Query 017919
Match_columns 364
No_of_seqs 133 out of 249
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 04:34:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017919.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017919hhsearch_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 4.2E-37 9.2E-42 237.5 3.8 63 73-135 1-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 94.4 0.023 4.9E-07 50.6 2.0 34 77-112 105-140 (146)
3 PF03811 Zn_Tnp_IS1: InsA N-te 92.4 0.082 1.8E-06 37.4 1.7 31 77-109 5-36 (36)
4 PF12760 Zn_Tnp_IS1595: Transp 91.7 0.21 4.6E-06 36.1 3.2 38 66-110 8-45 (46)
5 COG3677 Transposase and inacti 91.6 0.13 2.7E-06 45.0 2.3 36 77-114 30-65 (129)
6 smart00440 ZnF_C2C2 C2C2 Zinc 88.8 0.43 9.4E-06 34.1 2.7 37 78-114 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 86.8 0.57 1.2E-05 33.2 2.4 36 78-113 1-39 (39)
8 PHA02998 RNA polymerase subuni 80.3 1.6 3.4E-05 41.3 3.1 39 76-114 142-183 (195)
9 cd00202 ZnF_GATA Zinc finger D 77.3 1.9 4.2E-05 32.6 2.2 41 79-122 1-41 (54)
10 PF13453 zf-TFIIB: Transcripti 74.4 0.99 2.2E-05 31.9 0.0 37 79-120 1-37 (41)
11 TIGR01384 TFS_arch transcripti 74.2 3.6 7.7E-05 33.7 3.2 41 75-115 60-103 (104)
12 PF04216 FdhE: Protein involve 69.3 2.3 5E-05 40.8 1.2 37 77-113 211-249 (290)
13 PF04981 NMD3: NMD3 family ; 67.5 2.9 6.2E-05 39.3 1.4 36 80-115 1-48 (236)
14 TIGR01385 TFSII transcription 67.4 5.8 0.00012 39.4 3.5 37 77-113 258-297 (299)
15 smart00401 ZnF_GATA zinc finge 65.5 4.8 0.0001 30.2 2.0 39 77-118 3-41 (52)
16 TIGR01562 FdhE formate dehydro 63.6 5 0.00011 40.0 2.3 37 76-113 223-263 (305)
17 PF14690 zf-ISL3: zinc-finger 59.7 4.7 0.0001 28.3 1.0 32 77-108 2-47 (47)
18 TIGR00244 transcriptional regu 59.1 6.8 0.00015 35.8 2.1 44 79-122 2-48 (147)
19 PRK03564 formate dehydrogenase 59.1 6.5 0.00014 39.4 2.2 37 77-114 226-264 (309)
20 PHA00626 hypothetical protein 54.8 8.4 0.00018 30.5 1.7 37 79-117 2-38 (59)
21 PRK14810 formamidopyrimidine-D 54.5 7.8 0.00017 37.3 1.9 29 77-110 244-272 (272)
22 PRK14811 formamidopyrimidine-D 52.8 8.9 0.00019 37.0 1.9 29 77-110 235-263 (269)
23 PRK00464 nrdR transcriptional 48.3 12 0.00027 33.9 2.0 45 78-122 1-48 (154)
24 PRK01103 formamidopyrimidine/5 48.1 12 0.00025 36.0 1.9 29 77-110 245-273 (274)
25 COG4260 Membrane protease subu 46.8 11 0.00024 38.3 1.6 41 68-110 297-342 (345)
26 PRK10445 endonuclease VIII; Pr 46.5 13 0.00027 35.8 1.9 29 77-110 235-263 (263)
27 PF06220 zf-U1: U1 zinc finger 45.7 8.6 0.00019 27.4 0.5 17 100-116 1-17 (38)
28 PRK00432 30S ribosomal protein 45.4 12 0.00025 28.2 1.2 26 77-110 20-45 (50)
29 PRK13945 formamidopyrimidine-D 45.2 14 0.0003 35.7 2.0 29 77-110 254-282 (282)
30 PF09526 DUF2387: Probable met 43.2 17 0.00038 29.2 1.9 31 77-110 8-38 (71)
31 TIGR00577 fpg formamidopyrimid 40.6 18 0.00039 34.8 1.9 28 77-109 245-272 (272)
32 COG1997 RPL43A Ribosomal prote 40.4 16 0.00034 31.1 1.3 62 56-124 14-75 (89)
33 PRK14892 putative transcriptio 39.7 17 0.00037 31.0 1.4 35 76-114 20-54 (99)
34 PF14599 zinc_ribbon_6: Zinc-r 37.1 13 0.00029 29.2 0.4 13 77-89 48-60 (61)
35 PF14354 Lar_restr_allev: Rest 36.0 30 0.00064 25.6 2.1 36 75-110 1-37 (61)
36 KOG2906 RNA polymerase III sub 35.0 29 0.00063 30.3 2.1 38 76-113 64-104 (105)
37 PF06827 zf-FPG_IleRS: Zinc fi 32.3 20 0.00044 23.6 0.6 27 78-109 2-28 (30)
38 COG1327 Predicted transcriptio 31.9 27 0.00059 32.3 1.6 44 79-122 2-48 (156)
39 PF07282 OrfB_Zn_ribbon: Putat 31.6 33 0.00072 25.9 1.8 37 71-114 22-58 (69)
40 KOG2691 RNA polymerase II subu 30.3 42 0.00092 29.7 2.4 37 76-114 72-113 (113)
