Query 021641
Match_columns 309
No_of_seqs 136 out of 251
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 04:33:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021641.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021641hhsearch_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 3.6E-37 7.8E-42 233.7 3.9 63 43-105 1-63 (63)
2 TIGR02159 PA_CoA_Oxy4 phenylac 93.7 0.041 8.8E-07 48.0 2.0 34 47-82 105-140 (146)
3 PF12760 Zn_Tnp_IS1595: Transp 92.6 0.1 2.3E-06 36.8 2.4 29 46-80 17-45 (46)
4 COG3677 Transposase and inacti 92.4 0.091 2E-06 44.9 2.3 35 48-84 31-65 (129)
5 PF03811 Zn_Tnp_IS1: InsA N-te 92.2 0.089 1.9E-06 36.5 1.6 30 48-79 6-36 (36)
6 smart00440 ZnF_C2C2 C2C2 Zinc 89.3 0.37 8.1E-06 33.6 2.7 37 48-84 1-40 (40)
7 PF01096 TFIIS_C: Transcriptio 87.1 0.46 9.9E-06 33.0 2.0 36 48-83 1-39 (39)
8 TIGR01384 TFS_arch transcripti 81.9 1.7 3.6E-05 34.8 3.3 42 44-85 59-103 (104)
9 PHA02998 RNA polymerase subuni 80.6 1.6 3.4E-05 40.5 3.0 38 47-84 143-183 (195)
10 PF04216 FdhE: Protein involve 76.9 1.2 2.5E-05 41.9 1.1 36 48-83 212-249 (290)
11 PF13453 zf-TFIIB: Transcripti 76.1 0.79 1.7E-05 31.6 -0.1 37 49-90 1-37 (41)
12 cd00202 ZnF_GATA Zinc finger D 73.2 3.2 6.9E-05 30.8 2.4 41 49-92 1-41 (54)
13 TIGR01385 TFSII transcription 63.7 5.6 0.00012 38.6 2.6 37 47-83 258-297 (299)
14 PHA00626 hypothetical protein 62.8 5.7 0.00012 30.8 2.0 36 49-86 2-37 (59)
15 PF04981 NMD3: NMD3 family ; 62.1 4.2 9.2E-05 37.3 1.4 26 61-86 19-49 (236)
16 smart00401 ZnF_GATA zinc finge 56.4 9 0.00019 28.0 2.0 39 47-88 3-41 (52)
17 TIGR00244 transcriptional regu 56.1 7.9 0.00017 34.6 2.0 40 49-88 2-44 (147)
18 PF06220 zf-U1: U1 zinc finger 53.4 5.5 0.00012 27.7 0.5 17 70-86 1-17 (38)
19 PRK14810 formamidopyrimidine-D 52.0 9.1 0.0002 36.1 1.8 28 48-80 245-272 (272)
20 PF14690 zf-ISL3: zinc-finger 51.5 8 0.00017 26.5 1.0 31 48-78 3-47 (47)
21 PRK03564 formate dehydrogenase 50.4 11 0.00023 37.1 2.0 36 48-84 227-264 (309)
22 PRK14811 formamidopyrimidine-D 47.1 13 0.00028 35.1 2.0 28 48-80 236-263 (269)
23 PRK00464 nrdR transcriptional 46.7 14 0.00029 32.9 2.0 44 48-91 1-47 (154)
24 TIGR01562 FdhE formate dehydro 46.5 13 0.00028 36.4 2.0 35 48-83 225-263 (305)
25 PRK10445 endonuclease VIII; Pr 45.7 13 0.00029 34.8 1.9 29 47-80 235-263 (263)
26 KOG2906 RNA polymerase III sub 44.7 19 0.00042 30.7 2.5 37 47-83 65-104 (105)
27 PRK00432 30S ribosomal protein 42.6 14 0.00029 27.2 1.1 25 48-80 21-45 (50)
28 PRK01103 formamidopyrimidine/5 41.8 17 0.00038 34.0 2.0 28 48-80 246-273 (274)
29 PF09526 DUF2387: Probable met 40.6 21 0.00045 28.2 2.0 31 47-80 8-38 (71)
30 PRK13945 formamidopyrimidine-D 40.2 19 0.00042 34.0 2.1 28 48-80 255-282 (282)
31 KOG2691 RNA polymerase II subu 38.4 24 0.00053 30.5 2.2 36 47-84 73-113 (113)
32 TIGR00577 fpg formamidopyrimid 38.0 21 0.00045 33.6 1.9 27 48-79 246-272 (272)
33 PF14599 zinc_ribbon_6: Zinc-r 37.3 13 0.00028 28.6 0.4 13 47-59 48-60 (61)
34 PF05129 Elf1: Transcription e 34.5 23 0.00049 28.3 1.3 47 36-83 11-57 (81)
35 COG0266 Nei Formamidopyrimidin 34.1 22 0.00047 34.5 1.4 28 48-80 246-273 (273)
36 COG1327 Predicted transcriptio 28.8 35 0.00076 31.0 1.7 41 49-89 2-45 (156)
