Query 019668
Match_columns 337
No_of_seqs 142 out of 258
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 03:35:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019668.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019668hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02701 zf-Dof: Dof domain, z 100.0 1.2E-37 2.6E-42 238.5 4.2 63 71-133 1-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 95.1 0.014 3E-07 51.5 2.2 34 75-110 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 92.5 0.097 2.1E-06 37.5 2.2 36 66-108 10-45 (46)
4 COG3677 Transposase and inacti 91.9 0.11 2.3E-06 45.1 2.2 36 75-112 30-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 91.6 0.1 2.2E-06 36.6 1.5 30 76-107 6-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 88.4 0.44 9.4E-06 33.7 2.5 37 76-112 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 85.8 0.61 1.3E-05 32.7 2.1 36 76-111 1-39 (39)
8 PHA02998 RNA polymerase subuni 79.8 1.6 3.5E-05 40.8 2.9 39 74-112 142-183 (195)
9 cd00202 ZnF_GATA Zinc finger D 79.1 2 4.2E-05 32.3 2.7 42 77-121 1-42 (54)
10 PF04216 FdhE: Protein involve 77.0 1 2.3E-05 42.8 0.8 37 75-111 211-249 (290)
11 PF13453 zf-TFIIB: Transcripti 76.5 0.71 1.5E-05 32.3 -0.3 37 77-118 1-37 (41)
12 TIGR01384 TFS_arch transcripti 71.1 4.3 9.4E-05 32.9 3.0 39 75-113 62-103 (104)
13 PF04981 NMD3: NMD3 family ; 67.2 2.8 6.1E-05 39.0 1.3 36 78-113 1-48 (236)
14 TIGR01385 TFSII transcription 65.5 6.2 0.00013 38.8 3.3 37 75-111 258-297 (299)
15 smart00401 ZnF_GATA zinc finge 62.6 5.7 0.00012 29.4 1.9 40 74-116 2-41 (52)
16 PRK14810 formamidopyrimidine-D 62.0 4.7 0.0001 38.5 1.7 29 75-108 244-272 (272)
17 TIGR00244 transcriptional regu 59.9 6.1 0.00013 35.7 2.0 44 77-120 2-48 (147)
18 PRK14811 formamidopyrimidine-D 59.7 5.6 0.00012 38.0 1.8 29 75-108 235-263 (269)
19 PRK03564 formate dehydrogenase 58.4 6.4 0.00014 39.1 2.0 37 75-112 226-264 (309)
20 PF14690 zf-ISL3: zinc-finger 57.6 5 0.00011 27.9 0.8 32 75-106 2-47 (47)
21 TIGR01562 FdhE formate dehydro 55.6 7.4 0.00016 38.5 1.9 36 75-111 224-263 (305)
22 PRK01103 formamidopyrimidine/5 55.6 7.1 0.00015 37.1 1.8 29 75-108 245-273 (274)
23 PHA00626 hypothetical protein 54.0 8.4 0.00018 30.2 1.6 38 76-115 1-38 (59)
24 PRK10445 endonuclease VIII; Pr 53.7 7.9 0.00017 36.8 1.8 29 75-108 235-263 (263)
25 PF06220 zf-U1: U1 zinc finger 53.1 5.7 0.00012 28.0 0.5 17 98-114 1-17 (38)
26 PRK13945 formamidopyrimidine-D 52.6 8.7 0.00019 36.8 1.9 29 75-108 254-282 (282)
27 PF09526 DUF2387: Probable met 52.0 9.9 0.00021 30.3 1.8 31 75-108 8-38 (71)
28 PF14599 zinc_ribbon_6: Zinc-r 47.9 7.1 0.00015 30.4 0.4 14 74-87 47-60 (61)
29 TIGR00577 fpg formamidopyrimid 47.6 11 0.00025 35.8 1.8 28 75-107 245-272 (272)
30 PRK00464 nrdR transcriptional 47.5 12 0.00027 33.6 1.9 45 76-120 1-48 (154)
31 PRK00432 30S ribosomal protein 43.3 12 0.00027 27.7 1.0 26 75-108 20-45 (50)
32 PF06827 zf-FPG_IleRS: Zinc fi 39.9 12 0.00026 24.4 0.5 28 75-107 1-28 (30)
33 KOG2906 RNA polymerase III sub 38.6 24 0.00053 30.4 2.2 38 74-111 64-104 (105)
34 COG0266 Nei Formamidopyrimidin 37.5 19 0.00041 35.3 1.6 30 74-108 244-273 (273)
35 COG1997 RPL43A Ribosomal prote 36.8 15 0.00034 30.8 0.8 65 50-122 8-75 (89)
36 PF08273 Prim_Zn_Ribbon: Zinc- 34.8 24 0.00052 25.4 1.4 33 74-108 2-34 (40)
37 COG1327 Predicted transcriptio 33.3 24 0.00052 32.4 1.4 44 77-120 2-48 (156)
38 COG4260 Membrane protease subu 33.2 23 0.0005 35.7 1.5 40 67-108 298-342 (345)
