Query psy7380
Match_columns 72
No_of_seqs 93 out of 95
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 16:45:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7380.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7380hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3586|consensus 99.6 4.5E-17 9.8E-22 130.0 2.2 53 10-62 248-304 (437)
2 cd00182 TBOX T-box DNA binding 99.2 3.2E-12 7E-17 91.6 0.4 25 10-34 163-187 (188)
3 smart00425 TBOX Domain first f 99.1 4.2E-11 9E-16 85.6 0.9 26 10-35 164-189 (190)
4 PF00907 T-box: T-box; InterP 98.7 9E-10 1.9E-14 75.7 -1.6 24 9-32 161-184 (184)
5 KOG3585|consensus 98.6 1E-08 2.2E-13 78.3 0.7 26 10-35 187-212 (328)
6 smart00811 Alpha_kinase Alpha- 71.4 2.2 4.7E-05 30.6 1.2 16 13-28 7-22 (198)
7 PF13516 LRR_6: Leucine Rich r 33.8 27 0.00058 16.5 1.1 15 12-26 1-15 (24)
8 COG1825 RplY Ribosomal protein 32.9 11 0.00024 24.6 -0.6 23 13-35 35-57 (93)
9 PF08540 HMG_CoA_synt_C: Hydro 32.1 7.7 0.00017 29.5 -1.6 25 46-70 15-39 (282)
10 PF08218 Citrate_ly_lig: Citra 31.7 23 0.00049 26.3 0.8 17 15-31 1-17 (182)
11 PF10053 DUF2290: Uncharacteri 30.9 29 0.00062 25.7 1.3 40 22-61 79-119 (196)
12 TIGR03032 conserved hypothetic 22.4 31 0.00068 27.7 0.2 8 65-72 117-124 (335)
13 PF13130 DUF3952: Domain of un 21.5 33 0.00071 23.8 0.1 53 17-71 11-65 (107)
14 PF11228 DUF3027: Protein of u 21.3 56 0.0012 24.5 1.3 17 56-72 170-186 (193)
15 KOG0884|consensus 20.3 61 0.0013 23.7 1.3 20 7-26 140-160 (161)
No 1
>KOG3586|consensus
Probab=99.64 E-value=4.5e-17 Score=130.00 Aligned_cols=53 Identities=42% Similarity=0.432 Sum_probs=45.9
Q ss_pred hhhhccceeeecCCccccccccCCCch----hhhhhhhhhhccccccCCCCCCCCCC
Q psy7380 10 AYYKEITKLKIDSNPFAKGFRDSSRLT----EFERQNVLFDRHFMGRILRDEYPPDT 62 (72)
Q Consensus 10 ~qnqqIT~LKID~NPFAKgFRd~s~~~----~~~~eail~~q~~~rsp~r~~~~~~~ 62 (72)
-|||+||+||||+|||||||||.+++. +...++++..+++||+|+++...+..
T Consensus 248 YQNq~ITkLKI~sNPFAKGFRD~~~~~~~~~~~~~~~l~~~~~~~r~p~~~~~~~~~ 304 (437)
T KOG3586|consen 248 YQNQRITKLKIESNPFAKGFRDCGRNDWPDNEPGGDALLSAFARSRAPLRFPTQPSL 304 (437)
T ss_pred cccceeeeeeeccCccccccccCCccCccccCcchhhhhhhhhhccCccccccccch
Confidence 499999999999999999999998875 24456688899999999999887763
No 2
>cd00182 TBOX T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors.
Probab=99.19 E-value=3.2e-12 Score=91.55 Aligned_cols=25 Identities=68% Similarity=1.034 Sum_probs=23.5
Q ss_pred hhhhccceeeecCCccccccccCCC
Q psy7380 10 AYYKEITKLKIDSNPFAKGFRDSSR 34 (72)
Q Consensus 10 ~qnqqIT~LKID~NPFAKgFRd~s~ 34 (72)
-||++||+|||++|||||||||.++
T Consensus 163 YqN~~It~lKi~~NpfAkgfr~~~~ 187 (188)
T cd00182 163 YQNQEITQLKIDNNPFAKGFRDNGR 187 (188)
T ss_pred ecCHhHhhhhhcCCcccccccccCC
Confidence 4899999999999999999999876
No 3
>smart00425 TBOX Domain first found in the mice T locus (Brachyury) protein.
Probab=99.05 E-value=4.2e-11 Score=85.55 Aligned_cols=26 Identities=65% Similarity=0.948 Sum_probs=23.7
Q ss_pred hhhhccceeeecCCccccccccCCCc
Q psy7380 10 AYYKEITKLKIDSNPFAKGFRDSSRL 35 (72)
Q Consensus 10 ~qnqqIT~LKID~NPFAKgFRd~s~~ 35 (72)
-||++||+|||++||||||||+.++.
