Query 044150
Match_columns 381
No_of_seqs 224 out of 786
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 11:54:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044150.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044150hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.5 2.3E-14 4.9E-19 108.5 4.1 43 297-342 1-43 (54)
2 smart00401 ZnF_GATA zinc finge 99.4 6E-14 1.3E-18 105.2 3.6 39 295-333 3-41 (52)
3 PF00320 GATA: GATA zinc finge 99.4 5E-14 1.1E-18 98.5 0.5 35 298-332 1-35 (36)
4 KOG1601 GATA-4/5/6 transcripti 99.1 4.8E-11 1E-15 105.2 4.5 71 295-365 199-303 (340)
5 COG5641 GAT1 GATA Zn-finger-co 97.8 9E-06 2E-10 85.1 2.2 53 293-348 156-213 (498)
6 KOG3554 Histone deacetylase co 89.0 0.4 8.6E-06 51.1 3.7 38 292-329 383-422 (693)
7 PF14803 Nudix_N_2: Nudix N-te 67.2 1.7 3.7E-05 30.7 -0.1 30 296-325 1-30 (34)
8 PRK03988 translation initiatio 63.2 2.3 5E-05 38.2 -0.1 31 296-327 103-133 (138)
9 COG5641 GAT1 GATA Zn-finger-co 62.5 4.4 9.6E-05 43.4 1.8 37 295-331 297-334 (498)
10 TIGR00311 aIF-2beta translatio 60.9 2.8 6E-05 37.5 0.0 31 296-327 98-128 (133)
11 PRK14892 putative transcriptio 60.2 5.3 0.00011 34.3 1.6 34 295-329 21-54 (99)
12 smart00653 eIF2B_5 domain pres 57.2 3.4 7.5E-05 35.8 -0.0 29 296-325 81-109 (110)
13 PRK12336 translation initiatio 55.5 3.7 8.1E-05 38.6 -0.1 32 296-328 99-130 (201)
14 PF01783 Ribosomal_L32p: Ribos 53.7 4.4 9.5E-05 31.0 0.0 25 294-328 25-49 (56)
15 PRK12286 rpmF 50S ribosomal pr 53.3 7.1 0.00015 30.3 1.1 25 293-326 25-49 (57)
16 KOG3740 Uncharacterized conser 51.9 7.8 0.00017 42.8 1.5 40 292-331 459-501 (706)
17 COG5347 GTPase-activating prot 51.2 6.4 0.00014 39.9 0.8 32 295-328 20-51 (319)
18 PF08271 TF_Zn_Ribbon: TFIIB z 47.0 6.3 0.00014 28.2 -0.0 30 297-329 2-31 (43)
19 PF01873 eIF-5_eIF-2B: Domain 45.7 6.7 0.00015 34.7 -0.1 29 296-325 94-122 (125)
20 PF01412 ArfGap: Putative GTPa 44.9 14 0.00031 31.5 1.8 33 295-329 13-45 (116)
21 PRK13130 H/ACA RNA-protein com 39.7 23 0.00049 27.7 2.0 49 295-362 5-53 (56)
22 COG2816 NPY1 NTP pyrophosphohy 39.3 13 0.00027 37.4 0.7 31 294-328 110-140 (279)
23 PLN03114 ADP-ribosylation fact 38.7 16 0.00035 38.2 1.4 33 295-329 22-54 (395)
24 PF07282 OrfB_Zn_ribbon: Putat 36.6 15 0.00033 28.1 0.7 31 294-328 27-57 (69)
25 PF02701 zf-Dof: Dof domain, z 35.0 47 0.001 26.8 3.1 43 294-336 4-49 (63)
26 smart00105 ArfGap Putative GTP 33.1 30 0.00066 29.4 2.0 34 295-330 3-36 (112)
27 TIGR01385 TFSII transcription 33.1 18 0.0004 36.3 0.7 38 291-328 254-297 (299)
28 PHA03309 transcriptional regul 32.9 33 0.00072 39.9 2.7 39 205-244 1794-1832(2033)
29 PF01096 TFIIS_C: Transcriptio 32.6 7.4 0.00016 27.7 -1.5 32 297-328 2-39 (39)
30 KOG0909 Peptide:N-glycanase [P 31.5 21 0.00045 38.3 0.9 49 296-362 162-221 (500)
31 COG3529 Predicted nucleic-acid 31.3 10 0.00022 30.6 -1.1 33 296-328 11-43 (66)
32 PF06677 Auto_anti-p27: Sjogre 31.1 19 0.00041 26.4 0.4 25 295-324 17-41 (41)
33 TIGR00244 transcriptional regu 30.8 24 0.00053 32.5 1.1 34 296-329 1-40 (147)
34 KOG1598 Transcription initiati 30.7 25 0.00054 38.1 1.3 31 296-329 1-31 (521)
35 PF13717 zinc_ribbon_4: zinc-r 30.6 15 0.00032 25.9 -0.3 32 296-327 3-35 (36)
36 PF04810 zf-Sec23_Sec24: Sec23 30.3 21 0.00046 25.4 0.5 32 295-326 2-33 (40)
37 COG3952 Predicted membrane pro 27.4 19 0.0004 31.9 -0.3 19 308-328 76-94 (113)
38 PF09538 FYDLN_acid: Protein o 27.1 36 0.00078 29.5 1.5 15 314-328 6-20 (108)
39 PF11781 RRN7: RNA polymerase 27.0 27 0.0006 24.7 0.6 26 295-325 8-33 (36)
40 TIGR01031 rpmF_bact ribosomal 26.7 34 0.00073 26.4 1.1 26 293-328 24-49 (55)
41 PRK00420 hypothetical protein; 26.3 27 0.00058 30.7 0.5 30 295-329 23-52 (112)
42 PF09297 zf-NADH-PPase: NADH p 25.6 12 0.00026 25.3 -1.4 29 295-327 3-31 (32)
43 PF12760 Zn_Tnp_IS1595: Transp 25.2 28 0.00061 25.3 0.4 27 296-325 19-45 (46)
44 PRK00241 nudC NADH pyrophospha 25.1 26 0.00056 34.0 0.2 32 293-328 97-128 (256)
