Query T0616 Ryanodine receptor, Bacteroides thetaiotaomicron, 103 residues
Match_columns 103
No_of_seqs 103 out of 138
Neff 5.2
Searched_HMMs 11830
Date Mon Jul 5 08:58:56 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0616.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0616.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02026 RyR: RyR domain; Int 100.0 3.9E-41 2.8E-45 253.7 10.1 94 10-103 1-94 (94)
2 PF08676 MutL_C: MutL C termin 56.7 3.9 0.00033 19.5 3.2 55 37-101 29-84 (142)
3 PF01352 KRAB: KRAB box; Inte 48.3 2.2 0.00018 20.9 0.8 29 68-96 13-41 (41)
4 PF06504 RepC: Replication pro 41.8 10 0.00086 17.1 3.4 58 34-100 205-266 (281)
5 PF09011 DUF1898: Domain of un 27.9 14 0.0012 16.4 2.2 57 34-90 6-63 (158)
6 PF02965 Met_synt_B12: Vitamin 24.2 17 0.0014 15.8 2.1 23 23-45 34-56 (136)
7 PF06794 UPF0270: Uncharacteri 21.8 11 0.00094 16.9 0.8 11 66-76 1-11 (70)
8 PF00505 HMG_box: HMG (high mo 19.7 26 0.0022 14.7 2.9 23 68-90 37-59 (69)
9 PF03186 CobD_Cbib: CobD/Cbib 14.8 31 0.0027 14.3 1.8 32 15-46 123-154 (292)
10 PF11971 CAMSAP_CH: CAMSAP CH 13.6 38 0.0032 13.8 2.6 35 63-99 33-73 (85)
No 1
>PF02026 RyR: RyR domain; InterPro: IPR003032 This domain is called RyR for Ryanodine receptor . The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.
Probab=100.00 E-value=3.9e-41 Score=253.73 Aligned_cols=94 Identities=56% Similarity=0.984 Sum_probs=92.7
Q ss_pred CCCCCCCCCCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHCCCHHHHHHHHHHHHHHH
Q ss_conf 78888766752140789999999998888899999999820002774376668898412321189889987789999999
Q T0616 10 DYIPEPMDLSLVDLPESLIQLSERIAENVHEVWAKARIDEGWTYGEKRDDIHKKHPCLVPYDELPEEEKEYDRNTAMNTI 89 (103)
Q Consensus 10 ~y~P~PvD~s~v~L~~~l~~l~e~lAen~H~~Wa~~k~~~GW~yG~~~d~~~k~HP~Lvpy~~L~e~eK~~dr~~~~e~l 89 (103)
+|+|+|||||+|+||++++.|+|+||||+|++||++|+.+||+||+++|+..|+|||||||++||++||++||++++|+|
T Consensus 1 ~y~P~PvD~s~v~L~~~l~~lveklAEn~H~~Wa~~k~~~GW~yG~~~d~~~k~HP~Lvpy~~L~e~eK~~~r~~~~e~l 80 (94)
T PF02026_consen 1 GYKPKPVDTSNVTLPEELEELVEKLAENEHDRWAKEKIEQGWTYGEVRDDGGKTHPCLVPYDLLPEKEKEKDRDPARETL 80 (94)
T ss_pred CCCCCCCCCCCEECCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHH
T ss_conf 99898736466035888999999999999999999999748520023035789898756843399999998799999999
Q ss_pred HHHHHCCCCCCCCC
Q ss_conf 99988394114689
Q T0616 90 KMVKKLGFRIEKED 103 (103)
Q Consensus 90 k~l~~~Gy~I~~~d 103 (103)
|+|+++||+|++++
T Consensus 81 k~L~~~Gy~I~~~~ 94 (94)
T PF02026_consen 81 KTLLALGYSIERPK 94 (94)
T ss_pred HHHHHCCCEEECCC
T ss_conf 99999594530799
No 2
>PF08676 MutL_C: MutL C terminal dimerisation domain; InterPro: IPR014790 MutL and MutS are key components of the DNA repair machinery that corrects replication errors . MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signalling complex for repair. The N-terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation . ; PDB: 1x9z_B.
