Query 021974
Match_columns 304
No_of_seqs 135 out of 255
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 07:03:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021974.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021974hhsearch_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 8.6E-38 1.9E-42 236.6 4.4 63 34-96 1-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 93.3 0.038 8.2E-07 47.7 1.2 34 38-73 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 92.4 0.1 2.2E-06 36.6 2.2 28 38-71 18-45 (46)
4 COG3677 Transposase and inacti 92.0 0.1 2.2E-06 44.2 2.1 36 38-75 30-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 92.0 0.094 2E-06 36.3 1.6 31 38-70 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 88.8 0.4 8.6E-06 33.3 2.5 37 39-75 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 85.8 0.57 1.2E-05 32.3 1.9 36 39-74 1-39 (39)
8 TIGR01384 TFS_arch transcripti 78.4 2.4 5.3E-05 33.4 3.2 40 37-76 61-103 (104)
9 PF04216 FdhE: Protein involve 77.2 1.1 2.5E-05 41.3 1.2 37 38-74 211-249 (290)
10 PF13453 zf-TFIIB: Transcripti 76.6 0.69 1.5E-05 31.7 -0.3 37 40-81 1-37 (41)
11 PHA02998 RNA polymerase subuni 75.9 2.2 4.7E-05 39.5 2.5 39 37-75 142-183 (195)
12 cd00202 ZnF_GATA Zinc finger D 75.4 3.2 7E-05 30.6 2.9 39 41-82 2-40 (54)
13 PF04981 NMD3: NMD3 family ; 64.8 3.2 7E-05 37.5 1.1 26 52-77 19-49 (236)
14 TIGR01385 TFSII transcription 60.4 6.8 0.00015 37.7 2.5 38 37-74 257-297 (299)
15 PF14690 zf-ISL3: zinc-finger 59.9 4.1 8.8E-05 27.7 0.7 32 38-69 2-47 (47)
16 PF06220 zf-U1: U1 zinc finger 59.0 3.8 8.1E-05 28.4 0.4 17 61-77 1-17 (38)
17 smart00401 ZnF_GATA zinc finge 56.6 7.6 0.00016 28.2 1.7 39 38-79 3-41 (52)
18 TIGR00244 transcriptional regu 55.5 8.2 0.00018 34.3 2.0 44 40-83 2-48 (147)
19 PHA00626 hypothetical protein 54.9 8 0.00017 30.0 1.6 37 40-78 2-38 (59)
20 PRK14810 formamidopyrimidine-D 54.0 7.7 0.00017 36.1 1.7 30 37-71 243-272 (272)
21 PRK00464 nrdR transcriptional 51.1 11 0.00025 33.1 2.2 45 39-83 1-48 (154)
22 PRK14811 formamidopyrimidine-D 50.3 9.9 0.00021 35.4 1.8 29 38-71 235-263 (269)
23 PRK03564 formate dehydrogenase 47.8 12 0.00026 36.5 1.9 36 38-74 226-263 (309)
24 PRK01103 formamidopyrimidine/5 46.7 12 0.00026 34.7 1.7 29 38-71 245-273 (274)
25 PRK00432 30S ribosomal protein 46.3 9.9 0.00021 27.8 0.9 26 38-71 20-45 (50)
26 PRK10445 endonuclease VIII; Pr 44.9 13 0.00029 34.4 1.7 29 38-71 235-263 (263)
27 TIGR01562 FdhE formate dehydro 44.5 14 0.0003 35.9 1.8 36 38-74 224-263 (305)
28 PRK13945 formamidopyrimidine-D 43.9 15 0.00032 34.4 1.8 29 38-71 254-282 (282)
29 PF14599 zinc_ribbon_6: Zinc-r 43.9 9.5 0.00021 29.2 0.5 13 38-50 48-60 (61)
30 PF09526 DUF2387: Probable met 43.3 16 0.00036 28.6 1.8 31 38-71 8-38 (71)
31 KOG2906 RNA polymerase III sub 41.1 23 0.00049 30.3 2.3 37 38-74 65-104 (105)
32 TIGR00577 fpg formamidopyrimid 37.8 20 0.00044 33.3 1.8 28 38-70 245-272 (272)
33 COG0266 Nei Formamidopyrimidin 36.6 18 0.00038 34.9 1.2 30 37-71 244-273 (273)
34 PF06827 zf-FPG_IleRS: Zinc fi 34.5 17 0.00038 23.2 0.6 27 39-70 2-28 (30)
35 PF14354 Lar_restr_allev: Rest 32.7 35 0.00075 24.4 1.9 35 37-71 2-37 (61)
36 PF08273 Prim_Zn_Ribbon: Zinc- 31.3 28 0.0006 24.7 1.2 32 38-71 3-34 (40)
