Query 018277
Match_columns 358
No_of_seqs 290 out of 801
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 07:38:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018277.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018277hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00202 ZnF_GATA Zinc finger D 99.5 5.3E-14 1.2E-18 105.6 4.1 44 224-269 1-44 (54)
2 PF06200 tify: tify domain; I 99.4 1.8E-13 3.9E-18 95.3 4.8 34 86-119 2-35 (36)
3 smart00401 ZnF_GATA zinc finge 99.4 1.2E-13 2.6E-18 102.8 3.2 45 222-268 3-48 (52)
4 PF00320 GATA: GATA zinc finge 99.4 1.8E-13 3.9E-18 94.7 1.6 36 225-262 1-36 (36)
5 PF06203 CCT: CCT motif; Inte 99.2 5.8E-12 1.3E-16 91.7 3.1 44 153-196 1-44 (45)
6 KOG1601 GATA-4/5/6 transcripti 98.4 1.5E-07 3.3E-12 84.4 3.3 46 222-269 199-244 (340)
7 COG5641 GAT1 GATA Zn-finger-co 98.0 4.7E-06 1E-10 86.8 3.8 53 217-271 153-210 (498)
8 PF09425 CCT_2: Divergent CCT 96.8 0.00075 1.6E-08 44.6 1.5 25 151-176 2-26 (27)
9 COG5641 GAT1 GATA Zn-finger-co 86.8 0.29 6.4E-06 51.7 1.3 50 222-272 297-346 (498)
10 KOG3554 Histone deacetylase co 68.6 6.1 0.00013 42.1 4.1 40 222-263 386-427 (693)
11 KOG1601 GATA-4/5/6 transcripti 67.0 2.2 4.9E-05 38.2 0.6 41 150-190 290-330 (340)
12 PF14803 Nudix_N_2: Nudix N-te 58.2 3.6 7.7E-05 28.5 0.2 30 223-254 1-30 (34)
13 PF10777 YlaC: Inner membrane 57.0 12 0.00027 34.1 3.4 26 91-116 95-120 (155)
14 PF13717 zinc_ribbon_4: zinc-r 56.8 2.7 5.9E-05 29.1 -0.6 33 223-256 3-35 (36)
15 KOG1819 FYVE finger-containing 54.1 12 0.00025 40.4 3.2 45 2-50 393-448 (990)
16 PF09889 DUF2116: Uncharacteri 47.9 9.9 0.00021 29.5 1.2 29 223-261 4-33 (59)
17 PRK11823 DNA repair protein Ra 47.3 6.5 0.00014 40.8 0.1 17 222-239 7-23 (446)
18 PF13619 KTSC: KTSC domain 46.4 35 0.00075 25.7 3.9 30 87-116 13-43 (60)
19 TIGR00416 sms DNA repair prote 46.3 7 0.00015 40.7 0.2 17 222-239 7-23 (454)
20 PF04810 zf-Sec23_Sec24: Sec23 45.2 9.6 0.00021 26.8 0.7 31 222-254 2-32 (40)
21 TIGR02098 MJ0042_CXXC MJ0042 f 42.0 4.5 9.8E-05 27.6 -1.4 33 223-256 3-35 (38)
22 smart00653 eIF2B_5 domain pres 40.2 11 0.00024 32.3 0.4 28 223-254 81-109 (110)
23 PF06689 zf-C4_ClpX: ClpX C4-t 39.1 17 0.00037 25.8 1.2 33 223-256 2-34 (41)
24 cd01121 Sms Sms (bacterial rad 37.5 12 0.00026 38.1 0.3 12 224-238 2-13 (372)
25 PF02701 zf-Dof: Dof domain, z 36.9 36 0.00077 27.0 2.7 46 222-269 5-53 (63)
26 PF01412 ArfGap: Putative GTPa 34.4 34 0.00074 29.0 2.5 36 222-261 13-48 (116)
27 PRK11788 tetratricopeptide rep 32.8 17 0.00037 35.0 0.5 24 222-255 354-377 (389)
28 PRK05978 hypothetical protein; 32.4 17 0.00037 32.9 0.4 33 222-259 33-65 (148)
29 COG5349 Uncharacterized protei 32.1 21 0.00046 31.7 0.9 40 215-259 14-53 (126)
30 COG1631 RPL42A Ribosomal prote 31.8 28 0.00062 29.4 1.5 21 221-241 67-87 (94)
31 PRK05342 clpX ATP-dependent pr 31.1 27 0.00058 36.1 1.6 30 222-253 9-38 (412)
32 PRK12775 putative trifunctiona 30.7 19 0.00042 41.2 0.6 36 219-261 818-855 (1006)
