Query 018626
Match_columns 353
No_of_seqs 305 out of 805
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 02:40:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018626.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018626hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.4 7.3E-14 1.6E-18 104.6 3.3 42 224-267 1-42 (54)
2 smart00401 ZnF_GATA zinc finge 99.4 1.4E-13 3E-18 102.2 2.8 43 222-266 3-46 (52)
3 PF06203 CCT: CCT motif; Inte 99.4 2.5E-13 5.5E-18 98.4 3.3 44 153-196 1-44 (45)
4 PF00320 GATA: GATA zinc finge 99.4 1.4E-13 3E-18 95.0 1.4 35 225-261 1-35 (36)
5 PF06200 tify: tify domain; I 99.4 9.6E-13 2.1E-17 91.3 4.8 34 86-119 2-35 (36)
6 KOG1601 GATA-4/5/6 transcripti 98.4 1.2E-07 2.6E-12 85.3 2.7 41 222-264 199-239 (340)
7 COG5641 GAT1 GATA Zn-finger-co 97.8 1.7E-05 3.8E-10 82.5 3.6 48 217-266 153-205 (498)
8 PF09425 CCT_2: Divergent CCT 96.6 0.0012 2.5E-08 43.5 1.5 24 152-176 3-26 (27)
9 KOG3554 Histone deacetylase co 89.1 1.8 4E-05 45.6 8.6 39 222-262 386-426 (693)
10 COG5641 GAT1 GATA Zn-finger-co 85.7 0.4 8.6E-06 50.7 1.6 45 222-267 297-341 (498)
11 KOG1601 GATA-4/5/6 transcripti 78.1 0.81 1.8E-05 41.2 0.4 41 150-190 290-330 (340)
12 PF14803 Nudix_N_2: Nudix N-te 57.8 3.3 7.2E-05 28.5 -0.1 30 223-254 1-30 (34)
13 PF01783 Ribosomal_L32p: Ribos 56.0 3.3 7.1E-05 31.2 -0.3 25 222-258 26-50 (56)
14 COG5349 Uncharacterized protei 53.8 6.1 0.00013 34.8 0.9 43 214-261 13-55 (126)
15 PF09889 DUF2116: Uncharacteri 52.2 7.8 0.00017 29.9 1.2 29 223-261 4-33 (59)
16 TIGR00416 sms DNA repair prote 51.8 5.6 0.00012 41.4 0.5 17 222-239 7-23 (454)
17 PF13717 zinc_ribbon_4: zinc-r 47.0 4.6 0.0001 27.8 -0.7 33 223-256 3-35 (36)
18 COG1631 RPL42A Ribosomal prote 45.5 12 0.00027 31.4 1.4 21 221-241 67-87 (94)
19 PF06689 zf-C4_ClpX: ClpX C4-t 44.8 12 0.00026 26.4 1.2 33 223-256 2-34 (41)
20 PF06677 Auto_anti-p27: Sjogre 43.4 9.3 0.0002 27.4 0.4 25 222-253 17-41 (41)
21 smart00653 eIF2B_5 domain pres 42.3 9.8 0.00021 32.6 0.4 28 223-254 81-109 (110)
22 PRK05978 hypothetical protein; 41.5 12 0.00025 33.9 0.8 34 222-260 33-66 (148)
23 PRK11823 DNA repair protein Ra 40.0 9.9 0.00021 39.4 0.1 17 222-239 7-23 (446)
24 PF10777 YlaC: Inner membrane 39.8 33 0.00071 31.3 3.4 26 91-116 95-120 (155)
25 PRK00420 hypothetical protein; 38.3 14 0.0003 32.0 0.7 30 222-258 23-52 (112)
26 PF02701 zf-Dof: Dof domain, z 37.3 21 0.00045 28.1 1.5 44 222-267 5-51 (63)
27 KOG1819 FYVE finger-containing 37.0 32 0.00069 37.2 3.2 45 2-50 393-448 (990)
28 COG1645 Uncharacterized Zn-fin 36.1 12 0.00025 33.3 -0.0 29 222-258 28-56 (131)
29 PRK11788 tetratricopeptide rep 35.1 15 0.00033 35.3 0.5 10 222-231 354-363 (389)
30 PRK05342 clpX ATP-dependent pr 34.8 24 0.00051 36.5 1.9 29 222-252 9-37 (412)
31 PF01412 ArfGap: Putative GTPa 34.6 34 0.00075 28.9 2.6 36 222-261 13-48 (116)
32 COG2331 Uncharacterized protei 33.4 13 0.00027 30.5 -0.3 38 222-262 12-49 (82)
33 TIGR02098 MJ0042_CXXC MJ0042 f 32.9 8.2 0.00018 26.2 -1.2 34 223-257 3-36 (38)
34 TIGR00311 aIF-2beta translatio 32.1 15 0.00033 32.4 0.0 30 223-255 98-127 (133)
35 PRK03988 translation initiatio 31.0 16 0.00035 32.5 -0.0 30 223-255 103-132 (138)
36 PRK12775 putative trifunctiona 30.9 19 0.00041 41.2 0.5 37 219-262 818-856 (1006)
37 PRK12286 rpmF 50S ribosomal pr 30.8 17 0.00036 27.8 0.0 23 222-255 27-49 (57)
38 PF04810 zf-Sec23_Sec24: Sec23 30.6 22 0.00047 24.9 0.6 31 222-254 2-32 (40)
39 PF13619 KTSC: KTSC domain 30.5 95 0.0021 23.2 4.1 31 86-116 12-43 (60)
40 PF09297 zf-NADH-PPase: NADH p 30.3 10 0.00022 25.2 -1.1 28 222-255 3-30 (32)
41 cd01121 Sms Sms (bacterial rad 30.2 19 0.00041 36.7 0.3 12 224-238 2-13 (372)