37 TIGR03655 anti_R_Lar restricti 28.5 48 0.001 24.0 2.1 32 48-80 2-34 (53)
38 TIGR00686 phnA alkylphosphonat 26.7 43 0.00094 28.8 1.8 30 49-86 4-33 (109)
39 PF06827 zf-FPG_IleRS: Zinc fi 25.8 30 0.00066 22.2 0.6 27 48-79 2-28 (30)
40 PF06682 DUF1183: Protein of u 25.3 23 0.0005 35.0 -0.0 40 37-76 38-84 (318)
41 COG1997 RPL43A Ribosomal prote 25.2 38 0.00083 28.2 1.2 40 48-94 36-75 (89)
42 PF08273 Prim_Zn_Ribbon: Zinc- 24.8 56 0.0012 23.3 1.8 31 48-80 4-34 (40)
43 PF07282 OrfB_Zn_ribbon: Putat 24.6 44 0.00095 24.6 1.3 30 48-84 29-58 (69)
44 PF01807 zf-CHC2: CHC2 zinc fi 23.5 51 0.0011 26.5 1.6 29 48-80 34-62 (97)
45 PRK10220 hypothetical protein; 23.3 51 0.0011 28.5 1.6 30 49-86 5-34 (111)
46 PF08274 PhnA_Zn_Ribbon: PhnA 22.9 39 0.00084 22.8 0.7 27 49-83 4-30 (30)
47 COG5175 MOT2 Transcriptional r 21.5 22 0.00047 36.4 -1.1 49 44-96 27-76 (480)
48 TIGR02443 conserved hypothetic 21.3 67 0.0015 25.0 1.8 30 47-79 9-38 (59)
49 COG1594 RPB9 DNA-directed RNA 21.2 93 0.002 26.2 2.8 37 48-84 73-112 (113)
50 PRK12496 hypothetical protein; 21.1 56 0.0012 28.9 1.5 24 73-96 128-151 (164)
51 PF10613 Lig_chan-Glu_bd: Liga 21.0 22 0.00048 27.4 -0.9 9 297-305 53-61 (65)
52 smart00661 RPOL9 RNA polymeras 20.8 67 0.0014 22.3 1.6 34 49-87 2-35 (52)
No 1
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=100.00 E-value=3.6e-37 Score=233.65 Aligned_cols=63 Identities=79% Similarity=1.583 Sum_probs=60.2
Q ss_pred CCccCCCCCCCCCCCcceeeeccccCCCCcccccccccccccCCccccccCCCCcCCCCCCCC
Q 021641 43 RPQEQLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNVPVGGGSRKNKRSIS 105 (309)
Q Consensus 43 ~p~~~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvPvGgG~RK~k~sss 105 (309)
+|++.++||||+|.||||||||||++.||||||++|+||||+||+|||||||||+||+|+++|
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 467779999999999999999999999999999999999999999999999999999999875
No 2
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=93.66 E-value=0.041 Score=47.97 Aligned_cols=34 Identities=26% Similarity=0.819 Sum_probs=26.8
Q ss_pred CCCCCCCCCCCcceeeeccc--cCCCCccccccccccc
Q 021641 47 QLNCPRCNSTNTKFCYYNNY--SLTQPRYFCKTCRRYW 82 (309)
Q Consensus 47 ~~~CPRC~S~~TKfcyyNNy--~~~QPR~fCk~CrRyW 82 (309)
...||||.|.+|+.. +.+ +.++.-|.|++|+.=+
T Consensus 105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence 489999999999964 555 4457779999998643
No 3
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=92.57 E-value=0.1 Score=36.85 Aligned_cols=29 Identities=41% Similarity=0.957 Sum_probs=22.4
Q ss_pred cCCCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 46 EQLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 46 ~~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
.+..||+|.+. ++..+.+ +.+|.|+.|++
T Consensus 17 ~g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCPHCGST--KHYRLKT----RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence 34679999998 5544444 78999999986
No 4
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.35 E-value=0.091 Score=44.90 Aligned_cols=35 Identities=37% Similarity=0.782 Sum_probs=28.0
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTE 84 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~ 84 (309)
..||+|.+.+ +-=+.-+.....||.|++|++-|+.