33 PF06677 Auto_anti-p27: Sjogre 30.0 20 0.00044 25.8 0.4 25 222-253 17-41 (41)
34 KOG3740 Uncharacterized conser 29.2 23 0.00049 39.0 0.7 36 222-259 462-500 (706)
35 COG3952 Predicted membrane pro 28.5 16 0.00035 31.7 -0.4 19 237-257 76-94 (113)
36 PF08271 TF_Zn_Ribbon: TFIIB z 27.9 24 0.00051 24.9 0.4 30 224-258 2-31 (43)
37 PF01783 Ribosomal_L32p: Ribos 27.8 15 0.00033 27.7 -0.7 21 222-253 26-46 (56)
38 TIGR00311 aIF-2beta translatio 27.6 20 0.00044 31.7 0.0 30 223-255 98-127 (133)
39 PRK03988 translation initiatio 27.2 21 0.00045 31.9 0.0 30 223-255 103-132 (138)
40 PRK12286 rpmF 50S ribosomal pr 26.9 21 0.00045 27.3 -0.0 22 223-255 28-49 (57)
41 PRK00420 hypothetical protein; 26.5 28 0.00061 30.2 0.7 30 222-258 23-52 (112)
42 PF14812 PBP1_TM: Transmembran 25.3 23 0.00051 29.2 0.0 19 30-48 37-55 (81)
43 PF13719 zinc_ribbon_5: zinc-r 25.1 16 0.00034 25.3 -0.9 33 223-256 3-35 (37)
44 PRK12336 translation initiatio 24.4 25 0.00053 33.0 -0.0 31 223-256 99-129 (201)
45 COG1645 Uncharacterized Zn-fin 24.1 27 0.00058 31.2 0.1 27 222-256 28-54 (131)
46 PRK14892 putative transcriptio 22.1 23 0.00049 30.1 -0.7 35 222-259 21-55 (99)
47 TIGR00244 transcriptional regu 22.1 34 0.00075 31.1 0.4 38 224-261 2-43 (147)
48 PF09297 zf-NADH-PPase: NADH p 21.4 31 0.00067 22.9 -0.0 28 222-255 3-30 (32)
49 COG2331 Uncharacterized protei 21.2 30 0.00064 28.6 -0.2 35 222-259 12-46 (82)
50 COG2816 NPY1 NTP pyrophosphohy 21.1 35 0.00075 34.0 0.2 30 223-258 112-141 (279)
51 KOG1598 Transcription initiati 21.1 45 0.00098 35.9 1.1 31 224-259 2-32 (521)
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=99.45 E-value=5.3e-14 Score=105.61 Aligned_cols=44 Identities=55% Similarity=1.149 Sum_probs=40.0
Q ss_pred cccccccCCCCccccccCCCCCcccchHHHHHHHhcCCCCCCCCCC
Q 018277 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTLRDLSKGG 269 (358)
Q Consensus 224 ~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~r~~sk~~ 269 (358)
.|+||+++ .||+||+||.|..+|||||||+|++++..|+..+..
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 49999994 699999999998999999999999999999887754
No 2
>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=99.43 E-value=1.8e-13 Score=95.28 Aligned_cols=34 Identities=38% Similarity=0.701 Sum_probs=32.0
Q ss_pred CCCcceeeeeecceEEEeCCCCHHHHHHHHHHhC
Q 018277 86 ASRTSELTLSFEGEVYVFPAVTPEKVQAVLLLLG 119 (358)
Q Consensus 86 ~~~tsQLTisy~GeV~VFdsVspeKvqaVLlLlG 119 (358)
++.++||||||+|+|+|||+|+++||++||+|++
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 5678999999999999999999999999999986
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.41 E-value=1.2e-13 Score=102.77 Aligned_cols=45 Identities=53% Similarity=1.060 Sum_probs=39.7
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHHHHhcCCC-CCCCCC
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTL-RDLSKG 268 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~-r~~sk~ 268 (358)
...|++|+++ .||+||+||.|..+|||||||+|++++.+ |+..+.