Probab=56.70 E-value=3.9 Score=19.49 Aligned_cols=55 Identities=22% Similarity=0.305 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHC-CCHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 888999999998200027743766688984123211-89889987789999999999883941146
Q T0616 37 NVHEVWAKARIDEGWTYGEKRDDIHKKHPCLVPYDE-LPEEEKEYDRNTAMNTIKMVKKLGFRIEK 101 (103)
Q Consensus 37 n~H~~Wa~~k~~~GW~yG~~~d~~~k~HP~Lvpy~~-L~e~eK~~dr~~~~e~lk~l~~~Gy~I~~ 101 (103)
..|++...+++...|.-|. ...|+|+|... |++.+ .....+....|..+||.++.
T Consensus 29 AA~ERi~~E~l~~~~~~~~------~~Q~Ll~P~~l~l~~~e----~~~l~~~~~~L~~~Gf~~~~ 84 (142)
T PF08676_consen 29 AAHERILYEKLLRQLQSGT------PSQPLLFPLRLELSPQE----AELLEEYKEELEQLGFEFEP 84 (142)
T ss_dssp HHHHHHHHHHH---------------EEEEEEEEEEE--HHH----HHHHHHHHHHHHH---EEE-
T ss_pred HHHHHHHHHHHHHHHHCCC------CCEEECCCCEEECCHHH----HHHHHHHHHHHHHCCCEEEE
T ss_conf 9999999999999872678------75663688458629999----99999999999977959997
No 3
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) . It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box . The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain , . Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin , . KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome . Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1v65_A.
Probab=48.30 E-value=2.2 Score=20.91 Aligned_cols=29 Identities=17% Similarity=0.298 Sum_probs=25.4
Q ss_pred CCHHCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 23211898899877899999999998839
Q T0616 68 VPYDELPEEEKEYDRNTAMNTIKMVKKLG 96 (103)
Q Consensus 68 vpy~~L~e~eK~~dr~~~~e~lk~l~~~G 96 (103)
-.|..|+...|.-||+.+.|..+.|..+|
T Consensus 13 eEW~~Ld~~Qk~Ly~dvm~en~~~l~slg 41 (41)
T PF01352_consen 13 EEWGLLDPAQKNLYRDVMLENYRNLVSLG 41 (41)
T ss_dssp HHHHTS-HHHHHHHHHHHHHTTTS-----
T ss_pred HHHHHCCHHHHHHHHHHHHHHHCCCEECC
T ss_conf 78645899999876888987516343269
No 4
>PF06504 RepC: Replication protein C (RepC); InterPro: IPR010522 This family consists of several bacterial replication protein C (RepC) sequences.
Probab=41.83 E-value=10 Score=17.08 Aligned_cols=58 Identities=16% Similarity=0.275 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCCHH---CCCHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9888889999999982000277437666889-8412321---18988998778999999999988394114
Q T0616 34 IAENVHEVWAKARIDEGWTYGEKRDDIHKKH-PCLVPYD---ELPEEEKEYDRNTAMNTIKMVKKLGFRIE 100 (103)
Q Consensus 34 lAen~H~~Wa~~k~~~GW~yG~~~d~~~k~H-P~Lvpy~---~L~e~eK~~dr~~~~e~lk~l~~~Gy~I~ 100 (103)
-|.-.|.+-| ||.--+.. .+.+ -.|.+|- .-+.+...+-|..+|+.|+-|.+.||+|+
T Consensus 205 ~ArLlH~rLc------~wI~pGks---~~v~idTL~~yVW~~~a~~~~~rkRr~~vR~aL~El~~~GW~V~ 266 (281)
T PF06504_consen 205 PARLLHQRLC------SWIDPGKS---RRVEIDTLCGYVWPDEANPSAMRKRRQRVRKALPELEAVGWTVD 266 (281)
T ss_pred HHHHHHHHHH------HCCCCCCC---CCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEE
T ss_conf 8999999997------23787767---86314441121368999878999999999999999998596677
No 5
>PF09011 DUF1898: Domain of unknown function (DUF1898); InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; PDB: 2cto_A.