39 PRK14892 putative transcriptio 32.1 26 0.00056 29.6 1.4 36 73-112 19-54 (99)
40 PF08274 PhnA_Zn_Ribbon: PhnA 31.7 22 0.00048 24.3 0.7 28 76-111 3-30 (30)
41 TIGR02443 conserved hypothetic 30.3 36 0.00077 26.8 1.8 30 75-107 9-38 (59)
42 PF14354 Lar_restr_allev: Rest 30.3 38 0.00082 24.8 1.8 36 73-108 1-37 (61)
43 PF01807 zf-CHC2: CHC2 zinc fi 27.5 39 0.00085 27.5 1.7 30 76-109 34-63 (97)
44 PF07282 OrfB_Zn_ribbon: Putat 26.2 39 0.00084 25.3 1.3 37 69-112 22-58 (69)
45 TIGR03655 anti_R_Lar restricti 26.0 52 0.0011 24.1 1.9 32 76-108 2-34 (53)
46 KOG2691 RNA polymerase II subu 24.6 60 0.0013 28.5 2.3 37 74-112 72-113 (113)
47 COG4049 Uncharacterized protei 24.1 29 0.00063 27.5 0.3 11 73-83 15-25 (65)
48 PF06044 DRP: Dam-replacing fa 21.5 35 0.00076 33.5 0.4 34 74-111 30-64 (254)
49 TIGR00686 phnA alkylphosphonat 21.0 62 0.0013 28.2 1.7 31 76-114 3-33 (109)
50 PF01783 Ribosomal_L32p: Ribos 21.0 54 0.0012 24.6 1.2 26 69-107 21-46 (56)
51 PRK10220 hypothetical protein; 20.6 60 0.0013 28.4 1.5 31 76-114 4-34 (111)
No 1
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=100.00 E-value=1.2e-37 Score=238.47 Aligned_cols=63 Identities=78% Similarity=1.575 Sum_probs=60.4
Q ss_pred CCcccCCCCCCCCCCcceeeeccccCCCCcccchhcccccccCcccccccCCCCcccCCCCCC
Q 019668 71 QPETALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRNVPVGGGCRRNKRSKG 133 (337)
Q Consensus 71 ~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~lRnvPvGgG~Rknkr~~~ 133 (337)
.||+.++||||+|+||||||||||+++||||||++|+||||+||+||||||||||||+|++++
T Consensus 1 ~~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~s 63 (63)
T PF02701_consen 1 KPEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSSS 63 (63)
T ss_pred CCccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCCC
Confidence 478999999999999999999999999999999999999999999999999999999998753
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=95.08 E-value=0.014 Score=51.54 Aligned_cols=34 Identities=24% Similarity=0.705 Sum_probs=27.3
Q ss_pred cCCCCCCCCCCcceeeecccc--CCCCcccchhccccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYS--LSQPRHFCKTCRRYW 110 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~--~~QPR~fCk~CrRyW 110 (337)
...||||.|.+|+. .+.|- .++.-|+|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~--~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTI--TSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEe--ecCCCChhhHHHhhhhhhCCcH
Confidence 47999999999997 56664 457779999998644
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=92.48 E-value=0.097 Score=37.46 Aligned_cols=36 Identities=33% Similarity=0.787 Sum_probs=25.9
Q ss_pred hcCCCCCcccCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 66 MAKMPQPETALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 66 ~a~~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
|+.+-=|+. ..||+|.+. +...+.+ ..++.|++|++
T Consensus 10 l~~~RW~~g-~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 10 LEEIRWPDG-FVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred HHHhcCCCC-CCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 344444453 669999998 6555555 78899999985
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.88 E-value=0.11 Score=45.06 Aligned_cols=36 Identities=31% Similarity=0.652 Sum_probs=28.3
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhccccccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTR 112 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~ 112 (337)
...||+|.+.+.+ =++-+.....|+.|++|++-|+.