T Consensus 31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred CcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 7899999999 2225555566999999999999874
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=92.19 E-value=0.089 Score=36.50 Aligned_cols=30 Identities=47% Similarity=0.885 Sum_probs=21.2
Q ss_pred CCCCCCCCCCcceeeeccccC-CCCcccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSL-TQPRYFCKTCR 79 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~-~QPR~fCk~Cr 79 (309)
+.||+|.+++.- |=|-.+. -..||+|++|+
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 789999998721 1233433 36899999996
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.34 E-value=0.37 Score=33.63 Aligned_cols=37 Identities=30% Similarity=0.823 Sum_probs=27.6
Q ss_pred CCCCCCCCCCcceeeeccccCCCC---ccccccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQP---RYFCKTCRRYWTE 84 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QP---R~fCk~CrRyWT~ 84 (309)
.+||+|...+.-|-..+-.+...| -|.|..|...|.+
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 369999977777655555555555 3999999999964
No 7
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=87.13 E-value=0.46 Score=32.96 Aligned_cols=36 Identities=28% Similarity=0.829 Sum_probs=24.4
Q ss_pred CCCCCCCCCCcceeeeccccCCCCc---ccccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWT 83 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT 83 (309)
.+||.|...+.-|--.+..+...|- |.|.+|..-|+
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 3699999988766555555555553 89999999985
No 8
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=81.91 E-value=1.7 Score=34.79 Aligned_cols=42 Identities=24% Similarity=0.745 Sum_probs=29.5
Q ss_pred CccCCCCCCCCCCCcceeeeccccCCCCc---ccccccccccccC
Q 021641 44 PQEQLNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWTEG 85 (309)
Q Consensus 44 p~~~~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT~G 85 (309)
|.-...||+|...+.-|-..+-.+...|- |.|..|+-.|+++
T Consensus 59 ~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 59 PTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred CcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 33348999998777666555444444333 9999999999875
No 9
>PHA02998 RNA polymerase subunit; Provisional
Probab=80.57 E-value=1.6 Score=40.53 Aligned_cols=38 Identities=24% Similarity=0.602 Sum_probs=32.4
Q ss_pred CCCCCCCCCCCcceeeeccccCCCCc---cccccccccccc
Q 021641 47 QLNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWTE 84 (309)
Q Consensus 47 ~~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT~ 84 (309)
...||+|...++-|--.|-.+...|- |.|..|..-|.-
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 38899999999998888888877775 899999999963
No 10
>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=76.92 E-value=1.2 Score=41.86 Aligned_cols=36 Identities=25% Similarity=0.653 Sum_probs=18.5
Q ss_pred CCCCCCCCCCc-ceeeecc-ccCCCCcccccccccccc
Q 021641 48 LNCPRCNSTNT-KFCYYNN-YSLTQPRYFCKTCRRYWT 83 (309)
Q Consensus 48 ~~CPRC~S~~T-KfcyyNN-y~~~QPR~fCk~CrRyWT 83 (309)
..||.|...+. ++-||.. -....--+.|+.|+.|+-
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 68999988554 5666632 223233389999999983
No 11
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.06 E-value=0.79 Score=31.62 Aligned_cols=37 Identities=24% Similarity=0.622 Sum_probs=27.1
Q ss_pred CCCCCCCCCcceeeeccccCCCCcccccccccccccCCcccc
Q 021641 49 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRN 90 (309)
Q Consensus 49 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRn 90 (309)
+||+|...-...-+ ..-+-+.|..|.-.|=..|.+..
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 69999985555433 23566889999999988776654
No 12
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=73.23 E-value=3.2 Score=30.78 Aligned_cols=41 Identities=24% Similarity=0.667 Sum_probs=29.8
Q ss_pred CCCCCCCCCcceeeeccccCCCCcccccccccccccCCcccccc
Q 021641 49 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNVP 92 (309)
Q Consensus 49 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvP 92 (309)
.|-.|...+|..=.- .......+|-+|.-||.+.|..|.+-
T Consensus 1 ~C~~C~~~~Tp~WR~---g~~~~~~LCNaCgl~~~k~~~~rp~~ 41 (54)
T cd00202 1 ACSNCGTTTTPLWRR---GPSGGSTLCNACGLYWKKHGVMRPLS 41 (54)
T ss_pred CCCCCCCCCCccccc---CCCCcchHHHHHHHHHHhcCCCCCcc
Confidence 377888888763221 22467899999999999999766553
No 13
>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=63.65 E-value=5.6 Score=38.59 Aligned_cols=37 Identities=19% Similarity=0.631 Sum_probs=26.9
Q ss_pred CCCCCCCCCCCcceeeeccccCCCCc---ccccccccccc
Q 021641 47 QLNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWT 83 (309)
Q Consensus 47 ~~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT 83 (309)
...||+|...+..|-..+..+...|- |.|..|...|.
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 38999999777766555555544453 78999999984
No 14
>PHA00626 hypothetical protein
Probab=62.77 E-value=5.7 Score=30.82 Aligned_cols=36 Identities=22% Similarity=0.382 Sum_probs=24.4
Q ss_pred CCCCCCCCCcceeeeccccCCCCcccccccccccccCC
Q 021641 49 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGG 86 (309)
Q Consensus 49 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG 86 (309)
.||+|.|.+.-=|=. -....-||.|++|.=.+|+..
