Query 029010
Match_columns 200
No_of_seqs 150 out of 340
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:03:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029010.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029010hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04755 PAP_fibrillin: PAP_fi 100.0 5E-29 1.1E-33 206.2 15.5 123 71-194 1-133 (198)
2 TIGR02116 toxin_Txe_YoeB toxin 76.7 7.6 0.00016 27.7 5.1 31 92-123 17-47 (80)
3 PF05973 Gp49: Phage derived p 61.7 30 0.00066 24.9 5.7 43 90-132 6-50 (91)
4 PF06251 Caps_synth_GfcC: Caps 57.3 13 0.00027 31.8 3.4 66 68-135 53-131 (229)
5 PF12283 Protein_K: Bacterioph 48.5 50 0.0011 22.5 4.5 36 70-108 5-41 (56)
6 PF14834 GST_C_4: Glutathione 39.7 41 0.00089 26.6 3.5 40 83-126 33-72 (117)
7 PHA00097 K protein K 38.5 86 0.0019 21.4 4.4 35 71-108 6-41 (56)
8 COG3880 Modulator of heat shoc 36.0 56 0.0012 27.6 3.9 39 69-113 137-175 (176)
9 TIGR00053 addiction module tox 35.5 36 0.00079 24.3 2.5 32 93-124 23-54 (89)
10 cd03715 RT_ZFREV_like RT_ZFREV 34.8 83 0.0018 25.9 4.9 44 86-129 5-57 (210)
11 PF07624 PSD2: Protein of unkn 34.5 61 0.0013 23.0 3.5 38 72-109 22-59 (76)
12 PF05015 Plasmid_killer: Plasm 34.1 1.1E+02 0.0024 22.4 5.0 31 78-108 10-40 (93)
13 PF03724 META: META domain; I 31.2 1.9E+02 0.0042 20.4 7.7 59 118-186 1-59 (101)
14 cd01645 RT_Rtv RT_Rtv: Reverse 31.1 1.1E+02 0.0024 25.5 5.0 43 86-128 5-55 (213)
15 KOG1513 Nuclear helicase MOP-3 29.0 56 0.0012 34.2 3.3 33 69-106 775-807 (1300)
16 TIGR02530 flg_new flagellar op 28.6 77 0.0017 24.2 3.3 26 85-110 27-52 (96)
17 PF12644 DUF3782: Protein of u 28.4 1.4E+02 0.003 20.0 4.4 35 69-109 9-43 (64)
18 PF07240 Turandot: Stress-indu 27.1 1.4E+02 0.0031 22.3 4.4 38 73-110 11-48 (85)
19 PF14869 DUF4488: Domain of un 27.0 2.7E+02 0.0059 22.5 6.3 43 119-167 2-45 (133)
20 PHA00440 host protein H-NS-int 23.6 1.6E+02 0.0034 22.7 4.2 40 64-103 15-55 (98)
21 smart00550 Zalpha Z-DNA-bindin 23.5 1.1E+02 0.0024 21.1 3.1 55 70-127 4-65 (68)
22 PLN03014 carbonic anhydrase 23.3 1.4E+02 0.003 27.8 4.6 31 92-122 102-135 (347)
23 PF10047 DUF2281: Protein of u 23.2 1.8E+02 0.0039 20.2 4.2 46 74-126 2-47 (66)
24 TIGR02683 upstrm_HI1419 probab 22.9 2E+02 0.0044 20.9 4.7 35 91-128 18-52 (95)
25 PF14357 DUF4404: Domain of un 22.3 1.2E+02 0.0026 22.2 3.3 19 89-107 18-36 (85)
26 PF11247 DUF2675: Protein of u 21.6 2E+02 0.0044 22.1 4.5 39 64-102 15-54 (98)
27 PF14252 DUF4347: Domain of un 21.1 80 0.0017 26.0 2.4 35 98-132 107-146 (165)
28 PF00356 LacI: Bacterial regul 20.8 1.2E+02 0.0026 19.7 2.7 18 88-105 24-41 (46)
29 cd07828 nitrobindin nitrobindi 20.7 4.4E+02 0.0095 21.0 7.3 46 121-169 36-81 (148)
30 PF02295 z-alpha: Adenosine de 20.6 1.1E+02 0.0024 21.3 2.7 40 70-110 2-49 (66)
No 1
>PF04755 PAP_fibrillin: PAP_fibrillin; InterPro: IPR006843 This family identifies a conserved domain found in a number of plastid lipid-associated proteins (PAPs) that are thought to form together with other plastoglobulins a coat on the surface of the lipoprotein particle. The coat may contain receptors for attachment to the thylakoid membrane as well as regulatory proteins that may function in the transfer of lipids to and from the thylakoid membranes.). This entry also represents a number of putative fibrillin proteins.; GO: 0005198 structural molecule activity, 0009507 chloroplast
