Query 021633
Match_columns 310
No_of_seqs 148 out of 256
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 04:29:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021633.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021633hhsearch_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 2.9E-37 6.3E-42 234.1 3.8 62 52-113 2-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 93.4 0.032 6.9E-07 48.1 0.9 34 55-90 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 93.1 0.085 1.8E-06 37.0 2.5 27 56-88 19-45 (46)
4 COG3677 Transposase and inacti 92.7 0.076 1.6E-06 44.9 2.2 35 56-92 31-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 91.8 0.11 2.4E-06 36.0 1.7 31 55-87 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 89.1 0.42 9.2E-06 33.2 2.8 37 56-92 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 86.6 0.55 1.2E-05 32.4 2.1 36 56-91 1-39 (39)
8 PF13453 zf-TFIIB: Transcripti 79.5 0.62 1.3E-05 31.9 0.1 37 57-98 1-37 (41)
9 PF04216 FdhE: Protein involve 79.4 0.95 2E-05 41.8 1.3 36 55-90 211-248 (290)
10 PHA02998 RNA polymerase subuni 78.8 2.1 4.6E-05 39.6 3.3 43 50-92 138-183 (195)
11 TIGR01384 TFS_arch transcripti 77.6 2.3 5E-05 33.5 2.8 39 55-93 62-103 (104)
12 cd00202 ZnF_GATA Zinc finger D 74.6 2.6 5.7E-05 31.1 2.2 40 57-99 1-40 (54)
13 PF04981 NMD3: NMD3 family ; 66.7 3 6.6E-05 37.7 1.3 26 69-94 19-49 (236)
14 PF14690 zf-ISL3: zinc-finger 66.6 2.9 6.3E-05 28.4 0.9 32 55-86 2-47 (47)
15 TIGR01385 TFSII transcription 60.1 7.4 0.00016 37.4 2.7 38 54-91 257-297 (299)
16 TIGR00244 transcriptional regu 59.5 6.7 0.00014 34.9 2.1 43 57-99 2-47 (147)
17 PF06220 zf-U1: U1 zinc finger 59.3 3.8 8.2E-05 28.5 0.4 17 78-94 1-17 (38)
18 PRK14810 formamidopyrimidine-D 57.5 6.9 0.00015 36.4 1.9 30 54-88 243-272 (272)
19 smart00401 ZnF_GATA zinc finge 57.1 7.9 0.00017 28.2 1.8 39 55-96 3-41 (52)
20 PRK14811 formamidopyrimidine-D 54.2 8.6 0.00019 35.7 2.0 29 55-88 235-263 (269)
21 PHA00626 hypothetical protein 52.0 10 0.00023 29.5 1.8 37 57-95 2-38 (59)
22 TIGR01562 FdhE formate dehydro 51.8 10 0.00023 36.6 2.2 37 54-91 223-263 (305)
23 PRK01103 formamidopyrimidine/5 51.1 10 0.00022 35.0 2.0 30 54-88 244-273 (274)
24 PRK00464 nrdR transcriptional 50.8 11 0.00024 33.2 2.0 45 56-100 1-48 (154)
25 PRK03564 formate dehydrogenase 50.4 11 0.00023 36.7 2.0 36 55-91 226-263 (309)
26 PRK10445 endonuclease VIII; Pr 49.5 11 0.00024 34.8 2.0 29 55-88 235-263 (263)
27 PRK13945 formamidopyrimidine-D 47.2 13 0.00029 34.6 2.1 29 55-88 254-282 (282)
28 PRK00432 30S ribosomal protein 44.5 12 0.00026 27.4 1.1 25 56-88 21-45 (50)
29 TIGR00577 fpg formamidopyrimid 41.1 18 0.0004 33.5 2.0 28 55-87 245-272 (272)
30 PF14599 zinc_ribbon_6: Zinc-r 39.8 12 0.00026 28.7 0.5 18 50-67 43-60 (61)
31 KOG2906 RNA polymerase III sub 39.7 24 0.00053 30.1 2.3 38 54-91 64-104 (105)
32 smart00064 FYVE Protein presen 34.1 36 0.00079 24.7 2.3 35 48-91 3-37 (68)
33 PF09526 DUF2387: Probable met 34.0 32 0.00069 27.0 2.1 31 55-88 8-38 (71)
34 COG1997 RPL43A Ribosomal prote 33.5 24 0.00053 29.4 1.4 42 54-102 34-75 (89)
35 COG0094 RplE Ribosomal protein 33.1 34 0.00073 31.6 2.4 31 235-265 121-154 (180)
36 PF07282 OrfB_Zn_ribbon: Putat 33.0 26 0.00056 25.6 1.4 32 54-92 27-58 (69)
37 TIGR00155 pqiA_fam integral me 32.7 42 0.00091 33.3 3.1 19 49-67 27-45 (403)