37 TIGR03655 anti_R_Lar restricti 28.6 47 0.001 23.9 2.0 32 39-71 2-34 (53)
38 COG1327 Predicted transcriptio 27.3 36 0.00079 30.8 1.5 43 40-82 2-47 (156)
39 COG1997 RPL43A Ribosomal prote 27.1 34 0.00073 28.5 1.2 41 38-85 35-75 (89)
40 PF08274 PhnA_Zn_Ribbon: PhnA 25.6 32 0.0007 23.2 0.7 28 39-74 3-30 (30)
41 PF07282 OrfB_Zn_ribbon: Putat 25.4 52 0.0011 24.0 1.8 32 37-75 27-58 (69)
42 PRK14892 putative transcriptio 24.3 51 0.0011 27.4 1.8 38 33-74 16-53 (99)
43 TIGR02443 conserved hypothetic 24.1 57 0.0012 25.3 1.9 30 38-70 9-38 (59)
44 COG4260 Membrane protease subu 24.0 41 0.00089 33.6 1.3 39 31-71 299-342 (345)
45 PF01807 zf-CHC2: CHC2 zinc fi 23.4 50 0.0011 26.3 1.5 30 38-71 33-62 (97)
46 TIGR00155 pqiA_fam integral me 22.9 55 0.0012 32.5 2.0 19 30-48 25-43 (403)
47 PF06044 DRP: Dam-replacing fa 22.1 35 0.00075 33.0 0.4 33 38-74 31-64 (254)
48 COG4049 Uncharacterized protei 21.5 35 0.00076 26.8 0.3 11 36-46 15-25 (65)
49 PF05129 Elf1: Transcription e 21.4 47 0.001 26.3 1.0 44 30-74 14-57 (81)
50 TIGR00686 phnA alkylphosphonat 21.2 63 0.0014 27.8 1.8 31 39-77 3-33 (109)
51 PF09723 Zn-ribbon_8: Zinc rib 21.0 72 0.0016 22.1 1.8 14 36-49 24-37 (42)
52 PF08271 TF_Zn_Ribbon: TFIIB z 20.8 54 0.0012 22.5 1.1 28 40-73 2-29 (43)
53 KOG2691 RNA polymerase II subu 20.7 71 0.0015 27.7 2.0 37 37-75 72-113 (113)
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=8.6e-38 Score=236.65 Aligned_cols=63 Identities=92% Similarity=1.704 Sum_probs=60.3
Q ss_pred CCcccCCCCCCCCCCceeeeecccCCCCCcchhhhhccccccCcccccccCCCCccCCCCCCC
Q 021974 34 QPEQALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTLRNVPVGGGCRKNKRSSS 96 (304)
Q Consensus 34 ~pe~~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT~GGtLRnVPVGgG~RKnkrssS 96 (304)
+|++.++||||+|+||||||||||+++||||||++|+||||+||+||||||||||||+|+++|
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 367799999999999999999999999999999999999999999999999999999999874
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=93.26 E-value=0.038 Score=47.70 Aligned_cols=34 Identities=26% Similarity=0.819 Sum_probs=27.1
Q ss_pred cCCCCCCCCCCceeeeecccC--CCCCcchhhhhcccc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYS--LSQPRYFCKSCRRYW 73 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys--~~QPRhfCksCrRYW 73 (304)
...||||.|.+|+. .+.+- .++.-|+|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~--~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTI--TSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEe--ecCCCChhhHHHhhhhhhCCcH
Confidence 47999999999997 46664 447779999998643
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=92.36 E-value=0.1 Score=36.57 Aligned_cols=28 Identities=43% Similarity=0.985 Sum_probs=22.4
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
+..||+|.+. +...+.+ ..+|.|+.|++
T Consensus 18 g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 4679999998 6555555 78999999985
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.02 E-value=0.1 Score=44.21 Aligned_cols=36 Identities=36% Similarity=0.731 Sum_probs=28.1
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcccccc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTK 75 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT~ 75 (304)
...||+|.+.+.+ =+.-+.....||.|++|++-|+.
