Query 023228
Match_columns 285
No_of_seqs 150 out of 263
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 02:28:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023228.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023228hhsearch_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 1.9E-37 4E-42 233.0 4.1 62 40-101 2-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 93.2 0.038 8.2E-07 47.7 1.1 34 43-78 105-140 (146)
3 COG3677 Transposase and inacti 92.6 0.076 1.7E-06 44.9 2.1 36 43-80 30-65 (129)
4 PF12760 Zn_Tnp_IS1595: Transp 92.4 0.09 1.9E-06 36.8 1.9 27 44-76 19-45 (46)
5 PF03811 Zn_Tnp_IS1: InsA N-te 91.3 0.12 2.5E-06 35.5 1.4 31 43-75 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 88.5 0.38 8.3E-06 33.2 2.2 37 44-80 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 85.8 0.48 1E-05 32.5 1.5 36 44-79 1-39 (39)
8 PF04216 FdhE: Protein involve 75.7 1.3 2.7E-05 41.2 1.0 37 43-79 211-249 (290)
9 PF13453 zf-TFIIB: Transcripti 75.3 0.76 1.7E-05 31.4 -0.4 37 45-86 1-37 (41)
10 TIGR01384 TFS_arch transcripti 74.7 2.4 5.2E-05 33.5 2.2 39 43-81 62-103 (104)
11 PHA02998 RNA polymerase subuni 74.4 2.6 5.6E-05 38.7 2.6 39 42-80 142-183 (195)
12 cd00202 ZnF_GATA Zinc finger D 73.8 3.7 8E-05 30.1 2.9 40 45-87 1-40 (54)
13 PF04981 NMD3: NMD3 family ; 61.1 4 8.6E-05 37.1 1.0 26 57-82 19-49 (236)
14 TIGR01385 TFSII transcription 58.1 7.1 0.00015 37.5 2.2 38 42-79 257-297 (299)
15 PF14690 zf-ISL3: zinc-finger 56.9 4.9 0.00011 27.3 0.7 32 43-74 2-47 (47)
16 PF06220 zf-U1: U1 zinc finger 55.2 4.5 9.8E-05 27.8 0.3 17 66-82 1-17 (38)
17 smart00401 ZnF_GATA zinc finge 54.6 8.4 0.00018 27.9 1.6 39 43-84 3-41 (52)
18 TIGR00244 transcriptional regu 53.8 8.6 0.00019 34.0 1.8 42 45-86 2-46 (147)
19 PHA00626 hypothetical protein 52.0 8.7 0.00019 29.5 1.4 36 45-82 2-37 (59)
20 TIGR01562 FdhE formate dehydro 51.2 10 0.00022 36.6 2.1 36 43-79 224-263 (305)
21 KOG2906 RNA polymerase III sub 49.7 16 0.00034 30.9 2.7 38 42-79 64-104 (105)
22 PRK14810 formamidopyrimidine-D 48.9 9.3 0.0002 35.6 1.4 29 43-76 244-272 (272)
23 PRK03564 formate dehydrogenase 47.7 12 0.00026 36.4 1.9 37 43-80 226-264 (309)
24 PRK00464 nrdR transcriptional 47.1 13 0.00029 32.6 2.0 45 44-88 1-48 (154)
25 PRK14811 formamidopyrimidine-D 44.4 12 0.00027 34.8 1.4 29 43-76 235-263 (269)
26 PRK00432 30S ribosomal protein 42.6 11 0.00025 27.3 0.8 26 43-76 20-45 (50)
27 PRK01103 formamidopyrimidine/5 41.3 15 0.00032 34.2 1.4 29 43-76 245-273 (274)
28 PF14599 zinc_ribbon_6: Zinc-r 40.1 11 0.00024 28.6 0.4 16 40-55 45-60 (61)
29 PRK10445 endonuclease VIII; Pr 38.8 17 0.00036 33.8 1.4 29 43-76 235-263 (263)