45 PRK00464 nrdR transcriptional 25.1 31 0.00068 31.6 0.7 33 296-328 1-39 (154)
46 PF12773 DZR: Double zinc ribb 24.9 42 0.00091 24.1 1.3 30 294-328 11-40 (50)
47 COG5349 Uncharacterized protei 24.2 36 0.00077 30.8 0.9 33 295-330 21-53 (126)
48 PLN03131 hypothetical protein; 23.7 38 0.00082 37.8 1.2 32 295-328 23-54 (705)
49 KOG0703 Predicted GTPase-activ 23.5 30 0.00066 34.9 0.4 28 295-324 25-52 (287)
50 COG4260 Membrane protease subu 23.0 58 0.0013 33.5 2.2 30 294-326 314-343 (345)
51 PLN03119 putative ADP-ribosyla 23.0 39 0.00085 37.4 1.1 32 295-328 23-54 (648)
52 PF10083 DUF2321: Uncharacteri 22.9 47 0.001 31.0 1.5 33 295-327 39-78 (158)
53 smart00778 Prim_Zn_Ribbon Zinc 22.6 49 0.0011 23.8 1.2 30 296-325 4-33 (37)
54 PF05361 PP1_inhibitor: PKC-ac 22.3 68 0.0015 29.6 2.3 19 78-96 69-87 (144)
55 PRK00085 recO DNA repair prote 22.0 38 0.00083 31.6 0.7 30 294-324 148-177 (247)
56 PF09526 DUF2387: Probable met 21.7 26 0.00055 28.4 -0.4 33 296-328 9-41 (71)
57 PRK00423 tfb transcription ini 21.5 42 0.00092 33.3 0.9 9 295-303 30-38 (310)
58 COG1601 GCD7 Translation initi 21.0 36 0.00078 31.3 0.3 32 295-327 105-136 (151)
59 KOG0706 Predicted GTPase-activ 20.5 38 0.00081 36.2 0.4 34 294-329 22-55 (454)
No 1
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.48 E-value=2.3e-14 Score=108.50 Aligned_cols=43 Identities=49% Similarity=1.042 Sum_probs=38.0
Q ss_pred ccccCCCCCCCcccCCCCCCchhhhhhhhhHHhCCCCCCCCCCCCC
Q 044150 297 RCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKSGRLFPEYRPACSP 342 (381)
Q Consensus 297 ~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykkgrllp~yrpa~sP 342 (381)
.|+||++++||+||+||.|.++||||||+||++++ ..||...+
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~---~~rp~~~~ 43 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG---VMRPLSKR 43 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC---CCCCcccC
Confidence 59999999999999999888999999999999876 56776544
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.44 E-value=6e-14 Score=105.17 Aligned_cols=39 Identities=56% Similarity=1.152 Sum_probs=35.9
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHHhCCCC
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKSGRLF 333 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykkgrll 333 (381)
.++|+||+++.||+||+||.|..+|||||||+|++.+.+
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 578999999999999999999889999999999986644
No 3
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.40 E-value=5e-14 Score=98.45 Aligned_cols=35 Identities=60% Similarity=1.257 Sum_probs=28.1
Q ss_pred cccCCCCCCCcccCCCCCCchhhhhhhhhHHhCCC
Q 044150 298 CSHCGVQKTPQWRTGPLGAKTLCNACGVRYKSGRL 332 (381)
Q Consensus 298 Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykkgrl 332 (381)
|.||++++||+||+||.|..+||||||++|++.+.
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 89999999999999999988899999999998763
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=99.12 E-value=4.8e-11 Score=105.22 Aligned_cols=71 Identities=61% Similarity=1.172 Sum_probs=62.3
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHHhC---CCCCCCCCCCCCC--------------Cccchhhc------
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKSG---RLFPEYRPACSPT--------------FSSELHSN------ 351 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykkg---rllp~yrpa~sPt--------------~~~~~hsn------ 351 (381)
...|.+|+++.||+||+++.|.+.+|||||++|+++ +.++.++.+..++ +....+.+
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPRNVSPKGSGAVKGRTFTKSLHSNSAQLLL 278 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhcCccccccccCccccccccCCCccccccCCCCCcccccchhhhhh
Confidence 589999999999999999999999999999999998 7889999888877 45566665
Q ss_pred -----------hhhHHHHHHHhhcC
Q 044150 352 -----------HHRKVMEMRRKKEG 365 (381)
Q Consensus 352 -----------~hrkvie~Rr~k~~ 365 (381)
.+.++.+++|.++.