T Consensus 164 YqN~~it~lKi~~NpfAkgfr~~~~~ 189 (190)
T smart00425 164 YQNQKITKLKIDNNPFAKGFRDQGRR 189 (190)
T ss_pred ecccchhhccccCCCCcCccccccCC
Confidence 48999999999999999999998653
No 4
>PF00907 T-box: T-box; InterPro: IPR001699 Transcription factors of the T-box family are required both for early cell-fate decisions, such as those necessary for formation of the basic vertebrate body plan, and for differentiation and organogenesis []. The T-box is defined as the minimal region within the T-box protein that is both necessary and sufficient for sequence-specific DNA binding, all members of the family so far examined bind to the DNA consensus sequence TCACACCT. The T-box is a relatively large DNA-binding domain, generally comprising about a third of the entire protein (17-26 kDa). These genes were uncovered on the basis of similarity to the DNA binding domain [] of Mus musculus (Mouse) Brachyury (T) gene product, which similarity is the defining feature of the family. The Brachyury gene is named for its phenotype, which was identified 70 years ago as a mutant mouse strain with a short blunted tail. The gene, and its paralogues, have become a well-studied model for the family, and hence much of what is known about the T-box family is derived from the murine Brachyury gene. Consistent with its nuclear location, Brachyury protein has a sequence-specific DNA-binding activity and can act as a transcriptional regulator []. Homozygous mutants for the gene undergo extensive developmental anomalies, thus rendering the mutation lethal []. The postulated role of Brachyury is as a transcription factor, regulating the specification and differentiation of posterior mesoderm during gastrulation in a dose-dependent manner []. T-box proteins tend to be expressed in specific organs or cell types, especially during development, and they are generally required for the development of those tissues, for example, Brachyury is expressed in posterior mesoderm and in the developing notochord, and it is required for the formation of these cells in mice []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1H6F_B 4A04_A 1XBR_B 2X6V_B 2X6U_A.
Probab=98.73 E-value=9e-10 Score=75.70 Aligned_cols=24 Identities=63% Similarity=0.951 Sum_probs=20.0
Q ss_pred hhhhhccceeeecCCccccccccC
Q psy7380 9 QAYYKEITKLKIDSNPFAKGFRDS 32 (72)
Q Consensus 9 ~~qnqqIT~LKID~NPFAKgFRd~ 32 (72)
.-||++|++|||++|||||||||.
T Consensus 161 ~Yqn~~I~~lK~~~Npfak~fr~~ 184 (184)
T PF00907_consen 161 AYQNEEIRQLKIDNNPFAKGFRDK 184 (184)
T ss_dssp S-SSHHHHHHHHHH-GGGGGGHH-
T ss_pred ccchhhhhhhhhccCCCccccCCC
Confidence 458999999999999999999983
No 5
>KOG3585|consensus
Probab=98.60 E-value=1e-08 Score=78.25 Aligned_cols=26 Identities=65% Similarity=0.876 Sum_probs=23.3
Q ss_pred hhhhccceeeecCCccccccccCCCc
Q psy7380 10 AYYKEITKLKIDSNPFAKGFRDSSRL 35 (72)
Q Consensus 10 ~qnqqIT~LKID~NPFAKgFRd~s~~ 35 (72)
-||++||+|||++||||||||+....
T Consensus 187 YQn~~it~lKi~~Npfakgfr~~~~~ 212 (328)
T KOG3585|consen 187 YQNQEITKLKIDNNPFAKGFRDNIEG 212 (328)
T ss_pred eecceehhhcccCCcccccccccccc
Confidence 48999999999999999999998443
No 6
>smart00811 Alpha_kinase Alpha-kinase family. This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a bifunctional ion channel. This family is known as the alpha-kinase family. The structure of the kinase domain revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains.
Probab=71.39 E-value=2.2 Score=30.62 Aligned_cols=16 Identities=50% Similarity=0.717 Sum_probs=13.5
Q ss_pred hccceeeecCCccccc
Q psy7380 13 KEITKLKIDSNPFAKG 28 (72)
Q Consensus 13 qqIT~LKID~NPFAKg 28 (72)
.+.+.+||+.+|||+|
T Consensus 7 ~~~~~v~i~~~pFa~G 22 (198)
T smart00811 7 VSETGVKIELKPFAKG 22 (198)
T ss_pred cccEEEEEcCCccCCC
Confidence 3566799999999996
No 7
>PF13516 LRR_6: Leucine Rich repeat; PDB: 3RGZ_A 3RJ0_A 3RIZ_A 3RGX_A 1DFJ_I 2BNH_A 3VQ1_A 3VQ2_A 2Z64_A 2OMX_A ....