30 PRK13945 formamidopyrimidine-D 38.0 18 0.00039 33.8 1.5 29 43-76 254-282 (282)
31 PF09526 DUF2387: Probable met 37.2 22 0.00048 27.7 1.6 32 42-76 7-38 (71)
32 TIGR00577 fpg formamidopyrimid 32.1 25 0.00055 32.7 1.4 28 43-75 245-272 (272)
33 PF08273 Prim_Zn_Ribbon: Zinc- 26.6 37 0.00079 23.9 1.1 32 43-76 3-34 (40)
34 PF07282 OrfB_Zn_ribbon: Putat 25.7 36 0.00077 24.8 1.0 32 42-80 27-58 (69)
35 COG1997 RPL43A Ribosomal prote 25.7 34 0.00074 28.2 1.0 42 42-90 34-75 (89)
36 PF08274 PhnA_Zn_Ribbon: PhnA 25.6 26 0.00057 23.3 0.3 28 44-79 3-30 (30)
37 PF06827 zf-FPG_IleRS: Zinc fi 24.5 31 0.00067 21.9 0.4 27 44-75 2-28 (30)
38 COG1327 Predicted transcriptio 24.0 44 0.00096 30.0 1.4 43 45-87 2-47 (156)
39 TIGR03655 anti_R_Lar restricti 23.3 62 0.0013 23.1 1.9 32 44-76 2-34 (53)
40 TIGR00686 phnA alkylphosphonat 21.7 53 0.0011 28.0 1.4 31 44-82 3-33 (109)
41 TIGR02443 conserved hypothetic 21.1 68 0.0015 24.6 1.8 31 42-75 8-38 (59)
42 PF06682 DUF1183: Protein of u 20.8 29 0.00063 33.9 -0.3 41 31-73 38-85 (318)
43 PRK10220 hypothetical protein; 20.5 60 0.0013 27.8 1.5 31 44-82 4-34 (111)
44 PF01807 zf-CHC2: CHC2 zinc fi 20.3 60 0.0013 25.8 1.4 31 42-76 32-62 (97)
45 COG0266 Nei Formamidopyrimidin 20.1 54 0.0012 31.5 1.3 29 43-76 245-273 (273)
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=1.9e-37 Score=233.01 Aligned_cols=62 Identities=82% Similarity=1.588 Sum_probs=59.3
Q ss_pred ccccCCCCCCCCCCcceeeecccCCCCCchhhhccccccccCCccccccCCCCcCCCCCCCC
Q 023228 40 KEQALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNIPVGGGSRKNKRSSS 101 (285)
Q Consensus 40 ~~~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GG~lRnvPvGgg~RK~k~sss 101 (285)
+++.++||||+|.||||||||||+++||||||++|+||||+||+|||||||||+||+|+++|
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 45679999999999999999999999999999999999999999999999999999999875
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=93.20 E-value=0.038 Score=47.68 Aligned_cols=34 Identities=26% Similarity=0.828 Sum_probs=26.9
Q ss_pred cCCCCCCCCCCcceeeeccc--CCCCCchhhhcccccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNY--SLTQPRYFCKTCRRYW 78 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy--~~~QPR~fCk~CrRyW 78 (285)
...||||.|.+|+.. +.+ +.++.-|.|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence 479999999999964 555 4457779999998643
No 3
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.58 E-value=0.076 Score=44.91 Aligned_cols=36 Identities=36% Similarity=0.756 Sum_probs=28.4
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhcccccccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTE 80 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~ 80 (285)
...||+|.+.+ +-=+.-+.....||.|++|++-|+.
