Query 033924
Match_columns 108
No_of_seqs 111 out of 193
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 07:50:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033924.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033924hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1722 60s ribosomal protein 100.0 1.3E-32 2.7E-37 206.2 6.2 102 1-105 54-155 (155)
2 PTZ00033 60S ribosomal protein 99.9 5.3E-23 1.1E-27 150.7 3.8 67 1-68 58-124 (125)
3 PF14493 HTH_40: Helix-turn-he 37.5 24 0.00051 23.4 1.6 18 31-48 12-29 (91)
4 PF09278 MerR-DNA-bind: MerR, 28.8 33 0.00072 20.8 1.1 12 31-42 13-24 (65)
5 PRK00247 putative inner membra 15.4 4.5E+02 0.0097 23.1 5.7 13 11-23 299-311 (429)
6 cd04777 HTH_MerR-like_sg1 Heli 13.4 1.2E+02 0.0025 20.5 1.3 12 31-42 54-65 (107)
7 PF11973 NQRA_SLBB: NQRA C-ter 12.4 48 0.0011 20.7 -0.8 18 25-42 13-30 (51)
8 cd06539 CIDE_N_A CIDE_N domain 10.1 1.7E+02 0.0036 20.1 1.2 17 26-42 14-30 (78)
9 PF12653 DUF3785: Protein of u 10.0 1.6E+02 0.0034 22.4 1.2 21 28-48 28-48 (138)
10 cd06537 CIDE_N_B CIDE_N domain 9.5 1.8E+02 0.0039 20.1 1.2 17 27-43 15-31 (81)
No 1
>KOG1722 consensus 60s ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.3e-32 Score=206.17 Aligned_cols=102 Identities=51% Similarity=0.730 Sum_probs=92.4
Q ss_pred ChhhcccchHHHHHHHhhhhccCCCcccCccccCHHHHHHHhhcCHHHHHHHHHHHHHHHHHHhHhhHHHHHhhhhhhhh
Q 033924 1 MYRKQHKKDIAAEAVKKKRRSTKKPYSRSIVGATLEVIQKRRTEKPEVRDAAREAALREIKERIKKTKDEKRAKKAEVTS 80 (108)
Q Consensus 1 lyRR~hKKg~~ee~~kKr~rk~~k~~qRaIvGaSLe~I~~kRnqkpevR~A~Re~AireaKekkkakk~~kKa~ka~~~~ 80 (108)
|||++|+||++||++++|+|++++.|||+|||+|||+|+++|||+||||+|+||++|+++||++++.++++++.+++.++
T Consensus 54 LyR~khkKg~~ee~~kkrtrrt~k~~qRaI~GasL~~I~~KRn~kpevR~a~Re~alK~aKe~~ka~k~ak~A~K~~~as 133 (155)
T KOG1722|consen 54 LYRKKHKKGIQEEAAKKRTRRTVKKFQRAIVGASLDVILEKRNQKPEVRKAAREAALKKAKEKKKATKAAKKAKKAKSAS 133 (155)
T ss_pred HHHHHhhcchhHHHHHHHhhhhhhhhhhhhccccHHHHHHHhccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccc
Confidence 79999999999999999999999889999999999999999999999999999999999999999999999876666555
Q ss_pred hhhhccCCCCCCCCCCCCCccCCCC
Q 033924 81 KSKTQSKGSMPKGAAPKGPKLGGGG 105 (108)
Q Consensus 81 ~~k~~~k~~~~k~~~~~~p~~gg~~ 105 (108)
.. .++.+.+++.+++|+|||+.
