Query 046549
Match_columns 250
No_of_seqs 131 out of 184
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 13:14:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046549.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046549hhsearch_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 1.5E-36 3.4E-41 224.9 3.9 57 17-73 3-59 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 93.4 0.031 6.7E-07 47.0 0.8 36 19-54 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 93.4 0.068 1.5E-06 36.5 2.3 29 18-52 17-45 (46)
4 COG3677 Transposase and inacti 92.1 0.11 2.3E-06 43.0 2.2 36 19-56 30-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 90.2 0.2 4.3E-06 33.8 1.7 31 19-51 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 89.2 0.41 8.9E-06 32.4 2.7 37 20-56 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 86.6 0.6 1.3E-05 31.4 2.2 36 20-55 1-39 (39)
8 PHA02998 RNA polymerase subuni 82.7 1.3 2.7E-05 40.0 3.1 43 14-56 138-183 (195)
9 PF04216 FdhE: Protein involve 81.1 0.74 1.6E-05 41.4 1.1 37 19-55 211-249 (290)
10 TIGR01384 TFS_arch transcripti 81.0 2 4.3E-05 33.0 3.3 45 12-57 56-103 (104)
11 cd00202 ZnF_GATA Zinc finger D 80.2 1.5 3.2E-05 31.5 2.2 41 21-64 1-41 (54)
12 PF13453 zf-TFIIB: Transcripti 79.3 0.57 1.2E-05 31.3 -0.1 37 21-62 1-37 (41)
13 PF04981 NMD3: NMD3 family ; 64.1 3.7 8.1E-05 36.2 1.4 38 22-59 1-50 (236)
14 TIGR00244 transcriptional regu 64.1 5.2 0.00011 34.7 2.2 45 21-65 2-49 (147)
15 smart00401 ZnF_GATA zinc finge 64.0 5.6 0.00012 28.2 2.0 40 18-60 2-41 (52)
16 PF14690 zf-ISL3: zinc-finger 61.7 4 8.6E-05 27.0 0.9 32 19-50 2-47 (47)
17 TIGR01562 FdhE formate dehydro 57.4 7.5 0.00016 36.7 2.2 36 19-55 224-263 (305)
18 PRK00464 nrdR transcriptional 57.3 7.7 0.00017 33.3 2.1 45 20-64 1-48 (154)
19 PRK03564 formate dehydrogenase 55.2 8.1 0.00018 36.6 2.1 36 19-55 226-263 (309)
20 PF06220 zf-U1: U1 zinc finger 54.2 5.3 0.00011 27.0 0.5 17 42-58 1-17 (38)
21 PHA00626 hypothetical protein 52.1 10 0.00023 28.7 1.8 37 21-59 2-38 (59)
22 PRK00432 30S ribosomal protein 46.3 11 0.00024 26.8 1.1 26 19-52 20-45 (50)
23 PF09526 DUF2387: Probable met 45.9 15 0.00033 28.0 1.9 31 19-52 8-38 (71)
24 KOG2691 RNA polymerase II subu 45.5 17 0.00036 30.6 2.2 43 12-56 66-113 (113)
25 KOG2906 RNA polymerase III sub 41.0 22 0.00048 29.6 2.2 38 18-55 64-104 (105)
26 PF14599 zinc_ribbon_6: Zinc-r 39.8 12 0.00026 27.9 0.5 13 19-31 48-60 (61)
27 COG1327 Predicted transcriptio 35.5 23 0.0005 31.2 1.7 44 21-64 2-48 (156)
28 PF06827 zf-FPG_IleRS: Zinc fi 32.1 23 0.00049 22.0 0.8 27 20-51 2-28 (30)
29 PF07282 OrfB_Zn_ribbon: Putat 30.8 29 0.00062 24.7 1.2 32 18-56 27-58 (69)
30 PRK14892 putative transcriptio 29.3 45 0.00099 26.9 2.3 36 16-55 18-53 (99)
31 COG1997 RPL43A Ribosomal prote 28.9 36 0.00077 27.6 1.6 42 18-66 34-75 (89)
32 PF14354 Lar_restr_allev: Rest 26.5 55 0.0012 22.7 2.1 35 18-52 2-37 (61)
33 TIGR02443 conserved hypothetic 26.0 50 0.0011 24.9 1.8 30 19-51 9-38 (59)