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 37899999999 3335555555999999999999874
No 4
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=92.42 E-value=0.09 Score=36.78 Aligned_cols=27 Identities=44% Similarity=1.006 Sum_probs=22.3
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 44 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 44 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
..||+|.+. ++..+.+ +.+|.|++|++
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 679999998 6655655 78999999985
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=91.29 E-value=0.12 Score=35.55 Aligned_cols=31 Identities=45% Similarity=0.881 Sum_probs=21.7
Q ss_pred cCCCCCCCCCCcceeeecccCCC-CCchhhhccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLT-QPRYFCKTCR 75 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~-QPR~fCk~Cr 75 (285)
.+.||+|.+++.- |=|-.+.. ..||+|++|+
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 23444433 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.46 E-value=0.38 Score=33.21 Aligned_cols=37 Identities=30% Similarity=0.823 Sum_probs=28.2
Q ss_pred CCCCCCCCCCcceeeecccCCCCC---chhhhcccccccc
Q 023228 44 LNCPRCNSTNTKFCYYNNYSLTQP---RYFCKTCRRYWTE 80 (285)
Q Consensus 44 ~~CPRC~S~~TkfcyyNNy~~~QP---R~fCk~CrRyWT~ 80 (285)
.+||+|...+.-|-..+-.+...| -|.|..|...|.+
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 379999977777666666665555 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=85.79 E-value=0.48 Score=32.49 Aligned_cols=36 Identities=28% Similarity=0.829 Sum_probs=24.5
Q ss_pred CCCCCCCCCCcceeeecccCCCCCc---hhhhccccccc
Q 023228 44 LNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWT 79 (285)
Q Consensus 44 ~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT 79 (285)
.+||.|...+.-|=-.+..+...|- |.|.+|..-|+
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 3799999988766555666555553 99999999985
No 8
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=75.69 E-value=1.3 Score=41.23 Aligned_cols=37 Identities=24% Similarity=0.643 Sum_probs=18.7
Q ss_pred cCCCCCCCCCC-cceeeeccc-CCCCCchhhhccccccc
Q 023228 43 ALNCPRCNSTN-TKFCYYNNY-SLTQPRYFCKTCRRYWT 79 (285)
Q Consensus 43 ~~~CPRC~S~~-TkfcyyNNy-~~~QPR~fCk~CrRyWT 79 (285)
...||.|..++ .++-||..- ....--+.|+.|+.|+-
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 46899998855 456666433 33333499999999983
No 9
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=75.30 E-value=0.76 Score=31.36 Aligned_cols=37 Identities=24% Similarity=0.622 Sum_probs=27.0
Q ss_pred CCCCCCCCCcceeeecccCCCCCchhhhccccccccCCcccc
Q 023228 45 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRN 86 (285)
Q Consensus 45 ~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GG~lRn 86 (285)
+||+|...-...-+ ..-+-+.|..|.-.|=..|.+..
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 69999985554444 23566889999999988776643
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=74.67 E-value=2.4 Score=33.53 Aligned_cols=39 Identities=23% Similarity=0.720 Sum_probs=28.7
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCc---hhhhccccccccC
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWTEG 81 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT~G 81 (285)
...||+|...+.-|-..+-.+...|- |.|..|.-.|+++
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 48999998777666555555544443 9999999999875
No 11
>PHA02998 RNA polymerase subunit; Provisional
Probab=74.43 E-value=2.6 Score=38.72 Aligned_cols=39 Identities=23% Similarity=0.564 Sum_probs=33.7
Q ss_pred ccCCCCCCCCCCcceeeecccCCCCCc---hhhhcccccccc
Q 023228 42 QALNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWTE 80 (285)
Q Consensus 42 ~~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT~ 80 (285)
....||+|...++-|--.|-.+...|- |.|..|..-|.-
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 458999999999999888888888875 899999999963
No 12
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=73.82 E-value=3.7 Score=30.10 Aligned_cols=40 Identities=25% Similarity=0.688 Sum_probs=28.5
Q ss_pred CCCCCCCCCcceeeecccCCCCCchhhhccccccccCCccccc
Q 023228 45 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNI 87 (285)
Q Consensus 45 ~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GG~lRnv 87 (285)
.|-.|..++|..=.-. ......+|-+|.-||.+.|..|.+
T Consensus 1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~ 40 (54)
T cd00202 1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPL 40 (54)
T ss_pred CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCc
Confidence 3777888777532221 246779999999999999976544
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=61.12 E-value=4 Score=37.07 Aligned_cols=26 Identities=27% Similarity=0.809 Sum_probs=18.4
Q ss_pred eeecccCCCC-----CchhhhccccccccCC
Q 023228 57 CYYNNYSLTQ-----PRYFCKTCRRYWTEGG 82 (285)
Q Consensus 57 cyyNNy~~~Q-----PR~fCk~CrRyWT~GG 82 (285)
||...+.+.. --.+|+.|.||+..|.
