Query 038013
Match_columns 494
No_of_seqs 143 out of 258
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 06:38:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038013.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038013hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02701 zf-Dof: Dof domain, z 100.0 8.2E-36 1.8E-40 237.8 4.3 62 143-204 1-62 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 88.4 0.19 4.1E-06 46.6 0.9 34 147-182 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 86.9 0.51 1.1E-05 35.5 2.3 31 143-180 15-45 (46)
4 PF03811 Zn_Tnp_IS1: InsA N-te 85.1 0.55 1.2E-05 34.6 1.6 30 148-179 6-36 (36)
5 COG3677 Transposase and inacti 82.8 0.85 1.8E-05 41.5 2.2 35 148-184 31-65 (129)
6 smart00440 ZnF_C2C2 C2C2 Zinc 80.1 1.6 3.5E-05 32.4 2.5 37 148-184 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 73.9 2.4 5.3E-05 31.3 1.9 36 148-183 1-39 (39)
8 cd00202 ZnF_GATA Zinc finger D 70.0 4 8.6E-05 32.2 2.4 40 149-191 1-40 (54)
9 PF13453 zf-TFIIB: Transcripti 66.0 1.8 3.9E-05 31.8 -0.2 37 149-190 1-37 (41)
10 smart00401 ZnF_GATA zinc finge 58.3 7.5 0.00016 30.3 2.0 39 147-188 3-41 (52)
11 TIGR01384 TFS_arch transcripti 58.0 10 0.00022 32.3 3.0 39 147-185 62-103 (104)
12 PHA02998 RNA polymerase subuni 57.7 9 0.0002 37.7 2.8 39 146-184 142-183 (195)
13 PRK14810 formamidopyrimidine-D 51.1 8.9 0.00019 38.5 1.7 29 147-180 244-272 (272)
14 TIGR01385 TFSII transcription 51.0 11 0.00024 38.8 2.5 41 143-183 254-297 (299)
15 PF04981 NMD3: NMD3 family ; 50.6 7.9 0.00017 37.8 1.2 26 161-186 19-49 (236)
16 PRK14811 formamidopyrimidine-D 46.5 12 0.00026 37.6 1.8 30 147-181 235-264 (269)
17 KOG1819 FYVE finger-containing 46.0 18 0.0004 40.6 3.2 31 149-185 900-930 (990)
18 PF09526 DUF2387: Probable met 44.6 15 0.00032 30.9 1.8 31 147-180 8-38 (71)
19 PF04216 FdhE: Protein involve 44.4 11 0.00023 37.8 1.1 37 147-183 211-249 (290)
20 PRK01103 formamidopyrimidine/5 43.7 14 0.0003 37.0 1.8 29 147-180 245-273 (274)
21 PF14690 zf-ISL3: zinc-finger 42.6 12 0.00026 27.4 0.9 32 147-178 2-47 (47)
22 PRK13945 formamidopyrimidine-D 40.7 17 0.00036 36.6 1.9 29 147-180 254-282 (282)
23 PRK10445 endonuclease VIII; Pr 40.6 16 0.00036 36.4 1.7 29 147-180 235-263 (263)
24 TIGR00244 transcriptional regu 38.6 21 0.00045 33.9 2.0 44 149-192 2-48 (147)
25 PF06220 zf-U1: U1 zinc finger 38.4 13 0.00029 27.5 0.5 17 170-186 1-17 (38)
26 PRK00464 nrdR transcriptional 36.9 22 0.00047 33.6 1.9 44 149-192 2-48 (154)
27 TIGR00577 fpg formamidopyrimid 36.9 21 0.00045 35.8 1.8 28 147-179 245-272 (272)
28 PHA00626 hypothetical protein 36.3 24 0.00053 29.1 1.8 37 149-187 2-38 (59)
29 KOG2691 RNA polymerase II subu 35.8 25 0.00055 32.2 2.0 69 102-184 39-113 (113)
30 TIGR01562 FdhE formate dehydro 33.5 29 0.00062 36.2 2.2 10 173-182 253-262 (305)
31 PRK00432 30S ribosomal protein 31.9 23 0.00051 27.7 1.0 25 148-180 21-45 (50)
32 PF14354 Lar_restr_allev: Rest 31.3 38 0.00082 26.2 2.1 35 146-180 2-37 (61)
33 PRK14892 putative transcriptio 31.0 32 0.0007 30.6 1.8 35 144-182 18-52 (99)
34 TIGR03655 anti_R_Lar restricti 29.7 42 0.00092 25.9 2.1 32 148-180 2-34 (53)
35 COG0266 Nei Formamidopyrimidin 29.5 30 0.00066 35.6 1.6 29 147-180 245-273 (273)
36 KOG0132 RNA polymerase II C-te 29.1 4.4E+02 0.0094 31.6 10.6 8 319-326 591-598 (894)
