Query T0576 3NA2, Leptospirillum rubarum, 172 residues
Match_columns 172
No_of_seqs 2 out of 4
Neff 1.1
Searched_HMMs 11830
Date Fri Jun 4 14:26:30 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0576.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0576.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09550 DUF2376: Conserved hy 35.9 4.6 0.00039 18.3 0.9 15 133-147 4-18 (43)
2 PF06228 DUF1008: ChuX-like fa 30.7 14 0.0012 15.3 7.1 110 29-142 27-139 (141)
3 PF09497 Med12: Transcription 27.4 6 0.00051 17.6 0.3 24 101-124 38-63 (64)
4 PF11066 DUF2867: Protein of u 25.1 18 0.0015 14.7 5.8 60 56-123 71-135 (149)
5 PF00312 Ribosomal_S15: Riboso 24.7 9.3 0.00078 16.4 0.9 24 125-148 12-35 (83)
6 PF05171 HemS: Haemin-degradin 20.8 21 0.0018 14.1 8.0 90 29-120 21-111 (129)
7 PF10387 DUF2442: Protein of u 20.0 22 0.0019 14.0 2.2 28 75-102 8-35 (76)
8 PF11812 DUF3333: Domain of un 17.9 12 0.001 15.7 0.3 15 139-153 44-58 (155)
9 PF10597 U5_2-snRNA_bdg: U5-sn 16.9 18 0.0015 14.6 0.9 20 89-109 104-123 (135)
10 PF11005 DUF2844: Protein of u 16.5 14 0.0012 15.2 0.4 13 120-132 116-128 (132)
No 1
>PF09550 DUF2376: Conserved hypothetical phage protein (DUF2376)
Probab=35.92 E-value=4.6 Score=18.32 Aligned_cols=15 Identities=40% Similarity=0.842 Sum_probs=11.8
Q ss_pred CHHHHHHHHHHHCCC
Q ss_conf 767887765542014
Q T0576 133 PPEQFWAFTQRYIDL 147 (172)
Q Consensus 133 ppeqfwaftqryidl 147 (172)
+|++||+.|-+-..+
T Consensus 4 ~P~~FW~lTP~El~a 18 (43)
T PF09550_consen 4 RPEEFWALTPAELRA 18 (43)
T ss_pred CHHHHHHCCHHHHHH
T ss_conf 879999579999998
No 2
>PF06228 DUF1008: ChuX-like family; InterPro: IPR010413 This family consists of several hypothetical bacterial proteins of unknown function.; PDB: 2ph0_A 2ovi_C 3fm2_A 2hqv_A.
Probab=30.68 E-value=14 Score=15.28 Aligned_cols=110 Identities=22% Similarity=0.280 Sum_probs=74.8
Q ss_pred HHHHHHHHHHHHCCEEEEEECCCCCHHHHCCCCCEEEEEECCEEEE---EECCEEEEEEEEEEEEEEEECCCCCCCCEEE
Q ss_conf 6889999999736816887418875021217841067740534676---5012167775322237767427575786489
Q T0576 29 DRIGQMILEMFRTGMCLFSVRSPGGVAELYGGEARKVEITGTSLTI---EREDWHLHCKLETVETVVFDLSPKDNGGIRM 105 (172)
Q Consensus 29 drig~milemfr~gmclfsvrspg~vaelyggearkv~i~gtslti---ere~whlhc~letvetvvfdlspk~nggirm 105 (172)
