Query 024832
Match_columns 262
No_of_seqs 238 out of 850
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:44:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024832.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024832hhsearch_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 99.6 4.4E-16 9.5E-21 111.8 3.7 44 172-217 1-44 (54)
2 smart00401 ZnF_GATA zinc finge 99.6 1.6E-15 3.4E-20 108.0 3.4 48 169-218 2-50 (52)
3 PF00320 GATA: GATA zinc finge 99.5 1.3E-14 2.9E-19 96.0 0.8 35 173-209 1-35 (36)
4 PF06203 CCT: CCT motif; Inte 99.2 1.6E-11 3.6E-16 85.4 2.8 43 104-146 1-43 (45)
5 KOG1601 GATA-4/5/6 transcripti 98.7 8.8E-09 1.9E-13 88.8 3.2 50 170-221 199-248 (340)
6 COG5641 GAT1 GATA Zn-finger-co 98.5 5.5E-08 1.2E-12 96.7 3.0 54 168-224 156-215 (498)
7 PF06200 tify: tify domain; I 95.6 0.0058 1.3E-07 40.8 1.3 24 67-90 3-26 (36)
8 COG5641 GAT1 GATA Zn-finger-co 92.2 0.11 2.4E-06 52.4 3.1 49 168-217 295-343 (498)
9 KOG3554 Histone deacetylase co 89.8 1.3 2.9E-05 44.8 7.9 39 170-210 386-426 (693)
10 PF09425 CCT_2: Divergent CCT 83.4 0.74 1.6E-05 29.1 1.4 19 103-121 3-21 (27)
11 PF14803 Nudix_N_2: Nudix N-te 69.8 1.1 2.5E-05 29.4 -0.5 30 171-202 1-30 (34)
12 KOG1601 GATA-4/5/6 transcripti 63.4 2.5 5.4E-05 36.3 0.2 41 101-141 290-330 (340)
13 PF01783 Ribosomal_L32p: Ribos 59.8 2.2 4.8E-05 30.6 -0.7 25 169-205 25-49 (56)
14 PF06677 Auto_anti-p27: Sjogre 55.3 5.2 0.00011 27.3 0.6 25 170-201 17-41 (41)
15 PF01412 ArfGap: Putative GTPa 51.0 13 0.00028 30.0 2.4 38 168-209 11-48 (116)
16 PRK03988 translation initiatio 49.9 5.3 0.00012 33.9 -0.0 30 170-202 102-131 (138)
17 PF13248 zf-ribbon_3: zinc-rib 48.6 11 0.00023 22.9 1.2 23 170-202 2-24 (26)
18 PRK12286 rpmF 50S ribosomal pr 48.2 6.9 0.00015 28.5 0.3 25 168-203 25-49 (57)
19 TIGR00311 aIF-2beta translatio 47.4 6.3 0.00014 33.3 0.0 29 171-202 98-126 (133)
20 COG3952 Predicted membrane pro 46.3 5.1 0.00011 33.1 -0.7 20 185-206 76-95 (113)
21 smart00653 eIF2B_5 domain pres 45.0 7.4 0.00016 31.8 0.1 29 171-202 81-109 (110)
22 PRK12336 translation initiatio 41.6 8.5 0.00018 34.4 -0.1 30 170-202 98-127 (201)
23 PF13717 zinc_ribbon_4: zinc-r 40.9 5.1 0.00011 26.3 -1.2 33 171-204 3-35 (36)
24 PF13240 zinc_ribbon_2: zinc-r 38.5 18 0.00039 21.6 1.0 21 172-202 1-21 (23)
25 PRK11823 DNA repair protein Ra 38.1 12 0.00025 37.1 0.3 25 169-203 6-30 (446)
26 KOG3740 Uncharacterized conser 37.4 13 0.00028 39.0 0.4 39 168-208 460-501 (706)
27 PRK14892 putative transcriptio 36.8 11 0.00025 30.3 -0.0 37 168-207 19-55 (99)
28 KOG1598 Transcription initiati 36.7 16 0.00034 37.5 1.0 33 171-208 1-33 (521)
29 TIGR00416 sms DNA repair prote 36.3 13 0.00029 36.9 0.4 25 169-203 6-30 (454)
30 PF08271 TF_Zn_Ribbon: TFIIB z 36.3 13 0.00028 25.0 0.2 29 172-205 2-30 (43)
31 PRK00420 hypothetical protein; 35.0 18 0.00039 29.9 0.9 30 170-206 23-52 (112)
32 PF02701 zf-Dof: Dof domain, z 34.0 26 0.00057 26.3 1.5 47 169-217 4-53 (63)
33 PF01873 eIF-5_eIF-2B: Domain 33.9 15 0.00033 30.6 0.2 29 171-202 94-122 (125)
34 TIGR01031 rpmF_bact ribosomal 33.3 15 0.00032 26.5 0.1 25 168-203 24-48 (55)
35 PF09889 DUF2116: Uncharacteri 32.5 29 0.00062 25.6 1.5 29 170-208 3-32 (59)
36 PF09297 zf-NADH-PPase: NADH p 31.1 16 0.00034 23.0 -0.0 28 170-203 3-30 (32)
37 smart00834 CxxC_CXXC_SSSS Puta 31.0 19 0.00041 23.2 0.3 29 171-202 6-34 (41)
38 COG1645 Uncharacterized Zn-fin 30.7 19 0.00041 30.6 0.4 27 169-203 27-53 (131)
39 smart00105 ArfGap Putative GTP 30.6 46 0.001 26.7 2.6 37 169-209 2-38 (112)
40 PF04810 zf-Sec23_Sec24: Sec23 30.2 19 0.00041 24.0 0.2 31 170-202 2-32 (40)
41 PRK12496 hypothetical protein; 29.7 26 0.00057 30.3 1.1 35 169-211 126-160 (164)
42 COG3529 Predicted nucleic-acid 29.6 13 0.00028 27.9 -0.8 34 170-205 10-43 (66)
43 TIGR02098 MJ0042_CXXC MJ0042 f 28.5 8.8 0.00019 24.8 -1.6 33 171-204 3-35 (38)
44 COG2331 Uncharacterized protei 28.2 19 0.00042 28.1 0.0 34 171-207 13-46 (82)
45 PF09723 Zn-ribbon_8: Zinc rib 26.1 25 0.00055 23.6 0.3 29 171-202 6-34 (42)
46 PRK01110 rpmF 50S ribosomal pr 25.8 24 0.00052 25.9 0.1 25 168-204 25-49 (60)
47 PF09526 DUF2387: Probable met 25.7 25 0.00054 26.7 0.2 35 170-206 8-42 (71)
48 COG4260 Membrane protease subu 25.3 34 0.00075 33.0 1.1 28 170-202 315-342 (345)
49 TIGR02605 CxxC_CxxC_SSSS putat 25.1 29 0.00062 23.8 0.4 29 171-202 6-34 (52)