Probab=99.96 E-value=5e-29 Score=206.24 Aligned_cols=123 Identities=34% Similarity=0.584 Sum_probs=111.5
Q ss_pred HHHHHHHHHHhccCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCcC-CCCCceEEEEEecccccccc---CCCCccccc
Q 029010 71 ESFKEELFQAIKPLDRGAEASPEDQARVDQIARKLEAVNDIKEPLKS-NLLNGKWELLYTTSQSLLQT---KRPKFLRPN 146 (200)
Q Consensus 71 ~~lK~~LL~ai~~t~RG~~as~~~r~~I~elI~~LEalNPt~~P~~s-~lL~G~W~L~YTSs~~~l~~---~~p~~l~~v 146 (200)
+++|++||+++++++||+.+++++|++|+++|++||++||+++|+++ ++|+|+|+|+|||+.++.+. .++++ ..+
T Consensus 1 ~~~K~~Ll~~~~~~~rG~~~~~~~~~~i~~~v~~LE~~np~~~p~~s~~~L~G~W~Lvytt~~~~~~~l~~~~~~~-~~~ 79 (198)
T PF04755_consen 1 QDLKQELLQAVAGTNRGLRASPEDREEIEELVEELEALNPTPDPADSLPLLDGRWELVYTTSPEIRSLLQRGRLPG-VRV 79 (198)
T ss_pred ChHHHHHHHHHhccCCCccCCHHHHHHHHHHHHHHHHhCCCCCCcCCchhcCcEEEEEeecCCCcccccccccccc-ccc
Confidence 47999999999999999999999999999999999999999999998 99999999999999998854 44444 369
Q ss_pred cceEEEEeCCCCeEEEEEeC---CCc---ceeeeEEEEcCCceEEEEEeeEEEE
Q 029010 147 GKIYQAINIDTLRAQNIETW---PFF---NQATANLVPLNSKRVAVKFDYFRIA 194 (200)
Q Consensus 147 g~i~Q~Id~~~~~v~N~v~f---p~~---~~V~A~~~v~s~~Rv~V~F~~~~i~ 194 (200)
|+|||+||.+++++.|+|.| |++ ..+.|.+++.+++|+.|+|+++.+.
T Consensus 80 ~~v~Q~id~~~~~~~N~v~~~~~~~~~~~~~v~a~~~~~~~~rv~v~f~~~~l~ 133 (198)
T PF04755_consen 80 GRVFQTIDADNGRVENVVELSGFPLLEGSVSVRASLEVRSPRRVEVTFERASLK 133 (198)
T ss_pred cceEEEEECCCceEEEEEEEeccCceEEEEEEEEEEEEccccEEEEEEEeeEEc
Confidence 99999999999999999994 533 4888999999999999999998873
No 2
>TIGR02116 toxin_Txe_YoeB toxin-antitoxin system, toxin component, Txe/YoeB family. The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by matches to TIGR01552 and/or pfam02604.
Probab=76.67 E-value=7.6 Score=27.67 Aligned_cols=31 Identities=13% Similarity=0.290 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCCcCCCCCce
Q 029010 92 PEDQARVDQIARKLEAVNDIKEPLKSNLLNGK 123 (200)
Q Consensus 92 ~~~r~~I~elI~~LEalNPt~~P~~s~lL~G~ 123 (200)
++.+.+|.++|.+|+ .||.+.......|.|.
T Consensus 17 ~~~~~~i~~~i~~l~-~~P~~~~~~~~~L~G~ 47 (80)
T TIGR02116 17 KKLKKKINELIKDVR-RDPFKGKGKPEPLKGD 47 (80)
T ss_pred HHHHHHHHHHHHHHH-cCCCCCCCCcccCCCC
Confidence 567889999999887 5665422333335554
No 3
>PF05973 Gp49: Phage derived protein Gp49-like (DUF891); InterPro: IPR009241 This entry consists of several hypothetical viral and bacterial proteins some are annotated as addiction module killer proteins.
Probab=61.66 E-value=30 Score=24.86 Aligned_cols=43 Identities=16% Similarity=0.142 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCCCCCcCCCC--CceEEEEEeccc
Q 029010 90 ASPEDQARVDQIARKLEAVNDIKEPLKSNLL--NGKWELLYTTSQ 132 (200)
Q Consensus 90 as~~~r~~I~elI~~LEalNPt~~P~~s~lL--~G~W~L~YTSs~ 132 (200)
.++..+++|...++.|+..+|...+.....| +|-|||......
T Consensus 6 L~~~~~~~i~~~l~~l~~~G~~l~~~~~k~l~~~~i~ElR~~~~~ 50 (91)
T PF05973_consen 6 LPDKERAKILAQLERLEEHGPSLGEPLFKHLKGDGIYELRVRGGS 50 (91)
T ss_pred CCHHHHHHHHHHHHHHHhcCCccCCCcccccCcCCeEEEEEeecC
Confidence 3567889999999999988854333333334 699999987665
No 4
>PF06251 Caps_synth_GfcC: Capsule biosynthesis GfcC; InterPro: IPR010425 This entry represents uncharacterised bacterial proteins that contain a central beta-grasp like domain related to the SLBB domain [].; PDB: 3P42_B.
