Query 042156
Match_columns 336
No_of_seqs 143 out of 202
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 03:23:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042156.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042156hhsearch_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 7.8E-37 1.7E-41 233.7 4.0 62 35-96 2-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 92.8 0.043 9.3E-07 47.7 0.8 34 38-73 105-140 (146)
3 COG3677 Transposase and inacti 91.9 0.12 2.6E-06 44.1 2.4 37 37-75 29-65 (129)
4 PF12760 Zn_Tnp_IS1595: Transp 90.6 0.25 5.3E-06 35.0 2.6 28 38-71 18-45 (46)
5 PF03811 Zn_Tnp_IS1: InsA N-te 90.2 0.2 4.3E-06 35.1 1.8 31 38-70 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 87.8 0.59 1.3E-05 32.8 2.8 37 39-75 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 84.5 0.84 1.8E-05 31.8 2.2 36 39-74 1-39 (39)
8 PF04216 FdhE: Protein involve 82.0 0.68 1.5E-05 43.0 1.3 37 37-73 210-248 (290)
9 cd00202 ZnF_GATA Zinc finger D 80.7 1.3 2.9E-05 32.9 2.2 42 40-84 1-42 (54)
10 PF13453 zf-TFIIB: Transcripti 78.9 0.71 1.5E-05 31.9 0.2 37 40-81 1-37 (41)
11 TIGR01384 TFS_arch transcripti 76.4 3.3 7.3E-05 32.9 3.4 42 35-76 59-103 (104)
12 PHA02998 RNA polymerase subuni 75.0 3.1 6.6E-05 38.9 3.2 39 37-75 142-183 (195)
13 PF04981 NMD3: NMD3 family ; 68.9 2.6 5.7E-05 38.3 1.4 36 41-76 1-48 (236)
14 PF14690 zf-ISL3: zinc-finger 67.8 2.7 5.9E-05 28.8 1.0 32 38-69 2-47 (47)
15 smart00401 ZnF_GATA zinc finge 64.7 5.3 0.00012 29.3 2.1 39 38-79 3-41 (52)
16 TIGR01385 TFSII transcription 61.5 8.1 0.00018 37.4 3.2 40 35-74 255-297 (299)
17 TIGR00244 transcriptional regu 59.4 6.9 0.00015 35.1 2.2 43 40-82 2-47 (147)
18 PRK03564 formate dehydrogenase 57.8 7.1 0.00015 38.2 2.2 38 36-74 224-263 (309)
19 PRK00464 nrdR transcriptional 54.3 9.3 0.0002 33.9 2.2 44 39-82 1-47 (154)
20 TIGR01562 FdhE formate dehydro 53.4 8.8 0.00019 37.4 2.0 38 36-74 222-263 (305)
21 PRK14810 formamidopyrimidine-D 52.4 10 0.00022 35.5 2.2 31 36-71 242-272 (272)
22 PF06220 zf-U1: U1 zinc finger 51.9 5.9 0.00013 27.8 0.5 17 61-77 1-17 (38)
23 PHA00626 hypothetical protein 51.0 11 0.00024 29.6 1.8 37 40-78 2-38 (59)
24 PRK14811 formamidopyrimidine-D 48.7 13 0.00028 34.9 2.3 32 36-72 233-264 (269)
25 PRK10445 endonuclease VIII; Pr 48.0 11 0.00025 35.0 1.8 31 36-71 233-263 (263)
26 PRK01103 formamidopyrimidine/5 46.8 14 0.00031 34.4 2.3 31 36-71 243-273 (274)
27 PRK00432 30S ribosomal protein 44.0 13 0.00028 27.5 1.2 27 37-71 19-45 (50)
28 PRK13945 formamidopyrimidine-D 42.8 19 0.0004 33.9 2.3 31 36-71 252-282 (282)
29 COG4049 Uncharacterized protei 38.1 12 0.00027 29.7 0.4 24 18-46 2-25 (65)
30 TIGR00577 fpg formamidopyrimid 36.6 26 0.00056 32.8 2.3 30 36-70 243-272 (272)
31 COG4260 Membrane protease subu 36.3 20 0.00042 36.1 1.5 36 33-70 301-341 (345)
