Query 041099
Match_columns 361
No_of_seqs 162 out of 230
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 03:48:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041099.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041099hhsearch_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 3.7E-37 8E-42 237.3 4.9 62 49-110 2-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 93.3 0.039 8.4E-07 48.5 1.3 34 52-87 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 92.7 0.087 1.9E-06 37.7 2.2 29 51-85 17-45 (46)
4 COG3677 Transposase and inacti 91.7 0.11 2.3E-06 44.9 2.0 37 51-89 29-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 91.1 0.12 2.7E-06 36.4 1.5 31 52-84 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 87.4 0.52 1.1E-05 33.4 2.4 37 53-89 1-40 (40)
7 PF04216 FdhE: Protein involve 84.1 0.46 9.9E-06 44.7 1.0 38 51-88 210-249 (290)
8 PF01096 TFIIS_C: Transcriptio 82.4 0.9 2E-05 32.0 1.7 36 53-88 1-39 (39)
9 cd00202 ZnF_GATA Zinc finger D 81.4 1.8 4E-05 32.5 3.2 42 54-98 1-42 (54)
10 PHA02998 RNA polymerase subuni 76.1 2.3 5.1E-05 40.0 2.9 39 51-89 142-183 (195)
11 PF13453 zf-TFIIB: Transcripti 75.0 0.77 1.7E-05 32.1 -0.4 37 54-95 1-37 (41)
12 TIGR01384 TFS_arch transcripti 74.4 2.7 5.8E-05 33.9 2.4 39 52-90 62-103 (104)
13 PF12251 zf-SNAP50_C: snRNA-ac 68.5 8.4 0.00018 35.3 4.6 38 50-87 137-175 (196)
14 PF04981 NMD3: NMD3 family ; 67.0 2.5 5.5E-05 38.9 0.9 38 55-92 1-50 (236)
15 PRK14810 formamidopyrimidine-D 65.5 3.8 8.3E-05 38.8 1.8 31 50-85 242-272 (272)
16 PF14690 zf-ISL3: zinc-finger 64.3 3.1 6.7E-05 28.9 0.7 32 52-83 2-47 (47)
17 PRK14811 formamidopyrimidine-D 61.4 5.1 0.00011 37.9 1.8 31 50-85 233-263 (269)
18 TIGR01385 TFSII transcription 61.0 6.2 0.00013 38.6 2.4 38 51-88 257-297 (299)
19 smart00401 ZnF_GATA zinc finge 58.9 6.8 0.00015 29.1 1.8 40 51-93 2-41 (52)
20 PRK01103 formamidopyrimidine/5 58.7 6.1 0.00013 37.2 1.9 31 50-85 243-273 (274)
21 PF06220 zf-U1: U1 zinc finger 56.3 4.3 9.4E-05 28.7 0.3 17 75-91 1-17 (38)
22 PRK10445 endonuclease VIII; Pr 56.2 7.1 0.00015 36.8 1.9 31 50-85 233-263 (263)
23 PRK13945 formamidopyrimidine-D 54.8 7.9 0.00017 36.8 1.9 31 50-85 252-282 (282)
24 TIGR00244 transcriptional regu 53.6 8.9 0.00019 34.8 1.9 44 54-97 2-48 (147)
25 TIGR01562 FdhE formate dehydro 51.9 9.8 0.00021 37.5 2.1 37 51-88 223-263 (305)
26 PRK00464 nrdR transcriptional 49.9 10 0.00023 34.0 1.8 45 53-97 1-48 (154)
27 TIGR00577 fpg formamidopyrimid 49.4 11 0.00023 35.7 1.9 30 50-84 243-272 (272)
28 PRK03564 formate dehydrogenase 49.3 11 0.00024 37.4 2.0 38 51-89 225-264 (309)
29 PHA00626 hypothetical protein 48.6 11 0.00023 30.0 1.5 36 54-91 2-37 (59)
30 PRK00432 30S ribosomal protein 43.4 11 0.00024 28.2 0.8 27 51-85 19-45 (50)
31 KOG2906 RNA polymerase III sub 42.7 21 0.00045 31.1 2.4 41 48-88 61-104 (105)
32 PF09526 DUF2387: Probable met 41.3 18 0.0004 28.9 1.8 32 51-85 7-38 (71)
33 COG0266 Nei Formamidopyrimidin 40.5 17 0.00036 35.7 1.7 31 50-85 243-273 (273)
34 KOG3419 Mitochondrial/chloropl 35.1 15 0.00032 32.3 0.4 16 319-334 27-42 (112)
35 PF06827 zf-FPG_IleRS: Zinc fi 35.0 18 0.00039 23.7 0.7 27 53-84 2-28 (30)
36 PF14599 zinc_ribbon_6: Zinc-r 34.8 16 0.00035 28.6 0.5 14 51-64 47-60 (61)
37 COG1997 RPL43A Ribosomal prote 34.1 16 0.00034 31.1 0.4 43 50-99 33-75 (89)
38 PF07282 OrfB_Zn_ribbon: Putat 32.3 22 0.00049 26.5 0.9 32 51-89 27-58 (69)