38 COG1327 Predicted transcriptio 29.8 32 0.0007 31.1 1.7 44 57-100 2-48 (156)
39 PF06827 zf-FPG_IleRS: Zinc fi 29.5 26 0.00057 22.4 0.8 27 56-87 2-28 (30)
40 PF08274 PhnA_Zn_Ribbon: PhnA 28.9 26 0.00057 23.7 0.7 28 56-91 3-30 (30)
41 COG0266 Nei Formamidopyrimidin 28.5 36 0.00079 32.7 1.9 30 54-88 244-273 (273)
42 TIGR03655 anti_R_Lar restricti 28.1 52 0.0011 23.6 2.2 33 56-89 2-35 (53)
43 PF01807 zf-CHC2: CHC2 zinc fi 27.0 43 0.00094 26.6 1.8 30 55-88 33-62 (97)
44 PF14354 Lar_restr_allev: Rest 26.2 61 0.0013 23.1 2.3 35 54-88 2-37 (61)
45 PF08273 Prim_Zn_Ribbon: Zinc- 24.9 53 0.0011 23.4 1.7 32 55-88 3-34 (40)
46 COG5426 Uncharacterized membra 24.0 44 0.00095 32.0 1.5 71 183-277 98-177 (254)
47 PF05129 Elf1: Transcription e 23.5 50 0.0011 26.2 1.5 42 49-91 16-57 (81)
48 TIGR00686 phnA alkylphosphonat 23.0 54 0.0012 28.2 1.7 31 56-94 3-33 (109)
49 PF06044 DRP: Dam-replacing fa 22.8 34 0.00074 33.0 0.6 33 55-91 31-64 (254)
50 PRK10220 hypothetical protein; 22.3 60 0.0013 28.1 1.8 31 56-94 4-34 (111)
51 KOG1819 FYVE finger-containing 22.1 56 0.0012 35.2 2.0 46 47-101 893-938 (990)
52 PRK14892 putative transcriptio 21.3 71 0.0015 26.6 2.0 37 51-91 17-53 (99)
53 PF01873 eIF-5_eIF-2B: Domain 20.8 89 0.0019 26.7 2.6 31 54-88 92-122 (125)
54 KOG2691 RNA polymerase II subu 20.3 73 0.0016 27.6 2.0 37 54-92 72-113 (113)
55 PF08271 TF_Zn_Ribbon: TFIIB z 20.3 67 0.0015 22.0 1.5 28 57-90 2-29 (43)
56 smart00661 RPOL9 RNA polymeras 20.2 72 0.0016 21.9 1.6 32 57-93 2-33 (52)
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=2.9e-37 Score=234.13 Aligned_cols=62 Identities=82% Similarity=1.625 Sum_probs=59.3
Q ss_pred CCCCcCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCCCCcccCCCCCC
Q 021633 52 HDQALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTLRNIPVGGGCRKNKKVSS 113 (310)
Q Consensus 52 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~GGtLRNVPVGGG~RKnkr~ss 113 (310)
++++++||||+|.+|||||||||+++||||||++|+||||+||+|||||||||+||+|++++
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 46789999999999999999999999999999999999999999999999999999998764
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=93.38 E-value=0.032 Score=48.12 Aligned_cols=34 Identities=26% Similarity=0.821 Sum_probs=27.1
Q ss_pred CcCCCCCCCCCceeeeeccc--CCCCCccccccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNY--SLSQPRYFCKTCRRYW 90 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy--~~~QPR~fCksCrRyW 90 (310)
...||||.|.+|+.. +.+ +.++.-|+|++|+.=+
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 589999999999964 566 4457779999998644
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=93.06 E-value=0.085 Score=37.00 Aligned_cols=27 Identities=44% Similarity=1.009 Sum_probs=22.1
Q ss_pred cCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
..||+|.+. +...+.+ +.+|.|+.|++
T Consensus 19 ~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 679999998 6655555 78999999986
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.74 E-value=0.076 Score=44.93 Aligned_cols=35 Identities=31% Similarity=0.742 Sum_probs=27.8
Q ss_pred cCCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTK 92 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~ 92 (310)
..||+|.+.+ +-=+.-+.....||.|++|++-||.