++.-.+.-++-.-|--.+.|+++++|.|.-|- --+-.+..--.++ +-+.+|.|-+++.+..+-|---|.- |+---
T Consensus 27 ~~~~~ll~~l~~wG~vt~IV~t~~~I~E~kg~-~p~g~~~~Gy~Nl~~~~g~~lhgHL~~d~~~~i~fv~~pf~-g~~s~ 104 (141)
T PF06228_consen 27 ERFDELLEELPGWGEVTTIVHTEGAIFEVKGP-FPKGKYAHGYYNLMHKDGGPLHGHLKLDNIAAIAFVSRPFM-GRESY 104 (141)
T ss_dssp GGHHHHHHHHTT---EEEEEE-SSEEEEEEE----S-EB----BEEEE------EEEEEGGGEEEEEEEEEE-----EEE
T ss_pred HHHHHHHHHHHCCCCEEEEEECCCEEEEEECC-CCCCEECCCCEECCCCCCCEEEEEECHHHCCEEEEEECCCC-CCCCE
T ss_conf 99999999733248668999769889998458-99971156016636888731788972655011214403226-98618
Q ss_pred EEEEECCCCCCEEHHHHCHHHCCCCCCCHHHHHHHHH
Q ss_conf 9997036667420110010006798787678877655
Q T0576 106 AVVFRDKHQAPVLRAAWLPRLMPETPSPPEQFWAFTQ 142 (172)
Q Consensus 106 avvf~dkhq~pvlraawlprlmp~tpsppeqfwaftq 142 (172)
++.|-|+..-.++. .+|.|=- .----|+|.=+|-+
T Consensus 105 si~F~~~~G~~~fK-vflgrd~-~~~l~~~Qv~~f~~ 139 (141)
T PF06228_consen 105 SIRFFDAQGEAMFK-VFLGRDE-KRELFPEQVEAFRA 139 (141)
T ss_dssp EEEEEETTS-EEEE-EEE-B-T-TSSB-HHHHHHHHH
T ss_pred EEEEECCCCCEEEE-EEEECCC-CCCCCHHHHHHHHH
T ss_conf 99998689988999-9963599-87548899999985
No 3
>PF09497 Med12: Transcription mediator complex subunit Med12
Probab=27.38 E-value=6 Score=17.56 Aligned_cols=24 Identities=33% Similarity=0.552 Sum_probs=14.5
Q ss_pred CCEEEEEEEE--CCCCCCEEHHHHCH
Q ss_conf 8648999970--36667420110010
Q T0576 101 GGIRMAVVFR--DKHQAPVLRAAWLP 124 (172)
Q Consensus 101 ggirmavvf~--dkhq~pvlraawlp 124 (172)
.|+|--.+|. -..++|+.||.|+-
T Consensus 38 hg~r~~~lle~l~~~~VPl~RAiWli 63 (64)
T PF09497_consen 38 HGIRKEELLEQLCDYNVPLPRAIWLI 63 (64)
T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHCC
T ss_conf 82049999999987698714763110
No 4
>PF11066 DUF2867: Protein of unknown function (DUF2867)
Probab=25.07 E-value=18 Score=14.66 Aligned_cols=60 Identities=22% Similarity=0.429 Sum_probs=42.9
Q ss_pred HHCCCCC----EEEEEECCEEEEEECCEEEEEEEEEEEEEEEECCCCCCCC-EEEEEEEECCCCCCEEHHHHC
Q ss_conf 1217841----0677405346765012167775322237767427575786-489999703666742011001
Q T0576 56 ELYGGEA----RKVEITGTSLTIEREDWHLHCKLETVETVVFDLSPKDNGG-IRMAVVFRDKHQAPVLRAAWL 123 (172)
Q Consensus 56 elyggea----rkv~i~gtsltiere~whlhc~letvetvvfdlspk~ngg-irmavvf~dkhq~pvlraawl 123 (172)
++-.|++ +-++++...+-++.+++||+.++. +...+..+|+ +.++.+|+-+.-. =|+-|.