T Consensus 3 ~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~ 48 (52)
T smart00401 3 GRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLK 48 (52)
T ss_pred CCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCCCCccccc
Confidence 4689999995 69999999999999999999999999988 766543
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=99.36 E-value=1.8e-13 Score=94.74 Aligned_cols=36 Identities=56% Similarity=1.239 Sum_probs=28.0
Q ss_pred ccccccCCCCccccccCCCCCcccchHHHHHHHhcCCC
Q 018277 225 CQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTL 262 (358)
Q Consensus 225 C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~ 262 (358)
|.+|+++ .||+||+||.|..+|||+||++|++++++
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 8999995 69999999999889999999999998763
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=99.23 E-value=5.8e-12 Score=91.67 Aligned_cols=44 Identities=50% Similarity=0.761 Sum_probs=41.5
Q ss_pred HHHHHHHHHHhhhccccccceecchhHHHHhhhccccccccccc
Q 018277 153 RIASLVRFREKRKERCFDKKIRYSVRKEVAQRMHRKNGQFASLK 196 (358)
Q Consensus 153 R~AsL~RfREKRKeR~~~KkirYs~RK~~Aerm~RkKGrFas~k 196 (358)
|.++|.||++||+.|+|+|+|+|++||.+|+.++|.||||++..
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 57899999999999999999999999999999999999998654
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.41 E-value=1.5e-07 Score=84.40 Aligned_cols=46 Identities=48% Similarity=1.068 Sum_probs=38.6
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHHHHhcCCCCCCCCCC
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTLRDLSKGG 269 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~r~~sk~~ 269 (358)
...|.+|++ +.||+||++|.|+..||||||++|+++...|.+....
T Consensus 199 ~~~c~~~~~--~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~ 244 (340)
T KOG1601|consen 199 LRQCSNCGT--TKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKR 244 (340)
T ss_pred CcccCCCCC--CCCcceecCCCCCccccccchhhhhhcCccccccccC
Confidence 468999999 4799999999999999999999999997555544443
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=97.98 E-value=4.7e-06 Score=86.80 Aligned_cols=53 Identities=32% Similarity=0.574 Sum_probs=43.7
Q ss_pred CcccccccccccccCCCCccccccCCCC----CcccchHHHHHHHhcCCCC-CCCCCCCC
Q 018277 217 RPETVVRRCQHCGVSENNTPAMRRGPAG----PRTLCNACGLMWANKGTLR-DLSKGGRS 271 (358)
Q Consensus 217 ~~e~~~~~C~~Cg~~~~~TP~WR~GP~G----~~~LCNACGl~~~~~~~~r-~~sk~~~~ 271 (358)
..+.+...|.+|.+ +.||+|||+..+ +-.|||||||+|+-|+.+| +++.+...
T Consensus 153 ~~s~~~~vc~Nc~t--~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~ 210 (498)
T COG5641 153 DNSNQPHVCSNCKT--TSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDS 210 (498)
T ss_pred ccccccchhccccc--cCCccccccccccccCCccccccccccccccCCcCCCccccccc
Confidence 44455669999999 579999999994 4899999999999999999 77655433
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=96.75 E-value=0.00075 Score=44.60 Aligned_cols=25 Identities=52% Similarity=0.578 Sum_probs=10.0
Q ss_pred hHHHHHHHHHHHhhhccccccceecc
Q 018277 151 SRRIASLVRFREKRKERCFDKKIRYS 176 (358)
Q Consensus 151 s~R~AsL~RfREKRKeR~~~KkirYs 176 (358)
..|.+||.||.||||+|... +..|.
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 35899999999999999988 77775
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=86.85 E-value=0.29 Score=51.74 Aligned_cols=50 Identities=24% Similarity=0.240 Sum_probs=42.2
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHHHHhcCCCCCCCCCCCCC
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGTLRDLSKGGRSL 272 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~~r~~sk~~~~~ 272 (358)
...|.+|++. +.||.||+...-.-.+||+||++-+..+..+++.++....
T Consensus 297 ~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n 346 (498)
T COG5641 297 DKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPN 346 (498)
T ss_pred hcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCCChh
Confidence 5689999876 5799999998887899999999999999999888754433
No 10
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=68.57 E-value=6.1 Score=42.06 Aligned_cols=40 Identities=25% Similarity=0.581 Sum_probs=31.4
Q ss_pred cccccccccCCCCcccc--ccCCCCCcccchHHHHHHHhcCCCC
Q 018277 222 VRRCQHCGVSENNTPAM--RRGPAGPRTLCNACGLMWANKGTLR 263 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~W--R~GP~G~~~LCNACGl~~~~~~~~r 263 (358)
.+.|-.|+++ ..-+| +-+|.-...||..|=++|+|-+-+.
