Query 043617
Match_columns 291
No_of_seqs 143 out of 202
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 06:40:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043617.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043617hhsearch_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 1.2E-37 2.7E-42 234.6 3.8 62 11-72 2-63 (63)
2 PF12760 Zn_Tnp_IS1595: Transp 94.2 0.033 7.1E-07 38.8 2.1 28 14-47 18-45 (46)
3 TIGR02159 PA_CoA_Oxy4 phenylac 93.2 0.034 7.4E-07 47.6 0.8 34 14-49 105-140 (146)
4 COG3677 Transposase and inacti 92.6 0.09 1.9E-06 44.2 2.5 35 15-51 31-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 90.2 0.21 4.5E-06 34.4 1.8 31 14-46 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 89.1 0.46 1E-05 32.8 2.9 37 15-51 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 86.0 0.63 1.4E-05 31.9 2.1 35 16-50 2-39 (39)
8 PF13453 zf-TFIIB: Transcripti 81.1 0.45 9.8E-06 32.4 -0.2 37 16-57 1-37 (41)
9 cd00202 ZnF_GATA Zinc finger D 79.1 1.6 3.5E-05 31.9 2.2 40 16-58 1-40 (54)
10 TIGR01384 TFS_arch transcripti 77.3 3.3 7.2E-05 32.4 3.6 39 14-52 62-103 (104)
11 PHA02998 RNA polymerase subuni 76.8 2.7 5.8E-05 38.6 3.4 39 13-51 142-183 (195)
12 PF04216 FdhE: Protein involve 76.6 1.2 2.5E-05 40.9 1.0 37 14-50 211-249 (290)
13 PF04981 NMD3: NMD3 family ; 71.7 2.2 4.9E-05 38.2 1.6 37 17-53 1-49 (236)
14 KOG2906 RNA polymerase III sub 62.1 7.2 0.00016 33.0 2.6 45 4-50 57-104 (105)
15 smart00401 ZnF_GATA zinc finge 61.9 6.7 0.00014 28.3 2.1 40 13-55 2-41 (52)
16 TIGR00244 transcriptional regu 61.6 6.4 0.00014 34.7 2.4 45 16-60 2-49 (147)
17 PF14690 zf-ISL3: zinc-finger 59.6 4.8 0.0001 27.1 1.0 32 14-45 2-47 (47)
18 PRK00464 nrdR transcriptional 55.4 8.8 0.00019 33.6 2.1 44 16-59 2-48 (154)
19 PHA00626 hypothetical protein 54.9 8.5 0.00018 29.7 1.7 36 16-53 2-37 (59)
20 PF06220 zf-U1: U1 zinc finger 54.6 5.2 0.00011 27.5 0.5 17 37-53 1-17 (38)
21 PF09526 DUF2387: Probable met 52.4 11 0.00024 29.3 2.1 32 13-47 7-38 (71)
22 PRK03564 formate dehydrogenase 51.5 13 0.00028 36.0 2.7 37 14-51 226-264 (309)
23 PRK00432 30S ribosomal protein 47.5 11 0.00024 27.4 1.3 26 14-47 20-45 (50)
24 TIGR01562 FdhE formate dehydro 46.4 16 0.00036 35.1 2.6 36 14-50 224-263 (305)
25 PF14599 zinc_ribbon_6: Zinc-r 46.1 8.4 0.00018 29.3 0.5 14 13-26 47-60 (61)
26 PF14354 Lar_restr_allev: Rest 38.8 29 0.00063 24.6 2.3 36 12-47 1-37 (61)
27 PF07282 OrfB_Zn_ribbon: Putat 36.6 32 0.00068 24.9 2.3 32 13-51 27-58 (69)
28 PF06827 zf-FPG_IleRS: Zinc fi 33.3 18 0.00039 23.0 0.5 28 14-46 1-28 (30)
29 TIGR02443 conserved hypothetic 31.7 36 0.00078 26.2 1.9 31 13-46 8-38 (59)
30 COG1327 Predicted transcriptio 29.2 36 0.00078 30.6 1.8 44 16-59 2-48 (156)
31 TIGR03655 anti_R_Lar restricti 29.1 55 0.0012 23.3 2.4 32 15-47 2-34 (53)
32 COG1997 RPL43A Ribosomal prote 29.1 37 0.00081 28.1 1.7 41 14-61 35-75 (89)
33 TIGR00686 phnA alkylphosphonat 28.9 43 0.00094 28.5 2.2 32 14-53 2-33 (109)
34 PRK10220 hypothetical protein; 25.5 55 0.0012 28.0 2.2 32 14-53 3-34 (111)
35 PF08274 PhnA_Zn_Ribbon: PhnA 25.3 35 0.00075 22.9 0.8 28 15-50 3-30 (30)
36 PF08273 Prim_Zn_Ribbon: Zinc- 24.8 52 0.0011 23.2 1.6 32 14-47 3-34 (40)
37 PF01807 zf-CHC2: CHC2 zinc fi 24.1 50 0.0011 26.1 1.6 29 15-47 34-62 (97)
38 smart00661 RPOL9 RNA polymeras 22.1 64 0.0014 22.0 1.7 32 16-52 2-33 (52)
