Query 022924
Match_columns 290
No_of_seqs 257 out of 1048
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:08:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022924.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022924hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06200 tify: tify domain; I 99.7 4.5E-17 9.8E-22 109.5 5.2 34 66-99 2-35 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.6 8.8E-16 1.9E-20 111.7 3.9 44 200-245 1-44 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 3.3E-15 7.2E-20 107.7 3.5 48 197-246 2-50 (52)
4 PF00320 GATA: GATA zinc finge 99.4 2.1E-14 4.5E-19 96.3 0.7 36 201-238 1-36 (36)
5 PF06203 CCT: CCT motif; Inte 99.1 6.9E-11 1.5E-15 83.2 2.9 43 132-174 1-43 (45)
6 PF09425 CCT_2: Divergent CCT 98.9 3.8E-10 8.2E-15 71.3 1.5 25 130-155 2-26 (27)
7 KOG1601 GATA-4/5/6 transcripti 98.7 1.2E-08 2.5E-13 89.7 3.2 52 198-251 199-250 (340)
8 COG5641 GAT1 GATA Zn-finger-co 98.4 1.3E-07 2.9E-12 95.3 3.4 54 197-252 157-215 (498)
9 COG5641 GAT1 GATA Zn-finger-co 92.2 0.1 2.3E-06 53.3 2.9 52 196-248 295-346 (498)
10 KOG3554 Histone deacetylase co 91.8 1 2.3E-05 46.1 9.2 39 198-238 386-426 (693)
11 PF13619 KTSC: KTSC domain 73.4 6.4 0.00014 28.7 4.1 30 67-96 13-43 (60)
12 PF14803 Nudix_N_2: Nudix N-te 70.6 1.1 2.4E-05 29.9 -0.5 30 199-230 1-30 (34)
13 PF01783 Ribosomal_L32p: Ribos 56.5 2.6 5.6E-05 30.7 -0.8 27 197-235 25-51 (56)
14 PF01412 ArfGap: Putative GTPa 49.5 14 0.0003 30.4 2.3 37 197-237 12-48 (116)
15 PF02701 zf-Dof: Dof domain, z 48.4 12 0.00025 28.5 1.6 47 197-245 4-53 (63)
16 PF06677 Auto_anti-p27: Sjogre 48.1 7.1 0.00015 27.1 0.4 26 197-229 16-41 (41)
17 PF09889 DUF2116: Uncharacteri 46.9 13 0.00028 27.7 1.6 30 197-236 2-32 (59)
18 PF13248 zf-ribbon_3: zinc-rib 46.3 12 0.00027 23.0 1.2 23 198-230 2-24 (26)
19 PRK03988 translation initiatio 46.2 5.8 0.00013 34.2 -0.4 30 198-230 102-131 (138)
20 TIGR00311 aIF-2beta translatio 43.3 7 0.00015 33.5 -0.3 29 199-230 98-126 (133)
21 KOG1598 Transcription initiati 42.2 12 0.00026 38.9 1.1 33 199-236 1-33 (521)
22 COG3952 Predicted membrane pro 41.7 7.3 0.00016 32.6 -0.4 20 213-234 76-95 (113)
23 smart00653 eIF2B_5 domain pres 41.0 8.2 0.00018 32.0 -0.2 29 199-230 81-109 (110)
24 PF13240 zinc_ribbon_2: zinc-r 38.6 18 0.00039 21.9 1.0 21 200-230 1-21 (23)
25 smart00105 ArfGap Putative GTP 38.4 27 0.00059 28.5 2.4 42 198-243 3-48 (112)
26 KOG1601 GATA-4/5/6 transcripti 38.2 9.5 0.00021 33.3 -0.3 39 131-169 292-330 (340)
27 PRK12336 translation initiatio 38.2 9.2 0.0002 34.7 -0.4 29 199-230 99-127 (201)
28 PRK12286 rpmF 50S ribosomal pr 38.1 12 0.00026 27.6 0.3 25 196-231 25-49 (57)
29 PF13717 zinc_ribbon_4: zinc-r 38.0 8 0.00017 25.8 -0.6 33 199-232 3-35 (36)
30 PF04810 zf-Sec23_Sec24: Sec23 34.9 14 0.00031 25.0 0.2 31 198-230 2-32 (40)
31 COG2331 Uncharacterized protei 34.8 14 0.0003 29.2 0.2 36 199-237 13-48 (82)
32 PRK11823 DNA repair protein Ra 33.9 14 0.0003 37.3 0.0 25 197-231 6-30 (446)
33 PRK00420 hypothetical protein; 33.1 19 0.00041 30.1 0.7 31 197-234 22-52 (112)
34 COG5349 Uncharacterized protei 33.1 17 0.00037 31.0 0.5 35 197-236 20-54 (126)
35 COG1645 Uncharacterized Zn-fin 32.8 15 0.00034 31.5 0.2 26 197-230 27-52 (131)
36 KOG3740 Uncharacterized conser 31.8 18 0.0004 38.4 0.5 38 196-235 460-500 (706)
37 PF01873 eIF-5_eIF-2B: Domain 30.7 16 0.00035 30.9 -0.1 29 199-230 94-122 (125)
38 smart00834 CxxC_CXXC_SSSS Puta 29.9 18 0.00039 23.7 0.1 29 199-230 6-34 (41)
39 PF08271 TF_Zn_Ribbon: TFIIB z 29.8 17 0.00036 24.7 -0.1 28 200-232 2-29 (43)
40 cd01121 Sms Sms (bacterial rad 29.2 19 0.00042 35.5 0.2 22 200-231 2-23 (372)
41 PRK11788 tetratricopeptide rep 29.0 21 0.00046 33.4 0.4 23 197-229 353-375 (389)
42 TIGR00416 sms DNA repair prote 28.8 19 0.00042 36.4 0.1 24 197-230 6-29 (454)
43 COG4260 Membrane protease subu 27.8 29 0.00063 33.9 1.1 28 198-230 315-342 (345)
44 TIGR03831 YgiT_finger YgiT-typ 27.3 68 0.0015 21.1 2.6 20 70-89 14-33 (46)
45 PF08114 PMP1_2: ATPase proteo 27.3 23 0.00051 24.8 0.3 10 130-139 34-43 (43)
46 PF09723 Zn-ribbon_8: Zinc rib 26.7 21 0.00046 24.3 -0.0 29 199-230 6-34 (42)
47 PF08152 GUCT: GUCT (NUC152) d 26.6 37 0.00081 27.3 1.4 33 67-100 48-80 (97)