T Consensus 2 ~CP~CGS~~Ivrcg~--cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKT--MRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeece--ecccCcceEcCCCCCeechhh
Confidence 699999975432211 012246899999999998754
No 15
>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=62.14 E-value=4.2 Score=37.27 Aligned_cols=26 Identities=27% Similarity=0.809 Sum_probs=17.7
Q ss_pred eeeccccCCC-----CcccccccccccccCC
Q 021641 61 CYYNNYSLTQ-----PRYFCKTCRRYWTEGG 86 (309)
Q Consensus 61 cyyNNy~~~Q-----PR~fCk~CrRyWT~GG 86 (309)
||...+.+.. --.+|+.|.||+..|.
T Consensus 19 C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~ 49 (236)
T PF04981_consen 19 CYLKRFDIIEIPDRIEVTICPKCGRYRIGGR 49 (236)
T ss_pred HhcccCCeeecCCccCceECCCCCCEECCCE
Confidence 5555554433 2379999999999843
No 16
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=56.38 E-value=9 Score=28.03 Aligned_cols=39 Identities=23% Similarity=0.603 Sum_probs=28.9
Q ss_pred CCCCCCCCCCCcceeeeccccCCCCcccccccccccccCCcc
Q 021641 47 QLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSL 88 (309)
Q Consensus 47 ~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GGtl 88 (309)
+..|-.|....|..=. ....-++.+|-+|.-||.+.|.+
T Consensus 3 ~~~C~~C~~~~T~~WR---~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 3 GRSCSNCGTTETPLWR---RGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCcCCCCCCCCCccc---cCCCCCCcEeecccHHHHHcCCC
Confidence 3579999988886321 12333479999999999998887
No 17
>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=56.06 E-value=7.9 Score=34.58 Aligned_cols=40 Identities=23% Similarity=0.389 Sum_probs=29.6
Q ss_pred CCCCCCCCCcceeee---ccccCCCCcccccccccccccCCcc
Q 021641 49 NCPRCNSTNTKFCYY---NNYSLTQPRYFCKTCRRYWTEGGSL 88 (309)
Q Consensus 49 ~CPRC~S~~TKfcyy---NNy~~~QPR~fCk~CrRyWT~GGtl 88 (309)
.||.|...+||+-== ...+.-+-|.-|..|.+-||-==.+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERA 44 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeec
Confidence 699999999998622 2333456779999999999854443
No 18
>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=53.45 E-value=5.5 Score=27.73 Aligned_cols=17 Identities=41% Similarity=1.208 Sum_probs=7.1
Q ss_pred CCcccccccccccccCC
Q 021641 70 QPRYFCKTCRRYWTEGG 86 (309)
Q Consensus 70 QPR~fCk~CrRyWT~GG 86 (309)
+|||+|.=|..|.|..-
T Consensus 1 m~ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDS 17 (38)
T ss_dssp --S-B-TTT--B-S--S
T ss_pred CcCeecccccceecCCC
Confidence 69999999999997654
No 19
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=52.03 E-value=9.1 Score=36.06 Aligned_cols=28 Identities=14% Similarity=0.571 Sum_probs=20.9
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
..||||...=.|.-+ . .+.-|||..||+
T Consensus 245 ~pCprCG~~I~~~~~-~----gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPIRRVVV-A----GRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCeeEEEEE-C----CCccEECcCCcC
Confidence 679999986666442 2 366799999985
No 20
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=51.53 E-value=8 Score=26.53 Aligned_cols=31 Identities=32% Similarity=0.773 Sum_probs=18.2
Q ss_pred CCCCCCCCCCcce-eeeccc-------------cCCCCccccccc
Q 021641 48 LNCPRCNSTNTKF-CYYNNY-------------SLTQPRYFCKTC 78 (309)
Q Consensus 48 ~~CPRC~S~~TKf-cyyNNy-------------~~~QPR~fCk~C 78 (309)
..||.|.+...+. -++... .+..+|++|++|
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 4699999876221 111110 344678888887
No 21
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=50.41 E-value=11 Score=37.10 Aligned_cols=36 Identities=22% Similarity=0.531 Sum_probs=23.4
Q ss_pred CCCCCCCCCCcceeeecccc--CCCCccccccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYS--LTQPRYFCKTCRRYWTE 84 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~--~~QPR~fCk~CrRyWT~ 84 (309)
..||.|... .|.-|+.--. ..---+.|.+|++|+--
T Consensus 227 ~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 227 VKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred ccCCCCCCC-CceeeeeecCCCcceEeeeccccccccee
Confidence 678999874 4666663222 12223899999999854
No 22
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=47.13 E-value=13 Score=35.08 Aligned_cols=28 Identities=29% Similarity=0.736 Sum_probs=21.1
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
..||||...=.|.- +. .+.-|||..||+
T Consensus 236 ~pC~~Cg~~I~~~~-~~----gR~ty~Cp~CQ~ 263 (269)