34 PF08274 PhnA_Zn_Ribbon: PhnA 25.4 34 0.00074 22.4 0.7 28 20-55 3-30 (30)
35 PRK12496 hypothetical protein; 24.8 42 0.00091 28.6 1.4 29 45-73 128-156 (164)
36 TIGR03655 anti_R_Lar restricti 24.6 65 0.0014 22.5 2.1 32 20-52 2-34 (53)
37 PF01873 eIF-5_eIF-2B: Domain 24.5 63 0.0014 26.8 2.3 30 19-52 93-122 (125)
38 PF08273 Prim_Zn_Ribbon: Zinc- 24.0 48 0.001 22.9 1.3 32 19-52 3-34 (40)
39 PF01807 zf-CHC2: CHC2 zinc fi 24.0 49 0.0011 25.6 1.6 30 19-52 33-62 (97)
40 TIGR00155 pqiA_fam integral me 23.3 44 0.00095 32.3 1.4 18 9-26 3-20 (403)
41 TIGR00686 phnA alkylphosphonat 22.1 58 0.0013 27.3 1.7 31 20-58 3-33 (109)
42 PF06044 DRP: Dam-replacing fa 21.9 35 0.00076 32.1 0.4 33 19-55 31-64 (254)
43 smart00661 RPOL9 RNA polymeras 21.1 64 0.0014 21.5 1.5 32 21-57 2-33 (52)
44 PRK10220 hypothetical protein; 20.2 68 0.0015 27.0 1.7 31 20-58 4-34 (111)
45 PRK15103 paraquat-inducible me 20.1 60 0.0013 31.6 1.6 14 18-31 9-22 (419)
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=1.5e-36 Score=224.89 Aligned_cols=57 Identities=75% Similarity=1.560 Sum_probs=55.8
Q ss_pred cccccCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCCCcccCCC
Q 046549 17 SEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIGGGTRKSN 73 (250)
Q Consensus 17 ~~~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GGtlRnVPVGGG~RKnk 73 (250)
++.++||||+|.+|||||||||++.||||||++|+||||+||+|||||||||+||+|
T Consensus 3 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k 59 (63)
T PF02701_consen 3 EQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNK 59 (63)
T ss_pred ccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCC
Confidence 478999999999999999999999999999999999999999999999999999998
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=93.39 E-value=0.031 Score=47.05 Aligned_cols=36 Identities=22% Similarity=0.559 Sum_probs=27.4
Q ss_pred cccCCCCCCCCceeeeecccCCCCCccccccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYW 54 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyW 54 (250)
...||||.|.+|+..--=-=+.++.-|+|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence 479999999999965322235568889999998644
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=93.38 E-value=0.068 Score=36.54 Aligned_cols=29 Identities=38% Similarity=0.824 Sum_probs=23.2
Q ss_pred ccccCCCCCCCCceeeeecccCCCCCccccccccc
Q 046549 18 EQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRR 52 (250)
Q Consensus 18 ~~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrR 52 (250)
++..||+|.+. ++..+.+ +.++.|++|++
T Consensus 17 ~g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 35779999998 6655555 78999999985
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.08 E-value=0.11 Score=42.99 Aligned_cols=36 Identities=31% Similarity=0.670 Sum_probs=28.2
Q ss_pred cccCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTR 56 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~ 56 (250)
...||+|.+.+ +-=+.-+.....|+.|++|++-|+.