T Consensus 386 g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGLk 427 (693)
T KOG3554|consen 386 GRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGLK 427 (693)
T ss_pred CCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCcC
Confidence 4689999995 56666 4456667899999999999987553
No 11
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=66.96 E-value=2.2 Score=38.25 Aligned_cols=41 Identities=44% Similarity=0.680 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHHHhhhccccccceecchhHHHHhhhccccc
Q 018277 150 LSRRIASLVRFREKRKERCFDKKIRYSVRKEVAQRMHRKNG 190 (358)
Q Consensus 150 ls~R~AsL~RfREKRKeR~~~KkirYs~RK~~Aerm~RkKG 190 (358)
...|.+.+.|++++++.|.|+++++|..++..++.+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 45789999999999999999999999999998888888776
No 12
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=58.24 E-value=3.6 Score=28.52 Aligned_cols=30 Identities=30% Similarity=0.744 Sum_probs=14.6
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGL 254 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl 254 (358)
+.|.+||.. .+..-=.|-.-.+..|.+||.
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 369999973 122222445556899999995
No 13
>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=56.99 E-value=12 Score=34.14 Aligned_cols=26 Identities=23% Similarity=0.473 Sum_probs=22.0
Q ss_pred eeeeeecceEEEeCCCCHHHHHHHHH
Q 018277 91 ELTLSFEGEVYVFPAVTPEKVQAVLL 116 (358)
Q Consensus 91 QLTisy~GeV~VFdsVspeKvqaVLl 116 (358)
-|..-|+||||+...||++-+++||.
T Consensus 95 DLRVCYNGEWy~tr~vs~~ai~~iL~ 120 (155)
T PF10777_consen 95 DLRVCYNGEWYNTRFVSDQAIDKILQ 120 (155)
T ss_pred EEeEEEcceeeeeccCCHHHHHHHHc
Confidence 45668999999999999998887763
No 14
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=56.84 E-value=2.7 Score=29.11 Aligned_cols=33 Identities=21% Similarity=0.627 Sum_probs=28.6
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~ 256 (358)
..|.+|++. ...+..+-.+.|...-|-.||-.|
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 479999987 578999989999999999999776
No 15
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=54.08 E-value=12 Score=40.44 Aligned_cols=45 Identities=42% Similarity=0.673 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCCcccc-----------cCCCCccccCCCCCCCCCCCcccccCCCccccc
Q 018277 2 AAANPQPLQARPFEEH-----------ARAPPIQIEDEDGDYEDGEGMDDIDEGNINSIN 50 (358)
Q Consensus 2 ~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (358)
+++-|-|- +.|+| .+.|+++.+|+|++.+|||.. |++|.+|+|-+
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 346888888877655555443 35666676643
No 16
>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=47.92 E-value=9.9 Score=29.50 Aligned_cols=29 Identities=21% Similarity=0.697 Sum_probs=22.2
Q ss_pred ccccccccCCCCccccccCCCCCcccc-hHHHHHHHhcCC
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLC-NACGLMWANKGT 261 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LC-NACGl~~~~~~~ 261 (358)
++|..||.+. | .. +..| ..|+.-|.++.+
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 6899999863 3 22 7899 599999988743
No 17
>PRK11823 DNA repair protein RadA; Provisional
Probab=47.35 E-value=6.5 Score=40.79 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=11.1
Q ss_pred cccccccccCCCCccccc
Q 018277 222 VRRCQHCGVSENNTPAMR 239 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR 239 (358)
..+|.+||.. ...|.||
T Consensus 7 ~y~C~~Cg~~-~~~~~g~ 23 (446)
T PRK11823 7 AYVCQECGAE-SPKWLGR 23 (446)
T ss_pred eEECCcCCCC-CcccCee
Confidence 4689999985 2344443
No 18
>PF13619 KTSC: KTSC domain
Probab=46.37 E-value=35 Score=25.73 Aligned_cols=30 Identities=33% Similarity=0.439 Sum_probs=24.4
Q ss_pred CCcceeee-eecceEEEeCCCCHHHHHHHHH
Q 018277 87 SRTSELTL-SFEGEVYVFPAVTPEKVQAVLL 116 (358)
Q Consensus 87 ~~tsQLTi-sy~GeV~VFdsVspeKvqaVLl 116 (358)
..+..|.| |-.|.+|.|..||++.++++|.
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 34567887 4578999999999999999875
No 19
>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=46.34 E-value=7 Score=40.73 Aligned_cols=17 Identities=29% Similarity=0.512 Sum_probs=11.9
Q ss_pred cccccccccCCCCccccc
Q 018277 222 VRRCQHCGVSENNTPAMR 239 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR 239 (358)
..+|.+||.. ...|+||
T Consensus 7 ~y~C~~Cg~~-~~~~~g~ 23 (454)
T TIGR00416 7 KFVCQHCGAD-SPKWQGK 23 (454)
T ss_pred eEECCcCCCC-CccccEE
Confidence 4789999996 2455554
No 20
>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=45.22 E-value=9.6 Score=26.81 Aligned_cols=31 Identities=29% Similarity=0.632 Sum_probs=20.6
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHH
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGL 254 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl 254 (358)
+.+|.+|++ -.-|...-...|....|+-|+.
