Query 022872
Match_columns 291
No_of_seqs 129 out of 254
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 06:45:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022872.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022872hhsearch_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 2.5E-37 5.3E-42 233.1 4.2 63 25-87 1-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 92.7 0.048 1E-06 47.1 1.1 34 29-64 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 92.1 0.12 2.5E-06 36.3 2.2 29 28-62 17-45 (46)
4 PF03811 Zn_Tnp_IS1: InsA N-te 91.8 0.094 2E-06 36.1 1.4 30 30-61 6-36 (36)
5 COG3677 Transposase and inacti 91.3 0.13 2.9E-06 43.5 2.1 35 30-66 31-65 (129)
6 smart00440 ZnF_C2C2 C2C2 Zinc 88.5 0.39 8.5E-06 33.2 2.3 37 30-66 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 85.9 0.48 1E-05 32.6 1.5 36 30-65 1-39 (39)
8 TIGR01384 TFS_arch transcripti 80.7 1.7 3.7E-05 34.4 2.9 39 29-67 62-103 (104)
9 PHA02998 RNA polymerase subuni 77.3 1.9 4.2E-05 39.6 2.6 38 29-66 143-183 (195)
10 cd00202 ZnF_GATA Zinc finger D 74.8 3.2 7E-05 30.5 2.7 41 31-74 1-41 (54)
11 PF13453 zf-TFIIB: Transcripti 71.7 1.1 2.4E-05 30.7 -0.3 37 31-72 1-37 (41)
12 TIGR01385 TFSII transcription 60.6 6.2 0.00013 37.9 2.3 36 30-65 259-297 (299)
13 PF04981 NMD3: NMD3 family ; 59.6 4.4 9.5E-05 36.8 1.0 26 43-68 19-49 (236)
14 PHA00626 hypothetical protein 56.8 7.3 0.00016 30.0 1.6 36 31-68 2-37 (59)
15 PF04216 FdhE: Protein involve 55.3 5.1 0.00011 37.2 0.8 36 30-65 212-249 (290)
16 smart00401 ZnF_GATA zinc finge 54.1 8.9 0.00019 27.8 1.7 39 29-70 3-41 (52)
17 TIGR01562 FdhE formate dehydro 48.2 12 0.00026 36.2 2.1 35 30-65 225-263 (305)
18 TIGR00244 transcriptional regu 47.9 12 0.00027 33.1 1.9 40 31-70 2-44 (147)
19 PF06220 zf-U1: U1 zinc finger 47.5 7 0.00015 27.0 0.3 17 52-68 1-17 (38)
20 PRK14811 formamidopyrimidine-D 44.4 13 0.00028 34.7 1.6 28 30-62 236-263 (269)
21 PF14690 zf-ISL3: zinc-finger 43.7 9.1 0.0002 26.0 0.4 10 30-39 3-12 (47)
22 KOG2906 RNA polymerase III sub 43.2 23 0.0005 30.0 2.7 37 29-65 65-104 (105)
23 PRK03564 formate dehydrogenase 43.2 15 0.00033 35.7 1.9 36 30-66 227-264 (309)
24 PRK00464 nrdR transcriptional 41.4 19 0.00041 31.7 2.1 44 30-73 1-47 (154)
25 PRK00432 30S ribosomal protein 39.2 14 0.00031 26.9 0.8 25 30-62 21-45 (50)
26 PF09526 DUF2387: Probable met 38.5 21 0.00046 27.8 1.7 31 29-62 8-38 (71)
27 PF14599 zinc_ribbon_6: Zinc-r 35.3 15 0.00032 28.1 0.4 12 30-41 49-60 (61)
28 KOG2691 RNA polymerase II subu 30.8 33 0.00071 29.5 1.8 36 29-66 73-113 (113)
29 PF05129 Elf1: Transcription e 30.5 26 0.00056 27.7 1.1 45 20-65 13-57 (81)
30 PF06682 DUF1183: Protein of u 27.6 20 0.00043 35.1 -0.0 40 19-58 38-84 (318)
31 PF10613 Lig_chan-Glu_bd: Liga 25.4 16 0.00035 27.9 -0.9 9 279-287 53-61 (65)
32 TIGR03655 anti_R_Lar restricti 25.2 55 0.0012 23.4 1.9 32 30-62 2-34 (53)
33 COG1327 Predicted transcriptio 24.9 45 0.00097 30.1 1.7 40 31-70 2-44 (156)
