Query 011169
Match_columns 492
No_of_seqs 145 out of 260
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 08:53:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011169.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011169hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02701 zf-Dof: Dof domain, z 100.0 4.6E-36 9.9E-41 239.0 4.3 63 97-159 1-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 87.5 0.23 5E-06 46.1 0.9 34 101-136 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 86.4 0.57 1.2E-05 35.3 2.3 31 97-134 15-45 (46)
4 COG3677 Transposase and inacti 84.2 0.63 1.4E-05 42.4 1.9 35 102-138 31-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 84.1 0.51 1.1E-05 34.8 1.1 31 101-133 5-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 80.3 1.5 3.2E-05 32.6 2.3 37 102-138 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 72.2 2.7 5.9E-05 31.0 1.8 36 102-137 1-39 (39)
8 cd00202 ZnF_GATA Zinc finger D 63.7 6.6 0.00014 31.0 2.5 40 103-145 1-40 (54)
9 PF13453 zf-TFIIB: Transcripti 61.4 2.3 4.9E-05 31.3 -0.4 37 103-144 1-37 (41)
10 TIGR01384 TFS_arch transcripti 56.7 11 0.00023 32.3 2.9 39 101-139 62-103 (104)
11 PHA02998 RNA polymerase subuni 55.8 9.8 0.00021 37.5 2.7 39 100-138 142-183 (195)
12 smart00401 ZnF_GATA zinc finge 52.5 12 0.00026 29.2 2.3 39 101-142 3-41 (52)
13 PRK14810 formamidopyrimidine-D 50.4 9.1 0.0002 38.5 1.7 29 101-134 244-272 (272)
14 TIGR01385 TFSII transcription 49.3 14 0.0003 38.3 2.9 41 97-137 254-297 (299)
15 PF04981 NMD3: NMD3 family ; 49.0 8.2 0.00018 37.9 1.1 37 104-140 1-49 (236)
16 PRK14811 formamidopyrimidine-D 45.5 13 0.00027 37.6 1.8 28 102-134 236-263 (269)
17 PF14690 zf-ISL3: zinc-finger 44.7 12 0.00025 27.5 1.1 31 102-132 3-47 (47)
18 PF04216 FdhE: Protein involve 44.0 11 0.00023 38.0 1.1 36 101-136 211-248 (290)
19 PRK01103 formamidopyrimidine/5 41.7 15 0.00033 36.8 1.8 29 101-134 245-273 (274)
20 PRK10445 endonuclease VIII; Pr 40.7 16 0.00035 36.6 1.7 29 101-134 235-263 (263)
21 PRK13945 formamidopyrimidine-D 40.1 17 0.00038 36.7 1.9 29 101-134 254-282 (282)
22 PRK00464 nrdR transcriptional 39.8 19 0.0004 34.2 1.9 41 102-142 1-44 (154)
23 TIGR00244 transcriptional regu 38.2 21 0.00047 33.9 2.0 41 103-143 2-45 (147)
24 PF06220 zf-U1: U1 zinc finger 37.9 12 0.00027 27.7 0.3 17 124-140 1-17 (38)
25 PF09526 DUF2387: Probable met 37.4 23 0.0005 29.7 1.9 31 101-134 8-38 (71)
26 PHA00626 hypothetical protein 36.7 23 0.0005 29.2 1.7 37 103-141 2-38 (59)
27 KOG2691 RNA polymerase II subu 35.3 25 0.00055 32.2 1.9 46 89-138 62-113 (113)
28 TIGR00577 fpg formamidopyrimid 35.1 23 0.00049 35.7 1.8 28 101-133 245-272 (272)
29 PF14354 Lar_restr_allev: Rest 34.7 31 0.00068 26.7 2.1 35 100-134 2-37 (61)
30 TIGR01562 FdhE formate dehydro 34.3 28 0.0006 36.3 2.3 10 127-136 253-262 (305)
31 COG0266 Nei Formamidopyrimidin 30.8 28 0.00061 35.9 1.6 34 94-134 240-273 (273)
32 TIGR03655 anti_R_Lar restricti 29.7 43 0.00093 25.9 2.1 32 102-134 2-34 (53)
33 PRK03564 formate dehydrogenase 27.4 44 0.00095 35.1 2.4 10 127-136 253-262 (309)
34 PRK00432 30S ribosomal protein 27.3 32 0.00069 27.0 1.0 25 102-134 21-45 (50)
35 PF06827 zf-FPG_IleRS: Zinc fi 24.7 29 0.00062 23.9 0.3 28 102-134 2-29 (30)
36 PRK14892 putative transcriptio 23.5 54 0.0012 29.2 1.9 36 97-136 17-52 (99)
