Query T0642 J0KE1, Homo sapiens, 387 residues
Match_columns 387
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 11830
Date Thu Jul 22 14:56:05 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0642.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0642.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10479 FSA_C: Fragile site-a 25.2 9.4 0.00079 14.9 1.0 31 201-231 460-492 (615)
2 PF09664 DUF2399: Protein of u 21.1 17 0.0015 13.3 2.4 37 200-239 41-77 (155)
3 PF09582 AnfO_nitrog: Iron onl 20.8 9.1 0.00077 14.9 0.2 20 190-209 54-73 (202)
4 PF06531 DUF1108: Protein of u 14.1 23 0.0019 12.7 0.9 29 80-108 48-83 (86)
5 PF08772 NOB1_Zn_bind: Nin one 12.0 28 0.0024 12.2 0.9 15 171-185 4-18 (73)
6 PF11352 DUF3155: Protein of u 11.5 31 0.0026 11.9 1.0 45 168-214 17-62 (90)
7 PF04034 DUF367: Domain of unk 9.7 17 0.0014 13.5 -1.0 22 200-221 73-94 (127)
8 PF01249 Ribosomal_S21e: Ribos 7.4 40 0.0033 11.3 0.2 10 150-159 24-33 (81)
9 PF07405 DUF1506: Protein of u 6.7 35 0.003 11.6 -0.4 20 252-271 60-79 (133)
10 PF01463 LRRCT: Leucine rich r 6.7 39 0.0033 11.3 -0.1 11 4-14 2-12 (25)
No 1
>PF10479 FSA_C: Fragile site-associated protein C-terminus
Probab=25.22 E-value=9.4 Score=14.86 Aligned_cols=31 Identities=26% Similarity=0.494 Sum_probs=12.7
Q ss_pred EEEEEECCHHHHH--HHHHHHHHHHHHHHHHHH
Q ss_conf 1267751202334--566677887777754312
Q T0642 201 ACIFICGRVEHAH--ALASTWCFINALISTSIT 231 (387)
Q Consensus 201 acificgrvehah--alastwcfinalistsit 231 (387)
-|-|+|---.|-- .-|...-|...||+.-|.
T Consensus 460 ~~SfvteF~dhI~v~~da~~~~FLhdLi~sYlk 492 (615)
T PF10479_consen 460 ECSFVTEFEDHIFVTMDAEAFFFLHDLISSYLK 492 (615)
T ss_pred EEEEEEEECCEEEEEECHHHHHHHHHHHHHHHH
T ss_conf 899998752506898262676488999999752
No 2
>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399)
Probab=21.06 E-value=17 Score=13.34 Aligned_cols=37 Identities=22% Similarity=0.420 Sum_probs=29.7
Q ss_pred CEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHEECCCCC
Q ss_conf 2126775120233456667788777775431200001212
Q T0642 200 PACIFICGRVEHAHALASTWCFINALISTSITALYANDFR 239 (387)
Q Consensus 200 pacificgrvehahalastwcfinalistsitalyandfr 239 (387)
+.+.+||.. .+.-..+|-||..|.....+..|..||-
T Consensus 41 ~~~~LIct~---G~p~~a~~~ll~~L~~~g~~~~y~gDfD 77 (155)
T PF09664_consen 41 SDAPLICTS---GQPSAATRRLLDRLAAAGARLYYSGDFD 77 (155)
T ss_pred CCCEEEECC---CCHHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf 996399779---9323999999999984898799962798
No 3
>PF09582 AnfO_nitrog: Iron only nitrogenase protein AnfO (AnfO_nitrog)
Probab=20.84 E-value=9.1 Score=14.92 Aligned_cols=20 Identities=25% Similarity=0.411 Sum_probs=7.8
Q ss_pred HHHHHHCCCCCEEEEEECCH
Q ss_conf 67876416782126775120
Q T0642 190 EMEETINGINPACIFICGRV 209 (387)
Q Consensus 190 emeetinginpacificgrv 209 (387)
.|-+.++-+..--||+-+.+
T Consensus 54 ~~~~~v~~L~dCkifva~~v 73 (202)
T PF09582_consen 54 SLAEIVNFLGDCKIFVAKSV 73 (202)
T ss_pred HHHHHHHHHCCEEEEEEEEC
T ss_conf 99999997468189997111
No 4
>PF06531 DUF1108: Protein of unknown function (DUF1108); InterPro: IPR009494 This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. The function of this family is unknown.
Probab=14.09 E-value=23 Score=12.67 Aligned_cols=29 Identities=48% Similarity=0.512 Sum_probs=20.5
Q ss_pred CCCHHHHHCCCC-------CCCCCCCHHHHHHHHHH
Q ss_conf 122012210122-------00000102568886432
Q T0642 80 TEDANDLETASS-------ESSMENTDETERMINET 108 (387)
Q Consensus 80 tedandletass-------essmentdeterminet 108 (387)
.-|.|||-+|+. |---|||||..|.||-.
T Consensus 48 v~d~ndLy~A~D~~~~~i~EWIeeNTDeqDrLiNLV 83 (86)
T PF06531_consen 48 VTDENDLYIALDAMNQVINEWIEENTDEQDRLINLV 83 (86)
T ss_pred ECCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf 615799899999999999999985861788899896
No 5
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2con_A.