39 PF14354 Lar_restr_allev: Rest 32.2 36 0.00079 24.8 2.0 35 51-85 2-37 (61)
40 TIGR03655 anti_R_Lar restricti 30.7 38 0.00082 24.9 1.9 32 53-85 2-34 (53)
41 PRK00040 rpsP 30S ribosomal pr 29.8 17 0.00037 29.4 -0.0 10 325-334 32-41 (75)
42 TIGR00002 S16 ribosomal protei 28.3 19 0.00041 29.3 -0.0 10 325-334 31-40 (78)
43 PF00886 Ribosomal_S16: Riboso 27.1 14 0.0003 28.6 -1.0 11 325-335 25-35 (62)
44 PRK14524 rpsP 30S ribosomal pr 26.5 22 0.00047 30.0 0.0 11 325-335 32-42 (94)
45 CHL00005 rps16 ribosomal prote 24.9 24 0.00051 29.2 -0.1 11 325-335 32-42 (82)
46 PRK14522 rpsP 30S ribosomal pr 24.4 27 0.00059 30.8 0.2 10 325-334 33-42 (116)
47 PF01807 zf-CHC2: CHC2 zinc fi 24.4 45 0.00098 27.1 1.5 30 52-85 33-62 (97)
48 TIGR00686 phnA alkylphosphonat 24.3 43 0.00093 29.4 1.4 31 53-91 3-33 (109)
49 PF08274 PhnA_Zn_Ribbon: PhnA 23.9 32 0.0007 23.7 0.5 28 53-88 3-30 (30)
50 COG1327 Predicted transcriptio 23.9 45 0.00097 30.8 1.5 44 54-97 2-48 (156)
51 TIGR02443 conserved hypothetic 23.6 60 0.0013 25.8 1.9 31 51-84 8-38 (59)
52 KOG2691 RNA polymerase II subu 23.6 49 0.0011 29.2 1.6 39 49-89 70-113 (113)
53 PF08273 Prim_Zn_Ribbon: Zinc- 23.4 54 0.0012 23.8 1.5 32 52-85 3-34 (40)
54 COG4049 Uncharacterized protei 23.3 30 0.00066 27.8 0.3 11 50-60 15-25 (65)
55 PRK14525 rpsP 30S ribosomal pr 23.1 28 0.0006 29.2 0.0 10 325-334 33-42 (88)
56 PRK10220 hypothetical protein; 22.1 51 0.0011 29.0 1.4 31 53-91 4-34 (111)
No 1
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=100.00 E-value=3.7e-37 Score=237.35 Aligned_cols=62 Identities=79% Similarity=1.578 Sum_probs=59.1
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCCcchhhhhhhccccCcccccccCCCcccCCCCCCC
Q 041099 49 QQPPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGCRKNKRVKR 110 (361)
Q Consensus 49 ~~~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVGGG~RKnKr~~~ 110 (361)
++++++||||+|.+|||||||||++.||||||++|+||||+||+|||||||||+||+|++++
T Consensus 2 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~s 63 (63)
T PF02701_consen 2 PEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSSS 63 (63)
T ss_pred CccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCCC
Confidence 46789999999999999999999999999999999999999999999999999999998763
No 2
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=93.29 E-value=0.039 Score=48.51 Aligned_cols=34 Identities=29% Similarity=0.762 Sum_probs=27.3
Q ss_pred CCCCCCCCCCCceeeeeccc--CCCCCcchhhhhhhcc
Q 041099 52 PLKCPRCDSSNTKFCYYNNY--SLSQPRHFCKACKRYW 87 (361)
Q Consensus 52 ~l~CPRC~S~nTKFcYyNNy--~~~QPRhfCksCrRYW 87 (361)
...||||.|.+|+-. +.| +.++.-|+|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence 489999999999964 555 4567789999998644
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=92.74 E-value=0.087 Score=37.70 Aligned_cols=29 Identities=34% Similarity=0.785 Sum_probs=23.3
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
.+..||+|.+. +...+.+ +.++.|++|++
T Consensus 17 ~g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 45779999998 6655555 78999999986
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.73 E-value=0.11 Score=44.87 Aligned_cols=37 Identities=32% Similarity=0.630 Sum_probs=29.1
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcchhhhhhhcccc
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTR 89 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~ 89 (361)
....||+|.+.+ +-=+.-+.....||.|++|++-|+.
