Query psy8582
Match_columns 161
No_of_seqs 58 out of 60
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 22:29:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8582.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8582hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07809 RTP801_C: RTP801 C-te 100.0 1.1E-60 2.4E-65 366.8 8.4 115 38-153 1-116 (116)
2 cd00539 MCR_gamma Methyl-coenz 58.3 7.5 0.00016 33.9 2.2 28 56-83 126-155 (246)
3 TIGR03259 met_CoM_red_gam meth 57.6 7.9 0.00017 33.8 2.2 28 56-83 126-155 (244)
4 PF02240 MCR_gamma: Methyl-coe 52.8 7.1 0.00015 34.1 1.2 26 58-83 129-156 (247)
5 COG4057 McrG Methyl coenzyme M 43.6 18 0.00039 31.6 2.2 26 58-83 133-160 (257)
6 PF02641 DUF190: Uncharacteriz 42.5 24 0.00052 25.9 2.4 26 60-87 20-45 (101)
7 PHA02613 48 baseplate subunit; 25.5 58 0.0013 30.0 2.5 39 71-114 308-346 (361)
8 PF11980 DUF3481: Domain of un 23.2 56 0.0012 24.7 1.6 16 102-117 64-79 (87)
9 PF08361 TetR_C_2: MAATS-type 22.6 2.5E+02 0.0054 20.7 5.1 40 24-69 48-87 (121)
10 KOG3468|consensus 21.3 52 0.0011 26.3 1.2 19 95-113 11-29 (128)
11 PF13093 FTA4: Kinetochore com 20.7 1.4E+02 0.003 25.1 3.7 59 3-68 20-83 (213)
No 1
>PF07809 RTP801_C: RTP801 C-terminal region; InterPro: IPR012918 The members of this family are sequences similar to the C-terminal region of RTP801, the protein product of a hypoxia-inducible factor 1 (HIF-1)- responsive gene []. Two members of this family expressed by Drosophila melanogaster, Scylla (Q9NHN4 from SWISSPROT) and Charybde (Q9NHN5 from SWISSPROT), are designated as Hox targets []. RTP801 is thought to be involved in various cellular processes []. Over expression of the gene caused the apoptosis-resistant phenotype in cycling cells, and apoptosis sensitivity in growth arrested cells []. Moreover, the protein product of the mouse homologue of RTP801 (dig2 (Q9D3F7 from SWISSPROT)) is thought to be induced by diverse apoptotic signals, and also by dexamethasone treatment []. ; GO: 0009968 negative regulation of signal transduction, 0005737 cytoplasm; PDB: 3LQ9_A.
Probab=100.00 E-value=1.1e-60 Score=366.82 Aligned_cols=115 Identities=54% Similarity=0.922 Sum_probs=82.8
Q ss_pred HHHhhccccccceeecCCCchHHHHHHHHHhhhcCCCcccceEEEEEeecc-cceeeeeeEeeCCCCCceeEEEEEEEec
Q psy8582 38 LRAAKSAQLACGEVLLPSDLLPNVARDILRLAEVEPYGLKGCTLFINFETD-QECRKIATITCDPNTVSTFELYLTLRQD 116 (161)
Q Consensus 38 Lr~AK~~~L~C~~lLlP~~L~~rIa~dvLrls~~EPCGlRGc~I~v~~E~~-~~~~~l~~i~~DP~~VpTFELtLvlrqd 116 (161)
|++||+++|+|+|||+|++|++|||+||||+|++||||+|||+|||+||+| ++|+++|+|+|||+||||||||||||||
T Consensus 1 L~~AK~~~L~C~~vLlP~~L~~~Ia~dvL~ls~~EPCGlRGc~i~v~~E~~~~~~~~l~~i~~Dp~~vpTFEL~Lvlr~d 80 (116)
T PF07809_consen 1 LRKAKRSHLRCSEVLLPEDLTRRIARDVLRLSESEPCGLRGCLIDVCFEDEPDNCRRLGQIKVDPSTVPTFELTLVLRQD 80 (116)
T ss_dssp HTTEESSSSSEE-EE--HHHHHHHHHHHHHHHTTSTTGGGGEEEEEEEEET-TEEEEEEEEES-TTS---EEEEEEEE--
