology domain
Probab=99.86 E-value=1.7e-22 Score=183.51 Aligned_cols=123 Identities=35% Similarity=0.354 Sum_probs=112.4
Q ss_pred chhhhhhhhccchhhhhhhcccCCCCceeeccccccchHHHhhhcCHHHHHHHHhcCCCCCCCC----CCchhh---hhh
Q 009221 272 GMQQDQLKRDKSQQEKLQILGSHTSPLCEIDLNDILNFKEFVGHLTHEEQQQLLKYLPLNDTTV----FPDSLN---SMF 344 (540)
Q Consensus 272 ~~~~~~lkr~k~~~~~~~vl~~~~spL~~idl~d~~nf~ef~~~~t~eeq~~l~k~lp~~d~~~----~p~sl~---~mf 344 (540)
.+..+++|+++.. .+||+++.||||.+||++|+|+++| ..||+||||+||+|||.||... .+++|+ +||
T Consensus 7 ~~~~~~~k~~~~~---~~~l~sp~SpL~~~dLr~L~N~~tw-~~L~~eeq~eLl~LLP~~D~~~~~~~~~~~~~l~~S~l 82 (138)
T PF13919_consen 7 KPSKAQLKRKWSE---EIDLTSPKSPLVNADLRALLNPETW-SCLPEEEQQELLKLLPEVDRQVGPDPPDDSLPLSESAL 82 (138)
T ss_pred CCCcccccCCccc---ceeecCCCCcccccCHHHHhCHHHH-hcCCHHHHHHHHHhCCCCCcccccCCCcccccCCHHHh
Confidence 3455677877744 7799999999999999999999999 9999999999999999999966 688898 999
Q ss_pred chhhhhhhhhHHHHHHhhhccccccCCCchhhhHHHHHHH-hhcCCcchhHHHHHhh
Q 009221 345 DSLQFKENISSFQQLLAEGVFDLSFLGVATEDCRTLKRLA-LSNLTTSNWVEHYQSL 400 (540)
Q Consensus 345 ~s~qfk~n~~~fqqll~~gvf~~s~~~~k~e~~~~~~~l~-ls~~~ks~~~e~y~~l 400 (540)
+|.+|.+++..||+.|++|.|+..+. +.+...+.+|.+ ..|..|.+|.|.|.--
T Consensus 83 nn~~F~~a~~~fqe~L~~G~~~pe~~--~~~~~~~~~r~~g~~d~~K~~~fE~~wG~ 137 (138)
T PF13919_consen 83 NNEFFRDACQEFQERLAEGEFDPEWQ--RQAWKAEEEREAGKFDPWKEEEFEEYWGQ 137 (138)
T ss_pred cCHHHHHHHHHHHHHHHcCCCChHHH--HHHHHHHHHHHhccchhHHHHHHHHHhCC
Confidence 99999999999999999999999876 688899999999 9999999999999754
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=99.50 E-value=1.3e-14 Score=113.94 Aligned_cols=47 Identities=47% Similarity=1.107 Sum_probs=42.4
Q ss_pred ccccCCCCCCCcccCCCCCCCccchhhhhhHHhcCCCCCCCCCCCCC-CCC
Q 009221 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARA-EPD 55 (540)
Q Consensus 6 ~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~G~l~~~RPLs~r~-d~i 55 (540)
+|+||+++.||+||+||.|..+|||||||||++++.. ||+.++. +.+
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 5999999999999999988899999999999999976 8888877 444
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.45 E-value=5.6e-14 Score=109.28 Aligned_cols=49 Identities=45% Similarity=1.000 Sum_probs=42.4
Q ss_pred CCCCccccCCCCCCCcccCCCCCCCccchhhhhhHHhcCCCCCCCCCCCCC
Q 009221 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARA 52 (540)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~G~l~~~RPLs~r~ 52 (540)
+..+.|+||+++.||+||+||.|..+|||||||||++++.+ .||+.+.+
T Consensus 1 ~~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~--~rp~~~~~ 49 (52)
T smart00401 1 GSGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL--KRPLSLKK 49 (52)
T ss_pred CCCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC--CCcccccc
Confidence 45789999999999999999999889999999999999986 36655544
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=99.36 E-value=1.2e-13 Score=100.23 Aligned_cols=36 Identities=47% Similarity=1.127 Sum_probs=29.0
Q ss_pred cccCCCCCCCcccCCCCCCCccchhhhhhHHhcCCC
Q 009221 7 CYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTL 42 (540)
Q Consensus 7 CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~G~l 42 (540)
|.+|+++.||+||+||.|..+||||||+||++++++
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 899999999999999999888999999999999863
No 5
