Query T0557 NeR70A, , 145 residues
Match_columns 145
No_of_seqs 116 out of 927
Neff 8.2
Searched_HMMs 11830
Date Tue May 25 15:42:32 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0557.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0557.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04326 AAA_4: Divergent AAA 99.9 2.4E-25 2.1E-29 148.0 13.4 116 16-144 1-121 (122)
2 PF08854 DUF1824: Domain of un 64.1 1.1 9.5E-05 20.5 1.5 80 30-145 22-101 (125)
3 PF01899 MNHE: Na+/H+ ion anti 19.5 22 0.0019 13.9 3.3 43 16-62 34-76 (106)
4 PF06153 DUF970: Protein of un 15.7 28 0.0023 13.4 4.6 51 48-113 42-104 (109)
5 PF01739 CheR: CheR methyltran 12.9 30 0.0026 13.1 1.3 10 48-57 64-73 (196)
6 PF08532 Glyco_hydro_42M: Beta 7.4 55 0.0047 11.8 2.0 23 28-54 69-91 (207)
7 PF05271 Tobravirus_2B: Tobrav 6.8 59 0.005 11.6 2.2 24 32-55 47-74 (116)
8 PF10223 DUF2181: Uncharacteri 6.4 62 0.0053 11.5 2.2 24 2-25 58-81 (244)
9 PF10820 DUF2543: Protein of u 6.2 27 0.0023 13.4 -1.2 28 16-43 51-78 (81)
10 PF09837 DUF2064: Uncharacteri 5.6 70 0.0059 11.3 0.6 26 27-55 45-71 (122)
No 1
>PF04326 AAA_4: Divergent AAA domain; InterPro: IPR007421 This entry is related to IPR003959 from INTERPRO, and presumably has the same function (ATP-binding). A number of the archaeal members of this group are annotated as ATP-dependent DNA helicases 3.6.1 from EC.
Probab=99.93 E-value=2.4e-25 Score=147.98 Aligned_cols=116 Identities=34% Similarity=0.549 Sum_probs=93.0
Q ss_pred CCCEEEEEECCCCHHH-----HHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCCCCEEECCCHHHHHHHHHHHHHCCCC
Q ss_conf 9965777415788479-----99999997088778970799986327763366532202202035789999998760388
Q T0557 16 ESARIEAKRASDMGKS-----VMETVIAFANEPGLDGGYLLLGVDWAINDKGDTVYRPVGLPDPDKVQRDLASQCASMLN 90 (145)
Q Consensus 16 E~~~lEfK~~~~~~~~-----l~k~i~AFAN~~~~~GG~liiGV~d~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 90 (145)
|++++|||+.+....+ ++|+||||||+ +||+|+|||+|++...+. ..........+.+.+.+...+.
T Consensus 1 E~~~~EfK~~~~~~~~~~~~~~~k~i~AfaN~---~GG~i~iGV~D~~~i~G~-----~~~~~~~~~~~~~~~~~~~~~~ 72 (122)
T PF04326_consen 1 ESQRLEFKSALNPSSKKKKKEIAKTICAFANS---EGGYIVIGVDDDGEIVGV-----SDSDDQDDDQDIIQNKINDLIN 72 (122)
T ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHHHHHCC---CCCEEEEEECCCCCEEEE-----ECCCHHHHHHHHHHHHHHHHCC
T ss_conf 99879998567777630378899998787638---998999997789818712-----7554056789999999997579
Q ss_pred CCCEEEEEEEEECCCEEEEEEEECCCCCCCCEEECCCCCCCCEEEEECCCCCEE
Q ss_conf 530245889984697899998335999888588758799861689826875211
Q T0557 91 VALRPEMQLEQVGGKTLLVVYVPEADVTHKPIYKKATGLPGGAYRRIGSSDQRC 144 (145)
Q Consensus 91 p~~~~~i~~~~~~g~~i~vi~Ip~s~~~~~P~~~~~~~~~~~~Y~R~g~~~~~~ 144 (145)
|++.++++.+.++++.|++|.||++.. .|++.+.+ +.+|+|.|+++++|
T Consensus 73 p~~~~~~~~~~~~~~~v~vi~I~~~~~--~~~~~~~~---~~~y~R~g~~~~~~ 121 (122)
T PF04326_consen 73 PPIRPEIEEIEIDGKYVIVIEIPPSDN--KPYYYKND---GRYYIRVGDSNKPA 121 (122)
T ss_pred CCCCEEEEEEEECCCEEEEEEEECCCC--CCCEECCC---CEEEEECCCCCEEC
T ss_conf 997139999998995999999918878--57478269---86999889998089
No 2
>PF08854 DUF1824: Domain of unknown function (DUF1824); InterPro: IPR014953 This uncharacterised group of proteins are principally found in cyanobacteria. ; PDB: 2q22_C.