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 3689999999922 25555555999999999998874
No 5
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=91.98 E-value=0.094 Score=36.28 Aligned_cols=31 Identities=48% Similarity=0.890 Sum_probs=21.6
Q ss_pred cCCCCCCCCCCceeeeecccCCC-CCcchhhhhc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLS-QPRYFCKSCR 70 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~-QPRhfCksCr 70 (304)
.+.||+|.+++.- |=|-.+.. ..||+|++|+
T Consensus 5 ~v~CP~C~s~~~v--~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEGV--KKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCcc--eeCCCCCCCCEeEecCcCC
Confidence 4789999998721 12334333 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.83 E-value=0.4 Score=33.32 Aligned_cols=37 Identities=27% Similarity=0.806 Sum_probs=28.3
Q ss_pred CCCCCCCCCCceeeeecccCCCCC---cchhhhhcccccc
Q 021974 39 LKCPRCDSTNTKFCYYNNYSLSQP---RYFCKSCRRYWTK 75 (304)
Q Consensus 39 l~CPRC~S~nTKFcYyNNys~~QP---RhfCksCrRYWT~ 75 (304)
.+||+|...+.-|-..+-.+...| -|.|.+|...|..
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 379999988877766666665555 3999999999963
No 7
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=85.83 E-value=0.57 Score=32.33 Aligned_cols=36 Identities=31% Similarity=0.857 Sum_probs=24.7
Q ss_pred CCCCCCCCCCceeeeecccCCCCCc---chhhhhccccc
Q 021974 39 LKCPRCDSTNTKFCYYNNYSLSQPR---YFCKSCRRYWT 74 (304)
Q Consensus 39 l~CPRC~S~nTKFcYyNNys~~QPR---hfCksCrRYWT 74 (304)
.+||.|...+.-|--.+..+..-|- |.|.+|+.-|+
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 3799999988776555565555553 89999999985
No 8
>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=78.38 E-value=2.4 Score=33.44 Aligned_cols=40 Identities=20% Similarity=0.687 Sum_probs=29.3
Q ss_pred ccCCCCCCCCCCceeeeecccCCCCCc---chhhhhccccccC
Q 021974 37 QALKCPRCDSTNTKFCYYNNYSLSQPR---YFCKSCRRYWTKG 76 (304)
Q Consensus 37 ~~l~CPRC~S~nTKFcYyNNys~~QPR---hfCksCrRYWT~G 76 (304)
...+||+|...+.-|-..+-.+...|- |.|..|+-.|+.+
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 358999999877766555554444443 9999999999875
No 9
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=77.19 E-value=1.1 Score=41.34 Aligned_cols=37 Identities=30% Similarity=0.673 Sum_probs=18.7
Q ss_pred cCCCCCCCCCC-ceeeeeccc-CCCCCcchhhhhccccc
Q 021974 38 ALKCPRCDSTN-TKFCYYNNY-SLSQPRYFCKSCRRYWT 74 (304)
Q Consensus 38 ~l~CPRC~S~n-TKFcYyNNy-s~~QPRhfCksCrRYWT 74 (304)
...||.|...+ .++-||..- ....--+.|+.|+.|+-
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 46899999855 566676433 33333389999999983
No 10
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.59 E-value=0.69 Score=31.72 Aligned_cols=37 Identities=30% Similarity=0.629 Sum_probs=27.1
Q ss_pred CCCCCCCCCceeeeecccCCCCCcchhhhhccccccCccccc
Q 021974 40 KCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTLRN 81 (304)
Q Consensus 40 ~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT~GGtLRn 81 (304)
+||+|...-...-+ ..-+-+.|..|.-.|=..|.+..
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 69999986555444 23456889999999988776643
No 11
>PHA02998 RNA polymerase subunit; Provisional
Probab=75.91 E-value=2.2 Score=39.49 Aligned_cols=39 Identities=23% Similarity=0.571 Sum_probs=33.7
Q ss_pred ccCCCCCCCCCCceeeeecccCCCCCc---chhhhhcccccc
Q 021974 37 QALKCPRCDSTNTKFCYYNNYSLSQPR---YFCKSCRRYWTK 75 (304)
Q Consensus 37 ~~l~CPRC~S~nTKFcYyNNys~~QPR---hfCksCrRYWT~ 75 (304)
...+||+|...++-|--.|-.+...|- |.|..|..-|.-
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 468999999999999888888888775 899999999963
No 12
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=75.42 E-value=3.2 Score=30.56 Aligned_cols=39 Identities=31% Similarity=0.733 Sum_probs=27.5
Q ss_pred CCCCCCCCceeeeecccCCCCCcchhhhhccccccCcccccc
Q 021974 41 CPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTLRNV 82 (304)
Q Consensus 41 CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT~GGtLRnV 82 (304)
|--|..+.|..=.- ....+..+|-+|..||.+.|..|.+
T Consensus 2 C~~C~~~~Tp~WR~---g~~~~~~LCNaCgl~~~k~~~~rp~ 40 (54)
T cd00202 2 CSNCGTTTTPLWRR---GPSGGSTLCNACGLYWKKHGVMRPL 40 (54)
T ss_pred CCCCCCCCCccccc---CCCCcchHHHHHHHHHHhcCCCCCc
Confidence 67777777753221 1246779999999999999966543
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=64.76 E-value=3.2 Score=37.55 Aligned_cols=26 Identities=27% Similarity=0.790 Sum_probs=17.8
Q ss_pred eeecccCCCC-----CcchhhhhccccccCc
Q 021974 52 CYYNNYSLSQ-----PRYFCKSCRRYWTKGG 77 (304)
Q Consensus 52 cYyNNys~~Q-----PRhfCksCrRYWT~GG 77 (304)
||...+.+.. --.+|+.|.||+..|.