41 COG4888 Uncharacterized Zn rib 30.0 29 0.00062 30.3 1.3 36 76-112 21-56 (104)
42 COG0266 Nei Formamidopyrimidin 29.5 33 0.00071 34.1 1.8 30 76-110 244-273 (273)
43 TIGR03655 anti_R_Lar restricti 28.1 51 0.0011 24.4 2.2 32 78-110 2-34 (53)
44 PRK12286 rpmF 50S ribosomal pr 27.6 41 0.00088 26.0 1.7 25 76-112 26-50 (57)
45 PF08273 Prim_Zn_Ribbon: Zinc- 27.3 39 0.00085 24.6 1.4 32 77-110 3-34 (40)
46 PF01807 zf-CHC2: CHC2 zinc fi 27.3 42 0.0009 27.6 1.8 31 77-111 33-63 (97)
47 PTZ00303 phosphatidylinositol 27.2 83 0.0018 36.3 4.5 31 77-111 460-490 (1374)
48 PF08274 PhnA_Zn_Ribbon: PhnA 26.6 31 0.00067 23.8 0.7 28 78-113 3-30 (30)
49 PF01783 Ribosomal_L32p: Ribos 23.5 51 0.0011 25.0 1.5 27 70-109 20-46 (56)
50 COG4049 Uncharacterized protei 23.0 31 0.00068 27.6 0.3 11 75-85 15-25 (65)
51 TIGR02443 conserved hypothetic 22.6 65 0.0014 25.6 1.9 30 77-109 9-38 (59)
52 PF10122 Mu-like_Com: Mu-like 22.4 34 0.00074 26.5 0.4 15 74-88 21-35 (51)
53 TIGR00686 phnA alkylphosphonat 20.6 66 0.0014 28.3 1.8 31 78-116 3-33 (109)
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=4.2e-37 Score=237.46 Aligned_cols=63 Identities=78% Similarity=1.559 Sum_probs=60.3
Q ss_pred CCccCcCCCCCCCCCcceeeecCCCCCCCcccccccccccccCccccccccCCccccCCCCCC
Q 017919 73 MPEAALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRNVPVGGGCRRNKRSKG 135 (364)
Q Consensus 73 ~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~lRnVPvGgG~Rknkrs~~ 135 (364)
.||+.++||||+|+||||||||||+++|||||||+|+||||+||+||||||||||||+|++++
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=94.43 E-value=0.023 Score=50.63 Aligned_cols=34 Identities=24% Similarity=0.694 Sum_probs=27.6
Q ss_pred CcCCCCCCCCCcceeeecCCCC--CCCccccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSL--SQPRHFCKTCRRYW 112 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~--~QPR~fCk~CrRyW 112 (364)
...||||.|.+|+. .+.|-. ++.-|+|++|+.=+
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 48999999999997 577744 57779999998643
No 3
>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=92.37 E-value=0.082 Score=37.45 Aligned_cols=31 Identities=42% Similarity=0.754 Sum_probs=22.1
Q ss_pred CcCCCCCCCCCcceeeecCCCC-CCCcccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSL-SQPRHFCKTCR 109 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~-~QPR~fCk~Cr 109 (364)
.+.||+|.+++.= |=|-.+. -..||+|++|+
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 5789999998821 1344443 35899999996
No 4
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=91.74 E-value=0.21 Score=36.08 Aligned_cols=38 Identities=32% Similarity=0.761 Sum_probs=27.2
Q ss_pred hhhhcCCCCccCcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 66 ARMANVPMPEAALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 66 ar~a~~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
.-++.+-=|+. ..||+|.+. ++..+.+ ..++.|++|++
T Consensus 8 ~~l~~~RW~~g-~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 8 EYLEEIRWPDG-FVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred HHHHHhcCCCC-CCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 33444444554 669999998 6655655 78899999985
No 5
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.61 E-value=0.13 Score=45.05 Aligned_cols=36 Identities=31% Similarity=0.652 Sum_probs=28.6
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCccccccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTR 114 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~ 114 (364)
...||+|.+.+.+ =++-+.....|+.|++|++=|+.