42 COG3952 Predicted membrane pro 29.0 15 0.00032 31.8 -0.6 20 237-258 76-95 (113)
43 PRK14892 putative transcriptio 28.7 18 0.00039 30.6 -0.1 37 222-261 21-57 (99)
44 TIGR00244 transcriptional regu 28.4 28 0.0006 31.6 1.0 48 224-271 2-53 (147)
45 PRK12336 translation initiatio 28.1 19 0.00041 33.7 -0.1 30 223-255 99-128 (201)
46 PF08271 TF_Zn_Ribbon: TFIIB z 25.8 26 0.00057 24.6 0.3 31 224-259 2-32 (43)
47 PF07282 OrfB_Zn_ribbon: Putat 25.3 18 0.0004 27.3 -0.6 29 223-257 29-57 (69)
48 PF14812 PBP1_TM: Transmembran 24.1 26 0.00055 28.8 0.0 20 29-48 36-55 (81)
49 COG2816 NPY1 NTP pyrophosphohy 24.1 29 0.00062 34.5 0.3 31 223-259 112-142 (279)
50 KOG1598 Transcription initiati 23.6 39 0.00086 36.2 1.2 34 224-262 2-35 (521)
51 PF13248 zf-ribbon_3: zinc-rib 23.6 41 0.00089 21.4 0.9 23 223-255 3-25 (26)
52 PF01873 eIF-5_eIF-2B: Domain 23.3 31 0.00067 30.1 0.4 29 223-254 94-122 (125)
53 KOG3740 Uncharacterized conser 23.2 33 0.00071 37.7 0.6 42 222-265 462-506 (706)
54 smart00834 CxxC_CXXC_SSSS Puta 22.3 24 0.00052 23.8 -0.4 30 223-255 6-35 (41)
55 PF10083 DUF2321: Uncharacteri 22.2 41 0.00089 30.8 0.9 35 222-256 39-78 (158)
56 TIGR03573 WbuX N-acetyl sugar 20.0 72 0.0016 31.9 2.2 32 223-258 2-33 (343)
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=99.43 E-value=7.3e-14 Score=104.57 Aligned_cols=42 Identities=45% Similarity=1.005 Sum_probs=37.9
Q ss_pred cCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCCCCCCCC
Q 018626 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKETPMDVKP 267 (353)
Q Consensus 224 ~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~~~~~~ 267 (353)
.|+||+++ .||+||+||.|..+|||||||+|++++..++...
T Consensus 1 ~C~~C~~~--~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~ 42 (54)
T cd00202 1 ACSNCGTT--TTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSK 42 (54)
T ss_pred CCCCCCCC--CCcccccCCCCcchHHHHHHHHHHhcCCCCCccc
Confidence 49999996 5999999999989999999999999998877753
No 2
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.39 E-value=1.4e-13 Score=102.16 Aligned_cols=43 Identities=44% Similarity=0.946 Sum_probs=38.1
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCCC-CCCC
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKETP-MDVK 266 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~-~~~~ 266 (353)
...|++|+++ .||+||+||.|..+|||||||+|++++.+ ++..
T Consensus 3 ~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~ 46 (52)
T smart00401 3 GRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLS 46 (52)
T ss_pred CCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCCCCccc
Confidence 4689999986 59999999999999999999999999887 5543
No 3
>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=99.38 E-value=2.5e-13 Score=98.36 Aligned_cols=44 Identities=50% Similarity=0.761 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhhhcccccccccchhhHHHHHhhhcccCcccccc
Q 018626 153 RIASLVRFREKRKERCFDKKIRYSVRKEVAQRMHRKNGQFASLK 196 (353)
Q Consensus 153 R~asl~RfREKRK~R~f~KkiRY~~RK~~A~r~~R~KGrF~s~k 196 (353)
|.++|+||++||+.|+|+|+|+|++||.+|+.++|+||||++..
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~~ 44 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKKS 44 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCCC
Confidence 57899999999999999999999999999999999999998764
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=99.37 E-value=1.4e-13 Score=95.00 Aligned_cols=35 Identities=54% Similarity=1.178 Sum_probs=28.0
Q ss_pred CcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCC
Q 018626 225 CQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKET 261 (353)
Q Consensus 225 C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~ 261 (353)
|.+|+++ .||+||+||.|..+||||||++|++++.