T PRK14811 236 QPCPRCGTPIEKIV-VG----GRGTHFCPQCQP 263 (269)
T ss_pred CCCCcCCCeeEEEE-EC----CCCcEECCCCcC
Confidence 57999998766643 22 367799999996
No 23
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=46.72 E-value=14 Score=32.92 Aligned_cols=44 Identities=20% Similarity=0.406 Sum_probs=29.9
Q ss_pred CCCCCCCCCCccee---eeccccCCCCcccccccccccccCCccccc
Q 021641 48 LNCPRCNSTNTKFC---YYNNYSLTQPRYFCKTCRRYWTEGGSLRNV 91 (309)
Q Consensus 48 ~~CPRC~S~~TKfc---yyNNy~~~QPR~fCk~CrRyWT~GGtlRnv 91 (309)
..||.|.+..|++- |+-.-++-.-||-|+.|.+-++.==++-..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELV 47 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCc
Confidence 36999999887764 333333445569999999988765444433
No 24
>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=46.52 E-value=13 Score=36.37 Aligned_cols=35 Identities=17% Similarity=0.569 Sum_probs=23.5
Q ss_pred CCCCCCCCCCcceeeecccc----CCCCcccccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYS----LTQPRYFCKTCRRYWT 83 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~----~~QPR~fCk~CrRyWT 83 (309)
..||.|.+.+ +.-|+.-.. ..---..|.+|+.|+-
T Consensus 225 ~~C~~Cg~~~-~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 225 VKCSHCEESK-HLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred ccCCCCCCCC-ceeeEeecCCCCCcceEEeeccccccchh
Confidence 6899999864 566664332 1122278999999985
No 25
>PRK10445 endonuclease VIII; Provisional
Probab=45.65 E-value=13 Score=34.78 Aligned_cols=29 Identities=28% Similarity=0.760 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 47 QLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 47 ~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
+..||||...=.|.-+ . .+.-|||..|++
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 3679999987666543 2 367799999985
No 26
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=44.75 E-value=19 Score=30.73 Aligned_cols=37 Identities=27% Similarity=0.748 Sum_probs=32.0
Q ss_pred CCCCCCCCCCCcceeeeccccCCCCc---ccccccccccc
Q 021641 47 QLNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWT 83 (309)
Q Consensus 47 ~~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT 83 (309)
+..||+|...+.-|--+|-.+..-|- |.|-.|.--|-
T Consensus 65 ~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 65 EATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred cCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 47899999999988888888887776 99999999885
No 27
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=42.59 E-value=14 Score=27.20 Aligned_cols=25 Identities=36% Similarity=0.776 Sum_probs=18.1
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
.-||+|.+. |..-.. .|+.|..|..
T Consensus 21 ~fCP~Cg~~---~m~~~~-----~r~~C~~Cgy 45 (50)
T PRK00432 21 KFCPRCGSG---FMAEHL-----DRWHCGKCGY 45 (50)
T ss_pred CcCcCCCcc---hheccC-----CcEECCCcCC
Confidence 479999874 544332 7999999974
No 28
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=41.81 E-value=17 Score=34.04 Aligned_cols=28 Identities=25% Similarity=0.731 Sum_probs=20.9
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
.+||||...=.|.- ++ .+.-|||..|++
T Consensus 246 ~pC~~Cg~~I~~~~-~~----gR~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCRRCGTPIEKIK-QG----GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCeeEEEE-EC----CCCcEECcCCCC
Confidence 57999998766533 33 366799999996
No 29
>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=40.64 E-value=21 Score=28.15 Aligned_cols=31 Identities=23% Similarity=0.495 Sum_probs=24.1
Q ss_pred CCCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 47 QLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 47 ~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
+..||+|.+.+|-..|..|. ..-.-|-.|.=
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 47899999999888777665 55567888853
No 30
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.24 E-value=19 Score=33.97 Aligned_cols=28 Identities=14% Similarity=0.592 Sum_probs=20.9
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
.+||||...=.|.-+ ..+.-|||..||+
T Consensus 255 ~pC~~Cg~~I~~~~~-----~gR~t~~CP~CQ~ 282 (282)
T PRK13945 255 KPCRKCGTPIERIKL-----AGRSTHWCPNCQK 282 (282)
T ss_pred CCCCcCCCeeEEEEE-----CCCccEECCCCcC
Confidence 579999987666543 2366699999985
No 31
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=38.42 E-value=24 Score=30.49 Aligned_cols=36 Identities=28% Similarity=0.802 Sum_probs=24.6