T Consensus 2 p~rC~~C~a--ylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRA--YLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT----BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCC--EECCcceEcCCCCEEECcCCCC
Confidence 358999998 4688888888888899999986
No 21
>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=42.00 E-value=4.5 Score=27.57 Aligned_cols=33 Identities=27% Similarity=0.735 Sum_probs=24.2
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~ 256 (358)
..|.+|++. ...+...-+..|....|-.||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 469999886 356666666667778899998765
No 22
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=40.19 E-value=11 Score=32.34 Aligned_cols=28 Identities=29% Similarity=0.670 Sum_probs=20.4
Q ss_pred ccccccccCCCCccccccCCCCC-cccchHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGP-RTLCNACGL 254 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~-~~LCNACGl 254 (358)
-.|..|+-+. |-+-+.+ +- -.-|+|||-
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 4799999974 8888772 22 245999994
No 23
>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=39.06 E-value=17 Score=25.79 Aligned_cols=33 Identities=30% Similarity=0.749 Sum_probs=21.7
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~ 256 (358)
.+|+-||.++..+-..=.||.+ ...|+.|=...
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 4799999987666666688977 79999996543
No 24
>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=37.46 E-value=12 Score=38.10 Aligned_cols=12 Identities=33% Similarity=0.938 Sum_probs=8.7
Q ss_pred cccccccCCCCcccc
Q 018277 224 RCQHCGVSENNTPAM 238 (358)
Q Consensus 224 ~C~~Cg~~~~~TP~W 238 (358)
.|.+||.. +|.|
T Consensus 2 ~c~~cg~~---~~~~ 13 (372)
T cd01121 2 VCSECGYV---SPKW 13 (372)
T ss_pred CCCCCCCC---CCCc
Confidence 69999985 4555
No 25
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=36.88 E-value=36 Score=26.95 Aligned_cols=46 Identities=33% Similarity=0.715 Sum_probs=32.6
Q ss_pred cccccccccCCCCccccc---cCCCCCcccchHHHHHHHhcCCCCCCCCCC
Q 018277 222 VRRCQHCGVSENNTPAMR---RGPAGPRTLCNACGLMWANKGTLRDLSKGG 269 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR---~GP~G~~~LCNACGl~~~~~~~~r~~sk~~ 269 (358)
...|..|... .|-+-= --..-|+..|-+|-.+|-..|++|.+.-++
T Consensus 5 ~~~CPRC~S~--nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvgg 53 (63)
T PF02701_consen 5 PLPCPRCDST--NTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGG 53 (63)
T ss_pred CCCCCCcCCC--CCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCC
Confidence 4678888874 342211 123346899999999999999999885554
No 26
>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=34.36 E-value=34 Score=29.00 Aligned_cols=36 Identities=25% Similarity=0.527 Sum_probs=26.2
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHHHHhcCC
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANKGT 261 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~~~ 261 (358)
...|+.|+.. -|.|-.=..| ..||-.|.-.++.-|.
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 4689999984 6899999999 8999999988887664
No 27
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=32.83 E-value=17 Score=34.98 Aligned_cols=24 Identities=29% Similarity=0.692 Sum_probs=14.9
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHH
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (358)
.|.|.|||.. ..+|.| +|-.||-+
T Consensus 354 ~~~c~~cg~~-~~~~~~---------~c~~c~~~ 377 (389)
T PRK11788 354 RYRCRNCGFT-ARTLYW---------HCPSCKAW 377 (389)
T ss_pred CEECCCCCCC-Ccccee---------ECcCCCCc
Confidence 4788888885 234443 56666643
No 28
>PRK05978 hypothetical protein; Provisional
Probab=32.42 E-value=17 Score=32.93 Aligned_cols=33 Identities=30% Similarity=0.640 Sum_probs=25.1
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHHHHhc
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~ 259 (358)
..+|-+||.- .++ +|...-..-|.+||+.|..+