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 8999997 4999999999998999999999999875
No 5
>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=99.36 E-value=9.6e-13 Score=91.26 Aligned_cols=34 Identities=38% Similarity=0.701 Sum_probs=32.0
Q ss_pred cCCCceeeeeecceEEEeCCCCHHHHHHHHHHhC
Q 018626 86 ASRTSELTLSFEGEVYVFPAVTPEKVQAVLLLLG 119 (353)
Q Consensus 86 ~~~~sqLTI~y~GeV~VFdsVspeKvqaVllLlg 119 (353)
.+.++||||||+|+|+|||+|+++||++||+|++
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 4678899999999999999999999999999986
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.42 E-value=1.2e-07 Score=85.28 Aligned_cols=41 Identities=46% Similarity=1.077 Sum_probs=35.8
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCCCCC
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKETPMD 264 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~~~ 264 (353)
...|.+|+++ .||+||++|.|+..||||||++|+++...+.
T Consensus 199 ~~~c~~~~~~--~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~ 239 (340)
T KOG1601|consen 199 LRQCSNCGTT--KTPLWRRGPEGPKSLCNACGLRYKKGGVRRP 239 (340)
T ss_pred CcccCCCCCC--CCcceecCCCCCccccccchhhhhhcCcccc
Confidence 4689999986 5999999999999999999999999963333
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.76 E-value=1.7e-05 Score=82.50 Aligned_cols=48 Identities=29% Similarity=0.607 Sum_probs=40.6
Q ss_pred CCCCccccCcccCCCCCCCcccccCCCC----CcccchHHHHHHHhcCCCC-CCC
Q 018626 217 RPETVVRRCQHCGVSENNTPAMRRGPAG----PRTLCNACGLMWANKETPM-DVK 266 (353)
Q Consensus 217 ~~e~~~~~C~~C~~~~~~TP~WR~GP~G----~~~LCNACGl~~~~~~~~~-~~~ 266 (353)
..+.+...|.+|.++ .||+|||+..+ .-.|||||||+|+-+++++ ++.
T Consensus 153 ~~s~~~~vc~Nc~t~--stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t 205 (498)
T COG5641 153 DNSNQPHVCSNCKTT--STPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPIS 205 (498)
T ss_pred ccccccchhcccccc--CCccccccccccccCCccccccccccccccCCcCCCcc
Confidence 444556699999996 69999999994 3799999999999999999 664
No 8
>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=96.58 E-value=0.0012 Score=43.47 Aligned_cols=24 Identities=54% Similarity=0.627 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHhhhcccccccccch
Q 018626 152 RRIASLVRFREKRKERCFDKKIRYS 176 (353)
Q Consensus 152 ~R~asl~RfREKRK~R~f~KkiRY~ 176 (353)
.|.+||.||.||||+|... +..|.
T Consensus 3 aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 3 ARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp ---HHHHHHHHHH------------
T ss_pred hHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 5899999999999999987 66664
No 9
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=89.15 E-value=1.8 Score=45.61 Aligned_cols=39 Identities=21% Similarity=0.461 Sum_probs=31.5
Q ss_pred cccCcccCCCCCCCccccc--CCCCCcccchHHHHHHHhcCCC
Q 018626 222 VRRCQHCGVSENNTPAMRR--GPAGPRTLCNACGLMWANKETP 262 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~--GP~G~~~LCNACGl~~~~~~~~ 262 (353)
.+.|-+|+++ ..-+|-. +|.-...||..|.++|+|.+.+
T Consensus 386 g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 386 GRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred CCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 5789999996 4677754 5555779999999999998776
No 10
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=85.70 E-value=0.4 Score=50.67 Aligned_cols=45 Identities=22% Similarity=0.262 Sum_probs=39.6
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCCCCCCCC
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKETPMDVKP 267 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~~~~~~ 267 (353)
...|.+|++. +.||.||+...-.-.+|||||++.+..+..+++.|
T Consensus 297 ~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~p 341 (498)
T COG5641 297 DKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLP 341 (498)
T ss_pred hcCccccccc-ccCcccccccccccccccccccccCCcccccccCC
Confidence 4678999875 57999999988778999999999999999998877
No 11
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=78.07 E-value=0.81 Score=41.15 Aligned_cols=41 Identities=44% Similarity=0.680 Sum_probs=37.9
Q ss_pred hHHHHHHHHHHHHhhhcccccccccchhhHHHHHhhhcccC
Q 018626 150 LSRRIASLVRFREKRKERCFDKKIRYSVRKEVAQRMHRKNG 190 (353)
Q Consensus 150 ls~R~asl~RfREKRK~R~f~KkiRY~~RK~~A~r~~R~KG 190 (353)
...|.+.+.|++++++.|.|.++++|..|+..++.+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 46789999999999999999999999999999999999886
No 12
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=57.76 E-value=3.3 Score=28.54 Aligned_cols=30 Identities=30% Similarity=0.747 Sum_probs=14.7
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGL 254 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl 254 (353)
+.|.+||..- +..-=.|-...+..|.+||.
T Consensus 1 kfC~~CG~~l--~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPL--ERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChh--hhhcCCCCCccceECCCCCC
Confidence 3699999641 22222455567789999985
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=55.95 E-value=3.3 Score=31.19 Aligned_cols=25 Identities=28% Similarity=0.937 Sum_probs=18.0
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHh
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWAN 258 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~ 258 (353)
.-.|.+||.. .-+..+|..|| +|+.