T ss_pred CchhhhCcccCceEEchHHHHHHHHHHHHHhhcCCCCcceeeEEEEEEccccchheeeccEecCCCCCCcEEEEEEEeeC
Confidence 789999999999999999999999999999999999999999999999999 9999999999999999999999999999
Q ss_pred CCCCCccchhhhhhccCCCceEEeCCCcEEeeecccc
Q psy8582 117 FRHSWHSLLPQFLKNLTKGGTIMISRGFTLEKKRLYR 153 (161)
Q Consensus 117 ~~~~W~~~~~~F~~~~~~~~tl~Lsp~frliKkKLYs 153 (161)
+ ++||+++|+|.++.++++||+||||||+|||||||
T Consensus 81 ~-~~W~~l~~~F~~~~~~~~tl~ls~~frliKkKLYS 116 (116)
T PF07809_consen 81 S-SGWPSLRPLFLKNPGRGRTLRLSPGFRLIKKKLYS 116 (116)
T ss_dssp T-T-------S--T-------EE--S-EEEEEEE---
T ss_pred C-CCCHhHHHHhccCcCCCceEEECCCCEEEeccccC
Confidence 9 69999999999999999999999999999999997
No 2
>cd00539 MCR_gamma Methyl-coenzyme M reductase (MCR) gamma subunit. MCR catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea, in which methyl-coenzyme M and coenzyme B are converted to methane and the heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). MCR is a dimer of trimers, each of which consists of one alpha, one beta, and one gamma subunit, with two identical active sites containing nickel porphinoid factor 430 (F430).
Probab=58.28 E-value=7.5 Score=33.92 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=20.1
Q ss_pred CchHHHHHHHHHhhhcC--CCcccceEEEE
Q psy8582 56 DLLPNVARDILRLAEVE--PYGLKGCTLFI 83 (161)
Q Consensus 56 ~L~~rIa~dvLrls~~E--PCGlRGc~I~v 83 (161)
.=+..||++++...--- -||+|||++|=
T Consensus 126 rDlEk~sK~l~ete~fDpArtGiRGaTVHG 155 (246)
T cd00539 126 RDLEKIAKELLETELFDPARTGVRGATVHG 155 (246)
T ss_pred hhHHHHHHHHHhhhccCchhccccccceec
Confidence 34577888877654333 49999999984
No 3
>TIGR03259 met_CoM_red_gam methyl-coenzyme M reductase, gamma subunit. Members of this protein family are the gamma subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes.
Probab=57.57 E-value=7.9 Score=33.77 Aligned_cols=28 Identities=14% Similarity=0.350 Sum_probs=20.1
Q ss_pred CchHHHHHHHHHhhhcC--CCcccceEEEE
Q psy8582 56 DLLPNVARDILRLAEVE--PYGLKGCTLFI 83 (161)
Q Consensus 56 ~L~~rIa~dvLrls~~E--PCGlRGc~I~v 83 (161)
.=+..||++++...--- -||+|||++|=
T Consensus 126 rDlEk~sK~l~ete~fDpArtGiRGaTVHG 155 (244)
T TIGR03259 126 RDLEQISKELVETELFDPATTGVRGATVHG 155 (244)
T ss_pred hhHHHHHHHHHhhhccCchhccccccceec
Confidence 34577888877654333 49999999984
No 4
>PF02240 MCR_gamma: Methyl-coenzyme M reductase gamma subunit; InterPro: IPR003178 Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (2.8.4.1 from EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry []. MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [, ]. This entry represents the gamma subunit, which has a complex alpha-helical/beta-sheet topology.; GO: 0050524 coenzyme-B sulfoethylthiotransferase activity, 0015948 methanogenesis; PDB: 1MRO_C 3M32_C 3POT_F 1HBU_F 3M2U_C 3M2V_C 3M2R_F 1HBM_C 3M1V_C 1HBO_C ....