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~r~~~~ 303 (340)
T KOG1601|consen 279 APSKSEPPLLSSHQRVAEVRRYRES 303 (340)
T ss_pred hhcccCccccccchHHHHHhhccCc
Confidence 78899999988774
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.80 E-value=9e-06 Score=85.07 Aligned_cols=53 Identities=32% Similarity=0.575 Sum_probs=40.2
Q ss_pred CCCcccccCCCCCCCcccCCCCC----CchhhhhhhhhHHhCCCCCCCC-CCCCCCCccch
Q 044150 293 QVTRRCSHCGVQKTPQWRTGPLG----AKTLCNACGVRYKSGRLFPEYR-PACSPTFSSEL 348 (381)
Q Consensus 293 ~~~r~Cs~Cgt~~TP~WRrGP~G----~~tLCNACGl~ykkgrllp~yr-pa~sPt~~~~~ 348 (381)
.....|.||.+..||+|||+..+ .-+|||||||+|+-.+ ..| |...++.....
T Consensus 156 ~~~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg---~~r~P~t~ks~~~ks 213 (498)
T COG5641 156 NQPHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHG---SPRAPISLKSDSIKS 213 (498)
T ss_pred cccchhccccccCCccccccccccccCCccccccccccccccC---CcCCCcccccccccc
Confidence 34459999999999999999993 3799999999999544 344 66555444433
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=88.98 E-value=0.4 Score=51.14 Aligned_cols=38 Identities=29% Similarity=0.579 Sum_probs=31.8
Q ss_pred CCCCcccccCCCCCCCcc--cCCCCCCchhhhhhhhhHHh
Q 044150 292 GQVTRRCSHCGVQKTPQW--RTGPLGAKTLCNACGVRYKS 329 (381)
Q Consensus 292 ~~~~r~Cs~Cgt~~TP~W--RrGP~G~~tLCNACGl~ykk 329 (381)
.+..+.|.+|++++.-+| .-+|.-...||-.|-+||||
T Consensus 383 ~~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKK 422 (693)
T KOG3554|consen 383 NQDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKK 422 (693)
T ss_pred CCCCCcccccccccccceeccCCCCccchhhHHHHHHHHH
Confidence 344789999999999999 44556666899999999998
No 7
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=67.18 E-value=1.7 Score=30.66 Aligned_cols=30 Identities=27% Similarity=0.646 Sum_probs=16.0
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhh
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGV 325 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl 325 (381)
+.|.+||..-+-.--.|..-.+..|.+||-
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 469999987544334667777789999984
No 8
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=63.24 E-value=2.3 Score=38.22 Aligned_cols=31 Identities=29% Similarity=0.617 Sum_probs=23.9
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhhhH
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGVRY 327 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~y 327 (381)
..|..|+...|-.=+.+-.- -.-|+|||-..
T Consensus 103 VlC~~C~spdT~l~k~~r~~-~l~C~ACGa~~ 133 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIW-VLKCEACGAET 133 (138)
T ss_pred EECCCCCCCCcEEEEcCCeE-EEEcccCCCCC
Confidence 68999999999998753322 46899999653
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=62.55 E-value=4.4 Score=43.40 Aligned_cols=37 Identities=27% Similarity=0.399 Sum_probs=30.7
Q ss_pred CcccccCCC-CCCCcccCCCCCCchhhhhhhhhHHhCC
Q 044150 295 TRRCSHCGV-QKTPQWRTGPLGAKTLCNACGVRYKSGR 331 (381)
Q Consensus 295 ~r~Cs~Cgt-~~TP~WRrGP~G~~tLCNACGl~ykkgr 331 (381)
...|.+|++ +.||.||+...-..++|||||.+.+..+
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~~~ 334 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPG 334 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCCcc
Confidence 467888887 6799999988777899999999998543
No 10
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=60.88 E-value=2.8 Score=37.51 Aligned_cols=31 Identities=26% Similarity=0.588 Sum_probs=23.6
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhhhH
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGVRY 327 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~y 327 (381)
..|..|+...|-.-+.+.. --.-|+|||-..
T Consensus 98 VlC~~C~sPdT~l~k~~r~-~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRV-SLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEEeCCe-EEEecccCCCCC
Confidence 6799999999998875332 135899999653
No 11
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=60.17 E-value=5.3 Score=34.29 Aligned_cols=34 Identities=21% Similarity=0.374 Sum_probs=22.8
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHHh
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKS 329 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykk 329 (381)
.-.|.+|+.. +-.-..+-...+..|..||.|+..