48 PRK12496 hypothetical protein; 26.6 32 0.00069 30.2 1.1 34 197-238 126-159 (164)
49 PF09297 zf-NADH-PPase: NADH p 26.4 19 0.00042 23.0 -0.2 28 198-231 3-30 (32)
50 KOG0706 Predicted GTPase-activ 26.2 33 0.00071 35.1 1.2 38 196-237 21-58 (454)
51 TIGR02605 CxxC_CxxC_SSSS putat 26.0 24 0.00052 24.5 0.2 29 199-230 6-34 (52)
52 PRK14892 putative transcriptio 25.6 21 0.00045 29.2 -0.3 35 197-234 20-54 (99)
53 PF06689 zf-C4_ClpX: ClpX C4-t 25.1 30 0.00065 23.6 0.5 32 199-231 2-33 (41)
54 PF11781 RRN7: RNA polymerase 24.8 28 0.00061 23.3 0.3 26 198-230 8-33 (36)
55 PRK05978 hypothetical protein; 24.6 30 0.00064 30.3 0.5 34 197-235 32-65 (148)
56 TIGR01031 rpmF_bact ribosomal 24.4 26 0.00056 25.6 0.1 25 196-231 24-48 (55)
57 COG2816 NPY1 NTP pyrophosphohy 24.4 28 0.0006 33.5 0.3 31 196-232 109-139 (279)
58 TIGR02098 MJ0042_CXXC MJ0042 f 23.9 14 0.0003 24.2 -1.3 33 199-232 3-35 (38)
59 PRK05342 clpX ATP-dependent pr 23.1 44 0.00096 33.5 1.5 30 198-229 9-38 (412)
60 PF10083 DUF2321: Uncharacteri 23.1 37 0.0008 30.2 0.8 33 198-232 39-78 (158)
61 COG3529 Predicted nucleic-acid 23.1 22 0.00048 27.0 -0.5 34 198-233 10-43 (66)
62 COG5347 GTPase-activating prot 22.7 46 0.00099 32.6 1.4 36 197-236 19-54 (319)
63 PRK14559 putative protein seri 22.4 82 0.0018 33.7 3.3 22 200-231 3-24 (645)
64 COG1066 Sms Predicted ATP-depe 21.2 33 0.00071 35.1 0.1 25 197-231 6-30 (456)
65 smart00778 Prim_Zn_Ribbon Zinc 20.4 52 0.0011 22.3 0.9 29 199-229 4-32 (37)
No 1
>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=99.68 E-value=4.5e-17 Score=109.47 Aligned_cols=34 Identities=47% Similarity=0.763 Sum_probs=32.2
Q ss_pred cCCCCceeEEeCcEEEEECCCChHHHHHHHHHhc
Q 022924 66 LSNSSQLTLSFRGQVYVFDSVTPDKVQAVLLLLG 99 (290)
Q Consensus 66 ~~~~aQLTIfY~G~V~Vfd~vp~dKaqaIm~lA~ 99 (290)
.+.++||||||+|+|+|||+||+|||++||+||+
T Consensus 2 ~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~ 35 (36)
T PF06200_consen 2 SPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLAS 35 (36)
T ss_pred CCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhc
Confidence 4678999999999999999999999999999996
No 2
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.59 E-value=8.8e-16 Score=111.70 Aligned_cols=44 Identities=52% Similarity=1.258 Sum_probs=41.9
Q ss_pred ccceecccCCCCCccccCCCCCCccchhhhHHHHhcCCCCCCCccc
Q 022924 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKM 245 (290)
Q Consensus 200 ~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~~r~~~~~~ 245 (290)
.|+||+++ .||+||+||.+..+|||||||||++++..||+.+..
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 999999999888999999999999999999999877
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.54 E-value=3.3e-15 Score=107.75 Aligned_cols=48 Identities=52% Similarity=1.112 Sum_probs=43.7
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHHHHhcCCC-CCCCcccC
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL-RDLGKKME 246 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~~-r~~~~~~~ 246 (290)
...+|+||+++ .||+||+||.|...|||||||||++++.+ ||..+.++
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 4
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.44 E-value=2.1e-14 Score=96.29 Aligned_cols=36 Identities=53% Similarity=1.278 Sum_probs=28.6
Q ss_pred cceecccCCCCCccccCCCCCCccchhhhHHHHhcCCC
Q 022924 201 CTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL 238 (290)
Q Consensus 201 C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~~ 238 (290)
|+||+++ .||+||++|.|..+|||+|||||++++++
T Consensus 1 C~~C~tt--~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGTT--ETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT--S--T-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcCC--CCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 8999998 89999999999888999999999999863
No 5
>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=99.08 E-value=6.9e-11 Score=83.23 Aligned_cols=43 Identities=47% Similarity=0.779 Sum_probs=41.4
Q ss_pred HHHHHHHHHHhhhhhhccccchhhhhHHHHHHhhhhccccccc
Q 022924 132 RAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKGQFTSA 174 (290)
Q Consensus 132 RkASL~RFlEKRK~R~~~kk~~Y~~rke~a~R~~R~kGqf~~s 174 (290)
|.++|+||+|||+.|+|.++++|++|+..|+.++|.+|+|++.