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 4789999999922 25555566999999999998874
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.76 E-value=0.43 Score=34.06 Aligned_cols=37 Identities=24% Similarity=0.719 Sum_probs=28.3
Q ss_pred cCCCCCCCCCcceeeecCCCCCCC---ccccccccccccc
Q 017919 78 LKCPRCESTNTKFCYFNNYSLSQP---RHFCKTCRRYWTR 114 (364)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QP---R~fCk~CrRyWT~ 114 (364)
.+||+|...+.-|-..+-.+...| -|.|.+|...|.+
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 379999988777766666665555 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=86.84 E-value=0.57 Score=33.20 Aligned_cols=36 Identities=28% Similarity=0.768 Sum_probs=24.8
Q ss_pred cCCCCCCCCCcceeeecCCCCCCCc---ccccccccccc
Q 017919 78 LKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWT 113 (364)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT 113 (364)
.+||.|...+..|--.+..+...|- |.|.+|..-|+
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 3799999988776555666555553 89999999985
No 8
>PHA02998 RNA polymerase subunit; Provisional
Probab=80.30 E-value=1.6 Score=41.28 Aligned_cols=39 Identities=26% Similarity=0.651 Sum_probs=34.0
Q ss_pred cCcCCCCCCCCCcceeeecCCCCCCCc---cccccccccccc
Q 017919 76 AALKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWTR 114 (364)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT~ 114 (364)
...+||+|...++-|--.+-.+...|- |.|..|..-|.-
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 679999999999999888888888775 899999999853
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=77.28 E-value=1.9 Score=32.64 Aligned_cols=41 Identities=27% Similarity=0.696 Sum_probs=29.4
Q ss_pred CCCCCCCCCcceeeecCCCCCCCcccccccccccccCccccccc
Q 017919 79 KCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRNVP 122 (364)
Q Consensus 79 ~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~lRnVP 122 (364)
.|--|..++|..=.-.. .....+|-+|..||.+.|..|-+-
T Consensus 1 ~C~~C~~~~Tp~WR~g~---~~~~~LCNaCgl~~~k~~~~rp~~ 41 (54)
T cd00202 1 ACSNCGTTTTPLWRRGP---SGGSTLCNACGLYWKKHGVMRPLS 41 (54)
T ss_pred CCCCCCCCCCcccccCC---CCcchHHHHHHHHHHhcCCCCCcc
Confidence 37788888886422222 466789999999999999655443
No 10
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=74.44 E-value=0.99 Score=31.85 Aligned_cols=37 Identities=27% Similarity=0.637 Sum_probs=26.8
Q ss_pred CCCCCCCCCcceeeecCCCCCCCcccccccccccccCccccc
Q 017919 79 KCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRN 120 (364)
Q Consensus 79 ~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~lRn 120 (364)
+||+|...=.+.-+ ..-+-+.|..|.-.|=..+.+..