T Consensus 29 ~~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 29 TKVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred ccCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 347899999999 2225555566999999999999874
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=91.11 E-value=0.12 Score=36.42 Aligned_cols=31 Identities=35% Similarity=0.718 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCceeeeecccCC-CCCcchhhhhh
Q 041099 52 PLKCPRCDSSNTKFCYYNNYSL-SQPRHFCKACK 84 (361)
Q Consensus 52 ~l~CPRC~S~nTKFcYyNNy~~-~QPRhfCksCr 84 (361)
.+.||||.+.+.- |=|-... -..||+|++|+
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 3689999998721 2344443 35899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=87.38 E-value=0.52 Score=33.43 Aligned_cols=37 Identities=24% Similarity=0.704 Sum_probs=27.5
Q ss_pred CCCCCCCCCCceeeeecccCCCCC---cchhhhhhhcccc
Q 041099 53 LKCPRCDSSNTKFCYYNNYSLSQP---RHFCKACKRYWTR 89 (361)
Q Consensus 53 l~CPRC~S~nTKFcYyNNy~~~QP---RhfCksCrRYWT~ 89 (361)
.+||+|...+.-|-..+-.+...| -|.|.+|...|..
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 379999977777655555555555 4999999999963
No 7
>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=84.14 E-value=0.46 Score=44.70 Aligned_cols=38 Identities=24% Similarity=0.645 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCC-ceeeeeccc-CCCCCcchhhhhhhccc
Q 041099 51 PPLKCPRCDSSN-TKFCYYNNY-SLSQPRHFCKACKRYWT 88 (361)
Q Consensus 51 ~~l~CPRC~S~n-TKFcYyNNy-~~~QPRhfCksCrRYWT 88 (361)
....||.|...+ .++-||..- ....--+.|+.|+.|+-
T Consensus 210 ~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 210 VRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp -TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred cCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 567899999988 667777433 33333499999999983
No 8
>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=82.37 E-value=0.9 Score=31.99 Aligned_cols=36 Identities=28% Similarity=0.756 Sum_probs=23.6
Q ss_pred CCCCCCCCCCceeeeecccCCCCCc---chhhhhhhccc
Q 041099 53 LKCPRCDSSNTKFCYYNNYSLSQPR---HFCKACKRYWT 88 (361)
Q Consensus 53 l~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT 88 (361)
.+||+|...+.-|=-.+......|- |.|.+|..-|+
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 3799999987665444555555443 89999999885
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=81.43 E-value=1.8 Score=32.53 Aligned_cols=42 Identities=26% Similarity=0.678 Sum_probs=29.0
Q ss_pred CCCCCCCCCceeeeecccCCCCCcchhhhhhhccccCcccccccC
Q 041099 54 KCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPV 98 (361)
Q Consensus 54 ~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPV 98 (361)
.|--|...+|..=.- ....+..+|-+|.-||.+.|..|.+-.
T Consensus 1 ~C~~C~~~~Tp~WR~---g~~~~~~LCNaCgl~~~k~~~~rp~~~ 42 (54)
T cd00202 1 ACSNCGTTTTPLWRR---GPSGGSTLCNACGLYWKKHGVMRPLSK 42 (54)
T ss_pred CCCCCCCCCCccccc---CCCCcchHHHHHHHHHHhcCCCCCccc
Confidence 367787777643222 124678999999999999996655433
No 10
>PHA02998 RNA polymerase subunit; Provisional
Probab=76.12 E-value=2.3 Score=40.01 Aligned_cols=39 Identities=28% Similarity=0.619 Sum_probs=33.3
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCc---chhhhhhhcccc
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQPR---HFCKACKRYWTR 89 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT~ 89 (361)
...+||+|...++-|=-.|-++-..|- |.|..|..-|.-
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 568999999999998888888777775 899999999964
No 11
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=75.04 E-value=0.77 Score=32.13 Aligned_cols=37 Identities=27% Similarity=0.643 Sum_probs=27.0
Q ss_pred CCCCCCCCCceeeeecccCCCCCcchhhhhhhccccCccccc
Q 041099 54 KCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRN 95 (361)
Q Consensus 54 ~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRN 95 (361)
+||+|...=...-+ ..-+-+.|..|.-.|=..|.+..
T Consensus 1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEK 37 (41)
T ss_pred CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHH
Confidence 69999985554444 33566889999999988776654
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=74.37 E-value=2.7 Score=33.85 Aligned_cols=39 Identities=18% Similarity=0.605 Sum_probs=27.9
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCc---chhhhhhhccccC
Q 041099 52 PLKCPRCDSSNTKFCYYNNYSLSQPR---HFCKACKRYWTRG 90 (361)
Q Consensus 52 ~l~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT~G 90 (361)
..+||+|...+.-|=..+-.+...|- |.|..|+-.|+.+
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 48999998777665444444433332 8999999999875
No 13
>PF12251 zf-SNAP50_C: snRNA-activating protein of 50kDa MW C terminal; InterPro: IPR022042 This domain family is found in eukaryotes, and is typically between 196 and 207 amino acids in length. There is a conserved CEH sequence motif. SNAP50 is part of the snRNA-activating protein complex which activates RNA polymerases II and III. There is a cysteine-histidine cluster which contains two possible zinc finger motifs.