39 KOG2691 RNA polymerase II subu 21.9 64 0.0014 27.8 1.9 37 13-51 72-113 (113)
40 PF06044 DRP: Dam-replacing fa 21.9 35 0.00077 32.7 0.5 34 13-50 30-64 (254)
41 COG4049 Uncharacterized protei 20.4 37 0.00081 26.6 0.2 12 12-23 15-26 (65)
42 PRK00420 hypothetical protein; 20.3 76 0.0016 26.8 2.1 28 14-49 23-50 (112)
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=1.2e-37 Score=234.60 Aligned_cols=62 Identities=76% Similarity=1.541 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCCCCceeeeecCCCCCCCcccccccccccccCCccccccCCCCccCCCCCCC
Q 043617 11 VEISPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNRRGKS 72 (291)
Q Consensus 11 ~e~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnVPVGGG~RKnKrsss 72 (291)
+++.++||||+|.+|||||||||+++||||||++|+||||+||+||||||||||||+|+++|
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 57889999999999999999999999999999999999999999999999999999999875
No 2
>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=94.25 E-value=0.033 Score=38.79 Aligned_cols=28 Identities=43% Similarity=0.967 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCceeeeecCCCCCCCccccccccc
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRR 47 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 47 (291)
+..||+|.+. +...+.+ +.+|.|++|++
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 4779999998 6655655 78999999986
No 3
>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=93.21 E-value=0.034 Score=47.60 Aligned_cols=34 Identities=32% Similarity=0.868 Sum_probs=26.7
Q ss_pred CCCCCCCCCCCceeeeecCC--CCCCCccccccccccc
Q 043617 14 SPNCPRCGSSNTKFCYYNNY--SLTQPRYFCKGCRRYW 49 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy--~~~QPR~fCk~CrRYW 49 (291)
...||||.|.+|+.. +.+ +.++.-|+|++|+.=+
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 379999999999964 555 4457779999998643
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.60 E-value=0.09 Score=44.18 Aligned_cols=35 Identities=40% Similarity=0.728 Sum_probs=28.0
Q ss_pred CCCCCCCCCCceeeeecCCCCCCCccccccccccccc
Q 043617 15 PNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTK 51 (291)
Q Consensus 15 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~ 51 (291)
..||+|.+.+ +-=+.-+.....||.|++|++-|+.
T Consensus 31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred CcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 6899999999 3335555556999999999999874
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=90.19 E-value=0.21 Score=34.39 Aligned_cols=31 Identities=42% Similarity=0.842 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCceeeeecCCCCC-CCcccccccc
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLT-QPRYFCKGCR 46 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~-QPR~fCk~Cr 46 (291)
.+.||+|.+.+. -|=|-.+.. ..||+|++|+
T Consensus 5 ~v~CP~C~s~~~--v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEG--VKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCc--ceeCCCCCCCCEeEecCcCC
Confidence 468999999872 123444433 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.06 E-value=0.46 Score=32.78 Aligned_cols=37 Identities=30% Similarity=0.860 Sum_probs=27.8
Q ss_pred CCCCCCCCCCceeeeecCCCCCCC---ccccccccccccc
Q 043617 15 PNCPRCGSSNTKFCYYNNYSLTQP---RYFCKGCRRYWTK 51 (291)
Q Consensus 15 ~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRYWT~ 51 (291)
.+||+|...+.-|-..+-.+...| -|.|.+|...|..