T Consensus 19 C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 19 CYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred HhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 4555555433 2378999999999843
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=60.38 E-value=6.8 Score=37.67 Aligned_cols=38 Identities=18% Similarity=0.627 Sum_probs=28.9
Q ss_pred ccCCCCCCCCCCceeeeecccCCCCCc---chhhhhccccc
Q 021974 37 QALKCPRCDSTNTKFCYYNNYSLSQPR---YFCKSCRRYWT 74 (304)
Q Consensus 37 ~~l~CPRC~S~nTKFcYyNNys~~QPR---hfCksCrRYWT 74 (304)
...+||+|...+..|-..+..+...|- |.|..|...|.
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 368999999888877555555555553 78999999984
No 15
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=59.86 E-value=4.1 Score=27.71 Aligned_cols=32 Identities=31% Similarity=0.778 Sum_probs=19.1
Q ss_pred cCCCCCCCCCCcee-eeeccc-------------CCCCCcchhhhh
Q 021974 38 ALKCPRCDSTNTKF-CYYNNY-------------SLSQPRYFCKSC 69 (304)
Q Consensus 38 ~l~CPRC~S~nTKF-cYyNNy-------------s~~QPRhfCksC 69 (304)
...||.|.+..-+. -++... .+..+|++|++|
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 45799999876221 111111 345778888887
No 16
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=59.00 E-value=3.8 Score=28.44 Aligned_cols=17 Identities=41% Similarity=1.212 Sum_probs=7.1
Q ss_pred CCcchhhhhccccccCc
Q 021974 61 QPRYFCKSCRRYWTKGG 77 (304)
Q Consensus 61 QPRhfCksCrRYWT~GG 77 (304)
+|||||.=|..|.|..-
T Consensus 1 m~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDS 17 (38)
T ss_dssp --S-B-TTT--B-S--S
T ss_pred CcCeecccccceecCCC
Confidence 69999999999997654
No 17
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=56.62 E-value=7.6 Score=28.25 Aligned_cols=39 Identities=28% Similarity=0.639 Sum_probs=28.9
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhccccccCccc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTL 79 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT~GGtL 79 (304)
...|--|..+.|..= - ....-++.+|-+|.-||.+.|.+
T Consensus 3 ~~~C~~C~~~~T~~W--R-~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 3 GRSCSNCGTTETPLW--R-RGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCcCCCCCCCCCcc--c-cCCCCCCcEeecccHHHHHcCCC
Confidence 568999998888642 1 12233369999999999998886
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=55.46 E-value=8.2 Score=34.30 Aligned_cols=44 Identities=23% Similarity=0.397 Sum_probs=32.0
Q ss_pred CCCCCCCCCceeeee---cccCCCCCcchhhhhccccccCccccccc
Q 021974 40 KCPRCDSTNTKFCYY---NNYSLSQPRYFCKSCRRYWTKGGTLRNVP 83 (304)
Q Consensus 40 ~CPRC~S~nTKFcYy---NNys~~QPRhfCksCrRYWT~GGtLRnVP 83 (304)
+||.|...+||+-== ...+.-+-|..|..|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 699999999998432 33344567799999999998655544433
No 19
>PHA00626 hypothetical protein
Probab=54.92 E-value=8 Score=30.03 Aligned_cols=37 Identities=24% Similarity=0.348 Sum_probs=24.5
Q ss_pred CCCCCCCCCceeeeecccCCCCCcchhhhhccccccCcc
Q 021974 40 KCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGT 78 (304)
Q Consensus 40 ~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT~GGt 78 (304)
.||+|.|.+--=|=.= ....-||.|++|.=.+|+..-
T Consensus 2 ~CP~CGS~~Ivrcg~c--r~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIAKEKTM--RGWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceeeeecee--cccCcceEcCCCCCeechhhh
Confidence 6999999754311110 111457999999999998653
No 20
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=54.05 E-value=7.7 Score=36.09 Aligned_cols=30 Identities=13% Similarity=0.535 Sum_probs=22.0
Q ss_pred ccCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 37 QALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 37 ~~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
+..+||||...=.|.-+= .+.-|||-.|++
T Consensus 243 ~g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 367999999866654332 366699999985
No 21
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=51.08 E-value=11 Score=33.13 Aligned_cols=45 Identities=22% Similarity=0.465 Sum_probs=31.5
Q ss_pred CCCCCCCCCCceee---eecccCCCCCcchhhhhccccccCccccccc
Q 021974 39 LKCPRCDSTNTKFC---YYNNYSLSQPRYFCKSCRRYWTKGGTLRNVP 83 (304)
Q Consensus 39 l~CPRC~S~nTKFc---YyNNys~~QPRhfCksCrRYWT~GGtLRnVP 83 (304)
.+||-|.+..|++- |+-.-++-.-|+-|+.|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999987763 3334334555699999999887665554444
No 22
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=50.28 E-value=9.9 Score=35.41 Aligned_cols=29 Identities=28% Similarity=0.736 Sum_probs=21.6
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