T Consensus 30 ~~~cP~C~s~~~~--k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 30 KVNCPRCKSSNVV--KIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred cCcCCCCCcccee--eECCccccccccccCCcCcceee
Confidence 3789999999922 25555555999999999998874
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=91.65 E-value=0.1 Score=36.60 Aligned_cols=30 Identities=43% Similarity=0.782 Sum_probs=21.2
Q ss_pred CCCCCCCCCCcceeeeccccC-CCCcccchhcc
Q 019668 76 LKCPRCESTNTKFCYFNNYSL-SQPRHFCKTCR 107 (337)
Q Consensus 76 ~~CPRC~S~~Tkfcy~NNy~~-~QPR~fCk~Cr 107 (337)
+.||+|.+++.- |=|-.+. -..||+|++|+
T Consensus 6 v~CP~C~s~~~v--~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTEGV--KKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCCcc--eeCCCCCCCCEeEecCcCC
Confidence 789999998721 1334433 35899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.43 E-value=0.44 Score=33.70 Aligned_cols=37 Identities=24% Similarity=0.719 Sum_probs=28.1
Q ss_pred CCCCCCCCCCcceeeeccccCCCC---cccchhccccccc
Q 019668 76 LKCPRCESTNTKFCYFNNYSLSQP---RHFCKTCRRYWTR 112 (337)
Q Consensus 76 ~~CPRC~S~~Tkfcy~NNy~~~QP---R~fCk~CrRyWT~ 112 (337)
.+||+|...+.-|-..+-.+...| -|.|.+|...|..
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 379999988777755555655555 4999999999963
No 7
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=85.82 E-value=0.61 Score=32.72 Aligned_cols=36 Identities=28% Similarity=0.768 Sum_probs=24.4
Q ss_pred CCCCCCCCCCcceeeeccccCCCCc---ccchhcccccc
Q 019668 76 LKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWT 111 (337)
Q Consensus 76 ~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT 111 (337)
.+||.|...+..|=-.+..+...|- |.|.+|..-|+
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 3799999988776545555555553 89999999985
No 8
>PHA02998 RNA polymerase subunit; Provisional
Probab=79.78 E-value=1.6 Score=40.82 Aligned_cols=39 Identities=26% Similarity=0.653 Sum_probs=33.9
Q ss_pred ccCCCCCCCCCCcceeeeccccCCCCc---ccchhccccccc
Q 019668 74 TALKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWTR 112 (337)
Q Consensus 74 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT~ 112 (337)
...+||+|...++-|--.+-.+...|- |.|..|..-|.-
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 569999999999999888888888885 799999999853
No 9
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=79.05 E-value=2 Score=32.29 Aligned_cols=42 Identities=26% Similarity=0.666 Sum_probs=29.9
Q ss_pred CCCCCCCCCcceeeeccccCCCCcccchhcccccccCcccccccC
Q 019668 77 KCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRNVPV 121 (337)
Q Consensus 77 ~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~lRnvPv 121 (337)
.|--|..++|..=.-.. .....+|-+|..||.+.|..|.+-.
T Consensus 1 ~C~~C~~~~Tp~WR~g~---~~~~~LCNaCgl~~~k~~~~rp~~~ 42 (54)
T cd00202 1 ACSNCGTTTTPLWRRGP---SGGSTLCNACGLYWKKHGVMRPLSK 42 (54)
T ss_pred CCCCCCCCCCcccccCC---CCcchHHHHHHHHHHhcCCCCCccc
Confidence 37788887776422222 4677999999999999996655443
No 10
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=76.96 E-value=1 Score=42.77 Aligned_cols=37 Identities=30% Similarity=0.692 Sum_probs=19.0
Q ss_pred cCCCCCCCCCC-cceeeecc-ccCCCCcccchhcccccc
Q 019668 75 ALKCPRCESTN-TKFCYFNN-YSLSQPRHFCKTCRRYWT 111 (337)
Q Consensus 75 ~~~CPRC~S~~-Tkfcy~NN-y~~~QPR~fCk~CrRyWT 111 (337)
...||.|..++ .++-||.. -....--+.|++|+.|+-
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 56799999855 56777743 333333499999999983
No 11
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.46 E-value=0.71 Score=32.27 Aligned_cols=37 Identities=27% Similarity=0.637 Sum_probs=26.8
Q ss_pred CCCCCCCCCcceeeeccccCCCCcccchhcccccccCccccc
Q 019668 77 KCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRN 118 (337)
Q Consensus 77 ~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~lRn 118 (337)
+||+|...-.+.-+ ..-+-+.|..|.-.|=..+.+..