34 COG1997 RPL43A Ribosomal prote 24.6 35 0.00077 28.2 0.9 40 30-76 36-75 (89)
35 PF06827 zf-FPG_IleRS: Zinc fi 23.6 34 0.00074 21.7 0.5 27 30-61 2-28 (30)
36 PF07282 OrfB_Zn_ribbon: Putat 23.2 43 0.00093 24.4 1.0 30 30-66 29-58 (69)
37 TIGR00686 phnA alkylphosphonat 23.0 48 0.001 28.3 1.4 30 31-68 4-33 (109)
38 PF08273 Prim_Zn_Ribbon: Zinc- 21.8 61 0.0013 22.9 1.5 31 30-62 4-34 (40)
39 TIGR02443 conserved hypothetic 21.5 67 0.0015 24.8 1.8 30 29-61 9-38 (59)
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=2.5e-37 Score=233.05 Aligned_cols=63 Identities=79% Similarity=1.583 Sum_probs=60.2
Q ss_pred CCccCCCCCCCCCCCcceeeecccCCCCCchhhhccccccccCCccccccCCCCcCCCCCCCC
Q 022872 25 RPQEQLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNVPVGGGSRKNKRSIS 87 (291)
Q Consensus 25 ~p~~~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG~lRnvPVGgG~RKnkrsss 87 (291)
+|++.++||||+|.||||||||||+++||||||++|+||||+||+|||||||||+||+|+++|
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 467779999999999999999999999999999999999999999999999999999999874
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=92.73 E-value=0.048 Score=47.09 Aligned_cols=34 Identities=26% Similarity=0.808 Sum_probs=26.8
Q ss_pred CCCCCCCCCCCcceeeecccC--CCCCchhhhcccccc
Q 022872 29 QLNCPRCNSTNTKFCYYNNYS--LTQPRYFCKTCRRYW 64 (291)
Q Consensus 29 ~~~CPRC~S~~TKfcyyNNy~--~~QPR~fCk~CrRyW 64 (291)
...||||.|.+|+.. +.+- .++.-|.|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence 489999999999964 5564 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=92.06 E-value=0.12 Score=36.26 Aligned_cols=29 Identities=41% Similarity=0.957 Sum_probs=22.5
Q ss_pred cCCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 022872 28 EQLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 62 (291)
Q Consensus 28 ~~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 62 (291)
.+..||+|.+. ++..+.+ +.+|.|++|++
T Consensus 17 ~g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 44779999998 5544444 78999999985
No 4
>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=91.85 E-value=0.094 Score=36.10 Aligned_cols=30 Identities=47% Similarity=0.885 Sum_probs=21.3
Q ss_pred CCCCCCCCCCcceeeecccCC-CCCchhhhccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSL-TQPRYFCKTCR 61 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~-~QPR~fCk~Cr 61 (291)
+.||+|.+++.- |=|-.+. -..||+|++|+
T Consensus 6 v~CP~C~s~~~v--~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTEGV--KKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCCcc--eeCCCCCCCCEeEecCcCC
Confidence 789999998821 1333433 36899999996
No 5
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.35 E-value=0.13 Score=43.53 Aligned_cols=35 Identities=37% Similarity=0.782 Sum_probs=28.1
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhcccccccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTE 66 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~ 66 (291)
..||+|.+.+ +-=+.-+.....||.|++|++-|+.