50 PRK14559 putative protein seri 25.0 58 0.0013 34.2 2.8 9 195-203 42-50 (645)
51 COG5349 Uncharacterized protei 24.3 27 0.00059 29.5 0.2 34 170-208 21-54 (126)
52 PF11781 RRN7: RNA polymerase 24.2 31 0.00068 22.7 0.4 26 170-202 8-33 (36)
53 PRK05342 clpX ATP-dependent pr 24.0 42 0.00092 33.1 1.5 30 170-201 9-38 (412)
54 KOG0706 Predicted GTPase-activ 23.5 42 0.00091 33.9 1.3 40 167-210 20-59 (454)
55 TIGR03573 WbuX N-acetyl sugar 23.4 51 0.0011 31.4 1.9 32 171-206 2-33 (343)
56 COG2816 NPY1 NTP pyrophosphohy 23.4 30 0.00064 32.9 0.3 34 167-206 108-141 (279)
57 PF07282 OrfB_Zn_ribbon: Putat 23.3 39 0.00084 24.3 0.8 29 170-204 28-56 (69)
58 cd01121 Sms Sms (bacterial rad 23.2 29 0.00062 33.8 0.1 22 172-203 2-23 (372)
59 PF06689 zf-C4_ClpX: ClpX C4-t 23.1 33 0.00072 23.0 0.4 32 171-203 2-33 (41)
60 PF12773 DZR: Double zinc ribb 22.5 50 0.0011 22.3 1.2 11 169-179 11-21 (50)
61 PRK05978 hypothetical protein; 21.7 36 0.00079 29.3 0.5 34 170-208 33-66 (148)
62 KOG1561 CCAAT-binding factor, 20.2 1E+02 0.0023 29.6 3.2 29 122-150 217-246 (307)
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=99.61 E-value=4.4e-16 Score=111.83 Aligned_cols=44 Identities=52% Similarity=1.258 Sum_probs=41.7
Q ss_pred cceeeccCCCCCCceecCCCCCCccchhhhhHHHhcCCCCCCCccc
Q 024832 172 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKM 217 (262)
Q Consensus 172 ~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g~~Rp~s~~~ 217 (262)
.|+||+++ .||+||+||.|..+|||||||||++++..||+.+..
T Consensus 1 ~C~~C~~~--~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTT--TTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCC--CCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 59999998 999999999888999999999999999999999876
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.57 E-value=1.6e-15 Score=108.02 Aligned_cols=48 Identities=52% Similarity=1.112 Sum_probs=43.7
Q ss_pred CCccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcCCC-CCCCcccC
Q 024832 169 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL-RDLGKKME 218 (262)
Q Consensus 169 ~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g~~-Rp~s~~~~ 218 (262)
....|+||+++ .||+||+||.|.++|||||||||++++.+ ||..+.++
T Consensus 2 ~~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~~ 50 (52)
T smart00401 2 SGRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKKD 50 (52)
T ss_pred CCCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCCCCccccccc
Confidence 35799999998 99999999999889999999999999998 88887764
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=99.45 E-value=1.3e-14 Score=96.04 Aligned_cols=35 Identities=54% Similarity=1.288 Sum_probs=28.5
Q ss_pred ceeeccCCCCCCceecCCCCCCccchhhhhHHHhcCC
Q 024832 173 CTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 209 (262)
Q Consensus 173 C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g~ 209 (262)
|+||+++ .||+||++|.|..+|||+|||+|+++++
T Consensus 1 C~~C~tt--~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTT--ETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--S--T-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCC--CCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 8999998 8999999999988899999999999985
No 4
>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction. The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding
Probab=99.16 E-value=1.6e-11 Score=85.36 Aligned_cols=43 Identities=47% Similarity=0.779 Sum_probs=41.2
Q ss_pred HHHHHHHHHhhhhhhcccceeeeehhHHHHHHhhhccCccccc
Q 024832 104 RAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKGQFTSA 146 (262)
Q Consensus 104 R~a~l~rfrekrk~r~f~KkirY~~Rqe~A~r~~R~kGqfas~ 146 (262)
|.+.|.+|++||+.|+|+|+|+|++||.+|+.+||.+|+|++.
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~ 43 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKK 43 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCC
Confidence 6789999999999999999999999999999999999999974
No 5
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.70 E-value=8.8e-09 Score=88.78 Aligned_cols=50 Identities=46% Similarity=0.951 Sum_probs=44.2
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcCCCCCCCcccCCCC
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKMEDQP 221 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g~~Rp~s~~~~~~~ 221 (262)
...|.+|+++ .||+||++|.|+++||||||+++++++..|++.+++....
