Query 024229
Match_columns 270
No_of_seqs 139 out of 266
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 03:01:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024229.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024229hhsearch_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 1.7E-37 3.6E-42 232.0 4.3 62 54-115 2-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 92.9 0.046 9.9E-07 46.7 1.2 33 57-91 105-139 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 91.1 0.15 3.2E-06 35.4 1.8 27 58-90 19-45 (46)
4 PF03811 Zn_Tnp_IS1: InsA N-te 91.0 0.13 2.7E-06 35.1 1.4 31 57-89 5-36 (36)
5 COG3677 Transposase and inacti 91.0 0.14 3.1E-06 42.9 2.0 35 58-94 31-65 (129)
6 smart00440 ZnF_C2C2 C2C2 Zinc 86.8 0.52 1.1E-05 32.3 2.1 37 58-94 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 85.1 0.55 1.2E-05 31.9 1.5 36 58-93 1-39 (39)
8 cd00202 ZnF_GATA Zinc finger D 74.1 3.9 8.4E-05 29.7 3.0 39 60-101 2-40 (54)
9 TIGR01384 TFS_arch transcripti 72.3 2.9 6.2E-05 32.7 2.1 39 57-95 62-103 (104)
10 PHA02998 RNA polymerase subuni 69.9 3.6 7.9E-05 37.5 2.5 39 56-94 142-183 (195)
11 PF13453 zf-TFIIB: Transcripti 67.9 1.3 2.8E-05 30.0 -0.6 37 59-100 1-37 (41)
12 PF04981 NMD3: NMD3 family ; 54.8 5.6 0.00012 35.7 0.9 26 71-96 19-49 (236)
13 PF04216 FdhE: Protein involve 53.6 5.6 0.00012 36.5 0.7 37 57-93 211-249 (290)
14 TIGR01385 TFSII transcription 52.7 9.6 0.00021 36.3 2.1 37 57-93 258-297 (299)
15 smart00401 ZnF_GATA zinc finge 52.1 9.6 0.00021 27.3 1.6 39 57-98 3-41 (52)
16 PF14690 zf-ISL3: zinc-finger 47.9 7.6 0.00017 26.1 0.5 10 58-67 3-12 (47)
17 PF06220 zf-U1: U1 zinc finger 46.9 7.2 0.00016 26.6 0.2 17 80-96 1-17 (38)
18 TIGR00244 transcriptional regu 44.3 14 0.00031 32.4 1.8 41 59-99 2-45 (147)
19 TIGR01562 FdhE formate dehydro 43.6 15 0.00033 35.2 2.0 37 57-94 224-264 (305)
20 PHA00626 hypothetical protein 41.0 15 0.00033 28.0 1.2 36 59-96 2-37 (59)
21 PRK00432 30S ribosomal protein 39.9 13 0.00027 26.8 0.6 25 58-90 21-45 (50)
22 PF14599 zinc_ribbon_6: Zinc-r 39.0 12 0.00026 28.3 0.4 14 56-69 47-60 (61)
23 PRK03564 formate dehydrogenase 38.7 19 0.00042 34.6 1.8 37 57-94 226-264 (309)
24 PRK14810 formamidopyrimidine-D 38.7 16 0.00035 33.7 1.3 30 56-90 243-272 (272)
25 PRK14811 formamidopyrimidine-D 35.9 19 0.00042 33.2 1.3 29 57-90 235-263 (269)
26 PF07815 Abi_HHR: Abl-interact 34.0 19 0.0004 28.8 0.8 14 209-222 46-59 (79)
27 KOG2906 RNA polymerase III sub 33.8 35 0.00076 28.7 2.4 37 57-93 65-104 (105)
28 PRK01103 formamidopyrimidine/5 32.1 24 0.00052 32.4 1.3 29 57-90 245-273 (274)
29 PF09526 DUF2387: Probable met 31.8 29 0.00063 26.8 1.5 31 56-89 7-37 (71)
30 PRK00464 nrdR transcriptional 30.8 30 0.00064 30.2 1.5 44 59-102 2-48 (154)
31 PRK10445 endonuclease VIII; Pr 29.8 28 0.0006 32.0 1.3 29 57-90 235-263 (263)
32 PRK13945 formamidopyrimidine-D 29.6 29 0.00063 32.1 1.4 29 57-90 254-282 (282)