T Consensus 19 C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 19 CYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred HhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 5666665543 2278999999999843
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=58.15 E-value=7.1 Score=37.52 Aligned_cols=38 Identities=18% Similarity=0.626 Sum_probs=28.3
Q ss_pred ccCCCCCCCCCCcceeeecccCCCCCc---hhhhccccccc
Q 023228 42 QALNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWT 79 (285)
Q Consensus 42 ~~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT 79 (285)
....||+|...+..|-..+..+...|- |.|..|...|.
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 358999999877776555555555553 78999999984
No 15
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=56.88 E-value=4.9 Score=27.27 Aligned_cols=32 Identities=31% Similarity=0.752 Sum_probs=18.9
Q ss_pred cCCCCCCCCCCcce-eeeccc-------------CCCCCchhhhcc
Q 023228 43 ALNCPRCNSTNTKF-CYYNNY-------------SLTQPRYFCKTC 74 (285)
Q Consensus 43 ~~~CPRC~S~~Tkf-cyyNNy-------------~~~QPR~fCk~C 74 (285)
...||.|.+...+. -++... .+..+|++|++|
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred CccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 35799999876221 111111 345778888877
No 16
>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=55.24 E-value=4.5 Score=27.82 Aligned_cols=17 Identities=41% Similarity=1.208 Sum_probs=7.1
Q ss_pred CCchhhhccccccccCC
Q 023228 66 QPRYFCKTCRRYWTEGG 82 (285)
Q Consensus 66 QPR~fCk~CrRyWT~GG 82 (285)
+|||+|.=|..|.|..-
T Consensus 1 m~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDS 17 (38)
T ss_dssp --S-B-TTT--B-S--S
T ss_pred CcCeecccccceecCCC
Confidence 69999999999997654
No 17
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=54.65 E-value=8.4 Score=27.86 Aligned_cols=39 Identities=23% Similarity=0.616 Sum_probs=28.8
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhccccccccCCcc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSL 84 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GG~l 84 (285)
...|-.|..+.|..=.- ...-++.+|-+|.-||.+.|.+
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 46899999888863211 2223369999999999998886
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=53.84 E-value=8.6 Score=34.01 Aligned_cols=42 Identities=21% Similarity=0.350 Sum_probs=31.2
Q ss_pred CCCCCCCCCcceeee---cccCCCCCchhhhccccccccCCcccc
Q 023228 45 NCPRCNSTNTKFCYY---NNYSLTQPRYFCKTCRRYWTEGGSLRN 86 (285)
Q Consensus 45 ~CPRC~S~~Tkfcyy---NNy~~~QPR~fCk~CrRyWT~GG~lRn 86 (285)
.||.|...+||+-== ..-+.-+-|.-|..|.+-||-==.+-.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~ 46 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAEL 46 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccc
Confidence 699999999998532 344455678999999999986544433
No 19
>PHA00626 hypothetical protein
Probab=52.04 E-value=8.7 Score=29.49 Aligned_cols=36 Identities=22% Similarity=0.363 Sum_probs=24.1
Q ss_pred CCCCCCCCCcceeeecccCCCCCchhhhccccccccCC
Q 023228 45 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGG 82 (285)
Q Consensus 45 ~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GG 82 (285)
.||+|.|.+.-=|=.= ....-||.|++|.=.+|+..