Probab=33.84 E-value=27 Score=16.51 Aligned_cols=15 Identities=13% Similarity=0.348 Sum_probs=9.5
Q ss_pred hhccceeeecCCccc
Q psy7380 12 YKEITKLKIDSNPFA 26 (72)
Q Consensus 12 nqqIT~LKID~NPFA 26 (72)
|..++.|.|.+|.+.
T Consensus 1 ~~~L~~L~l~~n~i~ 15 (24)
T PF13516_consen 1 NPNLETLDLSNNQIT 15 (24)
T ss_dssp -TT-SEEE-TSSBEH
T ss_pred CCCCCEEEccCCcCC
Confidence 457889999998753
No 8
>COG1825 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]
Probab=32.92 E-value=11 Score=24.55 Aligned_cols=23 Identities=30% Similarity=0.437 Sum_probs=18.4
Q ss_pred hccceeeecCCccccccccCCCc
Q psy7380 13 KEITKLKIDSNPFAKGFRDSSRL 35 (72)
Q Consensus 13 qqIT~LKID~NPFAKgFRd~s~~ 35 (72)
+..--+.+|+++|+|.||..+.+
T Consensus 35 ~~~v~i~l~~~~~~k~~~~~~~~ 57 (93)
T COG1825 35 KEPVNIALDHHEFAKALRKLGYS 57 (93)
T ss_pred CCCceEEEcHHHHHHHHhhcccc
Confidence 34456899999999999988743
No 9
>PF08540 HMG_CoA_synt_C: Hydroxymethylglutaryl-coenzyme A synthase C terminal; InterPro: IPR013746 Synonym(s): 3-hydroxy-3-methylglutaryl-coenzyme A synthase, HMG-CoA synthase. Hydroxymethylglutaryl-CoA synthase (2.3.3.10 from EC) catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA []. HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria []. In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi []. In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes [, ]. This entry represents the C-terminal domain of HMG-CoA synthase enzymes from both eukaryotes and prokaryotes.; GO: 0004421 hydroxymethylglutaryl-CoA synthase activity, 0008299 isoprenoid biosynthetic process; PDB: 1TXT_D 1TVZ_A 1X9E_B 2HDB_B 3V4X_A 3V4N_C 2P8U_A 2FA0_A 2F9A_A 2F82_A ....
Probab=32.12 E-value=7.7 Score=29.55 Aligned_cols=25 Identities=32% Similarity=0.393 Sum_probs=17.2
Q ss_pred hccccccCCCCCCCCCCcceeceee
Q psy7380 46 DRHFMGRILRDEYPPDTGKVVNTLY 70 (72)
Q Consensus 46 ~q~~~rsp~r~~~~~~~g~~~~~~~ 70 (72)
.+.||||-+..++|.-+|+.+|+.|
T Consensus 15 ~yDFyKP~~~seyP~VDG~~S~~~Y 39 (282)
T PF08540_consen 15 VYDFYKPDLSSEYPVVDGKLSIQCY 39 (282)
T ss_dssp --SEE-BTTT-SS-EE-HHHHHHHH
T ss_pred chhccCCCCCCCCcEEchHHHHHHH
Confidence 4889999889999999999998876
No 10
>PF08218 Citrate_ly_lig: Citrate lyase ligase C-terminal domain; InterPro: IPR013166 [Citrate (pro-3S)-lyase] ligase (6.2.1.22 from EC), also known as citrate lyase ligase, is responsible for acetylation of the prosthetic group (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase. It converts the inactive thiol form of the enzyme to the active form. In Clostridium sphenoides, citrate lyase ligase actively degrades citrate. In Clostridium sporosphaeroides and Lactococcus lactis, however, the enzyme is under stringent regulatory control. The enzyme's activity in anaerobic bacteria is modulated by phosphorylation and dephosphorylation []. The proteins in this entry represent the C-terminal domain of citrate lyase ligase.; GO: 0008771 [citrate (pro-3S)-lyase] ligase activity
Probab=31.67 E-value=23 Score=26.26 Aligned_cols=17 Identities=35% Similarity=0.681 Sum_probs=13.6
Q ss_pred cceeeecCCcccccccc
Q psy7380 15 ITKLKIDSNPFAKGFRD 31 (72)
Q Consensus 15 IT~LKID~NPFAKgFRd 31 (72)
|..+-+..|||++|-|-
T Consensus 1 IgaIVMNaNPFT~GH~y 17 (182)
T PF08218_consen 1 IGAIVMNANPFTLGHRY 17 (182)
T ss_pred CceEEEcCCCCccHHHH
Confidence 44667889999999883
No 11
>PF10053 DUF2290: Uncharacterized conserved protein (DUF2290); InterPro: IPR018742 Members of this family of hypothetical bacterial proteins have no known function.