T Consensus 33 ~grCP~CG~G----~LF-~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 33 RGRCPACGEG----KLF-RAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred cCcCCCCCCC----ccc-ccccccCCCccccCCccccC
Confidence 5689999983 344 46666678999999998765
No 29
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.12 E-value=21 Score=31.66 Aligned_cols=40 Identities=33% Similarity=0.606 Sum_probs=28.6
Q ss_pred CCCcccccccccccccCCCCccccccCCCCCcccchHHHHHHHhc
Q 018277 215 TPRPETVVRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (358)
Q Consensus 215 ~~~~e~~~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~ 259 (358)
++-......+|-+||.- .-.+|.--...-|.|||+-|-.+
T Consensus 14 ~pi~~Gl~grCP~CGeG-----rLF~gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 14 TPIKRGLRGRCPRCGEG-----RLFRGFLKVVPACEACGLDYGFA 53 (126)
T ss_pred cHHHHHhcCCCCCCCCc-----hhhhhhcccCchhhhccccccCC
Confidence 33333445689999973 34567777788999999988665
No 30
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=31.80 E-value=28 Score=29.45 Aligned_cols=21 Identities=33% Similarity=0.767 Sum_probs=17.4
Q ss_pred ccccccccccCCCCccccccC
Q 018277 221 VVRRCQHCGVSENNTPAMRRG 241 (358)
Q Consensus 221 ~~~~C~~Cg~~~~~TP~WR~G 241 (358)
+..+|.-|+.....+|.||-+
T Consensus 67 Lr~~Ct~Cgkah~~~~~~Rak 87 (94)
T COG1631 67 LRLRCTECGKAHQRTPGFRAK 87 (94)
T ss_pred EEEEehhhccccccCcceeee
Confidence 467899999988777899965
No 31
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=31.07 E-value=27 Score=36.14 Aligned_cols=30 Identities=27% Similarity=0.703 Sum_probs=24.6
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHH
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACG 253 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACG 253 (358)
..+|+.||.+...++..-.||.. ..|+.|=
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~Ci 38 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDECI 38 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchHH
Confidence 35899999988778888888844 7999993
No 32
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=30.73 E-value=19 Score=41.19 Aligned_cols=36 Identities=28% Similarity=0.559 Sum_probs=25.7
Q ss_pred ccccccccccccCCCCccccccCCCCCcccchHHHH--HHHhcCC
Q 018277 219 ETVVRRCQHCGVSENNTPAMRRGPAGPRTLCNACGL--MWANKGT 261 (358)
Q Consensus 219 e~~~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl--~~~~~~~ 261 (358)
..+.|+|..|+. |.+=...|+| .|-+||- .|-++++
T Consensus 818 ~~~~~~~~~~~~----~~~~~~~~~~---~~~~~~~~~~~~~~~~ 855 (1006)
T PRK12775 818 SELQWRCDDCGK----VSEGFAFPYG---MCPACGGKLQALDRRK 855 (1006)
T ss_pred cceeeehhhhcc----ccccccCCcC---cCcccccchhhhhccC
Confidence 346799999987 6666777887 8999994 3444444
No 33
>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=30.00 E-value=20 Score=25.77 Aligned_cols=25 Identities=44% Similarity=1.095 Sum_probs=18.6
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHH
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACG 253 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACG 253 (358)
...|..|+ +|++| .-.| +.+|-+|+
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 35799995 69999 2345 78999885
No 34
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.17 E-value=23 Score=39.01 Aligned_cols=36 Identities=22% Similarity=0.482 Sum_probs=28.9
Q ss_pred cccccccccCCCCccccccCCCC---CcccchHHHHHHHhc
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAG---PRTLCNACGLMWANK 259 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G---~~~LCNACGl~~~~~ 259 (358)
+..|..|.+ ..||.|+.-+.+ ...+|.+|=---.|+
T Consensus 462 P~~caqckt--dftp~wk~ekstq~d~~i~cE~cvtSnqkk 500 (706)
T KOG3740|consen 462 PYACAQCKT--DFTPAWKKEKSTQADAAIVCENCVTSNQKK 500 (706)
T ss_pred chhhhhccc--ccccccccccccCcchHHHHHhhhhhcccc
Confidence 568999999 579999998888 458999997655443
No 35
>COG3952 Predicted membrane protein [Function unknown]
Probab=28.54 E-value=16 Score=31.73 Aligned_cols=19 Identities=37% Similarity=0.546 Sum_probs=14.6
Q ss_pred ccccCCCCCcccchHHHHHHH
Q 018277 237 AMRRGPAGPRTLCNACGLMWA 257 (358)
Q Consensus 237 ~WR~GP~G~~~LCNACGl~~~ 257 (358)
.||.+|-+ .||++||++-.