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 7899999999999999999999999999999999999999974
No 6
>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=98.92 E-value=3.8e-10 Score=71.33 Aligned_cols=25 Identities=48% Similarity=0.612 Sum_probs=10.0
Q ss_pred hhHHHHHHHHHHhhhhhhccccchhh
Q 022924 130 PQRAASLDRFRQKRKERCFDKKVRYS 155 (290)
Q Consensus 130 paRkASL~RFlEKRK~R~~~kk~~Y~ 155 (290)
.+|++||||||||||+|++. +.||.
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp ----HHHHHHHHHH------------
T ss_pred chHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 38999999999999999987 88996
No 7
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.67 E-value=1.2e-08 Score=89.72 Aligned_cols=52 Identities=44% Similarity=0.898 Sum_probs=45.9
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhhHHHHhcCCCCCCCcccCCCCCC
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKMEDQPLT 251 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~~r~~~~~~~~~~~~ 251 (290)
...|++|+++ .||+||+++.|..++|||||+++++++..|++.+++......
T Consensus 199 ~~~c~~~~~~--~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~~~~~~ 250 (340)
T KOG1601|consen 199 LRQCSNCGTT--KTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRPASSPR 250 (340)
T ss_pred CcccCCCCCC--CCcceecCCCCCccccccchhhhhhcCccccccccCcccccc
Confidence 5899999998 999999999999999999999999999888888877554443
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.42 E-value=1.3e-07 Score=95.30 Aligned_cols=54 Identities=33% Similarity=0.653 Sum_probs=46.4
Q ss_pred CCCccceecccCCCCCccccCCCC----CCccchhhhHHHHhcCCCC-CCCcccCCCCCCC
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSG----PRSLCNACGLFWANKGALR-DLGKKMEDQPLTP 252 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G----~~~LCNACGl~~~~~g~~r-~~~~~~~~~~~~~ 252 (290)
...+|.||.++ .||+|||+..+ +-.||||||||++.||++| |++++..-+....
T Consensus 157 ~~~vc~Nc~t~--stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 157 QPHVCSNCKTT--STPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred ccchhcccccc--CCccccccccccccCCccccccccccccccCCcCCCcccccccccccc
Confidence 34499999998 99999999993 3799999999999999999 9999886554444
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=92.23 E-value=0.1 Score=53.34 Aligned_cols=52 Identities=29% Similarity=0.365 Sum_probs=44.0
Q ss_pred CCCCccceecccCCCCCccccCCCCCCccchhhhHHHHhcCCCCCCCcccCCC
Q 022924 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGALRDLGKKMEDQ 248 (290)
Q Consensus 196 ~~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~~r~~~~~~~~~ 248 (290)
.....|.+|++. ..||.||+...-.-.+||+||++.+.++..||+.++....
T Consensus 295 ps~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n 346 (498)
T COG5641 295 PSDKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPN 346 (498)
T ss_pred hhhcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCCChh
Confidence 346789999975 5899999998777899999999999999999999876443
No 10
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=91.77 E-value=1 Score=46.06 Aligned_cols=39 Identities=23% Similarity=0.604 Sum_probs=31.8
Q ss_pred CCccceecccCCCCCcc--ccCCCCCCccchhhhHHHHhcCCC
Q 022924 198 ETSCTHCGISSKSTPMM--RRGPSGPRSLCNACGLFWANKGAL 238 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~W--RrGp~G~~~LCNACGl~~~~~g~~ 238 (290)
.+.|.+|+|+ ..-+| |-+|.-...||-.|=+||++-|.+
T Consensus 386 g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 6799999998 55566 556777678999999999998853
No 11
>PF13619 KTSC: KTSC domain
Probab=73.36 E-value=6.4 Score=28.70 Aligned_cols=30 Identities=30% Similarity=0.558 Sum_probs=26.2
Q ss_pred CCCCceeEEe-CcEEEEECCCChHHHHHHHH
Q 022924 67 SNSSQLTLSF-RGQVYVFDSVTPDKVQAVLL 96 (290)
Q Consensus 67 ~~~aQLTIfY-~G~V~Vfd~vp~dKaqaIm~ 96 (290)
+.+..|.|.| +|.++.|.+||++-.+++|.