Probab=64.15 E-value=1.1 Score=20.55 Aligned_cols=80 Identities=14% Similarity=0.180 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCCCCEEECCCHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCEEEE
Q ss_conf 79999999970887789707999863277633665322022020357899999987603885302458899846978999
Q T0557 30 KSVMETVIAFANEPGLDGGYLLLGVDWAINDKGDTVYRPVGLPDPDKVQRDLASQCASMLNVALRPEMQLEQVGGKTLLV 109 (145)
Q Consensus 30 ~~l~k~i~AFAN~~~~~GG~liiGV~d~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~p~~~~~i~~~~~~g~~i~v 109 (145)
+.|.+.+.+.+.. --|+.|||=-.. .+.....+++.....-.|+ ++...
T Consensus 22 ~~Lr~~L~~~~~~----sdw~tiGIcA~s---------------~~~a~~ALrs~~~alg~~~----~~~~~-------- 70 (125)
T PF08854_consen 22 EKLRQALRLLMSN----SDWFTIGICAPS---------------AEEAIAALRSYEQALGYPP----LEPLD-------- 70 (125)
T ss_dssp HHHHHHHHHHHHT----SSEEEE-EEESS---------------S----HHHHHHHHH----------------------
T ss_pred HHHHHHHHHHHHC----CCCEEEEEECCC---------------HHHHHHHHHHHHHHCCCCC----CCCCC--------
T ss_conf 9999999998624----560589865688---------------8999999999999809985----57788--------
Q ss_pred EEEECCCCCCCCEEECCCCCCCCEEEEECCCCCEEC
Q ss_conf 983359998885887587998616898268752119
Q T0557 110 VYVPEADVTHKPIYKKATGLPGGAYRRIGSSDQRCV 145 (145)
Q Consensus 110 i~Ip~s~~~~~P~~~~~~~~~~~~Y~R~g~~~~~~~ 145 (145)
.+..+.|+|+|.|...+.+|+|.-.|..|=|
T Consensus 71 -----~~~~~GpVfLK~N~~tg~~y~~~y~G~~rGV 101 (125)
T PF08854_consen 71 -----SPPIEGPVFLKANQKTGSCYLRSYTGLGRGV 101 (125)
T ss_dssp ------------EEEEE------EEEEE-----B--
T ss_pred -----CCCCCCCEEEEECCCCCCEEEEECCCCCCEE
T ss_conf -----8788886799865878748986227755338
No 3
>PF01899 MNHE: Na+/H+ ion antiporter subunit; InterPro: IPR002758 This family contains both characterised and uncharacterised bacterial and archaeal proteins; some of which are possibly transmembrane proteins involved in Na^+/H^+ or K^+/H^+ transport. The characterised proteins are mnhE (Staphylococcus aureus) and phaE. (Rhizobium meliloti), which are subunits of the Na^+/H^+ or K^+/H^+ antiporters, that are required for sodium and potassium excretion, respectively , . ; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0016021 integral to membrane
Probab=19.54 E-value=22 Score=13.86 Aligned_cols=43 Identities=16% Similarity=0.057 Sum_probs=26.7
Q ss_pred CCCEEEEEECCCCHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCC
Q ss_conf 99657774157884799999999708877897079998632776336
Q T0557 16 ESARIEAKRASDMGKSVMETVIAFANEPGLDGGYLLLGVDWAINDKG 62 (145)
Q Consensus 16 E~~~lEfK~~~~~~~~l~k~i~AFAN~~~~~GG~liiGV~d~~~~~~ 62 (145)
....+++.... .+++ .++.+||+...--|++.++++++....-
T Consensus 34 ~P~iv~v~~~~--~~d~--~~~~lan~ITLTPGTl~vdv~~~~~~l~ 76 (106)
T PF01899_consen 34 NPGIVRVPLRL--RSDL--GITLLANSITLTPGTLTVDVDDDRRVLY 76 (106)
T ss_pred CCEEEEEECCC--CCHH--HHHHHHHHHCCCCCEEEEEECCCCCEEE
T ss_conf 97499996256--9878--9999999881699759999718998899
No 4
>PF06153 DUF970: Protein of unknown function (DUF970); InterPro: IPR010375 This is a family of uncharacterised bacterial proteins.