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 69999985554433 23466889999999988776654
No 11
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=74.17 E-value=3.6 Score=33.68 Aligned_cols=41 Identities=17% Similarity=0.595 Sum_probs=29.6
Q ss_pred ccCcCCCCCCCCCcceeeecCCCCCCCc---ccccccccccccC
Q 017919 75 EAALKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWTRG 115 (364)
Q Consensus 75 e~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT~G 115 (364)
....+||+|...+.-|-..+-.+...|- |.|..|.-.|+++
T Consensus 60 ~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 3358999998777766555555443333 9999999999874
No 12
>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=69.25 E-value=2.3 Score=40.83 Aligned_cols=37 Identities=27% Similarity=0.700 Sum_probs=19.1
Q ss_pred CcCCCCCCCCCcc-eeeec-CCCCCCCcccccccccccc
Q 017919 77 ALKCPRCESTNTK-FCYFN-NYSLSQPRHFCKTCRRYWT 113 (364)
Q Consensus 77 ~~~CPRC~S~~Tk-fcy~N-Ny~~~QPR~fCk~CrRyWT 113 (364)
..+||.|..++.. +-||. .-....--+.|++|+.|+-
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 5689999987764 55663 3333333499999999983
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=67.54 E-value=2.9 Score=39.26 Aligned_cols=36 Identities=31% Similarity=0.856 Sum_probs=24.4
Q ss_pred CCCCCCCCcc-------eeeecCCCCCC-----CcccccccccccccC
Q 017919 80 CPRCESTNTK-------FCYFNNYSLSQ-----PRHFCKTCRRYWTRG 115 (364)
Q Consensus 80 CPRC~S~~Tk-------fcy~NNy~~~Q-----PR~fCk~CrRyWT~G 115 (364)
||+|...... =||...+.+.. --.+|+.|.||+..|
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 6666654443 26777766644 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=67.38 E-value=5.8 Score=39.37 Aligned_cols=37 Identities=19% Similarity=0.649 Sum_probs=28.2
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCc---ccccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWT 113 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT 113 (364)
..+||+|...+..|-..+..+...|- |.|..|...|.
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 68999999888777555555555553 78999999984
No 15
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=65.55 E-value=4.8 Score=30.15 Aligned_cols=39 Identities=26% Similarity=0.620 Sum_probs=29.3
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCcccccccccccccCccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGAL 118 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~l 118 (364)
...|--|..++|..=.- ...-++.+|-+|.-||.+.+.+
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 57899999998864221 2223379999999999998886
No 16
>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=63.57 E-value=5 Score=40.01 Aligned_cols=37 Identities=22% Similarity=0.617 Sum_probs=25.2
Q ss_pred cCcCCCCCCCCCcceeeecCCC----CCCCcccccccccccc
Q 017919 76 AALKCPRCESTNTKFCYFNNYS----LSQPRHFCKTCRRYWT 113 (364)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~----~~QPR~fCk~CrRyWT 113 (364)
...+||.|.+.+ |.-||.--. ..---..|.+|+.|+-
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 367899999875 555665432 1122378999999974
No 17
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=59.69 E-value=4.7 Score=28.33 Aligned_cols=32 Identities=28% Similarity=0.648 Sum_probs=19.0
Q ss_pred CcCCCCCCCCCcce-eeecC---------C----CCCCCccccccc
Q 017919 77 ALKCPRCESTNTKF-CYFNN---------Y----SLSQPRHFCKTC 108 (364)
Q Consensus 77 ~~~CPRC~S~~Tkf-cy~NN---------y----~~~QPR~fCk~C 108 (364)
+..||.|.+...+. =++.. + .+..+|++|++|
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 46799999877221 11110 0 346778888887
No 18
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=59.07 E-value=6.8 Score=35.76 Aligned_cols=44 Identities=23% Similarity=0.406 Sum_probs=31.7
Q ss_pred CCCCCCCCCcceeee---cCCCCCCCcccccccccccccCccccccc
Q 017919 79 KCPRCESTNTKFCYF---NNYSLSQPRHFCKTCRRYWTRGGALRNVP 122 (364)
Q Consensus 79 ~CPRC~S~~Tkfcy~---NNy~~~QPR~fCk~CrRyWT~GG~lRnVP 122 (364)
+||.|...+||+-=- ...+.-+-|..|..|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 799999999999432 23334556799999999998655544444
No 19
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=59.06 E-value=6.5 Score=39.35 Aligned_cols=37 Identities=27% Similarity=0.588 Sum_probs=24.7