32 PF09526 DUF2387: Probable met 35.8 27 0.00059 27.6 2.0 32 38-72 8-39 (71)
33 COG0266 Nei Formamidopyrimidin 33.4 25 0.00054 34.1 1.7 32 35-71 242-273 (273)
34 KOG2906 RNA polymerase III sub 32.9 34 0.00074 29.5 2.2 39 36-74 63-104 (105)
35 PF14599 zinc_ribbon_6: Zinc-r 32.8 18 0.00039 28.0 0.5 16 35-50 45-60 (61)
36 PF14354 Lar_restr_allev: Rest 31.3 45 0.00098 24.0 2.3 35 37-71 2-37 (61)
37 TIGR03655 anti_R_Lar restricti 31.0 46 0.001 24.1 2.4 33 39-72 2-35 (53)
38 PF08273 Prim_Zn_Ribbon: Zinc- 30.5 29 0.00064 24.9 1.2 32 38-71 3-34 (40)
39 COG1327 Predicted transcriptio 30.2 32 0.00069 31.4 1.7 43 40-82 2-47 (156)
40 PF07282 OrfB_Zn_ribbon: Putat 28.7 33 0.00072 25.2 1.3 32 37-75 27-58 (69)
41 COG1997 RPL43A Ribosomal prote 28.7 23 0.0005 29.8 0.5 44 35-85 32-75 (89)
42 TIGR00686 phnA alkylphosphonat 28.4 47 0.001 28.8 2.3 31 39-77 3-33 (109)
43 PF01807 zf-CHC2: CHC2 zinc fi 27.5 39 0.00085 27.1 1.6 30 38-71 33-62 (97)
44 PRK00420 hypothetical protein; 25.0 45 0.00097 28.6 1.6 28 38-73 23-50 (112)
45 PRK10220 hypothetical protein; 23.9 59 0.0013 28.4 2.1 32 38-77 3-34 (111)
46 PF06044 DRP: Dam-replacing fa 23.2 33 0.00071 33.4 0.5 33 38-74 31-64 (254)
47 PF06827 zf-FPG_IleRS: Zinc fi 22.8 35 0.00077 22.0 0.5 27 39-70 2-28 (30)
48 PF08274 PhnA_Zn_Ribbon: PhnA 21.9 42 0.00091 22.9 0.7 28 39-74 3-30 (30)
49 PTZ00255 60S ribosomal protein 21.8 43 0.00093 28.0 0.9 44 35-85 33-76 (90)
50 PF08142 AARP2CN: AARP2CN (NUC 21.7 39 0.00084 27.0 0.6 14 320-333 58-71 (85)
51 PF01873 eIF-5_eIF-2B: Domain 20.3 88 0.0019 26.9 2.5 31 37-71 92-122 (125)
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=7.8e-37 Score=233.66 Aligned_cols=62 Identities=79% Similarity=1.600 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCCCCccCCCCCCC
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKT 96 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVGGG~RKnKrs~s 96 (336)
++++++||||+|++|||||||||+++||||||++|+||||+||+||||||||||||+|++++
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 57899999999999999999999999999999999999999999999999999999998753
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=92.77 E-value=0.043 Score=47.70 Aligned_cols=34 Identities=26% Similarity=0.773 Sum_probs=27.1
Q ss_pred CCCCCCCCCCCceeeeeccc--CCCCCccccccccccc
Q 042156 38 PQKCPRCESLNTKFCYYNNY--SLSQPRYFCKTCRRYW 73 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy--~~~QPRhfCksCrRYW 73 (336)
...||||.|.+|+.. +.| +.+..-|+|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence 579999999999974 555 4557779999998644
No 3
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.91 E-value=0.12 Score=44.12 Aligned_cols=37 Identities=32% Similarity=0.666 Sum_probs=29.0
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQ 75 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~ 75 (336)
....||+|.+.+ +-=+.-+.....||.|++|++-|+.