T Consensus 21 ~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 21 IFECPRCGKV-SISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred EeECCCCCCe-EeeeecCCCcceEECCCCCCccCE
Confidence 5779999953 322222223558899999999864
No 12
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=57.17 E-value=3.4 Score=35.78 Aligned_cols=29 Identities=31% Similarity=0.590 Sum_probs=22.5
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhh
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGV 325 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl 325 (381)
..|..|+...|-+=+.+..- -.-|+|||-
T Consensus 81 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeE-EEEccccCC
Confidence 67999999999998873221 346999995
No 13
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=55.52 E-value=3.7 Score=38.64 Aligned_cols=32 Identities=28% Similarity=0.564 Sum_probs=25.0
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
..|..|+...|-+-+.+..- -.-|+|||-..-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~-~l~C~aCGa~~~ 130 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVL-MLRCDACGAHRP 130 (201)
T ss_pred EECCCCCCCCcEEEEcCCeE-EEEcccCCCCcc
Confidence 68999999999998764221 358999998764
No 14
>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=53.66 E-value=4.4 Score=31.00 Aligned_cols=25 Identities=36% Similarity=0.887 Sum_probs=18.8
Q ss_pred CCcccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 294 VTRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 294 ~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
....|.+||... -++.+|.+|| +|+
T Consensus 25 ~l~~c~~cg~~~---------~~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------LPHRVCPSCG-YYK 49 (56)
T ss_dssp SEEESSSSSSEE---------STTSBCTTTB-BSS
T ss_pred ceeeeccCCCEe---------cccEeeCCCC-eEC
Confidence 467899999643 2378999999 554
No 15
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=53.27 E-value=7.1 Score=30.35 Aligned_cols=25 Identities=32% Similarity=0.817 Sum_probs=19.9
Q ss_pred CCCcccccCCCCCCCcccCCCCCCchhhhhhhhh
Q 044150 293 QVTRRCSHCGVQKTPQWRTGPLGAKTLCNACGVR 326 (381)
Q Consensus 293 ~~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ 326 (381)
...-.|.+||...-| +.+|..||.|
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcC
Confidence 346789999987655 7899999944
No 16
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.94 E-value=7.8 Score=42.84 Aligned_cols=40 Identities=20% Similarity=0.519 Sum_probs=32.2
Q ss_pred CCCCcccccCCCCCCCcccCCCCC---CchhhhhhhhhHHhCC
Q 044150 292 GQVTRRCSHCGVQKTPQWRTGPLG---AKTLCNACGVRYKSGR 331 (381)
Q Consensus 292 ~~~~r~Cs~Cgt~~TP~WRrGP~G---~~tLCNACGl~ykkgr 331 (381)
..+.-.|..|.+.-||.|+.-+.+ .+.+|.+|-.--.|+.
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtSnqkkA 501 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTSNQKKA 501 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhhhccccc
Confidence 455788999999999999988777 4589999987665543
No 17
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=51.22 E-value=6.4 Score=39.92 Aligned_cols=32 Identities=31% Similarity=0.859 Sum_probs=28.5
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
.+.|..||... |+|-.=..| -.||--|---.|
T Consensus 20 Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHR 51 (319)
T COG5347 20 NKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHR 51 (319)
T ss_pred cCccccCCCCC-CceEecccC-eEEEeecchhhh
Confidence 58999999999 999999999 899999965554
No 18
>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=47.01 E-value=6.3 Score=28.22 Aligned_cols=30 Identities=23% Similarity=0.684 Sum_probs=18.5
Q ss_pred ccccCCCCCCCcccCCCCCCchhhhhhhhhHHh
Q 044150 297 RCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKS 329 (381)
Q Consensus 297 ~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykk 329 (381)
+|.+||... .--.--.| ...|..||+-..-
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE--EEEETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCCc--eEEcCCCC-eEECCCCCCEeec
Confidence 688999866 22223344 6799999976653
No 19
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=45.74 E-value=6.7 Score=34.67 Aligned_cols=29 Identities=34% Similarity=0.668 Sum_probs=23.8
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhh
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGV 325 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl 325 (381)
..|..|+...|-+-+.+..- -.-|+|||-
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccCC
Confidence 57999999999998874443 578999994
No 20
>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=44.85 E-value=14 Score=31.54 Aligned_cols=33 Identities=30% Similarity=0.749 Sum_probs=24.1
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHHh
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKS 329 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykk 329 (381)
.+.|++||... |.|-.=..| -.||-.|.-.++.
T Consensus 13 N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~ 45 (116)
T PF01412_consen 13 NKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRS 45 (116)
T ss_dssp CTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHH
T ss_pred cCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHH
Confidence 58999999655 599998899 8999999988875
No 21
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=39.68 E-value=23 Score=27.72 Aligned_cols=49 Identities=35% Similarity=0.735 Sum_probs=34.0
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHHhCCCCCCCCCCCCCCCccchhhchhhHHHHHHHh
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKSGRLFPEYRPACSPTFSSELHSNHHRKVMEMRRK 362 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykkgrllp~yrpa~sPt~~~~~hsn~hrkvie~Rr~ 362 (381)
.+.|.+||+-.- +..|-.||... ..+..|.|+.+-.--.+|..+++|..
T Consensus 5 mr~C~~CgvYTL----------k~~CP~CG~~t---------~~~~P~rfSp~D~y~~yR~~~kk~~~ 53 (56)
T PRK13130 5 IRKCPKCGVYTL----------KEICPVCGGKT---------KNPHPPRFSPEDKYGKYRRALKKRRK 53 (56)
T ss_pred ceECCCCCCEEc----------cccCcCCCCCC---------CCCCCCCCCCCCccHHHHHHHHHHhh
Confidence 577888887654 45788888654 34555688887777778877766644
No 22
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=39.34 E-value=13 Score=37.40 Aligned_cols=31 Identities=29% Similarity=0.646 Sum_probs=24.5
Q ss_pred CCcccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 294 VTRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 294 ~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
..|.|.+||+...+. ..|-+.+|+.||.++.
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~f 140 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEHF 140 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCccC
Confidence 468999999987763 3455789999998875
No 23
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=38.75 E-value=16 Score=38.16 Aligned_cols=33 Identities=27% Similarity=0.718 Sum_probs=28.3
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHHh
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKS 329 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykk 329 (381)
.++|..|+... |.|-.=..| -.||..|.=..+.