T Consensus 31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred CcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 7899999999 2234555555999999999999874
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=91.79 E-value=0.11 Score=35.98 Aligned_cols=31 Identities=48% Similarity=0.879 Sum_probs=21.6
Q ss_pred CcCCCCCCCCCceeeeecccCCC-CCcccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLS-QPRYFCKTCR 87 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~-QPR~fCksCr 87 (310)
.+.||+|.+++.- |=|-.+.. ..||+|++|+
T Consensus 5 ~v~CP~C~s~~~v--~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEGV--KKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCcc--eeCCCCCCCCEeEecCcCC
Confidence 3789999998721 23344433 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.13 E-value=0.42 Score=33.22 Aligned_cols=37 Identities=27% Similarity=0.801 Sum_probs=27.8
Q ss_pred cCCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQP---RYFCKTCRRYWTK 92 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QP---R~fCksCrRyWT~ 92 (310)
.+||+|...+.-|-..+-.+...| -|.|..|...|.+
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 4999999999964
No 7
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=86.63 E-value=0.55 Score=32.40 Aligned_cols=36 Identities=31% Similarity=0.849 Sum_probs=24.1
Q ss_pred cCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQPR---YFCKTCRRYWT 91 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QPR---~fCksCrRyWT 91 (310)
.+||.|...+.-|=-.+..+...|- |.|.+|..-|+
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 3799999987766545555555443 89999999985
No 8
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=79.53 E-value=0.62 Score=31.94 Aligned_cols=37 Identities=27% Similarity=0.633 Sum_probs=27.4
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCccccc
Q 021633 57 KCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTLRN 98 (310)
Q Consensus 57 ~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~GGtLRN 98 (310)
+||+|...-...-+ ..-+-+.|..|.-.|=..+.+..
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 23566889999999988776643
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=79.38 E-value=0.95 Score=41.78 Aligned_cols=36 Identities=31% Similarity=0.710 Sum_probs=18.3
Q ss_pred CcCCCCCCCC-CceeeeecccCCC-CCccccccccccc
Q 021633 55 ALKCPRCDST-HTKFCYYNNYSLS-QPRYFCKTCRRYW 90 (310)
Q Consensus 55 ~~~CPRC~S~-nTKFcYyNNy~~~-QPR~fCksCrRyW 90 (310)
...||.|... ..++-||..-... .--+.|++|+.|+
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchH
Confidence 4789999985 4567777433333 3349999999998
No 10
>PHA02998 RNA polymerase subunit; Provisional
Probab=78.76 E-value=2.1 Score=39.56 Aligned_cols=43 Identities=19% Similarity=0.478 Sum_probs=35.4
Q ss_pred CCCCCCcCCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 021633 50 PPHDQALKCPRCDSTHTKFCYYNNYSLSQPR---YFCKTCRRYWTK 92 (310)
Q Consensus 50 pp~~~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCksCrRyWT~ 92 (310)
.|.....+||+|...++-|--.|-.+-..|- |.|..|..-|.-
T Consensus 138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 3444569999999999998888888888775 899999999963
No 11
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=77.62 E-value=2.3 Score=33.53 Aligned_cols=39 Identities=21% Similarity=0.700 Sum_probs=28.3
Q ss_pred CcCCCCCCCCCceeeeecccCCCCCc---ccccccccccccC
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLSQPR---YFCKTCRRYWTKG 93 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCksCrRyWT~G 93 (310)
..+||+|...+.-|-..+-.+-..|- |.|..|.-.|+++
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 48999998777666554544433333 9999999999875
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=74.56 E-value=2.6 Score=31.06 Aligned_cols=40 Identities=30% Similarity=0.709 Sum_probs=27.9
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccc
Q 021633 57 KCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTLRNI 99 (310)
Q Consensus 57 ~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~GGtLRNV 99 (310)
.|-.|...+|..=.-. ...+..+|-+|.-||.+.|..|.+
T Consensus 1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~ 40 (54)
T cd00202 1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPL 40 (54)
T ss_pred CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCc
Confidence 3677877777532221 246779999999999999965544
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=66.67 E-value=3 Score=37.66 Aligned_cols=26 Identities=27% Similarity=0.790 Sum_probs=17.9
Q ss_pred eeecccCCCC-----CcccccccccccccCc
Q 021633 69 CYYNNYSLSQ-----PRYFCKTCRRYWTKGG 94 (310)
Q Consensus 69 cYyNNy~~~Q-----PR~fCksCrRyWT~GG 94 (310)
||...+.+.. --.+|+.|.||+..|.