T Consensus 29 ~~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 29 TKVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred ccCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 458899999999 2235555555999999999998874
No 4
>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=90.62 E-value=0.25 Score=34.98 Aligned_cols=28 Identities=39% Similarity=0.844 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 38 PQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
...||+|.+. +...+.+ ..++.|++|++
T Consensus 18 g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 4669999998 6655555 78899999985
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=90.20 E-value=0.2 Score=35.06 Aligned_cols=31 Identities=42% Similarity=0.793 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCceeeeecccCC-CCCcccccccc
Q 042156 38 PQKCPRCESLNTKFCYYNNYSL-SQPRYFCKTCR 70 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy~~-~QPRhfCksCr 70 (336)
.+.||+|.+.+.- |=|-.+. -..||+|++|+
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 5789999998721 1233333 35899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=87.80 E-value=0.59 Score=32.80 Aligned_cols=37 Identities=27% Similarity=0.793 Sum_probs=28.1
Q ss_pred CCCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 042156 39 QKCPRCESLNTKFCYYNNYSLSQP---RYFCKTCRRYWTQ 75 (336)
Q Consensus 39 ~~CPRC~S~nTKFcYyNNy~~~QP---RhfCksCrRYWT~ 75 (336)
.+||+|...+.-|-..+-.+...| -|.|.+|...|..
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 379999988777766665655555 4999999999963
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=84.50 E-value=0.84 Score=31.79 Aligned_cols=36 Identities=31% Similarity=0.769 Sum_probs=24.5
Q ss_pred CCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 042156 39 QKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWT 74 (336)
Q Consensus 39 ~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT 74 (336)
.+||.|...+.-|--.+.....-|- |.|.+|..-|+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 3799999988776555555555553 89999999985
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=81.95 E-value=0.68 Score=43.00 Aligned_cols=37 Identities=24% Similarity=0.554 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCC-ceeeeecc-cCCCCCccccccccccc
Q 042156 37 QPQKCPRCESLN-TKFCYYNN-YSLSQPRYFCKTCRRYW 73 (336)
Q Consensus 37 ~~~~CPRC~S~n-TKFcYyNN-y~~~QPRhfCksCrRYW 73 (336)
....||.|...+ .++-||.. -....--+.|+.|+.|+
T Consensus 210 ~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 210 VRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp -TTS-TTT---SS-EEE--------SEEEEEETTTTEEE
T ss_pred cCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchH
Confidence 577899999855 56667633 33333348999999997
No 9
>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=80.72 E-value=1.3 Score=32.88 Aligned_cols=42 Identities=24% Similarity=0.613 Sum_probs=29.7
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccC
Q 042156 40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84 (336)
Q Consensus 40 ~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPV 84 (336)
.|-.|...+|..=.-. ......+|-+|..||.+.|..|-+-.
T Consensus 1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~~~ 42 (54)
T cd00202 1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPLSK 42 (54)
T ss_pred CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCccc
Confidence 3777888777532222 24677999999999999997655444
No 10
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=78.92 E-value=0.71 Score=31.94 Aligned_cols=37 Identities=27% Similarity=0.594 Sum_probs=27.4
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCccccc
Q 042156 40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRN 81 (336)
Q Consensus 40 ~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRN 81 (336)
+||+|...-...-+ ..-+-+.|..|.-.|=..|.+..
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 69999985555444 23566889999999988877654
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=76.41 E-value=3.3 Score=32.87 Aligned_cols=42 Identities=19% Similarity=0.604 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccccC
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWTQG 76 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT~G 76 (336)
+.....||+|...+.-|-..+-.+...|- |.|..|.-.|+.+
T Consensus 59 ~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 59 PTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred CcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 34468999998777766555544433333 8999999999875
No 12
>PHA02998 RNA polymerase subunit; Provisional
Probab=74.95 E-value=3.1 Score=38.90 Aligned_cols=39 Identities=23% Similarity=0.564 Sum_probs=33.7
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWTQ 75 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT~ 75 (336)