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 379999977777666655655555 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=85.98 E-value=0.63 Score=31.89 Aligned_cols=35 Identities=31% Similarity=0.888 Sum_probs=24.0
Q ss_pred CCCCCCCCCceeeeecCCCCCCCc---ccccccccccc
Q 043617 16 NCPRCGSSNTKFCYYNNYSLTQPR---YFCKGCRRYWT 50 (291)
Q Consensus 16 ~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT 50 (291)
+||.|...+.-|=-.+..+...|- |.|.+|..-|+
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 699999987766555665555453 89999999985
No 8
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=81.12 E-value=0.45 Score=32.37 Aligned_cols=37 Identities=27% Similarity=0.651 Sum_probs=27.3
Q ss_pred CCCCCCCCCceeeeecCCCCCCCcccccccccccccCCcccc
Q 043617 16 NCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSLRN 57 (291)
Q Consensus 16 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRn 57 (291)
+||+|...-...-+ ..-+-+.|.+|.-.|=..|.+..
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 69999986555444 23566889999999988776654
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=79.14 E-value=1.6 Score=31.91 Aligned_cols=40 Identities=28% Similarity=0.739 Sum_probs=28.4
Q ss_pred CCCCCCCCCceeeeecCCCCCCCcccccccccccccCCccccc
Q 043617 16 NCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSLRNV 58 (291)
Q Consensus 16 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnV 58 (291)
.|-.|...+|..=.-. ......+|-+|.-||.+.|..|.+
T Consensus 1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~ 40 (54)
T cd00202 1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPL 40 (54)
T ss_pred CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCc
Confidence 3777888777532221 246778999999999999965544
No 10
>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=77.32 E-value=3.3 Score=32.40 Aligned_cols=39 Identities=23% Similarity=0.715 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCceeeeecCCCCCCCc---ccccccccccccC
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLTQPR---YFCKGCRRYWTKG 52 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT~G 52 (291)
..+||+|...+.-|=..+-.+...|- |.|..|+-.|+.+
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 47999998777666555555444333 9999999999875
No 11
>PHA02998 RNA polymerase subunit; Provisional
Probab=76.82 E-value=2.7 Score=38.64 Aligned_cols=39 Identities=23% Similarity=0.578 Sum_probs=33.6
Q ss_pred CCCCCCCCCCCCceeeeecCCCCCCCc---cccccccccccc
Q 043617 13 ISPNCPRCGSSNTKFCYYNNYSLTQPR---YFCKGCRRYWTK 51 (291)
Q Consensus 13 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT~ 51 (291)
...+||+|...++-|=-.|-.+...|- |.|..|..-|.-
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 558999999999998888888888775 899999999964
No 12
>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=76.62 E-value=1.2 Score=40.92 Aligned_cols=37 Identities=24% Similarity=0.635 Sum_probs=18.6
Q ss_pred CCCCCCCCCCC-ceeeeecCC-CCCCCcccccccccccc
Q 043617 14 SPNCPRCGSSN-TKFCYYNNY-SLTQPRYFCKGCRRYWT 50 (291)
Q Consensus 14 ~~~CPRC~S~n-TKFcYyNNy-~~~QPR~fCk~CrRYWT 50 (291)
-..||.|...+ .++-||..- ....--+.|+.|+.|+-
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 35899999884 566677433 33333489999999983
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=71.67 E-value=2.2 Score=38.23 Aligned_cols=37 Identities=32% Similarity=0.860 Sum_probs=26.1
Q ss_pred CCCCCCCCce-------eeeecCCCCCC-----CcccccccccccccCC
Q 043617 17 CPRCGSSNTK-------FCYYNNYSLTQ-----PRYFCKGCRRYWTKGG 53 (291)
Q Consensus 17 CPRC~S~nTK-------FcYyNNy~~~Q-----PR~fCk~CrRYWT~GG 53 (291)
||+|...... =||...+.+.. --..|+.|.||+..|.