33 TIGR00577 fpg formamidopyrimid 24.6 40 0.00086 31.1 1.3 28 57-89 245-272 (272)
34 COG1997 RPL43A Ribosomal prote 23.9 29 0.00062 28.4 0.2 42 56-104 34-75 (89)
35 COG2343 Uncharacterized protei 23.8 26 0.00055 30.5 -0.1 37 226-267 54-91 (132)
36 PF06827 zf-FPG_IleRS: Zinc fi 22.1 36 0.00078 21.4 0.4 27 58-89 2-28 (30)
37 PF14354 Lar_restr_allev: Rest 21.8 65 0.0014 22.7 1.7 35 56-90 2-37 (61)
38 PF07282 OrfB_Zn_ribbon: Putat 21.6 45 0.00098 24.0 0.9 30 58-94 29-58 (69)
39 TIGR03655 anti_R_Lar restricti 20.4 76 0.0017 22.4 1.8 32 58-90 2-34 (53)
40 PF08274 PhnA_Zn_Ribbon: PhnA 20.2 36 0.00078 22.5 0.1 28 58-93 3-30 (30)
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=1.7e-37 Score=232.01 Aligned_cols=62 Identities=79% Similarity=1.495 Sum_probs=59.4
Q ss_pred cccccCCCCCCCCCcceeeecccCCCCCchhhhhcccccccCCccccccCCCCCCCCCCCCC
Q 024229 54 RERVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSLRNVPVGGGSRKNKRSSS 115 (270)
Q Consensus 54 ~~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvPVGgG~RKnk~sss 115 (270)
+++.++||||+|.||||||||||+++||||||++|+||||+||+|||||||||+||+|+++|
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 46679999999999999999999999999999999999999999999999999999999875
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=92.91 E-value=0.046 Score=46.73 Aligned_cols=33 Identities=27% Similarity=0.704 Sum_probs=26.4
Q ss_pred ccCCCCCCCCCcceeeecccC--CCCCchhhhhcccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYS--FSQPRHFCKTCRRY 91 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~--~~QPR~fCk~CrRy 91 (270)
...||||.|.+|+.. +.+- .++.-|.|++|+.=
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEP 139 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCc
Confidence 489999999999964 6664 44777999999863
No 3
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=91.08 E-value=0.15 Score=35.40 Aligned_cols=27 Identities=41% Similarity=0.883 Sum_probs=22.1
Q ss_pred cCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
..||+|.+. +...+.+ +.++.|++|++
T Consensus 19 ~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 669999998 6655555 78999999985
No 4
>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=91.00 E-value=0.13 Score=35.12 Aligned_cols=31 Identities=45% Similarity=0.757 Sum_probs=21.7
Q ss_pred ccCCCCCCCCCcceeeecccCCC-CCchhhhhcc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFS-QPRHFCKTCR 89 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~-QPR~fCk~Cr 89 (270)
.+.||+|.+++.- |=|-.+.. ..||+|++|+
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 3789999998721 23444433 5899999996
No 5
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=90.97 E-value=0.14 Score=42.87 Aligned_cols=35 Identities=31% Similarity=0.695 Sum_probs=27.8
Q ss_pred cCCCCCCCCCcceeeecccCCCCCchhhhhccccccc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTA 94 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~ 94 (270)
..||+|.+.+ +-=++-+.....||.|++|++-|+.