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.64 E-value=1.8e-08 Score=91.31 Aligned_cols=49 Identities=43% Similarity=0.938 Sum_probs=42.3
Q ss_pred CCccccCCCCCCCcccCCCCCCCccchhhhhhHHhcCCCCCCCCCCCCCCCC
Q 009221 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (540)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~G~l~~~RPLs~r~d~i 55 (540)
...|.+|+++.||+||+++.|...+|||||++++++++. |++.+....+
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 6766666655
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.33 E-value=2e-07 Score=100.43 Aligned_cols=48 Identities=35% Similarity=0.747 Sum_probs=43.7
Q ss_pred CccccCCCCCCCcccCCCC-----CCCccchhhhhhHHhcCCCCCCCCCCCCCCCC
Q 009221 5 GPCYHCGVTSTPLWRNGPP-----EKPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~-----G~~tLCNACGL~~k~~G~l~~~RPLs~r~d~i 55 (540)
.+|.||.|+.||+|||+.. | -+|||||||+++.||+++. |+.++.+.+
T Consensus 159 ~vc~Nc~t~stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r~--P~t~ks~~~ 211 (498)
T COG5641 159 HVCSNCKTTSTPLWRRASSESSLPG-NNLCNACGLYLKLHGSPRA--PISLKSDSI 211 (498)
T ss_pred chhccccccCCccccccccccccCC-ccccccccccccccCCcCC--Ccccccccc
Confidence 4899999999999999999 5 4699999999999999932 999999998
No 7
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=92.19 E-value=0.095 Score=57.61 Aligned_cols=39 Identities=28% Similarity=0.614 Sum_probs=33.3
Q ss_pred CCccccCCCCCCCcc--cCCCCCCCccchhhhhhHHhcCCC
Q 009221 4 QGPCYHCGVTSTPLW--RNGPPEKPVLCNACGSRWRTKGTL 42 (540)
Q Consensus 4 ~r~CsnCgTt~TPlW--RrGP~G~~tLCNACGL~~k~~G~l 42 (540)
.+.|.+|+|+..-.| .-+|+.+..||-.|.+||++.|-+
T Consensus 386 g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccccccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 468999999999999 445666778999999999998865
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=85.98 E-value=0.43 Score=52.71 Aligned_cols=48 Identities=31% Similarity=0.593 Sum_probs=39.5
Q ss_pred CccccCCC-CCCCcccCCCCCCCccchhhhhhHHhcCCCCCCCCCCCCCCCC
Q 009221 5 GPCYHCGV-TSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (540)
Q Consensus 5 r~CsnCgT-t~TPlWRrGP~G~~tLCNACGL~~k~~G~l~~~RPLs~r~d~i 55 (540)
..|.+|++ +.||.|||...-.-++|||||++.+.++.. +|+.-+.+..
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 45778877 789999998877778999999999999887 7777666665
No 9
>KOG3037 consensus Cell membrane glycoprotein [General function prediction only]
Probab=64.13 E-value=6.1 Score=42.00 Aligned_cols=65 Identities=25% Similarity=0.438 Sum_probs=57.3
Q ss_pred eeccccccchHHHhhhcCH-HHHHHHHhcCCCCCCCCCCchhhhhhchhhhhhhhhHHHHHHhhhccc
Q 009221 300 EIDLNDILNFKEFVGHLTH-EEQQQLLKYLPLNDTTVFPDSLNSMFDSLQFKENISSFQQLLAEGVFD 366 (540)
Q Consensus 300 ~idl~d~~nf~ef~~~~t~-eeq~~l~k~lp~~d~~~~p~sl~~mf~s~qfk~n~~~fqqll~~gvf~ 366 (540)
.|||-+||-=++-++.|++ .-|.+||-+||.=+... +-+.+..+|+||..-|..|-+-|+-|--+
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 46889999999866644 99999999999999999999999988655
No 10
>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=58.34 E-value=8.4 Score=29.13 Aligned_cols=33 Identities=27% Similarity=0.783 Sum_probs=24.8
Q ss_pred CCCCccccCCCCCCCcccCCCCCCCccchhhhh
Q 009221 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (540)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL 34 (540)
++..+|..|+.+..-.|.+.......+|+.||.