T Consensus 30 ~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 30 KVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred cCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 47899999999 3334555555999999999999874
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=90.16 E-value=0.2 Score=33.78 Aligned_cols=31 Identities=39% Similarity=0.789 Sum_probs=21.4
Q ss_pred cccCCCCCCCCceeeeecccCC-CCCcccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYNL-SQPRHFCKNCR 51 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~~-~QPR~fCk~Cr 51 (250)
.+.||+|.+.+.= |=|-.+. -..||+|++|+
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 4789999998721 2233333 35899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.17 E-value=0.41 Score=32.40 Aligned_cols=37 Identities=22% Similarity=0.696 Sum_probs=28.0
Q ss_pred ccCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 046549 20 LKCPRCESTNTKFCYYNNYNLSQP---RHFCKNCRRYWTR 56 (250)
Q Consensus 20 ~~CPRC~S~~TKFcYyNNy~~~QP---R~fCk~CrRyWT~ 56 (250)
.+||+|...+.-|-..+-.....| -|.|.+|...|..
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 379999877777766666655555 3999999999963
No 7
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=86.57 E-value=0.6 Score=31.36 Aligned_cols=36 Identities=28% Similarity=0.771 Sum_probs=24.6
Q ss_pred ccCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 046549 20 LKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWT 55 (250)
Q Consensus 20 ~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT 55 (250)
.+||.|...+.-|--.+......|- |.|.+|..-|+
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 3799999988766655666555553 89999999885
No 8
>PHA02998 RNA polymerase subunit; Provisional
Probab=82.69 E-value=1.3 Score=40.01 Aligned_cols=43 Identities=26% Similarity=0.626 Sum_probs=35.8
Q ss_pred CCCcccccCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 046549 14 FPESEQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWTR 56 (250)
Q Consensus 14 ~pe~~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT~ 56 (250)
+|+....+||+|...++-|--.|-++-..|- |.|..|..-|.-
T Consensus 138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 3444679999999999999888888887775 899999999964
No 9
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=81.06 E-value=0.74 Score=41.45 Aligned_cols=37 Identities=27% Similarity=0.695 Sum_probs=19.0
Q ss_pred cccCCCCCCCC-ceeeeecc-cCCCCCcccccccccccc
Q 046549 19 QLKCPRCESTN-TKFCYYNN-YNLSQPRHFCKNCRRYWT 55 (250)
Q Consensus 19 ~~~CPRC~S~~-TKFcYyNN-y~~~QPR~fCk~CrRyWT 55 (250)
...||.|...+ .++-||.. -....--+.|..|+.|+-
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 57899999855 55667643 333333499999999983
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=80.96 E-value=2 Score=33.04 Aligned_cols=45 Identities=18% Similarity=0.612 Sum_probs=31.2
Q ss_pred CCCCCcccccCCCCCCCCceeeeecccCCCCCc---ccccccccccccC
Q 046549 12 PHFPESEQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWTRG 57 (250)
Q Consensus 12 p~~pe~~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT~G 57 (250)
|.+|. -...||+|...+.-|-..+-.+...|- |.|..|.-.|+.+
T Consensus 56 ~~~~~-~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 56 ETLPT-TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cCCCc-ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 33444 258999998777666555555443343 9999999999865
No 11
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=80.21 E-value=1.5 Score=31.50 Aligned_cols=41 Identities=27% Similarity=0.697 Sum_probs=28.5
Q ss_pred cCCCCCCCCceeeeecccCCCCCcccccccccccccCccccccc
Q 046549 21 KCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIP 64 (250)
Q Consensus 21 ~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GGtlRnVP 64 (250)
.|-.|...+|..=.-. ......+|-+|.-||.+.|..|.+-
T Consensus 1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~~ 41 (54)
T cd00202 1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPLS 41 (54)
T ss_pred CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCcc
Confidence 3677777776432221 2467799999999999999665443
No 12
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=79.33 E-value=0.57 Score=31.27 Aligned_cols=37 Identities=27% Similarity=0.632 Sum_probs=26.9
Q ss_pred cCCCCCCCCceeeeecccCCCCCcccccccccccccCccccc
Q 046549 21 KCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRN 62 (250)
Q Consensus 21 ~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GGtlRn 62 (250)
+||+|...-...-+ ..-+-+.|..|.-.|=..|.+..