37 PF08273 Prim_Zn_Ribbon: Zinc- 28.6 34 0.00074 26.0 1.4 33 146-180 2-34 (40)
38 PRK03564 formate dehydrogenase 28.2 41 0.00089 35.2 2.3 10 173-182 253-262 (309)
39 PF06827 zf-FPG_IleRS: Zinc fi 25.1 27 0.00058 24.0 0.3 28 148-180 2-29 (30)
40 PF01783 Ribosomal_L32p: Ribos 24.2 45 0.00097 26.4 1.4 27 140-179 20-46 (56)
41 TIGR02443 conserved hypothetic 22.8 58 0.0013 26.9 1.8 31 146-179 8-38 (59)
42 PF06217 GAGA_bind: GAGA bindi 21.0 70 0.0015 33.6 2.4 24 331-362 206-230 (301)
43 PF05129 Elf1: Transcription e 20.1 57 0.0012 27.8 1.3 44 139-183 14-57 (81)
No 1
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=100.00 E-value=8.2e-36 Score=237.77 Aligned_cols=62 Identities=74% Similarity=1.480 Sum_probs=60.1
Q ss_pred CCCCccCCCCCcCCCCceeeecccCCCCCcccchhchhccccCCcccccccCcCcccCCCCC
Q 038013 143 KPDKILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTMRNVPVGAGRRKNKSSS 204 (494)
Q Consensus 143 ~p~~~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~RyWT~GG~lRnVPvGgG~RK~k~sS 204 (494)
+|++.++||||+|++|||||||||++.||||||++|+||||+||+|||||||||+||+|++|
T Consensus 1 ~~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~ 62 (63)
T PF02701_consen 1 KPEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSS 62 (63)
T ss_pred CCccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCC
Confidence 58899999999999999999999999999999999999999999999999999999999964
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=88.42 E-value=0.19 Score=46.56 Aligned_cols=34 Identities=26% Similarity=0.661 Sum_probs=27.6
Q ss_pred ccCCCCCcCCCCceeeeccc--CCCCCcccchhchhcc
Q 038013 147 ILPCPRCNSMDTKFCYYNNY--NVNQPRHFCKNCQRYW 182 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy--~~~QPRhfCk~C~RyW 182 (494)
...||||.|.+|+. .+.| +.++.-|+|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~--~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTI--TSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEe--ecCCCChhhHHHhhhhhhCCcH
Confidence 58999999999997 5666 4567889999998633
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=86.95 E-value=0.51 Score=35.49 Aligned_cols=31 Identities=35% Similarity=0.779 Sum_probs=23.7
Q ss_pred CCCCccCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 143 KPDKILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 143 ~p~~~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
=|+. ..||+|.+. ++..+.+ +.++.|++|++
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 3444 669999998 6655555 78899999985
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=85.13 E-value=0.55 Score=34.63 Aligned_cols=30 Identities=33% Similarity=0.731 Sum_probs=21.2
Q ss_pred cCCCCCcCCCCceeeecccCC-CCCcccchhch
Q 038013 148 LPCPRCNSMDTKFCYYNNYNV-NQPRHFCKNCQ 179 (494)
Q Consensus 148 ~~CPRC~S~~TkfcyyNNy~~-~QPRhfCk~C~ 179 (494)
+.||+|.+.+.= |=|-.+. -..||+|++|+
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 689999998721 2344443 35899999996
No 5
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.83 E-value=0.85 Score=41.51 Aligned_cols=35 Identities=29% Similarity=0.634 Sum_probs=27.8
Q ss_pred cCCCCCcCCCCceeeecccCCCCCcccchhchhcccc
Q 038013 148 LPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTA 184 (494)
Q Consensus 148 ~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~RyWT~ 184 (494)
..||+|.+.+ +-=++-+.....|+.|++|++=|+.