T Consensus 22 Nk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRs 54 (395)
T PLN03114 22 NKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRS 54 (395)
T ss_pred CCcCccCCCCC-CCceeeccc-eeehhhhhHhhcc
Confidence 58999999876 999999999 8999999766654
No 24
>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=36.64 E-value=15 Score=28.08 Aligned_cols=31 Identities=23% Similarity=0.637 Sum_probs=23.2
Q ss_pred CCcccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 294 VTRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 294 ~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
....|..||...-- ...+....|..||..+.
T Consensus 27 TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 45789999987644 44555789999998764
No 25
>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=35.03 E-value=47 Score=26.84 Aligned_cols=43 Identities=14% Similarity=0.339 Sum_probs=32.5
Q ss_pred CCcccccCCCCCCCcc---cCCCCCCchhhhhhhhhHHhCCCCCCC
Q 044150 294 VTRRCSHCGVQKTPQW---RTGPLGAKTLCNACGVRYKSGRLFPEY 336 (381)
Q Consensus 294 ~~r~Cs~Cgt~~TP~W---RrGP~G~~tLCNACGl~ykkgrllp~y 336 (381)
+...|..|.+.+|--= --...-|...|-+|..+|..|+.|...
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnV 49 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNV 49 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCC
Confidence 3578999999988652 122345578999999999999877655
No 26
>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=33.14 E-value=30 Score=29.39 Aligned_cols=34 Identities=32% Similarity=0.740 Sum_probs=29.2
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHHhC
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKSG 330 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykkg 330 (381)
.+.|++|+. .-|.|-.=..| -.||-.|.-..+.-
T Consensus 3 N~~CaDC~~-~~p~w~s~~~G-ifvC~~CsgiHR~l 36 (112)
T smart00105 3 NKKCFDCGA-PNPTWASVNLG-VFLCIECSGIHRSL 36 (112)
T ss_pred CCcccCCCC-CCCCcEEeccc-eeEhHHhHHHHHhc
Confidence 589999998 45999998889 89999998888753
No 27
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=33.09 E-value=18 Score=36.30 Aligned_cols=38 Identities=24% Similarity=0.471 Sum_probs=26.5
Q ss_pred CCCCCcccccCCCCCCCcc----cCCCCCCc--hhhhhhhhhHH
Q 044150 291 WGQVTRRCSHCGVQKTPQW----RTGPLGAK--TLCNACGVRYK 328 (381)
Q Consensus 291 ~~~~~r~Cs~Cgt~~TP~W----RrGP~G~~--tLCNACGl~yk 328 (381)
..+....|..|+-.++-.| |...++-. +.|..||-+|+
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 3455789999998876544 44444411 38999999986
No 28
>PHA03309 transcriptional regulator ICP4; Provisional
Probab=32.88 E-value=33 Score=39.92 Aligned_cols=39 Identities=44% Similarity=0.526 Sum_probs=16.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCC
Q 044150 205 IPAKARSKRSRTGLRIWSLGSPSLSDSSSTSSASSSSSPS 244 (381)
Q Consensus 205 vP~KaRSKRsR~~~~~Ws~~~~~l~~sssssSs~sSssp~ 244 (381)
||++.||--.-. +.-|-++.-..++++||+||++|++|+
T Consensus 1794 vpvrrrsgaanc-ggrwmisagrsssssssssssssssps 1832 (2033)
T PHA03309 1794 VPVRRRSGAANC-GGRWMISAGRSSSSSSSSSSSSSSSPS 1832 (2033)
T ss_pred cceeeccccccc-CcceeeecCcccCcccccccccCCCCC
Confidence 455444433222 234876544444333333333333333
No 29
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=32.59 E-value=7.4 Score=27.75 Aligned_cols=32 Identities=28% Similarity=0.720 Sum_probs=19.5
Q ss_pred ccccCCCCCCC----cccCCCCCCc--hhhhhhhhhHH
Q 044150 297 RCSHCGVQKTP----QWRTGPLGAK--TLCNACGVRYK 328 (381)
Q Consensus 297 ~Cs~Cgt~~TP----~WRrGP~G~~--tLCNACGl~yk 328 (381)
.|..||..++- |-|.+.++.. ..|..||-+|+
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 48888887643 3466666632 47999998774
No 30
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=31.46 E-value=21 Score=38.27 Aligned_cols=49 Identities=29% Similarity=0.590 Sum_probs=31.5
Q ss_pred cccccCCCCC-CCcccCCCCCCc----------hhhhhhhhhHHhCCCCCCCCCCCCCCCccchhhchhhHHHHHHHh
Q 044150 296 RRCSHCGVQK-TPQWRTGPLGAK----------TLCNACGVRYKSGRLFPEYRPACSPTFSSELHSNHHRKVMEMRRK 362 (381)
Q Consensus 296 r~Cs~Cgt~~-TP~WRrGP~G~~----------tLCNACGl~ykkgrllp~yrpa~sPt~~~~~hsn~hrkvie~Rr~ 362 (381)
-.|.+||... ++.-+.+|.+.. +.||+||---+. |.| |...|.++.|+-
T Consensus 162 PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RF----PRY--------------Ndp~kLLeTRkG 221 (500)
T KOG0909|consen 162 PPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRF----PRY--------------NDPIKLLETRKG 221 (500)
T ss_pred CCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccC----ccc--------------CCHHHHHhhccC
Confidence 5699999877 444444454322 689999976542 322 446778777753
No 31
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=31.33 E-value=10 Score=30.61 Aligned_cols=33 Identities=21% Similarity=0.352 Sum_probs=25.8
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
-.|-.|.+..|=+|.+...-...-|.+||-.-+
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 469999999996655555555789999998775