Q ss_pred CcCCCCCCCCCcceeeecCCC--CCCCccccccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYS--LSQPRHFCKTCRRYWTR 114 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~--~~QPR~fCk~CrRyWT~ 114 (364)
..+||.|... .|.-||.--. ..---+.|.+|+.|+--
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 6789999974 4666664222 12233899999999853
No 20
>PHA00626 hypothetical protein
Probab=54.76 E-value=8.4 Score=30.53 Aligned_cols=37 Identities=19% Similarity=0.242 Sum_probs=25.1
Q ss_pred CCCCCCCCCcceeeecCCCCCCCcccccccccccccCcc
Q 017919 79 KCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGA 117 (364)
Q Consensus 79 ~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~ 117 (364)
.||+|.|.+.-=|=.=+ ...-||.|++|.=++|+..-
T Consensus 2 ~CP~CGS~~Ivrcg~cr--~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR--GWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceeeeeceec--ccCcceEcCCCCCeechhhh
Confidence 69999997543221111 11457999999999998654
No 21
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=54.51 E-value=7.8 Score=37.33 Aligned_cols=29 Identities=17% Similarity=0.653 Sum_probs=21.6
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
..+||||...=.|.-+= .+.-|||..|++
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 57899999776665332 266699999985
No 22
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=52.76 E-value=8.9 Score=36.97 Aligned_cols=29 Identities=31% Similarity=0.817 Sum_probs=21.6
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
..+||||...=.|.-+ . .+.-|||..|++
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 4589999987766433 2 366799999996
No 23
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=48.29 E-value=12 Score=33.91 Aligned_cols=45 Identities=22% Similarity=0.467 Sum_probs=32.2
Q ss_pred cCCCCCCCCCccee---eecCCCCCCCcccccccccccccCccccccc
Q 017919 78 LKCPRCESTNTKFC---YFNNYSLSQPRHFCKTCRRYWTRGGALRNVP 122 (364)
Q Consensus 78 ~~CPRC~S~~Tkfc---y~NNy~~~QPR~fCk~CrRyWT~GG~lRnVP 122 (364)
.+||-|.+..|++- |+-.-++-.-|+-|++|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999998764 3444444555699999999888766655554
No 24
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=48.10 E-value=12 Score=36.02 Aligned_cols=29 Identities=24% Similarity=0.657 Sum_probs=21.4
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
..+||||...=.|. -++ .+.-|||..|++
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 56799999776654 333 266699999986
No 25
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=46.84 E-value=11 Score=38.30 Aligned_cols=41 Identities=29% Similarity=0.683 Sum_probs=26.7
Q ss_pred hhcCCCCccCcCCCCCCCCCcceeeecCCCCC-----CCccccccccc
Q 017919 68 MANVPMPEAALKCPRCESTNTKFCYFNNYSLS-----QPRHFCKTCRR 110 (364)
Q Consensus 68 ~a~~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~-----QPR~fCk~CrR 110 (364)
.|....|...-+||||...| ||.---...+ -..-||++|..
T Consensus 297 qaqaa~pa~t~~~~r~~k~n--fc~ncG~~~t~~~~ng~a~fcp~cgq 342 (345)
T COG4260 297 QAQAAAPAATWPCARCAKLN--FCLNCGCGTTADFDNGKAKFCPECGQ 342 (345)
T ss_pred hhhhcCCcccCcchhccccc--cccccCcccccCCccchhhhChhhcC
Confidence 34456778899999999988 7753331111 13578888853
No 26
>PRK10445 endonuclease VIII; Provisional
Probab=46.49 E-value=13 Score=35.76 Aligned_cols=29 Identities=28% Similarity=0.655 Sum_probs=21.1
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
...||||...=.|.-+ + .+.-|||..|++
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 5679999877666544 2 266699999984
No 27
>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=45.68 E-value=8.6 Score=27.38 Aligned_cols=17 Identities=35% Similarity=1.017 Sum_probs=7.1
Q ss_pred CCcccccccccccccCc
Q 017919 100 QPRHFCKTCRRYWTRGG 116 (364)
Q Consensus 100 QPR~fCk~CrRyWT~GG 116 (364)
+|||||.=|..|.|..-
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 28
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.35 E-value=12 Score=28.20 Aligned_cols=26 Identities=35% Similarity=0.646 Sum_probs=19.1
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
..-||+|.+. |..-.. .|+.|..|..
