Query 024786
Match_columns 262
No_of_seqs 154 out of 215
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 07:24:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024786.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024786hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02701 zf-Dof: Dof domain, z 100.0 1.1E-37 2.4E-42 232.2 4.0 62 33-94 2-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 94.1 0.027 5.9E-07 47.6 1.6 35 36-72 105-141 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 94.0 0.047 1E-06 37.5 2.5 29 35-69 17-45 (46)
4 COG3677 Transposase and inacti 93.8 0.043 9.3E-07 45.5 2.3 36 36-73 30-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 92.9 0.066 1.4E-06 36.3 1.7 31 36-68 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 91.7 0.2 4.3E-06 34.1 2.8 37 37-73 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 89.2 0.34 7.4E-06 32.7 2.3 35 38-72 2-39 (39)
8 PF04216 FdhE: Protein involve 84.5 0.44 9.5E-06 43.1 1.1 37 36-72 211-249 (290)
9 PHA02998 RNA polymerase subuni 84.3 1 2.2E-05 40.8 3.2 41 33-73 140-183 (195)
10 PF13453 zf-TFIIB: Transcripti 84.3 0.29 6.3E-06 32.9 -0.1 37 38-79 1-37 (41)
11 TIGR01384 TFS_arch transcripti 81.0 2.1 4.6E-05 33.1 3.5 39 36-74 62-103 (104)
12 cd00202 ZnF_GATA Zinc finger D 76.2 2.3 5.1E-05 30.7 2.3 40 38-80 1-40 (54)
13 TIGR01385 TFSII transcription 75.1 2.7 5.8E-05 39.5 3.0 41 32-72 254-297 (299)
14 TIGR00244 transcriptional regu 69.7 3.4 7.4E-05 35.9 2.2 44 38-81 2-48 (147)
15 PF04981 NMD3: NMD3 family ; 67.0 3 6.4E-05 37.0 1.3 36 39-74 1-48 (236)
16 PRK14810 formamidopyrimidine-D 66.9 4 8.6E-05 37.2 2.1 30 35-69 243-272 (272)
17 TIGR01562 FdhE formate dehydro 65.9 4.3 9.2E-05 38.5 2.2 36 36-72 224-263 (305)
18 PHA00626 hypothetical protein 65.3 4.5 9.8E-05 30.8 1.8 36 38-75 2-37 (59)
19 PF06220 zf-U1: U1 zinc finger 65.2 2.6 5.6E-05 28.6 0.5 17 59-75 1-17 (38)
20 smart00401 ZnF_GATA zinc finge 64.6 5.1 0.00011 28.5 1.9 40 35-77 2-41 (52)
21 PRK14811 formamidopyrimidine-D 62.9 5.3 0.00012 36.3 2.2 30 36-70 235-264 (269)
22 PRK00464 nrdR transcriptional 62.1 5.7 0.00012 34.3 2.1 45 37-81 1-48 (154)
23 PRK01103 formamidopyrimidine/5 60.8 6.1 0.00013 35.8 2.2 30 35-69 244-273 (274)
24 PRK03564 formate dehydrogenase 59.8 6.1 0.00013 37.6 2.1 36 37-73 227-264 (309)
25 KOG1819 FYVE finger-containing 57.9 6.2 0.00013 41.3 1.9 55 10-73 875-929 (990)
26 PRK10445 endonuclease VIII; Pr 57.6 7.1 0.00015 35.4 2.0 30 35-69 234-263 (263)
27 PF09526 DUF2387: Probable met 56.9 8.2 0.00018 29.6 2.0 32 36-70 8-39 (71)
28 PRK13945 formamidopyrimidine-D 56.4 8 0.00017 35.3 2.2 29 36-69 254-282 (282)
29 KOG2906 RNA polymerase III sub 51.7 12 0.00025 31.4 2.2 38 35-72 64-104 (105)
30 PF14690 zf-ISL3: zinc-finger 50.2 8 0.00017 25.7 0.9 11 36-46 2-12 (47)
31 TIGR00577 fpg formamidopyrimid 50.0 11 0.00025 34.2 2.1 29 35-68 244-272 (272)
32 PRK00432 30S ribosomal protein 47.8 10 0.00022 27.2 1.1 27 35-69 19-45 (50)
33 PF08273 Prim_Zn_Ribbon: Zinc- 44.1 14 0.00031 25.6 1.4 32 36-69 3-34 (40)
34 COG1327 Predicted transcriptio 44.0 14 0.00031 32.7 1.6 43 38-80 2-47 (156)
35 PRK14892 putative transcriptio 42.8 24 0.00051 28.7 2.7 42 27-72 12-53 (99)
36 PF05129 Elf1: Transcription e 42.2 14 0.00031 28.6 1.3 46 26-72 12-57 (81)
37 PF14354 Lar_restr_allev: Rest 41.2 23 0.0005 24.8 2.1 35 35-69 2-37 (61)
38 PF14599 zinc_ribbon_6: Zinc-r 40.7 11 0.00025 28.2 0.5 12 37-48 49-60 (61)
39 COG0266 Nei Formamidopyrimidin 37.2 23 0.0005 33.4 2.0 30 35-69 244-273 (273)
40 COG4260 Membrane protease subu 36.7 13 0.00028 36.3 0.3 35 33-69 303-342 (345)
41 TIGR03655 anti_R_Lar restricti 36.3 33 0.00071 24.1 2.2 33 37-70 2-35 (53)
42 PF01807 zf-CHC2: CHC2 zinc fi 36.1 24 0.00053 27.4 1.7 31 36-70 33-63 (97)
43 PF07282 OrfB_Zn_ribbon: Putat 34.4 23 0.00051 25.2 1.3 32 35-73 27-58 (69)
44 PF06827 zf-FPG_IleRS: Zinc fi 33.1 20 0.00042 22.5 0.6 27 37-68 2-28 (30)
45 KOG2691 RNA polymerase II subu 32.9 35 0.00077 28.9 2.3 41 31-73 68-113 (113)
46 PF08274 PhnA_Zn_Ribbon: PhnA 32.9 20 0.00044 23.6 0.7 28 37-72 3-30 (30)
47 TIGR02443 conserved hypothetic 31.4 37 0.00079 25.8 1.9 30 36-68 9-38 (59)
48 TIGR01031 rpmF_bact ribosomal 28.9 46 0.001 24.2 2.1 28 31-70 21-48 (55)
49 KOG3554 Histone deacetylase co 28.5 58 0.0013 34.0 3.4 72 8-80 358-429 (693)
50 smart00661 RPOL9 RNA polymeras 27.8 39 0.00085 22.7 1.4 32 38-74 2-33 (52)