..+||||...=.|.-+ . .+.-|||..|++
T Consensus 235 g~pC~~Cg~~I~~~~~-~----gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVV-G----GRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEE-C----CCCcEECCCCcC
Confidence 4689999987666433 2 366799999996
No 23
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=47.79 E-value=12 Score=36.45 Aligned_cols=36 Identities=25% Similarity=0.599 Sum_probs=21.9
Q ss_pred cCCCCCCCCCCceeeeecccC--CCCCcchhhhhccccc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYS--LSQPRYFCKSCRRYWT 74 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys--~~QPRhfCksCrRYWT 74 (304)
..+||.|... .|.-||.--. ..---..|.+|+.|+-
T Consensus 226 R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 226 RVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred CccCCCCCCC-CceeeeeecCCCcceEeeecccccccce
Confidence 4678888874 3555653221 1122278999999874
No 24
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=46.74 E-value=12 Score=34.66 Aligned_cols=29 Identities=24% Similarity=0.729 Sum_probs=21.4
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
..+||||...=.|.- ++ .+.-|||..|++
T Consensus 245 g~pC~~Cg~~I~~~~-~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIK-QG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEE-EC----CCCcEECcCCCC
Confidence 568999998765542 33 366699999986
No 25
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.30 E-value=9.9 Score=27.80 Aligned_cols=26 Identities=35% Similarity=0.736 Sum_probs=19.0
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
..-||+|.+. |..-.. .|+.|..|..
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 544433 6999999974
No 26
>PRK10445 endonuclease VIII; Provisional
Probab=44.88 E-value=13 Score=34.38 Aligned_cols=29 Identities=31% Similarity=0.797 Sum_probs=21.4
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
..+||||...=.|.-+ . .+.-|||..|++
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 5789999987666544 2 366799999984
No 27
>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=44.48 E-value=14 Score=35.87 Aligned_cols=36 Identities=22% Similarity=0.584 Sum_probs=22.5
Q ss_pred cCCCCCCCCCCceeeeecccC----CCCCcchhhhhccccc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYS----LSQPRYFCKSCRRYWT 74 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys----~~QPRhfCksCrRYWT 74 (304)
..+||.|.+.+ +.-||.-.. ..---..|.+|+.|+-
T Consensus 224 R~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 224 RVKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred CccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchh
Confidence 46788888864 455664332 1112268999999873
No 28
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.91 E-value=15 Score=34.40 Aligned_cols=29 Identities=14% Similarity=0.599 Sum_probs=21.6
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
..+||||...=.|.-+ -.+.-|||..|++
T Consensus 254 g~pC~~Cg~~I~~~~~-----~gR~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCRKCGTPIERIKL-----AGRSTHWCPNCQK 282 (282)
T ss_pred cCCCCcCCCeeEEEEE-----CCCccEECCCCcC
Confidence 5699999987666544 2256699999985
No 29
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=43.88 E-value=9.5 Score=29.24 Aligned_cols=13 Identities=46% Similarity=0.902 Sum_probs=5.6
Q ss_pred cCCCCCCCCCCce
Q 021974 38 ALKCPRCDSTNTK 50 (304)
Q Consensus 38 ~l~CPRC~S~nTK 50 (304)
+++|+.|.|.||+
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 7899999999997
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=43.27 E-value=16 Score=28.56 Aligned_cols=31 Identities=23% Similarity=0.522 Sum_probs=25.2
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
+..||+|.+.+|=..|..|. ..-.-|-.|.=
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 67899999999988888776 55667888864
No 31
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=41.09 E-value=23 Score=30.29 Aligned_cols=37 Identities=27% Similarity=0.731 Sum_probs=32.3
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCc---chhhhhccccc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPR---YFCKSCRRYWT 74 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPR---hfCksCrRYWT 74 (304)
...||+|.....-|--++-.+..-|- |.|-.|+--|-
T Consensus 65 ~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 65 EATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred cCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 57899999999998888888888876 89999999884
No 32
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.85 E-value=20 Score=33.30 Aligned_cols=28 Identities=25% Similarity=0.624 Sum_probs=20.7
