Query 021859
Match_columns 306
No_of_seqs 170 out of 754
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 06:13:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021859.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021859hhsearch_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 99.4 7.9E-14 1.7E-18 102.7 3.9 35 170-204 1-35 (54)
2 smart00401 ZnF_GATA zinc finge 99.4 6E-14 1.3E-18 102.3 2.6 38 167-204 2-39 (52)
3 PF00320 GATA: GATA zinc finge 99.4 3.5E-14 7.7E-19 96.5 1.3 34 171-204 1-34 (36)
4 KOG1601 GATA-4/5/6 transcripti 98.7 1E-08 2.2E-13 87.2 2.2 36 168-203 199-234 (340)
5 COG5641 GAT1 GATA Zn-finger-co 98.1 1.7E-06 3.6E-11 87.9 2.2 37 165-201 155-195 (498)
6 KOG3554 Histone deacetylase co 84.3 1 2.2E-05 47.0 3.7 38 166-203 384-423 (693)
7 PF14803 Nudix_N_2: Nudix N-te 76.0 0.68 1.5E-05 31.7 -0.5 30 169-198 1-30 (34)
8 COG5641 GAT1 GATA Zn-finger-co 71.2 1.7 3.7E-05 45.1 0.8 35 168-202 297-332 (498)
9 PF01412 ArfGap: Putative GTPa 64.5 6 0.00013 32.7 2.6 36 167-204 12-47 (116)
10 PRK03988 translation initiatio 62.9 2.2 4.7E-05 37.2 -0.3 30 168-198 102-131 (138)
11 TIGR00311 aIF-2beta translatio 60.6 2.6 5.6E-05 36.6 -0.3 30 168-198 97-126 (133)
12 KOG3740 Uncharacterized conser 59.7 4.1 8.9E-05 43.7 1.0 35 165-199 459-496 (706)
13 smart00653 eIF2B_5 domain pres 58.9 2.9 6.3E-05 35.1 -0.2 29 169-198 81-109 (110)
14 PRK12336 translation initiatio 56.1 3.3 7.2E-05 37.7 -0.3 32 168-200 98-129 (201)
15 COG5347 GTPase-activating prot 52.2 6.8 0.00015 38.6 1.1 34 167-202 19-52 (319)
16 PF08271 TF_Zn_Ribbon: TFIIB z 51.1 3.8 8.3E-05 28.4 -0.6 28 170-200 2-29 (43)
17 smart00105 ArfGap Putative GTP 50.0 13 0.00028 30.6 2.3 34 168-203 3-36 (112)
18 PF01873 eIF-5_eIF-2B: Domain 45.4 5.7 0.00012 34.0 -0.5 28 169-197 94-121 (125)
19 PLN03114 ADP-ribosylation fact 43.5 14 0.0003 37.6 1.7 34 167-202 21-54 (395)
20 PF06677 Auto_anti-p27: Sjogre 42.4 9.5 0.00021 27.1 0.3 25 168-197 17-41 (41)
21 PF07282 OrfB_Zn_ribbon: Putat 40.0 15 0.00032 27.2 1.0 32 166-201 26-57 (69)
22 PRK12286 rpmF 50S ribosomal pr 39.6 8.7 0.00019 29.0 -0.3 26 165-199 24-49 (57)
23 PF09889 DUF2116: Uncharacteri 38.8 35 0.00077 26.1 2.9 33 168-208 3-36 (59)
24 COG3529 Predicted nucleic-acid 38.3 9.9 0.00021 29.9 -0.1 37 167-203 9-45 (66)
25 PRK00420 hypothetical protein; 36.5 15 0.00033 31.3 0.7 29 168-201 23-51 (112)
26 PF11781 RRN7: RNA polymerase 34.4 18 0.00039 24.9 0.7 28 166-198 6-33 (36)
27 COG2816 NPY1 NTP pyrophosphohy 33.2 15 0.00033 35.8 0.2 30 167-200 110-139 (279)
28 COG4260 Membrane protease subu 32.9 45 0.00098 33.3 3.3 30 166-198 313-342 (345)
29 COG3952 Predicted membrane pro 32.7 23 0.0005 30.5 1.2 20 181-202 76-95 (113)
30 PRK14892 putative transcriptio 31.6 13 0.00028 31.0 -0.4 34 167-201 20-53 (99)
31 PF12760 Zn_Tnp_IS1595: Transp 31.3 20 0.00044 25.2 0.5 26 169-197 19-44 (46)
32 KOG0703 Predicted GTPase-activ 31.1 20 0.00042 35.2 0.6 33 168-202 25-57 (287)
33 KOG1598 Transcription initiati 29.9 26 0.00057 36.9 1.3 30 169-201 1-30 (521)
34 PRK00423 tfb transcription ini 29.3 22 0.00048 34.1 0.6 30 168-200 11-40 (310)
35 smart00778 Prim_Zn_Ribbon Zinc 26.8 36 0.00079 23.8 1.1 29 168-197 3-32 (37)
36 KOG1168 Transcription factor A 26.3 36 0.00077 34.1 1.4 33 260-294 257-291 (385)
37 PF01783 Ribosomal_L32p: Ribos 25.8 15 0.00032 27.3 -1.0 22 167-197 25-46 (56)
38 cd07169 NR_DBD_GCNF_like DNA-b 25.3 64 0.0014 26.0 2.5 33 165-202 3-35 (90)
39 PRK00085 recO DNA repair prote 24.7 32 0.0007 31.0 0.7 30 167-197 148-177 (247)
40 PF09723 Zn-ribbon_8: Zinc rib 24.4 21 0.00046 24.8 -0.4 28 170-198 7-34 (42)
41 PF04810 zf-Sec23_Sec24: Sec23 24.0 30 0.00065 23.9 0.3 31 168-198 2-32 (40)
42 PLN03131 hypothetical protein; 23.2 44 0.00095 36.3 1.5 34 167-202 22-55 (705)
43 PLN03119 putative ADP-ribosyla 23.1 44 0.00095 36.0 1.4 34 167-202 22-55 (648)
44 PF13248 zf-ribbon_3: zinc-rib 23.1 53 0.0011 20.7 1.3 22 169-198 3-24 (26)