T Consensus 19 C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 19 CYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred HhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 5555555543 2379999999999843
No 14
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=66.56 E-value=2.9 Score=28.42 Aligned_cols=32 Identities=31% Similarity=0.762 Sum_probs=19.3
Q ss_pred CcCCCCCCCCCcee-eeeccc-------------CCCCCccccccc
Q 021633 55 ALKCPRCDSTHTKF-CYYNNY-------------SLSQPRYFCKTC 86 (310)
Q Consensus 55 ~~~CPRC~S~nTKF-cYyNNy-------------~~~QPR~fCksC 86 (310)
+..||.|.+...+. -++... .+..+|++|++|
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 46899999876221 111111 345778888887
No 15
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=60.13 E-value=7.4 Score=37.37 Aligned_cols=38 Identities=18% Similarity=0.622 Sum_probs=28.2
Q ss_pred CCcCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQPR---YFCKTCRRYWT 91 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCksCrRyWT 91 (310)
...+||+|...+..|-..+..+-..|- |.|..|...|.
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 348999999887776555555555553 78999999984
No 16
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=59.54 E-value=6.7 Score=34.88 Aligned_cols=43 Identities=19% Similarity=0.332 Sum_probs=31.3
Q ss_pred CCCCCCCCCceeeee---cccCCCCCcccccccccccccCcccccc
Q 021633 57 KCPRCDSTHTKFCYY---NNYSLSQPRYFCKTCRRYWTKGGTLRNI 99 (310)
Q Consensus 57 ~CPRC~S~nTKFcYy---NNy~~~QPR~fCksCrRyWT~GGtLRNV 99 (310)
+||.|...+||+-== ..-+..+-|..|..|.+-||-==++-..
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELL 47 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecccc
Confidence 699999999998532 3344456779999999999865544333
No 17
>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=59.30 E-value=3.8 Score=28.47 Aligned_cols=17 Identities=41% Similarity=1.212 Sum_probs=7.2
Q ss_pred CCcccccccccccccCc
Q 021633 78 QPRYFCKTCRRYWTKGG 94 (310)
Q Consensus 78 QPR~fCksCrRyWT~GG 94 (310)
+|||||.-|..|.|..-
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 18
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=57.49 E-value=6.9 Score=36.36 Aligned_cols=30 Identities=13% Similarity=0.541 Sum_probs=22.0
Q ss_pred CCcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
+..+||||...=.|.-+= .+.-|||..|++
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 457899999866654432 366699999985
No 19
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=57.10 E-value=7.9 Score=28.16 Aligned_cols=39 Identities=28% Similarity=0.612 Sum_probs=28.7
Q ss_pred CcCCCCCCCCCceeeeecccCCCCCcccccccccccccCccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTL 96 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~GGtL 96 (310)
+..|--|....|..=. ....-++.+|-+|.-||.+.|.+
T Consensus 3 ~~~C~~C~~~~T~~WR---~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 3 GRSCSNCGTTETPLWR---RGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCcCCCCCCCCCccc---cCCCCCCcEeecccHHHHHcCCC
Confidence 5789999988885321 12233369999999999998876
No 20
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=54.16 E-value=8.6 Score=35.73 Aligned_cols=29 Identities=28% Similarity=0.740 Sum_probs=21.6
Q ss_pred CcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
..+||||...=.|.-+ . .+.-|||..|++
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 21
>PHA00626 hypothetical protein
Probab=52.02 E-value=10 Score=29.50 Aligned_cols=37 Identities=22% Similarity=0.320 Sum_probs=24.6
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccCcc
Q 021633 57 KCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGT 95 (310)
Q Consensus 57 ~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~GGt 95 (310)
.||.|.|.+--=|=.= ....-||.|++|.=.+|+..-
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 6999999754321110 112457999999999998643
No 22
>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=51.79 E-value=10 Score=36.62 Aligned_cols=37 Identities=19% Similarity=0.547 Sum_probs=24.6
Q ss_pred CCcCCCCCCCCCceeeeecccC----CCCCcccccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYS----LSQPRYFCKTCRRYWT 91 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~----~~QPR~fCksCrRyWT 91 (310)
...+||.|.+.+ +.-|+.--. ..---..|.+|+.|+-
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 358899999864 555665432 1122278999999974
No 23
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=51.07 E-value=10 Score=35.02 Aligned_cols=30 Identities=23% Similarity=0.730 Sum_probs=21.7
Q ss_pred CCcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
...+||+|...=.|.- ++ .+.-|||..|++
T Consensus 244 ~g~pC~~Cg~~I~~~~-~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPIEKIK-QG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCeeEEEE-EC----CCCcEECcCCCC
Confidence 3468999998765533 33 366799999986