T Consensus 26 l~~c~~cg~~-----------~~~H~vc~~cG-~y~~ 50 (56)
T PF01783_consen 26 LVKCPNCGEP-----------KLPHRVCPSCG-YYKG 50 (56)
T ss_dssp EEESSSSSSE-----------ESTTSBCTTTB-BSSS
T ss_pred eeeeccCCCE-----------ecccEeeCCCC-eECC
Confidence 4689999963 23478999999 4443
No 14
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.83 E-value=6.1 Score=34.80 Aligned_cols=43 Identities=30% Similarity=0.564 Sum_probs=30.9
Q ss_pred CCCCCCCccccCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCC
Q 018626 214 GTPRPETVVRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKET 261 (353)
Q Consensus 214 g~~~~e~~~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~ 261 (353)
+++......-+|-+||.- .-.+|..-...-|.|||+-|-.+..
T Consensus 13 ~~pi~~Gl~grCP~CGeG-----rLF~gFLK~~p~C~aCG~dyg~~~a 55 (126)
T COG5349 13 VTPIKRGLRGRCPRCGEG-----RLFRGFLKVVPACEACGLDYGFADA 55 (126)
T ss_pred CcHHHHHhcCCCCCCCCc-----hhhhhhcccCchhhhccccccCCcc
Confidence 334333445689999963 4567777778899999999987643
No 15
>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=52.24 E-value=7.8 Score=29.92 Aligned_cols=29 Identities=21% Similarity=0.728 Sum_probs=22.7
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccc-hHHHHHHHhcCC
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLC-NACGLMWANKET 261 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LC-NACGl~~~~~~~ 261 (353)
++|.+||.+. | .. +..| ..|+..|.++..
T Consensus 4 kHC~~CG~~I---p------~~-~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 4 KHCPVCGKPI---P------PD-ESFCSPKCREEYRKRQK 33 (59)
T ss_pred CcCCcCCCcC---C------cc-hhhhCHHHHHHHHHHHH
Confidence 6899999873 3 23 7899 599999998754
No 16
>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=51.84 E-value=5.6 Score=41.40 Aligned_cols=17 Identities=29% Similarity=0.512 Sum_probs=12.2
Q ss_pred cccCcccCCCCCCCcccc
Q 018626 222 VRRCQHCGVSENNTPAMR 239 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR 239 (353)
..+|.+||.+ ...|+||
T Consensus 7 ~y~C~~Cg~~-~~~~~g~ 23 (454)
T TIGR00416 7 KFVCQHCGAD-SPKWQGK 23 (454)
T ss_pred eEECCcCCCC-CccccEE
Confidence 5789999997 2555554
No 17
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=46.97 E-value=4.6 Score=27.84 Aligned_cols=33 Identities=21% Similarity=0.627 Sum_probs=27.7
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~ 256 (353)
..|-+|++. -..+..+-.+.|...-|-.||-.|
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 469999987 378888888999889999999776
No 18
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=45.46 E-value=12 Score=31.44 Aligned_cols=21 Identities=33% Similarity=0.767 Sum_probs=17.8
Q ss_pred ccccCcccCCCCCCCcccccC
Q 018626 221 VVRRCQHCGVSENNTPAMRRG 241 (353)
Q Consensus 221 ~~~~C~~C~~~~~~TP~WR~G 241 (353)
+..+|+-|+..++.+|.||-+
T Consensus 67 Lr~~Ct~Cgkah~~~~~~Rak 87 (94)
T COG1631 67 LRLRCTECGKAHQRTPGFRAK 87 (94)
T ss_pred EEEEehhhccccccCcceeee
Confidence 567899999998777899975
No 19
>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=44.84 E-value=12 Score=26.44 Aligned_cols=33 Identities=30% Similarity=0.749 Sum_probs=22.0
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~ 256 (353)
.+|+-||.+.+.+-..=.||.+ ...|+.|=...
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~~ 34 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQA 34 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHHH
Confidence 4799999987666666689977 79999996543
No 20
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=43.38 E-value=9.3 Score=27.40 Aligned_cols=25 Identities=44% Similarity=1.095 Sum_probs=18.7
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHH
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACG 253 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACG 253 (353)
...|..|+ +|++| .-.| +.+|-+|+
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 35799996 79999 2345 78998885
No 21
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=42.29 E-value=9.8 Score=32.58 Aligned_cols=28 Identities=29% Similarity=0.670 Sum_probs=20.7
Q ss_pred ccCcccCCCCCCCcccccCCCCC-cccchHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGP-RTLCNACGL 254 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~-~~LCNACGl 254 (353)
-.|..|+.+. |-+-+.+ +- -.-|+|||-
T Consensus 81 VlC~~C~spd--T~l~k~~--r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPD--TELIKEN--RLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCC--cEEEEeC--CeEEEEccccCC
Confidence 4699999985 8888873 22 245999995
No 22
>PRK05978 hypothetical protein; Provisional
Probab=41.54 E-value=12 Score=33.85 Aligned_cols=34 Identities=29% Similarity=0.625 Sum_probs=26.2
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcC
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKE 260 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~ 260 (353)
..+|-+||.- .++ +|...-..-|.+||+.|...+
T Consensus 33 ~grCP~CG~G----~LF-~g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 33 RGRCPACGEG----KLF-RAFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cCcCCCCCCC----ccc-ccccccCCCccccCCccccCC
Confidence 4689999973 344 466777889999999998764
No 23
>PRK11823 DNA repair protein RadA; Provisional
Probab=40.03 E-value=9.9 Score=39.43 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=11.4
Q ss_pred cccCcccCCCCCCCcccc
Q 018626 222 VRRCQHCGVSENNTPAMR 239 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR 239 (353)
..+|.+||.+ +..|+||
T Consensus 7 ~y~C~~Cg~~-~~~~~g~ 23 (446)
T PRK11823 7 AYVCQECGAE-SPKWLGR 23 (446)
T ss_pred eEECCcCCCC-CcccCee
Confidence 5789999986 2444443
No 24
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=39.83 E-value=33 Score=31.32 Aligned_cols=26 Identities=23% Similarity=0.473 Sum_probs=22.1
Q ss_pred eeeeeecceEEEeCCCCHHHHHHHHH
Q 018626 91 ELTLSFEGEVYVFPAVTPEKVQAVLL 116 (353)
Q Consensus 91 qLTI~y~GeV~VFdsVspeKvqaVll 116 (353)
-|-.-|.||||+...||++-++++|.