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 69999985555433 23456889999999987776544
No 12
>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=71.14 E-value=4.3 Score=32.86 Aligned_cols=39 Identities=18% Similarity=0.622 Sum_probs=28.4
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCc---ccchhcccccccC
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWTRG 113 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT~G 113 (337)
..+||+|...+.-|-..+-.+...|- |.|..|.-.|+.+
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 48999998777666444444443343 8999999999864
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=67.21 E-value=2.8 Score=38.96 Aligned_cols=36 Identities=31% Similarity=0.856 Sum_probs=24.2
Q ss_pred CCCCCCCCcc-------eeeeccccCCC-----CcccchhcccccccC
Q 019668 78 CPRCESTNTK-------FCYFNNYSLSQ-----PRHFCKTCRRYWTRG 113 (337)
Q Consensus 78 CPRC~S~~Tk-------fcy~NNy~~~Q-----PR~fCk~CrRyWT~G 113 (337)
||+|...... =||...+.+.. --.+|+.|.||+..|
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~ 48 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGG 48 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCC
Confidence 6666653333 26777776644 237999999999984
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=65.53 E-value=6.2 Score=38.79 Aligned_cols=37 Identities=19% Similarity=0.649 Sum_probs=28.1
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCc---ccchhcccccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWT 111 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT 111 (337)
..+||+|...+..|-..+..+...|- |.|..|...|.
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 48999999888777555555555553 78999999884
No 15
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=62.59 E-value=5.7 Score=29.43 Aligned_cols=40 Identities=25% Similarity=0.617 Sum_probs=29.4
Q ss_pred ccCCCCCCCCCCcceeeeccccCCCCcccchhcccccccCccc
Q 019668 74 TALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGAL 116 (337)
Q Consensus 74 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~l 116 (337)
....|--|..++|..=.- ...-++.+|-+|.-||.+.+.+
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 357899999988864211 2223379999999999998886
No 16
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=62.03 E-value=4.7 Score=38.49 Aligned_cols=29 Identities=17% Similarity=0.653 Sum_probs=21.5
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
+.+||||...=.|.-+= .+.-|||..|++
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 57899999866664332 366699999985
No 17
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=59.89 E-value=6.1 Score=35.71 Aligned_cols=44 Identities=23% Similarity=0.406 Sum_probs=32.3
Q ss_pred CCCCCCCCCcceeee---ccccCCCCcccchhcccccccCccccccc
Q 019668 77 KCPRCESTNTKFCYF---NNYSLSQPRHFCKTCRRYWTRGGALRNVP 120 (337)
Q Consensus 77 ~CPRC~S~~Tkfcy~---NNy~~~QPR~fCk~CrRyWT~GG~lRnvP 120 (337)
+||.|...+||+-== ...+.-+-|..|..|.+-||-==++-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 699999999998432 33344567799999999998655544444
No 18
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=59.69 E-value=5.6 Score=37.98 Aligned_cols=29 Identities=31% Similarity=0.817 Sum_probs=21.6
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
+.+||||...=.|.-+ . .+.-|||..|++
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 4689999987666433 2 366799999996
No 19
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=58.43 E-value=6.4 Score=39.05 Aligned_cols=37 Identities=27% Similarity=0.588 Sum_probs=24.3
Q ss_pred cCCCCCCCCCCcceeeecccc--CCCCcccchhccccccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYS--LSQPRHFCKTCRRYWTR 112 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~--~~QPR~fCk~CrRyWT~ 112 (337)
..+||.|... .|.-||.--. ..---+.|.+|+.|+--
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 5789999974 4666664222 12223889999999853
No 20
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=57.59 E-value=5 Score=27.90 Aligned_cols=32 Identities=28% Similarity=0.648 Sum_probs=19.2
Q ss_pred cCCCCCCCCCCcce-eeeccc-------------cCCCCcccchhc
Q 019668 75 ALKCPRCESTNTKF-CYFNNY-------------SLSQPRHFCKTC 106 (337)
Q Consensus 75 ~~~CPRC~S~~Tkf-cy~NNy-------------~~~QPR~fCk~C 106 (337)
...||.|.+...+. -++... .+..+|++|++|
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 346778888887
No 21