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 2225555666999999999999874
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.53 E-value=0.39 Score=33.25 Aligned_cols=37 Identities=30% Similarity=0.823 Sum_probs=27.8
Q ss_pred CCCCCCCCCCcceeeecccCCCCC---chhhhcccccccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQP---RYFCKTCRRYWTE 66 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QP---R~fCk~CrRyWT~ 66 (291)
..||+|...+.-|-..+-.+...| -|.|..|...|.+
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 369999977777655555555555 3999999999964
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=85.86 E-value=0.48 Score=32.58 Aligned_cols=36 Identities=28% Similarity=0.829 Sum_probs=24.4
Q ss_pred CCCCCCCCCCcceeeecccCCCCCc---hhhhccccccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWT 65 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT 65 (291)
.+||.|...+.-|--.+..+...|- |.|.+|..-|+
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 3699999988766555555555543 89999999995
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=80.69 E-value=1.7 Score=34.40 Aligned_cols=39 Identities=23% Similarity=0.738 Sum_probs=28.7
Q ss_pred CCCCCCCCCCCcceeeecccCCCCCc---hhhhccccccccC
Q 022872 29 QLNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWTEG 67 (291)
Q Consensus 29 ~~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT~G 67 (291)
...||+|...+.-|-..+-.+...|- |.|..|+-.|+++
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 48999998777666555544444333 8999999999875
No 9
>PHA02998 RNA polymerase subunit; Provisional
Probab=77.33 E-value=1.9 Score=39.61 Aligned_cols=38 Identities=24% Similarity=0.602 Sum_probs=32.5
Q ss_pred CCCCCCCCCCCcceeeecccCCCCCc---hhhhcccccccc
Q 022872 29 QLNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWTE 66 (291)
Q Consensus 29 ~~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT~ 66 (291)
...||+|...++-|--.|-.+...|- |.|..|..-|.-
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 38899999999998888888887775 899999999963
No 10
>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=74.80 E-value=3.2 Score=30.49 Aligned_cols=41 Identities=24% Similarity=0.667 Sum_probs=29.5
Q ss_pred CCCCCCCCCcceeeecccCCCCCchhhhccccccccCCcccccc
Q 022872 31 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNVP 74 (291)
Q Consensus 31 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG~lRnvP 74 (291)
.|-.|...+|..=.- .......+|-+|.-||.+.|..|.+-
T Consensus 1 ~C~~C~~~~Tp~WR~---g~~~~~~LCNaCgl~~~k~~~~rp~~ 41 (54)
T cd00202 1 ACSNCGTTTTPLWRR---GPSGGSTLCNACGLYWKKHGVMRPLS 41 (54)
T ss_pred CCCCCCCCCCccccc---CCCCcchHHHHHHHHHHhcCCCCCcc
Confidence 377888887763211 22467899999999999999766553
No 11
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=71.66 E-value=1.1 Score=30.66 Aligned_cols=37 Identities=24% Similarity=0.622 Sum_probs=26.9
Q ss_pred CCCCCCCCCcceeeecccCCCCCchhhhccccccccCCcccc
Q 022872 31 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRN 72 (291)
Q Consensus 31 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG~lRn 72 (291)
+||+|...=...-+ ..-+-+.|..|.-.|=..|.+..
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 59999985554433 33566889999999988776654
No 12
>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=60.56 E-value=6.2 Score=37.92 Aligned_cols=36 Identities=19% Similarity=0.663 Sum_probs=26.7
Q ss_pred CCCCCCCCCCcceeeecccCCCCCc---hhhhccccccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWT 65 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT 65 (291)
..||+|...+..|-..+..+...|- |.|..|...|.
T Consensus 259 ~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 259 FTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred ccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 8999999777766555555555453 78999999994
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=59.60 E-value=4.4 Score=36.80 Aligned_cols=26 Identities=27% Similarity=0.809 Sum_probs=17.4
Q ss_pred eeecccCCCC-----CchhhhccccccccCC
Q 022872 43 CYYNNYSLTQ-----PRYFCKTCRRYWTEGG 68 (291)
Q Consensus 43 cyyNNy~~~Q-----PR~fCk~CrRyWT~GG 68 (291)
||...+.... .-.+|+.|.||+..|.
T Consensus 19 C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 19 CYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred HhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 4555544433 2379999999999843
No 14
>PHA00626 hypothetical protein
Probab=56.84 E-value=7.3 Score=30.04 Aligned_cols=36 Identities=22% Similarity=0.382 Sum_probs=24.4
Q ss_pred CCCCCCCCCcceeeecccCCCCCchhhhccccccccCC
Q 022872 31 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGG 68 (291)
Q Consensus 31 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG 68 (291)
.||+|.|.+.-=|=. -....-||.|++|.=.+|+..