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 11
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=57.35 E-value=3.6 Score=30.47 Aligned_cols=30 Identities=27% Similarity=0.560 Sum_probs=15.6
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhh
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL 34 (540)
+-|.+||..-+..--.|.+-...+|.+||.
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 359999988543333466666779999985
No 12
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=44.53 E-value=8.1 Score=37.88 Aligned_cols=29 Identities=31% Similarity=0.678 Sum_probs=22.1
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhh
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL 34 (540)
-.|..|+...|-+-+.+.. --.-|+|||-
T Consensus 99 V~C~~C~~pdT~l~k~~~~-~~l~C~aCGa 127 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRV-LMLRCDACGA 127 (201)
T ss_pred EECCCCCCCCcEEEEcCCe-EEEEcccCCC
Confidence 3699999999999776421 1237999997
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=40.80 E-value=7.2 Score=29.20 Aligned_cols=30 Identities=20% Similarity=0.542 Sum_probs=19.4
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhhhHH
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k 37 (540)
..|.+|+.+. ..+- ...| ..+|..||+-+.
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 3699999977 3443 2334 459999998443
No 14
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=39.32 E-value=17 Score=38.36 Aligned_cols=37 Identities=27% Similarity=0.654 Sum_probs=29.8
Q ss_pred CCCccccCCCCCCCcccCCCCCCCccchhhhhhHHhcCC
Q 009221 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (540)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~G~ 41 (540)
....|+.|+++. |.|-.-.-| ..||-.|.=-.|.=|+
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 457899999999 999999999 6799999654444443
No 15
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.28 E-value=13 Score=42.70 Aligned_cols=37 Identities=22% Similarity=0.611 Sum_probs=28.8
Q ss_pred CCccccCCCCCCCcccCCCCC---CCccchhhhhhHHhcC
Q 009221 4 QGPCYHCGVTSTPLWRNGPPE---KPVLCNACGSRWRTKG 40 (540)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGP~G---~~tLCNACGL~~k~~G 40 (540)
.-.|..|.|..||.|+.-+.+ ..++|.+|----.++.
T Consensus 462 P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqkkA 501 (706)
T KOG3740|consen 462 PYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQKKA 501 (706)
T ss_pred chhhhhcccccccccccccccCcchHHHHHhhhhhccccc
Confidence 457999999999999987666 4569999977544433
No 16
>PF15396 FAM60A: Protein Family FAM60A
Probab=38.18 E-value=29 Score=35.22 Aligned_cols=17 Identities=29% Similarity=0.436 Sum_probs=14.0
Q ss_pred ccchhhhhhHHhcCCCC
Q 009221 27 VLCNACGSRWRTKGTLA 43 (540)
Q Consensus 27 tLCNACGL~~k~~G~l~ 43 (540)
.+||||-|..++...+|
T Consensus 50 eICNACVLLVKRwKKLP 66 (213)
T PF15396_consen 50 EICNACVLLVKRWKKLP 66 (213)
T ss_pred hhhHHHHHHHHHHhhCC
Confidence 38999999999877663
No 17
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=37.93 E-value=18 Score=40.66 Aligned_cols=30 Identities=27% Similarity=0.646 Sum_probs=20.2
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhhhHH
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k 37 (540)
+.|.|||.+.=- |+-..| -..|++||.-.-
T Consensus 1 ~~C~~C~~s~fe--~d~a~g-~~~C~~CG~v~E 30 (521)
T KOG1598|consen 1 MVCKNCGGSNFE--RDEATG-NLYCTACGTVLE 30 (521)
T ss_pred CcCCCCCCCCcc--cccccC-Cceeccccceee
Confidence 479999987632 223334 459999998443
No 18
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=34.81 E-value=19 Score=37.71 Aligned_cols=32 Identities=22% Similarity=0.481 Sum_probs=24.7
Q ss_pred CCCccccCCCCCCCcccCCCCCCCccchhhhhhHHh
Q 009221 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRT 38 (540)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~ 38 (540)
..+.|..||+...+. ..|-..+|+.||.++..