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 6799999999 3335555555999999999998874
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=86.79 E-value=0.52 Score=32.29 Aligned_cols=37 Identities=24% Similarity=0.712 Sum_probs=28.4
Q ss_pred cCCCCCCCCCcceeeecccCCCCC---chhhhhccccccc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQP---RHFCKTCRRYWTA 94 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QP---R~fCk~CrRyWT~ 94 (270)
.+||+|...+.-|-..+-.+...| -|.|..|...|.+
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 369999987777766666666655 4999999999964
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=85.09 E-value=0.55 Score=31.95 Aligned_cols=36 Identities=25% Similarity=0.748 Sum_probs=25.0
Q ss_pred cCCCCCCCCCcceeeecccCCCCCc---hhhhhcccccc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQPR---HFCKTCRRYWT 93 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT 93 (270)
.+||.|...+.-|=-.+..+...|- |.|.+|..-|+
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 3699999988776555666666553 89999999885
No 8
>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=74.13 E-value=3.9 Score=29.75 Aligned_cols=39 Identities=28% Similarity=0.689 Sum_probs=27.9
Q ss_pred CCCCCCCCcceeeecccCCCCCchhhhhcccccccCCccccc
Q 024229 60 CPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSLRNV 101 (270)
Q Consensus 60 CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnv 101 (270)
|-.|..++|..=.-. ......+|-+|.-||.+.|..|.+
T Consensus 2 C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~ 40 (54)
T cd00202 2 CSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPL 40 (54)
T ss_pred CCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCc
Confidence 677887777532221 246779999999999999976544
No 9
>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=72.33 E-value=2.9 Score=32.74 Aligned_cols=39 Identities=18% Similarity=0.603 Sum_probs=29.1
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCc---hhhhhcccccccC
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPR---HFCKTCRRYWTAG 95 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT~G 95 (270)
...||+|...+.-|-..+-.+...|- |.|-.|+-.|+++
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 47999998777766555555544443 8999999999875
No 10
>PHA02998 RNA polymerase subunit; Provisional
Probab=69.85 E-value=3.6 Score=37.53 Aligned_cols=39 Identities=23% Similarity=0.605 Sum_probs=33.7
Q ss_pred cccCCCCCCCCCcceeeecccCCCCCc---hhhhhccccccc
Q 024229 56 RVLNCPRCNSTDTKFCYYNNYSFSQPR---HFCKTCRRYWTA 94 (270)
Q Consensus 56 ~~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT~ 94 (270)
....||+|...++-|=-.|-.+...|- |.|..|..-|.-
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 348899999999999888888888885 899999999963
No 11
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=67.89 E-value=1.3 Score=29.96 Aligned_cols=37 Identities=24% Similarity=0.612 Sum_probs=26.4
Q ss_pred CCCCCCCCCcceeeecccCCCCCchhhhhcccccccCCcccc
Q 024229 59 NCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSLRN 100 (270)
Q Consensus 59 ~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRn 100 (270)
+||+|...=...-+ ..-+-+.|..|.-.|=..|.+..
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 59999885444433 23456889999999988776643
No 12
>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=54.76 E-value=5.6 Score=35.74 Aligned_cols=26 Identities=27% Similarity=0.807 Sum_probs=17.7
Q ss_pred eeecccCCCC-----CchhhhhcccccccCC
Q 024229 71 CYYNNYSFSQ-----PRHFCKTCRRYWTAGG 96 (270)
Q Consensus 71 cyyNNy~~~Q-----PR~fCk~CrRyWT~GG 96 (270)
||...+.+.. --.+|+.|.||+..|.
T Consensus 19 C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 19 CYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred HhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 5555555433 2378999999999843
No 13
>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=53.59 E-value=5.6 Score=36.53 Aligned_cols=37 Identities=24% Similarity=0.647 Sum_probs=18.4
Q ss_pred ccCCCCCCCCCcc-eeeecccCCC-CCchhhhhcccccc
Q 024229 57 VLNCPRCNSTDTK-FCYYNNYSFS-QPRHFCKTCRRYWT 93 (270)
Q Consensus 57 ~~~CPRC~S~~Tk-fcyyNNy~~~-QPR~fCk~CrRyWT 93 (270)
...||.|...+.. +-||..-... .--+.|+.|+.|+-
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 4779999888765 5555333333 33399999999983
No 14
>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=52.72 E-value=9.6 Score=36.29 Aligned_cols=37 Identities=19% Similarity=0.645 Sum_probs=28.2
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCc---hhhhhcccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPR---HFCKTCRRYWT 93 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT 93 (270)
...||+|...+..|-..+..+...|- |.|..|...|.
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 48999999888777555666555553 78999999884
No 15
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=52.10 E-value=9.6 Score=27.34 Aligned_cols=39 Identities=26% Similarity=0.592 Sum_probs=28.6
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhcccccccCCcc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSL 98 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtl 98 (270)
...|--|..++|..=.- ...-++.+|-+|.-||.+.|.+
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 36799999888863211 2223369999999999998886
No 16
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=47.92 E-value=7.6 Score=26.06 Aligned_cols=10 Identities=40% Similarity=1.079 Sum_probs=8.3
Q ss_pred cCCCCCCCCC
Q 024229 58 LNCPRCNSTD 67 (270)
Q Consensus 58 ~~CPRC~S~~ 67 (270)
..||.|.+..