No 24
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=50.76 E-value=11 Score=33.22 Aligned_cols=45 Identities=20% Similarity=0.446 Sum_probs=32.0
Q ss_pred cCCCCCCCCCceee---eecccCCCCCcccccccccccccCccccccc
Q 021633 56 LKCPRCDSTHTKFC---YYNNYSLSQPRYFCKTCRRYWTKGGTLRNIP 100 (310)
Q Consensus 56 ~~CPRC~S~nTKFc---YyNNy~~~QPR~fCksCrRyWT~GGtLRNVP 100 (310)
.+||-|.+..|++- |+-.-++-.-||.|+.|.+-++.==++-..+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 37999999887764 4444444556699999999888766554444
No 25
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=50.36 E-value=11 Score=36.73 Aligned_cols=36 Identities=25% Similarity=0.594 Sum_probs=23.9
Q ss_pred CcCCCCCCCCCceeeeecccC--CCCCcccccccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYS--LSQPRYFCKTCRRYWT 91 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~--~~QPR~fCksCrRyWT 91 (310)
..+||.|... .|.-|+.--. ..---+.|.+|+.|+-
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 5789999974 4666663222 1222389999999974
No 26
>PRK10445 endonuclease VIII; Provisional
Probab=49.52 E-value=11 Score=34.82 Aligned_cols=29 Identities=31% Similarity=0.787 Sum_probs=21.5
Q ss_pred CcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
...||||...=.|.-+ . .+.-|||..|++
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 4679999987666544 2 366799999984
No 27
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=47.21 E-value=13 Score=34.61 Aligned_cols=29 Identities=14% Similarity=0.602 Sum_probs=21.5
Q ss_pred CcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
..+||||...=.|.-+ -.+.-|||..|++
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 4689999987666544 1266699999985
No 28
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=44.45 E-value=12 Score=27.42 Aligned_cols=25 Identities=36% Similarity=0.769 Sum_probs=18.2
Q ss_pred cCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
.-||+|.+. |..-.. .|+.|..|..
T Consensus 21 ~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 21 KFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred CcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 589999873 544443 6999999974
No 29
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.08 E-value=18 Score=33.54 Aligned_cols=28 Identities=25% Similarity=0.629 Sum_probs=20.8
Q ss_pred CcCCCCCCCCCceeeeecccCCCCCcccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCR 87 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCr 87 (310)
..+||||...=.|.-+ . .+.-|||..|+
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 4689999987666443 2 36679999996
No 30
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=39.84 E-value=12 Score=28.73 Aligned_cols=18 Identities=39% Similarity=0.672 Sum_probs=7.5
Q ss_pred CCCCCCcCCCCCCCCCce
Q 021633 50 PPHDQALKCPRCDSTHTK 67 (310)
Q Consensus 50 pp~~~~~~CPRC~S~nTK 67 (310)
+-+--..+|+.|.|.||+
T Consensus 43 ~fH~lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 43 PFHFLGHKCSHCGSYNTR 60 (61)
T ss_dssp E--TT----TTTS---EE
T ss_pred eeeHhhhcCCCCCCcccC
Confidence 356678999999999997
No 31
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=39.73 E-value=24 Score=30.15 Aligned_cols=38 Identities=26% Similarity=0.714 Sum_probs=32.5
Q ss_pred CCcCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQPR---YFCKTCRRYWT 91 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCksCrRyWT 91 (310)
-...||+|.....-|--+|-.+-.-|- |.|-.|+--|-
T Consensus 64 t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 64 TEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred ccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 347899999999988888888888776 89999999885
No 32
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=33.98 E-value=32 Score=26.99 Aligned_cols=31 Identities=23% Similarity=0.500 Sum_probs=25.0
Q ss_pred CcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
+..||+|.+.+|=..|..|. ..-.-|-.|.=
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 57899999999888888776 55667888853
No 34
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=33.48 E-value=24 Score=29.37 Aligned_cols=42 Identities=24% Similarity=0.546 Sum_probs=31.2
Q ss_pred CCcCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCC
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTLRNIPVG 102 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~GGtLRNVPVG 102 (310)
+...||-|.+...| -...---.|+-|..-|+.|+-....|.|
T Consensus 34 ~~~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 34 AKHVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred cCCcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 45789999998555 1222338899999999999987766654
No 35
>COG0094 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=33.08 E-value=34 Score=31.56 Aligned_cols=31 Identities=29% Similarity=0.473 Sum_probs=24.6