T Consensus 76 i~~~DpV~--Vl~~~~glF~~ 94 (113)
T COG3952 76 IRRQDPVF--VLGQACGLFIY 94 (113)
T ss_pred HHhcchHH--HHHHhhhHHHH
Confidence 45667776 89999999754
No 36
>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=27.92 E-value=24 Score=24.91 Aligned_cols=30 Identities=27% Similarity=0.762 Sum_probs=17.6
Q ss_pred cccccccCCCCccccccCCCCCcccchHHHHHHHh
Q 018277 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWAN 258 (358)
Q Consensus 224 ~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~ 258 (358)
+|.+|+.. . .--+.-.| ...|..||+...-
T Consensus 2 ~Cp~Cg~~---~-~~~D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSK---E-IVFDPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSS---E-EEEETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCC---c-eEEcCCCC-eEECCCCCCEeec
Confidence 58888883 1 33333333 7799999976543
No 37
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=27.83 E-value=15 Score=27.71 Aligned_cols=21 Identities=33% Similarity=1.053 Sum_probs=16.0
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHH
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACG 253 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACG 253 (358)
.-.|.+||.. .-+..+|..||
T Consensus 26 l~~c~~cg~~-----------~~~H~vc~~cG 46 (56)
T PF01783_consen 26 LVKCPNCGEP-----------KLPHRVCPSCG 46 (56)
T ss_dssp EEESSSSSSE-----------ESTTSBCTTTB
T ss_pred eeeeccCCCE-----------ecccEeeCCCC
Confidence 4579999973 22368999999
No 38
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=27.64 E-value=20 Score=31.75 Aligned_cols=30 Identities=27% Similarity=0.622 Sum_probs=21.0
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (358)
-.|..|+-+. |-+-+++- ---.-|+|||-.
T Consensus 98 VlC~~C~sPd--T~l~k~~r-~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPD--TRIIKEGR-VSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCC--cEEEEeCC-eEEEecccCCCC
Confidence 4799999975 77777531 112479999954
No 39
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=27.22 E-value=21 Score=31.89 Aligned_cols=30 Identities=30% Similarity=0.604 Sum_probs=21.0
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (358)
-.|..|+-+. |-+-+++- ---.-|+|||-.
T Consensus 103 VlC~~C~spd--T~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGSPD--TKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred EECCCCCCCC--cEEEEcCC-eEEEEcccCCCC
Confidence 4799999975 77777531 113679999953
No 40
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=26.92 E-value=21 Score=27.34 Aligned_cols=22 Identities=32% Similarity=0.964 Sum_probs=16.4
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (358)
-.|.+||... -+..+|..||.|
T Consensus 28 ~~C~~CG~~~-----------~~H~vC~~CG~Y 49 (57)
T PRK12286 28 VECPNCGEPK-----------LPHRVCPSCGYY 49 (57)
T ss_pred eECCCCCCcc-----------CCeEECCCCCcC
Confidence 4799999842 226899999954
No 41
>PRK00420 hypothetical protein; Validated
Probab=26.52 E-value=28 Score=30.22 Aligned_cols=30 Identities=23% Similarity=0.691 Sum_probs=22.6
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHHHHh
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWAN 258 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~ 258 (358)
..+|..||+ |+.|. ..| ...|-.||..+..
T Consensus 23 ~~~CP~Cg~-----pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCGL-----PLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCCC-----cceec-CCC-ceECCCCCCeeee
Confidence 457999985 67764 444 8999999987654
No 42
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=25.35 E-value=23 Score=29.17 Aligned_cols=19 Identities=37% Similarity=0.588 Sum_probs=0.0
Q ss_pred CCCCCCCCcccccCCCccc
Q 018277 30 GDYEDGEGMDDIDEGNINS 48 (358)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~~ 48 (358)
++|.|||..|+.++.+|..
T Consensus 37 dd~~DDD~dDdeeee~m~r 55 (81)
T PF14812_consen 37 DDYEDDDDDDDEEEEPMPR 55 (81)
T ss_dssp -------------------
T ss_pred cccccccccchhhcccccc
Confidence 5555555545455555543
No 43
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=25.12 E-value=16 Score=25.32 Aligned_cols=33 Identities=21% Similarity=0.598 Sum_probs=25.1
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~ 256 (358)
..|-+|++. ...|.=+-++.|.+.-|-.||-.|
T Consensus 3 i~CP~C~~~-f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTR-FRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCce-EEcCHHHcccCCcEEECCCCCcEe
Confidence 468889886 467777777777788888888766
No 44
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=24.45 E-value=25 Score=32.99 Aligned_cols=31 Identities=26% Similarity=0.584 Sum_probs=21.8
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHHHH
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~ 256 (358)
-.|..|+-+. |-+-+.+- ---.-|+|||-..