51 smart00778 Prim_Zn_Ribbon Zinc 27.0 53 0.0011 22.5 1.9 31 35-68 2-32 (37)
52 PF05876 Terminase_GpA: Phage 26.2 42 0.00091 33.7 1.9 43 36-79 200-247 (557)
53 COG1997 RPL43A Ribosomal prote 26.2 43 0.00092 27.4 1.6 43 34-83 33-75 (89)
54 TIGR00686 phnA alkylphosphonat 25.8 47 0.001 28.0 1.8 31 37-75 3-33 (109)
55 PRK10220 hypothetical protein; 25.7 51 0.0011 27.8 2.0 31 37-75 4-34 (111)
56 PF07383 DUF1496: Protein of u 25.5 50 0.0011 24.6 1.7 15 47-61 12-26 (56)
57 PF01873 eIF-5_eIF-2B: Domain 24.8 66 0.0014 26.8 2.5 29 37-69 94-122 (125)
58 COG1594 RPB9 DNA-directed RNA 24.7 80 0.0017 25.8 3.0 38 36-73 72-112 (113)
59 PF03966 Trm112p: Trm112p-like 24.2 38 0.00082 24.7 0.9 17 55-71 47-63 (68)
60 PF06044 DRP: Dam-replacing fa 23.7 31 0.00067 32.6 0.5 34 36-73 31-65 (254)
61 PF06403 Lamprin: Lamprin; In 23.2 59 0.0013 27.9 2.0 34 171-206 41-74 (138)
62 smart00451 ZnF_U1 U1-like zinc 21.4 43 0.00093 20.6 0.6 16 60-75 2-17 (35)
63 PRK00564 hypA hydrogenase nick 20.3 70 0.0015 26.0 1.8 9 39-47 91-99 (117)
64 PF08271 TF_Zn_Ribbon: TFIIB z 20.0 68 0.0015 21.5 1.4 28 38-71 2-29 (43)
No 1
>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=100.00 E-value=1.1e-37 Score=232.19 Aligned_cols=62 Identities=76% Similarity=1.534 Sum_probs=59.0
Q ss_pred CCCCcCCCCCcCCCceeeeecccCCCCCcccccccccccccCcccccccCCCCcccCCCCCC
Q 024786 33 EQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCR 94 (262)
Q Consensus 33 e~e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnVPVGGG~RKnk~~s~ 94 (262)
+++.++||||+|++|||||||||+++||||||++|+||||+||+|||||||||+||+|++++
T Consensus 2 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~s 63 (63)
T PF02701_consen 2 PEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSSS 63 (63)
T ss_pred CccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCCC
Confidence 56789999999999999999999999999999999999999999999999999999987653
No 2
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=94.07 E-value=0.027 Score=47.62 Aligned_cols=35 Identities=23% Similarity=0.655 Sum_probs=27.5
Q ss_pred CcCCCCCcCCCceeeeecccCC--CCCcccccccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNF--SQPRHFCKSCRRYWT 72 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~--~QPR~fCk~CrRyWT 72 (262)
..+||||.|.+|+.. +.+-. ++.-|+|++|+.=|.
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf~ 141 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPFE 141 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcHh
Confidence 479999999999964 55544 467799999997554
No 3
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=94.02 E-value=0.047 Score=37.51 Aligned_cols=29 Identities=38% Similarity=0.839 Sum_probs=23.2
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 69 (262)
+...||+|.+. +...+.+ +.+|.|++|++
T Consensus 17 ~g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 34679999998 6655655 78999999986
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.80 E-value=0.043 Score=45.50 Aligned_cols=36 Identities=33% Similarity=0.657 Sum_probs=28.5
Q ss_pred CcCCCCCcCCCceeeeecccCCCCCccccccccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTH 73 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~ 73 (262)
...||+|.+.+ +-=+.-+.....||.|++|++-|+.
T Consensus 30 ~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 30 KVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred cCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 46899999999 3335555555999999999999974
No 5
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=92.94 E-value=0.066 Score=36.32 Aligned_cols=31 Identities=42% Similarity=0.756 Sum_probs=21.8
Q ss_pred CcCCCCCcCCCceeeeecccCCC-CCcccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFS-QPRHFCKSCR 68 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~-QPR~fCk~Cr 68 (262)
.+.||+|.+++.- |=|-.+.. ..||+|++|+
T Consensus 5 ~v~CP~C~s~~~v--~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEGV--KKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCcc--eeCCCCCCCCEeEecCcCC
Confidence 4689999998721 23444433 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=91.67 E-value=0.2 Score=34.14 Aligned_cols=37 Identities=24% Similarity=0.753 Sum_probs=28.6
Q ss_pred cCCCCCcCCCceeeeecccCCCCC---ccccccccccccc
Q 024786 37 LPCPRCESTNTKFCYYNNYNFSQP---RHFCKSCRRYWTH 73 (262)
Q Consensus 37 ~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRyWT~ 73 (262)
.+||+|...+.-|-..+-.+...| -|.|.+|...|..