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEHFP 141 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCccCC
Confidence 357899999998885 44556799999986654
No 19
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=34.65 E-value=17 Score=29.57 Aligned_cols=22 Identities=32% Similarity=0.807 Sum_probs=15.1
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhhh
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~ 35 (540)
-.|.+||...-| ..+|..||.|
T Consensus 28 ~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 28 VECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred eECCCCCCccCC---------eEECCCCCcC
Confidence 357888776554 4588888854
No 20
>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=34.61 E-value=13 Score=29.77 Aligned_cols=22 Identities=27% Similarity=0.863 Sum_probs=13.5
Q ss_pred ccccCCCCCCCcccCCCCCCCccchhhhhhHH
Q 009221 6 PCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (540)
Q Consensus 6 ~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k 37 (540)
.|.+||...- +..+|.+|| ||+
T Consensus 28 ~c~~cg~~~~---------~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 28 KCPNCGEPKL---------PHRVCPSCG-YYK 49 (56)
T ss_dssp ESSSSSSEES---------TTSBCTTTB-BSS
T ss_pred eeccCCCEec---------ccEeeCCCC-eEC
Confidence 5777774322 245888888 444
No 21
>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=34.51 E-value=22 Score=34.20 Aligned_cols=51 Identities=18% Similarity=0.217 Sum_probs=34.4
Q ss_pred CccccCCCCCCCcc--cCCCCCC----CccchhhhhhHHhcCCCCCCCCCCCCCCCC
Q 009221 5 GPCYHCGVTSTPLW--RNGPPEK----PVLCNACGSRWRTKGTLANYTPLHARAEPD 55 (540)
Q Consensus 5 r~CsnCgTt~TPlW--RrGP~G~----~tLCNACGL~~k~~G~l~~~RPLs~r~d~i 55 (540)
+.|..|+...|-+- |-..+|. .--|.+||-+|-..-+.....|+-.+++|.
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 4444552 238999999988877654334444444444
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=33.95 E-value=7.9 Score=28.91 Aligned_cols=32 Identities=31% Similarity=0.878 Sum_probs=20.0
Q ss_pred ccccCCCCCCCcc----cCCCCCCC--ccchhhhhhHH
Q 009221 6 PCYHCGVTSTPLW----RNGPPEKP--VLCNACGSRWR 37 (540)
Q Consensus 6 ~CsnCgTt~TPlW----RrGP~G~~--tLCNACGL~~k 37 (540)
.|.+||-..+-.| |.++++.- +.|..||-+|+
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 5899999886655 44544421 38999998774
No 23
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.62 E-value=9.4 Score=32.27 Aligned_cols=33 Identities=24% Similarity=0.404 Sum_probs=25.2
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhhhHH
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k 37 (540)
-.|..|.+..|-.|.+-..-...-|-+||-..+
T Consensus 11 A~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 11 AVCPACQAQDTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred CCCcccchhhHHHHHHhcCCceEehhhcchHhh
Confidence 579999999998755544445678999998654
No 24
>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=31.75 E-value=31 Score=30.72 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=25.7
Q ss_pred CCCccccCCCCCCCcccCCCCCCCccchhhhhhHHhcCC
Q 009221 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (540)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~G~ 41 (540)
..+.|+.|+.... .|-.-..| ..||-.|.-..|.-|+
T Consensus 12 ~N~~CaDCg~~~p-~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 12 GNKVCADCGAPNP-TWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp TCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred CcCcCCCCCCCCC-CEEEeecC-hhhhHHHHHHHHHhcc
Confidence 3578999996554 89998888 5699999888877774
No 25
>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=31.47 E-value=26 Score=31.80 Aligned_cols=34 Identities=26% Similarity=0.799 Sum_probs=22.2
Q ss_pred CCCCCccccCCCCCCCcccCCCCCCCccchhhhhhHHhc
Q 009221 1 MGKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTK 39 (540)
Q Consensus 1 mGk~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~ 39 (540)
+|.+|.|.+||+.===|=| .+.+|--||--|..-
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 4888888888886433311 234788888866543
No 26
>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=31.32 E-value=16 Score=31.03 Aligned_cols=33 Identities=24% Similarity=0.383 Sum_probs=26.3
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhhhHH
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k 37 (540)
-.|..|+...|.+|.+.......-|-+||..-.