Probab=57.27 E-value=13 Score=31.76 Aligned_cols=66 Identities=20% Similarity=0.335 Sum_probs=39.9
Q ss_pred hhHHHHHHHHHHHhccCCCCCCCCHHHHHHHHHHHHHHHhcCCCC-------------CCCcCCCCCceEEEEEeccccc
Q 029010 68 KRVESFKEELFQAIKPLDRGAEASPEDQARVDQIARKLEAVNDIK-------------EPLKSNLLNGKWELLYTTSQSL 134 (200)
Q Consensus 68 ~~~~~lK~~LL~ai~~t~RG~~as~~~r~~I~elI~~LEalNPt~-------------~P~~s~lL~G~W~L~YTSs~~~ 134 (200)
.+.++.|++|+..+..... ....+..+....++++|+....+. .+...++|+|..+|.....+..
T Consensus 53 ~~~~~~~~~ll~~L~~l~~--~~~~~~~~~~~~l~~qL~~~~~~gR~~i~lD~d~~r~~~~~n~~L~ggd~L~vP~rp~~ 130 (229)
T PF06251_consen 53 AEAEQQKQQLLAQLAQLEQ--SADSDQAAAAQQLIQQLQSLEATGRVVINLDPDWVRLNPEYNPLLEGGDRLYVPPRPNT 130 (229)
T ss_dssp HHHHHHHHHHHHHHHHHHH--HS-HHHHHHHHHHHHHHTT--B----S----TTS-EESTTSS-B-ECEEEEE-----SE
T ss_pred HHHHHHHHHHHHHHHHHhh--ccchhHHHHHHHHHHHHHhccccceEEEecCHHHhhccccCCCcCCCCcEEEECCCCCE
Confidence 3677888888887776544 556677888999999998876542 1223478999999999887754
Q ss_pred c
Q 029010 135 L 135 (200)
Q Consensus 135 l 135 (200)
.
T Consensus 131 V 131 (229)
T PF06251_consen 131 V 131 (229)
T ss_dssp E
T ss_pred E
Confidence 3
No 5
>PF12283 Protein_K: Bacteriophage protein K; InterPro: IPR020962 This family of proteins is found in the microviridae (isometric ssDNA phages) and are approximately 60 amino acids in length. The function of these proteins are unknown. In phi X174 site-directed mutagenesis of gene K produces small plaques on su- hosts. The mutant phage has an identical latent period, but a more reduced burst size than that of the wild-type phi X174. The reduced burst size in the gene K mutant suggests that the gene K protein, although not essential, has a role in increasing infectivity by increasing the burst size three to six fold [].
Probab=48.49 E-value=50 Score=22.54 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhccCCC-CCCCCHHHHHHHHHHHHHHHhc
Q 029010 70 VESFKEELFQAIKPLDR-GAEASPEDQARVDQIARKLEAV 108 (200)
Q Consensus 70 ~~~lK~~LL~ai~~t~R-G~~as~~~r~~I~elI~~LEal 108 (200)
.--+|++||-+.+..+| |+-+-. ++|.....+||.+
T Consensus 5 ~tli~qellll~yelnrsgllven---e~i~~~l~~le~l 41 (56)
T PF12283_consen 5 TTLIKQELLLLTYELNRSGLLVEN---EEIQSQLKQLEKL 41 (56)
T ss_pred HHHHHHHHHHHHHHhccccccccc---HHHHHHHHHHHHH
Confidence 34589999999999998 777644 4566667777764
No 6
>PF14834 GST_C_4: Glutathione S-transferase, C-terminal domain; PDB: 3BBY_A.
Probab=39.72 E-value=41 Score=26.62 Aligned_cols=40 Identities=20% Similarity=0.180 Sum_probs=23.7
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCcCCCCCceEEE
Q 029010 83 PLDRGAEASPEDQARVDQIARKLEAVNDIKEPLKSNLLNGKWEL 126 (200)
Q Consensus 83 ~t~RG~~as~~~r~~I~elI~~LEalNPt~~P~~s~lL~G~W~L 126 (200)
...+....|++-++++++|+...|.+-+.+. +-|.|+|-.
T Consensus 33 ~~~~~~pLs~~a~~~a~kL~~~a~~ll~~g~----~~LFGewsI 72 (117)
T PF14834_consen 33 RGARKPPLSEAAQAAAQKLIAVAERLLADGG----PNLFGEWSI 72 (117)
T ss_dssp S--------HHHHHHHHHHHHHHHHHTTT------SSTTSS--H
T ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHhccCC----CCccccchH
Confidence 3445577899999999999999999976433 349999954
No 7
>PHA00097 K protein K
Probab=38.50 E-value=86 Score=21.35 Aligned_cols=35 Identities=23% Similarity=0.300 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhccCCC-CCCCCHHHHHHHHHHHHHHHhc
Q 029010 71 ESFKEELFQAIKPLDR-GAEASPEDQARVDQIARKLEAV 108 (200)
Q Consensus 71 ~~lK~~LL~ai~~t~R-G~~as~~~r~~I~elI~~LEal 108 (200)
--++++||-+.+..+| |+-+-. ++|.....+||.+
T Consensus 6 tli~qelllltyelnrsgllven---eeiqs~lk~le~l 41 (56)
T PHA00097 6 TLILQELLLLTYELNRSGLLVEN---EEIQSQLKKLEKL 41 (56)
T ss_pred HHHHHHHHHHHHhhccccceecc---HHHHHHHHHHHHH
Confidence 3578999999999998 777644 3566666677664
No 8
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=36.01 E-value=56 Score=27.57 Aligned_cols=39 Identities=26% Similarity=0.304 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHhccCCCCCCCCHHHHHHHHHHHHHHHhcCCCCC
Q 029010 69 RVESFKEELFQAIKPLDRGAEASPEDQARVDQIARKLEAVNDIKE 113 (200)
Q Consensus 69 ~~~~lK~~LL~ai~~t~RG~~as~~~r~~I~elI~~LEalNPt~~ 113 (200)
++.+||++|-++|..-+- |+.+.|.+-|.+|++.|+..+
T Consensus 137 ~I~~L~e~Lq~~i~~Eef------EeAA~iRDqIr~Lk~k~~~dd 175 (176)
T COG3880 137 KIIALKEALQDLIEREEF------EEAAVIRDQIRALKAKNGGDD 175 (176)
T ss_pred HHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHhhcCCCC
Confidence 788899999999987644 778899999999999987644
No 9
>TIGR00053 addiction module toxin component, YafQ family. This model represents a cluster of eubacterial proteins and a cluster of archaeal proteins, all of which are uncharacterized, from 85 to 102 residues in length, and similar in sequence. These include YafQ, a ribosome-associated endoribonuclease that serves as part of a toxin-antitoxin system, for which DinJ is the antidote component.