T Consensus 20 ~~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 4589999874 554443 6999999974
No 29
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=45.20 E-value=14 Score=35.73 Aligned_cols=29 Identities=17% Similarity=0.689 Sum_probs=21.3
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
..+||||...=.|.-+ . .+--|||..|++
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 4689999987766544 2 256699999984
No 30
>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=43.23 E-value=17 Score=29.21 Aligned_cols=31 Identities=23% Similarity=0.503 Sum_probs=25.0
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
+..||+|.+.+|=..|..|. ..-.-|-.|.-
T Consensus 8 Ga~CP~C~~~D~i~~~~e~~---ve~vECV~CGy 38 (71)
T PF09526_consen 8 GAVCPKCQAMDTIMMWRENG---VEYVECVECGY 38 (71)
T ss_pred CccCCCCcCccEEEEEEeCC---ceEEEecCCCC
Confidence 67899999999888887776 55567888853
No 31
>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=40.57 E-value=18 Score=34.85 Aligned_cols=28 Identities=29% Similarity=0.723 Sum_probs=20.6
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCcccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCR 109 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 109 (364)
..+||||...=.|.- +. .+.-|||..|+
T Consensus 245 g~pC~~Cg~~I~~~~-~~----gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIK-VG----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEE-EC----CCCCEECCCCC
Confidence 458999998766643 33 26669999996
No 32
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=40.42 E-value=16 Score=31.14 Aligned_cols=62 Identities=24% Similarity=0.348 Sum_probs=39.3
Q ss_pred CCCCCchhhhhhhhcCCCCccCcCCCCCCCCCcceeeecCCCCCCCcccccccccccccCccccccccC
Q 017919 56 SIRPGSMADRARMANVPMPEAALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGGALRNVPVG 124 (364)
Q Consensus 56 ~~rp~sm~~rar~a~~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG~lRnVPvG 124 (364)
++|=|...+|.-.+-...--....||-|.+...|= ..--.-.|+.|..-|+.|+-....|+|
T Consensus 14 GpRYG~~~Rrrv~~ie~~~~~~~~Cp~C~~~~VkR-------~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 14 GPRYGSKLRRRVKEIEAQQRAKHVCPFCGRTTVKR-------IATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred ccccchHHHHHHHHHHHHHhcCCcCCCCCCcceee-------eccCeEEcCCCCCeeccccccccchHH
Confidence 34445555444322222223478899999985551 222347899999999999987766654
No 33
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.71 E-value=17 Score=31.03 Aligned_cols=35 Identities=20% Similarity=0.422 Sum_probs=24.9
Q ss_pred cCcCCCCCCCCCcceeeecCCCCCCCccccccccccccc
Q 017919 76 AALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTR 114 (364)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~ 114 (364)
....||.|.+ .+--|=+.. ..+.+.|..|.-|-..
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 5788999995 333344443 4789999999999543
No 34
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=37.06 E-value=13 Score=29.21 Aligned_cols=13 Identities=46% Similarity=0.879 Sum_probs=5.5
Q ss_pred CcCCCCCCCCCcc
Q 017919 77 ALKCPRCESTNTK 89 (364)
Q Consensus 77 ~~~CPRC~S~~Tk 89 (364)
+++|+.|.|.||+
T Consensus 48 g~KC~~C~SYNT~ 60 (61)
T PF14599_consen 48 GHKCSHCGSYNTR 60 (61)
T ss_dssp ----TTTS---EE
T ss_pred hhcCCCCCCcccC
Confidence 6789999999997
No 35
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=35.98 E-value=30 Score=25.64 Aligned_cols=36 Identities=19% Similarity=0.360 Sum_probs=20.9
Q ss_pred ccCcCCCCCCCCCcceeeecCCCCCC-Cccccccccc
Q 017919 75 EAALKCPRCESTNTKFCYFNNYSLSQ-PRHFCKTCRR 110 (364)
Q Consensus 75 e~~~~CPRC~S~~Tkfcy~NNy~~~Q-PR~fCk~CrR 110 (364)
|+..+||.|.+....+.+........ -.-+|.+|.-
T Consensus 1 ~~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 1 EELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 35678999966666554432221111 3445888866
No 36
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=34.98 E-value=29 Score=30.29 Aligned_cols=38 Identities=24% Similarity=0.639 Sum_probs=32.9
Q ss_pred cCcCCCCCCCCCcceeeecCCCCCCCc---ccccccccccc
Q 017919 76 AALKCPRCESTNTKFCYFNNYSLSQPR---HFCKTCRRYWT 113 (364)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR---~fCk~CrRyWT 113 (364)
....||+|...+--|--++-.+..-|- |.|-.|.--|-
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 467899999999999888888888876 89999998885
No 37
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=32.27 E-value=20 Score=23.55 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=14.9
Q ss_pred cCCCCCCCCCcceeeecCCCCCCCcccccccc
Q 017919 78 LKCPRCESTNTKFCYFNNYSLSQPRHFCKTCR 109 (364)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 109 (364)
.+||||...-.++-..+ +.-+||..|+