T Consensus 2 ~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeecee--cccCcceEcCCCCCeechhh
Confidence 6999999754321110 11246799999999998764
No 20
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=51.18 E-value=10 Score=36.63 Aligned_cols=36 Identities=17% Similarity=0.548 Sum_probs=23.1
Q ss_pred cCCCCCCCCCCcceeeecccC----CCCCchhhhccccccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYS----LTQPRYFCKTCRRYWT 79 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~----~~QPR~fCk~CrRyWT 79 (285)
...||.|.+.+ +.-|+.--. ..---..|.+|+.|+-
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 46888888864 555665332 1122268999999974
No 21
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=49.68 E-value=16 Score=30.86 Aligned_cols=38 Identities=26% Similarity=0.713 Sum_probs=33.0
Q ss_pred ccCCCCCCCCCCcceeeecccCCCCCc---hhhhccccccc
Q 023228 42 QALNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWT 79 (285)
Q Consensus 42 ~~~~CPRC~S~~TkfcyyNNy~~~QPR---~fCk~CrRyWT 79 (285)
-...||+|...+.-|--+|-.+..-|- |.|-.|.--|-
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 347899999999999888888888886 99999999885
No 22
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=48.89 E-value=9.3 Score=35.61 Aligned_cols=29 Identities=14% Similarity=0.535 Sum_probs=21.3
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
..+||||...=.|.-+= .+.-|||..|++
T Consensus 244 g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 57999999766554332 366699999985
No 23
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=47.69 E-value=12 Score=36.36 Aligned_cols=37 Identities=22% Similarity=0.512 Sum_probs=23.2
Q ss_pred cCCCCCCCCCCcceeeecccC--CCCCchhhhcccccccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYS--LTQPRYFCKTCRRYWTE 80 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~--~~QPR~fCk~CrRyWT~ 80 (285)
...||.|... .|.-|+.--. ..---+.|.+|+.|+--
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 4678888874 3566653222 12223889999999753
No 24
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=47.11 E-value=13 Score=32.61 Aligned_cols=45 Identities=20% Similarity=0.451 Sum_probs=31.4
Q ss_pred CCCCCCCCCCccee---eecccCCCCCchhhhccccccccCCcccccc
Q 023228 44 LNCPRCNSTNTKFC---YYNNYSLTQPRYFCKTCRRYWTEGGSLRNIP 88 (285)
Q Consensus 44 ~~CPRC~S~~Tkfc---yyNNy~~~QPR~fCk~CrRyWT~GG~lRnvP 88 (285)
..||.|.+..|++- |+-.-++-.-||-|+.|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999887764 4444444555699999999887655554443
No 25
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=44.39 E-value=12 Score=34.82 Aligned_cols=29 Identities=28% Similarity=0.716 Sum_probs=21.3
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
..+||||...=.|.-+ . .+.-|||..|++
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 3589999987665433 2 366799999996
No 26
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=42.62 E-value=11 Score=27.28 Aligned_cols=26 Identities=35% Similarity=0.742 Sum_probs=18.8
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
..-||+|.+. |..-.. .|+.|..|..
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 4589999874 554443 6999999974
No 27
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=41.33 E-value=15 Score=34.18 Aligned_cols=29 Identities=24% Similarity=0.720 Sum_probs=21.0
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
..+||||...=.|. -++ .+.-|||..|++
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 46899999776553 233 366799999986
No 28
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=40.07 E-value=11 Score=28.64 Aligned_cols=16 Identities=31% Similarity=0.588 Sum_probs=6.6
Q ss_pred ccccCCCCCCCCCCcc
Q 023228 40 KEQALNCPRCNSTNTK 55 (285)
Q Consensus 40 ~~~~~~CPRC~S~~Tk 55 (285)
.--+++|+.|.|.||+
T Consensus 45 H~lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 45 HFLGHKCSHCGSYNTR 60 (61)
T ss_dssp -TT----TTTS---EE
T ss_pred eHhhhcCCCCCCcccC
Confidence 3456899999999997
No 29
>PRK10445 endonuclease VIII; Provisional
Probab=38.76 E-value=17 Score=33.77 Aligned_cols=29 Identities=28% Similarity=0.777 Sum_probs=20.9
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
...||||...=.|.-+ . .+.-|||..|++
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 4689999887655544 2 366799999984
No 30
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.00 E-value=18 Score=33.81 Aligned_cols=29 Identities=14% Similarity=0.578 Sum_probs=21.3
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
..+||||...=.|.-+ -.+.-|||..|++
T Consensus 254 g~pC~~Cg~~I~~~~~-----~gR~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCRKCGTPIERIKL-----AGRSTHWCPNCQK 282 (282)
T ss_pred cCCCCcCCCeeEEEEE-----CCCccEECCCCcC
Confidence 4689999987666544 2266699999984
No 31
>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=37.15 E-value=22 Score=27.67 Aligned_cols=32 Identities=22% Similarity=0.493 Sum_probs=24.9
Q ss_pred ccCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 42 QALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 42 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