45 TIGR01385 TFSII transcription 23.0 23 0.0005 34.5 -0.5 36 166-201 256-297 (299)
46 PF09526 DUF2387: Probable met 22.8 24 0.00051 27.8 -0.4 35 167-201 7-41 (71)
47 smart00834 CxxC_CXXC_SSSS Puta 22.6 27 0.00058 23.1 -0.1 29 170-199 7-35 (41)
48 COG0675 Transposase and inacti 22.2 33 0.00072 30.8 0.4 28 165-201 306-333 (364)
49 smart00661 RPOL9 RNA polymeras 21.4 48 0.001 23.1 0.9 29 169-200 1-30 (52)
50 PF09297 zf-NADH-PPase: NADH p 21.0 18 0.0004 23.6 -1.2 28 168-199 3-30 (32)
51 PRK08351 DNA-directed RNA poly 21.0 59 0.0013 25.2 1.4 16 169-184 16-32 (61)
52 PF12773 DZR: Double zinc ribb 20.8 50 0.0011 23.0 0.9 27 168-199 12-38 (50)
53 KOG0706 Predicted GTPase-activ 20.8 43 0.00094 34.8 0.8 35 165-201 20-54 (454)
54 COG5236 Uncharacterized conser 20.3 1E+02 0.0022 31.7 3.3 42 160-203 53-94 (493)
55 PRK00241 nudC NADH pyrophospha 20.2 40 0.00087 31.7 0.4 29 168-200 99-127 (256)
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=99.44 E-value=7.9e-14 Score=102.70 Aligned_cols=35 Identities=54% Similarity=1.213 Sum_probs=32.2
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHHHHHHhh
Q 021859 170 VCADCNTTKTPLWRSGPRGPKSLCNACGIRQRKAR 204 (306)
Q Consensus 170 ~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK~~ 204 (306)
.|+||++++||+||+||.|..+|||||||||++..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999999999999999888999999999998543
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.43 E-value=6e-14 Score=102.29 Aligned_cols=38 Identities=55% Similarity=1.174 Sum_probs=34.9
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHHhh
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRKAR 204 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK~~ 204 (306)
.++.|+||++++||+||+||.|+..|||||||+|++..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 46899999999999999999998899999999998654
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=99.42 E-value=3.5e-14 Score=96.55 Aligned_cols=34 Identities=53% Similarity=1.237 Sum_probs=27.2
Q ss_pred cccCCCCCCCcccCCCCCCcccchHHHHHHHHhh
Q 021859 171 CADCNTTKTPLWRSGPRGPKSLCNACGIRQRKAR 204 (306)
Q Consensus 171 CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK~~ 204 (306)
|++|++++||+||+||.|..+|||||||+|++.+
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 8999999999999999998789999999998764
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.65 E-value=1e-08 Score=87.20 Aligned_cols=36 Identities=69% Similarity=1.478 Sum_probs=34.4
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHHHHh
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRKA 203 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK~ 203 (306)
...|++|+++.||+||+++.|+..+|||||+++++.
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~ 234 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKG 234 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhc
Confidence 689999999999999999999999999999999866
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.06 E-value=1.7e-06 Score=87.93 Aligned_cols=37 Identities=46% Similarity=1.022 Sum_probs=32.3
Q ss_pred CCCCcccccCCCCCCCcccCCCCC----CcccchHHHHHHH
Q 021859 165 TNTIRVCADCNTTKTPLWRSGPRG----PKSLCNACGIRQR 201 (306)
Q Consensus 165 ~~~~r~CsnC~tt~TP~WRrGP~G----~~~LCNACGL~~r 201 (306)
......|.||.++.||+|||+..+ +-+|||||||+++
T Consensus 155 s~~~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~k 195 (498)
T COG5641 155 SNQPHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLK 195 (498)
T ss_pred ccccchhccccccCCccccccccccccCCcccccccccccc
Confidence 345569999999999999999993 2799999999997
No 6
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=84.35 E-value=1 Score=46.97 Aligned_cols=38 Identities=34% Similarity=0.638 Sum_probs=30.6
Q ss_pred CCCcccccCCCCCCCcc-cCC-CCCCcccchHHHHHHHHh
Q 021859 166 NTIRVCADCNTTKTPLW-RSG-PRGPKSLCNACGIRQRKA 203 (306)
Q Consensus 166 ~~~r~CsnC~tt~TP~W-RrG-P~G~~~LCNACGL~~rK~ 203 (306)
..++.|-+|+|++.-+| ..| |+-...||-.|=+||+|.