T Consensus 99 V~C~~C~~pd--T~l~k~~~-~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPD--TRLVKEDR-VLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCC--cEEEEcCC-eEEEEcccCCCCc
Confidence 4799999975 77777641 1135799999654
No 45
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=24.06 E-value=27 Score=31.24 Aligned_cols=27 Identities=33% Similarity=0.950 Sum_probs=21.8
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHHH
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMW 256 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~ 256 (358)
..+|.-||+ |++| =+| ...|-.||.+.
T Consensus 28 ~~hCp~Cg~-----PLF~--KdG-~v~CPvC~~~~ 54 (131)
T COG1645 28 AKHCPKCGT-----PLFR--KDG-EVFCPVCGYRE 54 (131)
T ss_pred HhhCcccCC-----ccee--eCC-eEECCCCCceE
Confidence 568999985 8999 556 89999999744
No 46
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.12 E-value=23 Score=30.09 Aligned_cols=35 Identities=20% Similarity=0.431 Sum_probs=23.2
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHHHHhc
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~ 259 (358)
.-.|.+|+...-..+.-| ..+...|-.||.++.+.
T Consensus 21 ~f~CP~Cge~~v~v~~~k---~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 21 IFECPRCGKVSISVKIKK---NIAIITCGNCGLYTEFE 55 (99)
T ss_pred EeECCCCCCeEeeeecCC---CcceEECCCCCCccCEE
Confidence 357999995321223333 34578999999998664
No 47
>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=22.06 E-value=34 Score=31.09 Aligned_cols=38 Identities=18% Similarity=0.336 Sum_probs=27.2
Q ss_pred cccccccCCCCccccccCCCC----CcccchHHHHHHHhcCC
Q 018277 224 RCQHCGVSENNTPAMRRGPAG----PRTLCNACGLMWANKGT 261 (358)
Q Consensus 224 ~C~~Cg~~~~~TP~WR~GP~G----~~~LCNACGl~~~~~~~ 261 (358)
+|..|+...+..=-=|...+| .+.-|.+||.+|-.--+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyEr 43 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFER 43 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeee
Confidence 688998866555555666666 34799999999876543
No 48
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=21.45 E-value=31 Score=22.90 Aligned_cols=28 Identities=32% Similarity=0.756 Sum_probs=15.0
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHH
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLM 255 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~ 255 (358)
.+.|..||.. ...-+.|....|.+||..
T Consensus 3 ~rfC~~CG~~------t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAP------TKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--B------EEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCcc------ccCCCCcCEeECCCCcCE
Confidence 3579999984 233455667899999864
No 49
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.24 E-value=30 Score=28.55 Aligned_cols=35 Identities=29% Similarity=0.564 Sum_probs=24.4
Q ss_pred cccccccccCCCCccccccCCCCCcccchHHHHHHHhc
Q 018277 222 VRRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (358)
Q Consensus 222 ~~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~ 259 (358)
..+|..|+-.-.-...+++.| -+.|.+||-++++.
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~ 46 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDP---LTTCEECGARLKKL 46 (82)
T ss_pred EEeecccchHHHHHHhcccCc---cccChhhChHHHHh
Confidence 457999986422345555555 56999999988775
No 50
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=21.10 E-value=35 Score=34.02 Aligned_cols=30 Identities=27% Similarity=0.562 Sum_probs=19.3
Q ss_pred ccccccccCCCCccccccCCCCCcccchHHHHHHHh
Q 018277 223 RRCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWAN 258 (358)
Q Consensus 223 ~~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~ 258 (358)
+.|..||+. .. ....|....|+.||.++--
T Consensus 112 RFCg~CG~~--~~----~~~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 112 RFCGRCGTK--TY----PREGGWARVCPKCGHEHFP 141 (279)
T ss_pred cCCCCCCCc--Cc----cccCceeeeCCCCCCccCC
Confidence 458888883 12 2234556789999887643
No 51
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=21.09 E-value=45 Score=35.92 Aligned_cols=31 Identities=32% Similarity=0.726 Sum_probs=21.9
Q ss_pred cccccccCCCCccccccCCCCCcccchHHHHHHHhc
Q 018277 224 RCQHCGVSENNTPAMRRGPAGPRTLCNACGLMWANK 259 (358)
Q Consensus 224 ~C~~Cg~~~~~TP~WR~GP~G~~~LCNACGl~~~~~ 259 (358)
.|.||+.+ .+. |+--.| -..|.+||......
T Consensus 2 ~C~~C~~s---~fe-~d~a~g-~~~C~~CG~v~E~~ 32 (521)
T KOG1598|consen 2 VCKNCGGS---NFE-RDEATG-NLYCTACGTVLEYN 32 (521)
T ss_pred cCCCCCCC---Ccc-cccccC-Cceeccccceeecc
Confidence 69999984 444 333444 79999999876554
Done!