37 TIGR02443 conserved hypothetic 21.7 61 0.0013 26.8 1.7 31 100-133 8-38 (59)
38 PF08273 Prim_Zn_Ribbon: Zinc- 21.6 58 0.0013 24.7 1.5 33 100-134 2-34 (40)
No 1
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=100.00 E-value=4.6e-36 Score=239.03 Aligned_cols=63 Identities=67% Similarity=1.417 Sum_probs=60.9
Q ss_pred CCCCccCCCCCCCCCCceeeecccCCCCCccccccchhhhccCCcccccccCcccccCCCCcc
Q 011169 97 RPDKIIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQRYWTAGGTMRNVPVGAGRRKNKHFAS 159 (492)
Q Consensus 97 ~p~~~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~RywT~GG~lRnvPvGgG~RKnk~s~s 159 (492)
+|++.++||||+|++|||||||||++.||||||++|+||||+||+|||||||||+||+|+++|
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 588999999999999999999999999999999999999999999999999999999999764
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=87.51 E-value=0.23 Score=46.12 Aligned_cols=34 Identities=26% Similarity=0.687 Sum_probs=27.4
Q ss_pred ccCCCCCCCCCCceeeeccc--CCCCCccccccchhhh
Q 011169 101 IIPCPRCNSMDTKFCYFNNY--NVNQPRHFCKNCQRYW 136 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny--~~~qpR~~Ck~C~Ryw 136 (492)
...||||.|.+|+.. +.| +.++.-|+|++|+.=+
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 589999999999965 555 5568889999998643
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=86.39 E-value=0.57 Score=35.26 Aligned_cols=31 Identities=35% Similarity=0.810 Sum_probs=24.1
Q ss_pred CCCCccCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 97 RPDKIIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 97 ~p~~~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
=|+. ..||+|.+. ++..+.+ +.+|.|++|++
T Consensus 15 W~~g-~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 15 WPDG-FVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCC-CCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 4444 669999998 6666666 78899999985
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=84.20 E-value=0.63 Score=42.43 Aligned_cols=35 Identities=29% Similarity=0.662 Sum_probs=27.9
Q ss_pred cCCCCCCCCCCceeeecccCCCCCccccccchhhhcc
Q 011169 102 IPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQRYWTA 138 (492)
Q Consensus 102 ~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~RywT~ 138 (492)
.-||+|.+.+ +-=++-+.....|+.|++|++-|+.
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 4799999999 4445555556999999999998874
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=84.15 E-value=0.51 Score=34.77 Aligned_cols=31 Identities=32% Similarity=0.692 Sum_probs=21.7
Q ss_pred ccCCCCCCCCCCceeeecccCCC-CCccccccch
Q 011169 101 IIPCPRCNSMDTKFCYFNNYNVN-QPRHFCKNCQ 133 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny~~~-qpR~~Ck~C~ 133 (492)
.+.||||.+.+. -|=|-.+.. ..||+|++|+
T Consensus 5 ~v~CP~C~s~~~--v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPRCQSTEG--VKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCCCCCCCc--ceeCCCCCCCCEeEecCcCC
Confidence 368999999772 233444443 5899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=80.34 E-value=1.5 Score=32.64 Aligned_cols=37 Identities=24% Similarity=0.828 Sum_probs=27.8
Q ss_pred cCCCCCCCCCCceeeecccCCCCC---ccccccchhhhcc
Q 011169 102 IPCPRCNSMDTKFCYFNNYNVNQP---RHFCKNCQRYWTA 138 (492)
Q Consensus 102 ~~CPrc~s~~tkfcyynny~~~qp---R~~Ck~C~RywT~ 138 (492)
.+||+|...+.-|-..+-.....| -|.|.+|...|..