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 4899999999 3335555666999999999998874
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=80.13 E-value=1.6 Score=32.43 Aligned_cols=37 Identities=24% Similarity=0.806 Sum_probs=27.9
Q ss_pred cCCCCCcCCCCceeeecccCCCCC---cccchhchhcccc
Q 038013 148 LPCPRCNSMDTKFCYYNNYNVNQP---RHFCKNCQRYWTA 184 (494)
Q Consensus 148 ~~CPRC~S~~TkfcyyNNy~~~QP---RhfCk~C~RyWT~ 184 (494)
.+||+|...+.-|-..+-.....| -|.|.+|...|..
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 379999988877766655555555 4999999999963
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=73.94 E-value=2.4 Score=31.27 Aligned_cols=36 Identities=25% Similarity=0.753 Sum_probs=23.9
Q ss_pred cCCCCCcCCCCceeeecccCCCCC---cccchhchhccc
Q 038013 148 LPCPRCNSMDTKFCYYNNYNVNQP---RHFCKNCQRYWT 183 (494)
Q Consensus 148 ~~CPRC~S~~TkfcyyNNy~~~QP---RhfCk~C~RyWT 183 (494)
..||.|...+.-|--.+.....-| .|.|.+|..-|+
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 379999998877655555554444 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=69.98 E-value=4 Score=32.22 Aligned_cols=40 Identities=25% Similarity=0.668 Sum_probs=29.2
Q ss_pred CCCCCcCCCCceeeecccCCCCCcccchhchhccccCCccccc
Q 038013 149 PCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTMRNV 191 (494)
Q Consensus 149 ~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~RyWT~GG~lRnV 191 (494)
.|-.|....|..=.-. ......+|-+|..||...|.+|-+
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 3778888777542222 256789999999999999976544
No 9
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=65.99 E-value=1.8 Score=31.82 Aligned_cols=37 Identities=22% Similarity=0.596 Sum_probs=26.6
Q ss_pred CCCCCcCCCCceeeecccCCCCCcccchhchhccccCCcccc
Q 038013 149 PCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTMRN 190 (494)
Q Consensus 149 ~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~RyWT~GG~lRn 190 (494)
+||+|...=...-+ ..-+-+.|.+|...|-..|.+..