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 379999988777766666666555 3999999999963
No 7
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=89.15 E-value=0.34 Score=32.73 Aligned_cols=35 Identities=23% Similarity=0.692 Sum_probs=24.5
Q ss_pred CCCCCcCCCceeeeecccCCCCCc---ccccccccccc
Q 024786 38 PCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWT 72 (262)
Q Consensus 38 ~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT 72 (262)
+||.|...+.-|--.+......|- |.|.+|..-|+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 799999988776555666555553 99999999985
No 8
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=84.54 E-value=0.44 Score=43.10 Aligned_cols=37 Identities=27% Similarity=0.643 Sum_probs=18.4
Q ss_pred CcCCCCCcCC-CceeeeecccCCCCC-cccccccccccc
Q 024786 36 QLPCPRCEST-NTKFCYYNNYNFSQP-RHFCKSCRRYWT 72 (262)
Q Consensus 36 ~~~CPRC~S~-nTKFcYyNNy~~~QP-R~fCk~CrRyWT 72 (262)
...||.|..+ ..++-||..-....- -+.|..|+.|+-
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 3589999888 456777743333333 399999999983
No 9
>PHA02998 RNA polymerase subunit; Provisional
Probab=84.35 E-value=1 Score=40.83 Aligned_cols=41 Identities=29% Similarity=0.699 Sum_probs=34.6
Q ss_pred CCCCcCCCCCcCCCceeeeecccCCCCCc---cccccccccccc
Q 024786 33 EQEQLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWTH 73 (262)
Q Consensus 33 e~e~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~ 73 (262)
+....+||+|...++-|--.|-++-..|- |.|..|..-|.-
T Consensus 140 kkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 140 EKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 33568999999999999888888888885 899999999963
No 10
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=84.33 E-value=0.29 Score=32.87 Aligned_cols=37 Identities=27% Similarity=0.605 Sum_probs=27.7
Q ss_pred CCCCCcCCCceeeeecccCCCCCcccccccccccccCccccc
Q 024786 38 PCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRD 79 (262)
Q Consensus 38 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRn 79 (262)
+||+|...-...-+ ..-+-+.|.+|.-.|=..+.|..
T Consensus 1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHH
Confidence 69999987555444 23566889999999988777654
No 11
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=81.02 E-value=2.1 Score=33.07 Aligned_cols=39 Identities=18% Similarity=0.603 Sum_probs=29.1
Q ss_pred CcCCCCCcCCCceeeeecccCCCCCc---ccccccccccccC
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWTHG 74 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~G 74 (262)
..+||+|...+.-|-..|-.+-..|- |.|..|.-.|+..
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 57999998777766555555544443 9999999999864
No 12
>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=76.17 E-value=2.3 Score=30.66 Aligned_cols=40 Identities=28% Similarity=0.723 Sum_probs=28.9
Q ss_pred CCCCCcCCCceeeeecccCCCCCcccccccccccccCcccccc
Q 024786 38 PCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDI 80 (262)
Q Consensus 38 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnV 80 (262)
.|-.|...+|..=.-.. .....+|-+|.-||.+.+..|.+
T Consensus 1 ~C~~C~~~~Tp~WR~g~---~~~~~LCNaCgl~~~k~~~~rp~ 40 (54)
T cd00202 1 ACSNCGTTTTPLWRRGP---SGGSTLCNACGLYWKKHGVMRPL 40 (54)
T ss_pred CCCCCCCCCCcccccCC---CCcchHHHHHHHHHHhcCCCCCc
Confidence 37778887775332222 46779999999999999965554
No 13
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=75.07 E-value=2.7 Score=39.52 Aligned_cols=41 Identities=17% Similarity=0.575 Sum_probs=30.3
Q ss_pred CCCCCcCCCCCcCCCceeeeecccCCCCCc---ccccccccccc
Q 024786 32 AEQEQLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWT 72 (262)
Q Consensus 32 ~e~e~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT 72 (262)
.+....+||+|...+..|-..|..+-..|- |.|..|...|.
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 344568999999888777655666555553 78999999984
No 14
>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=69.66 E-value=3.4 Score=35.94 Aligned_cols=44 Identities=23% Similarity=0.403 Sum_probs=32.3
Q ss_pred CCCCCcCCCceeeee---cccCCCCCcccccccccccccCccccccc
Q 024786 38 PCPRCESTNTKFCYY---NNYNFSQPRHFCKSCRRYWTHGGTLRDIP 81 (262)
Q Consensus 38 ~CPRC~S~nTKFcYy---NNy~~~QPR~fCk~CrRyWT~GGtLRnVP 81 (262)
+||.|...+||+-== ..-+.-+-|..|..|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 699999999998643 34445667899999999988544444333
No 15
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=67.02 E-value=3 Score=36.99 Aligned_cols=36 Identities=31% Similarity=0.833 Sum_probs=23.2
Q ss_pred CCCCcCCCce-------eeeecccCCCC-----CcccccccccccccC
Q 024786 39 CPRCESTNTK-------FCYYNNYNFSQ-----PRHFCKSCRRYWTHG 74 (262)
Q Consensus 39 CPRC~S~nTK-------FcYyNNy~~~Q-----PR~fCk~CrRyWT~G 74 (262)
||+|...... =||...+.+.. --.+|+.|.||+..|
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~ 48 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGG 48 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCC
Confidence 5566553332 25666666544 227899999999984
No 16
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=66.87 E-value=4 Score=37.16 Aligned_cols=30 Identities=20% Similarity=0.707 Sum_probs=22.4
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 69 (262)
+..+||||...=.|.-+= .+.-|||..|++
T Consensus 243 ~g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 456999999876665442 266699999985
No 17
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=65.85 E-value=4.3 Score=38.46 Aligned_cols=36 Identities=22% Similarity=0.619 Sum_probs=23.7
Q ss_pred CcCCCCCcCCCceeeeecccC---CCC-Ccccccccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYN---FSQ-PRHFCKSCRRYWT 72 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~---~~Q-PR~fCk~CrRyWT 72 (262)
..+||.|.+.+ +.-||.-.. ... --+.|.+|+.|+-
T Consensus 224 R~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 224 RVKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred CccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchh
Confidence 35899999865 566765433 112 2268999999974
No 18
>PHA00626 hypothetical protein
Probab=65.25 E-value=4.5 Score=30.78 Aligned_cols=36 Identities=19% Similarity=0.253 Sum_probs=24.0
Q ss_pred CCCCCcCCCceeeeecccCCCCCcccccccccccccCc
Q 024786 38 PCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGG 75 (262)
Q Consensus 38 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GG 75 (262)
.||+|.|.+.-=|=.= ....-||.|++|.=++|+..