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 379999977777666666655555 4999999999863
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=72.17 E-value=2.7 Score=31.02 Aligned_cols=36 Identities=28% Similarity=0.779 Sum_probs=23.5
Q ss_pred cCCCCCCCCCCceeeecccCCCCC---ccccccchhhhc
Q 011169 102 IPCPRCNSMDTKFCYFNNYNVNQP---RHFCKNCQRYWT 137 (492)
Q Consensus 102 ~~CPrc~s~~tkfcyynny~~~qp---R~~Ck~C~RywT 137 (492)
..||+|...+.-|--.+......| .|.|.+|..-|+
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 379999997766555555555444 389999999885
No 8
>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=63.75 E-value=6.6 Score=31.03 Aligned_cols=40 Identities=25% Similarity=0.663 Sum_probs=28.7
Q ss_pred CCCCCCCCCCceeeecccCCCCCccccccchhhhccCCccccc
Q 011169 103 PCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQRYWTAGGTMRNV 145 (492)
Q Consensus 103 ~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~RywT~GG~lRnv 145 (492)
.|-.|...+|..=+-.. .....+|-+|.-||...|.+|-+
T Consensus 1 ~C~~C~~~~Tp~WR~g~---~~~~~LCNaCgl~~~k~~~~rp~ 40 (54)
T cd00202 1 ACSNCGTTTTPLWRRGP---SGGSTLCNACGLYWKKHGVMRPL 40 (54)
T ss_pred CCCCCCCCCCcccccCC---CCcchHHHHHHHHHHhcCCCCCc
Confidence 37778887775332222 46779999999999999976554
No 9
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=61.36 E-value=2.3 Score=31.33 Aligned_cols=37 Identities=22% Similarity=0.596 Sum_probs=26.4
Q ss_pred CCCCCCCCCCceeeecccCCCCCccccccchhhhccCCcccc
Q 011169 103 PCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQRYWTAGGTMRN 144 (492)
Q Consensus 103 ~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~RywT~GG~lRn 144 (492)
+||+|...=...-+ ..-+-+.|.+|.-.|-..|.+..
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 59999885444333 22456889999999988776643
No 10
>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=56.70 E-value=11 Score=32.30 Aligned_cols=39 Identities=18% Similarity=0.648 Sum_probs=28.2
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCc---cccccchhhhccC
Q 011169 101 IIPCPRCNSMDTKFCYFNNYNVNQPR---HFCKNCQRYWTAG 139 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny~~~qpR---~~Ck~C~RywT~G 139 (492)
...||+|...+.-|-..+-.....|- |.|.+|.-.|+.+
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 47999998777666555554433332 8999999999875
No 11
>PHA02998 RNA polymerase subunit; Provisional
Probab=55.82 E-value=9.8 Score=37.49 Aligned_cols=39 Identities=26% Similarity=0.709 Sum_probs=33.1
Q ss_pred CccCCCCCCCCCCceeeecccCCCCCc---cccccchhhhcc
Q 011169 100 KIIPCPRCNSMDTKFCYFNNYNVNQPR---HFCKNCQRYWTA 138 (492)
Q Consensus 100 ~~~~CPrc~s~~tkfcyynny~~~qpR---~~Ck~C~RywT~ 138 (492)
...+||+|...++-|--.|-+....|- |.|..|..-|.-
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 457999999999998888888877775 899999998864
No 12
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=52.47 E-value=12 Score=29.19 Aligned_cols=39 Identities=18% Similarity=0.520 Sum_probs=28.9
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCccccccchhhhccCCcc
Q 011169 101 IIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQRYWTAGGTM 142 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~RywT~GG~l 142 (492)
...|--|...+|..=.-.. .-++.+|-+|.-||...|.+
T Consensus 3 ~~~C~~C~~~~T~~WR~g~---~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGP---SGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCcCCCCCCCCCccccCC---CCCCcEeecccHHHHHcCCC
Confidence 4689999988886432222 22379999999999998887
No 13
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=50.44 E-value=9.1 Score=38.51 Aligned_cols=29 Identities=24% Similarity=0.677 Sum_probs=21.2
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 101 IIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