Q ss_pred cccCCCCccccccceeecc---CCcccccccccc
Q 021633 235 SLDGTGGTFIDGCQRIMLP---YDANEVQNAIDV 265 (310)
Q Consensus 235 s~~g~~~~~~~~cqrlmlp---y~~~~~~~~~dv 265 (310)
||||.|.|-++.-+++.+| ||..+.--.|||
T Consensus 121 sFDg~GN~sfGI~E~i~FPei~yD~~~~i~GMdi 154 (180)
T COG0094 121 SFDGRGNYSFGIKEQIIFPEIDYDPIIGIRGMDI 154 (180)
T ss_pred ccCCCCceEecchheeecCccccCccCCccCceE
Confidence 7899999999999999999 775544455665
No 36
>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=33.05 E-value=26 Score=25.58 Aligned_cols=32 Identities=25% Similarity=0.580 Sum_probs=23.9
Q ss_pred CCcCCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTK 92 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~ 92 (310)
....||.|.....+ .+.+-.+.|..|...+.+
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 34679999987777 666777889999876543
No 37
>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=32.65 E-value=42 Score=33.26 Aligned_cols=19 Identities=42% Similarity=0.711 Sum_probs=11.3
Q ss_pred CCCCCCCcCCCCCCCCCce
Q 021633 49 RPPHDQALKCPRCDSTHTK 67 (310)
Q Consensus 49 ~pp~~~~~~CPRC~S~nTK 67 (310)
+.++.+...||||.+.-.+
T Consensus 27 ~l~~g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 27 RIESGQKAACPRCGTTLTV 45 (403)
T ss_pred CCCCCCeeECCCCCCCCcC
Confidence 3344556778888765433
No 38
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=29.80 E-value=32 Score=31.10 Aligned_cols=44 Identities=25% Similarity=0.349 Sum_probs=30.3
Q ss_pred CCCCCCCCCceeeee---cccCCCCCcccccccccccccCccccccc
Q 021633 57 KCPRCDSTHTKFCYY---NNYSLSQPRYFCKTCRRYWTKGGTLRNIP 100 (310)
Q Consensus 57 ~CPRC~S~nTKFcYy---NNy~~~QPR~fCksCrRyWT~GGtLRNVP 100 (310)
.||.|.+.+||+-== ..-+..+-|.-|-+|..-+|-==++--+|
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~ 48 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRP 48 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeecc
Confidence 699999999998421 11233456789999998888655544443
No 39
>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=29.51 E-value=26 Score=22.41 Aligned_cols=27 Identities=30% Similarity=0.743 Sum_probs=13.8
Q ss_pred cCCCCCCCCCceeeeecccCCCCCcccccccc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCR 87 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCr 87 (310)
.+||||...-.++-..+ +.-+||..|+
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 47899988776654421 2336777775
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=28.94 E-value=26 Score=23.66 Aligned_cols=28 Identities=32% Similarity=0.687 Sum_probs=14.7
Q ss_pred cCCCCCCCCCceeeeecccCCCCCcccccccccccc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWT 91 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT 91 (310)
-+||-|.|..|= ...--+.|..|..=|+
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 479999998775 4567789999987774
No 41
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=28.48 E-value=36 Score=32.75 Aligned_cols=30 Identities=20% Similarity=0.633 Sum_probs=21.3
Q ss_pred CCcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
+..+|++|.+.=.|-- --.+..|||..|++
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 4578999999554431 12367799999985
No 42
>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=28.07 E-value=52 Score=23.62 Aligned_cols=33 Identities=27% Similarity=0.584 Sum_probs=19.4
Q ss_pred cCCCCCCCCCceeeeecccCCCCCccc-ccccccc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQPRYF-CKTCRRY 89 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QPR~f-CksCrRy 89 (310)
.+||.|.+..-.|=+ ........+++ |..|...
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCCC
Confidence 579999997665532 12233334444 8877643
No 43
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=26.99 E-value=43 Score=26.62 Aligned_cols=30 Identities=23% Similarity=0.508 Sum_probs=16.9
Q ss_pred CcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
...||-|+..+..|..+.+- -++.|-+|.+
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 47799999887777776543 3899999985
No 44
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=26.22 E-value=61 Score=23.15 Aligned_cols=35 Identities=17% Similarity=0.369 Sum_probs=19.7
Q ss_pred CCcCCCCCCCCCceeeeecccCCCC-Cccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQ-PRYFCKTCRR 88 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~Q-PR~fCksCrR 88 (310)
+-.+||.|.+....+.+........ -.-+|..|..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4578999966655554422211111 3445888866
No 45
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=24.93 E-value=53 Score=23.39 Aligned_cols=32 Identities=19% Similarity=0.652 Sum_probs=18.2
Q ss_pred CcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 55 ALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 55 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
..+||-|.. ..+|..|-+. ..+-..+|+.|..