Probab=35.52 E-value=36 Score=24.33 Aligned_cols=32 Identities=22% Similarity=0.353 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCcCCCCCceE
Q 029010 93 EDQARVDQIARKLEAVNDIKEPLKSNLLNGKW 124 (200)
Q Consensus 93 ~~r~~I~elI~~LEalNPt~~P~~s~lL~G~W 124 (200)
.++.+|.+++..|...+|.|.......|.|.|
T Consensus 23 ~~~~~i~~~i~~l~~~~~~p~~~~~~~L~G~~ 54 (89)
T TIGR00053 23 KDLKKLLKKMEELINTLPLPEHYKDHPLRGPW 54 (89)
T ss_pred ccHHHHHHHHHHHHcCCCCCcccCCccCcCCc
Confidence 45678888888888755544433333455544
No 10
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=34.83 E-value=83 Score=25.93 Aligned_cols=44 Identities=9% Similarity=0.197 Sum_probs=31.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhcC---CCCCCCcC-----CCCCc-eEEEEEe
Q 029010 86 RGAEASPEDQARVDQIARKLEAVN---DIKEPLKS-----NLLNG-KWELLYT 129 (200)
Q Consensus 86 RG~~as~~~r~~I~elI~~LEalN---Pt~~P~~s-----~lL~G-~W~L~YT 129 (200)
+....++++++.+.+.|++|+..+ |...|-.+ +.=+| +||++.-
T Consensus 5 ~~~~~~~~~~~~~~~~v~~ll~~G~I~~~~s~~~sp~~~V~Kk~g~~~R~~vD 57 (210)
T cd03715 5 KQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQD 57 (210)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCeECCCCCCCCceEEEEeCCCCcceEEEE
Confidence 455678999999999999999876 33333222 23378 9999753
No 11
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=34.53 E-value=61 Score=23.01 Aligned_cols=38 Identities=16% Similarity=0.253 Sum_probs=25.7
Q ss_pred HHHHHHHHHhccCCCCCCCCHHHHHHHHHHHHHHHhcC
Q 029010 72 SFKEELFQAIKPLDRGAEASPEDQARVDQIARKLEAVN 109 (200)
Q Consensus 72 ~lK~~LL~ai~~t~RG~~as~~~r~~I~elI~~LEalN 109 (200)
...+.+.+.+..-.-|...+..|+..|+++++++++.+
T Consensus 22 ~~~~~~~~kl~~YAlGR~~~~~D~~~i~~i~~~~~~~~ 59 (76)
T PF07624_consen 22 QFARCFAEKLLTYALGRPLEFSDRCEIDRIVEAFKANG 59 (76)
T ss_pred HHHHHHHHHHHHHHcCCCCCcchHHHHHHHHHHHHHcC
Confidence 33444444444444455666789999999999998866
No 12
>PF05015 Plasmid_killer: Plasmid maintenance system killer protein; InterPro: IPR007711 Several plasmids with proteic killer gene systems have been reported. All of them encode a stable toxin and an unstable antidote. Upon loss of the plasmid, the less stable inhibitor is inactivated more rapidly than the toxin, allowing the toxin to be activated. The activation of those systems result in cell filamentation and cessation of viable cell production. It has been verified that both the stable killer and the unstable inhibitor of the systems are short polypeptides. This family corresponds to the toxin.
Probab=34.05 E-value=1.1e+02 Score=22.44 Aligned_cols=31 Identities=6% Similarity=0.126 Sum_probs=18.5
Q ss_pred HHHhccCCCCCCCCHHHHHHHHHHHHHHHhc
Q 029010 78 FQAIKPLDRGAEASPEDQARVDQIARKLEAV 108 (200)
Q Consensus 78 L~ai~~t~RG~~as~~~r~~I~elI~~LEal 108 (200)
|+.+..+++-....++-...+...+++|++.