T Consensus 95 DLRVCYNGEWy~tr~vs~~ai~~iL~ 120 (155)
T PF10777_consen 95 DLRVCYNGEWYNTRFVSDQAIDKILQ 120 (155)
T ss_pred EEeEEEcceeeeeccCCHHHHHHHHc
Confidence 56678999999999999998777763
No 25
>PRK00420 hypothetical protein; Validated
Probab=38.32 E-value=14 Score=31.98 Aligned_cols=30 Identities=23% Similarity=0.657 Sum_probs=22.5
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHh
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWAN 258 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~ 258 (353)
..+|..|| +|+.|. ..| ...|-.||..+..
T Consensus 23 ~~~CP~Cg-----~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCG-----LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCC-----Ccceec-CCC-ceECCCCCCeeee
Confidence 45799999 577874 444 8999999986554
No 26
>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=37.35 E-value=21 Score=28.07 Aligned_cols=44 Identities=23% Similarity=0.478 Sum_probs=31.9
Q ss_pred cccCcccCCCCCCCcccc---cCCCCCcccchHHHHHHHhcCCCCCCCC
Q 018626 222 VRRCQHCGVSENNTPAMR---RGPAGPRTLCNACGLMWANKETPMDVKP 267 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR---~GP~G~~~LCNACGl~~~~~~~~~~~~~ 267 (353)
...|..|..+. |=+-= --..-|+..|-+|..+|-..+++|.++-
T Consensus 5 ~~~CPRC~S~n--TKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPv 51 (63)
T PF02701_consen 5 PLPCPRCDSTN--TKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPV 51 (63)
T ss_pred CCCCCCcCCCC--CEEEeecCCCCCCcchhhHHHHHHHHhcceecCCcc
Confidence 56799998753 32211 1234578999999999999999999864
No 27
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=36.96 E-value=32 Score=37.17 Aligned_cols=45 Identities=42% Similarity=0.673 Sum_probs=26.1
Q ss_pred CCCCCCCCCCCCcccc-----------cCCCCccccCCCCCCCCCCCcccccCCCccccc
Q 018626 2 AAANPQPLQARPFEEH-----------ARAPPIQIEDEDGDYEDGEGMDDIDEGNINSIN 50 (353)
Q Consensus 2 ~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (353)
+++-|.|- +.|+| .+.|+++.+|-|++.+|||.. |++|.+|+|-+
T Consensus 393 ~~aspaps---~s~~hsiastssaatsstnppad~~dgdde~eddddi-dvdeediessd 448 (990)
T KOG1819|consen 393 ALASPAPS---GSEEHSIASTSSAATSSTNPPADNEDGDDEAEDDDDI-DVDEEDIESSD 448 (990)
T ss_pred cccCCCCC---CCccccccccccccccCCCCccccccCcccccCcccc-ccccccccccc
Confidence 34556666 78888 346778776654444444333 34666676643
No 28
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=36.14 E-value=12 Score=33.33 Aligned_cols=29 Identities=34% Similarity=0.889 Sum_probs=23.3
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHh
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWAN 258 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~ 258 (353)
..+|.-|| ||++| -+| ...|--||.+...
T Consensus 28 ~~hCp~Cg-----~PLF~--KdG-~v~CPvC~~~~~~ 56 (131)
T COG1645 28 AKHCPKCG-----TPLFR--KDG-EVFCPVCGYREVV 56 (131)
T ss_pred HhhCcccC-----Cccee--eCC-eEECCCCCceEEE
Confidence 56899999 69999 567 8999999974433
No 29
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=35.06 E-value=15 Score=35.33 Aligned_cols=10 Identities=40% Similarity=1.158 Sum_probs=7.0
Q ss_pred cccCcccCCC
Q 018626 222 VRRCQHCGVS 231 (353)
Q Consensus 222 ~~~C~~C~~~ 231 (353)
.|.|.|||.+
T Consensus 354 ~~~c~~cg~~ 363 (389)
T PRK11788 354 RYRCRNCGFT 363 (389)
T ss_pred CEECCCCCCC
Confidence 3677777775
No 30
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=34.77 E-value=24 Score=36.48 Aligned_cols=29 Identities=28% Similarity=0.779 Sum_probs=24.4
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHH
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNAC 252 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNAC 252 (353)
..+|+.||.+...++..-.||.. .+|+.|
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~C 37 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDEC 37 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchH
Confidence 35899999998788888889844 699999
No 31
>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=34.55 E-value=34 Score=28.89 Aligned_cols=36 Identities=22% Similarity=0.458 Sum_probs=26.6
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCC
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKET 261 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~ 261 (353)
...|..|+.. -|.|-.=..| -.||-.|.-..+.-++
T Consensus 13 N~~CaDCg~~---~p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 13 NKVCADCGAP---NPTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp CTB-TTT-SB---S--EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred cCcCCCCCCC---CCCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 4789999976 6899999999 8999999988888765
No 32
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.41 E-value=13 Score=30.52 Aligned_cols=38 Identities=26% Similarity=0.503 Sum_probs=27.3
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCCC
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKETP 262 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~ 262 (353)
..+|..|+-..+-...+++.| -+.|.+||-++++.-..