T Consensus 2 ~CP~CGS~~Ivrcg~--cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKT--MRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeece--ecccCcceEcCCCCCeechhh
Confidence 699999975432211 012246899999999998754
No 15
>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=55.35 E-value=5.1 Score=37.20 Aligned_cols=36 Identities=22% Similarity=0.635 Sum_probs=18.0
Q ss_pred CCCCCCCCCCcc-eeeecc-cCCCCCchhhhccccccc
Q 022872 30 LNCPRCNSTNTK-FCYYNN-YSLTQPRYFCKTCRRYWT 65 (291)
Q Consensus 30 ~~CPRC~S~~TK-fcyyNN-y~~~QPR~fCk~CrRyWT 65 (291)
..||.|...+.. +-||.. -....--+.|+.|+.|+-
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 679999887765 455532 222233389999999983
No 16
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=54.05 E-value=8.9 Score=27.80 Aligned_cols=39 Identities=23% Similarity=0.603 Sum_probs=28.8
Q ss_pred CCCCCCCCCCCcceeeecccCCCCCchhhhccccccccCCcc
Q 022872 29 QLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSL 70 (291)
Q Consensus 29 ~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG~l 70 (291)
+..|--|...+|..=. ....-++.+|-+|.-||.+.|.+
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 3579999988886321 12333369999999999998886
No 17
>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=48.21 E-value=12 Score=36.22 Aligned_cols=35 Identities=17% Similarity=0.569 Sum_probs=23.6
Q ss_pred CCCCCCCCCCcceeeecccC----CCCCchhhhccccccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYS----LTQPRYFCKTCRRYWT 65 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~----~~QPR~fCk~CrRyWT 65 (291)
..||.|...+ +.-|+.-.. ..---..|.+|+.|+-
T Consensus 225 ~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 225 VKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred ccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchh
Confidence 7899999865 556664332 1122278999999985
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=47.94 E-value=12 Score=33.11 Aligned_cols=40 Identities=23% Similarity=0.389 Sum_probs=28.7
Q ss_pred CCCCCCCCCcceeee---cccCCCCCchhhhccccccccCCcc
Q 022872 31 NCPRCNSTNTKFCYY---NNYSLTQPRYFCKTCRRYWTEGGSL 70 (291)
Q Consensus 31 ~CPRC~S~~TKfcyy---NNy~~~QPR~fCk~CrRyWT~GG~l 70 (291)
.||.|...+||+-== ...+.-+-|.-|..|.+-||-==.+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERA 44 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeec
Confidence 699999999998622 2223335679999999998854443
No 19
>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=47.49 E-value=7 Score=26.96 Aligned_cols=17 Identities=41% Similarity=1.208 Sum_probs=7.1
Q ss_pred CCchhhhccccccccCC
Q 022872 52 QPRYFCKTCRRYWTEGG 68 (291)
Q Consensus 52 QPR~fCk~CrRyWT~GG 68 (291)
+|||+|.=|..|.|..-
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 68999999999997654
No 20
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=44.41 E-value=13 Score=34.70 Aligned_cols=28 Identities=29% Similarity=0.736 Sum_probs=21.3
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 62 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 62 (291)
.+||||...=.|.- +. .+.-|||..|++
T Consensus 236 ~pC~~Cg~~I~~~~-~~----gR~ty~Cp~CQ~ 263 (269)
T PRK14811 236 QPCPRCGTPIEKIV-VG----GRGTHFCPQCQP 263 (269)
T ss_pred CCCCcCCCeeEEEE-EC----CCCcEECCCCcC
Confidence 68999998776643 32 366799999996
No 21
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=43.67 E-value=9.1 Score=25.96 Aligned_cols=10 Identities=40% Similarity=1.092 Sum_probs=8.1
Q ss_pred CCCCCCCCCC
Q 022872 30 LNCPRCNSTN 39 (291)
Q Consensus 30 ~~CPRC~S~~ 39 (291)
..||.|.+..
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 4699999877
No 22
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=43.21 E-value=23 Score=30.04 Aligned_cols=37 Identities=27% Similarity=0.748 Sum_probs=32.2
Q ss_pred CCCCCCCCCCCcceeeecccCCCCCc---hhhhccccccc
Q 022872 29 QLNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWT 65 (291)
Q Consensus 29 ~~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT 65 (291)
+..||+|...+.-|--+|-.+..-|- |.|-.|.--|-
T Consensus 65 ~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 65 EATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred cCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 37899999999998888888888776 89999999885
No 23
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=43.16 E-value=15 Score=35.67 Aligned_cols=36 Identities=22% Similarity=0.531 Sum_probs=23.6
Q ss_pred CCCCCCCCCCcceeeecccC--CCCCchhhhcccccccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYS--LTQPRYFCKTCRRYWTE 66 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~--~~QPR~fCk~CrRyWT~ 66 (291)
..||.|... .+.-|+.--. ..---..|.+|+.|+--
T Consensus 227 ~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 227 VKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred ccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 678999874 4666663222 12223899999999854
No 24
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=41.44 E-value=19 Score=31.71 Aligned_cols=44 Identities=20% Similarity=0.406 Sum_probs=29.4
Q ss_pred CCCCCCCCCCccee---eecccCCCCCchhhhccccccccCCccccc
Q 022872 30 LNCPRCNSTNTKFC---YYNNYSLTQPRYFCKTCRRYWTEGGSLRNV 73 (291)
Q Consensus 30 ~~CPRC~S~~TKfc---yyNNy~~~QPR~fCk~CrRyWT~GG~lRnv 73 (291)
..||-|.+..|++- |+-.-+.-.-|+-|+.|.+-++.==++-..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELV 47 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCc
Confidence 36999999997764 333333344569999999888765444333
No 25
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=39.19 E-value=14 Score=26.89 Aligned_cols=25 Identities=36% Similarity=0.776 Sum_probs=18.1
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 62 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 62 (291)
.-||+|.+. |..-.. .|+.|..|..