T Consensus 2 ~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeecee--cccCcceEcCCCCCeechhh
Confidence 6999999754311110 11145799999999999864
No 19
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=65.24 E-value=2.6 Score=28.63 Aligned_cols=17 Identities=41% Similarity=1.122 Sum_probs=7.1
Q ss_pred CCcccccccccccccCc
Q 024786 59 QPRHFCKSCRRYWTHGG 75 (262)
Q Consensus 59 QPR~fCk~CrRyWT~GG 75 (262)
+|||+|.=|..|.+..-
T Consensus 1 m~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDS 17 (38)
T ss_dssp --S-B-TTT--B-S--S
T ss_pred CcCeecccccceecCCC
Confidence 69999999999997654
No 20
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=64.64 E-value=5.1 Score=28.54 Aligned_cols=40 Identities=25% Similarity=0.569 Sum_probs=29.4
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCcccccccccccccCccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTL 77 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtL 77 (262)
....|-.|...+|..=.- ...-++.+|-+|.-||.+.+.+
T Consensus 2 ~~~~C~~C~~~~T~~WR~---g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRR---GPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCcccc---CCCCCCcEeecccHHHHHcCCC
Confidence 356899999888864322 2223379999999999998886
No 21
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=62.88 E-value=5.3 Score=36.35 Aligned_cols=30 Identities=33% Similarity=0.817 Sum_probs=22.2
Q ss_pred CcCCCCCcCCCceeeeecccCCCCCcccccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRY 70 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRy 70 (262)
..+||||...=.|.-+= .+.-|||..|++-
T Consensus 235 g~pC~~Cg~~I~~~~~~-----gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVG-----GRGTHFCPQCQPL 264 (269)
T ss_pred cCCCCcCCCeeEEEEEC-----CCCcEECCCCcCC
Confidence 45899999886664442 2666999999963
No 22
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=62.14 E-value=5.7 Score=34.26 Aligned_cols=45 Identities=22% Similarity=0.451 Sum_probs=33.7
Q ss_pred cCCCCCcCCCceee---eecccCCCCCcccccccccccccCccccccc
Q 024786 37 LPCPRCESTNTKFC---YYNNYNFSQPRHFCKSCRRYWTHGGTLRDIP 81 (262)
Q Consensus 37 ~~CPRC~S~nTKFc---YyNNy~~~QPR~fCk~CrRyWT~GGtLRnVP 81 (262)
.+||-|.+..|++- |+-.-+.-.-||.|++|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999987764 5555555666799999999998766655554
No 23
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=60.77 E-value=6.1 Score=35.75 Aligned_cols=30 Identities=30% Similarity=0.751 Sum_probs=21.9
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 69 (262)
+..+||||...=.|.-+ + .+.-|||..|++
T Consensus 244 ~g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEKIKQ-G----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCeeEEEEE-C----CCCcEECcCCCC
Confidence 44689999987655433 3 266699999986
No 24
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=59.78 E-value=6.1 Score=37.57 Aligned_cols=36 Identities=22% Similarity=0.549 Sum_probs=23.6
Q ss_pred cCCCCCcCCCceeeeecccCC--CCCccccccccccccc
Q 024786 37 LPCPRCESTNTKFCYYNNYNF--SQPRHFCKSCRRYWTH 73 (262)
Q Consensus 37 ~~CPRC~S~nTKFcYyNNy~~--~QPR~fCk~CrRyWT~ 73 (262)
.+||.|... .|.-||.--.. ..--+.|.+|++|+--
T Consensus 227 ~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 227 VKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred ccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 589999874 46667643222 2223889999999853
No 25
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=57.92 E-value=6.2 Score=41.28 Aligned_cols=55 Identities=20% Similarity=0.462 Sum_probs=30.4
Q ss_pred CCCCCCCCCCCCCccccCCCCCCCCCCcCCCCCcCCCceeeeecccCCCCCccccccccccccc
Q 024786 10 NNNNNNSSSSSSNKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTH 73 (262)
Q Consensus 10 ~~~~~~~~~~s~~~~~~a~~p~~e~e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~ 73 (262)
|.|.-.|+++|++..-...+=-|.....+|-.|...-+-| +-||.|++|.+.|-.
T Consensus 875 netqmpssatstsatlsppawipd~~a~~cmacq~pf~af---------rrrhhcrncggifcg 929 (990)
T KOG1819|consen 875 NETQMPSSATSTSATLSPPAWIPDEDAEQCMACQMPFNAF---------RRRHHCRNCGGIFCG 929 (990)
T ss_pred ccccCCccccccccccCCcccCCCCcchhhhhccCcHHHH---------HHhhhhcccCceeec
Confidence 3344445555544433222223344445666666544333 789999999887754
No 26
>PRK10445 endonuclease VIII; Provisional
Probab=57.64 E-value=7.1 Score=35.36 Aligned_cols=30 Identities=27% Similarity=0.640 Sum_probs=22.4
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 69 (262)
+..+||||...-.|.-+= .+.-|||..|++
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~-----gR~t~~CP~CQ~ 263 (263)
T PRK10445 234 DGEACERCGGIIEKTTLS-----SRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCCEeEEEEEC-----CCCcEECCCCcC
Confidence 346899999887665552 266699999985
No 27
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=56.90 E-value=8.2 Score=29.61 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=26.0
Q ss_pred CcCCCCCcCCCceeeeecccCCCCCcccccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRY 70 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRy 70 (262)
...||+|.+.+|-..|..|. ..-..|-.|.-.
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~---ve~vECV~CGy~ 39 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENG---VEYVECVECGYT 39 (71)
T ss_pred CccCCCCcCccEEEEEEeCC---ceEEEecCCCCe
Confidence 46899999999988888877 666789999643
No 28
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=56.44 E-value=8 Score=35.32 Aligned_cols=29 Identities=21% Similarity=0.748 Sum_probs=21.8
Q ss_pred CcCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 69 (262)
..+||||...=.|.-+= .+--|||..|++
T Consensus 254 g~pC~~Cg~~I~~~~~~-----gR~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCRKCGTPIERIKLA-----GRSTHWCPNCQK 282 (282)
T ss_pred cCCCCcCCCeeEEEEEC-----CCccEECCCCcC
Confidence 46999999887665552 256699999985
No 29
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=51.74 E-value=12 Score=31.36 Aligned_cols=38 Identities=21% Similarity=0.609 Sum_probs=32.9
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCc---ccccccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWT 72 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT 72 (262)
-...||+|...+--|-=+|-.+-..|- |.|-.|+--|-
T Consensus 64 t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 64 TEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred ccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 346899999999999888888888886 99999999884
No 30
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=50.19 E-value=8 Score=25.69 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=8.8
Q ss_pred CcCCCCCcCCC
Q 024786 36 QLPCPRCESTN 46 (262)
Q Consensus 36 ~~~CPRC~S~n 46 (262)
...||.|.+..