Q ss_pred CCCCCCCCCCCcceeeeccccCCCC-----ccccccccccccc
Q 021641 47 QLNCPRCNSTNTKFCYYNNYSLTQP-----RYFCKTCRRYWTE 84 (309)
Q Consensus 47 ~~~CPRC~S~~TKfcyyNNy~~~QP-----R~fCk~CrRyWT~ 84 (309)
...||+|...+.-| ||--+...- -|.|-.|.--||+
T Consensus 73 ~~~C~~C~~~eavf--fQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 73 DKHCPKCGHREAVF--FQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred cccCCccCCcceEE--EecccccccceEEEEEEeccccccccC
Confidence 36799999987765 533221111 1899999999985
No 32
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.01 E-value=21 Score=33.61 Aligned_cols=27 Identities=26% Similarity=0.620 Sum_probs=20.3
Q ss_pred CCCCCCCCCCcceeeeccccCCCCcccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCR 79 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~Cr 79 (309)
.+||||...=.|.- +. .+.-|||..|+
T Consensus 246 ~pC~~Cg~~I~~~~-~~----gR~t~~CP~CQ 272 (272)
T TIGR00577 246 EPCRRCGTPIEKIK-VG----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCeeEEEE-EC----CCCCEECCCCC
Confidence 57999998766643 32 36679999997
No 33
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=37.32 E-value=13 Score=28.61 Aligned_cols=13 Identities=38% Similarity=0.810 Sum_probs=5.6
Q ss_pred CCCCCCCCCCCcc
Q 021641 47 QLNCPRCNSTNTK 59 (309)
Q Consensus 47 ~~~CPRC~S~~TK 59 (309)
+++|+.|.|.||+
T Consensus 48 g~KC~~C~SYNT~ 60 (61)
T PF14599_consen 48 GHKCSHCGSYNTR 60 (61)
T ss_dssp ----TTTS---EE
T ss_pred hhcCCCCCCcccC
Confidence 3899999999997
No 34
>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=34.54 E-value=23 Score=28.30 Aligned_cols=47 Identities=17% Similarity=0.398 Sum_probs=20.5
Q ss_pred CccccCCCCccCCCCCCCCCCCcceeeeccccCCCCcccccccccccc
Q 021641 36 PMLERKARPQEQLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWT 83 (309)
Q Consensus 36 ~~~er~~~p~~~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT 83 (309)
+...++.+.++.-.||.|+..++=-|=.. ........-|+.|.-.+.
T Consensus 11 ~~kk~~~~l~~~F~CPfC~~~~sV~v~id-kk~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 11 PKKKKKPKLPKVFDCPFCNHEKSVSVKID-KKEGIGILSCRVCGESFQ 57 (81)
T ss_dssp ---------SS----TTT--SS-EEEEEE-TTTTEEEEEESSS--EEE
T ss_pred CccCcCCCCCceEcCCcCCCCCeEEEEEE-ccCCEEEEEecCCCCeEE
Confidence 33444555667799999998887777663 335566788999976553
No 35
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=34.11 E-value=22 Score=34.50 Aligned_cols=28 Identities=21% Similarity=0.649 Sum_probs=20.7
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
.+|++|.+.=.|.- --.+..|||..|++
T Consensus 246 epC~~CGt~I~k~~-----~~gR~t~~CP~CQ~ 273 (273)
T COG0266 246 EPCRRCGTPIEKIK-----LGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCccCCEeEEEE-----EcCCcCEeCCCCCC
Confidence 55999999665532 23477799999985
No 36
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=28.78 E-value=35 Score=30.98 Aligned_cols=41 Identities=22% Similarity=0.362 Sum_probs=28.4
Q ss_pred CCCCCCCCCcceeee---ccccCCCCcccccccccccccCCccc
Q 021641 49 NCPRCNSTNTKFCYY---NNYSLTQPRYFCKTCRRYWTEGGSLR 89 (309)
Q Consensus 49 ~CPRC~S~~TKfcyy---NNy~~~QPR~fCk~CrRyWT~GGtlR 89 (309)
.||.|.+.+||+-== -.-+..+-|.-|-.|..-+|-==++-
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~E 45 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAE 45 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheee
Confidence 699999999998521 11123356789999998887544433
No 37
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=28.51 E-value=48 Score=23.97 Aligned_cols=32 Identities=28% Similarity=0.636 Sum_probs=19.0
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccc-cccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYF-CKTCRR 80 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~f-Ck~CrR 80 (309)
.+||.|.+..-.|-+ ........+++ |..|..
T Consensus 2 kPCPfCGg~~~~~~~-~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRR-GFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEe-ccCCCCCEEEEECCCCCC
Confidence 359999997765542 12333344444 887764
No 38
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=26.67 E-value=43 Score=28.80 Aligned_cols=30 Identities=33% Similarity=0.821 Sum_probs=24.0
Q ss_pred CCCCCCCCCcceeeeccccCCCCcccccccccccccCC
Q 021641 49 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGG 86 (309)
Q Consensus 49 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG 86 (309)
.||.|.|..|-- .+.-+.|..|.-=|....