No 32
>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=31.14 E-value=19 Score=26.40 Aligned_cols=25 Identities=40% Similarity=0.921 Sum_probs=19.2
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhh
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACG 324 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACG 324 (381)
...|..| .||+.| ...| +..|-+|+
T Consensus 17 ~~~Cp~C---~~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDC---GTPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCC---CCeeEE-ecCC-CEECCCCC
Confidence 4578888 589999 3355 78999996
No 33
>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=30.76 E-value=24 Score=32.46 Aligned_cols=34 Identities=24% Similarity=0.495 Sum_probs=25.1
Q ss_pred cccccCCCCCCCcc--cCCCCCC----chhhhhhhhhHHh
Q 044150 296 RRCSHCGVQKTPQW--RTGPLGA----KTLCNACGVRYKS 329 (381)
Q Consensus 296 r~Cs~Cgt~~TP~W--RrGP~G~----~tLCNACGl~ykk 329 (381)
++|-.|+...|-.- |...+|. .--|.+||-+|-.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 47999999988775 4445552 2589999999863
No 34
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=30.71 E-value=25 Score=38.12 Aligned_cols=31 Identities=29% Similarity=0.680 Sum_probs=21.2
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhhhHHh
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKS 329 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykk 329 (381)
+.|.|||.+.= . |+--.| ...|++||.-.--
T Consensus 1 ~~C~~C~~s~f-e-~d~a~g-~~~C~~CG~v~E~ 31 (521)
T KOG1598|consen 1 MVCKNCGGSNF-E-RDEATG-NLYCTACGTVLEY 31 (521)
T ss_pred CcCCCCCCCCc-c-cccccC-Cceeccccceeec
Confidence 46999998652 1 222345 7899999987653
No 35
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.61 E-value=15 Score=25.90 Aligned_cols=32 Identities=25% Similarity=0.660 Sum_probs=22.7
Q ss_pred cccccCCCC-CCCcccCCCCCCchhhhhhhhhH
Q 044150 296 RRCSHCGVQ-KTPQWRTGPLGAKTLCNACGVRY 327 (381)
Q Consensus 296 r~Cs~Cgt~-~TP~WRrGP~G~~tLCNACGl~y 327 (381)
..|-+|++. .-+..+-.+.|...-|-.||-.|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 357788876 45777777777777888887654
No 36
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=30.32 E-value=21 Score=25.44 Aligned_cols=32 Identities=28% Similarity=0.622 Sum_probs=21.0
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhh
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVR 326 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ 326 (381)
..+|.+|++---|.-+-...|..-.||-||..
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 46899999998888877778878899999874
No 37
>COG3952 Predicted membrane protein [Function unknown]
Probab=27.43 E-value=19 Score=31.90 Aligned_cols=19 Identities=32% Similarity=0.431 Sum_probs=14.6
Q ss_pred cccCCCCCCchhhhhhhhhHH
Q 044150 308 QWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 308 ~WRrGP~G~~tLCNACGl~yk 328 (381)
.||.+|-+ .||++||++-.
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 35666665 79999999875
No 38
>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=27.10 E-value=36 Score=29.54 Aligned_cols=15 Identities=40% Similarity=1.077 Sum_probs=9.2
Q ss_pred CCCchhhhhhhhhHH
Q 044150 314 LGAKTLCNACGVRYK 328 (381)
Q Consensus 314 ~G~~tLCNACGl~yk 328 (381)
.|.|.+|..||.+|-
T Consensus 6 lGtKR~Cp~CG~kFY 20 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFY 20 (108)
T ss_pred cCCcccCCCCcchhc
Confidence 355666666666664
No 39
>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=26.96 E-value=27 Score=24.74 Aligned_cols=26 Identities=31% Similarity=0.819 Sum_probs=20.5
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhh
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGV 325 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl 325 (381)
...|..|+.. |-...+| ...|..||-
T Consensus 8 ~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 3569999987 6666678 899999984
No 40
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=26.70 E-value=34 Score=26.36 Aligned_cols=26 Identities=35% Similarity=0.828 Sum_probs=19.0
Q ss_pred CCCcccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 293 QVTRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 293 ~~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
...-.|.+||...- ++.+|-.|| +|+
T Consensus 24 p~l~~C~~cG~~~~---------~H~vc~~cG-~Y~ 49 (55)
T TIGR01031 24 PTLVVCPNCGEFKL---------PHRVCPSCG-YYK 49 (55)
T ss_pred CcceECCCCCCccc---------CeeECCccC-eEC
Confidence 34577999997543 378999999 443
No 41
>PRK00420 hypothetical protein; Validated
Probab=26.30 E-value=27 Score=30.73 Aligned_cols=30 Identities=27% Similarity=0.691 Sum_probs=22.9
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHHh
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKS 329 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykk 329 (381)
...|..|| +|..|- ..| +..|-+||..+..