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 5699999877
No 17
>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=46.87 E-value=7.2 Score=26.63 Aligned_cols=17 Identities=35% Similarity=0.989 Sum_probs=7.1
Q ss_pred CCchhhhhcccccccCC
Q 024229 80 QPRHFCKTCRRYWTAGG 96 (270)
Q Consensus 80 QPR~fCk~CrRyWT~GG 96 (270)
+|||+|.=|..|.|..-
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 68999999999997654
No 18
>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=44.34 E-value=14 Score=32.36 Aligned_cols=41 Identities=20% Similarity=0.379 Sum_probs=29.9
Q ss_pred CCCCCCCCCcceeee---cccCCCCCchhhhhcccccccCCccc
Q 024229 59 NCPRCNSTDTKFCYY---NNYSFSQPRHFCKTCRRYWTAGGSLR 99 (270)
Q Consensus 59 ~CPRC~S~~Tkfcyy---NNy~~~QPR~fCk~CrRyWT~GGtlR 99 (270)
+||-|...+||+-=- ...+.-+-|.-|..|.+-||-==.+-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAE 45 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecc
Confidence 699999999998532 23334456799999999888554443
No 19
>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=43.64 E-value=15 Score=35.17 Aligned_cols=37 Identities=16% Similarity=0.520 Sum_probs=25.0
Q ss_pred ccCCCCCCCCCcceeeecccC----CCCCchhhhhccccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYS----FSQPRHFCKTCRRYWTA 94 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~----~~QPR~fCk~CrRyWT~ 94 (270)
..+||.|.+.+ +.-|+.--. ..---..|.+|+.|+--
T Consensus 224 R~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~ 264 (305)
T TIGR01562 224 RVKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLKI 264 (305)
T ss_pred CccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchhh
Confidence 47899999875 555665432 11223789999999853
No 20
>PHA00626 hypothetical protein
Probab=41.04 E-value=15 Score=28.04 Aligned_cols=36 Identities=17% Similarity=0.236 Sum_probs=24.2
Q ss_pred CCCCCCCCCcceeeecccCCCCCchhhhhcccccccCC
Q 024229 59 NCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGG 96 (270)
Q Consensus 59 ~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GG 96 (270)
.||+|.|.+.-=|=.= ....-||.|++|.=.+|+..
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 5999999764322111 11246899999999998764
No 21
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=39.88 E-value=13 Score=26.84 Aligned_cols=25 Identities=36% Similarity=0.711 Sum_probs=18.2
Q ss_pred cCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
.-||+|.+. |..-.. .|+.|..|..
T Consensus 21 ~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 21 KFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred CcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 469999874 554443 6999999974
No 22
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=39.02 E-value=12 Score=28.31 Aligned_cols=14 Identities=29% Similarity=0.608 Sum_probs=6.0
Q ss_pred cccCCCCCCCCCcc
Q 024229 56 RVLNCPRCNSTDTK 69 (270)
Q Consensus 56 ~~~~CPRC~S~~Tk 69 (270)
-+++|+.|.|.||+
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 36899999999997
No 23
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=38.69 E-value=19 Score=34.62 Aligned_cols=37 Identities=22% Similarity=0.538 Sum_probs=24.8
Q ss_pred ccCCCCCCCCCcceeeecccC--CCCCchhhhhccccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYS--FSQPRHFCKTCRRYWTA 94 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~--~~QPR~fCk~CrRyWT~ 94 (270)
...||.|... .+.-|+.--. ..---..|.+|+.|+--
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 4789999974 4666653222 12223899999999854
No 24
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.67 E-value=16 Score=33.68 Aligned_cols=30 Identities=17% Similarity=0.569 Sum_probs=21.6
Q ss_pred cccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 56 RVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 56 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
+..+||||...=.|.-+= .+.-|||-.|++
T Consensus 243 ~g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 357899999766554332 366699999985
No 25
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=35.94 E-value=19 Score=33.19 Aligned_cols=29 Identities=31% Similarity=0.772 Sum_probs=21.3
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
..+||||...=.|.-+ . .+.-|||..|++
T Consensus 235 g~pC~~Cg~~I~~~~~-~----gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVV-G----GRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEE-C----CCCcEECCCCcC
Confidence 4579999977666433 2 366799999996
No 26
>PF07815 Abi_HHR: Abl-interactor HHR; InterPro: IPR012849 The region is found towards the N terminus of a number of adaptor proteins that interact with Abl-family tyrosine kinases []. More specifically, it is termed the homeo-domain homologous region (HHR), as it is similar to the DNA-binding region of homeo-domain proteins []. Other homeo-domain proteins have been implicated in specifying positional information during embryonic development, and in the regulation of the expression of cell-type specific genes []. The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved in cytoskeletal reorganisation, but their precise role remains unclear []. ; GO: 0005737 cytoplasm; PDB: 3P8C_F.