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 59999885444433 23566889999999988776543
No 10
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=58.26 E-value=7.5 Score=30.30 Aligned_cols=39 Identities=18% Similarity=0.526 Sum_probs=29.2
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCcccchhchhccccCCcc
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGTM 188 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~RyWT~GG~l 188 (494)
...|--|....|..=.-. ..-++.+|-+|.-||...|.+
T Consensus 3 ~~~C~~C~~~~T~~WR~g---~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 3 GRSCSNCGTTETPLWRRG---PSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCcCCCCCCCCCccccC---CCCCCcEeecccHHHHHcCCC
Confidence 468999999888643222 223379999999999998886
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=57.97 E-value=10 Score=32.31 Aligned_cols=39 Identities=18% Similarity=0.620 Sum_probs=28.2
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCc---ccchhchhccccC
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPR---HFCKNCQRYWTAG 185 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPR---hfCk~C~RyWT~G 185 (494)
...||+|...+.-|-..+-.....|- |.|.+|+-.|+.+
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 47999998777766555544433332 8999999999875
No 12
>PHA02998 RNA polymerase subunit; Provisional
Probab=57.69 E-value=9 Score=37.73 Aligned_cols=39 Identities=26% Similarity=0.688 Sum_probs=33.1
Q ss_pred CccCCCCCcCCCCceeeecccCCCCCc---ccchhchhcccc
Q 038013 146 KILPCPRCNSMDTKFCYYNNYNVNQPR---HFCKNCQRYWTA 184 (494)
Q Consensus 146 ~~~~CPRC~S~~TkfcyyNNy~~~QPR---hfCk~C~RyWT~ 184 (494)
....||+|...++-|--.|-.....|- |.|..|..-|.-
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 457999999999998888888777774 899999998864
No 13
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=51.10 E-value=8.9 Score=38.46 Aligned_cols=29 Identities=24% Similarity=0.677 Sum_probs=21.2
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
..+||||...=.+.-+= .+.-|||..||+
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 45999999766654332 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=50.98 E-value=11 Score=38.83 Aligned_cols=41 Identities=15% Similarity=0.592 Sum_probs=29.9
Q ss_pred CCCCccCCCCCcCCCCceeeecccCCCCCc---ccchhchhccc
Q 038013 143 KPDKILPCPRCNSMDTKFCYYNNYNVNQPR---HFCKNCQRYWT 183 (494)
Q Consensus 143 ~p~~~~~CPRC~S~~TkfcyyNNy~~~QPR---hfCk~C~RyWT 183 (494)
.......||+|...+..|-..+......|- |.|..|...|.
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 344568999999888777555555555553 78999999984
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=50.60 E-value=7.9 Score=37.85 Aligned_cols=26 Identities=27% Similarity=0.852 Sum_probs=17.6
Q ss_pred eeecccCCCC-----CcccchhchhccccCC
Q 038013 161 CYYNNYNVNQ-----PRHFCKNCQRYWTAGG 186 (494)
Q Consensus 161 cyyNNy~~~Q-----PRhfCk~C~RyWT~GG 186 (494)
||+..+.+.. --.+|+.|.||+..|.
T Consensus 19 C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 19 CYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred HhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 4555554422 3379999999999854
No 16
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=46.53 E-value=12 Score=37.58 Aligned_cols=30 Identities=37% Similarity=0.821 Sum_probs=21.7
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCcccchhchhc
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRY 181 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~Ry 181 (494)
+.+||||...=.|.-+ . .+.-|||..||+-
T Consensus 235 g~pC~~Cg~~I~~~~~-~----gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 235 GQPCPRCGTPIEKIVV-G----GRGTHFCPQCQPL 264 (269)
T ss_pred cCCCCcCCCeeEEEEE-C----CCCcEECCCCcCC
Confidence 3489999977666433 2 3667999999963
No 17