T Consensus 3 h~pCP~CGG-~DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 3 HGPCPICGG-KDRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp EE--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCCcC-ccccccCcCc-ccCCCEECCCCCC
Confidence 468999988 5688866543 3347899999943
No 46
>COG5426 Uncharacterized membrane protein [Function unknown]
Probab=23.98 E-value=44 Score=32.04 Aligned_cols=71 Identities=34% Similarity=0.499 Sum_probs=45.7
Q ss_pred hHHHHhhcccccccccCCCCCCccccCCCCCccccCCCCC--cccccCCCCCcccccCCCCccccccceeeccCCccccc
Q 021633 183 NKLEAIVGSSRNYDFMGNNGDMGMVGGLGNLSHHHQEGLT--PNVHNLCSPFGMSLDGTGGTFIDGCQRIMLPYDANEVQ 260 (310)
Q Consensus 183 ~kle~~~gss~~~~f~g~~~~~gm~~g~g~~~~~~~~gl~--~n~h~l~~~~g~s~~g~~~~~~~~cqrlmlpy~~~~~~ 260 (310)
++|+-| .|+.+|.|-+=|.+|- .+- .|+. ++||+ .-+.|.---.|||.|+|.|-
T Consensus 98 n~L~li------kdyV~~GGGLLMiGGY--~SF---~GIe~kA~yk~-------------T~v~dvLPV~~L~~DDRVE~ 153 (254)
T COG5426 98 NRLKLI------KDYVENGGGLLMIGGY--LSF---QGIEGKARYKN-------------TPVEDVLPVTCLPVDDRVEI 153 (254)
T ss_pred cHHHHH------HHHHhcCCcEEEEccE--EEE---eeecccccccc-------------CcHhhccceeeeccccceec
Confidence 457777 7788886666666551 000 1222 56655 55677777779999987665
Q ss_pred ----ccccccCCc---cccccccc
Q 021633 261 ----NAIDVKPNA---KLLSLDWQ 277 (310)
Q Consensus 261 ----~~~dvkp~~---kllsl~wq 277 (310)
.++-|||.- +=||=||-
T Consensus 154 PeG~~a~~v~peHpiv~g~s~ewP 177 (254)
T COG5426 154 PEGSTAVIVKPEHPIVAGLSGEWP 177 (254)
T ss_pred CCCccccccCCCCceecCCCCCCC
Confidence 568888854 55687885
No 47
>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=23.53 E-value=50 Score=26.18 Aligned_cols=42 Identities=14% Similarity=0.430 Sum_probs=20.8
Q ss_pred CCCCCCCcCCCCCCCCCceeeeecccCCCCCcccccccccccc
Q 021633 49 RPPHDQALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWT 91 (310)
Q Consensus 49 ~pp~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT 91 (310)
+++.+..-.||.|+..++=-|=... ......--|+.|.-.+.
T Consensus 16 ~~~l~~~F~CPfC~~~~sV~v~idk-k~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 16 KPKLPKVFDCPFCNHEKSVSVKIDK-KEGIGILSCRVCGESFQ 57 (81)
T ss_dssp ----SS----TTT--SS-EEEEEET-TTTEEEEEESSS--EEE
T ss_pred CCCCCceEcCCcCCCCCeEEEEEEc-cCCEEEEEecCCCCeEE
Confidence 3444567999999988887776643 35566788999976654
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=22.99 E-value=54 Score=28.21 Aligned_cols=31 Identities=26% Similarity=0.727 Sum_probs=24.9
Q ss_pred cCCCCCCCCCceeeeecccCCCCCcccccccccccccCc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGG 94 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~GG 94 (310)
..||.|.|..|-- .+.-+.|..|.-=|....