T Consensus 1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHH
Confidence 69999985555444 33566889999999987776543
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=64.10 E-value=3.7 Score=36.18 Aligned_cols=38 Identities=29% Similarity=0.774 Sum_probs=24.1
Q ss_pred CCCCCCCCce-------eeeecccCCCC-----CcccccccccccccCcc
Q 046549 22 CPRCESTNTK-------FCYYNNYNLSQ-----PRHFCKNCRRYWTRGGA 59 (250)
Q Consensus 22 CPRC~S~~TK-------FcYyNNy~~~Q-----PR~fCk~CrRyWT~GGt 59 (250)
||+|...... =||...+.+.. --.+|+.|.||+..|.=
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~W 50 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGRW 50 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCCEe
Confidence 5666553332 25666665533 22799999999998543
No 14
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=64.06 E-value=5.2 Score=34.65 Aligned_cols=45 Identities=22% Similarity=0.403 Sum_probs=33.7
Q ss_pred cCCCCCCCCceeeee---cccCCCCCcccccccccccccCcccccccC
Q 046549 21 KCPRCESTNTKFCYY---NNYNLSQPRHFCKNCRRYWTRGGALRNIPI 65 (250)
Q Consensus 21 ~CPRC~S~~TKFcYy---NNy~~~QPR~fCk~CrRyWT~GGtlRnVPV 65 (250)
+||.|...+||+-== ...+.-+-|.-|..|.+-||-==.+-..|+
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 444556778999999999986555444443
No 15
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=64.01 E-value=5.6 Score=28.17 Aligned_cols=40 Identities=25% Similarity=0.598 Sum_probs=29.3
Q ss_pred ccccCCCCCCCCceeeeecccCCCCCcccccccccccccCccc
Q 046549 18 EQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGAL 60 (250)
Q Consensus 18 ~~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GGtl 60 (250)
....|-.|...+|..=.- ...-++.+|-+|.-||.+.|.+
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 357899999888854311 2233369999999999998886
No 16
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=61.74 E-value=4 Score=27.01 Aligned_cols=32 Identities=31% Similarity=0.695 Sum_probs=19.1
Q ss_pred cccCCCCCCCCcee-eeeccc-------------CCCCCccccccc
Q 046549 19 QLKCPRCESTNTKF-CYYNNY-------------NLSQPRHFCKNC 50 (250)
Q Consensus 19 ~~~CPRC~S~~TKF-cYyNNy-------------~~~QPR~fCk~C 50 (250)
+..||.|.+..-+. -++... .+..+|++|++|
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 46799999876221 111110 346778888877
No 17
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=57.38 E-value=7.5 Score=36.66 Aligned_cols=36 Identities=22% Similarity=0.641 Sum_probs=20.8
Q ss_pred cccCCCCCCCCceeeeecccC----CCCCcccccccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYN----LSQPRHFCKNCRRYWT 55 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~----~~QPR~fCk~CrRyWT 55 (250)
..+||.|.+.+ +.-|+.--. ..---..|..|+.|+-
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 56788887754 455554322 1112267888888863
No 18
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=57.26 E-value=7.7 Score=33.28 Aligned_cols=45 Identities=22% Similarity=0.480 Sum_probs=33.1
Q ss_pred ccCCCCCCCCceee---eecccCCCCCcccccccccccccCccccccc
Q 046549 20 LKCPRCESTNTKFC---YYNNYNLSQPRHFCKNCRRYWTRGGALRNIP 64 (250)
Q Consensus 20 ~~CPRC~S~~TKFc---YyNNy~~~QPR~fCk~CrRyWT~GGtlRnVP 64 (250)