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=45.99 E-value=18 Score=40.63 Aligned_cols=31 Identities=23% Similarity=0.543 Sum_probs=20.3
Q ss_pred CCCCCcCCCCceeeecccCCCCCcccchhchhccccC
Q 038013 149 PCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAG 185 (494)
Q Consensus 149 ~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~RyWT~G 185 (494)
.|++|-.-.+-|-. -+-||.|++|.+.+-+-
T Consensus 900 ~a~~cmacq~pf~a------frrrhhcrncggifcg~ 930 (990)
T KOG1819|consen 900 DAEQCMACQMPFNA------FRRRHHCRNCGGIFCGK 930 (990)
T ss_pred cchhhhhccCcHHH------HHHhhhhcccCceeecc
Confidence 45665554554422 27899999998877543
No 18
>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=44.60 E-value=15 Score=30.87 Aligned_cols=31 Identities=29% Similarity=0.542 Sum_probs=24.9
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
+..||+|.++||=..|.-|. ..-.-|-.|.-
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 57899999999888877776 55667888864
No 19
>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=44.40 E-value=11 Score=37.83 Aligned_cols=37 Identities=22% Similarity=0.631 Sum_probs=18.1
Q ss_pred ccCCCCCcCCCCc-eeeec-ccCCCCCcccchhchhccc
Q 038013 147 ILPCPRCNSMDTK-FCYYN-NYNVNQPRHFCKNCQRYWT 183 (494)
Q Consensus 147 ~~~CPRC~S~~Tk-fcyyN-Ny~~~QPRhfCk~C~RyWT 183 (494)
...||.|...+.. +-||. .-....--+.|..|+.|+-
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 4578888877664 44553 2233333489999999983
No 20
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=43.74 E-value=14 Score=36.99 Aligned_cols=29 Identities=31% Similarity=0.697 Sum_probs=21.3
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
..+||||...=.|. .++ .+.-|||..||+
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 45899999776554 333 366799999996
No 21
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=42.56 E-value=12 Score=27.37 Aligned_cols=32 Identities=31% Similarity=0.624 Sum_probs=18.7
Q ss_pred ccCCCCCcCCCCce-eeec---------cc----CCCCCcccchhc
Q 038013 147 ILPCPRCNSMDTKF-CYYN---------NY----NVNQPRHFCKNC 178 (494)
Q Consensus 147 ~~~CPRC~S~~Tkf-cyyN---------Ny----~~~QPRhfCk~C 178 (494)
...||.|.+...+. -++. .+ .+..+|++|++|
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 35799999876221 1110 11 256778888887
No 22
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.72 E-value=17 Score=36.64 Aligned_cols=29 Identities=28% Similarity=0.751 Sum_probs=21.2
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
..+||||...=.|.-+ . .+--|||..||+
T Consensus 254 g~pC~~Cg~~I~~~~~-~----gR~t~~CP~CQ~ 282 (282)
T PRK13945 254 GKPCRKCGTPIERIKL-A----GRSTHWCPNCQK 282 (282)
T ss_pred cCCCCcCCCeeEEEEE-C----CCccEECCCCcC
Confidence 3599999977666544 2 256699999995
No 23
>PRK10445 endonuclease VIII; Provisional
Probab=40.55 E-value=16 Score=36.42 Aligned_cols=29 Identities=28% Similarity=0.660 Sum_probs=21.3
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
..+||||...=.+.-+ + .+.-|||..||+
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 4589999877665544 2 266799999985
No 24
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=38.64 E-value=21 Score=33.95 Aligned_cols=44 Identities=20% Similarity=0.403 Sum_probs=31.9
Q ss_pred CCCCCcCCCCceeee---cccCCCCCcccchhchhccccCCcccccc
Q 038013 149 PCPRCNSMDTKFCYY---NNYNVNQPRHFCKNCQRYWTAGGTMRNVP 192 (494)
Q Consensus 149 ~CPRC~S~~Tkfcyy---NNy~~~QPRhfCk~C~RyWT~GG~lRnVP 192 (494)
.||.|...+||+-=- ...+.-+-|..|.+|.+-||-==.+-..|
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~ 48 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLP 48 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccc
Confidence 699999999999532 33344556799999999998655544444
No 25
>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=38.38 E-value=13 Score=27.54 Aligned_cols=17 Identities=35% Similarity=0.976 Sum_probs=7.2