...+||+|...++-|--.+-.+-..|- |.|..|..-|.-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 578999999999999888888877775 799999999864
No 13
>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=68.91 E-value=2.6 Score=38.34 Aligned_cols=36 Identities=31% Similarity=0.798 Sum_probs=23.6
Q ss_pred CCCCCCCCce-------eeeecccCCCC-----CcccccccccccccC
Q 042156 41 CPRCESLNTK-------FCYYNNYSLSQ-----PRYFCKTCRRYWTQG 76 (336)
Q Consensus 41 CPRC~S~nTK-------FcYyNNy~~~Q-----PRhfCksCrRYWT~G 76 (336)
||+|...... =||...+.+.. --.+|+.|.||+..|
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 5666653333 26666666543 237999999999884
No 14
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=67.82 E-value=2.7 Score=28.79 Aligned_cols=32 Identities=34% Similarity=0.837 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCcee-eeeccc-------------CCCCCccccccc
Q 042156 38 PQKCPRCESLNTKF-CYYNNY-------------SLSQPRYFCKTC 69 (336)
Q Consensus 38 ~~~CPRC~S~nTKF-cYyNNy-------------~~~QPRhfCksC 69 (336)
+..||.|.+..-+. -++... .+..+|++|++|
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred CccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 56899999876221 111110 356778888887
No 15
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=64.69 E-value=5.3 Score=29.32 Aligned_cols=39 Identities=23% Similarity=0.576 Sum_probs=29.1
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCcccccccccccccCccc
Q 042156 38 PQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTL 79 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtL 79 (336)
...|--|...+|..=.- ...-++.+|-+|.-||.+.|.+
T Consensus 3 ~~~C~~C~~~~T~~WR~---g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 3 GRSCSNCGTTETPLWRR---GPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCcCCCCCCCCCcccc---CCCCCCcEeecccHHHHHcCCC
Confidence 57899999888864221 2223379999999999998886
No 16
>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=61.49 E-value=8.1 Score=37.40 Aligned_cols=40 Identities=18% Similarity=0.522 Sum_probs=29.5
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWT 74 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT 74 (336)
......||+|...+..|-..+..+..-|- |.|..|...|.
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 34578999999888777555555555553 78999999884
No 17
>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=59.40 E-value=6.9 Score=35.09 Aligned_cols=43 Identities=21% Similarity=0.338 Sum_probs=31.4
Q ss_pred CCCCCCCCCceeeee---cccCCCCCcccccccccccccCcccccc
Q 042156 40 KCPRCESLNTKFCYY---NNYSLSQPRYFCKTCRRYWTQGGTLRNV 82 (336)
Q Consensus 40 ~CPRC~S~nTKFcYy---NNy~~~QPRhfCksCrRYWT~GGtLRNV 82 (336)
+||.|...+||+-=- ...+.-+-|..|..|.+-||-==.+-..
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELL 47 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecccc
Confidence 699999999998532 3344556779999999998855444333
No 18
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=57.77 E-value=7.1 Score=38.21 Aligned_cols=38 Identities=26% Similarity=0.479 Sum_probs=24.6
Q ss_pred CCCCCCCCCCCCCceeeeecccC--CCCCcccccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYS--LSQPRYFCKTCRRYWT 74 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~--~~QPRhfCksCrRYWT 74 (336)
-...+||.|... .|.-||.--. ..---+.|.+|+.|+-
T Consensus 224 ~~R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 224 VVRVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred ccCccCCCCCCC-CceeeeeecCCCcceEeeecccccccce
Confidence 357889999974 4566653222 1222388999999964
No 19
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=54.26 E-value=9.3 Score=33.92 Aligned_cols=44 Identities=20% Similarity=0.360 Sum_probs=30.9
Q ss_pred CCCCCCCCCCceee---eecccCCCCCcccccccccccccCcccccc
Q 042156 39 QKCPRCESLNTKFC---YYNNYSLSQPRYFCKTCRRYWTQGGTLRNV 82 (336)
Q Consensus 39 ~~CPRC~S~nTKFc---YyNNy~~~QPRhfCksCrRYWT~GGtLRNV 82 (336)
.+||.|.+..|++- |+-.-++-.-|+-|..|.+-++.==++-..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELV 47 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCc
Confidence 37999999987764 444444555669999999988765444333
No 20
>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=53.43 E-value=8.8 Score=37.42 Aligned_cols=38 Identities=21% Similarity=0.452 Sum_probs=24.8
Q ss_pred CCCCCCCCCCCCCceeeeecccC----CCCCcccccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYS----LSQPRYFCKTCRRYWT 74 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~----~~QPRhfCksCrRYWT 74 (336)
-...+||.|.+.+ +.-|+.-.. ..---..|.+|+.|+-
T Consensus 222 ~~R~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 222 YVRVKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred ccCccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchh
Confidence 3578899999864 555664332 1122268999999963
No 21
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=52.39 E-value=10 Score=35.52 Aligned_cols=31 Identities=13% Similarity=0.515 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