T Consensus 199 ~~~c~~~~~~--~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~ 248 (340)
T KOG1601|consen 199 LRQCSNCGTT--KTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASS 248 (340)
T ss_pred CcccCCCCCC--CCcceecCCCCCccccccchhhhhhcCccccccccCcccc
Confidence 5899999997 9999999999988999999999999997788877764443
No 6
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.50 E-value=5.5e-08 Score=96.69 Aligned_cols=54 Identities=35% Similarity=0.703 Sum_probs=46.7
Q ss_pred CCCccceeeccCCCCCCceecCCC-----CCCccchhhhhHHHhcCCCC-CCCcccCCCCCCC
Q 024832 168 PSETSCTHCGISSKSTPMMRRGPS-----GPRSLCNACGLFWANKGALR-DLGKKMEDQPLTP 224 (262)
Q Consensus 168 ~~~~~C~nCgtt~~~TP~WRrGp~-----G~~~LCNACGl~~~~~g~~R-p~s~~~~~~~~~~ 224 (262)
....+|.||.++ .||+|||+.. | -+||||||||++.|+++| |++++..-+....
T Consensus 156 ~~~~vc~Nc~t~--stPlwrR~~~~~s~~~-n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 156 NQPHVCSNCKTT--STPLWRRASSESSLPG-NNLCNACGLYLKLHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred cccchhcccccc--CCccccccccccccCC-ccccccccccccccCCcCCCcccccccccccc
Confidence 344599999998 9999999999 6 599999999999999999 9999886555544
No 7
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=95.61 E-value=0.0058 Score=40.81 Aligned_cols=24 Identities=54% Similarity=0.888 Sum_probs=20.8
Q ss_pred CCCCcceeeecceeeeecccCCCC
Q 024832 67 SNSSQLTLSFRGQVYVFDSVTPDK 90 (262)
Q Consensus 67 ~~sS~ltlsf~g~~~vf~~v~pek 90 (262)
..+.+|||-|.|+|+||+.++|+|
T Consensus 3 ~~~~qLTIfY~G~V~Vfd~v~~~K 26 (36)
T PF06200_consen 3 PETAQLTIFYGGQVCVFDDVPPDK 26 (36)
T ss_pred CCCCcEEEEECCEEEEeCCCCHHH
Confidence 467899999999999999887665
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=92.20 E-value=0.11 Score=52.35 Aligned_cols=49 Identities=31% Similarity=0.369 Sum_probs=42.1
Q ss_pred CCCccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcCCCCCCCccc
Q 024832 168 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKM 217 (262)
Q Consensus 168 ~~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g~~Rp~s~~~ 217 (262)
+....|.+|++. +.||.|||...-.-++||+||++.+..+..||+..+.
T Consensus 295 ps~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~ 343 (498)
T COG5641 295 PSDKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKP 343 (498)
T ss_pred hhhcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCC
Confidence 346689999975 5899999998777799999999999999999998865
No 9
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=89.79 E-value=1.3 Score=44.76 Aligned_cols=39 Identities=23% Similarity=0.604 Sum_probs=31.9
Q ss_pred CccceeeccCCCCCCce--ecCCCCCCccchhhhhHHHhcCCC
Q 024832 170 ETSCTHCGISSKSTPMM--RRGPSGPRSLCNACGLFWANKGAL 210 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~W--RrGp~G~~~LCNACGl~~~~~g~~ 210 (262)
.+.|.+|+++ ..-.| |-+|.-...||-.|=+||++.|.+
T Consensus 386 g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 7799999998 65565 556777678999999999998853
No 10
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=83.39 E-value=0.74 Score=29.06 Aligned_cols=19 Identities=53% Similarity=0.688 Sum_probs=9.9
Q ss_pred cHHHHHHHHHhhhhhhccc
Q 024832 103 QRAASLDRFRQKRKERCFD 121 (262)
Q Consensus 103 ~R~a~l~rfrekrk~r~f~ 121 (262)
.|.++|.||-||||.|.+.
T Consensus 3 aRK~SLqRFLeKRK~R~~~ 21 (27)
T PF09425_consen 3 ARKASLQRFLEKRKDRLAA 21 (27)
T ss_dssp ---HHHHHHHHHH------
T ss_pred hHHHHHHHHHHHHHHhhcc
Confidence 4789999999999999765
No 11
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=69.80 E-value=1.1 Score=29.38 Aligned_cols=30 Identities=30% Similarity=0.708 Sum_probs=14.2
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
+.|.+||.. .+..-=.|.+-.+..|.+||.