T Consensus 134 ~~---k~qk~~k~~k~aaprVggkr 155 (155)
T KOG1722|consen 134 AP---KKQKAKKNAKVAAPRVGGKR 155 (155)
T ss_pred cc---cccchhhhhhhhcccccCCC
Confidence 32 22778889999999999874
No 2
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=99.87 E-value=5.3e-23 Score=150.71 Aligned_cols=67 Identities=30% Similarity=0.400 Sum_probs=63.3
Q ss_pred ChhhcccchHHHHHHHhhhhccCCCcccCccccCHHHHHHHhhcCHHHHHHHHHHHHHHHHHHhHhhH
Q 033924 1 MYRKQHKKDIAAEAVKKKRRSTKKPYSRSIVGATLEVIQKRRTEKPEVRDAAREAALREIKERIKKTK 68 (108)
Q Consensus 1 lyRR~hKKg~~ee~~kKr~rk~~k~~qRaIvGaSLe~I~~kRnqkpevR~A~Re~AireaKekkkakk 68 (108)
+|||+|+||++||+.++|+++++ ++||+|||+|||+|+++|||+||||.|++++||+++||++++.+
T Consensus 58 ~yRr~~kK~~~e~~~kkR~~rtv-K~qRaivg~sLe~I~~kR~~k~evr~aar~~a~r~~Ke~~~~~k 124 (125)
T PTZ00033 58 TYRRINRKTTTDRVQRRRAARTV-KVQRAIVGADLSYIQEVRAYVQKVDRSAKAKAVRAEKAERKAAK 124 (125)
T ss_pred HHHHHhCCcchhHHHHHHhcCCc-cchHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 59999999999999999999998 69999999999999999999999999999999999999988653
No 3
>PF14493 HTH_40: Helix-turn-helix domain
Probab=37.55 E-value=24 Score=23.37 Aligned_cols=18 Identities=33% Similarity=0.335 Sum_probs=15.5
Q ss_pred cccCHHHHHHHhhcCHHH
Q 033924 31 VGATLEVIQKRRTEKPEV 48 (108)
Q Consensus 31 vGaSLe~I~~kRnqkpev 48 (108)
-|.|+++|...|+-++..
T Consensus 12 ~G~si~eIA~~R~L~~sT 29 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKEST 29 (91)
T ss_pred cCCCHHHHHHHcCCCHHH
Confidence 499999999999987654
No 4
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=28.76 E-value=33 Score=20.80 Aligned_cols=12 Identities=33% Similarity=0.434 Sum_probs=8.7
Q ss_pred cccCHHHHHHHh
Q 033924 31 VGATLEVIQKRR 42 (108)
Q Consensus 31 vGaSLe~I~~kR 42 (108)
.|.||++|..-=
T Consensus 13 lGfsL~eI~~~l 24 (65)
T PF09278_consen 13 LGFSLEEIRELL 24 (65)
T ss_dssp TT--HHHHHHHH
T ss_pred cCCCHHHHHHHH
Confidence 699999999876
No 5
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=15.41 E-value=4.5e+02 Score=23.08 Aligned_cols=13 Identities=0% Similarity=-0.263 Sum_probs=6.5
Q ss_pred HHHHHHhhhhccC
Q 033924 11 AAEAVKKKRRSTK 23 (108)
Q Consensus 11 ~ee~~kKr~rk~~ 23 (108)
.+....+++|+..
T Consensus 299 ~~~~~~~~~~~~~ 311 (429)
T PRK00247 299 KEKKAFLWTLRRN 311 (429)
T ss_pred HHHHHHHHHHHhc
Confidence 3444455555554
No 6
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=13.44 E-value=1.2e+02 Score=20.47 Aligned_cols=12 Identities=42% Similarity=0.315 Sum_probs=10.1
Q ss_pred cccCHHHHHHHh
Q 033924 31 VGATLEVIQKRR 42 (108)
Q Consensus 31 vGaSLe~I~~kR 42 (108)
+|.||++|..-=
T Consensus 54 ~G~sL~eI~~~l 65 (107)
T cd04777 54 LGFSLIEIQKIF 65 (107)
T ss_pred CCCCHHHHHHHH
Confidence 599999999853
No 7
>PF11973 NQRA_SLBB: NQRA C-terminal domain; InterPro: IPR022615 This domain is found in bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration []. The function of this domain has not been characterised.; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=12.35 E-value=48 Score=20.70 Aligned_cols=18 Identities=22% Similarity=0.436 Sum_probs=15.0
Q ss_pred CcccCccccCHHHHHHHh
Q 033924 25 PYSRSIVGATLEVIQKRR 42 (108)
Q Consensus 25 ~~qRaIvGaSLe~I~~kR 42 (108)
.+-|.++|++|++|..-.