T Consensus 384 ~~g~~CEsC~ttqs~qWYsWGppnmqcrLCasCWiyWKKy 423 (693)
T KOG3554|consen 384 QDGRACESCYTTQSLQWYSWGPPNMQCRLCASCWIYWKKY 423 (693)
T ss_pred CCCCcccccccccccceeccCCCCccchhhHHHHHHHHHh
Confidence 34789999999999999 344 444456999999999875
No 7
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=75.97 E-value=0.68 Score=31.70 Aligned_cols=30 Identities=23% Similarity=0.636 Sum_probs=16.3
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHH
Q 021859 169 RVCADCNTTKTPLWRSGPRGPKSLCNACGI 198 (306)
Q Consensus 169 r~CsnC~tt~TP~WRrGP~G~~~LCNACGL 198 (306)
+.|.+||..-+-.--.|.+-.+.+|.+||.
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 469999988543334667777889999983
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=71.17 E-value=1.7 Score=45.08 Aligned_cols=35 Identities=31% Similarity=0.463 Sum_probs=28.9
Q ss_pred CcccccCCC-CCCCcccCCCCCCcccchHHHHHHHH
Q 021859 168 IRVCADCNT-TKTPLWRSGPRGPKSLCNACGIRQRK 202 (306)
Q Consensus 168 ~r~CsnC~t-t~TP~WRrGP~G~~~LCNACGL~~rK 202 (306)
...|.+|.+ +.||.||+...-.-++|||||++...
T Consensus 297 ~~~~s~~~~~~~tp~~~r~~~~~s~~~n~~~~~~~~ 332 (498)
T COG5641 297 DKKRSTLTTSTATPLWRRTSDKSSFSCNASGSALKP 332 (498)
T ss_pred hcCcccccccccCcccccccccccccccccccccCC
Confidence 567888887 78999999877768999999998754
No 9
>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=64.52 E-value=6 Score=32.72 Aligned_cols=36 Identities=36% Similarity=0.670 Sum_probs=25.4
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHHhh
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRKAR 204 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK~~ 204 (306)
..+.|++|++.. |.|-.=..| -.||-.|.-.+|...
T Consensus 12 ~N~~CaDCg~~~-p~w~s~~~G-iflC~~Cag~HR~lg 47 (116)
T PF01412_consen 12 GNKVCADCGAPN-PTWASLNYG-IFLCLECAGIHRSLG 47 (116)
T ss_dssp TCTB-TTT-SBS---EEETTTT-EEE-HHHHHHHHHHT
T ss_pred CcCcCCCCCCCC-CCEEEeecC-hhhhHHHHHHHHHhc
Confidence 458999999554 599999999 899999998887543
No 10
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=62.95 E-value=2.2 Score=37.24 Aligned_cols=30 Identities=30% Similarity=0.682 Sum_probs=23.3
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGI 198 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL 198 (306)
--.|..|+.+.|-+=+.+..- -..|+|||-
T Consensus 102 yVlC~~C~spdT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeE-EEEcccCCC
Confidence 368999999999998764322 458999994
No 11
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=60.56 E-value=2.6 Score=36.60 Aligned_cols=30 Identities=30% Similarity=0.723 Sum_probs=23.0
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGI 198 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL 198 (306)
--.|..|+.+.|-+-+.+.-- -.-|+|||-
T Consensus 97 yVlC~~C~sPdT~l~k~~r~~-~l~C~ACGa 126 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGRVS-LLKCEACGA 126 (133)
T ss_pred eEECCCCCCCCcEEEEeCCeE-EEecccCCC
Confidence 368999999999988764321 348999994
No 12
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.74 E-value=4.1 Score=43.72 Aligned_cols=35 Identities=26% Similarity=0.625 Sum_probs=29.6
Q ss_pred CCCCcccccCCCCCCCcccCCCCC---CcccchHHHHH
Q 021859 165 TNTIRVCADCNTTKTPLWRSGPRG---PKSLCNACGIR 199 (306)
Q Consensus 165 ~~~~r~CsnC~tt~TP~WRrGP~G---~~~LCNACGL~ 199 (306)
.+++-.|..|.|.-||.|+.-+.+ .+.+|.+|-.-
T Consensus 459 a~~P~~caqcktdftp~wk~ekstq~d~~i~cE~cvtS 496 (706)
T KOG3740|consen 459 ATEPYACAQCKTDFTPAWKKEKSTQADAAIVCENCVTS 496 (706)
T ss_pred cCCchhhhhcccccccccccccccCcchHHHHHhhhhh
Confidence 456889999999999999988777 45799999764
No 13
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=58.91 E-value=2.9 Score=35.13 Aligned_cols=29 Identities=28% Similarity=0.599 Sum_probs=22.5
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHH
Q 021859 169 RVCADCNTTKTPLWRSGPRGPKSLCNACGI 198 (306)
Q Consensus 169 r~CsnC~tt~TP~WRrGP~G~~~LCNACGL 198 (306)
-.|..|+.+.|-+=+.+..- -.-|+|||-
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 68999999999998873322 346999994
No 14
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=56.11 E-value=3.3 Score=37.75 Aligned_cols=32 Identities=25% Similarity=0.578 Sum_probs=24.3
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQ 200 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~ 200 (306)
--.|..|+...|-+-+.+..- -.-|+|||-..