Probab=68.52 E-value=8.4 Score=35.34 Aligned_cols=38 Identities=29% Similarity=0.606 Sum_probs=29.4
Q ss_pred CCCCCCCCCCCCCceeeeec-ccCCCCCcchhhhhhhcc
Q 041099 50 QPPLKCPRCDSSNTKFCYYN-NYSLSQPRHFCKACKRYW 87 (361)
Q Consensus 50 ~~~l~CPRC~S~nTKFcYyN-Ny~~~QPRhfCksCrRYW 87 (361)
...+.|--|.....++--+| ...+.-|.+||..|=+-.
T Consensus 137 ~~~~~C~vC~~~~A~~v~~~d~~~p~~P~~~C~~Cf~~l 175 (196)
T PF12251_consen 137 FRRRKCSVCGIYPAKWVTYNDELAPEDPCFFCDSCFRLL 175 (196)
T ss_pred cccccCCCCCCCCCEEEEECCccCCCCCchhHHHHHHHh
Confidence 35789999999986655555 456788999999998754
No 14
>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=67.00 E-value=2.5 Score=38.92 Aligned_cols=38 Identities=29% Similarity=0.760 Sum_probs=24.3
Q ss_pred CCCCCCCCce-------eeeecccCCCC-----CcchhhhhhhccccCcc
Q 041099 55 CPRCDSSNTK-------FCYYNNYSLSQ-----PRHFCKACKRYWTRGGT 92 (361)
Q Consensus 55 CPRC~S~nTK-------FcYyNNy~~~Q-----PRhfCksCrRYWT~GGt 92 (361)
||+|...... =||...+.+.. .-.+|+.|.||+..|.=
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~W 50 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGRW 50 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCCEe
Confidence 6666653333 25666665533 22789999999998543
No 15
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=65.54 E-value=3.8 Score=38.77 Aligned_cols=31 Identities=16% Similarity=0.597 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 50 QPPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 50 ~~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
.+..+||||...=.|.-+= .+.-|||..|++
T Consensus 242 R~g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 242 RTGEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCCCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 5678999999766554432 366699999985
No 16
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=64.30 E-value=3.1 Score=28.88 Aligned_cols=32 Identities=31% Similarity=0.741 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCcee-eeeccc-------------CCCCCcchhhhh
Q 041099 52 PLKCPRCDSSNTKF-CYYNNY-------------SLSQPRHFCKAC 83 (361)
Q Consensus 52 ~l~CPRC~S~nTKF-cYyNNy-------------~~~QPRhfCksC 83 (361)
+..||.|.+..-+. -++... .+..+|++|++|
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 46899999877221 111111 346778888877
No 17
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=61.35 E-value=5.1 Score=37.94 Aligned_cols=31 Identities=29% Similarity=0.763 Sum_probs=23.0
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 50 QPPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 50 ~~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
.++.+||||...=.|.-+ . .+.-|||..|++
T Consensus 233 R~g~pC~~Cg~~I~~~~~-~----gR~ty~Cp~CQ~ 263 (269)
T PRK14811 233 REGQPCPRCGTPIEKIVV-G----GRGTHFCPQCQP 263 (269)
T ss_pred CCcCCCCcCCCeeEEEEE-C----CCCcEECCCCcC
Confidence 456799999977666433 2 366799999996
No 18
>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=60.96 E-value=6.2 Score=38.63 Aligned_cols=38 Identities=18% Similarity=0.593 Sum_probs=27.9
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCc---chhhhhhhccc
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQPR---HFCKACKRYWT 88 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT 88 (361)
...+||+|...+..|-..+......|- |.|..|...|.