..-.+||||...=.|.-+= .+.-|||..|++
T Consensus 242 R~g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 242 RTGEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCCCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 4567999999866654332 366699999985
No 22
>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=51.95 E-value=5.9 Score=27.75 Aligned_cols=17 Identities=41% Similarity=1.224 Sum_probs=7.1
Q ss_pred CCcccccccccccccCc
Q 042156 61 QPRYFCKTCRRYWTQGG 77 (336)
Q Consensus 61 QPRhfCksCrRYWT~GG 77 (336)
+|||||.=|..|.|..-
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 58999999999987654
No 23
>PHA00626 hypothetical protein
Probab=50.96 E-value=11 Score=29.64 Aligned_cols=37 Identities=22% Similarity=0.291 Sum_probs=24.6
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCcc
Q 042156 40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGT 78 (336)
Q Consensus 40 ~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGt 78 (336)
.||.|.|.+--=|-.= ....-||.|++|.=++|+..-
T Consensus 2 ~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceeeeecee--cccCcceEcCCCCCeechhhh
Confidence 6999999754322110 112457999999999998643
No 24
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=48.68 E-value=13 Score=34.87 Aligned_cols=32 Identities=28% Similarity=0.662 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRY 72 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRY 72 (336)
....+||||...=.|.-+ . .+.-|||..|++-
T Consensus 233 R~g~pC~~Cg~~I~~~~~-~----gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 233 REGQPCPRCGTPIEKIVV-G----GRGTHFCPQCQPL 264 (269)
T ss_pred CCcCCCCcCCCeeEEEEE-C----CCCcEECCCCcCC
Confidence 345689999987666433 2 3667999999963
No 25
>PRK10445 endonuclease VIII; Provisional
Probab=47.99 E-value=11 Score=35.04 Aligned_cols=31 Identities=29% Similarity=0.783 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
....+||||...=.|.-+ . .+.-|||..|++
T Consensus 233 r~g~~Cp~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 263 (263)
T PRK10445 233 RDGEACERCGGIIEKTTL-S----SRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCCCEeEEEEE-C----CCCcEECCCCcC
Confidence 345789999987665544 2 366799999984
No 26
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=46.80 E-value=14 Score=34.35 Aligned_cols=31 Identities=23% Similarity=0.688 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
....+||||...=.|. -++ .+.-|||..|++
T Consensus 243 R~g~pC~~Cg~~I~~~-~~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 243 REGEPCRRCGTPIEKI-KQG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCCeeEEE-EEC----CCCcEECcCCCC
Confidence 3557899999876554 333 366799999986
No 27
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=44.03 E-value=13 Score=27.50 Aligned_cols=27 Identities=33% Similarity=0.712 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
...-||+|.+. |..-.. .|+.|..|..
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 45689999873 544443 6999999974
No 28
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=42.79 E-value=19 Score=33.92 Aligned_cols=31 Identities=13% Similarity=0.528 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
....+||||...=.|.-+ -.+.-|||..|++
T Consensus 252 R~g~pC~~Cg~~I~~~~~-----~gR~t~~CP~CQ~ 282 (282)
T PRK13945 252 RTGKPCRKCGTPIERIKL-----AGRSTHWCPNCQK 282 (282)
T ss_pred CCcCCCCcCCCeeEEEEE-----CCCccEECCCCcC
Confidence 345689999987666544 2266699999984
No 29
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=38.14 E-value=12 Score=29.71 Aligned_cols=24 Identities=29% Similarity=0.603 Sum_probs=15.0
Q ss_pred ccccccCCCCccccccCCCCCCCCCCCCC
Q 042156 18 RRLKTMQGGTENQQQQEQPQPQKCPRCES 46 (336)
Q Consensus 18 RRlk~~~~~~~~~q~~~~~~~~~CPRC~S 46 (336)
+|+|...-.+-. -+.-+.||||+-
T Consensus 2 ~R~KA~Kv~~RD-----GE~~lrCPRC~~ 25 (65)
T COG4049 2 VRLKAIKVRDRD-----GEEFLRCPRCGM 25 (65)
T ss_pred ccceeeEeeccC-----CceeeeCCchhH
Confidence 456655433311 357899999985
No 30
>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=36.62 E-value=26 Score=32.78 Aligned_cols=30 Identities=23% Similarity=0.577 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCR 70 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCr 70 (336)
....+||||...=.|.-+ . .+.-|||..|+
T Consensus 243 r~g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ 272 (272)
T TIGR00577 243 RKGEPCRRCGTPIEKIKV-G----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCCCeeEEEEE-C----CCCCEECCCCC
Confidence 445689999987666433 2 36679999996
No 31
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=36.29 E-value=20 Score=36.05 Aligned_cols=36 Identities=28% Similarity=0.663 Sum_probs=22.1
Q ss_pred cCCCCCCCCCCCCCCCceeeeecccCC-----CCCcccccccc
Q 042156 33 QEQPQPQKCPRCESLNTKFCYYNNYSL-----SQPRYFCKTCR 70 (336)
Q Consensus 33 ~~~~~~~~CPRC~S~nTKFcYyNNy~~-----~QPRhfCksCr 70 (336)
..+..--+||||...| ||.---.-. .-..-||+.|.