-+..||+|.+.+|-..|..|. ..-.-|-.|.=
T Consensus 7 AGa~CP~C~~~D~i~~~~e~~---ve~vECV~CGy 38 (71)
T PF09526_consen 7 AGAVCPKCQAMDTIMMWRENG---VEYVECVECGY 38 (71)
T ss_pred cCccCCCCcCccEEEEEEeCC---ceEEEecCCCC
Confidence 357899999999988888776 55566777753
No 32
>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=32.14 E-value=25 Score=32.72 Aligned_cols=28 Identities=25% Similarity=0.604 Sum_probs=20.4
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCR 75 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~Cr 75 (285)
..+||||...=.|.-+ . .+.-|||..|+
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 3589999987666433 2 36679999996
No 33
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=26.60 E-value=37 Score=23.91 Aligned_cols=32 Identities=19% Similarity=0.639 Sum_probs=18.4
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
+.+||-|.. ..+|..|-+. ..+-.++|..|..
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 468999988 5688866543 3347899999943
No 34
>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=25.69 E-value=36 Score=24.85 Aligned_cols=32 Identities=25% Similarity=0.583 Sum_probs=24.7
Q ss_pred ccCCCCCCCCCCcceeeecccCCCCCchhhhcccccccc
Q 023228 42 QALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTE 80 (285)
Q Consensus 42 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~ 80 (285)
-...||.|.....+ .+.+-.+.|..|...+.+
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 666777999999876653
No 35
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.67 E-value=34 Score=28.22 Aligned_cols=42 Identities=24% Similarity=0.549 Sum_probs=30.7
Q ss_pred ccCCCCCCCCCCcceeeecccCCCCCchhhhccccccccCCccccccCC
Q 023228 42 QALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNIPVG 90 (285)
Q Consensus 42 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GG~lRnvPvG 90 (285)
+...||-|.+...| -..---..|+.|..-|+.|+-....|+|
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 45789999998554 1122337899999999999987766654
No 36
>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=25.56 E-value=26 Score=23.32 Aligned_cols=28 Identities=29% Similarity=0.666 Sum_probs=14.4
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhccccccc
Q 023228 44 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWT 79 (285)
Q Consensus 44 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT 79 (285)
.+||-|.|..|= ...--+.|-.|..=|.
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 4566788999987774
No 37
>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=24.49 E-value=31 Score=21.90 Aligned_cols=27 Identities=26% Similarity=0.708 Sum_probs=13.5
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhccc
Q 023228 44 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCR 75 (285)
Q Consensus 44 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~Cr 75 (285)
.+||||...-.++-.. .+.-+||..|+
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 4788998876665441 12336777775
No 38
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=24.02 E-value=44 Score=30.01 Aligned_cols=43 Identities=21% Similarity=0.304 Sum_probs=29.4
Q ss_pred CCCCCCCCCcceeee---cccCCCCCchhhhccccccccCCccccc
Q 023228 45 NCPRCNSTNTKFCYY---NNYSLTQPRYFCKTCRRYWTEGGSLRNI 87 (285)
Q Consensus 45 ~CPRC~S~~Tkfcyy---NNy~~~QPR~fCk~CrRyWT~GG~lRnv 87 (285)
.||.|.+.+||+-== -.-+..+-|.-|-+|..-+|-==++--+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELR 47 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeec
Confidence 699999999998522 1223345678999999888755444333
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=23.30 E-value=62 Score=23.12 Aligned_cols=32 Identities=28% Similarity=0.636 Sum_probs=18.8
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchh-hhcccc
Q 023228 44 LNCPRCNSTNTKFCYYNNYSLTQPRYF-CKTCRR 76 (285)
Q Consensus 44 ~~CPRC~S~~TkfcyyNNy~~~QPR~f-Ck~CrR 76 (285)
.+||.|.+..-.|=+ ........+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 579999997665532 12233334444 777764
No 40
>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=21.66 E-value=53 Score=27.97 Aligned_cols=31 Identities=32% Similarity=0.747 Sum_probs=24.9
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhccccccccCC
Q 023228 44 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGG 82 (285)
Q Consensus 44 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GG 82 (285)
.+||.|.|..|- - .+.-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY---~-----dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTY---H-----DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceE---e-----cCCeeECccccccccccc
Confidence 589999998663 1 355699999999999876
No 41
>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=21.11 E-value=68 Score=24.65 Aligned_cols=31 Identities=23% Similarity=0.477 Sum_probs=22.6
Q ss_pred ccCCCCCCCCCCcceeeecccCCCCCchhhhccc
Q 023228 42 QALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCR 75 (285)
Q Consensus 42 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~Cr 75 (285)
-+..||+|...+|=..|..|.- .-.-|-.|.