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 458999999777776555555555553 78999999984
No 19
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=58.89 E-value=6.8 Score=29.08 Aligned_cols=40 Identities=25% Similarity=0.602 Sum_probs=29.4
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcchhhhhhhccccCccc
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTL 93 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtL 93 (361)
....|--|....|..=. ....-++.+|-+|.-||.+.|.+
T Consensus 2 ~~~~C~~C~~~~T~~WR---~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWR---RGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccc---cCCCCCCcEeecccHHHHHcCCC
Confidence 45789999988885321 12233369999999999998886
No 20
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=58.74 E-value=6.1 Score=37.24 Aligned_cols=31 Identities=23% Similarity=0.613 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 50 QPPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 50 ~~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
..+.+||||...=.|.- +. .+.-|||..|++
T Consensus 243 R~g~pC~~Cg~~I~~~~-~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 243 REGEPCRRCGTPIEKIK-QG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCCeeEEEE-EC----CCCcEECcCCCC
Confidence 46788999997765533 33 366799999986
No 21
>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=56.25 E-value=4.3 Score=28.74 Aligned_cols=17 Identities=41% Similarity=1.021 Sum_probs=7.1
Q ss_pred CCcchhhhhhhccccCc
Q 041099 75 QPRHFCKACKRYWTRGG 91 (361)
Q Consensus 75 QPRhfCksCrRYWT~GG 91 (361)
+|||||.=|..|.|..-
T Consensus 1 m~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDS 17 (38)
T ss_dssp --S-B-TTT--B-S--S
T ss_pred CcCeecccccceecCCC
Confidence 69999999999997654
No 22
>PRK10445 endonuclease VIII; Provisional
Probab=56.22 E-value=7.1 Score=36.81 Aligned_cols=31 Identities=26% Similarity=0.613 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 50 QPPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 50 ~~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
....+||||...=.|.-+ . .+.-|||..|++
T Consensus 233 r~g~~Cp~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 263 (263)
T PRK10445 233 RDGEACERCGGIIEKTTL-S----SRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCCCCEeEEEEE-C----CCCcEECCCCcC
Confidence 356789999977666544 2 366799999984
No 23
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=54.84 E-value=7.9 Score=36.78 Aligned_cols=31 Identities=16% Similarity=0.634 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 50 QPPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 50 ~~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
.+..+||||...=.|.-+ -.+.-|||..|++
T Consensus 252 R~g~pC~~Cg~~I~~~~~-----~gR~t~~CP~CQ~ 282 (282)
T PRK13945 252 RTGKPCRKCGTPIERIKL-----AGRSTHWCPNCQK 282 (282)
T ss_pred CCcCCCCcCCCeeEEEEE-----CCCccEECCCCcC
Confidence 356799999987666544 2266699999985
No 24
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=53.57 E-value=8.9 Score=34.77 Aligned_cols=44 Identities=23% Similarity=0.412 Sum_probs=31.8
Q ss_pred CCCCCCCCCceeeee---cccCCCCCcchhhhhhhccccCccccccc
Q 041099 54 KCPRCDSSNTKFCYY---NNYSLSQPRHFCKACKRYWTRGGTLRNVP 97 (361)
Q Consensus 54 ~CPRC~S~nTKFcYy---NNy~~~QPRhfCksCrRYWT~GGtLRNVP 97 (361)
+||-|...+||+-== ..-+.-+-|..|..|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 699999999998532 33445567799999999998654443333
No 25
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=51.90 E-value=9.8 Score=37.52 Aligned_cols=37 Identities=22% Similarity=0.574 Sum_probs=24.6
Q ss_pred CCCCCCCCCCCCceeeeecccC----CCCCcchhhhhhhccc
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYS----LSQPRHFCKACKRYWT 88 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~----~~QPRhfCksCrRYWT 88 (361)
...+||.|...+ +.-|+.--. ..---..|.+|++|+-
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 578899999865 555664332 1112268999999974
No 26
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=49.91 E-value=10 Score=34.01 Aligned_cols=45 Identities=24% Similarity=0.492 Sum_probs=32.1
Q ss_pred CCCCCCCCCCceee---eecccCCCCCcchhhhhhhccccCccccccc
Q 041099 53 LKCPRCDSSNTKFC---YYNNYSLSQPRHFCKACKRYWTRGGTLRNVP 97 (361)
Q Consensus 53 l~CPRC~S~nTKFc---YyNNy~~~QPRhfCksCrRYWT~GGtLRNVP 97 (361)
.+||-|.+..|++- |+-.-++-.-||-|+.|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999997764 4445445566699999999887655544443
No 27
>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=49.42 E-value=11 Score=35.74 Aligned_cols=30 Identities=27% Similarity=0.659 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcchhhhhh
Q 041099 50 QPPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACK 84 (361)
Q Consensus 50 ~~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCr 84 (361)
.++.+||||...=.|.-+ . .+.-|||..|+
T Consensus 243 r~g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ 272 (272)
T TIGR00577 243 RKGEPCRRCGTPIEKIKV-G----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCCCeeEEEEE-C----CCCCEECCCCC
Confidence 467899999977666433 2 36669999996
No 28
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=49.31 E-value=11 Score=37.37 Aligned_cols=38 Identities=26% Similarity=0.553 Sum_probs=24.6
Q ss_pred CCCCCCCCCCCCceeeeecccC--CCCCcchhhhhhhcccc
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYS--LSQPRHFCKACKRYWTR 89 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~--~~QPRhfCksCrRYWT~ 89 (361)
...+||.|... .|.-|+.--. ..---+.|..|++|+--
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 56889999974 4566653221 12223889999999854
No 29
>PHA00626 hypothetical protein
Probab=48.62 E-value=11 Score=30.00 Aligned_cols=36 Identities=19% Similarity=0.287 Sum_probs=24.2
Q ss_pred CCCCCCCCCceeeeecccCCCCCcchhhhhhhccccCc
Q 041099 54 KCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGG 91 (361)
Q Consensus 54 ~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GG 91 (361)
.||+|.+.+--=|=.= ....-||.|++|.=.+|+..