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~l~~ 49 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDP---LTTCEECGARLKKLLNA 49 (82)
T ss_pred EEeecccchHHHHHHhcccCc---cccChhhChHHHHhhcc
Confidence 357999987543455666665 46999999998886443
No 33
>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=32.93 E-value=8.2 Score=26.18 Aligned_cols=34 Identities=26% Similarity=0.685 Sum_probs=23.1
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWA 257 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~ 257 (353)
..|.+|+..- ..+..+.+..|....|-.||..|.
T Consensus 3 ~~CP~C~~~~-~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSF-RVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEE-EeCHHHcCCCCCEEECCCCCCEEE
Confidence 4688998752 455555555666788988887653
No 34
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=32.10 E-value=15 Score=32.44 Aligned_cols=30 Identities=27% Similarity=0.659 Sum_probs=21.4
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (353)
-.|..|+.+. |-+-+++-. --.-|+|||-.
T Consensus 98 VlC~~C~sPd--T~l~k~~r~-~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPD--TRIIKEGRV-SLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCC--cEEEEeCCe-EEEecccCCCC
Confidence 4699999985 888876321 12479999963
No 35
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=31.00 E-value=16 Score=32.50 Aligned_cols=30 Identities=30% Similarity=0.645 Sum_probs=21.4
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (353)
-.|..|+.+. |-+-+++-. --.-|+|||-.
T Consensus 103 VlC~~C~spd--T~l~k~~r~-~~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGSPD--TKLIKEGRI-WVLKCEACGAE 132 (138)
T ss_pred EECCCCCCCC--cEEEEcCCe-EEEEcccCCCC
Confidence 4799999975 888776321 13579999963
No 36
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=30.91 E-value=19 Score=41.23 Aligned_cols=37 Identities=27% Similarity=0.537 Sum_probs=25.7
Q ss_pred CCccccCcccCCCCCCCcccccCCCCCcccchHHHHH--HHhcCCC
Q 018626 219 ETVVRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM--WANKETP 262 (353)
Q Consensus 219 e~~~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~--~~~~~~~ 262 (353)
..+.|+|..|+. |.+=...|+| .|-+||-. |.++++.
T Consensus 818 ~~~~~~~~~~~~----~~~~~~~~~~---~~~~~~~~~~~~~~~~~ 856 (1006)
T PRK12775 818 SELQWRCDDCGK----VSEGFAFPYG---MCPACGGKLQALDRRKV 856 (1006)
T ss_pred cceeeehhhhcc----ccccccCCcC---cCcccccchhhhhccCc
Confidence 346799999986 5566667777 89999954 4444443
No 37
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=30.81 E-value=17 Score=27.76 Aligned_cols=23 Identities=30% Similarity=0.948 Sum_probs=17.0
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHH
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (353)
.-.|.+||... -+..+|..||.|
T Consensus 27 l~~C~~CG~~~-----------~~H~vC~~CG~Y 49 (57)
T PRK12286 27 LVECPNCGEPK-----------LPHRVCPSCGYY 49 (57)
T ss_pred ceECCCCCCcc-----------CCeEECCCCCcC
Confidence 34699999852 237899999954
No 38
>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=30.59 E-value=22 Score=24.91 Aligned_cols=31 Identities=29% Similarity=0.626 Sum_probs=20.1
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHH
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGL 254 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl 254 (353)
+.+|.+|+.= .-|..+-...|....|+-|+.
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 4589999885 478888888888899999986
No 39
>PF13619 KTSC: KTSC domain
Probab=30.48 E-value=95 Score=23.25 Aligned_cols=31 Identities=35% Similarity=0.564 Sum_probs=25.2
Q ss_pred cCCCceeeeee-cceEEEeCCCCHHHHHHHHH
Q 018626 86 ASRTSELTLSF-EGEVYVFPAVTPEKVQAVLL 116 (353)
Q Consensus 86 ~~~~sqLTI~y-~GeV~VFdsVspeKvqaVll 116 (353)
+..+..|.|.| .|.+|.|-.||++.++++|.
T Consensus 12 d~~~~~L~V~F~~G~~Y~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 12 DPETRTLEVEFKSGSVYRYFGVPPEVYEALLN 43 (60)
T ss_pred CCCCCEEEEEEcCCCEEEECCCCHHHHHHHHc
Confidence 44556788766 58889999999999999875
No 40
>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=30.27 E-value=10 Score=25.16 Aligned_cols=28 Identities=32% Similarity=0.762 Sum_probs=15.2
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHH
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (353)
.+.|..||... ..-+.|....|.+||+.