T Consensus 1 kfC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGP--LERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred CccccccCh--hhhhcCCCCCccceECCCCCC
Confidence 368999984 222222345556689999984
No 12
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=63.36 E-value=2.5 Score=36.26 Aligned_cols=41 Identities=41% Similarity=0.637 Sum_probs=36.8
Q ss_pred cccHHHHHHHHHhhhhhhcccceeeeehhHHHHHHhhhccC
Q 024832 101 QPQRAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKG 141 (262)
Q Consensus 101 ~p~R~a~l~rfrekrk~r~f~KkirY~~Rqe~A~r~~R~kG 141 (262)
.-.|.+.+.++++++..+.|+++++|..|+..+..+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 45788889999999999999999999999999999988776
No 13
>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=59.81 E-value=2.2 Score=30.65 Aligned_cols=25 Identities=28% Similarity=0.945 Sum_probs=18.6
Q ss_pred CCccceeeccCCCCCCceecCCCCCCccchhhhhHHH
Q 024832 169 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 205 (262)
Q Consensus 169 ~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~ 205 (262)
....|.+||.. .-++.+|..|| ||+
T Consensus 25 ~l~~c~~cg~~-----------~~~H~vc~~cG-~y~ 49 (56)
T PF01783_consen 25 NLVKCPNCGEP-----------KLPHRVCPSCG-YYK 49 (56)
T ss_dssp SEEESSSSSSE-----------ESTTSBCTTTB-BSS
T ss_pred ceeeeccCCCE-----------ecccEeeCCCC-eEC
Confidence 56799999974 22468999999 444
No 14
>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=55.28 E-value=5.2 Score=27.35 Aligned_cols=25 Identities=44% Similarity=1.204 Sum_probs=19.0
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 201 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACG 201 (262)
...|..|+ +|++| ..+| +.+|-+|+
T Consensus 17 ~~~Cp~C~-----~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCG-----TPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCCC-----CeeEE-ecCC-CEECCCCC
Confidence 46788886 48999 3466 68999985
No 15
>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=50.97 E-value=13 Score=30.01 Aligned_cols=38 Identities=26% Similarity=0.556 Sum_probs=28.0
Q ss_pred CCCccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcCC
Q 024832 168 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 209 (262)
Q Consensus 168 ~~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g~ 209 (262)
+....|..|+. .-|.|-.=.-| -.||-.|.-..+.-|+
T Consensus 11 ~~N~~CaDCg~---~~p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 11 PGNKVCADCGA---PNPTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp TTCTB-TTT-S---BS--EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred cCcCcCCCCCC---CCCCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 45799999997 67899999999 5999999988888774
No 16
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=49.90 E-value=5.3 Score=33.91 Aligned_cols=30 Identities=30% Similarity=0.671 Sum_probs=22.6
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
=-.|..|+.+ .|-+-+.+-.= -.-|+|||-
T Consensus 102 yVlC~~C~sp--dT~l~k~~r~~-~l~C~ACGa 131 (138)
T PRK03988 102 YVICPECGSP--DTKLIKEGRIW-VLKCEACGA 131 (138)
T ss_pred cEECCCCCCC--CcEEEEcCCeE-EEEcccCCC
Confidence 3689999998 88888753222 357999996
No 17
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=48.57 E-value=11 Score=22.94 Aligned_cols=23 Identities=30% Similarity=0.790 Sum_probs=16.0
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
.+.|.+||.. -+.+ ..+|-.||.
T Consensus 2 ~~~Cp~Cg~~---------~~~~-~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAE---------IDPD-AKFCPNCGA 24 (26)
T ss_pred cCCCcccCCc---------CCcc-cccChhhCC
Confidence 3678889884 2344 368888885
No 18
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=48.19 E-value=6.9 Score=28.46 Aligned_cols=25 Identities=32% Similarity=1.032 Sum_probs=19.0
Q ss_pred CCCccceeeccCCCCCCceecCCCCCCccchhhhhH
Q 024832 168 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 203 (262)
Q Consensus 168 ~~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~ 203 (262)
+....|.+||.. .- ++.+|..||.|
T Consensus 25 ~~l~~C~~CG~~--~~---------~H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEP--KL---------PHRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCc--cC---------CeEECCCCCcC
Confidence 456789999985 22 36899999965
No 19
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=47.39 E-value=6.3 Score=33.28 Aligned_cols=29 Identities=28% Similarity=0.694 Sum_probs=21.7
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
-.|..|+.+ .|-+-+.+.-= -.-|+|||-
T Consensus 98 VlC~~C~sP--dT~l~k~~r~~-~l~C~ACGa 126 (133)
T TIGR00311 98 VICRECNRP--DTRIIKEGRVS-LLKCEACGA 126 (133)
T ss_pred EECCCCCCC--CcEEEEeCCeE-EEecccCCC
Confidence 589999998 88888753211 247999996
No 20
>COG3952 Predicted membrane protein [Function unknown]
Probab=46.27 E-value=5.1 Score=33.05 Aligned_cols=20 Identities=40% Similarity=0.579 Sum_probs=16.0
Q ss_pred ceecCCCCCCccchhhhhHHHh
Q 024832 185 MMRRGPSGPRSLCNACGLFWAN 206 (262)
Q Consensus 185 ~WRrGp~G~~~LCNACGl~~~~ 206 (262)
+||.+|-+ .||++|||+-..
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 47778877 699999998654
No 21
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=45.03 E-value=7.4 Score=31.81 Aligned_cols=29 Identities=28% Similarity=0.621 Sum_probs=21.6
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
-.|..|+.+ .|-+-+.+..= -.-|+|||-
T Consensus 81 VlC~~C~sp--dT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSP--DTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred EECCCCCCC--CcEEEEeCCeE-EEEccccCC
Confidence 689999998 89888873211 245999994
No 22
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=41.57 E-value=8.5 Score=34.37 Aligned_cols=30 Identities=27% Similarity=0.674 Sum_probs=22.5
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
--.|..|+.+ .|-+-+.+..= -.-|+|||-
T Consensus 98 yV~C~~C~~p--dT~l~k~~~~~-~l~C~aCGa 127 (201)
T PRK12336 98 YVICSECGLP--DTRLVKEDRVL-MLRCDACGA 127 (201)
T ss_pred eEECCCCCCC--CcEEEEcCCeE-EEEcccCCC
Confidence 3689999998 88888763211 247999997
No 23
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=40.92 E-value=5.1 Score=26.32 Aligned_cols=33 Identities=21% Similarity=0.594 Sum_probs=25.2
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhhHH
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 204 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~ 204 (262)
..|.+|++. -..|..+-.+.|....|-.||-.|
T Consensus 3 i~Cp~C~~~-y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAK-YEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCE-EeCCHHHCCCCCcEEECCCCCCEe
Confidence 468888886 566777777888778888888655
No 24
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=38.55 E-value=18 Score=21.61 Aligned_cols=21 Identities=29% Similarity=0.835 Sum_probs=12.7
Q ss_pred cceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 172 SCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 172 ~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
.|.+||.. -+++ ..+|..||.
