Query T0545 MvR76 , , 158 residues
Match_columns 158
No_of_seqs 106 out of 499
Neff 6.5
Searched_HMMs 11830
Date Fri May 21 18:06:34 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0545.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0545.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03167 UDG: Uracil DNA glyco 99.7 3.4E-18 2.9E-22 119.9 9.8 132 7-155 1-145 (150)
2 PF05819 NolX: NolX protein; 36.0 4.5 0.00038 18.0 0.9 23 96-120 324-346 (624)
3 PF06898 YqfD: Putative stage 27.3 4.6 0.00039 17.9 -0.3 38 39-76 2-39 (385)
4 PF07799 DUF1643: Protein of u 19.5 16 0.0013 15.0 1.1 79 11-115 10-96 (136)
5 PF08353 DUF1727: Domain of un 18.8 24 0.002 13.9 2.8 45 95-141 44-91 (113)
6 PF08076 TetM_leader: Tetracyc 15.1 17 0.0015 14.7 0.5 14 17-30 6-19 (28)
7 PF10216 ChpXY: CO2 hydration 14.9 18 0.0015 14.6 0.6 24 27-51 137-160 (353)
8 PF04430 DUF498: Protein of un 10.1 43 0.0036 12.5 2.5 50 88-137 35-89 (110)
9 PF05590 DUF769: Xylella fasti 10.0 41 0.0035 12.6 1.1 14 126-139 230-243 (284)
10 PF01509 TruB_N: TruB family p 9.1 15 0.0013 15.0 -1.3 22 105-126 93-114 (149)
No 1
>PF03167 UDG: Uracil DNA glycosylase superfamily; InterPro: IPR005122 This entry represents various uracil-DNA glycosylases and related DNA glycosylases (3.2.2 from EC), such as uracil-DNA glycosylase , thermophilic uracil-DNA glycosylase , G:T/U mismatch-specific DNA glycosylase (Mug) , and single-strand selective monofunctional uracil-DNA glycosylase (SMUG1) . Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosylic bond, initiating the base excision repair pathway. Uracil in DNA can arise either through the deamination of cytosine to form mutagenic U:G mispairs, or through the incorporation of dUMP by DNA polymerase to form U:A pairs . These aberrant uracil residues are genotoxic . These proteins have a 3-layer alpha/beta/alpha structure. ; PDB: 2boo_A 1okb_B 1q3f_A 3fck_B 3fcf_A 1emj_A 2hxm_A 1yuo_A 1ssp_E 2oxm_A ....
Probab=99.74 E-value=3.4e-18 Score=119.90 Aligned_cols=132 Identities=22% Similarity=0.319 Sum_probs=101.3
Q ss_pred CCCCCCCCCEEEEECCCCHHHHHCCCCCCC-CCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEECCCCC-CCCCCC
Q ss_conf 863278884798714886777852556788-875068999997178876788478899999779602231100-235753
Q T0545 7 PAVLDENTEILILGSLPSDESIRKQQYYGN-PGNDFWRLVGHAIGENLQDMAYEKKLKTLKHNRIGLWDVFKA-GSREGS 84 (158)
Q Consensus 7 ~p~~~~~~~vLilGs~Pg~~S~~~g~yYa~-p~N~FW~il~~~~~~~~~~~~~e~~~~~L~~~gIgl~Dvv~~-~~R~gs 84 (158)
|+..+.+++|||||.+||..+.+.|++|++ ++|.||++|.+++ +....|++||++.. +.....