T Consensus 4 ~CP~C~seytY~--------dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTYH--------DGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceEe--------cCCeeECccccccccccc
Confidence 599999976632 255699999999998875
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=25.79 E-value=30 Score=22.20 Aligned_cols=27 Identities=26% Similarity=0.708 Sum_probs=14.3
Q ss_pred CCCCCCCCCCcceeeeccccCCCCcccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCR 79 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~Cr 79 (309)
.+||||...-.++-.. .+.-+||..|+
T Consensus 2 ~~C~rC~~~~~~~~~~-----~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGIN-----GRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEET-----TEEEEE-TTTC
T ss_pred CcCccCCCcceEeEec-----CCCCeECcCCc
Confidence 4699999887775532 23347787775
No 40
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=25.33 E-value=23 Score=34.98 Aligned_cols=40 Identities=25% Similarity=0.558 Sum_probs=23.5
Q ss_pred ccccCCCCccCCCCCC-----CCCCCcce--eeeccccCCCCccccc
Q 021641 37 MLERKARPQEQLNCPR-----CNSTNTKF--CYYNNYSLTQPRYFCK 76 (309)
Q Consensus 37 ~~er~~~p~~~~~CPR-----C~S~~TKf--cyyNNy~~~QPR~fCk 76 (309)
++.|+..|-++++|-. |+...-++ ||-.-|.-.-.---|+
T Consensus 38 Tt~RR~~pipQL~Cvggsa~~c~~~~p~vvqC~N~G~dg~dvqW~C~ 84 (318)
T PF06682_consen 38 TTSRRVSPIPQLKCVGGSARGCDLYEPDVVQCTNQGYDGEDVQWECK 84 (318)
T ss_pred cccccCCCCcceeecCCCcccccccCcceEEEEecCCCCcccceEEe
Confidence 6678888888899953 76543333 5554444334444444
No 41
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.22 E-value=38 Score=28.23 Aligned_cols=40 Identities=25% Similarity=0.586 Sum_probs=29.6
Q ss_pred CCCCCCCCCCcceeeeccccCCCCcccccccccccccCCccccccCC
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNVPVG 94 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvPvG 94 (309)
..||-|.....| -..---..|+.|..-|+.|+-....|.|
T Consensus 36 ~~Cp~C~~~~Vk-------R~a~GIW~C~kCg~~fAGgay~P~t~~~ 75 (89)
T COG1997 36 HVCPFCGRTTVK-------RIATGIWKCRKCGAKFAGGAYTPVTPAG 75 (89)
T ss_pred CcCCCCCCccee-------eeccCeEEcCCCCCeeccccccccchHH
Confidence 789999987544 1122337899999999999987766654
No 42
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=24.84 E-value=56 Score=23.26 Aligned_cols=31 Identities=19% Similarity=0.668 Sum_probs=17.5
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
.+||-|.. ..+|..|-+. ..+-.++|+.|..
T Consensus 4 ~pCP~CGG-~DrFri~~d~-~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 4 GPCPICGG-KDRFRIFDDK-DGRGTWICRQCGG 34 (40)
T ss_dssp E--TTTT--TTTEEEETT-----S-EEETTTTB
T ss_pred CCCCCCcC-ccccccCcCc-ccCCCEECCCCCC
Confidence 46999988 4588866543 3347899999943
No 43
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=24.57 E-value=44 Score=24.64 Aligned_cols=30 Identities=27% Similarity=0.609 Sum_probs=22.3
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTE 84 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~ 84 (309)
..||.|.....+ .+.+-.+.|..|...+.+
T Consensus 29 q~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 29 QTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred cCccCccccccc-------ccccceEEcCCCCCEECc
Confidence 559999887776 556667889988876643
No 44
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=23.49 E-value=51 Score=26.47 Aligned_cols=29 Identities=21% Similarity=0.544 Sum_probs=16.1
Q ss_pred CCCCCCCCCCcceeeeccccCCCCccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRR 80 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrR 80 (309)
..||-|+..+..|..+.+ .-++.|-+|.+
T Consensus 34 ~~CPfH~d~~pS~~i~~~----k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPD----KNRFKCFGCGK 62 (97)
T ss_dssp E--SSS--SS--EEEETT----TTEEEETTT--
T ss_pred EECcCCCCCCCceEEECC----CCeEEECCCCC
Confidence 779999988878776543 34899999985
No 45
>PRK10220 hypothetical protein; Provisional
Probab=23.30 E-value=51 Score=28.47 Aligned_cols=30 Identities=33% Similarity=0.871 Sum_probs=23.8
Q ss_pred CCCCCCCCCcceeeeccccCCCCcccccccccccccCC
Q 021641 49 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGG 86 (309)
Q Consensus 49 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GG 86 (309)
.||.|.|..|-- .+.-+.|..|.-=|+...
T Consensus 5 ~CP~C~seytY~--------d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTYE--------DNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcceEc--------CCCeEECCcccCcCCccc
Confidence 599999976632 256799999999998764
No 46
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=22.90 E-value=39 Score=22.81 Aligned_cols=27 Identities=30% Similarity=0.719 Sum_probs=14.8
Q ss_pred CCCCCCCCCcceeeeccccCCCCcccccccccccc
Q 021641 49 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWT 83 (309)
Q Consensus 49 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT 83 (309)
+||-|.|..|= ...--+.|-.|..=|.