T Consensus 1 ~Cp~CG~~---------~~~~-~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAE---------IEDD-AKFCPNCGT 21 (23)
T ss_pred CCcccCCC---------CCCc-CcchhhhCC
Confidence 36777774 2334 357777774
No 25
>PRK11823 DNA repair protein RadA; Provisional
Probab=38.06 E-value=12 Score=37.14 Aligned_cols=25 Identities=32% Similarity=0.906 Sum_probs=17.4
Q ss_pred CCccceeeccCCCCCCceecCCCCCCccchhhhhH
Q 024832 169 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 203 (262)
Q Consensus 169 ~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~ 203 (262)
...+|.+||. .+|.|. | .|.+||-+
T Consensus 6 ~~y~C~~Cg~---~~~~~~----g---~Cp~C~~w 30 (446)
T PRK11823 6 TAYVCQECGA---ESPKWL----G---RCPECGAW 30 (446)
T ss_pred CeEECCcCCC---CCcccC----e---eCcCCCCc
Confidence 4578999998 566663 3 58888764
No 26
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.38 E-value=13 Score=39.02 Aligned_cols=39 Identities=21% Similarity=0.428 Sum_probs=30.9
Q ss_pred CCCccceeeccCCCCCCceecCCCC---CCccchhhhhHHHhcC
Q 024832 168 PSETSCTHCGISSKSTPMMRRGPSG---PRSLCNACGLFWANKG 208 (262)
Q Consensus 168 ~~~~~C~nCgtt~~~TP~WRrGp~G---~~~LCNACGl~~~~~g 208 (262)
.+.-.|..|.+- .||.|+.-+.+ +..+|.+|----.++-
T Consensus 460 ~~P~~caqcktd--ftp~wk~ekstq~d~~i~cE~cvtSnqkkA 501 (706)
T KOG3740|consen 460 TEPYACAQCKTD--FTPAWKKEKSTQADAAIVCENCVTSNQKKA 501 (706)
T ss_pred CCchhhhhcccc--cccccccccccCcchHHHHHhhhhhccccc
Confidence 447899999995 99999998877 3489999977555543
No 27
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.77 E-value=11 Score=30.34 Aligned_cols=37 Identities=24% Similarity=0.514 Sum_probs=24.4
Q ss_pred CCCccceeeccCCCCCCceecCCCCCCccchhhhhHHHhc
Q 024832 168 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 207 (262)
Q Consensus 168 ~~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~ 207 (262)
+....|.+|+.. ..+ ...+-..++..|-.||+|+-+.
T Consensus 19 pt~f~CP~Cge~--~v~-v~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 19 PKIFECPRCGKV--SIS-VKIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred CcEeECCCCCCe--Eee-eecCCCcceEECCCCCCccCEE
Confidence 346789999952 332 2222245578999999987653
No 28
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=36.75 E-value=16 Score=37.46 Aligned_cols=33 Identities=27% Similarity=0.577 Sum_probs=23.1
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcC
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 208 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g 208 (262)
.+|.||+. +.+.-+- -.| -..|.+||.-.-...
T Consensus 1 ~~C~~C~~---s~fe~d~-a~g-~~~C~~CG~v~E~~~ 33 (521)
T KOG1598|consen 1 MVCKNCGG---SNFERDE-ATG-NLYCTACGTVLEYNN 33 (521)
T ss_pred CcCCCCCC---CCccccc-ccC-Cceeccccceeeccc
Confidence 47999998 4666333 455 489999999655443
No 29
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=36.29 E-value=13 Score=36.89 Aligned_cols=25 Identities=40% Similarity=0.982 Sum_probs=16.7
Q ss_pred CCccceeeccCCCCCCceecCCCCCCccchhhhhH
Q 024832 169 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 203 (262)
Q Consensus 169 ~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~ 203 (262)
...+|.+||. .+|.|- | .|.+||-+
T Consensus 6 ~~y~C~~Cg~---~~~~~~----g---~Cp~C~~w 30 (454)
T TIGR00416 6 SKFVCQHCGA---DSPKWQ----G---KCPACHAW 30 (454)
T ss_pred CeEECCcCCC---CCcccc----E---ECcCCCCc
Confidence 3578999998 455552 2 48888763
No 30
>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=36.25 E-value=13 Score=24.95 Aligned_cols=29 Identities=28% Similarity=0.762 Sum_probs=17.9
Q ss_pred cceeeccCCCCCCceecCCCCCCccchhhhhHHH
Q 024832 172 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 205 (262)
Q Consensus 172 ~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~ 205 (262)
.|.+|+.+ . .--..-.| ..+|..||+-+.
T Consensus 2 ~Cp~Cg~~--~--~~~D~~~g-~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSK--E--IVFDPERG-ELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSS--E--EEEETTTT-EEEETTT-BBEE
T ss_pred CCcCCcCC--c--eEEcCCCC-eEECCCCCCEee
Confidence 68899985 3 22233345 589999998543
No 31
>PRK00420 hypothetical protein; Validated
Probab=35.04 E-value=18 Score=29.88 Aligned_cols=30 Identities=23% Similarity=0.707 Sum_probs=23.0
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhhHHHh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 206 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~ 206 (262)
...|..||+ |+.|- ..| +.+|-.||-.+..
T Consensus 23 ~~~CP~Cg~-----pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCGL-----PLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCCC-----cceec-CCC-ceECCCCCCeeee
Confidence 478888886 78884 456 6999999986654
No 32
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=34.02 E-value=26 Score=26.26 Aligned_cols=47 Identities=26% Similarity=0.622 Sum_probs=32.5
Q ss_pred CCccceeeccCCCCCCcee---cCCCCCCccchhhhhHHHhcCCCCCCCccc
Q 024832 169 SETSCTHCGISSKSTPMMR---RGPSGPRSLCNACGLFWANKGALRDLGKKM 217 (262)
Q Consensus 169 ~~~~C~nCgtt~~~TP~WR---rGp~G~~~LCNACGl~~~~~g~~Rp~s~~~ 217 (262)
....|..|..+ .|---= -...-|+.+|-+|-.||-..|++|.++...