T Consensus 98 yV~C~~C~~pdT~l~k~~~~~-~l~C~aCGa~~ 129 (201)
T PRK12336 98 YVICSECGLPDTRLVKEDRVL-MLRCDACGAHR 129 (201)
T ss_pred eEECCCCCCCCcEEEEcCCeE-EEEcccCCCCc
Confidence 368999999999998764322 35899999653
No 15
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=52.16 E-value=6.8 Score=38.56 Aligned_cols=34 Identities=35% Similarity=0.720 Sum_probs=30.1
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHH
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRK 202 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK 202 (306)
..+.|++|+++. |+|-.-.-| -.||--|.=-.|.
T Consensus 19 ~Nk~CaDCga~~-P~W~S~nlG-vfiCi~CagvHRs 52 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVNLG-VFLCIDCAGVHRS 52 (319)
T ss_pred ccCccccCCCCC-CceEecccC-eEEEeecchhhhc
Confidence 458999999999 999999999 8999999766665
No 16
>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=51.11 E-value=3.8 Score=28.43 Aligned_cols=28 Identities=25% Similarity=0.809 Sum_probs=17.8
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHHHH
Q 021859 170 VCADCNTTKTPLWRSGPRGPKSLCNACGIRQ 200 (306)
Q Consensus 170 ~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~ 200 (306)
.|.+|+++. -.+ ....| ..+|..||+-+
T Consensus 2 ~Cp~Cg~~~-~~~-D~~~g-~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKE-IVF-DPERG-ELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSE-EEE-ETTTT-EEEETTT-BBE
T ss_pred CCcCCcCCc-eEE-cCCCC-eEECCCCCCEe
Confidence 588898876 233 23445 67999998643
No 17
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=50.02 E-value=13 Score=30.62 Aligned_cols=34 Identities=32% Similarity=0.636 Sum_probs=29.5
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHHHHh
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRKA 203 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK~ 203 (306)
.+.|++|+. .-|.|-.-.-| -.||-.|.-..|..
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 578999998 55999999999 89999999888744
No 18
>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=45.42 E-value=5.7 Score=34.05 Aligned_cols=28 Identities=32% Similarity=0.711 Sum_probs=23.1
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHH
Q 021859 169 RVCADCNTTKTPLWRSGPRGPKSLCNACG 197 (306)
Q Consensus 169 r~CsnC~tt~TP~WRrGP~G~~~LCNACG 197 (306)
-.|..|+.+.|-+=+.+..- -.-|+|||
T Consensus 94 VlC~~C~spdT~l~k~~r~~-~l~C~aCG 121 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLI-FLKCKACG 121 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCC-EEEETTTS
T ss_pred EEcCCCCCCccEEEEcCCEE-EEEecccC
Confidence 57999999999988874443 56899998
No 19
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=43.53 E-value=14 Score=37.59 Aligned_cols=34 Identities=35% Similarity=0.784 Sum_probs=28.2
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHH
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRK 202 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK 202 (306)
..+.|.+|+... |.|-.-..| -.||-.|.=..|.
T Consensus 21 gNk~CaDCga~n-PtWASvn~G-IFLCl~CSGVHRs 54 (395)
T PLN03114 21 DNKICFDCNAKN-PTWASVTYG-IFLCIDCSAVHRS 54 (395)
T ss_pred CCCcCccCCCCC-CCceeeccc-eeehhhhhHhhcc
Confidence 358899999875 999999999 8999999765554
No 20
>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=42.37 E-value=9.5 Score=27.14 Aligned_cols=25 Identities=48% Similarity=0.999 Sum_probs=19.5
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACG 197 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACG 197 (306)
...|..| .||+.| ...| +.+|-+|+
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 4678889 589999 4456 78999985
No 21
>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=40.03 E-value=15 Score=27.21 Aligned_cols=32 Identities=22% Similarity=0.525 Sum_probs=24.0
Q ss_pred CCCcccccCCCCCCCcccCCCCCCcccchHHHHHHH
Q 021859 166 NTIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQR 201 (306)
Q Consensus 166 ~~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~r 201 (306)
...+.|..||....- ...+....|..||..+.
T Consensus 26 ~TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKK----RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CCccCccCccccccc----ccccceEEcCCCCCEEC
Confidence 357899999998755 44455679999998653
No 22
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=39.57 E-value=8.7 Score=28.95 Aligned_cols=26 Identities=27% Similarity=0.800 Sum_probs=20.4
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHHHHH
Q 021859 165 TNTIRVCADCNTTKTPLWRSGPRGPKSLCNACGIR 199 (306)
Q Consensus 165 ~~~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~ 199 (306)
....-.|.+||...-| +.+|..||.|
T Consensus 24 ~~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 24 APGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CCcceECCCCCCccCC---------eEECCCCCcC
Confidence 3456789999987764 7899999955
No 23
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=38.82 E-value=35 Score=26.10 Aligned_cols=33 Identities=27% Similarity=0.626 Sum_probs=25.6
Q ss_pred CcccccCCCCCCCcccCCCCCCcccc-hHHHHHHHHhhhHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLC-NACGIRQRKARRAMA 208 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LC-NACGL~~rK~~k~~~ 208 (306)
-+.|.+||...-| . +..| ..|+-.|.+.+++..