T Consensus 3 ~rfC~~CG~~t------~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPT------KPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BE------EE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccc------cCCCCcCEeECCCCcCE
Confidence 36799999753 33445667899999875
No 41
>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=30.18 E-value=19 Score=36.67 Aligned_cols=12 Identities=33% Similarity=0.938 Sum_probs=8.8
Q ss_pred cCcccCCCCCCCccc
Q 018626 224 RCQHCGVSENNTPAM 238 (353)
Q Consensus 224 ~C~~C~~~~~~TP~W 238 (353)
+|.+||.. +|.|
T Consensus 2 ~c~~cg~~---~~~~ 13 (372)
T cd01121 2 VCSECGYV---SPKW 13 (372)
T ss_pred CCCCCCCC---CCCc
Confidence 69999986 4555
No 42
>COG3952 Predicted membrane protein [Function unknown]
Probab=28.98 E-value=15 Score=31.77 Aligned_cols=20 Identities=35% Similarity=0.469 Sum_probs=15.1
Q ss_pred ccccCCCCCcccchHHHHHHHh
Q 018626 237 AMRRGPAGPRTLCNACGLMWAN 258 (353)
Q Consensus 237 ~WR~GP~G~~~LCNACGl~~~~ 258 (353)
.||.+|-+ .||++||+.-.-
T Consensus 76 i~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHhcchHH--HHHHhhhHHHHH
Confidence 45667777 899999987543
No 43
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.67 E-value=18 Score=30.56 Aligned_cols=37 Identities=19% Similarity=0.391 Sum_probs=25.1
Q ss_pred cccCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCC
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKET 261 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~ 261 (353)
...|.+|+...-..++-| ..+...|-.||.++.+...
T Consensus 21 ~f~CP~Cge~~v~v~~~k---~~~h~~C~~CG~y~~~~V~ 57 (99)
T PRK14892 21 IFECPRCGKVSISVKIKK---NIAIITCGNCGLYTEFEVP 57 (99)
T ss_pred EeECCCCCCeEeeeecCC---CcceEECCCCCCccCEECC
Confidence 467999995432223333 3557899999999887633
No 44
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=28.35 E-value=28 Score=31.59 Aligned_cols=48 Identities=19% Similarity=0.376 Sum_probs=33.7
Q ss_pred cCcccCCCCCCCcccccCCCC----CcccchHHHHHHHhcCCCCCCCCCCcc
Q 018626 224 RCQHCGVSENNTPAMRRGPAG----PRTLCNACGLMWANKETPMDVKPSIME 271 (353)
Q Consensus 224 ~C~~C~~~~~~TP~WR~GP~G----~~~LCNACGl~~~~~~~~~~~~~~~~~ 271 (353)
+|..|+...|..=-=|.-.+| .+.-|.+||.+|-...+.-...+..++
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l~ViK 53 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIK 53 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccccEEEc
Confidence 599998876555555555555 457999999999888776555555444
No 45
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=28.05 E-value=19 Score=33.66 Aligned_cols=30 Identities=27% Similarity=0.659 Sum_probs=21.8
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (353)
-.|..|+-+. |-+-+.+-. --.-|+|||-.
T Consensus 99 V~C~~C~~pd--T~l~k~~~~-~~l~C~aCGa~ 128 (201)
T PRK12336 99 VICSECGLPD--TRLVKEDRV-LMLRCDACGAH 128 (201)
T ss_pred EECCCCCCCC--cEEEEcCCe-EEEEcccCCCC
Confidence 4799999985 888877411 12479999974
No 46
>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=25.80 E-value=26 Score=24.59 Aligned_cols=31 Identities=26% Similarity=0.746 Sum_probs=18.3
Q ss_pred cCcccCCCCCCCcccccCCCCCcccchHHHHHHHhc
Q 018626 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (353)
Q Consensus 224 ~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~ 259 (353)
+|.+|+.+ . .--+--.| ...|..||+.+.-.
T Consensus 2 ~Cp~Cg~~---~-~~~D~~~g-~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 2 KCPNCGSK---E-IVFDPERG-ELVCPNCGLVLEEN 32 (43)
T ss_dssp SBTTTSSS---E-EEEETTTT-EEEETTT-BBEE-T
T ss_pred CCcCCcCC---c-eEEcCCCC-eEECCCCCCEeecc
Confidence 58899874 2 33333333 67999999865543
No 47
>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=25.33 E-value=18 Score=27.34 Aligned_cols=29 Identities=24% Similarity=0.668 Sum_probs=19.9
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWA 257 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~ 257 (353)
..|..||..... ...+....|..||..+-
T Consensus 29 q~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHRNKK------RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCccccccc------ccccceEEcCCCCCEEC
Confidence 469999986311 44555678999998643
No 48
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=24.12 E-value=26 Score=28.83 Aligned_cols=20 Identities=40% Similarity=0.637 Sum_probs=0.0
Q ss_pred CCCCCCCCCcccccCCCccc
Q 018626 29 DGDYEDGEGMDDIDEGNINS 48 (353)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~~ 48 (353)
++||.|||..|+.++.+|..