.+||.|.+..|++- |+-.-++-.-|+-|++|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999997764 4445455666799999999888766655554
No 19
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=55.22 E-value=8.1 Score=36.59 Aligned_cols=36 Identities=25% Similarity=0.659 Sum_probs=20.7
Q ss_pred cccCCCCCCCCceeeeecccC--CCCCcccccccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYN--LSQPRHFCKNCRRYWT 55 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~--~~QPR~fCk~CrRyWT 55 (250)
..+||.|... .+.-|+.--. ..---+.|..|+.|+-
T Consensus 226 R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 226 RVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred CccCCCCCCC-CceeeeeecCCCcceEeeecccccccce
Confidence 5678888763 3555553211 1222277888888874
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=54.18 E-value=5.3 Score=26.97 Aligned_cols=17 Identities=35% Similarity=1.026 Sum_probs=7.1
Q ss_pred CCcccccccccccccCc
Q 046549 42 QPRHFCKNCRRYWTRGG 58 (250)
Q Consensus 42 QPR~fCk~CrRyWT~GG 58 (250)
+|||+|.=|..|.+..-
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 21
>PHA00626 hypothetical protein
Probab=52.06 E-value=10 Score=28.69 Aligned_cols=37 Identities=19% Similarity=0.265 Sum_probs=25.0
Q ss_pred cCCCCCCCCceeeeecccCCCCCcccccccccccccCcc
Q 046549 21 KCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGA 59 (250)
Q Consensus 21 ~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GGt 59 (250)
.||.|.|.+.-=|-.= ....-||.|++|.=.+|+..-
T Consensus 2 ~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceeeeecee--cccCcceEcCCCCCeechhhh
Confidence 6999999754322110 112467999999999998653
No 22
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.31 E-value=11 Score=26.81 Aligned_cols=26 Identities=35% Similarity=0.683 Sum_probs=19.0
Q ss_pred cccCCCCCCCCceeeeecccCCCCCccccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRR 52 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrR 52 (250)
..-||+|.+. |..-.. .|+.|..|..
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 4589999873 544443 6999999974
No 23
>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=45.86 E-value=15 Score=27.97 Aligned_cols=31 Identities=23% Similarity=0.512 Sum_probs=24.5
Q ss_pred cccCCCCCCCCceeeeecccCCCCCccccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRR 52 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrR 52 (250)
+..||+|.+.+|=..|..|. ..-.-|-.|.=
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~---ve~vECV~CGy 38 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENG---VEYVECVECGY 38 (71)
T ss_pred CccCCCCcCccEEEEEEeCC---ceEEEecCCCC
Confidence 67899999999888887776 55567888853
No 24
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=45.48 E-value=17 Score=30.61 Aligned_cols=43 Identities=23% Similarity=0.678 Sum_probs=29.9
Q ss_pred CCCCCcccccCCCCCCCCceeeeecccCCCC-----Cccccccccccccc
Q 046549 12 PHFPESEQLKCPRCESTNTKFCYYNNYNLSQ-----PRHFCKNCRRYWTR 56 (250)
Q Consensus 12 p~~pe~~~~~CPRC~S~~TKFcYyNNy~~~Q-----PR~fCk~CrRyWT~ 56 (250)
|-+|.-+...||+|...+.-| ||-.+... --|.|-+|.--||.
