Query 537021.9.peg.80_1 Match_columns 37 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 23 07:40:57 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_80.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01116 ATPase-IIA1_Ca calci 28.1 26 0.00066 18.1 1.0 23 7-31 590-614 (800) 2 TIGR02044 CueR Cu(I)-responsiv 27.7 53 0.0013 16.6 2.5 28 2-36 43-73 (127) 3 COG5111 RPC34 DNA-directed RNA 25.8 63 0.0016 16.2 2.6 31 7-37 32-65 (301) 4 pfam08874 DUF1835 Domain of un 20.0 66 0.0017 16.1 1.8 19 19-37 87-105 (115) 5 KOG0202 consensus 14.7 1.1E+02 0.0028 14.9 1.9 24 7-32 725-750 (972) 6 pfam11553 DUF3231 Protein of u 9.4 1.5E+02 0.0039 14.2 1.2 21 8-29 114-134 (166) 7 pfam09456 RcsC RcsC Alpha-Beta 9.4 2E+02 0.0051 13.6 1.9 17 19-35 5-21 (92) 8 COG2150 Predicted regulator of 8.9 73 0.0019 15.8 -0.6 17 8-24 21-37 (167) 9 pfam00846 Hanta_nucleocap Hant 8.5 1.5E+02 0.0038 14.3 0.8 13 14-26 331-343 (428) 10 pfam11707 Npa1 Ribosome 60S bi 8.4 2.2E+02 0.0057 13.4 1.7 16 19-35 127-142 (327) No 1 >TIGR01116 ATPase-IIA1_Ca calcium-translocating P-type ATPase, SERCA-type; InterPro: IPR005782 This model describes Ca2+ ATPases (3.6.3.8 from EC) from eukaryotes and includes significant representatives from plants. Plasma membrane Ca2+ ATPases are primarily responsible for extrusion of calcium from cytoplasmic milieu to outside, coupled to the hydrolyis of ATP. Besides Ca2+ ATPases, Na+/Ca2+ exchangers are also involved in the maintenance of Ca2+ homestasis in the cell. ; GO: 0005388 calcium-transporting ATPase activity, 0006816 calcium ion transport, 0016021 integral to membrane. Probab=28.06 E-value=26 Score=18.12 Aligned_cols=23 Identities=48% Similarity=0.920 Sum_probs=14.9 Q ss_pred HHHHHH--HHHHHHHHHHHHHHHHHHH Q ss_conf 688886--1276542135489999999 Q 537021.9.peg.8 7 TLLKAI--GFSVRNDMRNTCFIRYLLS 31 (37) Q Consensus 7 tllkai--gfsvrndmrntcfirylls 31 (37) |..+|. |=+.-|.|. -||||+.| T Consensus 590 TIV~AV~EGR~IyNNmK--qFIRYmIS 614 (800) T TIGR01116 590 TIVKAVEEGRAIYNNMK--QFIRYMIS 614 (800) T ss_pred HHHHHHCCCCHHHHCCH--HHHHHHHH T ss_conf 46533104641331232--46566552 No 2 >TIGR02044 CueR Cu(I)-responsive transcriptional regulator; InterPro: IPR011789 This entry represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue .; GO: 0003677 DNA binding, 0005507 copper ion binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription. Probab=27.73 E-value=53 Score=16.55 Aligned_cols=28 Identities=36% Similarity=0.717 Sum_probs=19.4 Q ss_pred CHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 54675688---886127654213548999999985027 Q 537021.9.peg.8 2 DVRKFTLL---KAIGFSVRNDMRNTCFIRYLLSLFRDK 36 (37) Q Consensus 2 dvrkftll---kaigfsvrndmrntcfiryllslfrdk 36 (37) +|..|+|+ +.+|||... |+-||+||.|. T Consensus 43 h~~~L~li~raR~~GFSLeE-------c~~ll~L~ndp 73 (127) T TIGR02044 43 HVDELRLISRARSVGFSLEE-------CKELLSLWNDP 73 (127) T ss_pred HHHHHHHHHHHHHHCCCHHH-------HHHHHHHHCCC T ss_conf 78888999999871898899-------99998752288 No 3 >COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription] Probab=25.75 E-value=63 Score=16.17 Aligned_cols=31 Identities=35% Similarity=0.471 Sum_probs=24.5 Q ss_pred HHHHHHHHHHHHHH---HHHHHHHHHHHHHHCCC Q ss_conf 68888612765421---35489999999850279 Q 537021.9.peg.8 7 TLLKAIGFSVRNDM---RNTCFIRYLLSLFRDKK 37 (37) Q Consensus 7 tllkaigfsvrndm---rntcfiryllslfrdkk 37 (37) .|.+++|-+--+|. -|.|.