Query 020288
Match_columns 328
No_of_seqs 141 out of 254
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 08:32:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020288.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020288hhsearch_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-42 237.7 4.5 63 73-135 1-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 94.7 0.022 4.9E-07 50.0 2.5 34 77-112 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 92.1 0.11 2.3E-06 37.1 2.0 36 68-110 10-45 (46)
4 COG3677 Transposase and inacti 91.8 0.1 2.3E-06 44.9 2.0 36 77-114 30-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 91.7 0.094 2E-06 36.6 1.3 31 77-109 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 87.7 0.42 9E-06 33.7 2.0 37 78-114 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 85.1 0.55 1.2E-05 32.8 1.5 36 78-113 1-39 (39)
8 cd00202 ZnF_GATA Zinc finger D 80.4 1.9 4.1E-05 32.2 2.9 42 79-123 1-42 (54)
9 PHA02998 RNA polymerase subuni 78.9 1.6 3.5E-05 40.7 2.6 39 76-114 142-183 (195)
10 PF13453 zf-TFIIB: Transcripti 78.0 0.65 1.4E-05 32.3 -0.2 37 79-120 1-37 (41)
11 PF04216 FdhE: Protein involve 77.9 0.98 2.1E-05 42.8 1.0 37 77-113 211-249 (290)
12 TIGR01384 TFS_arch transcripti 70.5 3.9 8.5E-05 33.0 2.6 39 77-115 62-103 (104)
13 PF04981 NMD3: NMD3 family ; 65.8 2.8 6E-05 38.8 0.9 36 80-115 1-48 (236)
14 TIGR00244 transcriptional regu 61.8 5.3 0.00011 36.0 1.9 44 79-122 2-48 (147)
15 TIGR01385 TFSII transcription 61.0 5.6 0.00012 38.9 2.1 37 77-113 258-297 (299)
16 smart00401 ZnF_GATA zinc finge 60.7 5.6 0.00012 29.4 1.6 39 77-118 3-41 (52)
17 PRK03564 formate dehydrogenase 59.5 6 0.00013 39.1 2.0 38 76-114 225-264 (309)
18 PF14690 zf-ISL3: zinc-finger 58.4 4.7 0.0001 27.9 0.8 32 77-108 2-47 (47)
19 PRK14810 formamidopyrimidine-D 57.8 5.4 0.00012 37.9 1.4 30 76-110 243-272 (272)
20 TIGR01562 FdhE formate dehydro 56.9 6.8 0.00015 38.6 1.9 37 76-113 223-263 (305)
21 PRK14811 formamidopyrimidine-D 55.4 6.3 0.00014 37.4 1.4 29 77-110 235-263 (269)
22 PRK01103 formamidopyrimidine/5 51.6 8 0.00017 36.6 1.4 30 76-110 244-273 (274)
23 PHA00626 hypothetical protein 51.4 8.3 0.00018 30.1 1.2 37 78-116 1-37 (59)
24 PF09526 DUF2387: Probable met 50.7 9.9 0.00021 30.2 1.6 32 76-110 7-38 (71)
25 PF06220 zf-U1: U1 zinc finger 50.6 5.8 0.00013 27.8 0.3 17 100-116 1-17 (38)
26 PRK10445 endonuclease VIII; Pr 49.6 8.9 0.00019 36.3 1.4 30 76-110 234-263 (263)
27 PRK00464 nrdR transcriptional 49.2 11 0.00023 33.9 1.7 45 78-122 1-48 (154)
28 PRK13945 formamidopyrimidine-D 48.4 9.9 0.00021 36.3 1.5 29 77-110 254-282 (282)
29 PF14599 zinc_ribbon_6: Zinc-r 46.6 7.7 0.00017 30.1 0.4 14 76-89 47-60 (61)
30 TIGR00577 fpg formamidopyrimid 43.2 13 0.00028 35.3 1.4 28 77-109 245-272 (272)
31 PF06827 zf-FPG_IleRS: Zinc fi 40.9 12 0.00027 24.2 0.6 28 77-109 1-28 (30)
32 PRK00432 30S ribosomal protein 40.8 12 0.00026 27.7 0.6 26 77-110 20-45 (50)
33 PRK14892 putative transcriptio 39.8 17 0.00037 30.6 1.5 35 76-114 20-54 (99)
34 KOG2906 RNA polymerase III sub 39.6 25 0.00054 30.3 2.4 38 76-113 64-104 (105)
35 COG1327 Predicted transcriptio 35.1 21 0.00046 32.6 1.4 43 79-121 2-47 (156)