T Consensus 13 ~~~~~L~V~F~~G~~Y~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 13 PETRTLEVEFKSGSVYRYFGVPPEVYEALLN 43 (60)
T ss_pred CCCCEEEEEEcCCCEEEECCCCHHHHHHHHc
Confidence 5578999988 89999999999998887775
No 12
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=70.57 E-value=1.1 Score=29.86 Aligned_cols=30 Identities=30% Similarity=0.708 Sum_probs=14.7
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
+.|.+||.+ .+..-=.|.+-.+.+|.+||-
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 369999985 322222456666789999984
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=56.54 E-value=2.6 Score=30.72 Aligned_cols=27 Identities=26% Similarity=0.913 Sum_probs=19.3
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHHHHhc
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 235 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~ 235 (290)
....|.+||.. . -+..+|..|| ||+.+
T Consensus 25 ~l~~c~~cg~~--~---------~~H~vc~~cG-~y~~r 51 (56)
T PF01783_consen 25 NLVKCPNCGEP--K---------LPHRVCPSCG-YYKGR 51 (56)
T ss_dssp SEEESSSSSSE--E---------STTSBCTTTB-BSSSS
T ss_pred ceeeeccCCCE--e---------cccEeeCCCC-eECCE
Confidence 46789999974 1 2368999999 55443
No 14
>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=49.48 E-value=14 Score=30.35 Aligned_cols=37 Identities=24% Similarity=0.503 Sum_probs=27.4
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 237 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~ 237 (290)
....|++|+. .-|.|-.=.-| ..||-.|.-..+.-|+
T Consensus 12 ~N~~CaDCg~---~~p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 12 GNKVCADCGA---PNPTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp TCTB-TTT-S---BS--EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred CcCcCCCCCC---CCCCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 4689999997 68899998889 7999999998888774
No 15
>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=48.43 E-value=12 Score=28.49 Aligned_cols=47 Identities=26% Similarity=0.622 Sum_probs=32.4
Q ss_pred CCCccceecccCCCCCccc---cCCCCCCccchhhhHHHHhcCCCCCCCccc
Q 022924 197 SETSCTHCGISSKSTPMMR---RGPSGPRSLCNACGLFWANKGALRDLGKKM 245 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WR---rGp~G~~~LCNACGl~~~~~g~~r~~~~~~ 245 (290)
....|..|... .|-.-= -...-++.+|-+|-.||-..|++|.++...
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 35678888765 332210 123345789999999999999999987653
No 16
>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=48.11 E-value=7.1 Score=27.06 Aligned_cols=26 Identities=38% Similarity=1.091 Sum_probs=19.7
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhh
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACG 229 (290)
....|..|++ |++| ..+| +.+|-+|+
T Consensus 16 L~~~Cp~C~~-----PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCGT-----PLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred hcCccCCCCC-----eeEE-ecCC-CEECCCCC
Confidence 4578988864 8999 3456 78998885
No 17
>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=46.86 E-value=13 Score=27.74 Aligned_cols=30 Identities=23% Similarity=0.640 Sum_probs=22.9
Q ss_pred CCCccceecccCCCCCccccCCCCCCccc-hhhhHHHHhcC
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLC-NACGLFWANKG 236 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LC-NACGl~~~~~g 236 (290)
.-+.|-+||.+ . |.. +.+| ..|+.-|.++.
T Consensus 2 ~HkHC~~CG~~--I-------p~~-~~fCS~~C~~~~~k~q 32 (59)
T PF09889_consen 2 PHKHCPVCGKP--I-------PPD-ESFCSPKCREEYRKRQ 32 (59)
T ss_pred CCCcCCcCCCc--C-------Ccc-hhhhCHHHHHHHHHHH
Confidence 35789999986 2 233 7899 69999998765
No 18
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=46.30 E-value=12 Score=22.99 Aligned_cols=23 Identities=30% Similarity=0.829 Sum_probs=15.8
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
.+.|.+||.. . +.+ ..+|-.||-
T Consensus 2 ~~~Cp~Cg~~--~-------~~~-~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAE--I-------DPD-AKFCPNCGA 24 (26)
T ss_pred cCCCcccCCc--C-------Ccc-cccChhhCC
Confidence 3678889884 2 333 578888885
No 19
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=46.23 E-value=5.8 Score=34.17 Aligned_cols=30 Identities=30% Similarity=0.671 Sum_probs=22.3
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
--.|..|+-+ .|-+-+.+-.= -.-|+|||-
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 3589999998 88887753222 357999996
No 20
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=43.26 E-value=7 Score=33.47 Aligned_cols=29 Identities=28% Similarity=0.694 Sum_probs=21.4
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
-.|..|+-+ .|-+-+.+.-- -.-|+|||-
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 88887753211 247999996
No 21
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=42.24 E-value=12 Score=38.88 Aligned_cols=33 Identities=24% Similarity=0.468 Sum_probs=22.8
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhHHHHhcC
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 236 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g 236 (290)
.+|.||+.+ .+.-+ ++..-..|++||.-.-...
T Consensus 1 ~~C~~C~~s---~fe~d--~a~g~~~C~~CG~v~E~~~ 33 (521)
T KOG1598|consen 1 MVCKNCGGS---NFERD--EATGNLYCTACGTVLEYNN 33 (521)
T ss_pred CcCCCCCCC---Ccccc--cccCCceeccccceeeccc
Confidence 479999984 55533 3444799999998554443
No 22
>COG3952 Predicted membrane protein [Function unknown]
Probab=41.66 E-value=7.3 Score=32.56 Aligned_cols=20 Identities=40% Similarity=0.579 Sum_probs=15.7
Q ss_pred ccccCCCCCCccchhhhHHHHh
Q 022924 213 MMRRGPSGPRSLCNACGLFWAN 234 (290)
Q Consensus 213 ~WRrGp~G~~~LCNACGl~~~~ 234 (290)
+||.+|-+ .||++|||+-..