..+||||...=.|.-+= .+.-|||..||+
T Consensus 244 g~pCprCG~~I~~~~~~-----gR~t~~CP~CQ~ 272 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVA-----GRSSHYCPHCQK 272 (272)
T ss_pred CCcCCCCCCeeEEEEEC-----CCccEECcCCcC
Confidence 45999999766554442 266699999995
No 14
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=49.29 E-value=14 Score=38.26 Aligned_cols=41 Identities=15% Similarity=0.599 Sum_probs=29.5
Q ss_pred CCCCccCCCCCCCCCCceeeecccCCCCCc---cccccchhhhc
Q 011169 97 RPDKIIPCPRCNSMDTKFCYFNNYNVNQPR---HFCKNCQRYWT 137 (492)
Q Consensus 97 ~p~~~~~CPrc~s~~tkfcyynny~~~qpR---~~Ck~C~RywT 137 (492)
.....++||+|...+..|-..+......|- |.|.+|...|.
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 344568999998777776555555555553 78999999884
No 15
>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=48.99 E-value=8.2 Score=37.90 Aligned_cols=37 Identities=30% Similarity=0.837 Sum_probs=23.6
Q ss_pred CCCCCCCCCc-------eeeecccCCCC-----CccccccchhhhccCC
Q 011169 104 CPRCNSMDTK-------FCYFNNYNVNQ-----PRHFCKNCQRYWTAGG 140 (492)
Q Consensus 104 CPrc~s~~tk-------fcyynny~~~q-----pR~~Ck~C~RywT~GG 140 (492)
||+|...... =||+..+.+-. --.+|+.|.||+..|.
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 5556553333 25666665533 2378999999999853
No 16
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=45.52 E-value=13 Score=37.56 Aligned_cols=28 Identities=39% Similarity=0.929 Sum_probs=20.9
Q ss_pred cCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 102 IPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 102 ~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
.+||||...=.|.-+ . .+.-|||..||+
T Consensus 236 ~pC~~Cg~~I~~~~~-~----gR~ty~Cp~CQ~ 263 (269)
T PRK14811 236 QPCPRCGTPIEKIVV-G----GRGTHFCPQCQP 263 (269)
T ss_pred CCCCcCCCeeEEEEE-C----CCCcEECCCCcC
Confidence 489999977665433 2 266799999996
No 17
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=44.66 E-value=12 Score=27.54 Aligned_cols=31 Identities=32% Similarity=0.656 Sum_probs=18.3
Q ss_pred cCCCCCCCCCCce-eeec---------cc----CCCCCccccccc
Q 011169 102 IPCPRCNSMDTKF-CYFN---------NY----NVNQPRHFCKNC 132 (492)
Q Consensus 102 ~~CPrc~s~~tkf-cyyn---------ny----~~~qpR~~Ck~C 132 (492)
..||.|.+...+. =++. .+ .+..+|++|++|
T Consensus 3 ~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 3 PRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred ccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 4799999776211 1111 11 346778888887
No 18
>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=44.02 E-value=11 Score=37.98 Aligned_cols=36 Identities=28% Similarity=0.676 Sum_probs=16.8
Q ss_pred ccCCCCCCCCCCc-eeeec-ccCCCCCccccccchhhh
Q 011169 101 IIPCPRCNSMDTK-FCYFN-NYNVNQPRHFCKNCQRYW 136 (492)
Q Consensus 101 ~~~CPrc~s~~tk-fcyyn-ny~~~qpR~~Ck~C~Ryw 136 (492)
...||.|...+.. +-||. .-....--+.|..|+.|+
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 4578888776654 44552 223333348899999987
No 19
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=41.74 E-value=15 Score=36.80 Aligned_cols=29 Identities=31% Similarity=0.687 Sum_probs=21.0
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 101 IIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
..+||||...=.|. .++ .+.-|||..||+
T Consensus 245 g~pC~~Cg~~I~~~-~~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKI-KQG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEE-EEC----CCCcEECcCCCC
Confidence 35899999775553 333 366699999996
No 20
>PRK10445 endonuclease VIII; Provisional
Probab=40.72 E-value=16 Score=36.59 Aligned_cols=29 Identities=28% Similarity=0.661 Sum_probs=21.4