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCR 70 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCr 70 (304)
..+||||...=.|.-+ . .+.-|||..|+
T Consensus 245 g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKV-G----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEEE-C----CCCCEECCCCC
Confidence 5699999987666433 2 36669999996
No 33
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=36.65 E-value=18 Score=34.86 Aligned_cols=30 Identities=20% Similarity=0.615 Sum_probs=21.4
Q ss_pred ccCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 37 QALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 37 ~~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
...+|++|.+.=.|-- --.+..|||..|++
T Consensus 244 ~GepC~~CGt~I~k~~-----~~gR~t~~CP~CQ~ 273 (273)
T COG0266 244 AGEPCRRCGTPIEKIK-----LGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCCccCCEeEEEE-----EcCCcCEeCCCCCC
Confidence 4679999999554431 13367799999985
No 34
>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=34.47 E-value=17 Score=23.22 Aligned_cols=27 Identities=30% Similarity=0.736 Sum_probs=14.1
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcchhhhhc
Q 021974 39 LKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCR 70 (304)
Q Consensus 39 l~CPRC~S~nTKFcYyNNys~~QPRhfCksCr 70 (304)
.+||||...-.++-.. .+.-+||..|+
T Consensus 2 ~~C~rC~~~~~~~~~~-----~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGIN-----GRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEET-----TEEEEE-TTTC
T ss_pred CcCccCCCcceEeEec-----CCCCeECcCCc
Confidence 5799999877665431 12337777775
No 35
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=32.66 E-value=35 Score=24.43 Aligned_cols=35 Identities=17% Similarity=0.391 Sum_probs=19.9
Q ss_pred ccCCCCCCCCCCceeeeecccCCCC-Ccchhhhhcc
Q 021974 37 QALKCPRCDSTNTKFCYYNNYSLSQ-PRYFCKSCRR 71 (304)
Q Consensus 37 ~~l~CPRC~S~nTKFcYyNNys~~Q-PRhfCksCrR 71 (304)
+..+||.|.+....+.+........ -.-+|..|..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4678999966665554422211111 3345888866
No 36
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=31.25 E-value=28 Score=24.75 Aligned_cols=32 Identities=19% Similarity=0.656 Sum_probs=18.2
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
..+||-|.. ..+|..|-+. ..+-..+|+.|..
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 568999988 5678855543 3347899999943
No 37
>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=28.59 E-value=47 Score=23.87 Aligned_cols=32 Identities=25% Similarity=0.631 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcch-hhhhcc
Q 021974 39 LKCPRCDSTNTKFCYYNNYSLSQPRYF-CKSCRR 71 (304)
Q Consensus 39 l~CPRC~S~nTKFcYyNNys~~QPRhf-CksCrR 71 (304)
.+||.|.+..-.|=+ ......-.+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 589999997765532 12233334444 877764
No 38
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=27.28 E-value=36 Score=30.76 Aligned_cols=43 Identities=23% Similarity=0.318 Sum_probs=29.4
Q ss_pred CCCCCCCCCceeeee---cccCCCCCcchhhhhccccccCcccccc
Q 021974 40 KCPRCDSTNTKFCYY---NNYSLSQPRYFCKSCRRYWTKGGTLRNV 82 (304)
Q Consensus 40 ~CPRC~S~nTKFcYy---NNys~~QPRhfCksCrRYWT~GGtLRnV 82 (304)
.||.|.+.+||+-== -.-+..+-|.-|-+|..-+|-==++--+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~ 47 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELR 47 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeec
Confidence 699999999998321 1123345678999999888855444333
No 39
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=27.12 E-value=34 Score=28.51 Aligned_cols=41 Identities=24% Similarity=0.548 Sum_probs=29.9
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhccccccCcccccccCC
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTLRNVPVG 85 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT~GGtLRnVPVG 85 (304)
...||-|.+...|= ..----.|+.|..-|+.|+-....|+|
T Consensus 35 ~~~Cp~C~~~~VkR-------~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 35 KHVCPFCGRTTVKR-------IATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred CCcCCCCCCcceee-------eccCeEEcCCCCCeeccccccccchHH
Confidence 56899999985441 112227899999999999987766654
No 40
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=25.58 E-value=32 Score=23.19 Aligned_cols=28 Identities=32% Similarity=0.700 Sum_probs=14.5
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcchhhhhccccc
Q 021974 39 LKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWT 74 (304)
Q Consensus 39 l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT 74 (304)
-+||-|.|..|= ....-+.|-.|..=|.