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 47777777 799999998643
No 23
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=41.04 E-value=8.2 Score=32.02 Aligned_cols=29 Identities=28% Similarity=0.621 Sum_probs=21.3
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
-.|..|+-+ .|-+-+.+..= -.-|+|||-
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 589999998 88887763211 235999994
No 24
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=38.55 E-value=18 Score=21.91 Aligned_cols=21 Identities=29% Similarity=0.835 Sum_probs=12.7
Q ss_pred ccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 200 ~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
.|.+||.. -+++ ..+|.-||-
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 37777774 2333 467777774
No 25
>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=38.39 E-value=27 Score=28.47 Aligned_cols=42 Identities=26% Similarity=0.499 Sum_probs=33.8
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhhHHHHhcCC----CCCCCc
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA----LRDLGK 243 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~----~r~~~~ 243 (290)
...|++|+. .-|.|=.=.-| ..||-.|.-..+..|+ .|.++|
T Consensus 3 N~~CaDC~~---~~p~w~s~~~G-ifvC~~CsgiHR~lg~his~VkSl~m 48 (112)
T smart00105 3 NKKCFDCGA---PNPTWASVNLG-VFLCIECSGIHRSLGVHISKVRSLTL 48 (112)
T ss_pred CCcccCCCC---CCCCcEEeccc-eeEhHHhHHHHHhcCCCcCeeeeccc
Confidence 578999998 56999888888 7999999998888764 444554
No 26
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=38.22 E-value=9.5 Score=33.30 Aligned_cols=39 Identities=44% Similarity=0.677 Sum_probs=35.5
Q ss_pred hHHHHHHHHHHhhhhhhccccchhhhhHHHHHHhhhhcc
Q 022924 131 QRAASLDRFRQKRKERCFDKKVRYSVRQEVALRMQRNKG 169 (290)
Q Consensus 131 aRkASL~RFlEKRK~R~~~kk~~Y~~rke~a~R~~R~kG 169 (290)
.|.+.+.|++++|+.|.|.++++|..++..+..+++-++
T Consensus 292 ~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 292 QRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred hHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 789999999999999999999999999998888877765
No 27
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=38.22 E-value=9.2 Score=34.67 Aligned_cols=29 Identities=28% Similarity=0.728 Sum_probs=21.9
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
-.|..|+-+ .|-+-+.+..= -.-|+|||-
T Consensus 99 V~C~~C~~p--dT~l~k~~~~~-~l~C~aCGa 127 (201)
T PRK12336 99 VICSECGLP--DTRLVKEDRVL-MLRCDACGA 127 (201)
T ss_pred EECCCCCCC--CcEEEEcCCeE-EEEcccCCC
Confidence 589999998 88887764211 347999997
No 28
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=38.10 E-value=12 Score=27.57 Aligned_cols=25 Identities=32% Similarity=1.032 Sum_probs=18.5
Q ss_pred CCCCccceecccCCCCCccccCCCCCCccchhhhHH
Q 022924 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (290)
Q Consensus 196 ~~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~ 231 (290)
.....|.+||.. .- +..+|..||.|
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 346789999985 22 26899999954
No 29
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=38.02 E-value=8 Score=25.77 Aligned_cols=33 Identities=21% Similarity=0.594 Sum_probs=25.8
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhHHH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~ 232 (290)
..|.+|++. ...+..+-.+.|....|-.||--|
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 667777778888888898888655
No 30
>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=34.89 E-value=14 Score=24.96 Aligned_cols=31 Identities=26% Similarity=0.634 Sum_probs=20.8
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
..+|.+|++- .-|..+-...|....||-|+.
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 4689999986 888888888888889999986
No 31
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.79 E-value=14 Score=29.25 Aligned_cols=36 Identities=22% Similarity=0.471 Sum_probs=24.7
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 237 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~ 237 (290)
-.|.+|+-. +-.+..=-+.+-+-|.+||-.+++--.
T Consensus 13 Y~c~~cg~~---~dvvq~~~ddplt~ce~c~a~~kk~l~ 48 (82)
T COG2331 13 YECTECGNR---FDVVQAMTDDPLTTCEECGARLKKLLN 48 (82)
T ss_pred EeecccchH---HHHHHhcccCccccChhhChHHHHhhc
Confidence 579999984 444444444556799999998876543
No 32
>PRK11823 DNA repair protein RadA; Provisional
Probab=33.91 E-value=14 Score=37.25 Aligned_cols=25 Identities=28% Similarity=0.824 Sum_probs=18.8
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHH
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~ 231 (290)
...+|.+||. .++.|. ..|.+||-+
T Consensus 6 ~~y~C~~Cg~---~~~~~~-------g~Cp~C~~w 30 (446)
T PRK11823 6 TAYVCQECGA---ESPKWL-------GRCPECGAW 30 (446)
T ss_pred CeEECCcCCC---CCcccC-------eeCcCCCCc
Confidence 4578999999 577763 369999763
No 33
>PRK00420 hypothetical protein; Validated
Probab=33.07 E-value=19 Score=30.14 Aligned_cols=31 Identities=23% Similarity=0.662 Sum_probs=23.2
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHHHHh
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 234 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~ 234 (290)
....|..||+ |+.|- ..| +.+|-.||..+..
T Consensus 22 l~~~CP~Cg~-----pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 22 LSKHCPVCGL-----PLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred ccCCCCCCCC-----cceec-CCC-ceECCCCCCeeee
Confidence 3478999986 67774 446 7999999986543
No 34
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.06 E-value=17 Score=31.04 Aligned_cols=35 Identities=26% Similarity=0.504 Sum_probs=23.5
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHHHHhcC
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 236 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g 236 (290)
..-+|-+||-- =+.|.- -...+-|.|||+-|-.+.
T Consensus 20 l~grCP~CGeG----rLF~gF-LK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 20 LRGRCPRCGEG----RLFRGF-LKVVPACEACGLDYGFAD 54 (126)
T ss_pred hcCCCCCCCCc----hhhhhh-cccCchhhhccccccCCc
Confidence 45689999963 344433 334679999999776543
No 35
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=32.76 E-value=15 Score=31.55 Aligned_cols=26 Identities=35% Similarity=1.036 Sum_probs=22.0
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
...+|.-||+ |++| -+| ..+|--||.