T Consensus 36 ddd~~DDD~dDdeeee~m~r 55 (81)
T PF14812_consen 36 DDDYEDDDDDDDEEEEPMPR 55 (81)
T ss_dssp --------------------
T ss_pred ccccccccccchhhcccccc
Confidence 44555555545455555543
No 49
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=24.06 E-value=29 Score=34.48 Aligned_cols=31 Identities=26% Similarity=0.566 Sum_probs=18.9
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHHHHhc
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~ 259 (353)
+.|..||+.. -. ...|-+..|+.||.++--+
T Consensus 112 RFCg~CG~~~---~~---~~~g~~~~C~~cg~~~fPR 142 (279)
T COG2816 112 RFCGRCGTKT---YP---REGGWARVCPKCGHEHFPR 142 (279)
T ss_pred cCCCCCCCcC---cc---ccCceeeeCCCCCCccCCC
Confidence 4588888752 21 2334557888888766543
No 50
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=23.57 E-value=39 Score=36.24 Aligned_cols=34 Identities=29% Similarity=0.647 Sum_probs=23.9
Q ss_pred cCcccCCCCCCCcccccCCCCCcccchHHHHHHHhcCCC
Q 018626 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKETP 262 (353)
Q Consensus 224 ~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~ 262 (353)
.|.||+.+ ++. |+--.| -..|.+||.........
T Consensus 2 ~C~~C~~s---~fe-~d~a~g-~~~C~~CG~v~E~~~iv 35 (521)
T KOG1598|consen 2 VCKNCGGS---NFE-RDEATG-NLYCTACGTVLEYNNIV 35 (521)
T ss_pred cCCCCCCC---Ccc-cccccC-Cceeccccceeecccee
Confidence 69999985 444 444455 79999999877665443
No 51
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.56 E-value=41 Score=21.37 Aligned_cols=23 Identities=26% Similarity=0.729 Sum_probs=14.4
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (353)
+.|.+||... +.+ ...|-.||..
T Consensus 3 ~~Cp~Cg~~~---------~~~-~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEI---------DPD-AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcC---------Ccc-cccChhhCCC
Confidence 5688888742 222 4678888753
No 52
>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=23.29 E-value=31 Score=30.14 Aligned_cols=29 Identities=31% Similarity=0.680 Sum_probs=21.8
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGL 254 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl 254 (353)
-.|..|+.+. |-+-+++-.- -.-|+|||-
T Consensus 94 VlC~~C~spd--T~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPD--TELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSS--EEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCCCc--cEEEEcCCEE-EEEecccCC
Confidence 4699999875 8888874333 467999994
No 53
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.20 E-value=33 Score=37.71 Aligned_cols=42 Identities=19% Similarity=0.404 Sum_probs=32.3
Q ss_pred cccCcccCCCCCCCcccccCCCC---CcccchHHHHHHHhcCCCCCC
Q 018626 222 VRRCQHCGVSENNTPAMRRGPAG---PRTLCNACGLMWANKETPMDV 265 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~WR~GP~G---~~~LCNACGl~~~~~~~~~~~ 265 (353)
+..|..|.+- -||.|+.-+.+ ...+|.+|----.|+--+.+.
T Consensus 462 P~~caqcktd--ftp~wk~ekstq~d~~i~cE~cvtSnqkkAlK~eh 506 (706)
T KOG3740|consen 462 PYACAQCKTD--FTPAWKKEKSTQADAAIVCENCVTSNQKKALKVEH 506 (706)
T ss_pred chhhhhcccc--cccccccccccCcchHHHHHhhhhhcccccccccc
Confidence 5689999986 49999998877 468999998776666444443
No 54
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=22.29 E-value=24 Score=23.83 Aligned_cols=30 Identities=27% Similarity=0.669 Sum_probs=20.5
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHH
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (353)
-+|..||.. -..|..--.+....|-.||..
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHT---FEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCE---EEEEEecCCCCCCCCCCCCCc
Confidence 479999974 345554444666789999973
No 55
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.21 E-value=41 Score=30.84 Aligned_cols=35 Identities=17% Similarity=0.510 Sum_probs=21.0
Q ss_pred cccCcccCCCCCCCccc-----ccCCCCCcccchHHHHHH
Q 018626 222 VRRCQHCGVSENNTPAM-----RRGPAGPRTLCNACGLMW 256 (353)
Q Consensus 222 ~~~C~~C~~~~~~TP~W-----R~GP~G~~~LCNACGl~~ 256 (353)
...|.+|++.+.--+-. -.+++-..+.|+.||..|
T Consensus 39 I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 39 ITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 45677887654211111 125556678999999765
No 56
>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=20.05 E-value=72 Score=31.86 Aligned_cols=32 Identities=22% Similarity=0.613 Sum_probs=23.2
Q ss_pred ccCcccCCCCCCCcccccCCCCCcccchHHHHHHHh
Q 018626 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWAN 258 (353)
Q Consensus 223 ~~C~~C~~~~~~TP~WR~GP~G~~~LCNACGl~~~~ 258 (353)
+.|..|..++ ..|--.-.-.| .||+|--+-.+
T Consensus 2 ~~C~~C~~~~-t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMPT-TRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCCC-CCCCeeECCCC---CchhhhhHHhh
Confidence 5799999874 55654455556 99999987643
Done!