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 479999874 544332 6999999974
No 26
>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=38.52 E-value=21 Score=27.85 Aligned_cols=31 Identities=23% Similarity=0.495 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 022872 29 QLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 62 (291)
Q Consensus 29 ~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 62 (291)
+..||+|.+.+|-..|..|. ..-.-|-.|.=
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 47899999999887777665 55567888753
No 27
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=35.29 E-value=15 Score=28.09 Aligned_cols=12 Identities=42% Similarity=0.905 Sum_probs=5.6
Q ss_pred CCCCCCCCCCcc
Q 022872 30 LNCPRCNSTNTK 41 (291)
Q Consensus 30 ~~CPRC~S~~TK 41 (291)
++|+.|.|.||+
T Consensus 49 ~KC~~C~SYNT~ 60 (61)
T PF14599_consen 49 HKCSHCGSYNTR 60 (61)
T ss_dssp ---TTTS---EE
T ss_pred hcCCCCCCcccC
Confidence 899999999997
No 28
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=30.80 E-value=33 Score=29.50 Aligned_cols=36 Identities=28% Similarity=0.787 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCcceeeecccCCCC-----Cchhhhcccccccc
Q 022872 29 QLNCPRCNSTNTKFCYYNNYSLTQ-----PRYFCKTCRRYWTE 66 (291)
Q Consensus 29 ~~~CPRC~S~~TKfcyyNNy~~~Q-----PR~fCk~CrRyWT~ 66 (291)
...||+|...+.-| ||--+... --|.|-.|.--||+
T Consensus 73 ~~~C~~C~~~eavf--fQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 73 DKHCPKCGHREAVF--FQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred cccCCccCCcceEE--EecccccccceEEEEEEeccccccccC
Confidence 37899999987765 53321111 11899999999985
No 29
>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=30.54 E-value=26 Score=27.71 Aligned_cols=45 Identities=16% Similarity=0.369 Sum_probs=20.6
Q ss_pred cccCCCCccCCCCCCCCCCCcceeeecccCCCCCchhhhccccccc
Q 022872 20 LERKARPQEQLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWT 65 (291)
Q Consensus 20 ~er~~~p~~~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT 65 (291)
..++.+.++.-.||.|+..++=-|=.. ........-|+.|.-.+.
T Consensus 13 kk~~~~l~~~F~CPfC~~~~sV~v~id-kk~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 13 KKKKPKLPKVFDCPFCNHEKSVSVKID-KKEGIGILSCRVCGESFQ 57 (81)
T ss_dssp -------SS----TTT--SS-EEEEEE-TTTTEEEEEESSS--EEE
T ss_pred cCcCCCCCceEcCCcCCCCCeEEEEEE-ccCCEEEEEecCCCCeEE
Confidence 344555667799999998888777663 335566788999976553
No 30
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=27.65 E-value=20 Score=35.12 Aligned_cols=40 Identities=25% Similarity=0.558 Sum_probs=21.6
Q ss_pred ccccCCCCccCCCCCC-----CCCCCcce--eeecccCCCCCchhhh
Q 022872 19 MLERKARPQEQLNCPR-----CNSTNTKF--CYYNNYSLTQPRYFCK 58 (291)
Q Consensus 19 ~~er~~~p~~~~~CPR-----C~S~~TKf--cyyNNy~~~QPR~fCk 58 (291)
++-|+..|-++|+|-. |....-++ ||-.-|.-.-.---|+
T Consensus 38 Tt~RR~~pipQL~Cvggsa~~c~~~~p~vvqC~N~G~dg~dvqW~C~ 84 (318)
T PF06682_consen 38 TTSRRVSPIPQLKCVGGSARGCDLYEPDVVQCTNQGYDGEDVQWECK 84 (318)
T ss_pred cccccCCCCcceeecCCCcccccccCcceEEEEecCCCCcccceEEe
Confidence 5667777888888843 65544333 5444433333333333
No 31
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=25.44 E-value=16 Score=27.92 Aligned_cols=9 Identities=67% Similarity=1.542 Sum_probs=7.8
Q ss_pred CcccccccC
Q 022872 279 TGYWNGMFG 287 (291)
Q Consensus 279 ~GyWnGMlG 287 (291)
+|=||||||
T Consensus 53 ~g~W~GmiG 61 (65)
T PF10613_consen 53 NGSWNGMIG 61 (65)
T ss_dssp TSEBEHHHH
T ss_pred CCcCcCHHH
Confidence 688999986
No 32
>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=25.19 E-value=55 Score=23.43 Aligned_cols=32 Identities=28% Similarity=0.636 Sum_probs=19.0
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchh-hhcccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPRYF-CKTCRR 62 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR~f-Ck~CrR 62 (291)
.+||.|.+..-.|-+ ........+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 359999997775542 12333344444 777764
No 33