Probab=34.01 E-value=19 Score=28.79 Aligned_cols=14 Identities=29% Similarity=0.529 Sum_probs=6.9
Q ss_pred CCCCCCCCCCCCCC
Q 024229 209 KKTLDFSSSDGFEN 222 (270)
Q Consensus 209 Kp~L~FSslDG~g~ 222 (270)
|.+++||.||.+|.
T Consensus 46 RkPIdys~LDdvGH 59 (79)
T PF07815_consen 46 RKPIDYSILDDVGH 59 (79)
T ss_dssp -----TTTTTTTTT
T ss_pred eccCccccccccCc
Confidence 56899999995554
No 27
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=33.83 E-value=35 Score=28.70 Aligned_cols=37 Identities=24% Similarity=0.615 Sum_probs=32.6
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCc---hhhhhcccccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPR---HFCKTCRRYWT 93 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT 93 (270)
...||+|...+.-|-=+|-.+..-|- |.|-.|.--|-
T Consensus 65 ~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 65 EATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred cCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 47899999999999989988888887 88999998885
No 28
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=32.13 E-value=24 Score=32.39 Aligned_cols=29 Identities=24% Similarity=0.622 Sum_probs=21.1
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
..+||||...=.|. -++ .+.-|||-.|++
T Consensus 245 g~pC~~Cg~~I~~~-~~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKI-KQG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEE-EEC----CCCcEECcCCCC
Confidence 46799999776553 333 366799999986
No 29
>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=31.76 E-value=29 Score=26.79 Aligned_cols=31 Identities=26% Similarity=0.501 Sum_probs=24.1
Q ss_pred cccCCCCCCCCCcceeeecccCCCCCchhhhhcc
Q 024229 56 RVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCR 89 (270)
Q Consensus 56 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~Cr 89 (270)
-+..||+|.+.+|=..|..|. ..-.-|-.|.
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~---ve~vECV~CG 37 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENG---VEYVECVECG 37 (71)
T ss_pred cCccCCCCcCccEEEEEEeCC---ceEEEecCCC
Confidence 357899999999888887776 4556677775
No 30
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=30.77 E-value=30 Score=30.20 Aligned_cols=44 Identities=25% Similarity=0.468 Sum_probs=30.7
Q ss_pred CCCCCCCCCccee---eecccCCCCCchhhhhcccccccCCcccccc
Q 024229 59 NCPRCNSTDTKFC---YYNNYSFSQPRHFCKTCRRYWTAGGSLRNVP 102 (270)
Q Consensus 59 ~CPRC~S~~Tkfc---yyNNy~~~QPR~fCk~CrRyWT~GGtlRnvP 102 (270)
.||-|.+..|++- |+-.-+.-.-|+-|..|.+-++.==++-..+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 6999999997764 3334344455699999999887655544443
No 31
>PRK10445 endonuclease VIII; Provisional
Probab=29.83 E-value=28 Score=32.01 Aligned_cols=29 Identities=28% Similarity=0.615 Sum_probs=20.8
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
...||||...=.|.-+ + .+.-|||-.|++
T Consensus 235 g~~Cp~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 263 (263)
T PRK10445 235 GEACERCGGIIEKTTL-S----SRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCEeEEEEE-C----CCCcEECCCCcC
Confidence 4679999877665544 2 266699999984
No 32
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.64 E-value=29 Score=32.13 Aligned_cols=29 Identities=17% Similarity=0.644 Sum_probs=21.1
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhccc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRR 90 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 90 (270)
..+||||...=.|.-+ . .+.-|||..|++
T Consensus 254 g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCRKCGTPIERIKL-A----GRSTHWCPNCQK 282 (282)
T ss_pred cCCCCcCCCeeEEEEE-C----CCccEECCCCcC
Confidence 4689999987666544 2 266699999984
No 33
>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=24.63 E-value=40 Score=31.10 Aligned_cols=28 Identities=29% Similarity=0.662 Sum_probs=20.3
Q ss_pred ccCCCCCCCCCcceeeecccCCCCCchhhhhcc
Q 024229 57 VLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCR 89 (270)