T Consensus 2 ~~~Cp~Cg~~~ 12 (47)
T PF14690_consen 2 PPRCPHCGSPS 12 (47)
T ss_pred CccCCCcCCCc
Confidence 35799999876
No 31
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.97 E-value=11 Score=34.15 Aligned_cols=29 Identities=31% Similarity=0.777 Sum_probs=21.3
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCcccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCR 68 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 68 (262)
+..+||||...=.|.-+ . .+.-|||..|+
T Consensus 244 ~g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ 272 (272)
T TIGR00577 244 KGEPCRRCGTPIEKIKV-G----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCCeeEEEEE-C----CCCCEECCCCC
Confidence 34699999988666543 2 26669999996
No 32
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=47.84 E-value=10 Score=27.19 Aligned_cols=27 Identities=33% Similarity=0.658 Sum_probs=19.3
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 69 (262)
...-||+|.+. |..-.. .|+.|..|..
T Consensus 19 ~~~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 34589999873 544433 6999999974
No 33
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=44.09 E-value=14 Score=25.64 Aligned_cols=32 Identities=22% Similarity=0.697 Sum_probs=18.7
Q ss_pred CcCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 69 (262)
+.+||-|.. ..||..|-+. .-+-..+|..|..
T Consensus 3 h~pCP~CGG-~DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGG-KDRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCCcC-ccccccCcCc-ccCCCEECCCCCC
Confidence 568999987 6689866654 3347799999943
No 34
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=44.03 E-value=14 Score=32.67 Aligned_cols=43 Identities=23% Similarity=0.300 Sum_probs=29.6
Q ss_pred CCCCCcCCCceeeee---cccCCCCCcccccccccccccCcccccc
Q 024786 38 PCPRCESTNTKFCYY---NNYNFSQPRHFCKSCRRYWTHGGTLRDI 80 (262)
Q Consensus 38 ~CPRC~S~nTKFcYy---NNy~~~QPR~fCk~CrRyWT~GGtLRnV 80 (262)
.||.|.+.+||+-== ..-+..+-|.-|.+|..-||-==++--+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELR 47 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeec
Confidence 699999999998532 1223345578999999888854443333
No 35
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=42.83 E-value=24 Score=28.72 Aligned_cols=42 Identities=17% Similarity=0.354 Sum_probs=28.0
Q ss_pred CCCCCCCCCCcCCCCCcCCCceeeeecccCCCCCcccccccccccc
Q 024786 27 AKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWT 72 (262)
Q Consensus 27 a~~p~~e~e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT 72 (262)
.+..+..+....||.|.+. +--|=+.. ..+.+.|..|.-|..
T Consensus 12 ~k~k~klpt~f~CP~Cge~-~v~v~~~k---~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 12 IRPKPKLPKIFECPRCGKV-SISVKIKK---NIAIITCGNCGLYTE 53 (99)
T ss_pred cccccCCCcEeECCCCCCe-EeeeecCC---CcceEECCCCCCccC
Confidence 3334445678899999953 33233333 478999999999854
No 36
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=42.17 E-value=14 Score=28.59 Aligned_cols=46 Identities=13% Similarity=0.267 Sum_probs=20.8
Q ss_pred cCCCCCCCCCCcCCCCCcCCCceeeeecccCCCCCcccccccccccc
Q 024786 26 TAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWT 72 (262)
Q Consensus 26 ~a~~p~~e~e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT 72 (262)
..+...+.+..-.||.|+..++=-|=...- .......|..|.-.+.
T Consensus 12 ~kk~~~~l~~~F~CPfC~~~~sV~v~idkk-~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 12 KKKKKPKLPKVFDCPFCNHEKSVSVKIDKK-EGIGILSCRVCGESFQ 57 (81)
T ss_dssp --------SS----TTT--SS-EEEEEETT-TTEEEEEESSS--EEE
T ss_pred ccCcCCCCCceEcCCcCCCCCeEEEEEEcc-CCEEEEEecCCCCeEE
Confidence 334445556778999999888777766433 5566788999976664
No 37
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=41.15 E-value=23 Score=24.75 Aligned_cols=35 Identities=23% Similarity=0.530 Sum_probs=19.9
Q ss_pred CCcCCCCCcCCCceeeeecccCCCC-Cccccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQ-PRHFCKSCRR 69 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~Q-PR~fCk~CrR 69 (262)
+..+||.|.+....+.+........ -.-+|..|.-
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5679999965555544422221111 3345888865
No 38
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=40.67 E-value=11 Score=28.23 Aligned_cols=12 Identities=42% Similarity=0.833 Sum_probs=5.6
Q ss_pred cCCCCCcCCCce
Q 024786 37 LPCPRCESTNTK 48 (262)
Q Consensus 37 ~~CPRC~S~nTK 48 (262)
++|+.|.|.||+
T Consensus 49 ~KC~~C~SYNT~ 60 (61)
T PF14599_consen 49 HKCSHCGSYNTR 60 (61)
T ss_dssp ---TTTS---EE
T ss_pred hcCCCCCCcccC
Confidence 599999999997
No 39
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.25 E-value=23 Score=33.40 Aligned_cols=30 Identities=23% Similarity=0.638 Sum_probs=21.7
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 69 (262)
+..+|++|.+.=.|--. -.+..|||..|++
T Consensus 244 ~GepC~~CGt~I~k~~~-----~gR~t~~CP~CQ~ 273 (273)
T COG0266 244 AGEPCRRCGTPIEKIKL-----GGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCccCCEeEEEEE-----cCCcCEeCCCCCC
Confidence 45699999998555322 3467799999985
No 40
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=36.71 E-value=13 Score=36.26 Aligned_cols=35 Identities=29% Similarity=0.758 Sum_probs=21.3
Q ss_pred CCCCcCCCCCcCCCceeeeecccCC-----CCCccccccccc
Q 024786 33 EQEQLPCPRCESTNTKFCYYNNYNF-----SQPRHFCKSCRR 69 (262)
Q Consensus 33 e~e~~~CPRC~S~nTKFcYyNNy~~-----~QPR~fCk~CrR 69 (262)
+.+.-+||||...| ||.-----. .-..-||+.|..