T Consensus 2 ~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeecee--cccCcceEcCCCCCeechhh
Confidence 6999999763311110 11246799999999999864
No 30
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.44 E-value=11 Score=28.16 Aligned_cols=27 Identities=33% Similarity=0.645 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
...-||+|.+. |..-.. .|+.|..|..
T Consensus 19 ~~~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 19 KNKFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred ccCcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 34589999873 544443 7999999974
No 31
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=42.71 E-value=21 Score=31.13 Aligned_cols=41 Identities=27% Similarity=0.595 Sum_probs=34.2
Q ss_pred CCCCCCCCCCCCCCCceeeeecccCCCCCc---chhhhhhhccc
Q 041099 48 QQQPPLKCPRCDSSNTKFCYYNNYSLSQPR---HFCKACKRYWT 88 (361)
Q Consensus 48 ~~~~~l~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT 88 (361)
.++-...||+|...+.-|--++-.+..-|- |.|-.|+--|-
T Consensus 61 v~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 61 VDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred hhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 445678999999999988888888877776 89999999884
No 32
>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=41.28 E-value=18 Score=28.89 Aligned_cols=32 Identities=22% Similarity=0.466 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
-+..||+|.+.+|=..|..|. ..-.-|-.|.-
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 468899999999988888776 55667888853
No 33
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=40.49 E-value=17 Score=35.68 Aligned_cols=31 Identities=19% Similarity=0.576 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 50 QPPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 50 ~~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
.++.+|+||...=.|--. -.+..|||..|++
T Consensus 243 R~GepC~~CGt~I~k~~~-----~gR~t~~CP~CQ~ 273 (273)
T COG0266 243 RAGEPCRRCGTPIEKIKL-----GGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCCccCCEeEEEEE-----cCCcCEeCCCCCC
Confidence 578899999987655321 2367799999985
No 34
>KOG3419 consensus Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=35.09 E-value=15 Score=32.33 Aligned_cols=16 Identities=31% Similarity=0.472 Sum_probs=12.9
Q ss_pred hhhhhhhhhhcccCCC
Q 041099 319 NVECQNQMEQIGLADP 334 (361)
Q Consensus 319 ~~~cqnq~e~~g~~dp 334 (361)
.-.=+.+||++|++||
T Consensus 27 ~~rdgk~iE~lG~ydP 42 (112)
T KOG3419|consen 27 KRRDGKPIEQLGTYDP 42 (112)
T ss_pred ccccCCchhheecccC
Confidence 3344679999999999
No 35
>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=34.96 E-value=18 Score=23.66 Aligned_cols=27 Identities=26% Similarity=0.608 Sum_probs=14.1
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcchhhhhh
Q 041099 53 LKCPRCDSSNTKFCYYNNYSLSQPRHFCKACK 84 (361)
Q Consensus 53 l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCr 84 (361)
.+||||...-.+.-..+ +.-+||..|+
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 57999988876654421 2337777775
No 36
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=34.81 E-value=16 Score=28.61 Aligned_cols=14 Identities=43% Similarity=0.733 Sum_probs=6.2
Q ss_pred CCCCCCCCCCCCce
Q 041099 51 PPLKCPRCDSSNTK 64 (361)
Q Consensus 51 ~~l~CPRC~S~nTK 64 (361)
-+++|+.|.|.||+
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 57899999999997
No 37
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=34.10 E-value=16 Score=31.07 Aligned_cols=43 Identities=21% Similarity=0.509 Sum_probs=32.4
Q ss_pred CCCCCCCCCCCCCceeeeecccCCCCCcchhhhhhhccccCcccccccCC
Q 041099 50 QPPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVG 99 (361)
Q Consensus 50 ~~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVG 99 (361)
.+...||-|.....| -..----.|+.|..-|+.|+-....|.|
T Consensus 33 ~~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 33 RAKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred hcCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 456899999998655 1122337899999999999997777665
No 38
>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=32.27 E-value=22 Score=26.46 Aligned_cols=32 Identities=31% Similarity=0.558 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcchhhhhhhcccc
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTR 89 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~ 89 (361)
.-..||.|.....+ .+.+-.+.|..|...+.+
T Consensus 27 TSq~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 45679999998877 666777999999876654
No 39