T Consensus 1 ~g~g~~~~~iliig~~P~~~~~~~g~~f~~~~g~~l~~~l~~~g---------------l~~~~v~~tn~~~~~~~~~~~ 65 (150)
T PF03167_consen 1 PGYGNPNARILIIGEAPGPGEDETGIPFSGPAGNRLWRILGEAG---------------LAREDVYLTNLVKCPPSNRKP 65 (150)
T ss_dssp --S-STT-SEEEE-----SHHHHHTSTT-CCTTHHHHHHHHHHH---------------HHTSGSEEGGSSSSCGEETTB
T ss_pred CCCCCCCCCEEEEECCCCHHHHHCCCEECCCCHHHHHHHHHHHC---------------CCCCCCEEEEECCCCCCCCCC
T ss_conf 99899999899997699965886298852674999999863532---------------154422698643555778999
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHH-----------CCCCCEEEEECCCCHHHHCCCHHHHHHHH
Q ss_conf 4444301355448999985698517987180578887641-----------24684588707987454326777999999
Q T0545 85 QDSKIGDEEINDFSGLKEMVPKLRLICFNGRKAGEYEPLL-----------RGMGYETKVLPSSSGANRRFSKNRESEWE 153 (158)
Q Consensus 85 ~D~~i~~~~~~d~~~l~~~~p~i~~i~f~G~~A~~~~~~~-----------~~~~~~~~vlPStSpana~~~~ek~~~W~ 153 (158)
.+++++...+ .+...++..+ ++.|++.|+.|++..... ...++.++.+|+||++|+.....+...|+
T Consensus 66 ~~~~i~~~~~-~L~~ei~~~~-p~~vv~lG~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~hPS~~~~~~~~~~~~~~~ 143 (150)
T PF03167_consen 66 TRSEIKECSP-FLLREIELLK-PKIVVLLGKKAARALLRVYKSAKIGRLRFKFGGVPVFPTPHPSPLNRNPNDKKPEAWQ 143 (150)
T ss_dssp TTTTCCHHHH-HHHHHHHHHT-SSEEEEES-HHHHHCHHS----CHHHHCCBTTTSEEEEEC-SSTTTCTSTSCCHHHHH
T ss_pred CHHHHHHHHH-HHHHHHHCCC-CCEEEEECHHHHHHHHHCCCCCCCCCEEECCCCCEEEEECCCHHHHHCCCCCCCHHHH
T ss_conf 9999998699-9999987379-9999998999999887105555433213158995599968819998584647846999
Q ss_pred HH
Q ss_conf 99
Q T0545 154 AV 155 (158)
Q Consensus 154 ~~ 155 (158)
++
T Consensus 144 ~~ 145 (150)
T PF03167_consen 144 EA 145 (150)
T ss_dssp HH
T ss_pred HH
T ss_conf 98
No 2
>PF05819 NolX: NolX protein; InterPro: IPR008718 This family consists of Rhizobium NolX and Xanthomonas HrpF proteins. The interaction between the plant pathogen Xanthomonas campestris pv. vesicatoria and its host plants is controlled by hrp genes (hypersensitive reaction and pathogenicity), which encode a type III protein secretion system. Among type III-secreted proteins are avirulence proteins, effectors involved in the induction of plant defence reactions. HrpF is dispensable for protein secretion but required for AvrBs3 recognition in planta, is thought to function as a translocator of effector proteins into the host cell . NolX, a Glycine max (Soybean) cultivar specificity protein, is secreted by a type III secretion system (TTSS) and shows homology to HrpF. It is not known whether NolX functions at the bacterium-plant interface or acts inside the host cell. NolX is expressed in planta only during the early stages of nodule development .; GO: 0009877 nodulation
Probab=35.95 E-value=4.5 Score=18.00 Aligned_cols=23 Identities=26% Similarity=0.557 Sum_probs=10.1
Q ss_pred HHHHHHHHCCCCCEEEECCCHHHHH
Q ss_conf 4899998569851798718057888
Q T0545 96 DFSGLKEMVPKLRLICFNGRKAGEY 120 (158)
Q Consensus 96 d~~~l~~~~p~i~~i~f~G~~A~~~ 120 (158)
|+.++..++|+|+ .|+.++|..|
T Consensus 324 Dl~~fs~~Hpqva--~y~~~qA~~Y 346 (624)
T PF05819_consen 324 DLSKFSDHHPQVA--EYNDKQAEGY 346 (624)
T ss_pred HHHHHHHHCHHHH--HHHHHHHHHH
T ss_conf 5889986478999--9889887656
No 3
>PF06898 YqfD: Putative stage IV sporulation protein YqfD; InterPro: IPR010690 This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis (P54469 from SWISSPROT) is known to be essential for efficient sporulation although its exact function is unknown .
Probab=27.32 E-value=4.6 Score=17.94 Aligned_cols=38 Identities=24% Similarity=0.420 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEECCC
Q ss_conf 50689999971788767884788999997796022311
Q T0545 39 NDFWRLVGHAIGENLQDMAYEKKLKTLKHNRIGLWDVF 76 (158)
Q Consensus 39 N~FW~il~~~~~~~~~~~~~e~~~~~L~~~gIgl~Dvv 76 (158)
|.||..+............-|.=..++.++||-+||+-
T Consensus 2 ~~~~~~~~Gyv~i~v~G~~~ErflN~~~~~gI~lw~v~ 39 (385)
T PF06898_consen 2 NKWWNFLRGYVRIEVEGYSPERFLNLCWRRGIYLWDVK 39 (385)
T ss_pred CHHHEEEEEEEEEEEEECCHHHHHHHHHHCCCEEEEEE
T ss_conf 20221114999999996788999999998898899999
No 4
>PF07799 DUF1643: Protein of unknown function (DUF1643); InterPro: IPR012441 The members of this family are all sequences found within hypothetical proteins expressed by various bacterial species. The region concerned is approximately 150 residues long.