T Consensus 3 p~Cp~C~se~~y--------~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTY--------EDGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----E--------E-SSSEEETTTTEEE-
T ss_pred CCCCCCCCccee--------ccCCEEeCCcccccCC
Confidence 479999998875 4566788999987774
No 41
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.43 E-value=52 Score=24.00 Aligned_cols=32 Identities=28% Similarity=0.611 Sum_probs=25.3
Q ss_pred ccCCCCCCCCCCceeeeecccCCCCCcchhhhhcccccc
Q 021974 37 QALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTK 75 (304)
Q Consensus 37 ~~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT~ 75 (304)
....||.|.....+ .+.+-.+.|..|...+.+
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 46779999998877 666777999999876654
No 42
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.27 E-value=51 Score=27.40 Aligned_cols=38 Identities=21% Similarity=0.498 Sum_probs=25.5
Q ss_pred CCCcccCCCCCCCCCCceeeeecccCCCCCcchhhhhccccc
Q 021974 33 PQPEQALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWT 74 (304)
Q Consensus 33 p~pe~~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT 74 (304)
+.......||.|.+ .+--|=+.. ..+.+.|..|.-|..
T Consensus 16 ~klpt~f~CP~Cge-~~v~v~~~k---~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 16 PKLPKIFECPRCGK-VSISVKIKK---NIAIITCGNCGLYTE 53 (99)
T ss_pred cCCCcEeECCCCCC-eEeeeecCC---CcceEECCCCCCccC
Confidence 33446889999995 233233333 478999999998853
No 43
>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=24.11 E-value=57 Score=25.32 Aligned_cols=30 Identities=23% Similarity=0.500 Sum_probs=22.7
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCR 70 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCr 70 (304)
+..||+|...+|=..|..|.- .-.-|-.|.
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 678999999999988866653 345677774
No 44
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=23.97 E-value=41 Score=33.55 Aligned_cols=39 Identities=26% Similarity=0.666 Sum_probs=23.2
Q ss_pred CCCCCcccCCCCCCCCCCceeeeecccCCC-----CCcchhhhhcc
Q 021974 31 PRPQPEQALKCPRCDSTNTKFCYYNNYSLS-----QPRYFCKSCRR 71 (304)
Q Consensus 31 p~p~pe~~l~CPRC~S~nTKFcYyNNys~~-----QPRhfCksCrR 71 (304)
+...|...-+||||...| ||.-----.+ -..-||+.|..
T Consensus 299 qaa~pa~t~~~~r~~k~n--fc~ncG~~~t~~~~ng~a~fcp~cgq 342 (345)
T COG4260 299 QAAAPAATWPCARCAKLN--FCLNCGCGTTADFDNGKAKFCPECGQ 342 (345)
T ss_pred hhcCCcccCcchhccccc--cccccCcccccCCccchhhhChhhcC
Confidence 334566688999999887 6643221111 13467777753
No 45
>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=23.42 E-value=50 Score=26.28 Aligned_cols=30 Identities=23% Similarity=0.534 Sum_probs=16.7
Q ss_pred cCCCCCCCCCCceeeeecccCCCCCcchhhhhcc
Q 021974 38 ALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRR 71 (304)
Q Consensus 38 ~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrR 71 (304)
...||-|+..+..|..+.+- -++.|-+|.+
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k----~~~~Cf~Cg~ 62 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDK----NRFKCFGCGK 62 (97)
T ss_dssp EE--SSS--SS--EEEETTT----TEEEETTT--
T ss_pred EEECcCCCCCCCceEEECCC----CeEEECCCCC
Confidence 57799999887777666433 3799999985
No 46
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=22.95 E-value=55 Score=32.53 Aligned_cols=19 Identities=42% Similarity=0.807 Sum_probs=10.4
Q ss_pred CCCCCCcccCCCCCCCCCC
Q 021974 30 KPRPQPEQALKCPRCDSTN 48 (304)
Q Consensus 30 ~p~p~pe~~l~CPRC~S~n 48 (304)
.++-++++...||||...-
T Consensus 25 ~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 25 LPRIESGQKAACPRCGTTL 43 (403)
T ss_pred ccCCCCCCeeECCCCCCCC
Confidence 3444455566677776543
No 47
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=22.14 E-value=35 Score=32.96 Aligned_cols=33 Identities=24% Similarity=0.757 Sum_probs=12.8
Q ss_pred cCCCCCCCCC-CceeeeecccCCCCCcchhhhhccccc