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 579999999999876555566779999998544
No 27
>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=31.19 E-value=25 Score=33.23 Aligned_cols=34 Identities=21% Similarity=0.422 Sum_probs=24.3
Q ss_pred CCCCCccccCCCCCCCcccCCCCCCCccchhhhhhHHhc
Q 009221 1 MGKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTK 39 (540)
Q Consensus 1 mGk~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~ 39 (540)
+|.++.|.+||+.-==+=| .+.+|-.||--|...
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 4889999999987544422 345899999876544
No 28
>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=30.09 E-value=17 Score=27.92 Aligned_cols=30 Identities=27% Similarity=0.654 Sum_probs=17.9
Q ss_pred CCCccccCCCCCCCc-ccCCCCCCCccchhh
Q 009221 3 KQGPCYHCGVTSTPL-WRNGPPEKPVLCNAC 32 (540)
Q Consensus 3 k~r~CsnCgTt~TPl-WRrGP~G~~tLCNAC 32 (540)
+..+|..|+.+.--. |..........|+.|
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 456899999988877 876444446799999
No 29
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=29.88 E-value=27 Score=35.96 Aligned_cols=30 Identities=20% Similarity=0.568 Sum_probs=21.3
Q ss_pred CCCCccccCCCCCCCcccCCCCCCCccchhhhh
Q 009221 2 GKQGPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (540)
Q Consensus 2 Gk~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL 34 (540)
++...|.+||.+ ..+.. -..| .++|..||+
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 33343 3456 469999999
No 30
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=28.59 E-value=32 Score=26.13 Aligned_cols=28 Identities=29% Similarity=0.497 Sum_probs=19.3
Q ss_pred CCCccccCCCCCCCcccCCCCCCCccchhhh
Q 009221 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACG 33 (540)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGP~G~~tLCNACG 33 (540)
....|.+||.+ ...|-++ ....-|++|+
T Consensus 17 ~g~~CP~Cg~~-~~~~~~~--~~~~~C~~C~ 44 (46)
T PF12760_consen 17 DGFVCPHCGST-KHYRLKT--RGRYRCKACR 44 (46)
T ss_pred CCCCCCCCCCe-eeEEeCC--CCeEECCCCC
Confidence 44679999988 5555555 2356799886
No 31
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=28.51 E-value=57 Score=27.65 Aligned_cols=42 Identities=31% Similarity=0.659 Sum_probs=30.6
Q ss_pred CCccccCCCCCCCc--ccCC-CCCCCccchhhhhhHHhcCCCCCC
Q 009221 4 QGPCYHCGVTSTPL--WRNG-PPEKPVLCNACGSRWRTKGTLANY 45 (540)
Q Consensus 4 ~r~CsnCgTt~TPl--WRrG-P~G~~tLCNACGL~~k~~G~l~~~ 45 (540)
...|..|..+.|-- .-+. ..-+...|-+|.-||...|.+++.
T Consensus 5 ~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnV 49 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNV 49 (63)
T ss_pred CCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCC
Confidence 46899999988754 2222 223557999999999999998543
No 32
>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=27.88 E-value=30 Score=25.80 Aligned_cols=27 Identities=30% Similarity=0.791 Sum_probs=19.0
Q ss_pred CCCccccCCCCCCCcccCCCCCCCccchhhhh
Q 009221 3 KQGPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (540)
Q Consensus 3 k~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL 34 (540)
....|..|+.. |-...+| .+.|..||-
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 4445557 458999984
No 33
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=27.82 E-value=21 Score=26.84 Aligned_cols=32 Identities=34% Similarity=0.996 Sum_probs=22.2
Q ss_pred ccccCCCCCCCcc----cCCCCCCC--ccchhhhhhHH
Q 009221 6 PCYHCGVTSTPLW----RNGPPEKP--VLCNACGSRWR 37 (540)
Q Consensus 6 ~CsnCgTt~TPlW----RrGP~G~~--tLCNACGL~~k 37 (540)
.|..|+-...-.| |.+.++.- +.|-.||-+|+
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 6999997776655 45544422 38999998875
No 34
>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=27.36 E-value=25 Score=30.43 Aligned_cols=18 Identities=39% Similarity=0.617 Sum_probs=13.3
Q ss_pred HHHhhhcCHHHHHHHHhc
Q 009221 310 KEFVGHLTHEEQQQLLKY 327 (540)
Q Consensus 310 ~ef~~~~t~eeq~~l~k~ 327 (540)
..|+|.||.+||++|=.|
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 469999999999999544
No 35
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.16 E-value=27 Score=31.41 Aligned_cols=44 Identities=16% Similarity=0.303 Sum_probs=26.4
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhhhHHhcCCCCCCCCCCCCCCC
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGTLANYTPLHARAEP 54 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~G~l~~~RPLs~r~d~ 54 (540)
-.|.+|+...-++ ..+.......|-.||.|+-.. + ++|..+-|+
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 3599999533322 112234567999999987652 2 555555443
No 36
>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=25.64 E-value=22 Score=25.16 Aligned_cols=28 Identities=29% Similarity=0.698 Sum_probs=16.6
Q ss_pred CCccccCCCCCCCcccCCCCCCCccchhhhhh
Q 009221 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (540)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~ 35 (540)
.+-|..||....+. +.|-...|.+||..