36 COG0266 Nei Formamidopyrimidin 32.5 23 0.0005 34.7 1.3 30 76-110 244-273 (273)
37 COG4260 Membrane protease subu 32.0 27 0.00059 35.1 1.7 40 69-110 298-342 (345)
38 PF14354 Lar_restr_allev: Rest 30.6 38 0.00081 24.7 1.9 36 75-110 1-37 (61)
39 TIGR02443 conserved hypothetic 29.6 38 0.00083 26.5 1.8 31 76-109 8-38 (59)
40 PF07282 OrfB_Zn_ribbon: Putat 28.5 33 0.00071 25.6 1.3 38 70-114 21-58 (69)
41 PF08274 PhnA_Zn_Ribbon: PhnA 28.3 22 0.00048 24.2 0.3 28 78-113 3-30 (30)
42 COG4888 Uncharacterized Zn rib 27.6 36 0.00078 29.3 1.5 36 76-112 21-56 (104)
43 PF01807 zf-CHC2: CHC2 zinc fi 26.9 37 0.00081 27.5 1.4 30 78-111 34-63 (97)
44 COG4049 Uncharacterized protei 26.2 25 0.00053 27.8 0.3 11 75-85 15-25 (65)
45 PF08273 Prim_Zn_Ribbon: Zinc- 26.1 31 0.00067 24.8 0.7 32 77-110 3-34 (40)
46 KOG2691 RNA polymerase II subu 24.9 50 0.0011 28.8 1.9 37 76-114 72-113 (113)
47 TIGR03655 anti_R_Lar restricti 23.9 55 0.0012 23.9 1.7 32 78-110 2-34 (53)
48 PF10122 Mu-like_Com: Mu-like 21.9 35 0.00076 26.0 0.4 14 75-88 22-35 (51)
49 PF06044 DRP: Dam-replacing fa 21.8 33 0.00071 33.5 0.2 33 77-113 31-64 (254)
50 COG1997 RPL43A Ribosomal prote 20.7 37 0.00081 28.5 0.3 42 76-124 34-75 (89)
51 PRK12286 rpmF 50S ribosomal pr 20.2 61 0.0013 24.7 1.4 24 76-111 26-49 (57)
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=237.72 Aligned_cols=63 Identities=79% Similarity=1.569 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCccccccccCCCcccCCCCCC
Q 020288 73 HTEVPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRNVPVGGGCRRNKKSKS 135 (328)
Q Consensus 73 ~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRnvPvGgG~Rknkr~~~ 135 (328)
.||+.++||||+|+||||||||||+++||||||++|+||||+||+||||||||||||+|++++
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 478999999999999999999999999999999999999999999999999999999998763
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=94.67 E-value=0.022 Score=50.00 Aligned_cols=34 Identities=26% Similarity=0.724 Sum_probs=27.5
Q ss_pred CCCCCCCCCCCcceeeecCCC--CCcCchhhhhhhccc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYS--LSQPRHFCKACRRYW 112 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~--~~QPR~fCk~CrRyw 112 (328)
...||||.|.+|+. .+.|- .++.-|+|++|+.=+
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=92.10 E-value=0.11 Score=37.12 Aligned_cols=36 Identities=39% Similarity=0.765 Sum_probs=26.1
Q ss_pred hccCCCCCCCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 68 LAKIPHTEVPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 68 ~a~~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
|+.+-=|+. ..||+|.+. ++..+.+ ..++.|++|++
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 444444444 669999998 6655555 78999999985
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.76 E-value=0.1 Score=44.95 Aligned_cols=36 Identities=31% Similarity=0.640 Sum_probs=28.4
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcCchhhhhhhccccc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTR 114 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~ 114 (328)
...||+|.+.+.+ =+.-+.....|+.|++|++-|+.