Probab=11.96 E-value=28 Score=12.16 Aligned_cols=15 Identities=40% Similarity=0.933 Sum_probs=11.0
Q ss_pred CCCCEEEEEECCEEE
Q ss_conf 797447876200321
Q T0642 171 HAPEWILLCHECKIT 185 (387)
Q Consensus 171 hapewillcheckit 185 (387)
+.--|+|.||-|--+
T Consensus 4 ~~k~~~lrC~aCf~~ 18 (73)
T PF08772_consen 4 RLKSWILRCHACFKI 18 (73)
T ss_dssp ----EEEE------E
T ss_pred HHHHHHHEEEHHHCC
T ss_conf 774254010221111
No 6
>PF11352 DUF3155: Protein of unknown function (DUF3155)
Probab=11.50 E-value=31 Score=11.91 Aligned_cols=45 Identities=36% Similarity=0.464 Sum_probs=32.0
Q ss_pred EECCCCCEEEEEECCEE-ECHHHHHHHHHCCCCCEEEEEECCHHHHHH
Q ss_conf 83479744787620032-101456787641678212677512023345
Q T0642 168 ICSHAPEWILLCHECKI-TATTHEMEETINGINPACIFICGRVEHAHA 214 (387)
Q Consensus 168 icshapewillchecki-tatthemeetinginpacificgrvehaha 214 (387)
|-.|.|.+-|-|-|.|- ||.-.-..+ +||.|..++..-|-||...
T Consensus 17 il~~vp~~~le~ge~KpVTAARr~i~e--~~i~pPA~l~VrRnehttd 62 (90)
T PF11352_consen 17 ILAHVPQFHLETGEDKPVTAARRFIAE--NGIVPPALLNVRRNEHTTD 62 (90)
T ss_pred HHHHCCCCEECCCCCCCCHHHHHHHHH--CCCCCCCEEEEECCCCCHH
T ss_conf 998687410025887840899999997--3889831046640543212
No 7
>PF04034 DUF367: Domain of unknown function (DUF367); InterPro: IPR007177 This domain is found in a family of proteins of unknown function. It appears to be found in eukaryotes and archaebacteria, and occurs associated with a potential metal-binding region in RNase L inhibitor, RLI (IPR007209 from INTERPRO).
Probab=9.66 E-value=17 Score=13.45 Aligned_cols=22 Identities=27% Similarity=0.478 Sum_probs=15.9
Q ss_pred CEEEEEECCHHHHHHHHHHHHH
Q ss_conf 2126775120233456667788
Q T0642 200 PACIFICGRVEHAHALASTWCF 221 (387)
Q Consensus 200 pacificgrvehahalastwcf 221 (387)
-|+.+|||..+.|..+.+..-+
T Consensus 73 AAaLyI~G~~~~A~~lL~~FkW 94 (127)
T PF04034_consen 73 AAALYILGFKDQAEELLSKFKW 94 (127)
T ss_pred HHHHHHCCCHHHHHHHHHHCCC
T ss_conf 9999993989999999974887
No 8
>PF01249 Ribosomal_S21e: Ribosomal protein S21e ; InterPro: IPR001931 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 , . A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 82 to 87 amino acids. The amino termini are all N alpha-acetylated. The N-terminal halves of the protein molecules are highly conserved in contrast to the carboxy-terminal parts .; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=7.36 E-value=40 Score=11.33 Aligned_cols=10 Identities=70% Similarity=0.777 Sum_probs=6.8
Q ss_pred CCCCCCCCHH
Q ss_conf 5543201010
Q T0642 150 NTANDHASVE 159 (387)
Q Consensus 150 ntandhasve 159 (387)
-+|.|||||.
T Consensus 24 I~akDHaSVQ 33 (81)
T PF01249_consen 24 ITAKDHASVQ 33 (81)
T ss_pred CCCCCCCEEE
T ss_conf 5257731589
No 9
>PF07405 DUF1506: Protein of unknown function (DUF1506); InterPro: IPR010875 This family consists of several bacterial proteins of around 130 residues in length. Members of this family seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.
Probab=6.74 E-value=35 Score=11.62 Aligned_cols=20 Identities=40% Similarity=0.634 Sum_probs=12.9
Q ss_pred EECCCCCCCCEEEEECCHHE
Q ss_conf 74346788522788701200
Q T0642 252 INATEDINPRELIMINARYM 271 (387)
Q Consensus 252 inatedinpreliminarym 271 (387)
+..--||+|.|+.||+.--|
T Consensus 60 ~Gv~i~I~P~El~~i~~sNi 79 (133)
T PF07405_consen 60 IGVIIDIKPQELVMIYDSNI 79 (133)
T ss_pred EEEEEEECHHHHHEECCCCC
T ss_conf 89999957578111116773
No 10
>PF01463 LRRCT: Leucine rich repeat C-terminal domain; InterPro: IPR000483 Leucine-rich repeats (LRR, see IPR001611 from INTERPRO) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape . LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions . Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response. LRRs are often flanked by cysteine-rich domains: an N-terminal LRR domain (IPR000372 from INTERPRO) and a C-terminal LRR domain. This entry represents the C-terminal LRR domain. ; PDB: 2wfh_B 2v9s_D 2v9t_B 1w8a_A 2v70_D.
Probab=6.69 E-value=39 Score=11.34 Aligned_cols=11 Identities=55% Similarity=0.833 Sum_probs=5.1
Q ss_pred CCCCCCCCCCC
Q ss_conf 33578653345
Q T0642 4 ARCASPERSTE 14 (387)
Q Consensus 4 arcasperste 14 (387)
+||++|+.-..
T Consensus 2 ~rC~~P~~lrg 12 (25)
T PF01463_consen 2 ARCASPPNLRG 12 (25)
T ss_dssp -BEEESGGGTT
T ss_pred CCCCCCHHHHC
T ss_conf 70588289806
Done!