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 46799999988775 34556689999974
No 37
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.84 E-value=52 Score=22.54 Aligned_cols=24 Identities=29% Similarity=0.886 Sum_probs=16.6
Q ss_pred CCccccCCCCCCCcccCCCCCCCccchhhhhh
Q 009221 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSR 35 (540)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~ 35 (540)
.+.|.+||+...+ +.. .|-.||-.
T Consensus 2 ~~~Cp~Cg~~~~~-------~~~-fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDP-------DAK-FCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCc-------ccc-cChhhCCC
Confidence 3679999995432 333 89999863
No 38
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=23.78 E-value=38 Score=37.87 Aligned_cols=25 Identities=20% Similarity=0.336 Sum_probs=18.4
Q ss_pred hhhhH--HHHHHHhhcCCcchhHHHHH
Q 009221 374 TEDCR--TLKRLALSNLTTSNWVEHYQ 398 (540)
Q Consensus 374 ~e~~~--~~~~l~ls~~~ks~~~e~y~ 398 (540)
..|++ -|.||..++...+-|-+.|.
T Consensus 417 e~Dw~mtylaR~~~~s~~~isw~fd~~ 443 (500)
T KOG0909|consen 417 ETDWKMTYLARLEGDSPGNISWHFDFK 443 (500)
T ss_pred HhhHHHHHHHHhcCCCCccccchhhhh
Confidence 34554 46677788999999988876
No 39
>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=23.05 E-value=29 Score=26.15 Aligned_cols=29 Identities=34% Similarity=0.651 Sum_probs=20.5
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhh
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGS 34 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL 34 (540)
-.|..||..-+-+..-.. .....|-+||-
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 369999987666554444 44568999986
No 40
>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=23.03 E-value=40 Score=26.93 Aligned_cols=29 Identities=21% Similarity=0.541 Sum_probs=20.3
Q ss_pred CCccccCCCCCCCcccCCCCCCCccchhhhhhH
Q 009221 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRW 36 (540)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~ 36 (540)
-..|..||....- ...+....|..||..+
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 3344566899999853
No 41
>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=22.81 E-value=64 Score=28.65 Aligned_cols=36 Identities=28% Similarity=0.732 Sum_probs=29.2
Q ss_pred CCccccCCCCCCCcccCCCCCCCccchhhhhhHHhcCC
Q 009221 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (540)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~G~ 41 (540)
.+.|++|+.. -|.|-.-..| ..+|-.|.-..|.-|+
T Consensus 3 N~~CaDC~~~-~p~w~s~~~G-ifvC~~CsgiHR~lg~ 38 (112)
T smart00105 3 NKKCFDCGAP-NPTWASVNLG-VFLCIECSGIHRSLGV 38 (112)
T ss_pred CCcccCCCCC-CCCcEEeccc-eeEhHHhHHHHHhcCC
Confidence 5789999984 5889988888 5699999877776664
No 42
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=22.06 E-value=30 Score=28.89 Aligned_cols=33 Identities=21% Similarity=0.349 Sum_probs=25.0
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhhhHH
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWR 37 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k 37 (540)
-.|..|+...|-+|.+...-...-|-+||..-+
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~ 42 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQEQ 42 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCccc
Confidence 479999999998865444445669999998543
No 43
>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=21.79 E-value=1.3e+02 Score=32.24 Aligned_cols=76 Identities=16% Similarity=0.123 Sum_probs=60.1
Q ss_pred hhhhhcccCCCCce---eeccccccchHHHhhhcCHHHHHHHHhcCCCCCCCCCCchhhhhhchhhhhhhhhHHHHHHhh
Q 009221 286 EKLQILGSHTSPLC---EIDLNDILNFKEFVGHLTHEEQQQLLKYLPLNDTTVFPDSLNSMFDSLQFKENISSFQQLLAE 362 (540)
Q Consensus 286 ~~~~vl~~~~spL~---~idl~d~~nf~ef~~~~t~eeq~~l~k~lp~~d~~~~p~sl~~mf~s~qfk~n~~~fqqll~~ 362 (540)
+-..-.+.++-++| +|-+-=++.=+.+-+.||++||++|.+.|-++-..+.|+ -|--+|+-|++.