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 25555556999999999998874
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=91.66 E-value=0.094 Score=36.65 Aligned_cols=31 Identities=42% Similarity=0.738 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCcceeeecCCCC-CcCchhhhhhh
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSL-SQPRHFCKACR 109 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~-~QPR~fCk~Cr 109 (328)
.+.||+|.+++.- |=|-.+. -..||+|++|+
T Consensus 5 ~v~CP~C~s~~~v--~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEGV--KKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCcc--eeCCCCCCCCEeEecCcCC
Confidence 3789999998721 1344433 35899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=87.71 E-value=0.42 Score=33.68 Aligned_cols=37 Identities=24% Similarity=0.722 Sum_probs=28.2
Q ss_pred CCCCCCCCCCcceeeecCCCCCcC---chhhhhhhccccc
Q 020288 78 LKCPRCDSTNTKFCYFNNYSLSQP---RHFCKACRRYWTR 114 (328)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QP---R~fCk~CrRywT~ 114 (328)
.+||+|...+.-|-..+-.+...| -|.|.+|...|.+
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 379999988777765556655555 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=85.06 E-value=0.55 Score=32.83 Aligned_cols=36 Identities=28% Similarity=0.755 Sum_probs=24.5
Q ss_pred CCCCCCCCCCcceeeecCCCCCcC---chhhhhhhcccc
Q 020288 78 LKCPRCDSTNTKFCYFNNYSLSQP---RHFCKACRRYWT 113 (328)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QP---R~fCk~CrRywT 113 (328)
.+||.|...+..|--.+..+...| .|.|.+|..-|+
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 379999998877655555555544 389999999985
No 8
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=80.41 E-value=1.9 Score=32.25 Aligned_cols=42 Identities=29% Similarity=0.687 Sum_probs=29.9
Q ss_pred CCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCcccccccc
Q 020288 79 KCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRNVPV 123 (328)
Q Consensus 79 ~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRnvPv 123 (328)
.|--|..++|..=.-.. .....+|-+|..||.+.|..|.+-.
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 37788888776422222 4678999999999999996655443
No 9
>PHA02998 RNA polymerase subunit; Provisional
Probab=78.86 E-value=1.6 Score=40.73 Aligned_cols=39 Identities=26% Similarity=0.646 Sum_probs=33.7
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCc---hhhhhhhccccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPR---HFCKACRRYWTR 114 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRywT~ 114 (328)
...+||+|...++-|--.+-.+...|- |.|..|..-|.-
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 569999999999999888888887775 899999999853
No 10
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=78.00 E-value=0.65 Score=32.34 Aligned_cols=37 Identities=27% Similarity=0.642 Sum_probs=27.2
Q ss_pred CCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCccccc
Q 020288 79 KCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRN 120 (328)
Q Consensus 79 ~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRn 120 (328)
+||+|...-.+.-+ ..-+-+.|..|.-.|=..+.+..
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 69999985555443 23566889999999988777654
No 11
>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=77.86 E-value=0.98 Score=42.76 Aligned_cols=37 Identities=30% Similarity=0.722 Sum_probs=19.3
Q ss_pred CCCCCCCCCCC-cceeeec-CCCCCcCchhhhhhhcccc
Q 020288 77 PLKCPRCDSTN-TKFCYFN-NYSLSQPRHFCKACRRYWT 113 (328)
Q Consensus 77 ~~~CPRC~S~~-Tkfcy~N-Ny~~~QPR~fCk~CrRywT 113 (328)
..+||.|..++ .++-||. .-....--+.|++|+.|+-
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 47899999855 5667773 3333444499999999983
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=70.48 E-value=3.9 Score=32.99 Aligned_cols=39 Identities=18% Similarity=0.592 Sum_probs=28.4
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcC---chhhhhhhcccccC
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQP---RHFCKACRRYWTRG 115 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QP---R~fCk~CrRywT~G 115 (328)
..+||+|...+.-|-..+-.+...| -|.|..|.-.|+++
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 4899999877776654454443333 38999999999874
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=65.83 E-value=2.8 Score=38.84 Aligned_cols=36 Identities=31% Similarity=0.860 Sum_probs=24.1
Q ss_pred CCCCCCCCcc-------eeeecCCCCCc-----CchhhhhhhcccccC
Q 020288 80 CPRCDSTNTK-------FCYFNNYSLSQ-----PRHFCKACRRYWTRG 115 (328)
Q Consensus 80 CPRC~S~~Tk-------fcy~NNy~~~Q-----PR~fCk~CrRywT~G 115 (328)
||+|...... =||...+.+.. --.+|+.|.||+..|
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 237899999999884
No 14
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=61.78 E-value=5.3 Score=35.97 Aligned_cols=44 Identities=23% Similarity=0.401 Sum_probs=32.3
Q ss_pred CCCCCCCCCcceeee---cCCCCCcCchhhhhhhcccccCccccccc
Q 020288 79 KCPRCDSTNTKFCYF---NNYSLSQPRHFCKACRRYWTRGGALRNVP 122 (328)
Q Consensus 79 ~CPRC~S~~Tkfcy~---NNy~~~QPR~fCk~CrRywT~GG~lRnvP 122 (328)
+||.|...+||+-== ...+.-+-|..|..|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 799999999998432 33445667899999999998655544333
No 15
>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=60.95 E-value=5.6 Score=38.93 Aligned_cols=37 Identities=19% Similarity=0.634 Sum_probs=28.1
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcCc---hhhhhhhcccc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQPR---HFCKACRRYWT 113 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRywT 113 (328)
..+||+|...+..|-..+..+...|- |.|..|...|.