T Consensus 10 l~~l~~~~~~k~~~~~~~~~~~~~L~~L~aa 40 (93)
T PF05015_consen 10 LEKLFEDGKTKKIPADIAKKLRRRLDQLDAA 40 (93)
T ss_pred HHHHHCCCCcCCcCHHHHHHHHHHHHHHHhC
Confidence 4444445544445566666777777777765
No 13
>PF03724 META: META domain; InterPro: IPR005184 A domain found in proteins of unknown function [], some of which are described as heat shock protein (HslJ). In Helicobacter pylori (Campylobacter pylori) the protein is secreted e.g. (O25998 from SWISSPROT) and implicated in motility. In Leishmania spp. it is described as an essential protein, over-expression of which, in Leishmania amazonensis increases virulence (O43987 from SWISSPROT; []). A pair of cysteine residues show correlated conservation, suggesting that they form a disulphide bond. ; PDB: 2KTS_A 2LA7_A.
Probab=31.21 E-value=1.9e+02 Score=20.41 Aligned_cols=59 Identities=15% Similarity=0.226 Sum_probs=30.4
Q ss_pred CCCCceEEEEEeccccccccCCCCccccccceEEEEeCCCCeEEEEEeCCCcceeeeEEEEcCCceEEE
Q 029010 118 NLLNGKWELLYTTSQSLLQTKRPKFLRPNGKIYQAINIDTLRAQNIETWPFFNQATANLVPLNSKRVAV 186 (200)
Q Consensus 118 ~lL~G~W~L~YTSs~~~l~~~~p~~l~~vg~i~Q~Id~~~~~v~N~v~fp~~~~V~A~~~v~s~~Rv~V 186 (200)
+|.+|+|.|.+.+....... + .-++.+=.||..++++. ..-.-|...+.+.+ .+.++.|
T Consensus 1 ~L~~~~W~l~~~~~~~~~~~--~----~~~~~~l~~~~~~~~~~---g~~gCN~~~g~~~~-~~~~l~~ 59 (101)
T PF03724_consen 1 PLQGGTWQLTSIDGDGKTGV--P----PPAKPTLTFDFEDGRVS---GSAGCNRFSGTYTI-EGNTLSF 59 (101)
T ss_dssp -TTTEEEEEEEE-SSS-B---------TTSSSEEEEECCCCEEE---EE-SSSEEEEEEEE-CTTEEEE
T ss_pred CccCCEEEEEEEecCCcccc--C----CCCCcEEEEEeCCCEEE---EEECCeeeEEEEEE-CCCEEEE
Confidence 57899999975544332111 1 02234445776666321 22234688888888 4444443
No 14
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=31.07 E-value=1.1e+02 Score=25.48 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=31.0
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhcC---CCCCCCcC-----CCCCceEEEEE
Q 029010 86 RGAEASPEDQARVDQIARKLEAVN---DIKEPLKS-----NLLNGKWELLY 128 (200)
Q Consensus 86 RG~~as~~~r~~I~elI~~LEalN---Pt~~P~~s-----~lL~G~W~L~Y 128 (200)
|....++++++.+.+.|++|-..+ |...|-.+ +.=+|+||++.
T Consensus 5 ~~~p~~~~~~~~~~~~i~~ll~~g~I~~~~s~~~sp~~~v~K~~g~~R~~~ 55 (213)
T cd01645 5 KQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLH 55 (213)
T ss_pred CccCCCHHHHHHHHHHHHHHHHCCceecCCCCCcCcEEEEEcCCCCeEEEe
Confidence 556788999999999999998765 33333332 23479999985
No 15
>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]
Probab=29.00 E-value=56 Score=34.21 Aligned_cols=33 Identities=36% Similarity=0.554 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHhccCCCCCCCCHHHHHHHHHHHHHHH
Q 029010 69 RVESFKEELFQAIKPLDRGAEASPEDQARVDQIARKLE 106 (200)
Q Consensus 69 ~~~~lK~~LL~ai~~t~RG~~as~~~r~~I~elI~~LE 106 (200)
.++++|++||+.|..++|-+.. +.+++||++|-
T Consensus 775 r~~~mkeeLL~kverLg~~LP~-----NTLDqLIdelG 807 (1300)
T KOG1513|consen 775 RVERMKEELLDKVERLGRELPP-----NTLDQLIDELG 807 (1300)
T ss_pred HHHHHHHHHHHHHHHhcccCCc-----chHHHHHHHhC
Confidence 5668999999999999988876 56788888873
No 16
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=28.59 E-value=77 Score=24.23 Aligned_cols=26 Identities=15% Similarity=0.279 Sum_probs=24.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHhcCC
Q 029010 85 DRGAEASPEDQARVDQIARKLEAVND 110 (200)
Q Consensus 85 ~RG~~as~~~r~~I~elI~~LEalNP 110 (200)
.||+..+++|-++|++.|.+.+..+-
T Consensus 27 ~R~I~l~~~~~~~i~~av~~A~~KG~ 52 (96)
T TIGR02530 27 ERNISINPDDWKKLLEAVEEAESKGV 52 (96)
T ss_pred HcCCCCCHHHHHHHHHHHHHHHhcCC
Confidence 48999999999999999999999874
No 17
>PF12644 DUF3782: Protein of unknown function (DUF3782); InterPro: IPR024271 This functionally uncharacterised family of proteins is found in bacteria and archaea. Proteins in this family are typically between 91 and 186 amino acids in length.