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeeee
Confidence 36788888 688874 355 7899999998763
No 42
>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=12 Score=25.26 Aligned_cols=29 Identities=31% Similarity=0.645 Sum_probs=15.8
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhH
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRY 327 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~y 327 (381)
.+.|..||....+.. .|....|.+||..+
T Consensus 3 ~rfC~~CG~~t~~~~----~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAP----GGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-S----SSS-EEESSSS-EE
T ss_pred CcccCcCCccccCCC----CcCEeECCCCcCEe
Confidence 478999998765432 35567899998753
No 43
>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=25.15 E-value=28 Score=25.26 Aligned_cols=27 Identities=30% Similarity=0.603 Sum_probs=19.6
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhh
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGV 325 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl 325 (381)
..|.+||.+ ..-|.++ .+ ..-|++|+-
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RG-RYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CC-eEECCCCCC
Confidence 569999998 5555554 33 789999974
No 44
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.09 E-value=26 Score=34.04 Aligned_cols=32 Identities=31% Similarity=0.614 Sum_probs=22.9
Q ss_pred CCCcccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 293 QVTRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 293 ~~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
...+.|.+||...... ..|....|.+||.++-
T Consensus 97 ~~~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 97 RSHRFCGYCGHPMHPS----KTEWAMLCPHCRERYY 128 (256)
T ss_pred hcCccccccCCCCeec----CCceeEECCCCCCEEC
Confidence 4468999999975432 3455678999996653
No 45
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=25.05 E-value=31 Score=31.62 Aligned_cols=33 Identities=33% Similarity=0.688 Sum_probs=21.5
Q ss_pred cccccCCCCCCCcccCC--CCC----CchhhhhhhhhHH
Q 044150 296 RRCSHCGVQKTPQWRTG--PLG----AKTLCNACGVRYK 328 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrG--P~G----~~tLCNACGl~yk 328 (381)
+.|-+||...|-.--.. +.| ...-|.+||-++.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence 46999998876553221 112 1368999998885
No 46
>PF12773 DZR: Double zinc ribbon
Probab=24.95 E-value=42 Score=24.14 Aligned_cols=30 Identities=30% Similarity=0.734 Sum_probs=19.7
Q ss_pred CCcccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 294 VTRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 294 ~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
..+.|.+||+.-. ........|..||-...
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENP 40 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCc
Confidence 3577888888766 33344567888887543
No 47
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.23 E-value=36 Score=30.75 Aligned_cols=33 Identities=33% Similarity=0.723 Sum_probs=22.6
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHHhC
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKSG 330 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykkg 330 (381)
..+|-+||.-+ -=+|=.-...-|.|||+.|-..
T Consensus 21 ~grCP~CGeGr---LF~gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 21 RGRCPRCGEGR---LFRGFLKVVPACEACGLDYGFA 53 (126)
T ss_pred cCCCCCCCCch---hhhhhcccCchhhhccccccCC
Confidence 46899999643 2233344457899999999753
No 48
>PLN03131 hypothetical protein; Provisional
Probab=23.74 E-value=38 Score=37.81 Aligned_cols=32 Identities=25% Similarity=0.560 Sum_probs=26.7
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
.++|.+|+... |.|-.=..| -.+|-.|.=..+
T Consensus 23 Nk~CADCga~~-P~WASiNlG-IFICi~CSGIHR 54 (705)
T PLN03131 23 NRRCINCNSLG-PQFVCTNFW-TFICMTCSGIHR 54 (705)
T ss_pred CCccccCCCCC-CCeeEeccc-eEEchhchhhhc
Confidence 58999999755 999998888 789999975544
No 49
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=23.51 E-value=30 Score=34.92 Aligned_cols=28 Identities=32% Similarity=0.969 Sum_probs=24.9
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhh
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACG 324 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACG 324 (381)
.+.|+.||+. .|.|-.=..| ..+|-.|-
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 6899999998 9999998899 88998873
No 50
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=23.04 E-value=58 Score=33.46 Aligned_cols=30 Identities=27% Similarity=0.706 Sum_probs=22.5
Q ss_pred CCcccccCCCCCCCcccCCCCCCchhhhhhhhh
Q 044150 294 VTRRCSHCGVQKTPQWRTGPLGAKTLCNACGVR 326 (381)
Q Consensus 294 ~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ 326 (381)
....|.+||...|+-.-. |..-.|-+||--
T Consensus 314 k~nfc~ncG~~~t~~~~n---g~a~fcp~cgq~ 343 (345)
T COG4260 314 KLNFCLNCGCGTTADFDN---GKAKFCPECGQG 343 (345)
T ss_pred ccccccccCcccccCCcc---chhhhChhhcCC
Confidence 456899999888886554 445699999954
No 51
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=22.96 E-value=39 Score=37.37 Aligned_cols=32 Identities=28% Similarity=0.584 Sum_probs=26.7
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
.++|.+|+... |.|-.=..| -.+|-.|.=..+
T Consensus 23 Nk~CADCgs~~-P~WASiNlG-IFICi~CSGIHR 54 (648)
T PLN03119 23 NRRCINCNSLG-PQYVCTTFW-TFVCMACSGIHR 54 (648)
T ss_pred CCccccCCCCC-CCceeeccc-eEEeccchhhhc
Confidence 58999999866 999988889 789999965444
No 52
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.93 E-value=47 Score=31.02 Aligned_cols=33 Identities=24% Similarity=0.699 Sum_probs=22.9
Q ss_pred CcccccCCCCCCCcccC-------CCCCCchhhhhhhhhH
Q 044150 295 TRRCSHCGVQKTPQWRT-------GPLGAKTLCNACGVRY 327 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRr-------GP~G~~tLCNACGl~y 327 (381)
...|.+|++..--.|-- ++.-...-|+.||..|
T Consensus 39 I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 39 ITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 56788888776544532 3444457899999998
No 53
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=22.62 E-value=49 Score=23.82 Aligned_cols=30 Identities=20% Similarity=0.557 Sum_probs=20.3
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhh
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGV 325 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl 325 (381)
..|-.|+....=.|..-.......||.||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 468899988766675532222679999974
No 54
>PF05361 PP1_inhibitor: PKC-activated protein phosphatase-1 inhibitor; InterPro: IPR008025 Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction [].; GO: 0042325 regulation of phosphorylation, 0005737 cytoplasm; PDB: 2RLT_A 1J2M_A 1K5O_A 1J2N_A.