Probab=15.70 E-value=28 Score=13.36 Aligned_cols=51 Identities=25% Similarity=0.254 Sum_probs=28.7
Q ss_pred CEEEEEEECCCCCCCCCCCCEEECCCHHHHHHHHHHHHHCCCC---CCCEEE---------EEEEEECCCEEEEEEEE
Q ss_conf 0799986327763366532202202035789999998760388---530245---------88998469789999833
Q T0557 48 GYLLLGVDWAINDKGDTVYRPVGLPDPDKVQRDLASQCASMLN---VALRPE---------MQLEQVGGKTLLVVYVP 113 (145)
Q Consensus 48 G~liiGV~d~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---p~~~~~---------i~~~~~~g~~i~vi~Ip 113 (145)
-++++||+|+. .++..+.|.+.|..... |+.... --.++..|-.|+++.|.
T Consensus 42 tTlLIGvede~---------------vd~vl~iIk~~c~~R~q~v~~~~~~~~~~~~~~~~pveV~VGGAtvFVl~ve 104 (109)
T PF06153_consen 42 TTLLIGVEDER---------------VDEVLDIIKKNCKEREQVVTPPSPMGGSGGMYVPYPVEVEVGGATVFVLDVE 104 (109)
T ss_pred EEEEEEEEHHH---------------HHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCEEEEECCCEEEEEEHH
T ss_conf 68999842888---------------8999999998502652663678776667665435225898668689998779
No 5
>PF01739 CheR: CheR methyltransferase, SAM binding domain; InterPro: IPR000780 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order . Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI ), shared by other AdoMet-Mtases , is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments , although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases , , , . The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences . Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains , . Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase , which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues , . The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A . The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region .; GO: 0008757 S-adenosylmethionine-dependent methyltransferase activity; PDB: 1bc5_A 1af7_A.
Probab=12.85 E-value=30 Score=13.13 Aligned_cols=10 Identities=20% Similarity=0.478 Sum_probs=5.1
Q ss_pred CEEEEEEECC
Q ss_conf 0799986327
Q T0557 48 GYLLLGVDWA 57 (145)
Q Consensus 48 G~liiGV~d~ 57 (145)
-+=|+|.+-+
T Consensus 64 ~~~I~atDi~ 73 (196)
T PF01739_consen 64 DFRILATDIS 73 (196)
T ss_dssp -EEEEEEES-
T ss_pred CEEEEEEECC
T ss_conf 5599999899
No 6
>PF08532 Glyco_hydro_42M: Beta-galactosidase trimerisation domain; InterPro: IPR013738 This is non catalytic domain B of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. This domain is related to glutamine amidotransferase enzymes, but the catalytic residues are replaced by non functional amino acids. This domain is involved in trimerisation. ; PDB: 1kwg_A 1kwk_A.