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=32.24 E-value=36 Score=24.82 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCCceeeeecccCCCC-Ccchhhhhhh
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQ-PRHFCKACKR 85 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~Q-PRhfCksCrR 85 (361)
+..+||.|......+.+........ -.-.|..|..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5688999966655544422211111 3345888866
No 40
>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=30.71 E-value=38 Score=24.86 Aligned_cols=32 Identities=22% Similarity=0.522 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcch-hhhhhh
Q 041099 53 LKCPRCDSSNTKFCYYNNYSLSQPRHF-CKACKR 85 (361)
Q Consensus 53 l~CPRC~S~nTKFcYyNNy~~~QPRhf-CksCrR 85 (361)
.+||.|.+..-.|=+ ........+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 589999997765532 12333344444 777764
No 41
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed
Probab=29.78 E-value=17 Score=29.37 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=9.1
Q ss_pred hhhhcccCCC
Q 041099 325 QMEQIGLADP 334 (361)
Q Consensus 325 q~e~~g~~dp 334 (361)
-||+||++||
T Consensus 32 ~iE~lG~ydP 41 (75)
T PRK00040 32 FIERVGFYNP 41 (75)
T ss_pred ceeEEeecCC
Confidence 4799999999
No 42
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=28.34 E-value=19 Score=29.32 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=9.1
Q ss_pred hhhhcccCCC
Q 041099 325 QMEQIGLADP 334 (361)
Q Consensus 325 q~e~~g~~dp 334 (361)
-||+||++||
T Consensus 31 ~iE~lG~YnP 40 (78)
T TIGR00002 31 YIEELGFYNP 40 (78)
T ss_pred ceeEeeeccC
Confidence 4799999999
No 43
>PF00886 Ribosomal_S16: Ribosomal protein S16; InterPro: IPR000307 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 S16 is one of the proteins from the small ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups: Eubacterial S16. Algal and plant chloroplast S16. Cyanelle S16. Neurospora crassa mitochondrial S24 (cyt-21). S16 proteins have about 100 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2Y14_P 3UZ6_S 2J02_P 1HNZ_P 3V26_P 3KNL_P 1N34_P 2J00_P 1HNW_P 3OHC_P ....
Probab=27.12 E-value=14 Score=28.65 Aligned_cols=11 Identities=36% Similarity=0.755 Sum_probs=9.4
Q ss_pred hhhhcccCCCC
Q 041099 325 QMEQIGLADPS 335 (361)
Q Consensus 325 q~e~~g~~dps 335 (361)
-||+||++||-
T Consensus 25 ~iE~lG~YdP~ 35 (62)
T PF00886_consen 25 FIEELGFYDPI 35 (62)
T ss_dssp ESEEEEEEETT
T ss_pred hhhccceEcCC
Confidence 47999999993
No 44
>PRK14524 rpsP 30S ribosomal protein S16; Provisional
Probab=26.49 E-value=22 Score=30.03 Aligned_cols=11 Identities=27% Similarity=0.591 Sum_probs=9.4
Q ss_pred hhhhcccCCCC
Q 041099 325 QMEQIGLADPS 335 (361)
Q Consensus 325 q~e~~g~~dps 335 (361)
-||+||+|||-
T Consensus 32 ~iE~lG~YnP~ 42 (94)
T PRK14524 32 YIESLGYYNPL 42 (94)
T ss_pred ceeEeeecCCC
Confidence 47999999993
No 45
>CHL00005 rps16 ribosomal protein S16
Probab=24.90 E-value=24 Score=29.17 Aligned_cols=11 Identities=36% Similarity=0.872 Sum_probs=9.4
Q ss_pred hhhhcccCCCC
Q 041099 325 QMEQIGLADPS 335 (361)
Q Consensus 325 q~e~~g~~dps 335 (361)
-||+||++||-
T Consensus 32 ~iE~lG~YnP~ 42 (82)
T CHL00005 32 DLEKVGFYDPI 42 (82)
T ss_pred ceeEeeeccCC
Confidence 37999999993
No 46
>PRK14522 rpsP 30S ribosomal protein S16; Provisional
Probab=24.45 E-value=27 Score=30.80 Aligned_cols=10 Identities=40% Similarity=0.720 Sum_probs=9.2
Q ss_pred hhhhcccCCC
Q 041099 325 QMEQIGLADP 334 (361)
Q Consensus 325 q~e~~g~~dp 334 (361)
-||+||++||
T Consensus 33 ~IE~lG~YdP 42 (116)
T PRK14522 33 YIELLGWYDP 42 (116)
T ss_pred cceeeeccCC
Confidence 5899999999
No 47
>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=24.40 E-value=45 Score=27.07 Aligned_cols=30 Identities=23% Similarity=0.513 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 52 PLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 52 ~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
...||-|+..+..|..+.. .-++.|-+|.+
T Consensus 33 ~~~CPfH~d~~pS~~i~~~----k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPD----KNRFKCFGCGK 62 (97)
T ss_dssp EE--SSS--SS--EEEETT----TTEEEETTT--
T ss_pred EEECcCCCCCCCceEEECC----CCeEEECCCCC
Confidence 4679999987777777654 34899999985
No 48
>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=24.25 E-value=43 Score=29.36 Aligned_cols=31 Identities=26% Similarity=0.684 Sum_probs=24.8
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcchhhhhhhccccCc
Q 041099 53 LKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGG 91 (361)
Q Consensus 53 l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GG 91 (361)
.+||.|.|..|- - .+.-+.|..|.-=|....