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 101 IIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
..+||||...=.|.-+ + .+.-|||..||+
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 4489999877665544 2 266799999995
No 21
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.05 E-value=17 Score=36.68 Aligned_cols=29 Identities=28% Similarity=0.728 Sum_probs=21.2
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 101 IIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
..+||||...=.|.-+= .+--|||..||+
T Consensus 254 g~pC~~Cg~~I~~~~~~-----gR~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCRKCGTPIERIKLA-----GRSTHWCPNCQK 282 (282)
T ss_pred cCCCCcCCCeeEEEEEC-----CCccEECCCCcC
Confidence 34999999776664442 256699999995
No 22
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=39.77 E-value=19 Score=34.15 Aligned_cols=41 Identities=24% Similarity=0.449 Sum_probs=30.5
Q ss_pred cCCCCCCCCCCcee---eecccCCCCCccccccchhhhccCCcc
Q 011169 102 IPCPRCNSMDTKFC---YFNNYNVNQPRHFCKNCQRYWTAGGTM 142 (492)
Q Consensus 102 ~~CPrc~s~~tkfc---yynny~~~qpR~~Ck~C~RywT~GG~l 142 (492)
..||.|.+.+|++- |+-.-|+..-||-|++|.+-++.==++
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERV 44 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEec
Confidence 36999999998764 555555666679999999887754444
No 23
>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=38.18 E-value=21 Score=33.90 Aligned_cols=41 Identities=20% Similarity=0.373 Sum_probs=30.8
Q ss_pred CCCCCCCCCCceeee---cccCCCCCccccccchhhhccCCccc
Q 011169 103 PCPRCNSMDTKFCYF---NNYNVNQPRHFCKNCQRYWTAGGTMR 143 (492)
Q Consensus 103 ~CPrc~s~~tkfcyy---nny~~~qpR~~Ck~C~RywT~GG~lR 143 (492)
.||.|...+||+-=- ..-+.-+-|..|.+|.+-+|-==.+-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAE 45 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecc
Confidence 699999999998753 34445566799999999888544443
No 24
>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=37.90 E-value=12 Score=27.66 Aligned_cols=17 Identities=35% Similarity=0.976 Sum_probs=7.2
Q ss_pred CCccccccchhhhccCC
Q 011169 124 QPRHFCKNCQRYWTAGG 140 (492)
Q Consensus 124 qpR~~Ck~C~RywT~GG 140 (492)
+|||||.=|..|.|..-
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 25
>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=37.36 E-value=23 Score=29.70 Aligned_cols=31 Identities=29% Similarity=0.532 Sum_probs=24.6
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 101 IIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
+..||+|.++||=..|+-|. ..-.-|-.|.-
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 57899999999888887776 45567888853
No 26
>PHA00626 hypothetical protein
Probab=36.66 E-value=23 Score=29.17 Aligned_cols=37 Identities=16% Similarity=0.220 Sum_probs=24.9
Q ss_pred CCCCCCCCCCceeeecccCCCCCccccccchhhhccCCc
Q 011169 103 PCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQRYWTAGGT 141 (492)
Q Consensus 103 ~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~RywT~GG~ 141 (492)
.||+|.+.+.--|-.=+ ...-||.|++|.=++|...-
T Consensus 2 ~CP~CGS~~Ivrcg~cr--~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR--GWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceeeeeceec--ccCcceEcCCCCCeechhhh
Confidence 69999997643222111 11357999999999998654
No 27
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=35.29 E-value=25 Score=32.17 Aligned_cols=46 Identities=24% Similarity=0.619 Sum_probs=31.3
Q ss_pred chhccccCC-CCCccCCCCCCCCCCceeeecccCCCC-----Cccccccchhhhcc
Q 011169 89 TDQEKAFKR-PDKIIPCPRCNSMDTKFCYFNNYNVNQ-----PRHFCKNCQRYWTA 138 (492)
Q Consensus 89 ~~~~~~~~~-p~~~~~CPrc~s~~tkfcyynny~~~q-----pR~~Ck~C~RywT~ 138 (492)
-.++.+||+ -++ .||+|...+.- |||--.... .-|.|-+|.-.||.