T Consensus 71 ~~~~gd~~~~f~V~~~~~~e~ll~~~d~hL~~~~~------l~~~~~~~~~~l~~tt~v~~~~~~--Gr~Y~~ 135 (149)
T PF11066_consen 71 DLRVGDRVDFFRVEEVSPDEILLGTDDKHLDFRLS------LEVQDDGEGRQLRVTTVVHPHNLL--GRLYWA 135 (149)
T ss_pred CCCCCCCCCCEEEEEECCCEEEECCCCCCCEEEEE------EEEEECCCCCEEEEEEEEEECCCC--HHHHHH
T ss_conf 46878844506999845893441026775528999------999987998689999999979954--899999
No 5
>PF00312 Ribosomal_S15: Ribosomal protein S15; InterPro: IPR000589 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , ,], groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1kuq_A 2hgr_R 2fkx_A 1f7y_A 1pns_O 1dk1_A 1ab3_A 1voq_O 3d5c_O 2qnh_p ....
Probab=24.72 E-value=9.3 Score=16.40 Aligned_cols=24 Identities=29% Similarity=0.213 Sum_probs=19.5
Q ss_pred HHCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf 006798787678877655420141
Q T0576 125 RLMPETPSPPEQFWAFTQRYIDLP 148 (172)
Q Consensus 125 rlmp~tpsppeqfwaftqryidlp 148 (172)
+--.||+|+|+|...+|.|...|-
T Consensus 12 ~~~~dtGs~evQia~LT~rI~~L~ 35 (83)
T PF00312_consen 12 RHPGDTGSSEVQIALLTERINNLT 35 (83)
T ss_dssp SHSS--SSHHHHHHHHHHHHHHHH
T ss_pred HCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 568988992999999999999999
No 6
>PF05171 HemS: Haemin-degrading HenS.ChuX domain; InterPro: IPR007845 The Yersinia enterocolitica O:8 periplasmic binding protein-dependent transport system consisted of four proteins: the periplasmic haemin-binding protein HemT, the haemin permease protein HemU, the ATP-binding hydrophilic protein HemV and the haemin-degrading protein HemS (this family).; GO: 0006826 iron ion transport; PDB: 2j0p_A 2j0r_A 1u9t_A 2hq2_A.
Probab=20.78 E-value=21 Score=14.13 Aligned_cols=90 Identities=16% Similarity=0.191 Sum_probs=68.8
Q ss_pred HHHHHHHHHHHHCC-EEEEEECCCCCHHHHCCCCCEEEEEECCEEEEEECCEEEEEEEEEEEEEEEECCCCCCCCEEEEE
Q ss_conf 68899999997368-16887418875021217841067740534676501216777532223776742757578648999
Q T0576 29 DRIGQMILEMFRTG-MCLFSVRSPGGVAELYGGEARKVEITGTSLTIEREDWHLHCKLETVETVVFDLSPKDNGGIRMAV 107 (172)
Q Consensus 29 drig~milemfr~g-mclfsvrspg~vaelyggearkv~i~gtsltiere~whlhc~letvetvvfdlspk~nggirmav 107 (172)
.....++-+.-..| ....-+|.+|.|-| .-|...++...|--+.+--++..||-.+.....+-.--.|.+ .|++..+
T Consensus 21 ~~~~~lL~~~~~~g~~vM~~trN~g~vq~-~~G~~~~~~~~g~~~~vl~~~~dLrl~~~~w~~~wav~~~t~-~G~~~Sl 98 (129)
T PF05171_consen 21 PAFRALLEALAALGLPVMAFTRNEGCVQE-HTGPYENLKPMGPWGNVLDPDFDLRLFFDHWASAWAVRKPTD-DGVVTSL 98 (129)
T ss_dssp THHHHHHHHHHHHT--EEEEEE-SSEEEE-E-----SEEEETTEEEEE-TTEEEEEEGGGEEEEEEEEE-------EEEE
T ss_pred HHHHHHHHHHHHCCCCEEEEECCCCEEEE-EEEECCCEECCCCEEEEECCCCEEEECHHHEEEEEEEECCCC-CCCEEEE
T ss_conf 76999999999759908999759961799-987607741159889996798419981354059999973589-9968999
Q ss_pred EEECCCCCCEEHH
Q ss_conf 9703666742011
Q T0576 108 VFRDKHQAPVLRA 120 (172)
Q Consensus 108 vf~dkhq~pvlra 120 (172)
-|-|++...|...