T Consensus 303 pa~t~~~~r~~k~n--fc~ncG~~~t~~~~ng~a~fcp~cgq 342 (345)
T COG4260 303 PAATWPCARCAKLN--FCLNCGCGTTADFDNGKAKFCPECGQ 342 (345)
T ss_pred CcccCcchhccccc--cccccCcccccCCccchhhhChhhcC
Confidence 34567999999988 765322111 113467877754
No 41
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=36.28 E-value=33 Score=24.12 Aligned_cols=33 Identities=21% Similarity=0.532 Sum_probs=20.0
Q ss_pred cCCCCCcCCCceeeeecccCCCCCccc-ccccccc
Q 024786 37 LPCPRCESTNTKFCYYNNYNFSQPRHF-CKSCRRY 70 (262)
Q Consensus 37 ~~CPRC~S~nTKFcYyNNy~~~QPR~f-Ck~CrRy 70 (262)
.+||.|.+..-.|-+ ...+....+++ |..|...
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCCC
Confidence 589999997665542 12333344444 8877643
No 42
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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 CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=36.07 E-value=24 Score=27.43 Aligned_cols=31 Identities=23% Similarity=0.467 Sum_probs=17.3
Q ss_pred CcCCCCCcCCCceeeeecccCCCCCcccccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRY 70 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRy 70 (262)
...||-|+..+..|..+.+.+ ++.|-+|.+.
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k~----~~~Cf~Cg~~ 63 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDKN----RFKCFGCGKG 63 (97)
T ss_dssp EE--SSS--SS--EEEETTTT----EEEETTT--E
T ss_pred EEECcCCCCCCCceEEECCCC----eEEECCCCCC
Confidence 357999998887877775543 7999999853
No 43
>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=34.44 E-value=23 Score=25.24 Aligned_cols=32 Identities=28% Similarity=0.510 Sum_probs=25.1
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCccccccccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTH 73 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~ 73 (262)
.-..||.|.....+ .+.+-.+.|..|...+.+
T Consensus 27 TSq~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 34579999998777 666777999999877654
No 44
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=33.10 E-value=20 Score=22.47 Aligned_cols=27 Identities=22% Similarity=0.577 Sum_probs=14.6
Q ss_pred cCCCCCcCCCceeeeecccCCCCCcccccccc
Q 024786 37 LPCPRCESTNTKFCYYNNYNFSQPRHFCKSCR 68 (262)
Q Consensus 37 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 68 (262)
.+||||.....++-..+ +.-+||..|+
T Consensus 2 ~~C~rC~~~~~~~~~~~-----r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGING-----RSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETT-----EEEEE-TTTC
T ss_pred CcCccCCCcceEeEecC-----CCCeECcCCc
Confidence 47999998877765422 2237787775
No 45
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=32.93 E-value=35 Score=28.89 Aligned_cols=41 Identities=22% Similarity=0.556 Sum_probs=28.5
Q ss_pred CCCCCCcCCCCCcCCCceeeeecccCCCCC-----ccccccccccccc
Q 024786 31 AAEQEQLPCPRCESTNTKFCYYNNYNFSQP-----RHFCKSCRRYWTH 73 (262)
Q Consensus 31 ~~e~e~~~CPRC~S~nTKFcYyNNy~~~QP-----R~fCk~CrRyWT~ 73 (262)
.|.-+...||+|...+.-| ||-.+...- -|.|-+|.--||+
T Consensus 68 LPrts~~~C~~C~~~eavf--fQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 68 LPRTSDKHCPKCGHREAVF--FQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred cCccccccCCccCCcceEE--EecccccccceEEEEEEeccccccccC
Confidence 4444678999999987664 654332211 1899999999985
No 46
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=32.90 E-value=20 Score=23.63 Aligned_cols=28 Identities=29% Similarity=0.609 Sum_probs=14.8
Q ss_pred cCCCCCcCCCceeeeecccCCCCCcccccccccccc
Q 024786 37 LPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWT 72 (262)
Q Consensus 37 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT 72 (262)
-+||-|.|..|= ...--+.|..|..=|.
T Consensus 3 p~Cp~C~se~~y--------~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTY--------EDGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----E--------E-SSSEEETTTTEEE-
T ss_pred CCCCCCCCccee--------ccCCEEeCCcccccCC
Confidence 379999998775 5567789999988774
No 47
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=31.45 E-value=37 Score=25.84 Aligned_cols=30 Identities=23% Similarity=0.458 Sum_probs=23.3
Q ss_pred CcCCCCCcCCCceeeeecccCCCCCcccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCR 68 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 68 (262)
...||+|...++=..|..|.- .-..|-.|.