Q 021974 38 ALKCPRCDST-NTKFCYYNNYSLSQPRYFCKSCRRYWT 74 (304)
Q Consensus 38 ~l~CPRC~S~-nTKFcYyNNys~~QPRhfCksCrRYWT 74 (304)
-..||+|.+. -.+| ..+.+-.-++|..|..=+-
T Consensus 31 n~yCP~Cg~~~L~~f----~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF----ENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp H---TTT--SS-EE------------EEE-TTT--EEE
T ss_pred CCcCCCCCChhHhhc----cCCCccceeECCCCchHHh
Confidence 4689999998 5665 3345566799999987654
No 48
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=21.49 E-value=35 Score=26.85 Aligned_cols=11 Identities=55% Similarity=1.322 Sum_probs=9.1
Q ss_pred cccCCCCCCCC
Q 021974 36 EQALKCPRCDS 46 (304)
Q Consensus 36 e~~l~CPRC~S 46 (304)
|.-+.||||+-
T Consensus 15 E~~lrCPRC~~ 25 (65)
T COG4049 15 EEFLRCPRCGM 25 (65)
T ss_pred ceeeeCCchhH
Confidence 45899999986
No 49
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=21.40 E-value=47 Score=26.33 Aligned_cols=44 Identities=16% Similarity=0.439 Sum_probs=20.6
Q ss_pred CCCCCCcccCCCCCCCCCCceeeeecccCCCCCcchhhhhccccc
Q 021974 30 KPRPQPEQALKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWT 74 (304)
Q Consensus 30 ~p~p~pe~~l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT 74 (304)
+.+++.+..-.||.|+..++=-|=... .......-|+.|.-.+.
T Consensus 14 k~~~~l~~~F~CPfC~~~~sV~v~idk-k~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 14 KKKPKLPKVFDCPFCNHEKSVSVKIDK-KEGIGILSCRVCGESFQ 57 (81)
T ss_dssp ------SS----TTT--SS-EEEEEET-TTTEEEEEESSS--EEE
T ss_pred CcCCCCCceEcCCcCCCCCeEEEEEEc-cCCEEEEEecCCCCeEE
Confidence 344455578999999988887776633 35566788999976654
No 50
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=21.15 E-value=63 Score=27.76 Aligned_cols=31 Identities=29% Similarity=0.743 Sum_probs=24.9
Q ss_pred CCCCCCCCCCceeeeecccCCCCCcchhhhhccccccCc
Q 021974 39 LKCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGG 77 (304)
Q Consensus 39 l~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYWT~GG 77 (304)
.+||.|.|..|-- .+.-+.|..|.-=|....
T Consensus 3 p~CP~C~seytY~--------dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTYH--------DGTQLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceEe--------cCCeeECccccccccccc
Confidence 5799999986632 355699999999999876
No 51
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.03 E-value=72 Score=22.09 Aligned_cols=14 Identities=36% Similarity=0.994 Sum_probs=10.6
Q ss_pred cccCCCCCCCCCCc
Q 021974 36 EQALKCPRCDSTNT 49 (304)
Q Consensus 36 e~~l~CPRC~S~nT 49 (304)
+....||+|.+.+.
T Consensus 24 ~~~~~CP~Cg~~~~ 37 (42)
T PF09723_consen 24 DDPVPCPECGSTEV 37 (42)
T ss_pred CCCCcCCCCCCCce
Confidence 45789999998443
No 52
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (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 seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=20.81 E-value=54 Score=22.52 Aligned_cols=28 Identities=29% Similarity=0.725 Sum_probs=18.7
Q ss_pred CCCCCCCCCceeeeecccCCCCCcchhhhhcccc
Q 021974 40 KCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYW 73 (304)
Q Consensus 40 ~CPRC~S~nTKFcYyNNys~~QPRhfCksCrRYW 73 (304)
.||.|.+...-+ . ..+--..|..|..-.
T Consensus 2 ~Cp~Cg~~~~~~---D---~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVF---D---PERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEEE---E---TTTTEEEETTT-BBE
T ss_pred CCcCCcCCceEE---c---CCCCeEECCCCCCEe
Confidence 699999976432 2 445667999996544
No 53
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=20.75 E-value=71 Score=27.69 Aligned_cols=37 Identities=27% Similarity=0.748 Sum_probs=26.4
Q ss_pred ccCCCCCCCCCCceeeeecccCCCCC-----cchhhhhcccccc
Q 021974 37 QALKCPRCDSTNTKFCYYNNYSLSQP-----RYFCKSCRRYWTK 75 (304)
Q Consensus 37 ~~l~CPRC~S~nTKFcYyNNys~~QP-----RhfCksCrRYWT~ 75 (304)
....||+|.....-| |+--+...- -|.|-+|.--||.
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 467899999988776 654322211 1899999999985
Done!