Probab=19.53 E-value=16 Score=14.99 Aligned_cols=79 Identities=15% Similarity=0.169 Sum_probs=40.5
Q ss_pred CCCCCEEEEECCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEECCCCC-CCCCCCCHHHH
Q ss_conf 78884798714886777852556788875068999997178876788478899999779602231100-23575344443
Q T0545 11 DENTEILILGSLPSDESIRKQQYYGNPGNDFWRLVGHAIGENLQDMAYEKKLKTLKHNRIGLWDVFKA-GSREGSQDSKI 89 (158)
Q Consensus 11 ~~~~~vLilGs~Pg~~S~~~g~yYa~p~N~FW~il~~~~~~~~~~~~~e~~~~~L~~~gIgl~Dvv~~-~~R~gs~D~~i 89 (158)
..+..++|+|-|||.... ...+.+-.....+..+.|+|-+-++-= +.|.++ -+++
T Consensus 10 ~~~~~~~~IglNPS~Ad~-----------------------~~~D~T~~r~~~~a~~~gy~~~~v~NLfa~rat~-p~~L 65 (136)
T PF07799_consen 10 EGGPVLLFIGLNPSTADA-----------------------EKDDPTVRRCINFARAWGYGGFIVVNLFAYRATD-PKDL 65 (136)
T ss_pred CCCCEEEEEEECCCCCCC-----------------------CCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCC-HHHH
T ss_conf 899879999975897886-----------------------6678689999999876698859999753203599-7898
Q ss_pred HH---HH-H-HH--HHHHHHHCCCCCEEEECCC
Q ss_conf 01---35-5-44--8999985698517987180
Q T0545 90 GD---EE-I-ND--FSGLKEMVPKLRLICFNGR 115 (158)
Q Consensus 90 ~~---~~-~-~d--~~~l~~~~p~i~~i~f~G~ 115 (158)
+. .+ + || +.++++.... .|+.=|.
T Consensus 66 ~~~~dpig~~Nd~~i~~~~~~a~~--vi~aWG~ 96 (136)
T PF07799_consen 66 KRAPDPIGPENDAHIREILKEADD--VIAAWGN 96 (136)
T ss_pred HHCCCCCCHHHHHHHHHHHHCCCC--EEEEECC
T ss_conf 646288783269999999836595--9999299
No 5
>PF08353 DUF1727: Domain of unknown function (DUF1727); InterPro: IPR013564 This domain of unknown function is found at the C terminus of bacterial proteins which include UDP-N-acetylmuramyl tripeptide synthase and the related Mur ligase.
Probab=18.84 E-value=24 Score=13.94 Aligned_cols=45 Identities=22% Similarity=0.321 Sum_probs=31.3
Q ss_pred HHHHHHHHHCCCCCEEEECCCHHHHHHHHHCCCCCE---EEEECCCCHHH
Q ss_conf 448999985698517987180578887641246845---88707987454
Q T0545 95 NDFSGLKEMVPKLRLICFNGRKAGEYEPLLRGMGYE---TKVLPSSSGAN 141 (158)
Q Consensus 95 ~d~~~l~~~~p~i~~i~f~G~~A~~~~~~~~~~~~~---~~vlPStSpan 141 (158)
.||+.|.. +.++.|.+.|.+++....+++=.|++ +.+.|+-..|-
T Consensus 44 vdfE~L~~--~~i~~vi~sG~R~~Dma~RLkyAgv~~~~i~v~~d~~~al 91 (113)
T PF08353_consen 44 VDFEKLAD--DNIKQVIVSGERAEDMALRLKYAGVPEEKITVEPDLEEAL 91 (113)
T ss_pred CCHHHHCC--CCCCEEEEEEEEHHHHHHHEEECCCCHHHEEECCCHHHHH
T ss_conf 68888554--8986799973578996757133583657838619999999
No 6
>PF08076 TetM_leader: Tetracycline resistance determinant leader peptide; InterPro: IPR012992 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification , : Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria . There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity . The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the tetracycline resistance leader peptide, which can be found in Tet(M) ribosomal protection proteins. A short open reading frame corresponding to a 28 amino acid peptide, which contains a number of inverted repeat sequences was found immediately upstream of tet(M). Transcriptional analyses has found that expression of tet(M) resulted from an extension of a small transcript representing the upstream leader region into the resistance determinant. Therefore, this leader sequence is responsible for transcriptional attenuation and thus regulation of the transcription of tet(M) .
Probab=15.11 E-value=17 Score=14.73 Aligned_cols=14 Identities=36% Similarity=0.660 Sum_probs=11.0
Q ss_pred EEEECCCCHHHHHC
Q ss_conf 98714886777852
Q T0545 17 LILGSLPSDESIRK 30 (158)
Q Consensus 17 LilGs~Pg~~S~~~ 30 (158)
.|+|.|||.+|...