T Consensus 3 HkHC~~CG~~Ip~-------~-~~fCS~~C~~~~~k~qk~~~ 36 (59)
T PF09889_consen 3 HKHCPVCGKPIPP-------D-ESFCSPKCREEYRKRQKRMR 36 (59)
T ss_pred CCcCCcCCCcCCc-------c-hhhhCHHHHHHHHHHHHHHH
Confidence 4789999977654 2 6899 599999988776644
No 24
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=38.26 E-value=9.9 Score=29.85 Aligned_cols=37 Identities=24% Similarity=0.375 Sum_probs=29.2
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHHh
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRKA 203 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK~ 203 (306)
.+..|..|.+..|-+|.+-..-+..-|-+||...+..
T Consensus 9 AGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~~ 45 (66)
T COG3529 9 AGAVCPACQAQDTLAMWRENNVEIVECVKCGHHMREA 45 (66)
T ss_pred ccCCCcccchhhHHHHHHhcCCceEehhhcchHhhhc
Confidence 3568999999999886655555578999999988644
No 25
>PRK00420 hypothetical protein; Validated
Probab=36.52 E-value=15 Score=31.26 Aligned_cols=29 Identities=24% Similarity=0.545 Sum_probs=22.7
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQR 201 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~r 201 (306)
...|..|+ +|+.|- ..| +..|-+||-.+.
T Consensus 23 ~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCC---Ccceec-CCC-ceECCCCCCeee
Confidence 37899998 677775 456 789999998764
No 26
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=34.41 E-value=18 Score=24.91 Aligned_cols=28 Identities=25% Similarity=0.682 Sum_probs=21.4
Q ss_pred CCCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 021859 166 NTIRVCADCNTTKTPLWRSGPRGPKSLCNACGI 198 (306)
Q Consensus 166 ~~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL 198 (306)
+....|..|+.. |-...+| ...|..||-
T Consensus 6 ~~~~~C~~C~~~----~~~~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR----WFYSDDG-FYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe----EeEccCC-EEEhhhCce
Confidence 344569999987 6666678 899999984
No 27
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.24 E-value=15 Score=35.76 Aligned_cols=30 Identities=30% Similarity=0.699 Sum_probs=24.1
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHH
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQ 200 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~ 200 (306)
.-|.|..||+...|. ..|-+.+|+.||.++
T Consensus 110 ~~RFCg~CG~~~~~~----~~g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRFCGRCGTKTYPR----EGGWARVCPKCGHEH 139 (279)
T ss_pred hCcCCCCCCCcCccc----cCceeeeCCCCCCcc
Confidence 359999999998763 345568999999987
No 28
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=32.87 E-value=45 Score=33.29 Aligned_cols=30 Identities=23% Similarity=0.705 Sum_probs=22.7
Q ss_pred CCCcccccCCCCCCCcccCCCCCCcccchHHHH
Q 021859 166 NTIRVCADCNTTKTPLWRSGPRGPKSLCNACGI 198 (306)
Q Consensus 166 ~~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL 198 (306)
.....|.|||.+.|+-.-.|. .-+|-+||-
T Consensus 313 ~k~nfc~ncG~~~t~~~~ng~---a~fcp~cgq 342 (345)
T COG4260 313 AKLNFCLNCGCGTTADFDNGK---AKFCPECGQ 342 (345)
T ss_pred cccccccccCcccccCCccch---hhhChhhcC
Confidence 445699999999998665544 459999984
No 29
>COG3952 Predicted membrane protein [Function unknown]
Probab=32.66 E-value=23 Score=30.46 Aligned_cols=20 Identities=30% Similarity=0.378 Sum_probs=15.2
Q ss_pred cccCCCCCCcccchHHHHHHHH
Q 021859 181 LWRSGPRGPKSLCNACGIRQRK 202 (306)
Q Consensus 181 ~WRrGP~G~~~LCNACGL~~rK 202 (306)
.||.+|-+ .||+|||++..-
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 36777766 799999998643
No 30
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=31.64 E-value=13 Score=30.97 Aligned_cols=34 Identities=18% Similarity=0.373 Sum_probs=22.6
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHH
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQR 201 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~r 201 (306)
..-.|.+|+.. +-.-..+...++..|-.||.|+.