Q Consensus 57 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~Cr 89 (270)
..+||||...=.|.-+ . .+.-|||-.|+
T Consensus 245 g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKV-G----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEE-C----CCCCEECCCCC
Confidence 4689999977666433 3 26669999996
No 34
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=23.86 E-value=29 Score=28.44 Aligned_cols=42 Identities=24% Similarity=0.498 Sum_probs=30.4
Q ss_pred cccCCCCCCCCCcceeeecccCCCCCchhhhhcccccccCCccccccCC
Q 024229 56 RVLNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTAGGSLRNVPVG 104 (270)
Q Consensus 56 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvPVG 104 (270)
+...||-|.....| -..----.|+.|..-|+.|+-....|.|
T Consensus 34 ~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 34 AKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred cCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 45789999998555 1111227899999999999987766654
No 35
>COG2343 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.83 E-value=26 Score=30.49 Aligned_cols=37 Identities=27% Similarity=0.539 Sum_probs=23.5
Q ss_pred eeeeecCCCCCcC-CCCcchhhhhhccccCCCCccccccccCC
Q 024229 226 RLWFPLQDIKPEI-SNTTTDRFELNRGQAQAESTGYWTRLLGG 267 (270)
Q Consensus 226 RLLFPFEDLKq~v-Ss~~~~~~d~nk~q~~GdS~GyWnGMLGG 267 (270)
+..||+||++++. ..+..|.+--=|| ..+||+-.+||
T Consensus 54 ~~YiP~~Di~~e~l~~t~~~T~Cp~KG-----~AsYysv~~~~ 91 (132)
T COG2343 54 VHYIPPEDIRFEYLIPTPTHTYCPYKG-----TASYYSVVVGG 91 (132)
T ss_pred eeecCHHHchHhhcccCCCccccCccc-----ccceEEEEcCC
Confidence 8899999997643 2332233333354 45899977776
No 36
>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=22.13 E-value=36 Score=21.40 Aligned_cols=27 Identities=22% Similarity=0.591 Sum_probs=13.1
Q ss_pred cCCCCCCCCCcceeeecccCCCCCchhhhhcc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCR 89 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~Cr 89 (270)
.+||||...-.++-.. .+.-+||..|+
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 4688888876665441 12336676665
No 37
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.78 E-value=65 Score=22.72 Aligned_cols=35 Identities=20% Similarity=0.466 Sum_probs=19.3
Q ss_pred cccCCCCCCCCCcceeeecccCCCC-Cchhhhhccc
Q 024229 56 RVLNCPRCNSTDTKFCYYNNYSFSQ-PRHFCKTCRR 90 (270)
Q Consensus 56 ~~~~CPRC~S~~TkfcyyNNy~~~Q-PR~fCk~CrR 90 (270)
+..+||.|.+....+.+........ -.-.|..|..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4577999966655544422211111 3445888866
No 38
>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=21.58 E-value=45 Score=24.03 Aligned_cols=30 Identities=27% Similarity=0.520 Sum_probs=23.3
Q ss_pred cCCCCCCCCCcceeeecccCCCCCchhhhhccccccc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWTA 94 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~ 94 (270)
..||.|.....+ .+.+-.+.|..|...+.+
T Consensus 29 q~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 29 QTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred cCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 449999998887 666777999999876643
No 39
>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=20.41 E-value=76 Score=22.44 Aligned_cols=32 Identities=25% Similarity=0.542 Sum_probs=18.6
Q ss_pred cCCCCCCCCCcceeeecccCCCCCchh-hhhccc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQPRHF-CKTCRR 90 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QPR~f-Ck~CrR 90 (270)
.+||.|.+..-.|=+ ........+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 479999997765531 12233334444 777754
No 40
>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=20.24 E-value=36 Score=22.55 Aligned_cols=28 Identities=29% Similarity=0.619 Sum_probs=14.1
Q ss_pred cCCCCCCCCCcceeeecccCCCCCchhhhhcccccc
Q 024229 58 LNCPRCNSTDTKFCYYNNYSFSQPRHFCKTCRRYWT 93 (270)
Q Consensus 58 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT 93 (270)
-+||-|.|..|= ...--+.|-+|..=|.
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 469999998875 4566688888887763
Done!