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 7777765443 37777776654 2278999999999843
No 14
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=62.07 E-value=7.2 Score=33.00 Aligned_cols=45 Identities=27% Similarity=0.733 Sum_probs=36.2
Q ss_pred ccCCCCCCCCCCCCCCCCCCCceeeeecCCCCCCCc---ccccccccccc
Q 043617 4 VWNHKPNVEISPNCPRCGSSNTKFCYYNNYSLTQPR---YFCKGCRRYWT 50 (291)
Q Consensus 4 ~w~~k~~~e~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRYWT 50 (291)
.| +-..+-...||+|...+.-|--+|-.+..-|- |.|-.|+--|-
T Consensus 57 a~--~nv~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 57 AW--ENVDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred cc--cchhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 57 33344557999999999998888888888776 99999999884
No 15
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=61.92 E-value=6.7 Score=28.32 Aligned_cols=40 Identities=25% Similarity=0.654 Sum_probs=29.1
Q ss_pred CCCCCCCCCCCCceeeeecCCCCCCCcccccccccccccCCcc
Q 043617 13 ISPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSL 55 (291)
Q Consensus 13 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtL 55 (291)
....|-.|....|..=.- ...-++.+|-+|.-||.+.|.+
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 346899999888853211 2223369999999999998886
No 16
>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=61.58 E-value=6.4 Score=34.72 Aligned_cols=45 Identities=22% Similarity=0.367 Sum_probs=33.4
Q ss_pred CCCCCCCCCceeeee---cCCCCCCCcccccccccccccCCccccccC
Q 043617 16 NCPRCGSSNTKFCYY---NNYSLTQPRYFCKGCRRYWTKGGSLRNVPV 60 (291)
Q Consensus 16 ~CPRC~S~nTKFcYy---NNy~~~QPR~fCk~CrRYWT~GGtLRnVPV 60 (291)
+||.|...+||+-== ...+.-+-|.-|.+|.+-||-==.+-..|+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l 49 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPP 49 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecccccc
Confidence 699999999998643 344455678999999999986555444443
No 17
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=59.65 E-value=4.8 Score=27.11 Aligned_cols=32 Identities=38% Similarity=0.922 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCcee-eeecCC-------------CCCCCccccccc
Q 043617 14 SPNCPRCGSSNTKF-CYYNNY-------------SLTQPRYFCKGC 45 (291)
Q Consensus 14 ~~~CPRC~S~nTKF-cYyNNy-------------~~~QPR~fCk~C 45 (291)
...||.|.+...+. -++... .+..+|++|++|
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 35799999876221 111111 344677888877
No 18
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=55.38 E-value=8.8 Score=33.56 Aligned_cols=44 Identities=25% Similarity=0.492 Sum_probs=32.1
Q ss_pred CCCCCCCCCceee---eecCCCCCCCcccccccccccccCCcccccc
Q 043617 16 NCPRCGSSNTKFC---YYNNYSLTQPRYFCKGCRRYWTKGGSLRNVP 59 (291)
Q Consensus 16 ~CPRC~S~nTKFc---YyNNy~~~QPR~fCk~CrRYWT~GGtLRnVP 59 (291)
+||.|.+..|++- |+-.-+.-.-|+-|++|.+-++.==++-..+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 7999999987764 4444445556699999999888765555444
No 19
>PHA00626 hypothetical protein
Probab=54.92 E-value=8.5 Score=29.74 Aligned_cols=36 Identities=28% Similarity=0.454 Sum_probs=24.3
Q ss_pred CCCCCCCCCceeeeecCCCCCCCcccccccccccccCC
Q 043617 16 NCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGG 53 (291)
Q Consensus 16 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GG 53 (291)
.||+|.|.+--=|-.= ....-||.|+.|.=.+|+..