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 579999998663 1 355699999999999876
No 49
>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=23.92 E-value=32 Score=23.71 Aligned_cols=28 Identities=32% Similarity=0.678 Sum_probs=14.6
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcchhhhhhhccc
Q 041099 53 LKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWT 88 (361)
Q Consensus 53 l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT 88 (361)
-+||.|.+..|= ....-+.|..|..=|.
T Consensus 3 p~Cp~C~se~~y--------~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTY--------EDGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----E--------E-SSSEEETTTTEEE-
T ss_pred CCCCCCCCccee--------ccCCEEeCCcccccCC
Confidence 479999998774 5567788999987774
No 50
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=23.88 E-value=45 Score=30.81 Aligned_cols=44 Identities=25% Similarity=0.384 Sum_probs=29.6
Q ss_pred CCCCCCCCCceeeee---cccCCCCCcchhhhhhhccccCccccccc
Q 041099 54 KCPRCDSSNTKFCYY---NNYSLSQPRHFCKACKRYWTRGGTLRNVP 97 (361)
Q Consensus 54 ~CPRC~S~nTKFcYy---NNy~~~QPRhfCksCrRYWT~GGtLRNVP 97 (361)
.||-|.+.+||+-== -.-+.-+-|.-|..|..-+|-==++--+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 699999999998421 11233455788999998888554443333
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=23.58 E-value=60 Score=25.76 Aligned_cols=31 Identities=23% Similarity=0.454 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCCceeeeecccCCCCCcchhhhhh
Q 041099 51 PPLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACK 84 (361)
Q Consensus 51 ~~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCr 84 (361)
-+..||+|...+|=..|..|.- .-.-|-.|.
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 4689999999999988865543 345677774
No 52
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=23.56 E-value=49 Score=29.22 Aligned_cols=39 Identities=21% Similarity=0.618 Sum_probs=27.2
Q ss_pred CCCCCCCCCCCCCCceeeeecccCCCCC-----cchhhhhhhcccc
Q 041099 49 QQPPLKCPRCDSSNTKFCYYNNYSLSQP-----RHFCKACKRYWTR 89 (361)
Q Consensus 49 ~~~~l~CPRC~S~nTKFcYyNNy~~~QP-----RhfCksCrRYWT~ 89 (361)
.-+...||+|...+.-| |+--....- -|.|-+|.--||.
T Consensus 70 rts~~~C~~C~~~eavf--fQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 70 RTSDKHCPKCGHREAVF--FQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred ccccccCCccCCcceEE--EecccccccceEEEEEEeccccccccC
Confidence 34668999999987765 554322111 1889999999985
No 53
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=23.36 E-value=54 Score=23.82 Aligned_cols=32 Identities=19% Similarity=0.597 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCceeeeecccCCCCCcchhhhhhh
Q 041099 52 PLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKR 85 (361)
Q Consensus 52 ~l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR 85 (361)
+.+||-|.. ..+|..|-+. .-+-..+|..|..
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 5688855543 2347799999943
No 54
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=23.32 E-value=30 Score=27.81 Aligned_cols=11 Identities=45% Similarity=1.153 Sum_probs=9.0
Q ss_pred CCCCCCCCCCC
Q 041099 50 QPPLKCPRCDS 60 (361)
Q Consensus 50 ~~~l~CPRC~S 60 (361)
++-+.||||+-
T Consensus 15 E~~lrCPRC~~ 25 (65)
T COG4049 15 EEFLRCPRCGM 25 (65)
T ss_pred ceeeeCCchhH
Confidence 46789999985
No 55
>PRK14525 rpsP 30S ribosomal protein S16; Provisional
Probab=23.13 E-value=28 Score=29.15 Aligned_cols=10 Identities=40% Similarity=0.939 Sum_probs=9.0
Q ss_pred hhhhcccCCC
Q 041099 325 QMEQIGLADP 334 (361)
Q Consensus 325 q~e~~g~~dp 334 (361)
-||+||+|||
T Consensus 33 ~IE~lG~YnP 42 (88)
T PRK14525 33 YLEDVGIYDP 42 (88)
T ss_pred ceeEEecccC
Confidence 4799999999
No 56
>PRK10220 hypothetical protein; Provisional
Probab=22.06 E-value=51 Score=28.99 Aligned_cols=31 Identities=26% Similarity=0.679 Sum_probs=24.9
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcchhhhhhhccccCc
Q 041099 53 LKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGG 91 (361)
Q Consensus 53 l~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GG 91 (361)
.+||.|.+..|- ..+..+.|..|.-=|+...
T Consensus 4 P~CP~C~seytY--------~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTY--------EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceE--------cCCCeEECCcccCcCCccc
Confidence 579999997662 2356799999999999875
Done!