T Consensus 13 ~y~rt~~Ga~i~~l~~g~ 30 (51)
T PF11973_consen 13 RYVRTRIGASISDLLAGN 30 (51)
T ss_pred cEEEEeCCcCHHHHhCcc
Confidence 467899999999998654
No 8
>cd06539 CIDE_N_A CIDE_N domain of CIDE-A proteins. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins. These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40, ICAD/DFF45, and CIDE nucleases during apoptosis. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, the CIDE proteins were initially characterized as mitochondrial activators of apoptosis. However, strong metabolic phenotypes of mice lacking CIDE-A and CIDE-B indicated that this family may play critical roles in energy balance.
Probab=10.12 E-value=1.7e+02 Score=20.12 Aligned_cols=17 Identities=12% Similarity=0.356 Sum_probs=14.4
Q ss_pred cccCccccCHHHHHHHh
Q 033924 26 YSRSIVGATLEVIQKRR 42 (108)
Q Consensus 26 ~qRaIvGaSLe~I~~kR 42 (108)
...+|+..||+|+..|=
T Consensus 14 ~k~GV~A~sL~EL~~K~ 30 (78)
T cd06539 14 SRRGVMASSLQELISKT 30 (78)
T ss_pred ceEEEEecCHHHHHHHH
Confidence 36799999999998874
No 9
>PF12653 DUF3785: Protein of unknown function (DUF3785); InterPro: IPR024210 This family of proteins is functionally uncharacterised. Proteins in this family are approximately 140 amino acids in length and share two CXXC motifs suggesting these are zinc binding proteins. In clostridia proteins are found in an operon with three signalling proteins, suggesting that they are involved in DNA-binding transcription regulator downstream of an as yet unknown signalling pathway.
Probab=9.99 E-value=1.6e+02 Score=22.37 Aligned_cols=21 Identities=29% Similarity=0.401 Sum_probs=17.6
Q ss_pred cCccccCHHHHHHHhhcCHHH
Q 033924 28 RSIVGATLEVIQKRRTEKPEV 48 (108)
Q Consensus 28 RaIvGaSLe~I~~kRnqkpev 48 (108)
-.|-|+|||.|+.-=|...+|
T Consensus 28 ~ev~G~s~d~il~~ln~~eeV 48 (138)
T PF12653_consen 28 EEVEGLSLDKILEALNESEEV 48 (138)
T ss_pred cccccccHHHHHHHhcccccc
Confidence 468899999999988886665
No 10
>cd06537 CIDE_N_B CIDE_N domain of CIDE-B proteins. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins. These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40, ICAD/DFF45 and CIDE nucleases during apoptosis. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, CIDE proteins were initially characterized as mitochondrial activators of apoptosis. However, strong metabolic phenotypes of mice lacking CIDE-A and CIDE-B indicated that this family may play critical roles in energy balance.
Probab=9.50 E-value=1.8e+02 Score=20.10 Aligned_cols=17 Identities=12% Similarity=0.305 Sum_probs=14.3
Q ss_pred ccCccccCHHHHHHHhh
Q 033924 27 SRSIVGATLEVIQKRRT 43 (108)
Q Consensus 27 qRaIvGaSLe~I~~kRn 43 (108)
..+|+..||+++..|=.
T Consensus 15 kkGV~A~sL~EL~~K~~ 31 (81)
T cd06537 15 RKGLTAASLQELLAKAL 31 (81)
T ss_pred eEeEEccCHHHHHHHHH
Confidence 57899999999998743
Done!