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 78999999984
No 16
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=60.69 E-value=5.6 Score=29.35 Aligned_cols=39 Identities=28% Similarity=0.625 Sum_probs=29.0
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCccc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGAL 118 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~l 118 (328)
...|--|..++|..=.- ...-++.+|-+|.-||.+.+.+
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 57899999988864211 1223379999999999998876
No 17
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=59.46 E-value=6 Score=39.10 Aligned_cols=38 Identities=26% Similarity=0.589 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCCcceeeecCCC--CCcCchhhhhhhccccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYS--LSQPRHFCKACRRYWTR 114 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~--~~QPR~fCk~CrRywT~ 114 (328)
...+||.|... .|.-||.--. ..---+.|.+|+.|+--
T Consensus 225 ~R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 225 VRVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred cCccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 35789999974 4666764222 22233899999999853
No 18
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=58.39 E-value=4.7 Score=27.93 Aligned_cols=32 Identities=31% Similarity=0.725 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCcce-eeecCC-------------CCCcCchhhhhh
Q 020288 77 PLKCPRCDSTNTKF-CYFNNY-------------SLSQPRHFCKAC 108 (328)
Q Consensus 77 ~~~CPRC~S~~Tkf-cy~NNy-------------~~~QPR~fCk~C 108 (328)
+..||.|.+...+. -++... .+..+|++|++|
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 346777888877
No 19
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=57.76 E-value=5.4 Score=37.90 Aligned_cols=30 Identities=17% Similarity=0.595 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
++.+||||...=.|.-+= .+.-|||..|++
T Consensus 243 ~g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 367899999866664332 366699999985
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=56.91 E-value=6.8 Score=38.60 Aligned_cols=37 Identities=22% Similarity=0.632 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCcceeeecCCC----CCcCchhhhhhhcccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYS----LSQPRHFCKACRRYWT 113 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~----~~QPR~fCk~CrRywT 113 (328)
...+||.|.+.+ |.-||.-.. ..---..|.+|+.|+-
T Consensus 223 ~R~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 223 VRVKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred cCccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchh
Confidence 358899999865 566765432 1122378999999974
No 21
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=55.40 E-value=6.3 Score=37.44 Aligned_cols=29 Identities=31% Similarity=0.801 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
+.+||||...=.|.-+ . .+.-|||..|++
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 5689999987666433 2 366799999996
No 22
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=51.56 E-value=8 Score=36.61 Aligned_cols=30 Identities=23% Similarity=0.596 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
.+.+||||...=.|. -++ .+.-|||..|++
T Consensus 244 ~g~pC~~Cg~~I~~~-~~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEKI-KQG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCeeEEE-EEC----CCCcEECcCCCC
Confidence 357899999876654 333 366799999986
No 23
>PHA00626 hypothetical protein
Probab=51.38 E-value=8.3 Score=30.14 Aligned_cols=37 Identities=19% Similarity=0.289 Sum_probs=24.6
Q ss_pred CCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCc
Q 020288 78 LKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGG 116 (328)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG 116 (328)
..||+|.|.+--=|=.= ....-||.|++|.=.+|+..