T Consensus 27 L~~hCp~Cg~-----PLF~--KdG-~v~CPvC~~ 52 (131)
T COG1645 27 LAKHCPKCGT-----PLFR--KDG-EVFCPVCGY 52 (131)
T ss_pred HHhhCcccCC-----ccee--eCC-eEECCCCCc
Confidence 4578999987 7999 668 799999995
No 36
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.77 E-value=18 Score=38.42 Aligned_cols=38 Identities=21% Similarity=0.434 Sum_probs=30.0
Q ss_pred CCCCccceecccCCCCCccccCCCC---CCccchhhhHHHHhc
Q 022924 196 PSETSCTHCGISSKSTPMMRRGPSG---PRSLCNACGLFWANK 235 (290)
Q Consensus 196 ~~~~~C~nCg~~~~~Tp~WRrGp~G---~~~LCNACGl~~~~~ 235 (290)
.....|..|.+- .||.|+.-+.+ ...+|..|----.++
T Consensus 460 ~~P~~caqcktd--ftp~wk~ekstq~d~~i~cE~cvtSnqkk 500 (706)
T KOG3740|consen 460 TEPYACAQCKTD--FTPAWKKEKSTQADAAIVCENCVTSNQKK 500 (706)
T ss_pred CCchhhhhcccc--cccccccccccCcchHHHHHhhhhhcccc
Confidence 346799999996 99999998777 457999997654444
No 37
>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=30.68 E-value=16 Score=30.92 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=22.5
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
-.|..|+.+ .|-+-+.+..- -.-|+|||-
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 579999998 88887774443 468999994
No 38
>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=29.92 E-value=18 Score=23.68 Aligned_cols=29 Identities=24% Similarity=0.678 Sum_probs=19.6
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
-+|..||.. -..|..-.++....|-.||.
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 478889873 44455444455678999987
No 39
>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=29.81 E-value=17 Score=24.71 Aligned_cols=28 Identities=29% Similarity=0.786 Sum_probs=16.8
Q ss_pred ccceecccCCCCCccccCCCCCCccchhhhHHH
Q 022924 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (290)
Q Consensus 200 ~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~ 232 (290)
+|.+|+.+ . ..+ ..-.| ..+|..||+-+
T Consensus 2 ~Cp~Cg~~--~-~~~-D~~~g-~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSK--E-IVF-DPERG-ELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSS--E-EEE-ETTTT-EEEETTT-BBE
T ss_pred CCcCCcCC--c-eEE-cCCCC-eEECCCCCCEe
Confidence 68889885 2 222 22334 67999999844
No 40
>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=29.15 E-value=19 Score=35.50 Aligned_cols=22 Identities=36% Similarity=1.019 Sum_probs=16.7
Q ss_pred ccceecccCCCCCccccCCCCCCccchhhhHH
Q 022924 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (290)
Q Consensus 200 ~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~ 231 (290)
+|.+||. .+|.|. | -|.+||-+
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 6999998 677774 2 68888863
No 41
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=28.97 E-value=21 Score=33.39 Aligned_cols=23 Identities=22% Similarity=0.707 Sum_probs=0.0
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhh
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACG 229 (290)
..+.|.+||. .+..| ..+|..||
T Consensus 353 p~~~c~~cg~---~~~~~-------~~~c~~c~ 375 (389)
T PRK11788 353 PRYRCRNCGF---TARTL-------YWHCPSCK 375 (389)
T ss_pred CCEECCCCCC---CCccc-------eeECcCCC
No 42
>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=28.78 E-value=19 Score=36.39 Aligned_cols=24 Identities=38% Similarity=0.887 Sum_probs=17.9
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
...+|.+||. .++.|- ..|.+||-
T Consensus 6 ~~y~C~~Cg~---~~~~~~-------g~Cp~C~~ 29 (454)
T TIGR00416 6 SKFVCQHCGA---DSPKWQ-------GKCPACHA 29 (454)
T ss_pred CeEECCcCCC---CCcccc-------EECcCCCC
Confidence 4579999999 566662 36999976
No 43
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=27.80 E-value=29 Score=33.88 Aligned_cols=28 Identities=29% Similarity=0.650 Sum_probs=20.7
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
...|.|||+. .|+- -+.|..-+|-+||.
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 4478999975 6664 35666679999986
No 44
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=27.31 E-value=68 Score=21.13 Aligned_cols=20 Identities=20% Similarity=0.380 Sum_probs=17.3
Q ss_pred CceeEEeCcEEEEECCCChH
Q 022924 70 SQLTLSFRGQVYVFDSVTPD 89 (290)
Q Consensus 70 aQLTIfY~G~V~Vfd~vp~d 89 (290)
..+++-|+|...++.+||+.
T Consensus 14 ~~~~~~~~~~~~~i~~vp~~ 33 (46)
T TIGR03831 14 TTETYEYGGELIVIENVPAL 33 (46)
T ss_pred EEEEEEeCCEEEEEeCCCcc
Confidence 36788899999999999975
No 45
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=27.25 E-value=23 Score=24.85 Aligned_cols=10 Identities=40% Similarity=0.700 Sum_probs=8.9
Q ss_pred hhHHHHHHHH
Q 022924 130 PQRAASLDRF 139 (290)
Q Consensus 130 paRkASL~RF 139 (290)
.+|+++|+||
T Consensus 34 ~aRkr~l~rf 43 (43)
T PF08114_consen 34 QARKRALQRF 43 (43)
T ss_pred HHHHHHHhcC
Confidence 5999999998
No 46
>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=26.67 E-value=21 Score=24.31 Aligned_cols=29 Identities=21% Similarity=0.538 Sum_probs=18.5
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
-+|..||.. --.|+..-+.....|-.||-
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 478888863 33344444455678888886
No 47
>PF08152 GUCT: GUCT (NUC152) domain; InterPro: IPR012562 This is the C-terminal domain found in the RNA helicase II / Gu protein family [].; GO: 0003723 RNA binding, 0004386 helicase activity, 0005524 ATP binding, 0005634 nucleus; PDB: 2E29_A.