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 6999999754321110 11146899999999999864
No 20
>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=54.59 E-value=5.2 Score=27.54 Aligned_cols=17 Identities=41% Similarity=1.171 Sum_probs=7.2
Q ss_pred CCcccccccccccccCC
Q 043617 37 QPRYFCKGCRRYWTKGG 53 (291)
Q Consensus 37 QPR~fCk~CrRYWT~GG 53 (291)
+|||+|.=|..|.|..-
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 21
>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=52.45 E-value=11 Score=29.26 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCCceeeeecCCCCCCCccccccccc
Q 043617 13 ISPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRR 47 (291)
Q Consensus 13 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 47 (291)
-++.||+|.+.+|-..|..|. ..-.-|-.|.=
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~---ve~vECV~CGy 38 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENG---VEYVECVECGY 38 (71)
T ss_pred cCccCCCCcCccEEEEEEeCC---ceEEEecCCCC
Confidence 467999999999988888777 55567888863
No 22
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=51.51 E-value=13 Score=35.95 Aligned_cols=37 Identities=24% Similarity=0.480 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCceeeeecCCC--CCCCccccccccccccc
Q 043617 14 SPNCPRCGSSNTKFCYYNNYS--LTQPRYFCKGCRRYWTK 51 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~--~~QPR~fCk~CrRYWT~ 51 (291)
-.+||.|... .|.-|+.--. ..---..|..|++|+--
T Consensus 226 R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 226 RVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred CccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 4589999874 4566653222 12223789999999754
No 23
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=47.48 E-value=11 Score=27.39 Aligned_cols=26 Identities=38% Similarity=0.860 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCceeeeecCCCCCCCccccccccc
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRR 47 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 47 (291)
..-||+|.+. |..-.. .|+.|..|..
T Consensus 20 ~~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 3489999873 544433 6999999974
No 24
>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=46.40 E-value=16 Score=35.06 Aligned_cols=36 Identities=19% Similarity=0.499 Sum_probs=23.3
Q ss_pred CCCCCCCCCCCceeeeecCCC----CCCCcccccccccccc
Q 043617 14 SPNCPRCGSSNTKFCYYNNYS----LTQPRYFCKGCRRYWT 50 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~----~~QPR~fCk~CrRYWT 50 (291)
-.+||.|.+.+ +.-|+.--. ..---..|..|+.|+-
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 46899999864 555665332 1122268999999974
No 25
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=46.13 E-value=8.4 Score=29.34 Aligned_cols=14 Identities=43% Similarity=1.018 Sum_probs=6.0
Q ss_pred CCCCCCCCCCCCce
Q 043617 13 ISPNCPRCGSSNTK 26 (291)
Q Consensus 13 ~~~~CPRC~S~nTK 26 (291)
.+.+|+.|.|.||+
T Consensus 47 lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 47 LGHKCSHCGSYNTR 60 (61)
T ss_dssp T----TTTS---EE
T ss_pred hhhcCCCCCCcccC
Confidence 35799999999997
No 26
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=38.80 E-value=29 Score=24.60 Aligned_cols=36 Identities=22% Similarity=0.422 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCCCceeeeecCCCCCC-Cccccccccc
Q 043617 12 EISPNCPRCGSSNTKFCYYNNYSLTQ-PRYFCKGCRR 47 (291)
Q Consensus 12 e~~~~CPRC~S~nTKFcYyNNy~~~Q-PR~fCk~CrR 47 (291)
++..+||.|.+....+.+........ -.-.|..|..
T Consensus 1 ~~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 1 EELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 35679999966655554422221111 3345888865
No 27
>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=36.64 E-value=32 Score=24.93 Aligned_cols=32 Identities=31% Similarity=0.690 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCCceeeeecCCCCCCCccccccccccccc
Q 043617 13 ISPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTK 51 (291)
Q Consensus 13 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~ 51 (291)
.+..||.|.....+ .+.+-.+.|..|...+.+
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 56789999998877 666777999999876543
No 28
>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=33.33 E-value=18 Score=22.99 Aligned_cols=28 Identities=25% Similarity=0.718 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCceeeeecCCCCCCCcccccccc
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCR 46 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 46 (291)
+.+||||...-.+.-..+ +.-+||..|+
T Consensus 1 G~~C~rC~~~~~~~~~~~-----r~~~~C~rCq 28 (30)
T PF06827_consen 1 GEKCPRCWNYIEDIGING-----RSTYLCPRCQ 28 (30)
T ss_dssp TSB-TTT--BBEEEEETT-----EEEEE-TTTC
T ss_pred CCcCccCCCcceEeEecC-----CCCeECcCCc
Confidence 357999998876654421 2337777775
No 29
>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=31.66 E-value=36 Score=26.24 Aligned_cols=31 Identities=23% Similarity=0.475 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCCceeeeecCCCCCCCcccccccc
Q 043617 13 ISPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCR 46 (291)
Q Consensus 13 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~Cr 46 (291)
-++.||+|...+|=..|..|.- .-.-|-.|.