T Consensus 99 e~FD~~G~~i~ki 111 (129)
T PF05171_consen 99 EFFDAAGEAIHKI 111 (129)
T ss_dssp EEEE----EEEEE
T ss_pred EEECCCCCEEEEE
T ss_conf 9996889799999
No 7
>PF10387 DUF2442: Protein of unknown function (DUF2442); PDB: 2auw_A.
Probab=19.96 E-value=22 Score=14.02 Aligned_cols=28 Identities=32% Similarity=0.415 Sum_probs=22.7
Q ss_pred EECCEEEEEEEEEEEEEEEECCCCCCCC
Q ss_conf 5012167775322237767427575786
Q T0576 75 EREDWHLHCKLETVETVVFDLSPKDNGG 102 (172)
Q Consensus 75 ere~whlhc~letvetvvfdlspk~ngg 102 (172)
--++|.|.+..++-++-+||++|--+++
T Consensus 8 ~~~~y~L~v~F~dG~~~~~Dl~~~l~~~ 35 (76)
T PF10387_consen 8 PLDDYRLLVTFSDGETGIVDLSPLLEGP 35 (76)
T ss_dssp E-STTEEEEEE----EEEEE---HHH-G
T ss_pred ECCCCEEEEEECCCCEEEEEHHHHHCCC
T ss_conf 8899499999849989999849950665
No 8
>PF11812 DUF3333: Domain of unknown function (DUF3333)
Probab=17.87 E-value=12 Score=15.66 Aligned_cols=15 Identities=60% Similarity=1.026 Sum_probs=7.7
Q ss_pred HHHHHHCCCCEEEEC
Q ss_conf 765542014157704
Q T0576 139 AFTQRYIDLPMVVDA 153 (172)
Q Consensus 139 aftqryidlp~vvda 153 (172)
||+|-||.+|+-.|+
T Consensus 44 AF~qT~I~l~V~~~~ 58 (155)
T PF11812_consen 44 AFTQTYITLPVTLDP 58 (155)
T ss_pred HHHEEEEEEEEEECH
T ss_conf 572258898778588
No 9
>PF10597 U5_2-snRNA_bdg: U5-snRNA binding site 2 of PrP8
Probab=16.92 E-value=18 Score=14.65 Aligned_cols=20 Identities=40% Similarity=0.649 Sum_probs=15.0
Q ss_pred EEEEEECCCCCCCCEEEEEEE
Q ss_conf 377674275757864899997
Q T0576 89 ETVVFDLSPKDNGGIRMAVVF 109 (172)
Q Consensus 89 etvvfdlspk~nggirmavvf 109 (172)
-.||| .+|||-||.-|--+.
T Consensus 104 PPvvF-YtPKElGGLGMLS~g 123 (135)
T PF10597_consen 104 PPVVF-YTPKELGGLGMLSMG 123 (135)
T ss_pred CCEEE-ECCHHCCCCCEECCC
T ss_conf 98466-581440763100145
No 10
>PF11005 DUF2844: Protein of unknown function (DUF2844)
Probab=16.50 E-value=14 Score=15.18 Aligned_cols=13 Identities=46% Similarity=0.910 Sum_probs=6.8
Q ss_pred HHHCHHHCCCCCC
Q ss_conf 1001000679878
Q T0576 120 AAWLPRLMPETPS 132 (172)
Q Consensus 120 aawlprlmp~tps 132 (172)
-||||+++|.--+
T Consensus 116 rAwlP~~lPaGV~ 128 (132)
T PF11005_consen 116 RAWLPAALPAGVS 128 (132)
T ss_pred CEECCCCCCCCCC
T ss_conf 1514110689877
Done!