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred cccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 468999999999988866653 456788885
No 48
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=28.89 E-value=46 Score=24.24 Aligned_cols=28 Identities=29% Similarity=0.745 Sum_probs=20.6
Q ss_pred CCCCCCcCCCCCcCCCceeeeecccCCCCCcccccccccc
Q 024786 31 AAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRY 70 (262)
Q Consensus 31 ~~e~e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRy 70 (262)
...+....||.|.+. .+|-+.|..|.-|
T Consensus 21 l~~p~l~~C~~cG~~------------~~~H~vc~~cG~Y 48 (55)
T TIGR01031 21 LTAPTLVVCPNCGEF------------KLPHRVCPSCGYY 48 (55)
T ss_pred ccCCcceECCCCCCc------------ccCeeECCccCeE
Confidence 444567789999874 3677888888855
No 49
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=28.51 E-value=58 Score=33.97 Aligned_cols=72 Identities=24% Similarity=0.374 Sum_probs=44.6
Q ss_pred CCCCCCCCCCCCCCCccccCCCCCCCCCCcCCCCCcCCCceeeeecccCCCCCcccccccccccccCcccccc
Q 024786 8 NNNNNNNNSSSSSSNKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDI 80 (262)
Q Consensus 8 ~~~~~~~~~~~~s~~~~~~a~~p~~e~e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnV 80 (262)
+.|.-|+++-+..-.|+..-..-.+.+..+.|-.|..... .-+|.=--+.--..+|-+|--||-+=|-|..-
T Consensus 358 ~ynKPnpnqI~~~n~k~g~~gtt~~~~~g~~CEsC~ttqs-~qWYsWGppnmqcrLCasCWiyWKKygGLk~p 429 (693)
T KOG3554|consen 358 TYNKPNPNQISPYNTKPGMNGTTFQNQDGRACESCYTTQS-LQWYSWGPPNMQCRLCASCWIYWKKYGGLKMP 429 (693)
T ss_pred CCCCCCcceecccCCCcCcccccccCCCCCcccccccccc-cceeccCCCCccchhhHHHHHHHHHhcCcCCc
Confidence 3344445555555555544444455556899999987654 22343333444457899999999987766543
No 50
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=27.83 E-value=39 Score=22.73 Aligned_cols=32 Identities=19% Similarity=0.426 Sum_probs=18.9
Q ss_pred CCCCCcCCCceeeeecccCCCCCcccccccccccccC
Q 024786 38 PCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHG 74 (262)
Q Consensus 38 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~G 74 (262)
-||.|.+. .|..... ...|+.|..|...+-..
T Consensus 2 FCp~Cg~~----l~~~~~~-~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNM----LIPKEGK-EKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCc----cccccCC-CCCEEECCcCCCeEECC
Confidence 58888773 3333221 11488899998665443
No 51
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=26.95 E-value=53 Score=22.55 Aligned_cols=31 Identities=26% Similarity=0.807 Sum_probs=20.8
Q ss_pred CCcCCCCCcCCCceeeeecccCCCCCcccccccc
Q 024786 35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCR 68 (262)
Q Consensus 35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 68 (262)
.+.+||.|.+ +.+|= |.+..- .-.++|..|.
T Consensus 2 ~~~pCP~CGG-~DrFr-~~d~~g-~G~~~C~~Cg 32 (37)
T smart00778 2 RHGPCPNCGG-SDRFR-FDDKDG-RGTWFCSVCG 32 (37)
T ss_pred CccCCCCCCC-ccccc-cccCCC-CcCEEeCCCC
Confidence 3679999988 45676 444222 3558999884
No 52
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=26.23 E-value=42 Score=33.75 Aligned_cols=43 Identities=19% Similarity=0.420 Sum_probs=29.8
Q ss_pred CcCCCCCcCCCc----eeeeeccc-CCCCCcccccccccccccCccccc
Q 024786 36 QLPCPRCESTNT----KFCYYNNY-NFSQPRHFCKSCRRYWTHGGTLRD 79 (262)
Q Consensus 36 ~~~CPRC~S~nT----KFcYyNNy-~~~QPR~fCk~CrRyWT~GGtLRn 79 (262)
.++||.|..... .|-| +.- .....+|.|..|..-|++.-..+.
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w-~~~~~~~~a~y~C~~Cg~~i~e~~k~~m 247 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKW-DKGEAPETARYVCPHCGCEIEEHDKRRM 247 (557)
T ss_pred EccCCCCCCCccccccceee-cCCCCccceEEECCCCcCCCCHHHHhhc
Confidence 469999987743 1333 322 566778999999999997654443
No 53
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.20 E-value=43 Score=27.38 Aligned_cols=43 Identities=23% Similarity=0.504 Sum_probs=31.4
Q ss_pred CCCcCCCCCcCCCceeeeecccCCCCCcccccccccccccCcccccccCC
Q 024786 34 QEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVG 83 (262)
Q Consensus 34 ~e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnVPVG 83 (262)
.+...||.|.+...| -...--..|+.|..-|+.|.-....|.|
T Consensus 33 ~~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 33 RAKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred hcCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 345689999998555 1222337899999999999987766654
No 54
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=25.84 E-value=47 Score=27.96 Aligned_cols=31 Identities=32% Similarity=0.765 Sum_probs=24.5
Q ss_pred cCCCCCcCCCceeeeecccCCCCCcccccccccccccCc
Q 024786 37 LPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGG 75 (262)
Q Consensus 37 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GG 75 (262)
.+||.|.|..|- - .+.-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY---~-----dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTY---H-----DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceE---e-----cCCeeECccccccccccc
Confidence 489999998663 2 355699999999998775
No 55
>PRK10220 hypothetical protein; Provisional
Probab=25.74 E-value=51 Score=27.84 Aligned_cols=31 Identities=26% Similarity=0.639 Sum_probs=24.4
Q ss_pred cCCCCCcCCCceeeeecccCCCCCcccccccccccccCc
Q 024786 37 LPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGG 75 (262)
Q Consensus 37 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GG 75 (262)
.+||.|.|..|- ..+..+.|..|.-=|+..-
T Consensus 4 P~CP~C~seytY--------~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTY--------EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceE--------cCCCeEECCcccCcCCccc
Confidence 589999997663 2356799999999998764
No 56
>PF07383 DUF1496: Protein of unknown function (DUF1496); InterPro: IPR009971 This family consists of several bacterial proteins of around 90 residues in length. Members of this family seem to be found exclusively in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown.
Probab=25.48 E-value=50 Score=24.64 Aligned_cols=15 Identities=27% Similarity=0.815 Sum_probs=11.0
Q ss_pred ceeeeecccCCCCCc
Q 024786 47 TKFCYYNNYNFSQPR 61 (262)
Q Consensus 47 TKFcYyNNy~~~QPR 61 (262)
.|+|||+|..-+.-.