T Consensus 20 t~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 20 KIFECPRCGKV-SISVKIKKNIAIITCGNCGLYTE 53 (99)
T ss_pred cEeECCCCCCe-EeeeecCCCcceEECCCCCCccC
Confidence 45789999953 32222222355889999999975
No 31
>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=31.30 E-value=20 Score=25.17 Aligned_cols=26 Identities=35% Similarity=0.739 Sum_probs=19.5
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHH
Q 021859 169 RVCADCNTTKTPLWRSGPRGPKSLCNACG 197 (306)
Q Consensus 169 r~CsnC~tt~TP~WRrGP~G~~~LCNACG 197 (306)
-.|.+|+.+ ...|.++ .+ ..-|++|+
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~-~~~C~~C~ 44 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RG-RYRCKACR 44 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CC-eEECCCCC
Confidence 569999998 5555555 34 68999996
No 32
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=31.10 E-value=20 Score=35.18 Aligned_cols=33 Identities=36% Similarity=0.721 Sum_probs=27.4
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRK 202 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK 202 (306)
.+.|++|++. .|.|-.---| -.+|=.|-=-.|+
T Consensus 25 N~~CADC~a~-~P~WaSwnlG-vFiC~~C~giHR~ 57 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASWNLG-VFICLRCAGIHRS 57 (287)
T ss_pred cCcccccCCC-CCCeEEeecC-eEEEeeccccccc
Confidence 6899999999 9999998889 7899888544443
No 33
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=29.92 E-value=26 Score=36.90 Aligned_cols=30 Identities=30% Similarity=0.668 Sum_probs=21.3
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHHHHH
Q 021859 169 RVCADCNTTKTPLWRSGPRGPKSLCNACGIRQR 201 (306)
Q Consensus 169 r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~r 201 (306)
+.|.||+.+.= =|+-..| ...|.+||.-.-
T Consensus 1 ~~C~~C~~s~f--e~d~a~g-~~~C~~CG~v~E 30 (521)
T KOG1598|consen 1 MVCKNCGGSNF--ERDEATG-NLYCTACGTVLE 30 (521)
T ss_pred CcCCCCCCCCc--ccccccC-Cceeccccceee
Confidence 47999998752 1333556 789999998653
No 34
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=29.29 E-value=22 Score=34.12 Aligned_cols=30 Identities=30% Similarity=0.702 Sum_probs=17.8
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQ 200 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~ 200 (306)
...|.+|+.+ +.--+-..| ..+|.-||+-.
T Consensus 11 ~~~Cp~Cg~~--~iv~d~~~G-e~vC~~CG~Vl 40 (310)
T PRK00423 11 KLVCPECGSD--KLIYDYERG-EIVCADCGLVI 40 (310)
T ss_pred CCcCcCCCCC--CeeEECCCC-eEeecccCCcc
Confidence 4567778752 332223456 67788888744
No 35
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=26.82 E-value=36 Score=23.79 Aligned_cols=29 Identities=24% Similarity=0.660 Sum_probs=21.4
Q ss_pred CcccccCCCCCCCcccCC-CCCCcccchHHH
Q 021859 168 IRVCADCNTTKTPLWRSG-PRGPKSLCNACG 197 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrG-P~G~~~LCNACG 197 (306)
...|..|+.+..=.|..- ..| ...|+.||
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G-~~~C~~Cg 32 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRG-TWFCSVCG 32 (37)
T ss_pred ccCCCCCCCccccccccCCCCc-CEEeCCCC
Confidence 357999999887677553 334 67999996
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=26.31 E-value=36 Score=34.11 Aligned_cols=33 Identities=45% Similarity=0.693 Sum_probs=21.7
Q ss_pred CCCcccccccccccccCchhhhhccCc--hhHHHHHH
Q 021859 260 KKKLCSFEDLTLILSKNNSSALQRVFP--QEEKEAAI 294 (306)
Q Consensus 260 ~~k~~~f~d~~~~ls~~~~~a~~~~f~--~de~~AAi 294 (306)
+-.+|+||.|+++ -|||-|+..+.. -||.|||+
T Consensus 257 QSTICRFESLTLS--HNNMiALKPILqaWLEeAE~a~ 291 (385)
T KOG1168|consen 257 QSTICRFESLTLS--HNNMIALKPILQAWLEEAEAAM 291 (385)
T ss_pred ccceeeeeeeccc--cCcchhhhHHHHHHHHHHHHHH
Confidence 4459999998864 577788876632 25555554
No 37
>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=25.76 E-value=15 Score=27.25 Aligned_cols=22 Identities=32% Similarity=0.967 Sum_probs=17.2
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHH
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACG 197 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACG 197 (306)
....|.+||... -++.+|.+||
T Consensus 25 ~l~~c~~cg~~~---------~~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPK---------LPHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEE---------STTSBCTTTB
T ss_pred ceeeeccCCCEe---------cccEeeCCCC
Confidence 568899999643 3478999999
No 38
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=25.33 E-value=64 Score=26.03 Aligned_cols=33 Identities=24% Similarity=0.418 Sum_probs=24.6
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHHHHHHHH
Q 021859 165 TNTIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRK 202 (306)
Q Consensus 165 ~~~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK 202 (306)
.++...|.-|+...+-.+ .| ...|+||..++|.