Probab=30.92 E-value=29 Score=25.73 Aligned_cols=40 Identities=15% Similarity=0.320 Sum_probs=30.2
Q ss_pred CCccccccccCCCchh-hhhhhhhhhccccccCCCCCCCCC
Q psy7380 22 SNPFAKGFRDSSRLTE-FERQNVLFDRHFMGRILRDEYPPD 61 (72)
Q Consensus 22 ~NPFAKgFRd~s~~~~-~~~eail~~q~~~rsp~r~~~~~~ 61 (72)
-+||.-.|.+.+-.-. .....-+++...+++|+|-+++|+
T Consensus 79 P~P~~~~~q~~~~~y~~D~~~~~i~~~~i~~~PiRfDyd~~ 119 (196)
T PF10053_consen 79 PSPYLEDFQEEPEIYIEDYIYADIEEKRIVPSPIRFDYDPD 119 (196)
T ss_pred cCcchhhhccCCcchHHHHHHHHHHhcccccCceEEecCcc
Confidence 4799999998866533 333355677888999999999993
No 12
>TIGR03032 conserved hypothetical protein TIGR03032. This protein family is uncharacterized. A number of motifs are conserved perfectly among all member sequences. The function of this protein is unknown.
Probab=22.41 E-value=31 Score=27.72 Aligned_cols=8 Identities=75% Similarity=1.356 Sum_probs=7.2
Q ss_pred eeceeecC
Q psy7380 65 VVNTLYSC 72 (72)
Q Consensus 65 ~~~~~~~~ 72 (72)
++||+|||
T Consensus 117 fVNT~fSC 124 (335)
T TIGR03032 117 FVNTLFSC 124 (335)
T ss_pred EEECccee
Confidence 68999999
No 13
>PF13130 DUF3952: Domain of unknown function (DUF3952)
Probab=21.52 E-value=33 Score=23.79 Aligned_cols=53 Identities=15% Similarity=0.155 Sum_probs=35.3
Q ss_pred eeeecCCccccccccCCCchhhhhhhhhhhccccccC--CCCCCCCCCcceeceeec
Q psy7380 17 KLKIDSNPFAKGFRDSSRLTEFERQNVLFDRHFMGRI--LRDEYPPDTGKVVNTLYS 71 (72)
Q Consensus 17 ~LKID~NPFAKgFRd~s~~~~~~~eail~~q~~~rsp--~r~~~~~~~g~~~~~~~~ 71 (72)
+-||++-||.|+-++-.+.. ...|--.+|+++... -++.-.-++|+-.+++|.
T Consensus 11 etKIeYe~~VKALDEGDMkt--VMSASDdGYAyV~e~~i~st~eekeDg~~~~~iyQ 65 (107)
T PF13130_consen 11 ETKIEYERFVKALDEGDMKT--VMSASDDGYAYVKERVIYSTFEEKEDGEHSKTIYQ 65 (107)
T ss_pred eeeeehHHHHHHhcccchhh--eeccCCCceeEEEEEeeeeeeeeccCcceeeEEEe
Confidence 46999999999988766542 223333456655433 455566678888888873
No 14
>PF11228 DUF3027: Protein of unknown function (DUF3027); InterPro: IPR021391 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.27 E-value=56 Score=24.50 Aligned_cols=17 Identities=35% Similarity=0.765 Sum_probs=14.9
Q ss_pred CCCCCCCcceeceeecC
Q psy7380 56 DEYPPDTGKVVNTLYSC 72 (72)
Q Consensus 56 ~~~~~~~g~~~~~~~~~ 72 (72)
.++.|++|+||..-|.|
T Consensus 170 Ne~sp~DGrVVs~d~GC 186 (193)
T PF11228_consen 170 NEWSPADGRVVSLDHGC 186 (193)
T ss_pred CCCCCCCCCEEccccCc
Confidence 46789999999999988
No 15
>KOG0884|consensus
Probab=20.26 E-value=61 Score=23.69 Aligned_cols=20 Identities=30% Similarity=0.571 Sum_probs=16.1
Q ss_pred Cchhhhh-ccceeeecCCccc
Q psy7380 7 NNQAYYK-EITKLKIDSNPFA 26 (72)
Q Consensus 7 ~~~~qnq-qIT~LKID~NPFA 26 (72)
+-||-|+ .|..+-|-.||||
T Consensus 140 tyrpl~~~~ik~itihanp~a 160 (161)
T KOG0884|consen 140 TYRPLNDVHIKDITIHANPFA 160 (161)
T ss_pred ccccchheeeeeeEEecCcCC
Confidence 4566665 5889999999998
Done!