T Consensus 6 ~~m~~fP~D~S~y~ 19 (28)
T PF08076_consen 6 MFMHHFPSDKSIYH 19 (28)
T ss_pred EEEECCCCCCCEEE
T ss_conf 02013888654531
No 7
>PF10216 ChpXY: CO2 hydration protein (ChpXY)
Probab=14.95 E-value=18 Score=14.62 Aligned_cols=24 Identities=29% Similarity=0.731 Sum_probs=16.9
Q ss_pred HHHCCCCCCCCCCCHHHHHHHHHCC
Q ss_conf 7852556788875068999997178
Q T0545 27 SIRKQQYYGNPGNDFWRLVGHAIGE 51 (158)
Q Consensus 27 S~~~g~yYa~p~N~FW~il~~~~~~ 51 (158)
..++--||.+- -.||++|+.+|.+
T Consensus 137 ~vR~~~yys~L-G~FWrVMsdiF~~ 160 (353)
T PF10216_consen 137 QVRQLAYYSGL-GQFWRVMSDIFLE 160 (353)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHHH
T ss_conf 99999999864-5799998999999
No 8
>PF04430 DUF498: Protein of unknown function (DUF498/DUF598); InterPro: IPR007523 This is a family of uncharacterised proteins possibly involved in DNA repair. The crystal structure of this protein revealed a 3-layer beta+alpha/beta/alpha topology .; PDB: 3cpk_A 2k2e_A 2q4q_B 2ab1_A 1ihn_A 2cyj_A 2fvt_A 2fi9_A 2gm2_A.
Probab=10.09 E-value=43 Score=12.52 Aligned_cols=50 Identities=22% Similarity=0.361 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHCCCCCEEE-ECCCHHH----HHHHHHCCCCCEEEEECCC
Q ss_conf 430135544899998569851798-7180578----8876412468458870798
Q T0545 88 KIGDEEINDFSGLKEMVPKLRLIC-FNGRKAG----EYEPLLRGMGYETKVLPSS 137 (158)
Q Consensus 88 ~i~~~~~~d~~~l~~~~p~i~~i~-f~G~~A~----~~~~~~~~~~~~~~vlPSt 137 (158)
...+..+.+++.++...|.+..|. -||++.. +....+...|+.+.+|++.
T Consensus 35 ~~~~l~~~~l~~l~~~~~~peiliiGTG~~~~~~~~~~~~~l~~~gi~vE~m~T~ 89 (110)
T PF04430_consen 35 SFSDLTPEDLAELLELEPDPEILIIGTGQRQRFLPPELREYLRKKGIGVEVMDTP 89 (110)
T ss_dssp STTCE-THHHHHHHCTCCS-SEEEE------SEE-HHHHHHHHTTT-EEEE--HH
T ss_pred CCCCCCHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHHHHHHCCCEEEEECHH
T ss_conf 7143999999999854589878999069988889999999999869979997869
No 9
>PF05590 DUF769: Xylella fastidiosa protein of unknown function (DUF769); InterPro: IPR008487 This family consists of several uncharacterised hypothetical proteins of unknown function from Xylella fastidiosa, the organism that causes Pierce's disease in plants.
Probab=10.04 E-value=41 Score=12.62 Aligned_cols=14 Identities=36% Similarity=0.529 Sum_probs=7.8
Q ss_pred CCCCEEEEECCCCH
Q ss_conf 46845887079874
Q T0545 126 GMGYETKVLPSSSG 139 (158)
Q Consensus 126 ~~~~~~~vlPStSp 139 (158)
..++++|.-|--++
T Consensus 230 G~gvE~wmtPig~g 243 (284)
T PF05590_consen 230 GDGVEMWMTPIGDG 243 (284)
T ss_pred CCCCEEEECCCCCC
T ss_conf 04505630367788
No 10
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine, specifically converting uracil-55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA .; GO: 0003723 RNA binding, 0016439 tRNA-pseudouridine synthase activity, 0031119 tRNA pseudouridine synthesis; PDB: 1ze1_C 1ze2_A 1r3e_A 2ab4_A 1zl3_A 1k8w_A 1r3f_A 1sgv_B 2apo_A 3hjy_A ....
Probab=9.13 E-value=15 Score=15.03 Aligned_cols=22 Identities=23% Similarity=0.190 Sum_probs=15.8
Q ss_pred CCCCEEEECCCHHHHHHHHHCC
Q ss_conf 9851798718057888764124
Q T0545 105 PKLRLICFNGRKAGEYEPLLRG 126 (158)
Q Consensus 105 p~i~~i~f~G~~A~~~~~~~~~ 126 (158)
|..-.|=.||++||++.++-..
T Consensus 93 P~ySAvKv~G~raYelAR~G~~ 114 (149)
T PF01509_consen 93 PMYSAVKVNGKRAYELARKGIE 114 (149)
T ss_dssp SSSSSSBT---BHHHHHH----
T ss_pred CHHHEEEECCHHHHHHHHCCCC
T ss_conf 6346564188219999867981
Done!