T Consensus 3 ~~~~~~C~VCg~~a~g~h----yG-v~sC~aCk~FFRR 35 (90)
T cd07169 3 RAEQRTCLICGDRATGLH----YG-IISCEGCKGFFKR 35 (90)
T ss_pred cccCCCCeecCCcCcceE----EC-cceehhhHHHHHH
Confidence 356778999998665443 34 4689999999984
No 39
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=24.69 E-value=32 Score=30.95 Aligned_cols=30 Identities=27% Similarity=0.666 Sum_probs=24.9
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHH
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACG 197 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACG 197 (306)
....|..|++.....|-.-..| ..+|..|+
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 3568999998887677777777 89999997
No 40
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=24.41 E-value=21 Score=24.85 Aligned_cols=28 Identities=21% Similarity=0.478 Sum_probs=17.7
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHH
Q 021859 170 VCADCNTTKTPLWRSGPRGPKSLCNACGI 198 (306)
Q Consensus 170 ~CsnC~tt~TP~WRrGP~G~~~LCNACGL 198 (306)
.|..|+.+-+-+..-.. .....|-+||-
T Consensus 7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 57888876654443333 44668888875
No 41
>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=23.97 E-value=30 Score=23.89 Aligned_cols=31 Identities=26% Similarity=0.589 Sum_probs=20.2
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGI 198 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL 198 (306)
+-+|.+|++---|.-+-...|..-.||-|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 4689999999988877777776779999986
No 42
>PLN03131 hypothetical protein; Provisional
Probab=23.15 E-value=44 Score=36.32 Aligned_cols=34 Identities=24% Similarity=0.470 Sum_probs=28.0
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHH
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRK 202 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK 202 (306)
..+.|++|+... |.|-.-.-| -.+|-.|.=..|.
T Consensus 22 gNk~CADCga~~-P~WASiNlG-IFICi~CSGIHRs 55 (705)
T PLN03131 22 PNRRCINCNSLG-PQFVCTNFW-TFICMTCSGIHRE 55 (705)
T ss_pred CCCccccCCCCC-CCeeEeccc-eEEchhchhhhcc
Confidence 458999999754 999998889 7899999766554
No 43
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=23.08 E-value=44 Score=36.03 Aligned_cols=34 Identities=26% Similarity=0.493 Sum_probs=28.3
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHHH
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRK 202 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK 202 (306)
..+.|++|+... |.|-.-.-| -.+|-.|.=..|.
T Consensus 22 gNk~CADCgs~~-P~WASiNlG-IFICi~CSGIHRs 55 (648)
T PLN03119 22 PNRRCINCNSLG-PQYVCTTFW-TFVCMACSGIHRE 55 (648)
T ss_pred CCCccccCCCCC-CCceeeccc-eEEeccchhhhcc
Confidence 358999999866 999999999 7899999766554
No 44
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.07 E-value=53 Score=20.73 Aligned_cols=22 Identities=27% Similarity=0.904 Sum_probs=13.6
Q ss_pred cccccCCCCCCCcccCCCCCCcccchHHHH
Q 021859 169 RVCADCNTTKTPLWRSGPRGPKSLCNACGI 198 (306)
Q Consensus 169 r~CsnC~tt~TP~WRrGP~G~~~LCNACGL 198 (306)
+.|.+|++...+ + ...|-.||-
T Consensus 3 ~~Cp~Cg~~~~~-------~-~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP-------D-AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc-------c-cccChhhCC
Confidence 567888875432 2 457777764
No 45
>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=22.97 E-value=23 Score=34.48 Aligned_cols=36 Identities=25% Similarity=0.604 Sum_probs=25.3
Q ss_pred CCCcccccCCCCCCCcc----cCCCCCCc--ccchHHHHHHH
Q 021859 166 NTIRVCADCNTTKTPLW----RSGPRGPK--SLCNACGIRQR 201 (306)
Q Consensus 166 ~~~r~CsnC~tt~TP~W----RrGP~G~~--~LCNACGL~~r 201 (306)
.....|..|+-..+-.| |...++-. +.|..||-+|+
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 34689999998887666 34443311 38999999885
No 46
>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=22.79 E-value=24 Score=27.78 Aligned_cols=35 Identities=23% Similarity=0.423 Sum_probs=28.1
Q ss_pred CCcccccCCCCCCCcccCCCCCCcccchHHHHHHH
Q 021859 167 TIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQR 201 (306)
Q Consensus 167 ~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~r 201 (306)
.+-.|..|.+..|-.|.+...-...-|-+||...+
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred cCccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 35789999999998866555565789999998775
No 47
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=22.63 E-value=27 Score=23.14 Aligned_cols=29 Identities=28% Similarity=0.604 Sum_probs=18.6
Q ss_pred ccccCCCCCCCcccCCCCCCcccchHHHHH
Q 021859 170 VCADCNTTKTPLWRSGPRGPKSLCNACGIR 199 (306)
Q Consensus 170 ~CsnC~tt~TP~WRrGP~G~~~LCNACGL~ 199 (306)
.|..|+..-+ .|..-..+....|-.||-.
T Consensus 7 ~C~~Cg~~fe-~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 7 RCEDCGHTFE-VLQKISDDPLATCPECGGD 35 (41)
T ss_pred EcCCCCCEEE-EEEecCCCCCCCCCCCCCc
Confidence 6888888655 3443333556678888873
No 48
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.25 E-value=33 Score=30.83 Aligned_cols=28 Identities=25% Similarity=0.530 Sum_probs=21.5
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHHHHHHH
Q 021859 165 TNTIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQR 201 (306)
Q Consensus 165 ~~~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~r 201 (306)
....+.|+.||. ..+....|..||..+.