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=24.95 E-value=45 Score=30.07 Aligned_cols=40 Identities=23% Similarity=0.363 Sum_probs=27.2
Q ss_pred CCCCCCCCCcceeeec---ccCCCCCchhhhccccccccCCcc
Q 022872 31 NCPRCNSTNTKFCYYN---NYSLTQPRYFCKTCRRYWTEGGSL 70 (291)
Q Consensus 31 ~CPRC~S~~TKfcyyN---Ny~~~QPR~fCk~CrRyWT~GG~l 70 (291)
.||.|.+.+||+-==- .-+.-+-|.-|-.|..-+|-==++
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~ 44 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERA 44 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhhee
Confidence 6999999999985111 112234568999999888754443
No 34
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.61 E-value=35 Score=28.22 Aligned_cols=40 Identities=25% Similarity=0.586 Sum_probs=29.7
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhccccccccCCccccccCC
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNVPVG 76 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG~lRnvPVG 76 (291)
..||-|.....| -..---..|+.|..-|+.|+-....|.|
T Consensus 36 ~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 36 HVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred CcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 789999988544 1122337899999999999987766654
No 35
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=23.60 E-value=34 Score=21.75 Aligned_cols=27 Identities=26% Similarity=0.708 Sum_probs=14.1
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCR 61 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~Cr 61 (291)
.+||||...-.++-.. .+.-+||..|+
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 4699998887776532 23346777775
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=23.25 E-value=43 Score=24.44 Aligned_cols=30 Identities=27% Similarity=0.609 Sum_probs=23.6
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhcccccccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTE 66 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~ 66 (291)
..||.|.....+ .+.+-.+.|..|...+.+
T Consensus 29 q~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 29 QTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred cCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 669999988877 566677999999877654
No 37
>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=22.98 E-value=48 Score=28.32 Aligned_cols=30 Identities=33% Similarity=0.821 Sum_probs=23.9
Q ss_pred CCCCCCCCCcceeeecccCCCCCchhhhccccccccCC
Q 022872 31 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGG 68 (291)
Q Consensus 31 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG 68 (291)
.||.|.|..|-- .+.-+.|..|.-=|....
T Consensus 4 ~CP~C~seytY~--------dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTYH--------DGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceEe--------cCCeeECccccccccccc
Confidence 599999976632 355699999999998875
No 38
>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=21.78 E-value=61 Score=22.91 Aligned_cols=31 Identities=19% Similarity=0.660 Sum_probs=17.5
Q ss_pred CCCCCCCCCCcceeeecccCCCCCchhhhcccc
Q 022872 30 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 62 (291)
Q Consensus 30 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 62 (291)
.+||-|... .+|..|-+. ..+-..+|+.|..
T Consensus 4 ~pCP~CGG~-DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 4 GPCPICGGK-DRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp E--TTTT-T-TTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCcCc-cccccCcCc-ccCCCEECCCCCC
Confidence 469999884 588866543 3347899999943
No 39
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=21.54 E-value=67 Score=24.78 Aligned_cols=30 Identities=23% Similarity=0.479 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCcceeeecccCCCCCchhhhccc
Q 022872 29 QLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCR 61 (291)
Q Consensus 29 ~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~Cr 61 (291)
+..||+|...+|=..|.-|.- .-.-|-.|.
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 478999999999887754443 334566664
Done!