T Consensus 4 ~~~~CPRC~S~--nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvgg 53 (63)
T PF02701_consen 4 QPLPCPRCDST--NTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGG 53 (63)
T ss_pred cCCCCCCcCCC--CCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCC
Confidence 45678888875 332200 012346789999999999999999887653
No 33
>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=33.87 E-value=15 Score=30.63 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=22.9
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
-.|..|+.+ .|-+-+.+..= -.-|+|||-
T Consensus 94 VlC~~C~sp--dT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSP--DTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSS--SEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCC--ccEEEEcCCEE-EEEecccCC
Confidence 589999998 88888874443 468999994
No 34
>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=33.28 E-value=15 Score=26.51 Aligned_cols=25 Identities=32% Similarity=0.947 Sum_probs=18.5
Q ss_pred CCCccceeeccCCCCCCceecCCCCCCccchhhhhH
Q 024832 168 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 203 (262)
Q Consensus 168 ~~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~ 203 (262)
+....|.+||.. --++.+|-.||.|
T Consensus 24 p~l~~C~~cG~~-----------~~~H~vc~~cG~Y 48 (55)
T TIGR01031 24 PTLVVCPNCGEF-----------KLPHRVCPSCGYY 48 (55)
T ss_pred CcceECCCCCCc-----------ccCeeECCccCeE
Confidence 456789999984 2346899999954
No 35
>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=32.52 E-value=29 Score=25.57 Aligned_cols=29 Identities=24% Similarity=0.671 Sum_probs=22.1
Q ss_pred CccceeeccCCCCCCceecCCCCCCccc-hhhhhHHHhcC
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLC-NACGLFWANKG 208 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LC-NACGl~~~~~g 208 (262)
-+.|.+||.+ -| .. +.+| ..|+.-|.++.
T Consensus 3 HkHC~~CG~~---Ip------~~-~~fCS~~C~~~~~k~q 32 (59)
T PF09889_consen 3 HKHCPVCGKP---IP------PD-ESFCSPKCREEYRKRQ 32 (59)
T ss_pred CCcCCcCCCc---CC------cc-hhhhCHHHHHHHHHHH
Confidence 5789999985 22 23 6899 69999998765
No 36
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=31.14 E-value=16 Score=23.05 Aligned_cols=28 Identities=29% Similarity=0.720 Sum_probs=15.3
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhhH
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 203 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~ 203 (262)
.+.|..||.. . ...+.|-...|.+||..
T Consensus 3 ~rfC~~CG~~--t----~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAP--T----KPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--B--E----EE-SSSS-EEESSSS-E
T ss_pred CcccCcCCcc--c----cCCCCcCEeECCCCcCE
Confidence 4689999985 2 23455667899999874
No 37
>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=31.03 E-value=19 Score=23.19 Aligned_cols=29 Identities=24% Similarity=0.678 Sum_probs=19.1
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
-+|..||.. -..|..-.++....|-.||.
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 368888873 34455443355678999987
No 38
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=30.72 E-value=19 Score=30.59 Aligned_cols=27 Identities=33% Similarity=0.958 Sum_probs=21.9
Q ss_pred CCccceeeccCCCCCCceecCCCCCCccchhhhhH
Q 024832 169 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 203 (262)
Q Consensus 169 ~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~ 203 (262)
....|.-||+ |++| -+| ..+|--||..
T Consensus 27 L~~hCp~Cg~-----PLF~--KdG-~v~CPvC~~~ 53 (131)
T COG1645 27 LAKHCPKCGT-----PLFR--KDG-EVFCPVCGYR 53 (131)
T ss_pred HHhhCcccCC-----ccee--eCC-eEECCCCCce
Confidence 3578888886 8999 578 6999999953
No 39
>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=30.61 E-value=46 Score=26.68 Aligned_cols=37 Identities=24% Similarity=0.500 Sum_probs=31.3
Q ss_pred CCccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcCC
Q 024832 169 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 209 (262)
Q Consensus 169 ~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g~ 209 (262)
....|..|+. .-|.|=.-.-| ..||-.|.-..+..|+
T Consensus 2 ~N~~CaDC~~---~~p~w~s~~~G-ifvC~~CsgiHR~lg~ 38 (112)
T smart00105 2 GNKKCFDCGA---PNPTWASVNLG-VFLCIECSGIHRSLGV 38 (112)
T ss_pred CCCcccCCCC---CCCCcEEeccc-eeEhHHhHHHHHhcCC
Confidence 3689999998 46999988889 5999999988887764
No 40
>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=30.24 E-value=19 Score=24.02 Aligned_cols=31 Identities=26% Similarity=0.634 Sum_probs=20.3
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
..+|.+|++- .-|...-...|..-.||-|+.