Probab=28.38 E-value=1.4e+02 Score=20.03 Aligned_cols=35 Identities=26% Similarity=0.257 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHhccCCCCCCCCHHHHHHHHHHHHHHHhcC
Q 029010 69 RVESFKEELFQAIKPLDRGAEASPEDQARVDQIARKLEAVN 109 (200)
Q Consensus 69 ~~~~lK~~LL~ai~~t~RG~~as~~~r~~I~elI~~LEalN 109 (200)
+...++++|-+.... +++++.+.|++.+..|.+..
T Consensus 9 ~i~a~~e~l~~~~~~------lt~e~~~~l~~~~~al~~~~ 43 (64)
T PF12644_consen 9 EIMATKEELEELEER------LTKEDKKRLEEYIDALGARW 43 (64)
T ss_pred HHHHHHHHHHHHHhh------cCHHHHHHHHHHHHHHHHHh
Confidence 566677777777654 78999999999999998764
No 18
>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].
Probab=27.11 E-value=1.4e+02 Score=22.27 Aligned_cols=38 Identities=21% Similarity=0.369 Sum_probs=30.4
Q ss_pred HHHHHHHHhccCCCCCCCCHHHHHHHHHHHHHHHhcCC
Q 029010 73 FKEELFQAIKPLDRGAEASPEDQARVDQIARKLEAVND 110 (200)
Q Consensus 73 lK~~LL~ai~~t~RG~~as~~~r~~I~elI~~LEalNP 110 (200)
--++|++.-.....-+..++++|+.+++.|.+-+..|-
T Consensus 11 ni~eLi~fY~ky~~~~~L~~~~r~~~d~~i~~y~~~~~ 48 (85)
T PF07240_consen 11 NIQELIAFYEKYSPRLPLTPQDRQRIDRFIRRYKEENN 48 (85)
T ss_pred hHHHHHHHHHHcCccCCCCHHHHHHHHHHHHHHHHHhh
Confidence 34566666666666678899999999999999999983
No 19
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=26.98 E-value=2.7e+02 Score=22.50 Aligned_cols=43 Identities=26% Similarity=0.445 Sum_probs=25.3
Q ss_pred CCCceEEEE-EeccccccccCCCCccccccceEEEEeCCCCeEEEEEeCC
Q 029010 119 LLNGKWELL-YTTSQSLLQTKRPKFLRPNGKIYQAINIDTLRAQNIETWP 167 (200)
Q Consensus 119 lL~G~W~L~-YTSs~~~l~~~~p~~l~~vg~i~Q~Id~~~~~v~N~v~fp 167 (200)
-|.|.|+|. |-+...-.... + ..+.++-+|. ++|+..|+.-.|
T Consensus 2 ~l~GVWQ~c~~~~~~~~~~g~----l-~~~~~lKilS-~Dgtf~Ni~~~~ 45 (133)
T PF14869_consen 2 SLQGVWQLCHYVSESPEVPGK----L-KPSNVLKILS-DDGTFVNITMIP 45 (133)
T ss_pred CceEEEEEEEEeecCcccCce----E-eecccEEEEc-CCCcEEEEEEeC
Confidence 378999999 54443222111 1 2335566676 457888886654
No 20
>PHA00440 host protein H-NS-interacting protein
Probab=23.64 E-value=1.6e+02 Score=22.67 Aligned_cols=40 Identities=18% Similarity=0.272 Sum_probs=31.3
Q ss_pred CcChhhH-HHHHHHHHHHhccCCCCCCCCHHHHHHHHHHHH
Q 029010 64 GFSTKRV-ESFKEELFQAIKPLDRGAEASPEDQARVDQIAR 103 (200)
Q Consensus 64 ~~~~~~~-~~lK~~LL~ai~~t~RG~~as~~~r~~I~elI~ 103 (200)
++.+.|. +..++.|+++..+...|-..++-||.-+.+.++
T Consensus 15 A~~~se~e~~~~e~l~~Lak~v~~GE~~~~~~re~lvqaLT 55 (98)
T PHA00440 15 AKMDSETEAILEEDILDLAKQAGAGEEVNPKDKELLVQALT 55 (98)
T ss_pred EEeChHHHHHHHHHHHHHHhhcCCcccCChHHHHHHHHHHh
Confidence 3444554 469999999999999999999999887766553
No 21
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=23.51 E-value=1.1e+02 Score=21.13 Aligned_cols=55 Identities=15% Similarity=0.240 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHhccCCC-CCCCCH------HHHHHHHHHHHHHHhcCCCCCCCcCCCCCceEEEE
Q 029010 70 VESFKEELFQAIKPLDR-GAEASP------EDQARVDQIARKLEAVNDIKEPLKSNLLNGKWELL 127 (200)
Q Consensus 70 ~~~lK~~LL~ai~~t~R-G~~as~------~~r~~I~elI~~LEalNPt~~P~~s~lL~G~W~L~ 127 (200)
.+..++++|+++...+. |+.+.. -++..|.+++..||..+=.-. + .--.+.|++-
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~--~-~~~~~~W~i~ 65 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK--Q-GGTPPLWKLT 65 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe--c-CCCCCceEee
Confidence 45678899999997754 565544 336789999999999875322 1 1133788874
No 22
>PLN03014 carbonic anhydrase
Probab=23.28 E-value=1.4e+02 Score=27.82 Aligned_cols=31 Identities=23% Similarity=0.340 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHhcCC-CCCCCcC--CCCCc
Q 029010 92 PEDQARVDQIARKLEAVND-IKEPLKS--NLLNG 122 (200)
Q Consensus 92 ~~~r~~I~elI~~LEalNP-t~~P~~s--~lL~G 122 (200)
+...++|+++..+|+.... .+.+-+. .+++|
T Consensus 102 ~~~~~~~~~~~~~l~~~~~~~~~~~~~lerL~~G 135 (347)
T PLN03014 102 TVAAAKVEQITAALQTGTSSDKKAFDPVETIKQG 135 (347)
T ss_pred hHHHHhHHHHHHHHhcccCCCCCCcCHHHHHHHH
Confidence 4456899999999986432 2333332 45555
No 23
>PF10047 DUF2281: Protein of unknown function (DUF2281); InterPro: IPR018739 This domain is found in putative uncharacterised proteins, though some proteins contaning this domain are described as a transcritional regulator of the Xre family.