T Consensus 8 AGA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 8 AGAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred ccccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 4679999999999988866653 335576664
No 30
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.18 E-value=36 Score=30.61 Aligned_cols=44 Identities=25% Similarity=0.398 Sum_probs=30.8
Q ss_pred CCCCCCCCCceeeeec---CCCCCCCcccccccccccccCCcccccc
Q 043617 16 NCPRCGSSNTKFCYYN---NYSLTQPRYFCKGCRRYWTKGGSLRNVP 59 (291)
Q Consensus 16 ~CPRC~S~nTKFcYyN---Ny~~~QPR~fCk~CrRYWT~GGtLRnVP 59 (291)
.||.|.+.+||+-==- .-+..+-|.-|.+|..-+|-==++--+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 6999999999985321 2234456789999998888655544443
No 31
>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=29.08 E-value=55 Score=23.32 Aligned_cols=32 Identities=28% Similarity=0.683 Sum_probs=18.6
Q ss_pred CCCCCCCCCCceeeeecCCCCCCCccc-cccccc
Q 043617 15 PNCPRCGSSNTKFCYYNNYSLTQPRYF-CKGCRR 47 (291)
Q Consensus 15 ~~CPRC~S~nTKFcYyNNy~~~QPR~f-Ck~CrR 47 (291)
.+||.|.+..-.|=+ ........+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 589999997664532 12233334444 777754
No 32
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=29.06 E-value=37 Score=28.09 Aligned_cols=41 Identities=24% Similarity=0.609 Sum_probs=30.2
Q ss_pred CCCCCCCCCCCceeeeecCCCCCCCcccccccccccccCCccccccCC
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSLRNVPVG 61 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GGtLRnVPVG 61 (291)
...||-|.+...| -...---.|+.|..-|+.|+-....|.|
T Consensus 35 ~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 35 KHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred CCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 4689999988555 1122337899999999999987766654
No 33
>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=28.89 E-value=43 Score=28.55 Aligned_cols=32 Identities=28% Similarity=0.736 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCceeeeecCCCCCCCcccccccccccccCC
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGG 53 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GG 53 (291)
...||.|.|..|- - .+.-+.|..|.-=|...+
T Consensus 2 lp~CP~C~seytY---~-----dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 2 LPPCPKCNSEYTY---H-----DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CCcCCcCCCcceE---e-----cCCeeECccccccccccc
Confidence 3689999998663 1 355699999999999876
No 34
>PRK10220 hypothetical protein; Provisional
Probab=25.49 E-value=55 Score=28.03 Aligned_cols=32 Identities=31% Similarity=0.823 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCceeeeecCCCCCCCcccccccccccccCC
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGG 53 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~GG 53 (291)
...||.|.|..|- ..+.-+.|..|.-=|+...
T Consensus 3 lP~CP~C~seytY--------~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 3 LPHCPKCNSEYTY--------EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCcCCCCCCcceE--------cCCCeEECCcccCcCCccc
Confidence 4689999998663 2355699999999999875
No 35
>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=25.28 E-value=35 Score=22.90 Aligned_cols=28 Identities=36% Similarity=0.852 Sum_probs=14.6
Q ss_pred CCCCCCCCCCceeeeecCCCCCCCcccccccccccc
Q 043617 15 PNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWT 50 (291)
Q Consensus 15 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT 50 (291)
.+||-|.|..|= ...--+.|..|..=|.