Probab=52.77 E-value=7.1 Score=34.08 Aligned_cols=26 Identities=15% Similarity=0.411 Sum_probs=13.9
Q ss_pred hHHHHHHHHHhhhc--CCCcccceEEEE
Q psy8582 58 LPNVARDILRLAEV--EPYGLKGCTLFI 83 (161)
Q Consensus 58 ~~rIa~dvLrls~~--EPCGlRGc~I~v 83 (161)
+..||++++...-- --||+|||++|=
T Consensus 129 lEk~sK~l~etE~fDpA~~g~RGaTVHG 156 (247)
T PF02240_consen 129 LEKISKELIETELFDPARTGIRGATVHG 156 (247)
T ss_dssp HHHHHHHHHHBTT--TTTEEE-SS----
T ss_pred HHHHHHHHHhhhccCchhcccccceecc
Confidence 56788877754333 349999999984
No 5
>COG4057 McrG Methyl coenzyme M reductase, gamma subunit [Coenzyme metabolism]
Probab=43.64 E-value=18 Score=31.58 Aligned_cols=26 Identities=23% Similarity=0.556 Sum_probs=19.2
Q ss_pred hHHHHHHHHHhhhcCC--CcccceEEEE
Q psy8582 58 LPNVARDILRLAEVEP--YGLKGCTLFI 83 (161)
Q Consensus 58 ~~rIa~dvLrls~~EP--CGlRGc~I~v 83 (161)
+..||++++...---| ||+|||++|=
T Consensus 133 lE~isK~l~eTe~fDPA~~GiRGatVHG 160 (257)
T COG4057 133 LEKISKELLETEFFDPARSGIRGATVHG 160 (257)
T ss_pred HHHHHHHHHHhhccChhhcccccceecc
Confidence 4667777776555444 8999999984
No 6
>PF02641 DUF190: Uncharacterized ACR, COG1993; InterPro: IPR003793 This is an uncharacterised domain found in proteins of unknown function.; PDB: 2DCL_C 1O51_A.
Probab=42.46 E-value=24 Score=25.88 Aligned_cols=26 Identities=27% Similarity=0.341 Sum_probs=21.0
Q ss_pred HHHHHHHHhhhcCCCcccceEEEEEeec
Q psy8582 60 NVARDILRLAEVEPYGLKGCTLFINFET 87 (161)
Q Consensus 60 rIa~dvLrls~~EPCGlRGc~I~v~~E~ 87 (161)
.+.+.|++.+.. +|++||+++--.++
T Consensus 20 ~l~~~ll~~~~~--~gi~GaTV~rgi~G 45 (101)
T PF02641_consen 20 PLYEWLLERARE--AGIAGATVFRGIEG 45 (101)
T ss_dssp EHHHHHHHHHHH--TT-SEEEEEE-SEE
T ss_pred EHHHHHHHHHHH--CCCCeEEEEcceee
Confidence 467889999988 99999999997776
No 7
>PHA02613 48 baseplate subunit; Provisional
Probab=25.50 E-value=58 Score=30.03 Aligned_cols=39 Identities=21% Similarity=0.287 Sum_probs=27.2
Q ss_pred cCCCcccceEEEEEeecccceeeeeeEeeCCCCCceeEEEEEEE
Q psy8582 71 VEPYGLKGCTLFINFETDQECRKIATITCDPNTVSTFELYLTLR 114 (161)
Q Consensus 71 ~EPCGlRGc~I~v~~E~~~~~~~l~~i~~DP~~VpTFELtLvlr 114 (161)
=-|||+---.++=-.++ ....+..-|+++.+|||-++||
T Consensus 308 FGPaqItSIRfdkTpDg-----~fNgLa~aPNlPssf~LEitFr 346 (361)
T PHA02613 308 FGPAQIQSIRFDKTPDG-----HFNGLAIAPNLPSSFVLEITFR 346 (361)
T ss_pred cCccceeEEeccCCchh-----ccchhccCCCCCceEEEEEEEe
Confidence 35888754333222221 3567888999999999999998
No 8
>PF11980 DUF3481: Domain of unknown function (DUF3481); InterPro: IPR022579 This domain of unknown function is located in the C terminus of the eukaryotic neuropilin receptor family of proteins. It is found in association with PF00754 from PFAM, PF00431 from PFAM and PF00629 from PFAM. There are two completely conserved residues (Y and E) that may be functionally important.
Probab=23.21 E-value=56 Score=24.70 Aligned_cols=16 Identities=19% Similarity=0.235 Sum_probs=13.2
Q ss_pred CCCceeEEEEEEEecC
Q psy8582 102 NTVSTFELYLTLRQDF 117 (161)
Q Consensus 102 ~~VpTFELtLvlrqd~ 117 (161)
.+.|+||+++++|++.