Probab=27.90 E-value=14 Score=16.36 Aligned_cols=57 Identities=19% Similarity=0.142 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCCHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 9888889999999982000277437666889-84123211898899877899999999
Q T0616 34 IAENVHEVWAKARIDEGWTYGEKRDDIHKKH-PCLVPYDELPEEEKEYDRNTAMNTIK 90 (103)
Q Consensus 34 lAen~H~~Wa~~k~~~GW~yG~~~d~~~k~H-P~Lvpy~~L~e~eK~~dr~~~~e~lk 90 (103)
-|.|.--.++.++|-+-=+.|-.-+..+-.- -|--.|..|++.+|+.|-+++++.-+
T Consensus 6 a~RNay~ff~qemIPElrRrGlqv~gvadaiplcs~dWall~e~eKe~Yae~Arelk~ 63 (158)
T PF09011_consen 6 AQRNAYFFFMQEMIPELRRRGLQVSGVADAIPLCSEDWALLSEDEKEAYAEKARELKN 63 (158)
T ss_dssp SS--HHHHHHHTTHHHHHH-----SSHHHHTGGGHHHHHHS-HHHHHHHHHHHHHHHH
T ss_pred CCCCEEEEEHHHHCHHHHHCCCCCCCHHHHCCCCCHHHHHCHHHHHHHHHHHHHHHHH
T ss_conf 3544478757876879897578610234322545854665608789999999999875
No 6
>PF02965 Met_synt_B12: Vitamin B12 dependent methionine synthase, activation domain; InterPro: IPR004223 Vitamin B12 dependent methionine synthase 2.1.1.13 from EC (5-methyltetrahydrofolate--homocysteine S-methyltransferase) catalyses the conversion of 5-methyltetrahydrofolate and L-homocysteine to tetrahydrofolate and L-methionine as the final step in de novo methionine biosynthesis. The enzyme requires methylcobalamin as a cofactor. In humans, defects in this enzyme are the cause of autosomal recessive inherited methylcobalamin deficiency (CBLG), which causes mental retardation, macrocytic anemia and homocystinuria. Mild deficiencies in activity may result in mild hyperhomocysteinemia, and mutations in the enzyme may be involved in tumorigenesis. Vitamin B12 dependent methionine synthase is found in prokaryotes and eukaryotes, but in prokaryotes the cofactor is cobalamin. In Escherichia coli, methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and tetrahydrofolate, the third module binds the B12 cofactor (IPR003759 from INTERPRO, IPR006158 from INTERPRO), and the C-terminal module (activation domain) binds S-adenosylmethionine. The activation domain is essential for the reductive activation of the enzyme. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain . The activation domain adopts an unusual alpha/beta fold.; GO: 0008705 methionine synthase activity, 0009086 methionine biosynthetic process, 0005622 intracellular; PDB: 1j6r_A 2o2k_A 3bul_A 1msk_A 1k98_A 1k7y_A.
Probab=24.17 E-value=17 Score=15.81 Aligned_cols=23 Identities=39% Similarity=0.397 Sum_probs=14.5
Q ss_pred ECHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 07899999999988888999999
Q T0616 23 LPESLIQLSERIAENVHEVWAKA 45 (103)
Q Consensus 23 L~~~l~~l~e~lAen~H~~Wa~~ 45 (103)
+.---..++|.+|+..|..-..+
T Consensus 34 ldala~~~~Ea~ae~~~~~ir~~ 56 (136)
T PF02965_consen 34 LDALASELAEALAEYVHEEIRKE 56 (136)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999999998
No 7
>PF06794 UPF0270: Uncharacterised protein family (UPF0270); InterPro: IPR010648 This is a group of proteins of unknown function.; PDB: 1y0n_A.