T Consensus 66 PTLPrts~~~C~~C~~~eavf--fQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 66 PTLPRTSDKHCPKCGHREAVF--FQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred CCcCccccccCCccCCcceEE--EecccccccceEEEEEEeccccccccC
Confidence 445666788999999887654 55432211 11899999999985
No 25
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=41.01 E-value=22 Score=29.58 Aligned_cols=38 Identities=21% Similarity=0.625 Sum_probs=32.7
Q ss_pred ccccCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 046549 18 EQLKCPRCESTNTKFCYYNNYNLSQPR---HFCKNCRRYWT 55 (250)
Q Consensus 18 ~~~~CPRC~S~~TKFcYyNNy~~~QPR---~fCk~CrRyWT 55 (250)
-...||+|...+.-|--+|-.+..-|- |.|-.|+--|-
T Consensus 64 t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 64 TEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred ccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 357899999999998888888888776 89999999884
No 26
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=39.82 E-value=12 Score=27.93 Aligned_cols=13 Identities=46% Similarity=0.841 Sum_probs=5.5
Q ss_pred cccCCCCCCCCce
Q 046549 19 QLKCPRCESTNTK 31 (250)
Q Consensus 19 ~~~CPRC~S~~TK 31 (250)
+++|+.|.|.||+
T Consensus 48 g~KC~~C~SYNT~ 60 (61)
T PF14599_consen 48 GHKCSHCGSYNTR 60 (61)
T ss_dssp ----TTTS---EE
T ss_pred hhcCCCCCCcccC
Confidence 5789999999997
No 27
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=35.51 E-value=23 Score=31.17 Aligned_cols=44 Identities=27% Similarity=0.398 Sum_probs=31.2
Q ss_pred cCCCCCCCCceeeee---cccCCCCCcccccccccccccCccccccc
Q 046549 21 KCPRCESTNTKFCYY---NNYNLSQPRHFCKNCRRYWTRGGALRNIP 64 (250)
Q Consensus 21 ~CPRC~S~~TKFcYy---NNy~~~QPR~fCk~CrRyWT~GGtlRnVP 64 (250)
.||.|.+.+||+-== -.-+.-+-|.-|-+|..-+|-==++--+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 699999999998532 22234556789999998888655544443
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=32.08 E-value=23 Score=22.04 Aligned_cols=27 Identities=26% Similarity=0.630 Sum_probs=14.0
Q ss_pred ccCCCCCCCCceeeeecccCCCCCcccccccc
Q 046549 20 LKCPRCESTNTKFCYYNNYNLSQPRHFCKNCR 51 (250)
Q Consensus 20 ~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~Cr 51 (250)
.+||||...-.++-.. .+.-+||..|+
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 5799998877665442 22336777775
No 29
>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=30.75 E-value=29 Score=24.66 Aligned_cols=32 Identities=34% Similarity=0.593 Sum_probs=25.1
Q ss_pred ccccCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 046549 18 EQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTR 56 (250)
Q Consensus 18 ~~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~ 56 (250)
.-..||.|.....+ .+..-.+.|..|...+.+
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 45679999998877 666777999999876654
No 30
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=29.32 E-value=45 Score=26.95 Aligned_cols=36 Identities=22% Similarity=0.457 Sum_probs=24.9
Q ss_pred CcccccCCCCCCCCceeeeecccCCCCCcccccccccccc
Q 046549 16 ESEQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWT 55 (250)
Q Consensus 16 e~~~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT 55 (250)
-+....||.|.+. +--|=+.. ..+.+.|..|.-|..
T Consensus 18 lpt~f~CP~Cge~-~v~v~~~k---~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 18 LPKIFECPRCGKV-SISVKIKK---NIAIITCGNCGLYTE 53 (99)
T ss_pred CCcEeECCCCCCe-EeeeecCC---CcceEECCCCCCccC
Confidence 3468899999952 32233333 478899999998853
No 31
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=28.86 E-value=36 Score=27.64 Aligned_cols=42 Identities=24% Similarity=0.524 Sum_probs=31.3
Q ss_pred ccccCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCC
Q 046549 18 EQLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGGALRNIPIG 66 (250)
Q Consensus 18 ~~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GGtlRnVPVG 66 (250)
....||-|.....| -...---.|+.|..-|+.|+-....|.|
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 45789999988555 1222337899999999999987766665
No 32
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=26.53 E-value=55 Score=22.71 Aligned_cols=35 Identities=20% Similarity=0.420 Sum_probs=19.3
Q ss_pred ccccCCCCCCCCceeeeecccCCCC-Cccccccccc
Q 046549 18 EQLKCPRCESTNTKFCYYNNYNLSQ-PRHFCKNCRR 52 (250)
Q Consensus 18 ~~~~CPRC~S~~TKFcYyNNy~~~Q-PR~fCk~CrR 52 (250)
+..+||.|.+....+.+........ -.-.|..|..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4678999955555544422211111 3345888865
No 33
>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=25.96 E-value=50 Score=24.93 Aligned_cols=30 Identities=23% Similarity=0.466 Sum_probs=22.0
Q ss_pred cccCCCCCCCCceeeeecccCCCCCcccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCR 51 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~Cr 51 (250)
+..||+|...++=..|..|.- .-.-|-.|.