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 4799999986631 355699999999999876
No 49
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=22.85 E-value=34 Score=33.02 Aligned_cols=33 Identities=24% Similarity=0.765 Sum_probs=12.7
Q ss_pred CcCCCCCCCC-CceeeeecccCCCCCcccccccccccc
Q 021633 55 ALKCPRCDST-HTKFCYYNNYSLSQPRYFCKTCRRYWT 91 (310)
Q Consensus 55 ~~~CPRC~S~-nTKFcYyNNy~~~QPR~fCksCrRyWT 91 (310)
...||.|.+. -.+| ..+.+-.-++|..|..=+-
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 4789999997 5665 3345566799999987654
No 50
>PRK10220 hypothetical protein; Provisional
Probab=22.29 E-value=60 Score=28.06 Aligned_cols=31 Identities=29% Similarity=0.779 Sum_probs=24.9
Q ss_pred cCCCCCCCCCceeeeecccCCCCCcccccccccccccCc
Q 021633 56 LKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGG 94 (310)
Q Consensus 56 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~GG 94 (310)
..||.|.|..|- ..+.-+.|..|.-=|+..-
T Consensus 4 P~CP~C~seytY--------~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTY--------EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceE--------cCCCeEECCcccCcCCccc
Confidence 579999998663 2356799999999998775
No 51
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=22.09 E-value=56 Score=35.20 Aligned_cols=46 Identities=20% Similarity=0.498 Sum_probs=30.5
Q ss_pred cCCCCCCCCcCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccC
Q 021633 47 RLRPPHDQALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTLRNIPV 101 (310)
Q Consensus 47 ~~~pp~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~GGtLRNVPV 101 (310)
+.|-|.+...+|-.|...-+-| +-||-|++|.+.|-.--.--..|+
T Consensus 893 pawipd~~a~~cmacq~pf~af---------rrrhhcrncggifcg~cs~asapi 938 (990)
T KOG1819|consen 893 PAWIPDEDAEQCMACQMPFNAF---------RRRHHCRNCGGIFCGKCSCASAPI 938 (990)
T ss_pred cccCCCCcchhhhhccCcHHHH---------HHhhhhcccCceeecccccCCCCC
Confidence 3455666667777777665554 789999999988765443333333
No 52
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.30 E-value=71 Score=26.59 Aligned_cols=37 Identities=19% Similarity=0.424 Sum_probs=25.0
Q ss_pred CCCCCcCCCCCCCCCceeeeecccCCCCCcccccccccccc
Q 021633 51 PHDQALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWT 91 (310)
Q Consensus 51 p~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT 91 (310)
..+....||.|.+ .+--|=... ..+.+.|..|.-|..
T Consensus 17 klpt~f~CP~Cge-~~v~v~~~k---~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 17 KLPKIFECPRCGK-VSISVKIKK---NIAIITCGNCGLYTE 53 (99)
T ss_pred CCCcEeECCCCCC-eEeeeecCC---CcceEECCCCCCccC
Confidence 3346789999995 233233333 478999999998843
No 53
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=20.75 E-value=89 Score=26.65 Aligned_cols=31 Identities=26% Similarity=0.460 Sum_probs=21.6
Q ss_pred CCcCCCCCCCCCceeeeecccCCCCCccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRR 88 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrR 88 (310)
+-+.||-|.+.+|.+--- ..---..|++|..
T Consensus 92 ~yVlC~~C~spdT~l~k~----~r~~~l~C~aCGa 122 (125)
T PF01873_consen 92 EYVLCPECGSPDTELIKE----GRLIFLKCKACGA 122 (125)
T ss_dssp HHSSCTSTSSSSEEEEEE----TTCCEEEETTTSC
T ss_pred HEEEcCCCCCCccEEEEc----CCEEEEEecccCC
Confidence 348999999999997543 1223367888863
No 54
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=20.35 E-value=73 Score=27.64 Aligned_cols=37 Identities=24% Similarity=0.737 Sum_probs=26.1
Q ss_pred CCcCCCCCCCCCceeeeecccCCCCC-----ccccccccccccc
Q 021633 54 QALKCPRCDSTHTKFCYYNNYSLSQP-----RYFCKTCRRYWTK 92 (310)
Q Consensus 54 ~~~~CPRC~S~nTKFcYyNNy~~~QP-----R~fCksCrRyWT~ 92 (310)
.-..||+|...+.-| ||--+...- -|.|-+|.--||+
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 457899999987664 654332211 1899999999985
No 55
>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=20.31 E-value=67 Score=22.05 Aligned_cols=28 Identities=29% Similarity=0.650 Sum_probs=18.5
Q ss_pred CCCCCCCCCceeeeecccCCCCCccccccccccc
Q 021633 57 KCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYW 90 (310)
Q Consensus 57 ~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyW 90 (310)
.||.|.+...-+. ..+--+.|..|..-.
T Consensus 2 ~Cp~Cg~~~~~~D------~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVFD------PERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEEEE------TTTTEEEETTT-BBE
T ss_pred CCcCCcCCceEEc------CCCCeEECCCCCCEe
Confidence 6999999764322 445667999996543
No 56
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.18 E-value=72 Score=21.92 Aligned_cols=32 Identities=19% Similarity=0.511 Sum_probs=17.8
Q ss_pred CCCCCCCCCceeeeecccCCCCCcccccccccccccC
Q 021633 57 KCPRCDSTHTKFCYYNNYSLSQPRYFCKTCRRYWTKG 93 (310)
Q Consensus 57 ~CPRC~S~nTKFcYyNNy~~~QPR~fCksCrRyWT~G 93 (310)
-||.|.+ ..|..... ...|+.|..|...+-..
T Consensus 2 FCp~Cg~----~l~~~~~~-~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGN----MLIPKEGK-EKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCC----ccccccCC-CCCEEECCcCCCeEECC
Confidence 4888866 22332211 11478888888665443
Done!