T Consensus 2 p~rC~~C~ay--lNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAY--LNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--B--S-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCE--ECCcceEcCCCCEEECcCCCC
Confidence 4689999996 888888888887779999986
No 41
>PRK12496 hypothetical protein; Provisional
Probab=29.73 E-value=26 Score=30.26 Aligned_cols=35 Identities=23% Similarity=0.399 Sum_probs=24.6
Q ss_pred CCccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcCCCC
Q 024832 169 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALR 211 (262)
Q Consensus 169 ~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g~~R 211 (262)
...+|.-|+.. .|. ++.+ ..|.-||...+++...+
T Consensus 126 w~~~C~gC~~~---~~~---~~~~--~~C~~CG~~~~r~~~~~ 160 (164)
T PRK12496 126 WRKVCKGCKKK---YPE---DYPD--DVCEICGSPVKRKMVKR 160 (164)
T ss_pred eeEECCCCCcc---ccC---CCCC--CcCCCCCChhhhcchhh
Confidence 45789999973 443 3333 58999999888776533
No 42
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.55 E-value=13 Score=27.92 Aligned_cols=34 Identities=24% Similarity=0.388 Sum_probs=26.1
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhhHHH
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 205 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~ 205 (262)
...|..|.+- .|-+||+-..=+..-|-+||..-+
T Consensus 10 GA~CP~C~~~--Dtl~mW~En~ve~vECV~CG~~~~ 43 (66)
T COG3529 10 GAVCPACQAQ--DTLAMWRENNVEIVECVKCGHHMR 43 (66)
T ss_pred cCCCcccchh--hHHHHHHhcCCceEehhhcchHhh
Confidence 3689999995 777766666666789999998653
No 43
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=28.51 E-value=8.8 Score=24.79 Aligned_cols=33 Identities=27% Similarity=0.690 Sum_probs=19.1
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhhHH
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 204 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~ 204 (262)
..|.+|++. -.-+....+..|....|-.||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 468888874 222333334455567788887654
No 44
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.23 E-value=19 Score=28.11 Aligned_cols=34 Identities=26% Similarity=0.558 Sum_probs=22.9
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhhHHHhc
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 207 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~ 207 (262)
-+|.+|+-.-..-..++..| -+-|.+||-.+++-
T Consensus 13 Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~ 46 (82)
T COG2331 13 YECTECGNRFDVVQAMTDDP---LTTCEECGARLKKL 46 (82)
T ss_pred EeecccchHHHHHHhcccCc---cccChhhChHHHHh
Confidence 47999998523334455544 56899999977654
No 45
>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=26.06 E-value=25 Score=23.58 Aligned_cols=29 Identities=21% Similarity=0.538 Sum_probs=17.4
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
-+|..||.. --.|+..-+.....|-+||-
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHE---FEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCE---EEEEEEcCCCCCCcCCCCCC
Confidence 368888853 33334433344578888885
No 46
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=25.78 E-value=24 Score=25.85 Aligned_cols=25 Identities=16% Similarity=0.198 Sum_probs=17.5
Q ss_pred CCCccceeeccCCCCCCceecCCCCCCccchhhhhHH
Q 024832 168 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 204 (262)
Q Consensus 168 ~~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~ 204 (262)
.....|.+||.. . -++.+|- ||.|.
T Consensus 25 ~~~~~c~~cg~~--~---------~pH~vc~-cG~Y~ 49 (60)
T PRK01110 25 PTLSVDKTTGEY--H---------LPHHVSP-KGYYK 49 (60)
T ss_pred CceeEcCCCCce--e---------ccceecC-CcccC
Confidence 346789999984 1 2357899 99653
No 47
>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=25.66 E-value=25 Score=26.71 Aligned_cols=35 Identities=26% Similarity=0.398 Sum_probs=27.3
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhhHHHh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 206 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~ 206 (262)
...|..|... .|-+|++...-...-|-+||..-..
T Consensus 8 Ga~CP~C~~~--D~i~~~~e~~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 8 GAVCPKCQAM--DTIMMWRENGVEYVECVECGYTERQ 42 (71)
T ss_pred CccCCCCcCc--cEEEEEEeCCceEEEecCCCCeecc
Confidence 3689999997 7777777666667899999985543
No 48
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=25.28 E-value=34 Score=32.96 Aligned_cols=28 Identities=29% Similarity=0.650 Sum_probs=20.2
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
...|.|||.. .|+- =++|.--+|-+||-
T Consensus 315 ~nfc~ncG~~--~t~~---~~ng~a~fcp~cgq 342 (345)
T COG4260 315 LNFCLNCGCG--TTAD---FDNGKAKFCPECGQ 342 (345)
T ss_pred cccccccCcc--cccC---CccchhhhChhhcC
Confidence 4478999965 6664 35666679999985
No 49
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=25.13 E-value=29 Score=23.76 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=19.4
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
-+|..|+. .--.|+.--+.....|-.||-
T Consensus 6 y~C~~Cg~---~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGH---RFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCC---EeEEEEecCCCCCCCCCCCCC
Confidence 47888887 344676543344567999986
No 50
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.96 E-value=58 Score=34.22 Aligned_cols=9 Identities=33% Similarity=0.833 Sum_probs=4.7
Q ss_pred ccchhhhhH
Q 024832 195 SLCNACGLF 203 (262)
Q Consensus 195 ~LCNACGl~ 203 (262)
.+|..||-.
T Consensus 42 ~fC~~CG~~ 50 (645)
T PRK14559 42 AHCPNCGAE 50 (645)
T ss_pred ccccccCCc
Confidence 455555553
No 51
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.28 E-value=27 Score=29.48 Aligned_cols=34 Identities=29% Similarity=0.627 Sum_probs=22.8
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcC
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 208 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g 208 (262)
.-+|-+||-- =+.| |=-...+-|.|||+-|-.+.