T Consensus 96 dyw~~~~~~dQ~~VEaa~la~aL~~a~~~lW~~L~~~~k~~l~~wL~~~~~~~~~~------------nNW~lF~v~v~~ 163 (361)
T PF10022_consen 96 DYWGFIGDYDQRLVEAASLALALLRAPEWLWDPLDEEEKENLVDWLKQIRGIKPPD------------NNWLLFRVMVEA 163 (361)
T ss_pred cccCCcccchhhHhHHHHHHHHHHHCHHHHHhhCCHHHHHHHHHHHHhcCcCCCcc------------chhHHHHHHHHH
Confidence 33445566667777 666666777889999999999999999999998888885 689999999999
Q ss_pred hccccccCCCc
Q 009221 363 GVFDLSFLGVA 373 (540)
Q Consensus 363 gvf~~s~~~~k 373 (540)
+...++..-..
T Consensus 164 ~L~~~G~~~d~ 174 (361)
T PF10022_consen 164 FLKKVGEEYDE 174 (361)
T ss_pred HHHHcCCCCcH
Confidence 98888543333
No 44
>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=20.88 E-value=40 Score=32.99 Aligned_cols=30 Identities=30% Similarity=0.714 Sum_probs=23.7
Q ss_pred CccccCCCCCCCcccCCCCC--CCccchhhhh
Q 009221 5 GPCYHCGVTSTPLWRNGPPE--KPVLCNACGS 34 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G--~~tLCNACGL 34 (540)
.+|.+||.....++|+-..| +-+-|..||-
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~ 32 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGK 32 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence 47999999999999886555 3357999975
No 45
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=20.86 E-value=31 Score=26.72 Aligned_cols=32 Identities=28% Similarity=0.417 Sum_probs=22.5
Q ss_pred CccccCCCCCCCcccCCCCCCCccchhhhhhHHhcCC
Q 009221 5 GPCYHCGVTSTPLWRNGPPEKPVLCNACGSRWRTKGT 41 (540)
Q Consensus 5 r~CsnCgTt~TPlWRrGP~G~~tLCNACGL~~k~~G~ 41 (540)
-.|.+||...+..+ +...-|..||-+.-.+.+
T Consensus 3 Y~C~~Cg~~~~~~~-----~~~irC~~CG~rIlyK~R 34 (44)
T smart00659 3 YICGECGRENEIKS-----KDVVRCRECGYRILYKKR 34 (44)
T ss_pred EECCCCCCEeecCC-----CCceECCCCCceEEEEeC
Confidence 36999999877651 234579999986665543
No 46
>COG3952 Predicted membrane protein [Function unknown]
Probab=20.44 E-value=27 Score=32.36 Aligned_cols=20 Identities=35% Similarity=0.418 Sum_probs=14.9
Q ss_pred cccCCCCCCCccchhhhhhHHh
Q 009221 17 LWRNGPPEKPVLCNACGSRWRT 38 (540)
Q Consensus 17 lWRrGP~G~~tLCNACGL~~k~ 38 (540)
+||.+|-+ .+|++||++-..
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 46777755 499999997654
No 47
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=20.06 E-value=43 Score=35.27 Aligned_cols=28 Identities=25% Similarity=0.686 Sum_probs=24.6
Q ss_pred CCccccCCCCCCCcccCCCCCCCccchhhh
Q 009221 4 QGPCYHCGVTSTPLWRNGPPEKPVLCNACG 33 (540)
Q Consensus 4 ~r~CsnCgTt~TPlWRrGP~G~~tLCNACG 33 (540)
.+.|+.|++. .|.|-.-.-| .-+|-.|.
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 5789999999 9999998888 66999984
Done!