Q ss_pred CCcccchhchhccccCC
Q 038013 170 QPRHFCKNCQRYWTAGG 186 (494)
Q Consensus 170 QPRhfCk~C~RyWT~GG 186 (494)
+|||||.=|..|.|..-
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 68999999999997665
No 26
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=36.86 E-value=22 Score=33.64 Aligned_cols=44 Identities=27% Similarity=0.464 Sum_probs=31.7
Q ss_pred CCCCCcCCCCcee---eecccCCCCCcccchhchhccccCCcccccc
Q 038013 149 PCPRCNSMDTKFC---YYNNYNVNQPRHFCKNCQRYWTAGGTMRNVP 192 (494)
Q Consensus 149 ~CPRC~S~~Tkfc---yyNNy~~~QPRhfCk~C~RyWT~GG~lRnVP 192 (494)
.||.|.+.+|++- |+-.-|+-.-||-|.+|.+-++.==++-..+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCcc
Confidence 6999999998764 4445555666799999999887655444443
No 27
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.85 E-value=21 Score=35.83 Aligned_cols=28 Identities=36% Similarity=0.742 Sum_probs=20.6
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCcccchhch
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQ 179 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~ 179 (494)
+.+||||...=.|.- ++ .+.-|||..||
T Consensus 245 g~pC~~Cg~~I~~~~-~~----gR~t~~CP~CQ 272 (272)
T TIGR00577 245 GEPCRRCGTPIEKIK-VG----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCCeeEEEE-EC----CCCCEECCCCC
Confidence 359999997766643 33 36679999997
No 28
>PHA00626 hypothetical protein
Probab=36.34 E-value=24 Score=29.11 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=24.7
Q ss_pred CCCCCcCCCCceeeecccCCCCCcccchhchhccccCCc
Q 038013 149 PCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGT 187 (494)
Q Consensus 149 ~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~RyWT~GG~ 187 (494)
.||+|.|.+.-=|-.= ....-||.|+.|.=++|...-
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 6999999754322111 111357999999999998653
No 29
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=35.82 E-value=25 Score=32.20 Aligned_cols=69 Identities=23% Similarity=0.382 Sum_probs=41.8
Q ss_pred CCCCCCCCCCCCchhhhhhccccccCccccccccccccccCC-CCCccCCCCCcCCCCceeeecccCCCC-----Ccccc
Q 038013 102 TSSGNSDNPKTLSVDRETRSLKSSKNGEQSETSNSQEKTLKK-PDKILPCPRCNSMDTKFCYYNNYNVNQ-----PRHFC 175 (494)
Q Consensus 102 ~~s~~~~~pktps~~~~~~~~~~~~~~~~~~~~~~q~~~~~~-p~~~~~CPRC~S~~TkfcyyNNy~~~Q-----PRhfC 175 (494)
+++.+-.|+-..+++|-+.- -..-.++.+||. -+ ..||+|...+.-| |+--.... --|.|
T Consensus 39 ~s~~vY~~~~~~e~dE~t~i----------i~Dl~~DPTLPrts~--~~C~~C~~~eavf--fQ~~~~r~d~~m~l~yvC 104 (113)
T KOG2691|consen 39 DSSRVYVNELSHEHDELTQI----------IMDLASDPTLPRTSD--KHCPKCGHREAVF--FQAQTRRADEAMRLFYVC 104 (113)
T ss_pred CCcceEcCCcccchhhHHHH----------HHhhccCCCcCcccc--ccCCccCCcceEE--EecccccccceEEEEEEe
Confidence 34455556655555443321 122446677765 44 4999999988766 65432211 11889
Q ss_pred hhchhcccc
Q 038013 176 KNCQRYWTA 184 (494)
Q Consensus 176 k~C~RyWT~ 184 (494)
-+|.-.||.
T Consensus 105 ~~C~h~wte 113 (113)
T KOG2691|consen 105 CSCGHRWTE 113 (113)
T ss_pred ccccccccC
Confidence 999999984
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=33.45 E-value=29 Score=36.18 Aligned_cols=10 Identities=40% Similarity=1.046 Sum_probs=5.7
Q ss_pred ccchhchhcc
Q 038013 173 HFCKNCQRYW 182 (494)
Q Consensus 173 hfCk~C~RyW 182 (494)
+.|..|+.|+
T Consensus 253 e~C~~C~~Yl 262 (305)
T TIGR01562 253 ETCDSCQGYL 262 (305)
T ss_pred eeccccccch
Confidence 4566665554
No 31
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=31.95 E-value=23 Score=27.70 Aligned_cols=25 Identities=36% Similarity=0.679 Sum_probs=18.5
Q ss_pred cCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 148 LPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 148 ~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
.-||+|.+. |..... .|+.|..|..