Probab=21.78 E-value=11 Score=16.87 Aligned_cols=11 Identities=36% Similarity=1.029 Sum_probs=5.7
Q ss_pred CCCCHHCCCHH
Q ss_conf 41232118988
Q T0616 66 CLVPYDELPEE 76 (103)
Q Consensus 66 ~Lvpy~~L~e~ 76 (103)
||+||+.|++.
T Consensus 1 MiIP~~~L~~e 11 (70)
T PF06794_consen 1 MIIPWQQLPPE 11 (70)
T ss_dssp EE--GGGS-HH
T ss_pred CCCCHHHCCHH
T ss_conf 90774769999
No 8
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair . The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins ; LEF1 lymphoid enhancer binding factor 1 ; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor ; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3f27_D 2yul_A 1i11_A 2gzk_A 1hry_A 1j46_A 1j47_A 1hrz_A 1gt0_D 1o4x_B ....
Probab=19.68 E-value=26 Score=14.71 Aligned_cols=23 Identities=26% Similarity=0.248 Sum_probs=18.9
Q ss_pred CCHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 23211898899877899999999
Q T0616 68 VPYDELPEEEKEYDRNTAMNTIK 90 (103)
Q Consensus 68 vpy~~L~e~eK~~dr~~~~e~lk 90 (103)
.-|..||+.+|..+.+.+.+...
T Consensus 37 ~~Wk~ls~~eK~~y~~~a~~~~~ 59 (69)
T PF00505_consen 37 EMWKSLSEEEKKKYEEKAEEDKE 59 (69)
T ss_dssp HHHHHSCHHHHHHHHHHHHHHHH
T ss_pred HHHHHCCHHHHHHHHHHHHHHHH
T ss_conf 88883999999999999999999
No 9
>PF03186 CobD_Cbib: CobD/Cbib protein; InterPro: IPR004485 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents the CbiB protein, which is involved in cobalamin biosynthesis and porphyrin biosynthesis. It converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon .; GO: 0009236 cobalamin biosynthetic process, 0016021 integral to membrane
Probab=14.85 E-value=31 Score=14.29 Aligned_cols=32 Identities=19% Similarity=0.015 Sum_probs=23.5
Q ss_pred CCCCCCCEECHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 76675214078999999999888889999999
Q T0616 15 PMDLSLVDLPESLIQLSERIAENVHEVWAKAR 46 (103)
Q Consensus 15 PvD~s~v~L~~~l~~l~e~lAen~H~~Wa~~k 46 (103)
.-||++..-..-....+|.+|||.++.|..--
T Consensus 123 ~Rdt~~l~~~~i~ra~iEslaen~~d~~~apl 154 (292)
T PF03186_consen 123 GRDTDNLDEEGIARAAIESLAENLSDGVFAPL 154 (292)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf 98802199889999999999999634109999
No 10
>PF11971 CAMSAP_CH: CAMSAP CH domain
Probab=13.59 E-value=38 Score=13.82 Aligned_cols=35 Identities=26% Similarity=0.430 Sum_probs=24.6
Q ss_pred CCCCCCCH------HCCCHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 89841232------11898899877899999999998839411
Q T0616 63 KHPCLVPY------DELPEEEKEYDRNTAMNTIKMVKKLGFRI 99 (103)
Q Consensus 63 ~HP~Lvpy------~~L~e~eK~~dr~~~~e~lk~l~~~Gy~I 99 (103)
-+|.++|+ ..+|...+.++...+.+.- --.+|+.+
T Consensus 33 y~P~~i~~~~i~~~~~~S~~~~l~N~~~l~~~~--~~~l~~~~ 73 (85)
T PF11971_consen 33 YCPQLIPLHEICLRPQMSQADSLYNIQLLNNFC--NEKLGFSC 73 (85)
T ss_pred HCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHH--HHHCCCCC
T ss_conf 682536587705676322999965799999999--99829987
Done!