T Consensus 21 ~grCP~CGeG----rLF~-gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 21 RGRCPRCGEG----RLFR-GFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred cCCCCCCCCc----hhhh-hhcccCchhhhccccccCCc
Confidence 4689999963 2333 33334578999999876654
No 52
>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=24.19 E-value=31 Score=22.74 Aligned_cols=26 Identities=27% Similarity=0.666 Sum_probs=20.4
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 202 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl 202 (262)
...|..|+.. |-...+| ...|..||-
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 4569999972 7777788 699999984
No 53
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=23.96 E-value=42 Score=33.10 Aligned_cols=30 Identities=27% Similarity=0.628 Sum_probs=24.9
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhh
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 201 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACG 201 (262)
...|+-||.+...++..-.||.. ..|+.|-
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~Ci 38 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDECI 38 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchHH
Confidence 46999999998888888888743 7999994
No 54
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=23.52 E-value=42 Score=33.88 Aligned_cols=40 Identities=25% Similarity=0.486 Sum_probs=33.6
Q ss_pred CCCCccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcCCC
Q 024832 167 SPSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL 210 (262)
Q Consensus 167 ~~~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g~~ 210 (262)
.+..++|..|+. .-|-|=.-+-| ..||--|---.+.-|++
T Consensus 20 ~~~NKvCFDCgA---knPtWaSVTYG-IFLCiDCSAvHRnLGVH 59 (454)
T KOG0706|consen 20 QSENKVCFDCGA---KNPTWASVTYG-IFLCIDCSAVHRNLGVH 59 (454)
T ss_pred CCCCceecccCC---CCCCceeecce-EEEEEecchhhhccccc
Confidence 356799999999 79999999999 69999998866666653
No 55
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=23.44 E-value=51 Score=31.43 Aligned_cols=32 Identities=25% Similarity=0.620 Sum_probs=25.4
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhhHHHh
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 206 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~ 206 (262)
..|..|.-+ .+.|--.-+.+| +||+|--+-.+
T Consensus 2 ~~C~~C~~~-~t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMP-TTRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCC-CCCCCeeECCCC---CchhhhhHHhh
Confidence 579999998 566776677777 89999997644
No 56
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=23.36 E-value=30 Score=32.86 Aligned_cols=34 Identities=26% Similarity=0.516 Sum_probs=24.4
Q ss_pred CCCCccceeeccCCCCCCceecCCCCCCccchhhhhHHHh
Q 024832 167 SPSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 206 (262)
Q Consensus 167 ~~~~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~ 206 (262)
-+..+.|..||+. ..| ...|-..+|+.||..+..
T Consensus 108 ~~~~RFCg~CG~~--~~~----~~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 108 YRSHRFCGRCGTK--TYP----REGGWARVCPKCGHEHFP 141 (279)
T ss_pred HhhCcCCCCCCCc--Ccc----ccCceeeeCCCCCCccCC
Confidence 3557999999995 333 234556899999987653
No 57
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.34 E-value=39 Score=24.33 Aligned_cols=29 Identities=31% Similarity=0.681 Sum_probs=20.1
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhhHH
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 204 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~ 204 (262)
...|..||..... ...+....|..||..+
T Consensus 28 Sq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc------ccccceEEcCCCCCEE
Confidence 4789999996222 3345457999999854
No 58
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=23.16 E-value=29 Score=33.76 Aligned_cols=22 Identities=36% Similarity=1.019 Sum_probs=15.4
Q ss_pred cceeeccCCCCCCceecCCCCCCccchhhhhH
Q 024832 172 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 203 (262)
Q Consensus 172 ~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~ 203 (262)
+|.+||. .+|.|. | -|.+||-+
T Consensus 2 ~c~~cg~---~~~~~~----g---~cp~c~~w 23 (372)
T cd01121 2 VCSECGY---VSPKWL----G---KCPECGEW 23 (372)
T ss_pred CCCCCCC---CCCCcc----E---ECcCCCCc
Confidence 6889988 566663 3 47778764
No 59
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=23.05 E-value=33 Score=23.05 Aligned_cols=32 Identities=25% Similarity=0.675 Sum_probs=20.5
Q ss_pred ccceeeccCCCCCCceecCCCCCCccchhhhhH
Q 024832 171 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 203 (262)
Q Consensus 171 ~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~ 203 (262)
..|+=||.+....-..=.||.+ ...|+.|-..
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHH
Confidence 5799999986666555588877 5899999754
No 60
>PF12773 DZR: Double zinc ribbon
Probab=22.54 E-value=50 Score=22.27 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=6.6
Q ss_pred CCccceeeccC
Q 024832 169 SETSCTHCGIS 179 (262)
Q Consensus 169 ~~~~C~nCgtt 179 (262)
....|.+||+.
T Consensus 11 ~~~fC~~CG~~ 21 (50)
T PF12773_consen 11 DAKFCPHCGTP 21 (50)
T ss_pred cccCChhhcCC
Confidence 35666666664
No 61
>PRK05978 hypothetical protein; Provisional
Probab=21.73 E-value=36 Score=29.35 Aligned_cols=34 Identities=26% Similarity=0.587 Sum_probs=23.8
Q ss_pred CccceeeccCCCCCCceecCCCCCCccchhhhhHHHhcC
Q 024832 170 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 208 (262)
Q Consensus 170 ~~~C~nCgtt~~~TP~WRrGp~G~~~LCNACGl~~~~~g 208 (262)
..+|-+||. -.+++ +--.-..-|.+||+.|..+.
T Consensus 33 ~grCP~CG~----G~LF~-g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 33 RGRCPACGE----GKLFR-AFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cCcCCCCCC----Ccccc-cccccCCCccccCCccccCC
Confidence 468999996 35555 34444678999999776553
No 62
>KOG1561 consensus CCAAT-binding factor, subunit B (HAP2) [Transcription]
Probab=20.23 E-value=1e+02 Score=29.58 Aligned_cols=29 Identities=24% Similarity=0.318 Sum_probs=23.9
Q ss_pred ceeeeehhHHHHHHhhh-ccCccccccccC
Q 024832 122 KKVRYSVRQEVALRMQR-NKGQFTSAKKCE 150 (262)
Q Consensus 122 KkirY~~Rqe~A~r~~R-~kGqfas~K~~~ 150 (262)
|++-=+.|+..|.+|+| ..|+|...|+..
T Consensus 217 kpYLHESRH~HAmkR~RG~GGRFln~k~~~ 246 (307)
T KOG1561|consen 217 KPYLHESRHLHAMKRARGEGGRFLNTKEYH 246 (307)
T ss_pred CccccchhhHHHhhcccCCCCCCCchhhhh
Confidence 35667899999999999 779999877743
Done!