T Consensus 4 ~Cp~C~se~~y--------~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 4 KCPLCGSEYTY--------EDGELLVCPECGHEWN 30 (30)
T ss_dssp --TTT-----E--------E-SSSEEETTTTEEE-
T ss_pred CCCCCCCccee--------ccCCEEeCCcccccCC
Confidence 69999998775 4477789999988774
No 47
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=21.45 E-value=22 Score=36.40 Aligned_cols=49 Identities=27% Similarity=0.602 Sum_probs=33.6
Q ss_pred CccC-CCCCCCCCCCcceeeeccccCCCCcccccccccccccCCccccccCCCC
Q 021641 44 PQEQ-LNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGSLRNVPVGGG 96 (309)
Q Consensus 44 p~~~-~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GGtlRnvPvGgG 96 (309)
-+|. .+|| |.=.--+|||-|=..- --..|.+|||.+|.-- .|-|||..-
T Consensus 27 tdknf~pc~-cgy~ic~fc~~~irq~--lngrcpacrr~y~den-v~~~~~s~e 76 (480)
T COG5175 27 TDKNFFPCP-CGYQICQFCYNNIRQN--LNGRCPACRRKYDDEN-VRYVTLSPE 76 (480)
T ss_pred ccCCcccCC-cccHHHHHHHHHHHhh--ccCCChHhhhhccccc-eeEEecCHH
Confidence 3444 6687 6666678996543322 3467999999999864 588888754
No 48
>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=21.32 E-value=67 Score=24.97 Aligned_cols=30 Identities=23% Similarity=0.479 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCcceeeeccccCCCCcccccccc
Q 021641 47 QLNCPRCNSTNTKFCYYNNYSLTQPRYFCKTCR 79 (309)
Q Consensus 47 ~~~CPRC~S~~TKfcyyNNy~~~QPR~fCk~Cr 79 (309)
+..||+|...+|=..|..|.- .-.-|-.|.
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~---e~vECv~Cg 38 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNI---ELVECVECG 38 (59)
T ss_pred cccCCCCcCccEEEEEEeCCc---eEEEeccCC
Confidence 478999999999888765543 345566664
No 49
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=21.19 E-value=93 Score=26.20 Aligned_cols=37 Identities=27% Similarity=0.766 Sum_probs=25.1
Q ss_pred CCCCCCCCCCcceeeeccccCCCCc---cccccccccccc
Q 021641 48 LNCPRCNSTNTKFCYYNNYSLTQPR---YFCKTCRRYWTE 84 (309)
Q Consensus 48 ~~CPRC~S~~TKfcyyNNy~~~QPR---~fCk~CrRyWT~ 84 (309)
..||+|...+--|-..|..+..-|- |.|..|.--|+.
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 6799999887665444333332222 899999999974
No 50
>PRK12496 hypothetical protein; Provisional
Probab=21.15 E-value=56 Score=28.94 Aligned_cols=24 Identities=21% Similarity=0.443 Sum_probs=12.1
Q ss_pred ccccccccccccCCccccccCCCC
Q 021641 73 YFCKTCRRYWTEGGSLRNVPVGGG 96 (309)
Q Consensus 73 ~fCk~CrRyWT~GGtlRnvPvGgG 96 (309)
|.|..|+|++...-.--.=|+=|.
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~ 151 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGS 151 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCC
Confidence 667777776654322222344444
No 51
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=21.04 E-value=22 Score=27.40 Aligned_cols=9 Identities=67% Similarity=1.542 Sum_probs=7.7
Q ss_pred CcccccccC
Q 021641 297 TGYWNGMFG 305 (309)
Q Consensus 297 ~G~WnGMlG 305 (309)
+|=||||||
T Consensus 53 ~g~W~GmiG 61 (65)
T PF10613_consen 53 NGSWNGMIG 61 (65)
T ss_dssp TSEBEHHHH
T ss_pred CCcCcCHHH
Confidence 578999986
No 52
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.76 E-value=67 Score=22.29 Aligned_cols=34 Identities=18% Similarity=0.469 Sum_probs=20.2
Q ss_pred CCCCCCCCCcceeeeccccCCCCcccccccccccccCCc
Q 021641 49 NCPRCNSTNTKFCYYNNYSLTQPRYFCKTCRRYWTEGGS 87 (309)
Q Consensus 49 ~CPRC~S~~TKfcyyNNy~~~QPR~fCk~CrRyWT~GGt 87 (309)
-||.|.. ..|..... ...|+.|..|...+-....
T Consensus 2 FCp~Cg~----~l~~~~~~-~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGN----MLIPKEGK-EKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCC----ccccccCC-CCCEEECCcCCCeEECCCc
Confidence 4888876 23333211 1248999999876655433
Done!