T Consensus 64 ~~~~~~Ep~ltikLek 79 (87)
T PF11980_consen 64 GAPPSVEPVLTIKLEK 79 (87)
T ss_pred CCCcccceeeeeEeec
Confidence 4556899999999886
No 9
>PF08361 TetR_C_2: MAATS-type transcriptional repressor, C-terminal region; InterPro: IPR013572 This entry is named after the various transcriptional regulatory proteins that it contains, including MtrR (Q6RV06 from SWISSPROT), AcrR (P34000 from SWISSPROT), ArpR (Q9KJC4 from SWISSPROT), TtgR (Q9AIU0 from SWISSPROT) and SmeT (Q8KLP4 from SWISSPROT). These are members of the TetR (tetracycline resistance) family of transcriptional repressors, that are involved in the control of expression of multidrug resistance proteins [, , ]. ; GO: 0003677 DNA binding; PDB: 3BCG_B 2QOP_A 2UXP_B 2XDN_C 2UXH_A 2UXI_B 2UXO_A 2UXU_B 2WUI_A 2W53_A ....
Probab=22.64 E-value=2.5e+02 Score=20.65 Aligned_cols=40 Identities=33% Similarity=0.352 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHHHHHHHhhccccccceeecCCCchHHHHHHHHHhh
Q psy8582 24 DSASIFLSNRLEQELRAAKSAQLACGEVLLPSDLLPNVARDILRLA 69 (161)
Q Consensus 24 ~~~~~~L~~~le~~Lr~AK~~~L~C~~lLlP~~L~~rIa~dvLrls 69 (161)
.++.++.-++|+..|++|-+.. .||+++..+.|.-.++..
T Consensus 48 ~~~~~~~~~~i~~~l~~A~~~g------~L~~~ld~~~AA~~l~a~ 87 (121)
T PF08361_consen 48 REAQREALARIERLLRRAQARG------QLPADLDPRLAAIMLHAL 87 (121)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT------SS-TTB-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHcC------CCCCCCCHHHHHHHHHHH
Confidence 3477788889999999777653 369999999999988754
No 10
>KOG3468|consensus
Probab=21.25 E-value=52 Score=26.27 Aligned_cols=19 Identities=16% Similarity=0.314 Sum_probs=14.4
Q ss_pred eeEeeCCCCCceeEEEEEE
Q psy8582 95 ATITCDPNTVSTFELYLTL 113 (161)
Q Consensus 95 ~~i~~DP~~VpTFELtLvl 113 (161)
..+..+|+.+|||-=-.-|
T Consensus 11 p~v~P~pd~~PTFdP~~gf 29 (128)
T KOG3468|consen 11 PEVAPRPDRPPTFDPQYGF 29 (128)
T ss_pred cccCCCCCCCCCCCcccCC
Confidence 6788999999999644433
No 11
>PF13093 FTA4: Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
Probab=20.71 E-value=1.4e+02 Score=25.11 Aligned_cols=59 Identities=15% Similarity=0.326 Sum_probs=41.0
Q ss_pred ccCcceeeccCcc-----chhhhcchhHHHHHHHHHHHHHHHHhhccccccceeecCCCchHHHHHHHHHh
Q psy8582 3 VLPNPVVFANNYE-----AFQQEDIEDSASIFLSNRLEQELRAAKSAQLACGEVLLPSDLLPNVARDILRL 68 (161)
Q Consensus 3 ~~~~~~~~~~~~~-----~~~~~~~e~~~~~~L~~~le~~Lr~AK~~~L~C~~lLlP~~L~~rIa~dvLrl 68 (161)
.|+.|+.-+...+ +.+.+++.+.+++.+-..+-..|++=-+. .+|.+-+++||+.|..+
T Consensus 20 iLsqPL~ps~~wr~~~~~~~~~~~l~~k~v~~vL~klN~~lkqH~r~-------vys~Qa~~hVaeQI~~l 83 (213)
T PF13093_consen 20 ILSQPLAPSRDWRSINSEPASEDPLSDKVVQDVLQKLNARLKQHNRR-------VYSPQAIRHVAEQIDKL 83 (213)
T ss_pred HcCCCCCCCHHHHHhcccccccCCCCHHHHHHHHHHHHHHHHHHHHH-------hCCHHHHHHHHHHHHHH
Confidence 4677776643211 22234577788888888888888643222 67999999999999875
Done!