T Consensus 2 ~~C~rC~~~~~~~~~~~-----r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGING-----RSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETT-----EEEEE-TTTC
T ss_pred CcCccCCCcceEeEecC-----CCCeECcCCc
Confidence 58999998877764421 2337888876
No 38
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=31.87 E-value=27 Score=32.35 Aligned_cols=44 Identities=25% Similarity=0.360 Sum_probs=29.8
Q ss_pred CCCCCCCCCcceeeec---CCCCCCCcccccccccccccCccccccc
Q 017919 79 KCPRCESTNTKFCYFN---NYSLSQPRHFCKTCRRYWTRGGALRNVP 122 (364)
Q Consensus 79 ~CPRC~S~~Tkfcy~N---Ny~~~QPR~fCk~CrRyWT~GG~lRnVP 122 (364)
+||.|.+.+||+-==- .-+.-+-|.-|-+|..-+|-==++--+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 6999999999983211 1123455689999998888655543343
No 39
>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=31.63 E-value=33 Score=25.90 Aligned_cols=37 Identities=30% Similarity=0.478 Sum_probs=28.5
Q ss_pred CCCCccCcCCCCCCCCCcceeeecCCCCCCCccccccccccccc
Q 017919 71 VPMPEAALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTR 114 (364)
Q Consensus 71 ~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~ 114 (364)
|+.-.....||.|.....+ .+..-.+.|..|...+.+
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 4444457889999998888 666777999999877654
No 40
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=30.33 E-value=42 Score=29.67 Aligned_cols=37 Identities=24% Similarity=0.647 Sum_probs=26.4
Q ss_pred cCcCCCCCCCCCcceeeecCCCCCC-----Cccccccccccccc
Q 017919 76 AALKCPRCESTNTKFCYFNNYSLSQ-----PRHFCKTCRRYWTR 114 (364)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~Q-----PR~fCk~CrRyWT~ 114 (364)
+...||+|...+.-| |+--+... --|.|-+|.--||+
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 456899999988766 65433221 12899999999985
No 41
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=30.05 E-value=29 Score=30.32 Aligned_cols=36 Identities=19% Similarity=0.617 Sum_probs=25.7
Q ss_pred cCcCCCCCCCCCcceeeecCCCCCCCccccccccccc
Q 017919 76 AALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYW 112 (364)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyW 112 (364)
....||||+...---|..-- +...--.-|+.|..+.
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 46789999999998887432 2233446799998765
No 42
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=29.50 E-value=33 Score=34.07 Aligned_cols=30 Identities=23% Similarity=0.610 Sum_probs=22.0
Q ss_pred cCcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 76 AALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
+..+|++|.+.=.|.-. -.+..|||..|++
T Consensus 244 ~GepC~~CGt~I~k~~~-----~gR~t~~CP~CQ~ 273 (273)
T COG0266 244 AGEPCRRCGTPIEKIKL-----GGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCccCCEeEEEEE-----cCCcCEeCCCCCC
Confidence 46789999997666421 2366799999985
No 43
>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=28.12 E-value=51 Score=24.41 Aligned_cols=32 Identities=25% Similarity=0.528 Sum_probs=19.3
Q ss_pred cCCCCCCCCCcceeeecCCCCCCCccc-cccccc
Q 017919 78 LKCPRCESTNTKFCYFNNYSLSQPRHF-CKTCRR 110 (364)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR~f-Ck~CrR 110 (364)
.+||.|.+..-.|=+ ......-.+++ |..|.-
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 589999997775532 12233334444 887764
No 44
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=27.61 E-value=41 Score=26.04 Aligned_cols=25 Identities=28% Similarity=0.873 Sum_probs=19.7
Q ss_pred cCcCCCCCCCCCcceeeecCCCCCCCccccccccccc
Q 017919 76 AALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYW 112 (364)
Q Consensus 76 ~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyW 112 (364)
....||.|.+. .+|.+.|..|.-|=
T Consensus 26 ~l~~C~~CG~~------------~~~H~vC~~CG~Y~ 50 (57)
T PRK12286 26 GLVECPNCGEP------------KLPHRVCPSCGYYK 50 (57)
T ss_pred cceECCCCCCc------------cCCeEECCCCCcCC
Confidence 46789999864 37899999999663
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=27.26 E-value=39 Score=24.59 Aligned_cols=32 Identities=22% Similarity=0.614 Sum_probs=18.3
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRR 110 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrR 110 (364)
..+||-|.. ..+|..|-+. ...-..+|+.|..
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 3347799999943
No 46
>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=27.26 E-value=42 Score=27.63 Aligned_cols=31 Identities=19% Similarity=0.362 Sum_probs=17.1
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCcccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRY 111 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRy 111 (364)
...||-|+..+..|..+.+. -++.|-+|...