T Consensus 62 l~~DPTLPrts~~--~C~~C~~~eav--ffQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 62 LASDPTLPRTSDK--HCPKCGHREAV--FFQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred hccCCCcCccccc--cCCccCCcceE--EEecccccccceEEEEEEeccccccccC
Confidence 456777876 444 99999987765 455432211 11899999999984
No 28
>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=35.14 E-value=23 Score=35.68 Aligned_cols=28 Identities=36% Similarity=0.743 Sum_probs=20.6
Q ss_pred ccCCCCCCCCCCceeeecccCCCCCccccccch
Q 011169 101 IIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQ 133 (492)
Q Consensus 101 ~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~ 133 (492)
..+||||...=.|.-+ . .+.-|||..||
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 3499999977665443 3 26669999998
No 29
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=34.74 E-value=31 Score=26.69 Aligned_cols=35 Identities=23% Similarity=0.513 Sum_probs=20.2
Q ss_pred CccCCCCCCCCCCceeeecccCCCC-Cccccccchh
Q 011169 100 KIIPCPRCNSMDTKFCYFNNYNVNQ-PRHFCKNCQR 134 (492)
Q Consensus 100 ~~~~CPrc~s~~tkfcyynny~~~q-pR~~Ck~C~R 134 (492)
++.+||.|.+....+.+........ -.-+|.+|.-
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 5679999965555544433222111 3455888866
No 30
>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=34.27 E-value=28 Score=36.33 Aligned_cols=10 Identities=40% Similarity=1.046 Sum_probs=6.2
Q ss_pred cccccchhhh
Q 011169 127 HFCKNCQRYW 136 (492)
Q Consensus 127 ~~Ck~C~Ryw 136 (492)
+.|.+|++|+
T Consensus 253 e~C~~C~~Yl 262 (305)
T TIGR01562 253 ETCDSCQGYL 262 (305)
T ss_pred eeccccccch
Confidence 4566666665
No 31
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=30.78 E-value=28 Score=35.95 Aligned_cols=34 Identities=26% Similarity=0.698 Sum_probs=23.7
Q ss_pred ccCCCCCccCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 94 AFKRPDKIIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 94 ~~~~p~~~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
+--+-++ +|+||.+.=.|.-. -.+..|||..||+
T Consensus 240 VYgR~Ge--pC~~CGt~I~k~~~-----~gR~t~~CP~CQ~ 273 (273)
T COG0266 240 VYGRAGE--PCRRCGTPIEKIKL-----GGRSTFYCPVCQK 273 (273)
T ss_pred EecCCCC--CCCccCCEeEEEEE-----cCCcCEeCCCCCC
Confidence 4445444 99999987666332 2366799999995
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=29.66 E-value=43 Score=25.91 Aligned_cols=32 Identities=25% Similarity=0.598 Sum_probs=19.9
Q ss_pred cCCCCCCCCCCceeeecccCCCCCccc-cccchh
Q 011169 102 IPCPRCNSMDTKFCYFNNYNVNQPRHF-CKNCQR 134 (492)
Q Consensus 102 ~~CPrc~s~~tkfcyynny~~~qpR~~-Ck~C~R 134 (492)
.+||.|.+.+-.|=| ...+....+++ |..|+.