Probab=26.56 E-value=37 Score=27.28 Aligned_cols=33 Identities=21% Similarity=0.166 Sum_probs=25.5
Q ss_pred CCCCceeEEeCcEEEEECCCChHHHHHHHHHhcC
Q 022924 67 SNSSQLTLSFRGQVYVFDSVTPDKVQAVLLLLGG 100 (290)
Q Consensus 67 ~~~aQLTIfY~G~V~Vfd~vp~dKaqaIm~lA~g 100 (290)
..-..|||.=++.=.||| ||.+.++.++.....
T Consensus 48 ~~v~~m~l~~d~~GavFD-vP~~~~~~~~~~~~~ 80 (97)
T PF08152_consen 48 DKVKGMTLLKDKMGAVFD-VPSEIAEEFLAKWED 80 (97)
T ss_dssp TT-EEEEE-TTSSEEEEE-EEHHHHHHHHHH--S
T ss_pred HhhCcEEEecCCCEEEEE-ChHHHHHHHHHhCcc
Confidence 456789999999999999 999999999887653
No 48
>PRK12496 hypothetical protein; Provisional
Probab=26.56 E-value=32 Score=30.19 Aligned_cols=34 Identities=21% Similarity=0.365 Sum_probs=23.8
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHHHHhcCCC
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGAL 238 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~~ 238 (290)
...+|..|+.. .+. ++.+ ..|.-||...+++...
T Consensus 126 w~~~C~gC~~~---~~~---~~~~--~~C~~CG~~~~r~~~~ 159 (164)
T PRK12496 126 WRKVCKGCKKK---YPE---DYPD--DVCEICGSPVKRKMVK 159 (164)
T ss_pred eeEECCCCCcc---ccC---CCCC--CcCCCCCChhhhcchh
Confidence 35789999974 332 3333 5899999988877653
No 49
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=26.43 E-value=19 Score=22.96 Aligned_cols=28 Identities=29% Similarity=0.720 Sum_probs=15.2
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhhHH
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~ 231 (290)
.+.|..||.. . ...+.|-...|..||..
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 4679999985 2 22455667899999874
No 50
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=26.16 E-value=33 Score=35.08 Aligned_cols=38 Identities=26% Similarity=0.526 Sum_probs=32.3
Q ss_pred CCCCccceecccCCCCCccccCCCCCCccchhhhHHHHhcCC
Q 022924 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKGA 237 (290)
Q Consensus 196 ~~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g~ 237 (290)
...++|+.|+. .-|-|=.=+.| ..||--|---.|.-|+
T Consensus 21 ~~NKvCFDCgA---knPtWaSVTYG-IFLCiDCSAvHRnLGV 58 (454)
T KOG0706|consen 21 SENKVCFDCGA---KNPTWASVTYG-IFLCIDCSAVHRNLGV 58 (454)
T ss_pred CCCceecccCC---CCCCceeecce-EEEEEecchhhhcccc
Confidence 35799999999 79999999999 8999999876666554
No 51
>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=25.96 E-value=24 Score=24.51 Aligned_cols=29 Identities=28% Similarity=0.686 Sum_probs=20.0
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
-+|.+||. .--.|+.--+.....|-.||-
T Consensus 6 y~C~~Cg~---~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGH---RFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCC---EeEEEEecCCCCCCCCCCCCC
Confidence 47899997 345676544444567999997
No 52
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.60 E-value=21 Score=29.23 Aligned_cols=35 Identities=23% Similarity=0.460 Sum_probs=23.0
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHHHHh
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWAN 234 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~ 234 (290)
....|.+|+.. .-+. ..+-..+...|-.||.|+.+
T Consensus 20 t~f~CP~Cge~--~v~v-~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKV--SISV-KIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCe--Eeee-ecCCCcceEECCCCCCccCE
Confidence 46789999942 2221 11223557899999999765
No 53
>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=25.12 E-value=30 Score=23.60 Aligned_cols=32 Identities=25% Similarity=0.675 Sum_probs=21.0
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhHH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~ 231 (290)
..|+=||.+....-..=.||.+ ...|+.|-..