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred cccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 688999999999988865543 335566664
No 34
>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=25.36 E-value=34 Score=22.45 Aligned_cols=28 Identities=32% Similarity=0.675 Sum_probs=14.4
Q ss_pred ccCCCCCCCCceeeeecccCCCCCcccccccccccc
Q 046549 20 LKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWT 55 (250)
Q Consensus 20 ~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT 55 (250)
-+||-|.|..+= ...--+.|..|..=|.
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 479999998774 5667788999987773
No 35
>PRK12496 hypothetical protein; Provisional
Probab=24.80 E-value=42 Score=28.64 Aligned_cols=29 Identities=21% Similarity=0.397 Sum_probs=16.8
Q ss_pred ccccccccccccCcccccccCCCcccCCC
Q 046549 45 HFCKNCRRYWTRGGALRNIPIGGGTRKSN 73 (250)
Q Consensus 45 ~fCk~CrRyWT~GGtlRnVPVGGG~RKnk 73 (250)
+.|..|+|++...-.--.=|+=|..=|.|
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPVKRK 156 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChhhhc
Confidence 77888888886443322346655543333
No 36
>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=24.61 E-value=65 Score=22.49 Aligned_cols=32 Identities=22% Similarity=0.493 Sum_probs=18.6
Q ss_pred ccCCCCCCCCceeeeecccCCCCCccc-cccccc
Q 046549 20 LKCPRCESTNTKFCYYNNYNLSQPRHF-CKNCRR 52 (250)
Q Consensus 20 ~~CPRC~S~~TKFcYyNNy~~~QPR~f-Ck~CrR 52 (250)
.+||.|.+..-.|=+ ......-.+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 579999997665532 12233333444 777764
No 37
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=24.49 E-value=63 Score=26.82 Aligned_cols=30 Identities=27% Similarity=0.441 Sum_probs=20.9
Q ss_pred cccCCCCCCCCceeeeecccCCCCCccccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRR 52 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrR 52 (250)
-+.||-|.+.+|.+--- ..---..|++|..
T Consensus 93 yVlC~~C~spdT~l~k~----~r~~~l~C~aCGa 122 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKE----GRLIFLKCKACGA 122 (125)
T ss_dssp HSSCTSTSSSSEEEEEE----TTCCEEEETTTSC
T ss_pred EEEcCCCCCCccEEEEc----CCEEEEEecccCC
Confidence 37899999999997544 1123366888853
No 38
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=23.98 E-value=48 Score=22.91 Aligned_cols=32 Identities=19% Similarity=0.622 Sum_probs=18.2
Q ss_pred cccCCCCCCCCceeeeecccCCCCCccccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRR 52 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrR 52 (250)
+.+||-|.. ..+|..|-+. .-+-..+|..|..