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 589999997775542 12333344444 888864
No 33
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=27.39 E-value=44 Score=35.05 Aligned_cols=10 Identities=30% Similarity=0.919 Sum_probs=5.3
Q ss_pred cccccchhhh
Q 011169 127 HFCKNCQRYW 136 (492)
Q Consensus 127 ~~Ck~C~Ryw 136 (492)
+.|..|++|+
T Consensus 253 e~C~~C~~Yl 262 (309)
T PRK03564 253 ESCGDCGTYL 262 (309)
T ss_pred eecccccccc
Confidence 4555555554
No 34
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.29 E-value=32 Score=26.95 Aligned_cols=25 Identities=36% Similarity=0.663 Sum_probs=18.5
Q ss_pred cCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 102 IPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 102 ~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
.-||+|.+. |..... .|+.|..|..
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 389999873 555544 6999999964
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=24.74 E-value=29 Score=23.85 Aligned_cols=28 Identities=25% Similarity=0.606 Sum_probs=15.6
Q ss_pred cCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 102 IPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 102 ~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
.+||||...-.++-..+ +.-+||..|+.
T Consensus 2 ~~C~rC~~~~~~~~~~~-----r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGING-----RSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETT-----EEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecC-----CCCeECcCCcC
Confidence 47999998877765522 33478888873
No 36
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=23.52 E-value=54 Score=29.19 Aligned_cols=36 Identities=31% Similarity=0.552 Sum_probs=25.5
Q ss_pred CCCCccCCCCCCCCCCceeeecccCCCCCccccccchhhh
Q 011169 97 RPDKIIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQRYW 136 (492)
Q Consensus 97 ~p~~~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~Ryw 136 (492)
+......||.|.. .+--|=+.. ..+.+.|..|.-|-
T Consensus 17 klpt~f~CP~Cge-~~v~v~~~k---~~~h~~C~~CG~y~ 52 (99)
T PRK14892 17 KLPKIFECPRCGK-VSISVKIKK---NIAIITCGNCGLYT 52 (99)
T ss_pred CCCcEeECCCCCC-eEeeeecCC---CcceEECCCCCCcc
Confidence 3347899999995 233344443 57899999999884
No 37
>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=21.72 E-value=61 Score=26.79 Aligned_cols=31 Identities=26% Similarity=0.424 Sum_probs=22.5
Q ss_pred CccCCCCCCCCCCceeeecccCCCCCccccccch
Q 011169 100 KIIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQ 133 (492)
Q Consensus 100 ~~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~ 133 (492)
-+..||+|..+||=..|.-|.- .-.-|-.|.
T Consensus 8 AGA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 8 AGAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred ccccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 3578999999999988865543 345677774
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=21.59 E-value=58 Score=24.71 Aligned_cols=33 Identities=27% Similarity=0.722 Sum_probs=19.0
Q ss_pred CccCCCCCCCCCCceeeecccCCCCCccccccchh
Q 011169 100 KIIPCPRCNSMDTKFCYFNNYNVNQPRHFCKNCQR 134 (492)
Q Consensus 100 ~~~~CPrc~s~~tkfcyynny~~~qpR~~Ck~C~R 134 (492)
+..+||-|.. ..+|..|-+. .-+-..+|..|..
T Consensus 2 ~h~pCP~CGG-~DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 2 KHGPCPICGG-KDRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp EEE--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCCCcC-ccccccCcCc-ccCCCEECCCCCC
Confidence 3568999988 5689866654 2347799999954
Done!