Probab=7.39 E-value=55 Score=11.80 Aligned_cols=23 Identities=26% Similarity=0.544 Sum_probs=18.9
Q ss_pred CHHHHHHHHHHHHCCCCCCCCEEEEEE
Q ss_conf 847999999997088778970799986
Q T0557 28 MGKSVMETVIAFANEPGLDGGYLLLGV 54 (145)
Q Consensus 28 ~~~~l~k~i~AFAN~~~~~GG~liiGV 54 (145)
.++.+++.+.+|+. .||.||+|-
T Consensus 69 l~~~~~~~L~~yV~----~GG~lv~~~ 91 (207)
T PF08532_consen 69 LSDEFAERLRAYVE----NGGTLVAGP 91 (207)
T ss_dssp --HHH---HHHHHT--------EEE--
T ss_pred ECHHHHHHHHHHHH----CCCEEEEEC
T ss_conf 48778899999997----899999975
No 7
>PF05271 Tobravirus_2B: Tobravirus 2B protein; InterPro: IPR007935 This family consists of several tobravirus 2B proteins. It is known that the 2B protein is required for transmission by both Paratrichodorus pachydermus and Paratrichodorus anemones nematodes . Transmission of the tobraviruses Tobacco rattle virus by trichodorid vector nematodes requires the viral coat protein (CP) and the 2B protein, a nonstructural protein encoded by RNA2, the smaller of the two viral genomic RNAs. It is hypothesized that the 2B protein functions by interacting with a small, flexible domain located at the C-terminus of the CP, forming a bridge between the virus particle and the internal surface of the vector nematode feeding apparatus .; GO: 0019089 transmission of virus
Probab=6.82 E-value=59 Score=11.64 Aligned_cols=24 Identities=17% Similarity=0.416 Sum_probs=11.5
Q ss_pred HHHHHHHHHCCC-C---CCCCEEEEEEE
Q ss_conf 999999970887-7---89707999863
Q T0557 32 VMETVIAFANEP-G---LDGGYLLLGVD 55 (145)
Q Consensus 32 l~k~i~AFAN~~-~---~~GG~liiGV~ 55 (145)
+-|...+|.... + ++-|+++|-|.
T Consensus 47 IPk~fiSFiDnRlPMCiNhkG~vyIrV~ 74 (116)
T PF05271_consen 47 IPKSFISFIDNRLPMCINHKGWVYIRVK 74 (116)
T ss_pred CCHHHHHHCCCCCCEEECCCCEEEEEEC
T ss_conf 6276764304776427746645999964
No 8
>PF10223 DUF2181: Uncharacterized conserved protein (DUF2181)
Probab=6.41 E-value=62 Score=11.53 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHCCCCCEEEEEEC
Q ss_conf 737999999971789965777415
Q T0557 2 RSATDLLDELNAVDESARIEAKRA 25 (145)
Q Consensus 2 ~~~~e~l~~L~~~~E~~~lEfK~~ 25 (145)
.+-+|.|+.+....-+..|+||+-
T Consensus 58 ltL~e~L~~v~~~~kgVKLDFKs~ 81 (244)
T PF10223_consen 58 LTLEEWLDEVLPSNKGVKLDFKSI 81 (244)
T ss_pred CCHHHHHHHHHCCCCEEEEEECCH
T ss_conf 659999999863483799850467
No 9
>PF10820 DUF2543: Protein of unknown function (DUF2543)
Probab=6.20 E-value=27 Score=13.39 Aligned_cols=28 Identities=21% Similarity=0.350 Sum_probs=15.1
Q ss_pred CCCEEEEEECCCCHHHHHHHHHHHHCCC
Q ss_conf 9965777415788479999999970887
Q T0557 16 ESARIEAKRASDMGKSVMETVIAFANEP 43 (145)
Q Consensus 16 E~~~lEfK~~~~~~~~l~k~i~AFAN~~ 43 (145)
|+..-|.-+..+.+..-+.+|+-|.|.+
T Consensus 51 EeAQ~EMA~eAgi~~~RIDdIA~FLNqW 78 (81)
T PF10820_consen 51 EEAQQEMAREAGIDERRIDDIANFLNQW 78 (81)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 9999999998299777689999999874
No 10
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); PDB: 3cgx_A.
Probab=5.56 E-value=70 Score=11.26 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=12.0
Q ss_pred CCHHHHHHHH-HHHHCCCCCCCCEEEEEEE
Q ss_conf 8847999999-9970887789707999863
Q T0557 27 DMGKSVMETV-IAFANEPGLDGGYLLLGVD 55 (145)
Q Consensus 27 ~~~~~l~k~i-~AFAN~~~~~GG~liiGV~ 55 (145)
+..+.+...+ .+|... -.-.++||-+
T Consensus 45 dLG~Rm~~a~~~~~~~g---~~~vvlIGsD 71 (122)
T PF09837_consen 45 DLGERMARAFQDAFERG---YEPVVLIGSD 71 (122)
T ss_dssp ----HHHHHHHHHHH-------EEEEE---
T ss_pred CHHHHHHHHHHHHHHCC---CCEEEEECCC
T ss_conf 98999999999999648---9849998188
Done!