T Consensus 301 a~pa~t~~~~r~~k~n--fc~ncG~~~t~~~~ng~a~fcp~cg 341 (345)
T COG4260 301 AAPAATWPCARCAKLN--FCLNCGCGTTADFDNGKAKFCPECG 341 (345)
T ss_pred cCCcccCcchhccccc--cccccCcccccCCccchhhhChhhc
Confidence 3456778999999887 765332111 11346777775
No 32
>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=35.84 E-value=27 Score=27.61 Aligned_cols=32 Identities=22% Similarity=0.515 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCcccccccccc
Q 042156 38 PQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRY 72 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRY 72 (336)
...||+|.+.+|=..|..|. ..-.-|-.|.=.
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 46799999999988888776 556778888643
No 33
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=33.39 E-value=25 Score=34.11 Aligned_cols=32 Identities=19% Similarity=0.580 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
-..-.+|++|.+.=.|--. -.+..|||..|++
T Consensus 242 gR~GepC~~CGt~I~k~~~-----~gR~t~~CP~CQ~ 273 (273)
T COG0266 242 GRAGEPCRRCGTPIEKIKL-----GGRSTFYCPVCQK 273 (273)
T ss_pred cCCCCCCCccCCEeEEEEE-----cCCcCEeCCCCCC
Confidence 4567789999995444311 3467799999985
No 34
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=32.88 E-value=34 Score=29.55 Aligned_cols=39 Identities=26% Similarity=0.665 Sum_probs=33.5
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 042156 36 PQPQKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWT 74 (336)
Q Consensus 36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT 74 (336)
+-...||+|...+.-|--++-.+..-|- |.|-.|+--|-
T Consensus 63 ~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 63 QTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred hccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 4577899999999999888888887776 89999999884
No 35
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=32.77 E-value=18 Score=28.01 Aligned_cols=16 Identities=38% Similarity=0.688 Sum_probs=6.7
Q ss_pred CCCCCCCCCCCCCCce
Q 042156 35 QPQPQKCPRCESLNTK 50 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTK 50 (336)
+--.++|+.|.|.||+
T Consensus 45 H~lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 45 HFLGHKCSHCGSYNTR 60 (61)
T ss_dssp -TT----TTTS---EE
T ss_pred eHhhhcCCCCCCcccC
Confidence 4567899999999997
No 36
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=31.27 E-value=45 Score=24.03 Aligned_cols=35 Identities=17% Similarity=0.384 Sum_probs=19.9
Q ss_pred CCCCCCCCCCCCceeeeecccCCCC-Cccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQ-PRYFCKTCRR 71 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~Q-PRhfCksCrR 71 (336)
+..+||.|.+....+.+........ -.-+|..|.-
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4678999966655554422211111 3345888866
No 37
>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=31.04 E-value=46 Score=24.11 Aligned_cols=33 Identities=27% Similarity=0.611 Sum_probs=19.7
Q ss_pred CCCCCCCCCCceeeeecccCCCCCccc-ccccccc
Q 042156 39 QKCPRCESLNTKFCYYNNYSLSQPRYF-CKTCRRY 72 (336)
Q Consensus 39 ~~CPRC~S~nTKFcYyNNy~~~QPRhf-CksCrRY 72 (336)
.+||.|.+..-.|=+ ......-.+++ |..|...