T Consensus 1 m~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCCceeeeecee--cccCcceEcCCCCCeechhh
Confidence 36999999754322111 11245799999999999864
No 24
>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=50.69 E-value=9.9 Score=30.18 Aligned_cols=32 Identities=22% Similarity=0.459 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
-+..||+|.+.+|-..|..|. ..-.-|-.|.-
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 368899999999988888776 55567888853
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=50.57 E-value=5.8 Score=27.81 Aligned_cols=17 Identities=35% Similarity=1.011 Sum_probs=7.1
Q ss_pred cCchhhhhhhcccccCc
Q 020288 100 QPRHFCKACRRYWTRGG 116 (328)
Q Consensus 100 QPR~fCk~CrRywT~GG 116 (328)
+|||||.=|..|.|..-
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 58999999999997654
No 26
>PRK10445 endonuclease VIII; Provisional
Probab=49.56 E-value=8.9 Score=36.28 Aligned_cols=30 Identities=27% Similarity=0.606 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
.+..||||...-.|.-+ + .+.-|||..|++
T Consensus 234 ~g~~Cp~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 263 (263)
T PRK10445 234 DGEACERCGGIIEKTTL-S----SRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCCEeEEEEE-C----CCCcEECCCCcC
Confidence 35689999987666544 2 366799999984
No 27
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=49.18 E-value=11 Score=33.87 Aligned_cols=45 Identities=24% Similarity=0.487 Sum_probs=32.4
Q ss_pred CCCCCCCCCCccee---eecCCCCCcCchhhhhhhcccccCccccccc
Q 020288 78 LKCPRCDSTNTKFC---YFNNYSLSQPRHFCKACRRYWTRGGALRNVP 122 (328)
Q Consensus 78 ~~CPRC~S~~Tkfc---y~NNy~~~QPR~fCk~CrRywT~GG~lRnvP 122 (328)
.+||-|.+.+|++- |+-.-++-.-|+-|++|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999987763 4445445556699999999888765554444
No 28
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=48.41 E-value=9.9 Score=36.28 Aligned_cols=29 Identities=17% Similarity=0.666 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
+.+||||...-.|.-+ . .+--|||..|++
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 5689999987766544 2 266699999984
No 29
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=46.62 E-value=7.7 Score=30.10 Aligned_cols=14 Identities=43% Similarity=0.831 Sum_probs=6.0
Q ss_pred CCCCCCCCCCCCcc
Q 020288 76 VPLKCPRCDSTNTK 89 (328)
Q Consensus 76 ~~~~CPRC~S~~Tk 89 (328)
-+++|+.|.|.||+
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 46899999999997
No 30
>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=43.25 E-value=13 Score=35.32 Aligned_cols=28 Identities=29% Similarity=0.692 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcCchhhhhhh
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACR 109 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 109 (328)
+.+||||...=.|.-+ . .+.-|||..|+
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 5689999987666433 3 36669999996
No 31
>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=40.85 E-value=12 Score=24.23 Aligned_cols=28 Identities=25% Similarity=0.547 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcCchhhhhhh
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACR 109 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 109 (328)
+.+||||.....++-.. .+.-+||..|+
T Consensus 1 G~~C~rC~~~~~~~~~~-----~r~~~~C~rCq 28 (30)
T PF06827_consen 1 GEKCPRCWNYIEDIGIN-----GRSTYLCPRCQ 28 (30)
T ss_dssp TSB-TTT--BBEEEEET-----TEEEEE-TTTC
T ss_pred CCcCccCCCcceEeEec-----CCCCeECcCCc
Confidence 46899999887766431 23347787775
No 32
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=40.84 E-value=12 Score=27.72 Aligned_cols=26 Identities=35% Similarity=0.644 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
..-||+|.+. |..-.. .|+.|..|..
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 6899999974
No 33
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.82 E-value=17 Score=30.58 Aligned_cols=35 Identities=20% Similarity=0.394 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhccccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTR 114 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~ 114 (328)
....||.|.+ .+--|=+.. ..+.+.|..|.-|-..