>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=55.62 E-value=7.4 Score=38.48 Aligned_cols=36 Identities=22% Similarity=0.633 Sum_probs=24.4
Q ss_pred cCCCCCCCCCCcceeeecccc----CCCCcccchhcccccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYS----LSQPRHFCKTCRRYWT 111 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~----~~QPR~fCk~CrRyWT 111 (337)
..+||.|.+.+ |.-||.-.. ..---..|.+|+.|+-
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 57899999864 555665432 1122368999999974
No 22
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=55.56 E-value=7.1 Score=37.10 Aligned_cols=29 Identities=24% Similarity=0.657 Sum_probs=21.5
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
+.+||||...=.|. -++ .+.-|||..|++
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 56899999876654 333 366799999986
No 23
>PHA00626 hypothetical protein
Probab=53.98 E-value=8.4 Score=30.21 Aligned_cols=38 Identities=18% Similarity=0.256 Sum_probs=25.0
Q ss_pred CCCCCCCCCCcceeeeccccCCCCcccchhcccccccCcc
Q 019668 76 LKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGA 115 (337)
Q Consensus 76 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~ 115 (337)
..||+|.|.+--=|=.= ....-||.|++|.=.+|+..-
T Consensus 1 m~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCCceeeeecee--cccCcceEcCCCCCeechhhh
Confidence 36999999754322111 111457999999999998643
No 24
>PRK10445 endonuclease VIII; Provisional
Probab=53.74 E-value=7.9 Score=36.77 Aligned_cols=29 Identities=28% Similarity=0.655 Sum_probs=21.2
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
+.+||||...-.|.-+ + .+.-|||..|++
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 5689999887666544 2 366699999984
No 25
>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=53.12 E-value=5.7 Score=27.99 Aligned_cols=17 Identities=35% Similarity=1.017 Sum_probs=7.1
Q ss_pred CCcccchhcccccccCc
Q 019668 98 QPRHFCKTCRRYWTRGG 114 (337)
Q Consensus 98 QPR~fCk~CrRyWT~GG 114 (337)
+|||||.-|..|.|..-
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 26
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=52.59 E-value=8.7 Score=36.78 Aligned_cols=29 Identities=17% Similarity=0.689 Sum_probs=21.4
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
+.+||||...-.|.-+ . .+--|||..|++
T Consensus 254 g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCRKCGTPIERIKL-A----GRSTHWCPNCQK 282 (282)
T ss_pred cCCCCcCCCeeEEEEE-C----CCccEECCCCcC
Confidence 4689999987666544 2 256699999985
No 27
>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=51.98 E-value=9.9 Score=30.29 Aligned_cols=31 Identities=23% Similarity=0.503 Sum_probs=25.2
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
+..||+|.+.+|=..|..|. ..-.-|-.|.-
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 68899999999988887776 55667888863
No 28
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=47.85 E-value=7.1 Score=30.40 Aligned_cols=14 Identities=43% Similarity=0.786 Sum_probs=5.9
Q ss_pred ccCCCCCCCCCCcc
Q 019668 74 TALKCPRCESTNTK 87 (337)
Q Consensus 74 ~~~~CPRC~S~~Tk 87 (337)
-+++|+.|.|.||+
T Consensus 47 lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 47 LGHKCSHCGSYNTR 60 (61)
T ss_dssp T----TTTS---EE
T ss_pred hhhcCCCCCCcccC
Confidence 35789999999997
No 29
>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=47.64 E-value=11 Score=35.82 Aligned_cols=28 Identities=29% Similarity=0.708 Sum_probs=20.6
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhcc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCR 107 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 107 (337)
+.+||||...=.|.-+ . .+.-|||..|+
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 4689999987666433 3 36669999996
No 30
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=47.51 E-value=12 Score=33.59 Aligned_cols=45 Identities=22% Similarity=0.467 Sum_probs=32.4
Q ss_pred CCCCCCCCCCccee---eeccccCCCCcccchhcccccccCccccccc
Q 019668 76 LKCPRCESTNTKFC---YFNNYSLSQPRHFCKTCRRYWTRGGALRNVP 120 (337)
Q Consensus 76 ~~CPRC~S~~Tkfc---y~NNy~~~QPR~fCk~CrRyWT~GG~lRnvP 120 (337)
.+||-|.+..|++- |+-.-++-.-|+-|++|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999887763 4444444555699999999888766655554
No 31
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.29 E-value=12 Score=27.75 Aligned_cols=26 Identities=35% Similarity=0.646 Sum_probs=18.8
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
..-||+|.+. |..-.. .|+.|..|..