-|-|+++||++. T Consensus 32 el~~qmg~~sltDl~s~ln~lL~r~li~l~rq~~ 65 (301) T COG5111 32 ELQMQMGKASLTDLASELNALLKRQLISLFRQKG 65 (301) T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 9999854020888999999999876666774199 No 4 >pfam08874 DUF1835 Domain of unknown function (DUF1835). This family of proteins are functionally uncharacterized. Probab=19.99 E-value=66 Score=16.06 Aligned_cols=19 Identities=37% Similarity=0.648 Sum_probs=15.3 Q ss_pred HHHHHHHHHHHHHHHHCCC Q ss_conf 2135489999999850279 Q 537021.9.peg.8 19 DMRNTCFIRYLLSLFRDKK 37 (37) Q Consensus 19 dmrntcfiryllslfrdkk 37 (37) ....-|..+|++++++||+ T Consensus 87 na~Dqlgl~~~~~~Lkd~~ 105 (115) T pfam08874 87 NAHDQLGLRYVLSLLKDKP 105 (115) T ss_pred CHHHHHHHHHHHHHHCCCC T ss_conf 8798998999999854678 No 5 >KOG0202 consensus Probab=14.69 E-value=1.1e+02 Score=14.91 Aligned_cols=24 Identities=50% Similarity=0.897 Sum_probs=15.8 Q ss_pred HHHHHH--HHHHHHHHHHHHHHHHHHHH Q ss_conf 688886--12765421354899999998 Q 537021.9.peg.8 7 TLLKAI--GFSVRNDMRNTCFIRYLLSL 32 (37) Q Consensus 7 tllkai--gfsvrndmrntcfiryllsl 32 (37) |.+.|| |-+.-|.|.| ||||+||- T Consensus 725 tIvaAVEEGr~IynNik~--Fir~~lSs 750 (972) T KOG0202 725 TIVAAVEEGRAIYNNIKN--FIRYLLSS 750 (972) T ss_pred HHHHHHHHHHHHHHHHHH--HHHHHHHH T ss_conf 999999976889999999--99999861 No 6 >pfam11553 DUF3231 Protein of unknown function (DUF3231). This bacterial family of proteins has no known function. Probab=9.37 E-value=1.5e+02 Score=14.19 Aligned_cols=21 Identities=38% Similarity=0.513 Sum_probs=14.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8888612765421354899999 Q 537021.9.peg.8 8 LLKAIGFSVRNDMRNTCFIRYL 29 (37) Q Consensus 8 llkaigfsvrndmrntcfiryl 29 (37) ...|++.|.|+|.|.. |.+++ T Consensus 114 ~~~al~~s~R~Di~~~-f~~~~ 134 (166) T pfam11553 114 YGLALSMSLRNDIRLL-YSRCL 134 (166) T ss_pred HHHHHHHHHHHHHHHH-HHHHH T ss_conf 9999999999999999-99999 No 7 >pfam09456 RcsC RcsC Alpha-Beta-Loop (ABL). This domain is found in the C-terminus of the phospho-relay kinase RcsC between pfam00512 and pfam00072, and forms a discrete alpha/beta/loop structure. Probab=9.35 E-value=2e+02 Score=13.61 Aligned_cols=17 Identities=24% Similarity=0.385 Sum_probs=13.3 Q ss_pred HHHHHHHHHHHHHHHHC Q ss_conf 21354899999998502 Q 537021.9.peg.8 19 DMRNTCFIRYLLSLFRD 35 (37) Q Consensus 19 dmrntcfiryllslfrd 35 (37) +.||.+.-+||+++.+. T Consensus 5 ~iRNa~Le~yL~~lL~~ 21 (92) T pfam09456 5 AIRNASLESFLERLLSY 21 (92) T ss_pred HHHHHHHHHHHHHHHHH T ss_conf 77788999999999997 No 8 >COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only] Probab=8.90 E-value=73 Score=15.84 Aligned_cols=17 Identities=35% Similarity=0.468 Sum_probs=12.7 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 88886127654213548 Q 537021.9.peg.8 8 LLKAIGFSVRNDMRNTC 24 (37) Q Consensus 8 llkaigfsvrndmrntc 24 (37) .|-..||||+|++.+.| T Consensus 21 ~l~~~GisV~~g~~~~~ 37 (167) T COG2150 21 KLLESGISVKNGGKIYC 37 (167) T ss_pred HHHHHCEEECCCCCEEE T ss_conf 99980836726983563 No 9 >pfam00846 Hanta_nucleocap Hantavirus nucleocapsid protein. Probab=8.46 E-value=1.5e+02 Score=14.29 Aligned_cols=13 Identities=54% Similarity=0.782 Sum_probs=10.5 Q ss_pred HHHHHHHHHHHHH Q ss_conf 2765421354899 Q 537021.9.peg.8 14 FSVRNDMRNTCFI 26 (37) Q Consensus 14 fsvrndmrntcfi 26 (37) ||+-.|||||-.- T Consensus 331 fsilQDmRntImA 343 (428) T pfam00846 331 FSILQDMRNTIMA 343 (428) T ss_pred HHHHHHHHHHHHH T ss_conf 9999998877877 No 10 >pfam11707 Npa1 Ribosome 60S biogenesis N-terminal. Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length. Probab=8.35 E-value=2.2e+02 Score=13.38 Aligned_cols=16 Identities=38% Similarity=0.675 Sum_probs=12.2 Q ss_pred HHHHHHHHHHHHHHHHC Q ss_conf 21354899999998502 Q 537021.9.peg.8 19 DMRNTCFIRYLLSLFRD 35 (37) Q Consensus 19 dmrntcfiryllslfrd 35 (37) ++| ++||+|+||+++. T Consensus 127 s~R-~~fI~F~lsfL~~ 142 (327) T pfam11707 127 SIR-RNFIRFALSFLSV 142 (327) T ss_pred CHH-HHHHHHHHHHHCC T ss_conf 789-9999999999703 Done!