Probab=23.17 E-value=1.8e+02 Score=20.16 Aligned_cols=46 Identities=33% Similarity=0.365 Sum_probs=31.4
Q ss_pred HHHHHHHhccCCCCCCCCHHHHHHHHHHHHHHHhcCCCCCCCcCCCCCceEEE
Q 029010 74 KEELFQAIKPLDRGAEASPEDQARVDQIARKLEAVNDIKEPLKSNLLNGKWEL 126 (200)
Q Consensus 74 K~~LL~ai~~t~RG~~as~~~r~~I~elI~~LEalNPt~~P~~s~lL~G~W~L 126 (200)
+++|++.+... +++.+.+|.+.|+=|...++.... ....+.|.|+=
T Consensus 2 ~~~l~~~i~~L------P~~~~~Evldfi~fL~~k~~~~~~-~~~~~~~~~~G 47 (66)
T PF10047_consen 2 EEELLEKIQQL------PEELQQEVLDFIEFLLQKYQQKES-KKKKLLGDWKG 47 (66)
T ss_pred hHHHHHHHHHC------CHHHHHHHHHHHHHHHHhcccccc-cccccccccCC
Confidence 45667777654 678899999999999988843222 23345666653
No 24
>TIGR02683 upstrm_HI1419 probable addiction module killer protein. Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the upstream member of a gene pair, where the downstream member is a predicted DNA-binding protein from a clade within Pfam helix-turn-helix family pfam01381. These gene pairs, when found on the bacterial chromosome, often are located with prophage regions, but also in both integrated plasmid regions and near housekeeping genes. Analysis suggests that the gene pair may serve as an addiction module.
Probab=22.93 E-value=2e+02 Score=20.92 Aligned_cols=35 Identities=20% Similarity=0.125 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHHHHHhcCCCCCCCcCCCCCceEEEEE
Q 029010 91 SPEDQARVDQIARKLEAVNDIKEPLKSNLLNGKWELLY 128 (200)
Q Consensus 91 s~~~r~~I~elI~~LEalNPt~~P~~s~lL~G~W~L~Y 128 (200)
++.++.+|...++.|+. ++ .|.--++-+|-|+|++
T Consensus 18 d~~~~~kI~~~i~~l~~-g~--~~~~K~l~~~~~ElR~ 52 (95)
T TIGR02683 18 DPRAKARILARIDRLAL-GN--FGDVKPVGEGVSELRI 52 (95)
T ss_pred CHHHHHHHHHHHHHHhc-cC--CCCccCCCCCcEEEEe
Confidence 45678899999999985 32 2322245557788877
No 25
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=22.29 E-value=1.2e+02 Score=22.22 Aligned_cols=19 Identities=21% Similarity=0.356 Sum_probs=10.2
Q ss_pred CCCHHHHHHHHHHHHHHHh
Q 029010 89 EASPEDQARVDQIARKLEA 107 (200)
Q Consensus 89 ~as~~~r~~I~elI~~LEa 107 (200)
..++++|+.+.++.+++|.
T Consensus 18 ~ld~~~~~~L~~l~~dIe~ 36 (85)
T PF14357_consen 18 PLDEETRAELSSLDDDIEA 36 (85)
T ss_pred CCCHHHHHHHHHHHHHHHH
Confidence 3445555555555555555
No 26
>PF11247 DUF2675: Protein of unknown function (DUF2675) ; InterPro: IPR022611 Members in this family of proteins include Bacteriophage T7 gene 5.5; they have no known function.