T Consensus 20 t~f~CP~Cge-~~v~v~~~k---~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGK-VSISVKIKK---NIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCC-eEeeeecCC---CcceEECCCCCCccCE
Confidence 5688999995 233333443 4789999999998543
No 34
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=39.64 E-value=25 Score=30.27 Aligned_cols=38 Identities=24% Similarity=0.633 Sum_probs=32.6
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCc---hhhhhhhcccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPR---HFCKACRRYWT 113 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRywT 113 (328)
....||+|...+.-|--++-.+..-|- |.|-.|.--|-
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 457899999999998888888888876 89999999885
No 35
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=35.10 E-value=21 Score=32.55 Aligned_cols=43 Identities=23% Similarity=0.322 Sum_probs=30.0
Q ss_pred CCCCCCCCCcceeee---cCCCCCcCchhhhhhhcccccCcccccc
Q 020288 79 KCPRCDSTNTKFCYF---NNYSLSQPRHFCKACRRYWTRGGALRNV 121 (328)
Q Consensus 79 ~CPRC~S~~Tkfcy~---NNy~~~QPR~fCk~CrRywT~GG~lRnv 121 (328)
+||.|.+.+||+-== ..-+..+-|.-|-+|..-+|-==++--+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELR 47 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeec
Confidence 699999999998421 1223455678999999888865553333
No 36
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=32.53 E-value=23 Score=34.65 Aligned_cols=30 Identities=20% Similarity=0.595 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
++.+|++|.+.-.|-- + -.+..|||..|++
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 5678999999655531 1 2366799999985
No 37
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=32.04 E-value=27 Score=35.12 Aligned_cols=40 Identities=25% Similarity=0.615 Sum_probs=25.3
Q ss_pred ccCCCCCCCCCCCCCCCCCcceeeecCCCC-----CcCchhhhhhhc
Q 020288 69 AKIPHTEVPLKCPRCDSTNTKFCYFNNYSL-----SQPRHFCKACRR 110 (328)
Q Consensus 69 a~~p~pe~~~~CPRC~S~~Tkfcy~NNy~~-----~QPR~fCk~CrR 110 (328)
|....|..--+||||...| ||.-----. .-..-||++|..
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 3445666778999999888 775333111 124578888853
No 38
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=30.60 E-value=38 Score=24.72 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCCCcceeeecCCCCCc-Cchhhhhhhc
Q 020288 75 EVPLKCPRCDSTNTKFCYFNNYSLSQ-PRHFCKACRR 110 (328)
Q Consensus 75 e~~~~CPRC~S~~Tkfcy~NNy~~~Q-PR~fCk~CrR 110 (328)
|+..+||.|.+....+.+........ -.-+|..|.-
T Consensus 1 ~~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 1 EELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 35678999966665554432221111 3445888865
No 39
>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=29.59 E-value=38 Score=26.50 Aligned_cols=31 Identities=23% Similarity=0.437 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhh
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACR 109 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 109 (328)
-+..||+|...+|=..|..|.- ...-|-.|.
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 3689999999999988866654 335566664
No 40
>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=28.48 E-value=33 Score=25.58 Aligned_cols=38 Identities=26% Similarity=0.487 Sum_probs=28.8
Q ss_pred cCCCCCCCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhccccc
Q 020288 70 KIPHTEVPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTR 114 (328)
Q Consensus 70 ~~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~ 114 (328)
.|+.-..-..||.|.....+ .+..-.+.|..|...+.+
T Consensus 21 ~v~~~~TSq~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 21 EVDEAYTSQTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred EECCCCCccCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 34444456889999998877 666778999999877654
No 41
>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=28.30 E-value=22 Score=24.17 Aligned_cols=28 Identities=32% Similarity=0.675 Sum_probs=14.4
Q ss_pred CCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccc
Q 020288 78 LKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWT 113 (328)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT 113 (328)
-+||-|.|..|= ...--+.|.+|..=|.
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 4566788999987774
No 42
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=27.56 E-value=36 Score=29.33 Aligned_cols=36 Identities=19% Similarity=0.601 Sum_probs=24.9
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYW 112 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyw 112 (328)
..-.||||+...---|..-- ....--.-|+.|..+.
T Consensus 21 k~FtCp~Cghe~vs~ctvkk-~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKK-TVNIGTAVCGNCGLSF 56 (104)
T ss_pred ceEecCccCCeeeeEEEEEe-cCceeEEEcccCcceE
Confidence 44679999999988887432 2233446788887665
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=26.91 E-value=37 Score=27.52 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=16.5
Q ss_pred CCCCCCCCCCcceeeecCCCCCcCchhhhhhhcc
Q 020288 78 LKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRY 111 (328)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRy 111 (328)
..||-|+..+..|..+.+. -++.|-+|.+.