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCCC
Confidence 589999997765532 12233334444 8887643
No 38
>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=30.53 E-value=29 Score=24.91 Aligned_cols=32 Identities=19% Similarity=0.677 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 38 PQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
+.+||-|.. ..+|..|-+. ...-..+|+.|..
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 568999988 5688866543 2347799999943
No 39
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=30.17 E-value=32 Score=31.42 Aligned_cols=43 Identities=23% Similarity=0.287 Sum_probs=29.4
Q ss_pred CCCCCCCCCceeeee---cccCCCCCcccccccccccccCcccccc
Q 042156 40 KCPRCESLNTKFCYY---NNYSLSQPRYFCKTCRRYWTQGGTLRNV 82 (336)
Q Consensus 40 ~CPRC~S~nTKFcYy---NNy~~~QPRhfCksCrRYWT~GGtLRNV 82 (336)
.||.|.+.+||+-== -.-+.-+-|.-|.+|..-+|-==++--+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELR 47 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeec
Confidence 699999999998421 1123445578999999888855443333
No 40
>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=28.69 E-value=33 Score=25.22 Aligned_cols=32 Identities=31% Similarity=0.601 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQ 75 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~ 75 (336)
.-..||.|.....+ .+..-.+.|..|...+..
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 35579999998877 566777999999876543
No 41
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=28.68 E-value=23 Score=29.78 Aligned_cols=44 Identities=23% Similarity=0.532 Sum_probs=32.4
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCC
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVG 85 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVG 85 (336)
......||-|.....| -..----.|+.|..-|+.|+-....|+|
T Consensus 32 ~~~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 32 QRAKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred HhcCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 3568899999998554 1222337899999999999987666654
No 42
>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=28.38 E-value=47 Score=28.83 Aligned_cols=31 Identities=26% Similarity=0.720 Sum_probs=25.1
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcccccccccccccCc
Q 042156 39 QKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGG 77 (336)
Q Consensus 39 ~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GG 77 (336)
..||.|.|..|-- ...-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY~--------dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTYH--------DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceEe--------cCCeeECccccccccccc
Confidence 5799999987632 455699999999999875
No 43
>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=27.46 E-value=39 Score=27.10 Aligned_cols=30 Identities=20% Similarity=0.458 Sum_probs=17.0
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 38 PQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
...||-|+..+..|..+.+- -++.|-+|.+
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~ 62 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDK----NRFKCFGCGK 62 (97)
T ss_dssp EE--SSS--SS--EEEETTT----TEEEETTT--
T ss_pred EEECcCCCCCCCceEEECCC----CeEEECCCCC
Confidence 56799999887787776543 3799999985
No 44
>PRK00420 hypothetical protein; Validated
Probab=25.04 E-value=45 Score=28.64 Aligned_cols=28 Identities=14% Similarity=0.441 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCccccccccccc
Q 042156 38 PQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYW 73 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYW 73 (336)
...||.|.+.-+++ .+-..||..|...-
T Consensus 23 ~~~CP~Cg~pLf~l--------k~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFEL--------KDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcceec--------CCCceECCCCCCee
Confidence 36799999887775 46789999998753
No 45
>PRK10220 hypothetical protein; Provisional
Probab=23.94 E-value=59 Score=28.37 Aligned_cols=32 Identities=28% Similarity=0.713 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCcccccccccccccCc
Q 042156 38 PQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGG 77 (336)
Q Consensus 38 ~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GG 77 (336)
...||.|.|..|-- ...-+.|..|.-=|+...