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 5799999986666556688877 6899999654
No 54
>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=24.82 E-value=28 Score=23.30 Aligned_cols=26 Identities=27% Similarity=0.666 Sum_probs=20.5
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhhH
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGL 230 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl 230 (290)
...|..|+.. |....+| ...|..||-
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 3569999972 7777888 799999984
No 55
>PRK05978 hypothetical protein; Provisional
Probab=24.55 E-value=30 Score=30.31 Aligned_cols=34 Identities=26% Similarity=0.569 Sum_probs=24.2
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHHHHhc
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANK 235 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~ 235 (290)
...+|-+||. -.+++ +--.-..-|.+||+.|..+
T Consensus 32 l~grCP~CG~----G~LF~-g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGE----GKLFR-AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCC----Ccccc-cccccCCCccccCCccccC
Confidence 3568999996 45665 4444467899999977655
No 56
>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=24.40 E-value=26 Score=25.59 Aligned_cols=25 Identities=32% Similarity=0.947 Sum_probs=17.9
Q ss_pred CCCCccceecccCCCCCccccCCCCCCccchhhhHH
Q 022924 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (290)
Q Consensus 196 ~~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~ 231 (290)
.....|.+||.. . -+..+|-.||.|
T Consensus 24 p~l~~C~~cG~~--~---------~~H~vc~~cG~Y 48 (55)
T TIGR01031 24 PTLVVCPNCGEF--K---------LPHRVCPSCGYY 48 (55)
T ss_pred CcceECCCCCCc--c---------cCeeECCccCeE
Confidence 356789999974 1 236799999943
No 57
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=24.40 E-value=28 Score=33.53 Aligned_cols=31 Identities=29% Similarity=0.621 Sum_probs=22.0
Q ss_pred CCCCccceecccCCCCCccccCCCCCCccchhhhHHH
Q 022924 196 PSETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (290)
Q Consensus 196 ~~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~ 232 (290)
+..+.|..||+. ..+ ...|-+.+|+.||.++
T Consensus 109 ~~~RFCg~CG~~--~~~----~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCGRCGTK--TYP----REGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCCCCCCc--Ccc----ccCceeeeCCCCCCcc
Confidence 346889999985 333 3446678999999865
No 58
>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=23.94 E-value=14 Score=24.19 Aligned_cols=33 Identities=27% Similarity=0.690 Sum_probs=18.7
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhhHHH
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFW 232 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~ 232 (290)
..|.+|++. -.-+..+.+..|....|-.||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 457788774 222333334455567787777644
No 59
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=23.11 E-value=44 Score=33.47 Aligned_cols=30 Identities=27% Similarity=0.628 Sum_probs=24.9
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhh
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACG 229 (290)
..+|+-||.+.......-.||.. ..|+.|-
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~Ci 38 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDECI 38 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchHH
Confidence 45999999998888888888743 7999993
No 60
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.10 E-value=37 Score=30.16 Aligned_cols=33 Identities=27% Similarity=0.520 Sum_probs=19.3
Q ss_pred CCccceecccCCCCCcccc-------CCCCCCccchhhhHHH
Q 022924 198 ETSCTHCGISSKSTPMMRR-------GPSGPRSLCNACGLFW 232 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRr-------Gp~G~~~LCNACGl~~ 232 (290)
...|.+|+++ .--.|-- ++......|+.||..|
T Consensus 39 I~~Cp~C~~~--IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 39 ITSCPNCSTP--IRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHHCcCCCCC--CCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 4567777665 3322322 3444557899999866
No 61
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.08 E-value=22 Score=27.02 Aligned_cols=34 Identities=24% Similarity=0.388 Sum_probs=27.0
Q ss_pred CCccceecccCCCCCccccCCCCCCccchhhhHHHH
Q 022924 198 ETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWA 233 (290)
Q Consensus 198 ~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~ 233 (290)
...|..|.+- .|-+||+-..-+..-|-+||-..+
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 3689999985 787777776666889999998653
No 62
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=22.67 E-value=46 Score=32.57 Aligned_cols=36 Identities=28% Similarity=0.549 Sum_probs=29.9
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHHHHhcC
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLFWANKG 236 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~~~~~g 236 (290)
....|+.|+.+ . |.|=.=.-| ..||-.|-=-.|.-|
T Consensus 19 ~Nk~CaDCga~--~-P~W~S~nlG-vfiCi~CagvHRsLG 54 (319)
T COG5347 19 SNKKCADCGAP--N-PTWASVNLG-VFLCIDCAGVHRSLG 54 (319)
T ss_pred ccCccccCCCC--C-CceEecccC-eEEEeecchhhhccc
Confidence 36899999997 5 999999999 799999976555544
No 63
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=22.42 E-value=82 Score=33.67 Aligned_cols=22 Identities=27% Similarity=0.907 Sum_probs=11.9
Q ss_pred ccceecccCCCCCccccCCCCCCccchhhhHH
Q 022924 200 SCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (290)
Q Consensus 200 ~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~ 231 (290)
.|.+||.. .|++ .-+|..||..
T Consensus 3 ~Cp~Cg~~---------n~~~-akFC~~CG~~ 24 (645)
T PRK14559 3 ICPQCQFE---------NPNN-NRFCQKCGTS 24 (645)
T ss_pred cCCCCCCc---------CCCC-CccccccCCC
Confidence 56666654 4444 3466666653
No 64
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=21.19 E-value=33 Score=35.11 Aligned_cols=25 Identities=36% Similarity=0.921 Sum_probs=19.7
Q ss_pred CCCccceecccCCCCCccccCCCCCCccchhhhHH
Q 022924 197 SETSCTHCGISSKSTPMMRRGPSGPRSLCNACGLF 231 (290)
Q Consensus 197 ~~~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACGl~ 231 (290)
....|.+||+ ..|.|- | -|..||-|
T Consensus 6 t~f~C~~CG~---~s~KW~----G---kCp~Cg~W 30 (456)
T COG1066 6 TAFVCQECGY---VSPKWL----G---KCPACGAW 30 (456)
T ss_pred cEEEcccCCC---CCcccc----c---cCCCCCCc
Confidence 4579999999 788883 4 69999963
No 65
>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=20.41 E-value=52 Score=22.29 Aligned_cols=29 Identities=24% Similarity=0.561 Sum_probs=17.2
Q ss_pred CccceecccCCCCCccccCCCCCCccchhhh
Q 022924 199 TSCTHCGISSKSTPMMRRGPSGPRSLCNACG 229 (290)
Q Consensus 199 ~~C~nCg~~~~~Tp~WRrGp~G~~~LCNACG 229 (290)
..|..|+-+ ..-.|..-......+|+.||
T Consensus 4 ~pCP~CGG~--DrFr~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 4 GPCPNCGGS--DRFRFDDKDGRGTWFCSVCG 32 (37)
T ss_pred cCCCCCCCc--cccccccCCCCcCEEeCCCC
Confidence 468888875 44445442222257888886
Done!