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~~ 63 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDK----NRFKCFGCGKG 63 (97)
T ss_dssp EE--SSS--SS--EEEETTT----TEEEETTT--E
T ss_pred EEECcCCCCCCCceEEECCC----CeEEECCCCCC
Confidence 46799999888787666543 37999999853
No 47
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=27.23 E-value=83 Score=36.33 Aligned_cols=31 Identities=23% Similarity=0.601 Sum_probs=20.2
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCcccccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRY 111 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRy 111 (364)
...|..|...-+-+ ...+..-||-||.|.+-
T Consensus 460 SdtC~~C~kkFfSl----sK~L~~RKHHCRkCGrV 490 (1374)
T PTZ00303 460 SDSCPSCGRAFISL----SRPLGTRAHHCRSCGIR 490 (1374)
T ss_pred CCcccCcCCccccc----ccccccccccccCCccc
Confidence 35699998654332 22234567999999764
No 48
>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=26.56 E-value=31 Score=23.82 Aligned_cols=28 Identities=32% Similarity=0.663 Sum_probs=14.5
Q ss_pred cCCCCCCCCCcceeeecCCCCCCCcccccccccccc
Q 017919 78 LKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWT 113 (364)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT 113 (364)
-+||-|.|..|= ...--+.|.+|..=|.
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 479999999875 4566789999987773
No 49
>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=23.47 E-value=51 Score=25.01 Aligned_cols=27 Identities=30% Similarity=0.872 Sum_probs=19.7
Q ss_pred cCCCCccCcCCCCCCCCCcceeeecCCCCCCCcccccccc
Q 017919 70 NVPMPEAALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCR 109 (364)
Q Consensus 70 ~~p~pe~~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 109 (364)
++..| ....||-|.. +..|.+.|.+|.
T Consensus 20 ~l~~~-~l~~c~~cg~------------~~~~H~vc~~cG 46 (56)
T PF01783_consen 20 KLKAP-NLVKCPNCGE------------PKLPHRVCPSCG 46 (56)
T ss_dssp S--TT-SEEESSSSSS------------EESTTSBCTTTB
T ss_pred ccccc-ceeeeccCCC------------EecccEeeCCCC
Confidence 34444 6789999984 348999999996
No 50
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=23.00 E-value=31 Score=27.63 Aligned_cols=11 Identities=55% Similarity=1.244 Sum_probs=9.1
Q ss_pred ccCcCCCCCCC
Q 017919 75 EAALKCPRCES 85 (364)
Q Consensus 75 e~~~~CPRC~S 85 (364)
|.-+.||||.-
T Consensus 15 E~~lrCPRC~~ 25 (65)
T COG4049 15 EEFLRCPRCGM 25 (65)
T ss_pred ceeeeCCchhH
Confidence 56899999975
No 51
>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=22.59 E-value=65 Score=25.62 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=22.8
Q ss_pred CcCCCCCCCCCcceeeecCCCCCCCcccccccc
Q 017919 77 ALKCPRCESTNTKFCYFNNYSLSQPRHFCKTCR 109 (364)
Q Consensus 77 ~~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~Cr 109 (364)
+..||+|...+|=..|.-|.- ...-|-.|.
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 678999999999988866553 345677774
No 52
>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=22.39 E-value=34 Score=26.47 Aligned_cols=15 Identities=47% Similarity=1.037 Sum_probs=11.9
Q ss_pred CccCcCCCCCCCCCc
Q 017919 74 PEAALKCPRCESTNT 88 (364)
Q Consensus 74 pe~~~~CPRC~S~~T 88 (364)
-+-..+||||...|.
T Consensus 21 ~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 21 IELEIKCPRCKTINH 35 (51)
T ss_pred cEEEEECCCCCccce
Confidence 345789999998775
No 53
>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=20.58 E-value=66 Score=28.32 Aligned_cols=31 Identities=26% Similarity=0.693 Sum_probs=24.6
Q ss_pred cCCCCCCCCCcceeeecCCCCCCCcccccccccccccCc
Q 017919 78 LKCPRCESTNTKFCYFNNYSLSQPRHFCKTCRRYWTRGG 116 (364)
Q Consensus 78 ~~CPRC~S~~Tkfcy~NNy~~~QPR~fCk~CrRyWT~GG 116 (364)
..||.|.|..|- - ...-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY---~-----dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTY---H-----DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceE---e-----cCCeeECccccccccccc
Confidence 579999998763 2 345689999999999875
Done!