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 554443 6999999974
No 32
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=31.34 E-value=38 Score=26.17 Aligned_cols=35 Identities=23% Similarity=0.529 Sum_probs=19.8
Q ss_pred CccCCCCCcCCCCceeeecccCCCC-Ccccchhchh
Q 038013 146 KILPCPRCNSMDTKFCYYNNYNVNQ-PRHFCKNCQR 180 (494)
Q Consensus 146 ~~~~CPRC~S~~TkfcyyNNy~~~Q-PRhfCk~C~R 180 (494)
+..+||.|.+....+.+........ -.-+|.+|..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 4679999965555544422221111 3455888866
No 33
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=30.96 E-value=32 Score=30.57 Aligned_cols=35 Identities=31% Similarity=0.579 Sum_probs=25.4
Q ss_pred CCCccCCCCCcCCCCceeeecccCCCCCcccchhchhcc
Q 038013 144 PDKILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYW 182 (494)
Q Consensus 144 p~~~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~RyW 182 (494)
......||.|.+. +--|=+.. ..+++.|..|.-|-
T Consensus 18 lpt~f~CP~Cge~-~v~v~~~k---~~~h~~C~~CG~y~ 52 (99)
T PRK14892 18 LPKIFECPRCGKV-SISVKIKK---NIAIITCGNCGLYT 52 (99)
T ss_pred CCcEeECCCCCCe-EeeeecCC---CcceEECCCCCCcc
Confidence 3478999999952 33334443 58899999999884
No 34
>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=29.69 E-value=42 Score=25.91 Aligned_cols=32 Identities=25% Similarity=0.598 Sum_probs=19.9
Q ss_pred cCCCCCcCCCCceeeecccCCCCCccc-chhchh
Q 038013 148 LPCPRCNSMDTKFCYYNNYNVNQPRHF-CKNCQR 180 (494)
Q Consensus 148 ~~CPRC~S~~TkfcyyNNy~~~QPRhf-Ck~C~R 180 (494)
.+||.|.+.+-.|=+ ...+....++| |..|+.
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 589999997775532 12333344454 887764
No 35
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=29.52 E-value=30 Score=35.62 Aligned_cols=29 Identities=28% Similarity=0.615 Sum_probs=21.2
Q ss_pred ccCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 147 ILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 147 ~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
+-+|+||.+.=.|--. -.+..|||..||+
T Consensus 245 GepC~~CGt~I~k~~~-----~gR~t~~CP~CQ~ 273 (273)
T COG0266 245 GEPCRRCGTPIEKIKL-----GGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCccCCEeEEEEE-----cCCcCEeCCCCCC
Confidence 3499999987666422 2366799999995
No 36
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=29.13 E-value=4.4e+02 Score=31.59 Aligned_cols=8 Identities=50% Similarity=0.899 Sum_probs=4.8
Q ss_pred CCCCCCCC
Q 038013 319 YFPGPPWP 326 (494)
Q Consensus 319 ~~pg~PWp 326 (494)
++||+|-+
T Consensus 591 ~~pg~P~~ 598 (894)
T KOG0132|consen 591 PRPGAPIP 598 (894)
T ss_pred CCCCCCCC
Confidence 67776543
No 37
>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=28.65 E-value=34 Score=25.95 Aligned_cols=33 Identities=24% Similarity=0.704 Sum_probs=19.1
Q ss_pred CccCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 146 KILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 146 ~~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
+..+||-|.. ..+|..|-+. .-+-..+|+.|..
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 3569999988 5688866654 3347899999954
No 38
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=28.21 E-value=41 Score=35.16 Aligned_cols=10 Identities=30% Similarity=0.919 Sum_probs=5.1
Q ss_pred ccchhchhcc
Q 038013 173 HFCKNCQRYW 182 (494)
Q Consensus 173 hfCk~C~RyW 182 (494)
+.|..|++|+
T Consensus 253 e~C~~C~~Yl 262 (309)
T PRK03564 253 ESCGDCGTYL 262 (309)
T ss_pred eecccccccc
Confidence 4455555554
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=25.14 E-value=27 Score=24.00 Aligned_cols=28 Identities=25% Similarity=0.625 Sum_probs=15.4
Q ss_pred cCCCCCcCCCCceeeecccCCCCCcccchhchh
Q 038013 148 LPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQR 180 (494)
Q Consensus 148 ~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~R 180 (494)
.+||||...-.++-..+ +.-+||..|+.