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 489999998775 4566788999987774
No 36
>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=24.80 E-value=52 Score=23.22 Aligned_cols=32 Identities=22% Similarity=0.728 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCceeeeecCCCCCCCccccccccc
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRR 47 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 47 (291)
..+||-|.. ..+|..|-+. ..+-..+|+.|..
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 458999987 5688866543 3347899999943
No 37
>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=24.10 E-value=50 Score=26.08 Aligned_cols=29 Identities=24% Similarity=0.549 Sum_probs=16.2
Q ss_pred CCCCCCCCCCceeeeecCCCCCCCccccccccc
Q 043617 15 PNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRR 47 (291)
Q Consensus 15 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR 47 (291)
..||-|+..+..|..+.+- -++.|-+|.+
T Consensus 34 ~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~ 62 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPDK----NRFKCFGCGK 62 (97)
T ss_dssp E--SSS--SS--EEEETTT----TEEEETTT--
T ss_pred EECcCCCCCCCceEEECCC----CeEEECCCCC
Confidence 4799999887777776543 3799999984
No 38
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.08 E-value=64 Score=21.98 Aligned_cols=32 Identities=22% Similarity=0.534 Sum_probs=19.6
Q ss_pred CCCCCCCCCceeeeecCCCCCCCcccccccccccccC
Q 043617 16 NCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKG 52 (291)
Q Consensus 16 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYWT~G 52 (291)
-||.|.+. .|..... ...|+.|..|...+-.+
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 59999773 2333221 12489999999765443
No 39
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=21.88 E-value=64 Score=27.78 Aligned_cols=37 Identities=27% Similarity=0.798 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCCceeeeecCCCCCCC-----ccccccccccccc
Q 043617 13 ISPNCPRCGSSNTKFCYYNNYSLTQP-----RYFCKGCRRYWTK 51 (291)
Q Consensus 13 ~~~~CPRC~S~nTKFcYyNNy~~~QP-----R~fCk~CrRYWT~ 51 (291)
....||+|...+.-| ||--+...- -|.|-+|.--||.
T Consensus 72 s~~~C~~C~~~eavf--fQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 72 SDKHCPKCGHREAVF--FQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred ccccCCccCCcceEE--EecccccccceEEEEEEeccccccccC
Confidence 456899999887654 554332211 1899999999985
No 40
>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=21.86 E-value=35 Score=32.67 Aligned_cols=34 Identities=26% Similarity=0.732 Sum_probs=13.0
Q ss_pred CCCCCCCCCCC-CceeeeecCCCCCCCcccccccccccc
Q 043617 13 ISPNCPRCGSS-NTKFCYYNNYSLTQPRYFCKGCRRYWT 50 (291)
Q Consensus 13 ~~~~CPRC~S~-nTKFcYyNNy~~~QPR~fCk~CrRYWT 50 (291)
+...||+|.+. -.+| .-+.+-.-.+|..|..=.-
T Consensus 30 ~n~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp HH---TTT--SS-EE------------EEE-TTT--EEE
T ss_pred HCCcCCCCCChhHhhc----cCCCccceeECCCCchHHh
Confidence 34579999998 5565 3344556699999987654
No 41
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=20.41 E-value=37 Score=26.58 Aligned_cols=12 Identities=50% Similarity=0.988 Sum_probs=9.1
Q ss_pred CCCCCCCCCCCC
Q 043617 12 EISPNCPRCGSS 23 (291)
Q Consensus 12 e~~~~CPRC~S~ 23 (291)
|+-+.||||+--
T Consensus 15 E~~lrCPRC~~~ 26 (65)
T COG4049 15 EEFLRCPRCGMV 26 (65)
T ss_pred ceeeeCCchhHH
Confidence 556799999853
No 42
>PRK00420 hypothetical protein; Validated
Probab=20.33 E-value=76 Score=26.81 Aligned_cols=28 Identities=21% Similarity=0.526 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCceeeeecCCCCCCCccccccccccc
Q 043617 14 SPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYW 49 (291)
Q Consensus 14 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRYW 49 (291)
...||.|.+.-+++ .+-..||..|.+.-
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 46899999887763 36789999997643
Done!