T Consensus 12 ~r~C~Yqdq~YSeGA 26 (56)
T PF07383_consen 12 QRCCYYQDQAYSEGA 26 (56)
T ss_pred ceEEEEcCCccCCCC
Confidence 499999997665443
No 57
>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=24.84 E-value=66 Score=26.84 Aligned_cols=29 Identities=28% Similarity=0.480 Sum_probs=20.7
Q ss_pred cCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786 37 LPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69 (262)
Q Consensus 37 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 69 (262)
+.||-|.+.+|.+--- ...--..|++|..
T Consensus 94 VlC~~C~spdT~l~k~----~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE----GRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEE----TTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEc----CCEEEEEecccCC
Confidence 6899999999997544 1223367888853
No 58
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=24.68 E-value=80 Score=25.81 Aligned_cols=38 Identities=18% Similarity=0.604 Sum_probs=25.7
Q ss_pred CcCCCCCcCCCceeeeecccCCCCCc---cccccccccccc
Q 024786 36 QLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWTH 73 (262)
Q Consensus 36 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~ 73 (262)
-..||+|...+--|-..|...-.-|- |.|..|.--|+.
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 46899999877655444333333332 899999999964
No 59
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=24.21 E-value=38 Score=24.75 Aligned_cols=17 Identities=18% Similarity=0.532 Sum_probs=12.5
Q ss_pred cCCCCCccccccccccc
Q 024786 55 YNFSQPRHFCKSCRRYW 71 (262)
Q Consensus 55 y~~~QPR~fCk~CrRyW 71 (262)
+..-.-...|..|+|.+
T Consensus 47 ~~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 47 VEIVEGELICPECGREY 63 (68)
T ss_dssp EETTTTEEEETTTTEEE
T ss_pred ccccCCEEEcCCCCCEE
Confidence 45666778899998865
No 60
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=23.72 E-value=31 Score=32.62 Aligned_cols=34 Identities=26% Similarity=0.676 Sum_probs=13.4
Q ss_pred CcCCCCCcCC-CceeeeecccCCCCCccccccccccccc
Q 024786 36 QLPCPRCEST-NTKFCYYNNYNFSQPRHFCKSCRRYWTH 73 (262)
Q Consensus 36 ~~~CPRC~S~-nTKFcYyNNy~~~QPR~fCk~CrRyWT~ 73 (262)
...||+|.+. -.+| ..|.+-.-++|..|..-+--
T Consensus 31 n~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyEL 65 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYEL 65 (254)
T ss_dssp H---TTT--SS-EE------------EEE-TTT--EEEE
T ss_pred CCcCCCCCChhHhhc----cCCCccceeECCCCchHHhh
Confidence 3589999998 5665 34455567999999876653
No 61
>PF06403 Lamprin: Lamprin; InterPro: IPR009437 This family consists of several lamprin proteins from the Sea lamprey Petromyzon marinus. Lamprin, an insoluble non-collagen, non-elastin protein, is the major connective tissue component of the fibrillar extracellular matrix of lamprey annular cartilage. Although not generally homologous to any other protein, soluble lamprins contain a tandemly repeated peptide sequence (GGLGY), which is present in both silkmoth chorion proteins and spider dragline silk. Strong homologies to this repeat sequence are also present in several mammalian and avian elastins. It is thought that these proteins share a structural motif which promotes self-aggregation and fibril formation in proteins through interdigitation of hydrophobic side chains in beta-sheet/beta-turn structures, a motif that has been preserved in recognisable form over several hundred million years of evolution [].; GO: 0005198 structural molecule activity, 0005578 proteinaceous extracellular matrix
Probab=23.23 E-value=59 Score=27.87 Aligned_cols=34 Identities=47% Similarity=0.978 Sum_probs=21.1
Q ss_pred CceeccccccccCCCcccccccccCCcccccccccc
Q 024786 171 GFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGVS 206 (262)
Q Consensus 171 Gf~~lgGfg~GlG~Gf~~dv~~~G~gr~~w~fpg~~ 206 (262)
|-++.+|.||| |-|+ +..+..|+|.+...|||..
T Consensus 41 ~glgygglgyg-glgy-~glg~aglgy~glgy~g~a 74 (138)
T PF06403_consen 41 GGLGYGGLGYG-GLGY-DGLGVAGLGYGGLGYPGAA 74 (138)
T ss_pred ccccccccccC-cccc-ccccccccccCccCCCccc
Confidence 44566676766 6666 6666566666666666544
No 62
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=21.36 E-value=43 Score=20.63 Aligned_cols=16 Identities=25% Similarity=0.503 Sum_probs=12.8
Q ss_pred CcccccccccccccCc
Q 024786 60 PRHFCKSCRRYWTHGG 75 (262)
Q Consensus 60 PR~fCk~CrRyWT~GG 75 (262)
++|+|.-|..+++.-.
T Consensus 2 ~~~~C~~C~~~~~~~~ 17 (35)
T smart00451 2 GGFYCKLCNVTFTDEI 17 (35)
T ss_pred cCeEccccCCccCCHH
Confidence 6799999999887433
No 63
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.29 E-value=70 Score=26.01 Aligned_cols=9 Identities=44% Similarity=1.173 Sum_probs=4.4
Q ss_pred CCCCcCCCc
Q 024786 39 CPRCESTNT 47 (262)
Q Consensus 39 CPRC~S~nT 47 (262)
||+|.+.+.
T Consensus 91 CP~Cgs~~~ 99 (117)
T PRK00564 91 CEKCHSKNV 99 (117)
T ss_pred CcCCCCCce
Confidence 555554443
No 64
>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=20.04 E-value=68 Score=21.54 Aligned_cols=28 Identities=21% Similarity=0.606 Sum_probs=18.2
Q ss_pred CCCCCcCCCceeeeecccCCCCCccccccccccc
Q 024786 38 PCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYW 71 (262)
Q Consensus 38 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyW 71 (262)
.||.|.+.+.- +. ..+--+.|..|..-.
T Consensus 2 ~Cp~Cg~~~~~---~D---~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIV---FD---PERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEE---EE---TTTTEEEETTT-BBE
T ss_pred CCcCCcCCceE---Ec---CCCCeEECCCCCCEe
Confidence 69999997642 22 345567899996543
Done!