Probab=22.34 E-value=68 Score=29.60 Aligned_cols=19 Identities=21% Similarity=0.457 Sum_probs=14.8
Q ss_pred CCCCCcccccccCCCCchh
Q 044150 78 VACDDFFVDDLLDFSNEDV 96 (381)
Q Consensus 78 ~~~ddFsVdDLLDfsn~d~ 96 (381)
-+.++.-||||||+++++.
T Consensus 69 ~~p~EIDIDeLLDl~sdee 87 (144)
T PF05361_consen 69 EMPEEIDIDELLDLESDEE 87 (144)
T ss_dssp TS-SSSHHHHHHCTSSTTH
T ss_pred CCCCcccHHHHhcCCchHH
Confidence 3445899999999998763
No 55
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=21.99 E-value=38 Score=31.55 Aligned_cols=30 Identities=23% Similarity=0.665 Sum_probs=24.4
Q ss_pred CCcccccCCCCCCCcccCCCCCCchhhhhhh
Q 044150 294 VTRRCSHCGVQKTPQWRTGPLGAKTLCNACG 324 (381)
Q Consensus 294 ~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACG 324 (381)
....|..||......|-.-..| +.+|..|+
T Consensus 148 ~l~~C~~Cg~~~~~~~f~~~~g-g~~c~~c~ 177 (247)
T PRK00085 148 DLDHCAVCGAPGDHRYFSPKEG-GAVCSECG 177 (247)
T ss_pred chhhHhcCCCCCCceEEecccC-Cccccccc
Confidence 3568999998877677776777 89999997
No 56
>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=21.70 E-value=26 Score=28.44 Aligned_cols=33 Identities=18% Similarity=0.283 Sum_probs=26.6
Q ss_pred cccccCCCCCCCcccCCCCCCchhhhhhhhhHH
Q 044150 296 RRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYK 328 (381)
Q Consensus 296 r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~yk 328 (381)
-.|-.|+...|=+|.+.......-|-+||-.-.
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 579999999997765555566789999997765
No 57
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.48 E-value=42 Score=33.28 Aligned_cols=9 Identities=33% Similarity=1.051 Sum_probs=5.1
Q ss_pred CcccccCCC
Q 044150 295 TRRCSHCGV 303 (381)
Q Consensus 295 ~r~Cs~Cgt 303 (381)
...|.+||.
T Consensus 30 e~vC~~CG~ 38 (310)
T PRK00423 30 EIVCADCGL 38 (310)
T ss_pred eEeecccCC
Confidence 455666664
No 58
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=21.00 E-value=36 Score=31.33 Aligned_cols=32 Identities=28% Similarity=0.515 Sum_probs=25.4
Q ss_pred CcccccCCCCCCCcccCCCCCCchhhhhhhhhH
Q 044150 295 TRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRY 327 (381)
Q Consensus 295 ~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~y 327 (381)
-..|.-|+...|+.-+.+-.= ..-|-|||-..
T Consensus 105 yv~C~~c~s~dt~l~~~~R~~-~l~c~acGa~~ 136 (151)
T COG1601 105 YVKCKECGSPDTELIKEERLL-FLKCEACGAIR 136 (151)
T ss_pred eeEeccCCCCchhhhhhhhhH-hhHHHHhCCcc
Confidence 478999999999999884333 46899999654
No 59
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=20.54 E-value=38 Score=36.24 Aligned_cols=34 Identities=26% Similarity=0.727 Sum_probs=28.9
Q ss_pred CCcccccCCCCCCCcccCCCCCCchhhhhhhhhHHh
Q 044150 294 VTRRCSHCGVQKTPQWRTGPLGAKTLCNACGVRYKS 329 (381)
Q Consensus 294 ~~r~Cs~Cgt~~TP~WRrGP~G~~tLCNACGl~ykk 329 (381)
+.+.|..|+.. -|-|-.-+.| -.||--|---.+.
T Consensus 22 ~NKvCFDCgAk-nPtWaSVTYG-IFLCiDCSAvHRn 55 (454)
T KOG0706|consen 22 ENKVCFDCGAK-NPTWASVTYG-IFLCIDCSAVHRN 55 (454)
T ss_pred CCceecccCCC-CCCceeecce-EEEEEecchhhhc
Confidence 46999999975 4999999999 8999999766654
Done!