T Consensus 306 ~~tS~~C~~cg~---------~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 306 YYTSKTCPCCGH---------LSGRLFKCPRCGFVHD 333 (364)
T ss_pred CCCcccccccCC---------ccceeEECCCCCCeeh
Confidence 455699999999 3354679999998654
No 49
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.37 E-value=48 Score=23.05 Aligned_cols=29 Identities=21% Similarity=0.681 Sum_probs=19.3
Q ss_pred cccccCCCCCCCc-ccCCCCCCcccchHHHHHH
Q 021859 169 RVCADCNTTKTPL-WRSGPRGPKSLCNACGIRQ 200 (306)
Q Consensus 169 r~CsnC~tt~TP~-WRrGP~G~~~LCNACGL~~ 200 (306)
+.|..||..-.+. |.. .....|..||..+
T Consensus 1 ~FCp~Cg~~l~~~~~~~---~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKE---KRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCC---CCEEECCcCCCeE
Confidence 3699999865443 322 2367999999654
No 50
>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=21.03 E-value=18 Score=23.63 Aligned_cols=28 Identities=32% Similarity=0.796 Sum_probs=15.4
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGIR 199 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~ 199 (306)
-+.|..||+...+. +.|-...|.+||..
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 47899999877654 33556788888864
No 51
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=21.00 E-value=59 Score=25.17 Aligned_cols=16 Identities=19% Similarity=0.621 Sum_probs=13.1
Q ss_pred cccccCCCCC-CCcccC
Q 021859 169 RVCADCNTTK-TPLWRS 184 (306)
Q Consensus 169 r~CsnC~tt~-TP~WRr 184 (306)
..|.+|+++. |..|+.
T Consensus 16 ~~CP~Cgs~~~T~~W~G 32 (61)
T PRK08351 16 DRCPVCGSRDLSDEWFD 32 (61)
T ss_pred CcCCCCcCCcccccccc
Confidence 3699999988 888974
No 52
>PF12773 DZR: Double zinc ribbon
Probab=20.77 E-value=50 Score=22.98 Aligned_cols=27 Identities=30% Similarity=0.813 Sum_probs=14.8
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGIR 199 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~ 199 (306)
.+.|.+||+.-. ........|..||-.
T Consensus 12 ~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLP-----PPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChh-----hccCCCCCCcCCcCC
Confidence 566777776655 222223456666643
No 53
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=20.75 E-value=43 Score=34.79 Aligned_cols=35 Identities=34% Similarity=0.736 Sum_probs=28.2
Q ss_pred CCCCcccccCCCCCCCcccCCCCCCcccchHHHHHHH
Q 021859 165 TNTIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQR 201 (306)
Q Consensus 165 ~~~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~r 201 (306)
..+.+.|.+|+.. -|-|-.-+.| -.||--|---.|
T Consensus 20 ~~~NKvCFDCgAk-nPtWaSVTYG-IFLCiDCSAvHR 54 (454)
T KOG0706|consen 20 QSENKVCFDCGAK-NPTWASVTYG-IFLCIDCSAVHR 54 (454)
T ss_pred CCCCceecccCCC-CCCceeecce-EEEEEecchhhh
Confidence 3456999999975 6899999999 899999964433
No 54
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=20.34 E-value=1e+02 Score=31.73 Aligned_cols=42 Identities=24% Similarity=0.518 Sum_probs=31.4
Q ss_pred CCCCCCCCCcccccCCCCCCCcccCCCCCCcccchHHHHHHHHh
Q 021859 160 NNNNNTNTIRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQRKA 203 (306)
Q Consensus 160 ss~~s~~~~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~rK~ 203 (306)
+..+...+...|.-|....| .--.-|-| +-.|-+||+++|.+
T Consensus 53 SaddtDEen~~C~ICA~~~T-Ys~~~PC~-H~~CH~Ca~RlRAL 94 (493)
T COG5236 53 SADDTDEENMNCQICAGSTT-YSARYPCG-HQICHACAVRLRAL 94 (493)
T ss_pred cccccccccceeEEecCCce-EEEeccCC-chHHHHHHHHHHHH
Confidence 44455677889999987665 34456778 78999999999854
No 55
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.19 E-value=40 Score=31.72 Aligned_cols=29 Identities=28% Similarity=0.501 Sum_probs=21.3
Q ss_pred CcccccCCCCCCCcccCCCCCCcccchHHHHHH
Q 021859 168 IRVCADCNTTKTPLWRSGPRGPKSLCNACGIRQ 200 (306)
Q Consensus 168 ~r~CsnC~tt~TP~WRrGP~G~~~LCNACGL~~ 200 (306)
.+.|..||+..... ..|....|.+||..+
T Consensus 99 ~~fC~~CG~~~~~~----~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 99 HRFCGYCGHPMHPS----KTEWAMLCPHCRERY 127 (256)
T ss_pred CccccccCCCCeec----CCceeEECCCCCCEE
Confidence 58999999976542 345567899999654
Done!