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 6799999887777666543 37999999853
No 44
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=26.22 E-value=25 Score=27.81 Aligned_cols=11 Identities=55% Similarity=1.168 Sum_probs=8.9
Q ss_pred CCCCCCCCCCC
Q 020288 75 EVPLKCPRCDS 85 (328)
Q Consensus 75 e~~~~CPRC~S 85 (328)
|.-+.||||+-
T Consensus 15 E~~lrCPRC~~ 25 (65)
T COG4049 15 EEFLRCPRCGM 25 (65)
T ss_pred ceeeeCCchhH
Confidence 45599999985
No 45
>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=26.10 E-value=31 Score=24.77 Aligned_cols=32 Identities=22% Similarity=0.618 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCcceeeecCCCCCcCchhhhhhhc
Q 020288 77 PLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRR 110 (328)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (328)
..+||-|.. ..+|..|-+. ...-..+|+.|..
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 3347789999943
No 46
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=24.93 E-value=50 Score=28.81 Aligned_cols=37 Identities=24% Similarity=0.629 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCc-----Cchhhhhhhccccc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQ-----PRHFCKACRRYWTR 114 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~Q-----PR~fCk~CrRywT~ 114 (328)
....||+|...+.-| |+--+... --|.|-+|.--||+
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 65533221 12889999999985
No 47
>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=23.92 E-value=55 Score=23.88 Aligned_cols=32 Identities=22% Similarity=0.517 Sum_probs=19.0
Q ss_pred CCCCCCCCCCcceeeecCCCCCcCchh-hhhhhc
Q 020288 78 LKCPRCDSTNTKFCYFNNYSLSQPRHF-CKACRR 110 (328)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR~f-Ck~CrR 110 (328)
.+||.|.+.+-.|=+ ......-.+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 579999997765532 12233334444 877764
No 48
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=21.89 E-value=35 Score=26.03 Aligned_cols=14 Identities=50% Similarity=1.215 Sum_probs=10.9
Q ss_pred CCCCCCCCCCCCCc
Q 020288 75 EVPLKCPRCDSTNT 88 (328)
Q Consensus 75 e~~~~CPRC~S~~T 88 (328)
+-..+||||...|.
T Consensus 22 ~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 22 ELEIKCPRCKTINH 35 (51)
T ss_pred EEEEECCCCCccce
Confidence 34589999998775
No 49
>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=21.77 E-value=33 Score=33.51 Aligned_cols=33 Identities=24% Similarity=0.687 Sum_probs=12.5
Q ss_pred CCCCCCCCCC-CcceeeecCCCCCcCchhhhhhhcccc
Q 020288 77 PLKCPRCDST-NTKFCYFNNYSLSQPRHFCKACRRYWT 113 (328)
Q Consensus 77 ~~~CPRC~S~-~Tkfcy~NNy~~~QPR~fCk~CrRywT 113 (328)
-..||.|.+. -.+| ..+.+-.-.+|..|..=+-
T Consensus 31 n~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp H---TTT--SS-EE------------EEE-TTT--EEE
T ss_pred CCcCCCCCChhHhhc----cCCCccceeECCCCchHHh
Confidence 4689999998 5554 3344556799999987554
No 50
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=20.68 E-value=37 Score=28.53 Aligned_cols=42 Identities=24% Similarity=0.490 Sum_probs=31.1
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcccccCccccccccC
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRYWTRGGALRNVPVG 124 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRywT~GG~lRnvPvG 124 (328)
....||-|.+...|= ..----.|+.|..-|+.|+-....|+|
T Consensus 34 ~~~~Cp~C~~~~VkR-------~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 34 AKHVCPFCGRTTVKR-------IATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred cCCcCCCCCCcceee-------eccCeEEcCCCCCeeccccccccchHH
Confidence 457899999985441 223347899999999999987766654
No 51
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=20.24 E-value=61 Score=24.69 Aligned_cols=24 Identities=29% Similarity=0.897 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCCcceeeecCCCCCcCchhhhhhhcc
Q 020288 76 VPLKCPRCDSTNTKFCYFNNYSLSQPRHFCKACRRY 111 (328)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRy 111 (328)
....||.|.+. .+|.+.|..|.-|
T Consensus 26 ~l~~C~~CG~~------------~~~H~vC~~CG~Y 49 (57)
T PRK12286 26 GLVECPNCGEP------------KLPHRVCPSCGYY 49 (57)
T ss_pred cceECCCCCCc------------cCCeEECCCCCcC
Confidence 44789999864 3788999999866
Done!