T Consensus 3 lP~CP~C~seytY~--------d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 3 LPHCPKCNSEYTYE--------DNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCcCCCCCCcceEc--------CCCeEECCcccCcCCccc
Confidence 35799999987632 456799999999998775
No 46
>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=23.19 E-value=33 Score=33.42 Aligned_cols=33 Identities=24% Similarity=0.678 Sum_probs=12.6
Q ss_pred CCCCCCCCCC-CceeeeecccCCCCCcccccccccccc
Q 042156 38 PQKCPRCESL-NTKFCYYNNYSLSQPRYFCKTCRRYWT 74 (336)
Q Consensus 38 ~~~CPRC~S~-nTKFcYyNNy~~~QPRhfCksCrRYWT 74 (336)
...||+|.+. -.+| ..+.+-.-.+|..|..=+-
T Consensus 31 n~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp H---TTT--SS-EE------------EEE-TTT--EEE
T ss_pred CCcCCCCCChhHhhc----cCCCccceeECCCCchHHh
Confidence 4679999998 5665 3344556799999986554
No 47
>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=22.79 E-value=35 Score=22.01 Aligned_cols=27 Identities=30% Similarity=0.826 Sum_probs=13.7
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcccccccc
Q 042156 39 QKCPRCESLNTKFCYYNNYSLSQPRYFCKTCR 70 (336)
Q Consensus 39 ~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCr 70 (336)
.+||||...-.++-.. .+.-+||..|+
T Consensus 2 ~~C~rC~~~~~~~~~~-----~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGIN-----GRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEET-----TEEEEE-TTTC
T ss_pred CcCccCCCcceEeEec-----CCCCeECcCCc
Confidence 4789998877665442 12336777775
No 48
>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=21.88 E-value=42 Score=22.94 Aligned_cols=28 Identities=32% Similarity=0.679 Sum_probs=14.6
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcccccccccccc
Q 042156 39 QKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWT 74 (336)
Q Consensus 39 ~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT 74 (336)
-+||-|.|..|= ...--+.|..|..=|.
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 479999998875 4667788999987774
No 49
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=21.84 E-value=43 Score=28.01 Aligned_cols=44 Identities=23% Similarity=0.380 Sum_probs=29.7
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCC
Q 042156 35 QPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVG 85 (336)
Q Consensus 35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVG 85 (336)
+...+.||.|....-|= ..----.|+.|.+-|+.|.-..+-|.|
T Consensus 33 q~a~y~CpfCgk~~vkR-------~a~GIW~C~~C~~~~AGGAy~~~T~~~ 76 (90)
T PTZ00255 33 QHAKYFCPFCGKHAVKR-------QAVGIWRCKGCKKTVAGGAWTLSTPAA 76 (90)
T ss_pred HhCCccCCCCCCCceee-------eeeEEEEcCCCCCEEeCCccccccchh
Confidence 35688999998665541 001227899999999888775554443
No 50
>PF08142 AARP2CN: AARP2CN (NUC121) domain; InterPro: IPR012948 This domain is the central domain of AARP2 (asparagine and aspartate rich protein 2). It is weakly similar to the GTP-binding domain of elongation factor TU []. PfAARP2 is an antigen from Plasmodium falciparum of 150 kDa, which is encoded by a unique gene on chromosome 1 []. The central region of Pfaarp2 contains blocks of repetitions encoding asparagine and aspartate residues. ; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=21.69 E-value=39 Score=27.05 Aligned_cols=14 Identities=43% Similarity=0.719 Sum_probs=12.8
Q ss_pred cCCCCcCCCCCCCC
Q 042156 320 SLNPNQWRDLPGYG 333 (336)
Q Consensus 320 sl~~nqW~~lpg~g 333 (336)
.|+.|+..|+||+|
T Consensus 58 ~l~~n~lVHIpG~G 71 (85)
T PF08142_consen 58 PLSVNQLVHIPGVG 71 (85)
T ss_pred cccCCCEEEeCCcC
Confidence 38899999999998
No 51
>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=20.35 E-value=88 Score=26.90 Aligned_cols=31 Identities=26% Similarity=0.399 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156 37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR 71 (336)
Q Consensus 37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 71 (336)
.-..||-|.+.+|.+--- ..---..|++|..
T Consensus 92 ~yVlC~~C~spdT~l~k~----~r~~~l~C~aCGa 122 (125)
T PF01873_consen 92 EYVLCPECGSPDTELIKE----GRLIFLKCKACGA 122 (125)
T ss_dssp HHSSCTSTSSSSEEEEEE----TTCCEEEETTTSC
T ss_pred HEEEcCCCCCCccEEEEc----CCEEEEEecccCC
Confidence 347899999999997544 1123366888853
Done!