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 47999998877764421 33478888863
No 40
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=24.22 E-value=45 Score=26.41 Aligned_cols=27 Identities=33% Similarity=0.972 Sum_probs=20.2
Q ss_pred ccCCCCCccCCCCCcCCCCceeeecccCCCCCcccchhch
Q 038013 140 TLKKPDKILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQ 179 (494)
Q Consensus 140 ~~~~p~~~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~ 179 (494)
.++.| .+..||-|... .+|.+.|.+|+
T Consensus 20 ~l~~~-~l~~c~~cg~~------------~~~H~vc~~cG 46 (56)
T PF01783_consen 20 KLKAP-NLVKCPNCGEP------------KLPHRVCPSCG 46 (56)
T ss_dssp S--TT-SEEESSSSSSE------------ESTTSBCTTTB
T ss_pred ccccc-ceeeeccCCCE------------ecccEeeCCCC
Confidence 45556 88899999852 38899999996
No 41
>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=22.78 E-value=58 Score=26.93 Aligned_cols=31 Identities=26% Similarity=0.432 Sum_probs=22.7
Q ss_pred CccCCCCCcCCCCceeeecccCCCCCcccchhch
Q 038013 146 KILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQ 179 (494)
Q Consensus 146 ~~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~ 179 (494)
-+..||+|..+||=..|.-|.- ...-|-.|.
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 3578999999999987755543 345677774
No 42
>PF06217 GAGA_bind: GAGA binding protein-like family; InterPro: IPR010409 This family includes gbp a protein from Soybean that binds to GAGA element dinucleotide repeat DNA []. It seems likely that the region which defines this family mediates DNA binding. This putative domain contains several conserved cysteines and a histidine suggesting this may be a zinc-binding DNA interaction domain.
Probab=20.95 E-value=70 Score=33.61 Aligned_cols=24 Identities=38% Similarity=0.829 Sum_probs=15.4
Q ss_pred CCCCCCCCCC-CCCcccccCCCCccCCCCCCCC
Q 038013 331 TPMPPPGFYP-SGFPVSFYPETTYWGCAVPGYC 362 (494)
Q Consensus 331 p~~PpP~fcP-pg~p~pfyPa~aYWgC~vPg~W 362 (494)
+.||.| +|- .|.|=++|= ||| |+|
T Consensus 206 s~mP~P-vCSCTG~pqqCYr----WG~---GGW 230 (301)
T PF06217_consen 206 STMPIP-VCSCTGVPQQCYR----WGN---GGW 230 (301)
T ss_pred CCCCCc-ccccCCCCccccc----cCC---Ccc
Confidence 345544 565 576666653 999 788
No 43
>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=20.10 E-value=57 Score=27.78 Aligned_cols=44 Identities=20% Similarity=0.346 Sum_probs=21.5
Q ss_pred cccCCCCCccCCCCCcCCCCceeeecccCCCCCcccchhchhccc
Q 038013 139 KTLKKPDKILPCPRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWT 183 (494)
Q Consensus 139 ~~~~~p~~~~~CPRC~S~~TkfcyyNNy~~~QPRhfCk~C~RyWT 183 (494)
+...+.+....||.|+..++=-|-+..- ......-|+.|+-++.
T Consensus 14 k~~~~l~~~F~CPfC~~~~sV~v~idkk-~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 14 KKKPKLPKVFDCPFCNHEKSVSVKIDKK-EGIGILSCRVCGESFQ 57 (81)
T ss_dssp ------SS----TTT--SS-EEEEEETT-TTEEEEEESSS--EEE
T ss_pred CcCCCCCceEcCCcCCCCCeEEEEEEcc-CCEEEEEecCCCCeEE
Confidence 3344667889999999888877777433 5567788999976654
Done!