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 3589999874 544443 6999999974
No 32
>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=39.90 E-value=12 Score=24.37 Aligned_cols=28 Identities=25% Similarity=0.587 Sum_probs=15.1
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhcc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCR 107 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 107 (337)
+.+||||.....++-..+ +.-+||..|+
T Consensus 1 G~~C~rC~~~~~~~~~~~-----r~~~~C~rCq 28 (30)
T PF06827_consen 1 GEKCPRCWNYIEDIGING-----RSTYLCPRCQ 28 (30)
T ss_dssp TSB-TTT--BBEEEEETT-----EEEEE-TTTC
T ss_pred CCcCccCCCcceEeEecC-----CCCeECcCCc
Confidence 468999998877764421 2337888876
No 33
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=38.57 E-value=24 Score=30.45 Aligned_cols=38 Identities=26% Similarity=0.655 Sum_probs=32.5
Q ss_pred ccCCCCCCCCCCcceeeeccccCCCCc---ccchhcccccc
Q 019668 74 TALKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWT 111 (337)
Q Consensus 74 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT 111 (337)
....||+|...+.-|--++-.+..-|- |.|-.|+--|-
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 347899999999988888888888876 89999999885
No 34
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=37.55 E-value=19 Score=35.31 Aligned_cols=30 Identities=20% Similarity=0.613 Sum_probs=21.5
Q ss_pred ccCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 74 TALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 74 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
++.+|++|.+.-.|-- + -.+..|||..|++
T Consensus 244 ~GepC~~CGt~I~k~~-~----~gR~t~~CP~CQ~ 273 (273)
T COG0266 244 AGEPCRRCGTPIEKIK-L----GGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCccCCEeEEEE-E----cCCcCEeCCCCCC
Confidence 4678999999655531 1 2366799999985
No 35
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=36.83 E-value=15 Score=30.84 Aligned_cols=65 Identities=26% Similarity=0.459 Sum_probs=40.4
Q ss_pred CCCCC--CCCCchhHHhhhcCCC-CCcccCCCCCCCCCCcceeeeccccCCCCcccchhcccccccCcccccccCC
Q 019668 50 GSTGA--IRPNSMTERARMAKMP-QPETALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRNVPVG 122 (337)
Q Consensus 50 g~ag~--~~p~sm~~rar~a~~p-~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~lRnvPvG 122 (337)
|.+|. +|=++..+| +...+- +--....||-|.+...|= ..----.|+.|..-|+.|+-....|+|
T Consensus 8 G~aGrfGpRYG~~~Rr-rv~~ie~~~~~~~~Cp~C~~~~VkR-------~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 8 GIAGRFGPRYGSKLRR-RVKEIEAQQRAKHVCPFCGRTTVKR-------IATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred ccCcccccccchHHHH-HHHHHHHHHhcCCcCCCCCCcceee-------eccCeEEcCCCCCeeccccccccchHH
Confidence 44553 344555443 444332 223458899999985541 222337899999999999887766654
No 36
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=34.83 E-value=24 Score=25.40 Aligned_cols=33 Identities=21% Similarity=0.596 Sum_probs=18.7
Q ss_pred ccCCCCCCCCCCcceeeeccccCCCCcccchhccc
Q 019668 74 TALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 108 (337)
Q Consensus 74 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 108 (337)
...+||-|.. ..+|..|-+. ...-..+|+.|..
T Consensus 2 ~h~pCP~CGG-~DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 2 KHGPCPICGG-KDRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp EEE--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCCCcC-ccccccCcCc-ccCCCEECCCCCC
Confidence 3568999988 5688866543 3347799999943
No 37
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=33.29 E-value=24 Score=32.36 Aligned_cols=44 Identities=25% Similarity=0.365 Sum_probs=30.3
Q ss_pred CCCCCCCCCcceeee---ccccCCCCcccchhcccccccCccccccc
Q 019668 77 KCPRCESTNTKFCYF---NNYSLSQPRHFCKTCRRYWTRGGALRNVP 120 (337)
Q Consensus 77 ~CPRC~S~~Tkfcy~---NNy~~~QPR~fCk~CrRyWT~GG~lRnvP 120 (337)
+||.|.+.+||+-== ..-+..+-|.-|-+|..-+|-==++--+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 699999999998321 11233456789999998888655544343
No 38
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=33.16 E-value=23 Score=35.70 Aligned_cols=40 Identities=28% Similarity=0.698 Sum_probs=25.3
Q ss_pred cCCCCCcccCCCCCCCCCCcceeeeccccCC-----CCcccchhccc
Q 019668 67 AKMPQPETALKCPRCESTNTKFCYFNNYSLS-----QPRHFCKTCRR 108 (337)
Q Consensus 67 a~~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~-----QPR~fCk~CrR 108 (337)
|....|..--+||||...| ||.-----.+ -..-||++|..