T Consensus 3 h~pCP~CGG-~DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGG-KDRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCCcC-ccccccCcCc-ccCCCEECCCCCC
Confidence 568999988 5688866543 3347799999943
No 39
>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=23.96 E-value=49 Score=25.59 Aligned_cols=30 Identities=20% Similarity=0.477 Sum_probs=16.8
Q ss_pred cccCCCCCCCCceeeeecccCCCCCccccccccc
Q 046549 19 QLKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRR 52 (250)
Q Consensus 19 ~~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrR 52 (250)
...||-|+..+..|..+.+. -++.|-+|.+
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~ 62 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDK----NRFKCFGCGK 62 (97)
T ss_dssp EE--SSS--SS--EEEETTT----TEEEETTT--
T ss_pred EEECcCCCCCCCceEEECCC----CeEEECCCCC
Confidence 46799999877777776543 3799999985
No 40
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=23.27 E-value=44 Score=32.33 Aligned_cols=18 Identities=28% Similarity=0.846 Sum_probs=11.4
Q ss_pred CCCCCCCCcccccCCCCC
Q 046549 9 PMKPHFPESEQLKCPRCE 26 (250)
Q Consensus 9 ~~kp~~pe~~~~~CPRC~ 26 (250)
.||.+.++.+...||.|+
T Consensus 3 ~~~~~~~~~~~~~C~~Cd 20 (403)
T TIGR00155 3 KMCEHHPAAKHILCSQCD 20 (403)
T ss_pred cccccCCCCCeeeCCCCC
Confidence 355556666666677776
No 41
>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=22.05 E-value=58 Score=27.25 Aligned_cols=31 Identities=26% Similarity=0.667 Sum_probs=24.8
Q ss_pred ccCCCCCCCCceeeeecccCCCCCcccccccccccccCc
Q 046549 20 LKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGG 58 (250)
Q Consensus 20 ~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GG 58 (250)
..||.|.|..|- ....-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY--------~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTY--------HDGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceE--------ecCCeeECccccccccccc
Confidence 579999997663 2355699999999999876
No 42
>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=21.94 E-value=35 Score=32.10 Aligned_cols=33 Identities=30% Similarity=0.765 Sum_probs=12.5
Q ss_pred cccCCCCCCC-CceeeeecccCCCCCcccccccccccc
Q 046549 19 QLKCPRCEST-NTKFCYYNNYNLSQPRHFCKNCRRYWT 55 (250)
Q Consensus 19 ~~~CPRC~S~-~TKFcYyNNy~~~QPR~fCk~CrRyWT 55 (250)
...||+|.+. -.+| ..+.+-.-.+|..|..=+-
T Consensus 31 n~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp H---TTT--SS-EE------------EEE-TTT--EEE
T ss_pred CCcCCCCCChhHhhc----cCCCccceeECCCCchHHh
Confidence 3579999997 5555 4455666799999987554
No 43
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.07 E-value=64 Score=21.55 Aligned_cols=32 Identities=19% Similarity=0.459 Sum_probs=18.9
Q ss_pred cCCCCCCCCceeeeecccCCCCCcccccccccccccC
Q 046549 21 KCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRG 57 (250)
Q Consensus 21 ~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~G 57 (250)
-||.|.. ..|..... ...|+.|..|...+-..
T Consensus 2 FCp~Cg~----~l~~~~~~-~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGN----MLIPKEGK-EKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCC----ccccccCC-CCCEEECCcCCCeEECC
Confidence 5888876 23333221 12488899998665443
No 44
>PRK10220 hypothetical protein; Provisional
Probab=20.23 E-value=68 Score=26.98 Aligned_cols=31 Identities=26% Similarity=0.669 Sum_probs=24.8
Q ss_pred ccCCCCCCCCceeeeecccCCCCCcccccccccccccCc
Q 046549 20 LKCPRCESTNTKFCYYNNYNLSQPRHFCKNCRRYWTRGG 58 (250)
Q Consensus 20 ~~CPRC~S~~TKFcYyNNy~~~QPR~fCk~CrRyWT~GG 58 (250)
..||.|.|..|- ..+.-+.|..|.-=|+...
T Consensus 4 P~CP~C~seytY--------~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTY--------EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceE--------cCCCeEECCcccCcCCccc
Confidence 579999997663 2355699999999999875
No 45
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=20.09 E-value=60 Score=31.64 Aligned_cols=14 Identities=21% Similarity=0.750 Sum_probs=8.8
Q ss_pred ccccCCCCCCCCce
Q 046549 18 EQLKCPRCESTNTK 31 (250)
Q Consensus 18 ~~~~CPRC~S~~TK 31 (250)
....||.|+.-...
T Consensus 9 ~~~~C~~Cd~l~~~ 22 (419)
T PRK15103 9 KHILCPQCDMLVAL 22 (419)
T ss_pred CcccCCCCCceeec
Confidence 44668888765443
Done!