Probab=21.65 E-value=2e+02 Score=22.07 Aligned_cols=39 Identities=21% Similarity=0.269 Sum_probs=31.0
Q ss_pred CcChh-hHHHHHHHHHHHhccCCCCCCCCHHHHHHHHHHH
Q 029010 64 GFSTK-RVESFKEELFQAIKPLDRGAEASPEDQARVDQIA 102 (200)
Q Consensus 64 ~~~~~-~~~~lK~~LL~ai~~t~RG~~as~~~r~~I~elI 102 (200)
++.++ .-+.+.+.|+++..+-..|-..++-||.-+.+.+
T Consensus 15 av~~se~e~~~~e~ll~Lak~v~~GE~~~~~~re~l~qaL 54 (98)
T PF11247_consen 15 AVIDSEQEEEFEEDLLELAKKVGAGEKVSGFQREMLVQAL 54 (98)
T ss_pred EEeCHHHHHHHHHHHHHHHhhcCCccccCHHHHHHHHHHH
Confidence 34444 4567999999999999999999999987766654
No 27
>PF14252 DUF4347: Domain of unknown function (DUF4347)
Probab=21.10 E-value=80 Score=26.00 Aligned_cols=35 Identities=17% Similarity=0.384 Sum_probs=23.6
Q ss_pred HHHHHHHHHhcCCCC-----CCCcCCCCCceEEEEEeccc
Q 029010 98 VDQIARKLEAVNDIK-----EPLKSNLLNGKWELLYTTSQ 132 (200)
Q Consensus 98 I~elI~~LEalNPt~-----~P~~s~lL~G~W~L~YTSs~ 132 (200)
=.++|++|+.+-... .++-+..+.|.|.|.|++..
T Consensus 107 G~~fv~~L~~ltga~VAAS~~~tG~~~~GGdW~Le~~~G~ 146 (165)
T PF14252_consen 107 GQEFVQRLAQLTGADVAASTDLTGNAALGGDWDLEVQTGD 146 (165)
T ss_pred HHHHHHHHHHHHCCCEEecCCCcCccccCCCCeeeeeecc
Confidence 356777777765432 22234678899999998765
No 28
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=20.80 E-value=1.2e+02 Score=19.70 Aligned_cols=18 Identities=28% Similarity=0.377 Sum_probs=15.7
Q ss_pred CCCCHHHHHHHHHHHHHH
Q 029010 88 AEASPEDQARVDQIARKL 105 (200)
Q Consensus 88 ~~as~~~r~~I~elI~~L 105 (200)
-..+++.|++|.+++++|
T Consensus 24 ~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 24 PRVSEETRERILEAAEEL 41 (46)
T ss_dssp SSSTHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHH
Confidence 368899999999999887
No 29
>cd07828 nitrobindin nitrobindin heme-binding domain. Nitrobindin is a heme-containing lipocalin that may reversibly bind nitric oxide. This heme-binding domain forms a beta barrel structure, and in a small family of proteins from tetrapods, it is found C-terminal to a THAP zinc finger domain (a sequence-specific DNA binding domain). Members of this group are putatively related to fatty acid-binding proteins (FABPs).
Probab=20.75 E-value=4.4e+02 Score=21.00 Aligned_cols=46 Identities=28% Similarity=0.316 Sum_probs=31.7
Q ss_pred CceEEEEEeccccccccCCCCccccccceEEEEeCCCCeEEEEEeCCCc
Q 029010 121 NGKWELLYTTSQSLLQTKRPKFLRPNGKIYQAINIDTLRAQNIETWPFF 169 (200)
Q Consensus 121 ~G~W~L~YTSs~~~l~~~~p~~l~~vg~i~Q~Id~~~~~v~N~v~fp~~ 169 (200)
.|..-|.|++..-.+...+| +-++.| |-.+|+++..+..++.-|..
T Consensus 36 ~g~p~L~Y~s~~w~~~~~~p-~h~E~G--fwr~~~~~~~V~~~la~p~G 81 (148)
T cd07828 36 DGQPFLNYTSRTWRLDDGRP-LHRETG--FWRIDPDTGEVELLLAHPTG 81 (148)
T ss_pred CCCCeEEEEEEEEeCCCCCc-ceEeeE--EEEEcCCCCEEEEEEEECCc
Confidence 46677888777544433444 445677 88899888888888887753
No 30
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=20.62 E-value=1.1e+02 Score=21.31 Aligned_cols=40 Identities=20% Similarity=0.428 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHhccCCCCCCCCHH--------HHHHHHHHHHHHHhcCC
Q 029010 70 VESFKEELFQAIKPLDRGAEASPE--------DQARVDQIARKLEAVND 110 (200)
Q Consensus 70 ~~~lK~~LL~ai~~t~RG~~as~~--------~r~~I~elI~~LEalNP 110 (200)
.+++++++|+.+...+ |..++.- .+.+|+...-.||..+-
T Consensus 2 ~~~~ee~Il~~L~~~g-~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~ 49 (66)
T PF02295_consen 2 MQDLEEKILDFLKELG-GSTATAIAKALGLSVPKKEVNRVLYRLEKQGK 49 (66)
T ss_dssp HHHHHHHHHHHHHHHT-SSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred chhHHHHHHHHHHhcC-CccHHHHHHHhCcchhHHHHHHHHHHHHHCCC
Confidence 5688999999999988 7666552 26899999999999864
Done!