T Consensus 298 aqaa~pa~t~~~~r~~k~n--fc~ncG~~~t~~~~ng~a~fcp~cgq 342 (345)
T COG4260 298 AQAAAPAATWPCARCAKLN--FCLNCGCGTTADFDNGKAKFCPECGQ 342 (345)
T ss_pred hhhcCCcccCcchhccccc--cccccCcccccCCccchhhhChhhcC
Confidence 3456677778999999888 7653321111 13467888753
No 39
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=32.13 E-value=26 Score=29.64 Aligned_cols=36 Identities=19% Similarity=0.410 Sum_probs=25.2
Q ss_pred cccCCCCCCCCCCcceeeeccccCCCCcccchhccccccc
Q 019668 73 ETALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTR 112 (337)
Q Consensus 73 e~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~ 112 (337)
.....||.|.+ .+--|=+.. ..+.+.|..|.-|-..
T Consensus 19 pt~f~CP~Cge-~~v~v~~~k---~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGK-VSISVKIKK---NIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCC-eEeeeecCC---CcceEECCCCCCccCE
Confidence 35688999995 233334443 4789999999998543
No 40
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=31.74 E-value=22 Score=24.26 Aligned_cols=28 Identities=32% Similarity=0.663 Sum_probs=14.7
Q ss_pred CCCCCCCCCCcceeeeccccCCCCcccchhcccccc
Q 019668 76 LKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWT 111 (337)
Q Consensus 76 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT 111 (337)
-+||-|.|..|= ...--+.|.+|..=|.
T Consensus 3 p~Cp~C~se~~y--------~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTY--------EDGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----E--------E-SSSEEETTTTEEE-
T ss_pred CCCCCCCCccee--------ccCCEEeCCcccccCC
Confidence 479999998875 4567789999987774
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=30.31 E-value=36 Score=26.76 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=22.9
Q ss_pred cCCCCCCCCCCcceeeeccccCCCCcccchhcc
Q 019668 75 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCR 107 (337)
Q Consensus 75 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 107 (337)
+..||+|...+|=..|..|.- ...-|-.|.
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 689999999999988866654 345677774
No 42
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=30.25 E-value=38 Score=24.80 Aligned_cols=36 Identities=19% Similarity=0.359 Sum_probs=20.3
Q ss_pred cccCCCCCCCCCCcceeeeccccCCC-Ccccchhccc
Q 019668 73 ETALKCPRCESTNTKFCYFNNYSLSQ-PRHFCKTCRR 108 (337)
Q Consensus 73 e~~~~CPRC~S~~Tkfcy~NNy~~~Q-PR~fCk~CrR 108 (337)
|+..+||.|.+....+.+........ -.-+|..|.-
T Consensus 1 ~~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 1 EELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 35678999966665554422211111 3345888865
No 43
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=27.52 E-value=39 Score=27.49 Aligned_cols=30 Identities=20% Similarity=0.381 Sum_probs=16.5
Q ss_pred CCCCCCCCCCcceeeeccccCCCCcccchhcccc
Q 019668 76 LKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRY 109 (337)
Q Consensus 76 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRy 109 (337)
..||-|+..+..|..+.+. -++.|-+|.+.