T Consensus 8 AGA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 8 AGAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred ccccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 4588999999999988866653 334566663
No 42
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=20.83 E-value=29 Score=33.93 Aligned_cols=41 Identities=22% Similarity=0.528 Sum_probs=24.6
Q ss_pred hhhhcCCCCccccCCCCC-----CCCCCcc--eeeecccCCCCCchhhhc
Q 023228 31 ALERKARPQKEQALNCPR-----CNSTNTK--FCYYNNYSLTQPRYFCKT 73 (285)
Q Consensus 31 ~~er~~~p~~~~~~~CPR-----C~S~~Tk--fcyyNNy~~~QPR~fCk~ 73 (285)
|+-|+..|.++ |+|-. |+...-+ =||-.-|.-.-.---||+
T Consensus 38 Tt~RR~~pipQ--L~Cvggsa~~c~~~~p~vvqC~N~G~dg~dvqW~C~A 85 (318)
T PF06682_consen 38 TTSRRVSPIPQ--LKCVGGSARGCDLYEPDVVQCTNQGYDGEDVQWECKA 85 (318)
T ss_pred cccccCCCCcc--eeecCCCcccccccCcceEEEEecCCCCcccceEEeC
Confidence 56688788777 89943 7664333 366555544444445543
No 43
>PRK10220 hypothetical protein; Provisional
Probab=20.51 E-value=60 Score=27.76 Aligned_cols=31 Identities=32% Similarity=0.830 Sum_probs=24.9
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhccccccccCC
Q 023228 44 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGG 82 (285)
Q Consensus 44 ~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrRyWT~GG 82 (285)
.+||.|.|..|- ..+.-+.|..|.-=|+..-
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 689999998663 2356799999999998775
No 44
>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=20.29 E-value=60 Score=25.79 Aligned_cols=31 Identities=19% Similarity=0.446 Sum_probs=17.2
Q ss_pred ccCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 42 QALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 42 ~~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
-...||-|+..+..|..+.+- -++.|-+|.+
T Consensus 32 ~~~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~ 62 (97)
T PF01807_consen 32 YRCLCPFHDDKTPSFSINPDK----NRFKCFGCGK 62 (97)
T ss_dssp EEE--SSS--SS--EEEETTT----TEEEETTT--
T ss_pred EEEECcCCCCCCCceEEECCC----CeEEECCCCC
Confidence 357799999887777776543 3899999985
No 45
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=20.15 E-value=54 Score=31.51 Aligned_cols=29 Identities=21% Similarity=0.633 Sum_probs=20.8
Q ss_pred cCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 023228 43 ALNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 76 (285)
Q Consensus 43 ~~~CPRC~S~~TkfcyyNNy~~~QPR~fCk~CrR 76 (285)
.-+|++|.+.=.|.- --.+..|||..|++
T Consensus 245 GepC~~CGt~I~k~~-----~~gR~t~~CP~CQ~ 273 (273)
T COG0266 245 GEPCRRCGTPIEKIK-----LGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCccCCEeEEEE-----EcCCcCEeCCCCCC
Confidence 468999999654432 13467799999985
Done!