T Consensus 34 ~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~~ 63 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPDK----NRFKCFGCGKG 63 (97)
T ss_dssp E--SSS--SS--EEEETTT----TEEEETTT--E
T ss_pred EECcCCCCCCCceEEECCC----CeEEECCCCCC
Confidence 6799999887777666443 37999999853
No 44
>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=26.18 E-value=39 Score=25.29 Aligned_cols=37 Identities=30% Similarity=0.512 Sum_probs=28.1
Q ss_pred CCCCcccCCCCCCCCCCcceeeeccccCCCCcccchhccccccc
Q 019668 69 MPQPETALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTR 112 (337)
Q Consensus 69 ~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~ 112 (337)
|+.-..-..||.|.....+ .+..-.+.|..|...+.+
T Consensus 22 v~~~~TSq~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 22 VDEAYTSQTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred ECCCCCccCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 4444455889999998877 666777999999877654
No 45
>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=25.96 E-value=52 Score=24.11 Aligned_cols=32 Identities=25% Similarity=0.528 Sum_probs=19.0
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccc-chhccc
Q 019668 76 LKCPRCESTNTKFCYFNNYSLSQPRHF-CKTCRR 108 (337)
Q Consensus 76 ~~CPRC~S~~Tkfcy~NNy~~~QPR~f-Ck~CrR 108 (337)
.+||.|.+..-.|=+ ......-.+++ |..|.-
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 589999997765532 12233334444 887764
No 46
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=24.63 E-value=60 Score=28.46 Aligned_cols=37 Identities=24% Similarity=0.665 Sum_probs=26.4
Q ss_pred ccCCCCCCCCCCcceeeeccccCCCC-----cccchhccccccc
Q 019668 74 TALKCPRCESTNTKFCYFNNYSLSQP-----RHFCKTCRRYWTR 112 (337)
Q Consensus 74 ~~~~CPRC~S~~Tkfcy~NNy~~~QP-----R~fCk~CrRyWT~ 112 (337)
.-..||+|...+.-| |+--+...- -|.|-+|.--||+
T Consensus 72 s~~~C~~C~~~eavf--fQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 72 SDKHCPKCGHREAVF--FQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred ccccCCccCCcceEE--EecccccccceEEEEEEeccccccccC
Confidence 447899999988766 654332211 1889999999985
No 47
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=24.15 E-value=29 Score=27.52 Aligned_cols=11 Identities=55% Similarity=1.241 Sum_probs=8.8
Q ss_pred cccCCCCCCCC
Q 019668 73 ETALKCPRCES 83 (337)
Q Consensus 73 e~~~~CPRC~S 83 (337)
|.-+.||||+-
T Consensus 15 E~~lrCPRC~~ 25 (65)
T COG4049 15 EEFLRCPRCGM 25 (65)
T ss_pred ceeeeCCchhH
Confidence 45599999986
No 48
>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=21.54 E-value=35 Score=33.46 Aligned_cols=34 Identities=24% Similarity=0.671 Sum_probs=13.0
Q ss_pred ccCCCCCCCCC-CcceeeeccccCCCCcccchhcccccc
Q 019668 74 TALKCPRCEST-NTKFCYFNNYSLSQPRHFCKTCRRYWT 111 (337)
Q Consensus 74 ~~~~CPRC~S~-~Tkfcy~NNy~~~QPR~fCk~CrRyWT 111 (337)
+-..||.|.+. -.+| ..+.+-.-.+|..|..=+-
T Consensus 30 ~n~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp HH---TTT--SS-EE------------EEE-TTT--EEE
T ss_pred HCCcCCCCCChhHhhc----cCCCccceeECCCCchHHh
Confidence 45789999998 5554 3344455699999987554
No 49
>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=21.03 E-value=62 Score=28.21 Aligned_cols=31 Identities=26% Similarity=0.693 Sum_probs=24.6
Q ss_pred CCCCCCCCCCcceeeeccccCCCCcccchhcccccccCc
Q 019668 76 LKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGG 114 (337)
Q Consensus 76 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG 114 (337)
..||.|.|..|-- ...-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY~--------dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTYH--------DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceEe--------cCCeeECccccccccccc
Confidence 4799999986632 355689999999999875
No 50
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=21.02 E-value=54 Score=24.61 Aligned_cols=26 Identities=31% Similarity=0.925 Sum_probs=19.2
Q ss_pred CCCCcccCCCCCCCCCCcceeeeccccCCCCcccchhcc
Q 019668 69 MPQPETALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCR 107 (337)
Q Consensus 69 ~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 107 (337)
+..| ....||-|.. +..|.+.|.+|.
T Consensus 21 l~~~-~l~~c~~cg~------------~~~~H~vc~~cG 46 (56)
T PF01783_consen 21 LKAP-NLVKCPNCGE------------PKLPHRVCPSCG 46 (56)
T ss_dssp --TT-SEEESSSSSS------------EESTTSBCTTTB
T ss_pred cccc-ceeeeccCCC------------EecccEeeCCCC
Confidence 4444 6789999984 348999999996
No 51
>PRK10220 hypothetical protein; Provisional
Probab=20.62 E-value=60 Score=28.39 Aligned_cols=31 Identities=26% Similarity=0.658 Sum_probs=24.7
Q ss_pred CCCCCCCCCCcceeeeccccCCCCcccchhcccccccCc
Q 019668 76 LKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGG 114 (337)
Q Consensus 76 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG 114 (337)
..||.|.|..|- .....+.|..|.-=|+..-
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 579999998663 1355699999999999875
Done!