Query psy9508
Match_columns 511
No_of_seqs 83 out of 85
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 21:19:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9508.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9508hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05217 STOP: STOP protein; 95.4 0.34 7.3E-06 46.0 12.9 37 420-456 165-204 (215)
2 PF05217 STOP: STOP protein; 95.3 0.31 6.7E-06 46.2 12.1 22 331-352 165-187 (215)
3 PF15373 DUF4601: Domain of un 5.4 2.3E+03 0.05 24.1 7.7 22 481-502 299-321 (440)
4 PRK09678 DNA-binding transcrip 3.1 8.7E+02 0.019 20.7 1.9 23 1-23 37-59 (72)
5 PF06773 Bim_N: Bim protein N- 2.3 1.2E+03 0.026 18.0 1.6 16 192-207 13-28 (41)
6 PF15643 Tox-PL-2: Papain fold 1.9 8.9E+02 0.019 22.1 0.5 11 234-244 78-88 (100)
7 PF15000 TUSC2: Tumour suppres 1.8 9.1E+02 0.02 22.5 0.3 42 28-69 47-93 (111)
8 PF06442 DHFR_2: R67 dihydrofo 1.6 9.5E+02 0.021 20.6 -0.0 31 185-215 13-54 (78)
9 PF07193 DUF1408: Protein of u 1.4 1.5E+03 0.033 19.4 0.9 18 25-42 37-54 (75)
10 cd00389 microbial_RNases micro 1.1 3.1E+03 0.068 17.1 2.1 28 9-36 39-66 (71)
No 1
>PF05217 STOP: STOP protein; InterPro: IPR007882 Neurons contain abundant subsets of highly stable microtubules that resist de-polymerising conditions such as exposure to the cold. Stable microtubules are thought to be essential for neuronal development, maintenance, and function. STOP is a major factor responsible for the intriguing stability properties of neuronal microtubules and is important for synaptic plasticity. STOPs (for stable tubule only polypeptides) are calmodulin-binding and calmodulin-regulated proteins which, in mammals, are encoded by a single gene but exhibit substantial cell specific variability due to mRNA splicing and alternative promoter use. STOP microtubule stabilising activity has been ascribed to two classes of new bifunctional calmodulin- and microtubule-binding motifs, with distinct microtubule binding properties in vivo. STOPs seem to be restricted to vertebrates and are composed of a conserved domain split by the apparent insertion of variable sequences that are completely unrelated among species []. N-STOP (for neuronal adult STOP) contains two repeat domains. The central repeat domain is composed of five repeated sequences of 46 amino acids. These sequences are almost completely identical, exhibiting an unusual degree of conservation of the repeat motif, compared to repeated sequences in other microtubule-associated proteins. The carboxy-terminal repeat domain is composed of 28 imperfect repeats of an 11 amino acid consensus sequence. Upstream of the carboxy-terminal repeat domain, rat N-STOP contains a highly basic sequence (called the "KR domain" after its high content in lysine and arginine residues) and a so-called "linker domain" located between the central repeat domain and the KR domain. To date, two splicing variants of STOP, E-STOP and F-STOP, have been characterised in rodents. Knowledge of STOPs function and properties may help in the treatment of neuroleptics in illnesses such as schizophrenia, currently thought to result from synaptic defects [].
Probab=95.43 E-value=0.34 Score=45.99 Aligned_cols=37 Identities=35% Similarity=0.664 Sum_probs=21.0
Q ss_pred CCCCccCC-CCCCCCCCCCCCCC--CCCCCCCCCCCcccc
Q psy9508 420 PEGDFEGR-PKDDYGPKVGDRAP--VKKPQDNLYPEGEFE 456 (511)
Q Consensus 420 peG~F~~~-~k~~y~pK~~eRp~--~~kP~DNL~peG~F~ 456 (511)
+.+.|.+. .+.+|.++.+++.. .++....+.+...|.
T Consensus 165 ~~~pF~~~T~~~~y~~~~~~~~~~~~~~~~~~~~~~~~F~ 204 (215)
T PF05217_consen 165 PSGPFDGTTYQSDYQPKQGEPAKSPCKPTSQPPQPSPSFQ 204 (215)
T ss_pred CCCcccCCccccccCCCCCCcccccccCccCCCCcCcCcc
Confidence 45556332 56788888888777 333344444444444
No 2
>PF05217 STOP: STOP protein; InterPro: IPR007882 Neurons contain abundant subsets of highly stable microtubules that resist de-polymerising conditions such as exposure to the cold. Stable microtubules are thought to be essential for neuronal development, maintenance, and function. STOP is a major factor responsible for the intriguing stability properties of neuronal microtubules and is important for synaptic plasticity. STOPs (for stable tubule only polypeptides) are calmodulin-binding and calmodulin-regulated proteins which, in mammals, are encoded by a single gene but exhibit substantial cell specific variability due to mRNA splicing and alternative promoter use. STOP microtubule stabilising activity has been ascribed to two classes of new bifunctional calmodulin- and microtubule-binding motifs, with distinct microtubule binding properties in vivo. STOPs seem to be restricted to vertebrates and are composed of a conserved domain split by the apparent insertion of variable sequences that are completely unrelated among species []. N-STOP (for neuronal adult STOP) contains two repeat domains. The central repeat domain is composed of five repeated sequences of 46 amino acids. These sequences are almost completely identical, exhibiting an unusual degree of conservation of the repeat motif, compared to repeated sequences in other microtubule-associated proteins. The carboxy-terminal repeat domain is composed of 28 imperfect repeats of an 11 amino acid consensus sequence. Upstream of the carboxy-terminal repeat domain, rat N-STOP contains a highly basic sequence (called the "KR domain" after its high content in lysine and arginine residues) and a so-called "linker domain" located between the central repeat domain and the KR domain. To date, two splicing variants of STOP, E-STOP and F-STOP, have been characterised in rodents. Knowledge of STOPs function and properties may help in the treatment of neuroleptics in illnesses such as schizophrenia, currently thought to result from synaptic defects [].
Probab=95.25 E-value=0.31 Score=46.21 Aligned_cols=22 Identities=45% Similarity=0.901 Sum_probs=12.1
Q ss_pred ccccccC-CCCCCCCCCCCCCCC
Q psy9508 331 PEGEFEG-RPKDDYGPKIGDRAP 352 (511)
Q Consensus 331 pEGef~~-~~k~dy~pk~~eRp~ 352 (511)
.++.|+. ..+.+|.+..+++..
T Consensus 165 ~~~pF~~~T~~~~y~~~~~~~~~ 187 (215)
T PF05217_consen 165 PSGPFDGTTYQSDYQPKQGEPAK 187 (215)
T ss_pred CCCcccCCccccccCCCCCCccc
Confidence 4455554 245566666666655
No 3
>PF15373 DUF4601: Domain of unknown function (DUF4601)
Probab=5.36 E-value=2.3e+03 Score=24.14 Aligned_cols=22 Identities=23% Similarity=0.126 Sum_probs=12.0
Q ss_pred CCccccC-CCCCCCccchhhhcc
Q psy9508 481 EGDFERP-VKEKPKQAEKVEAFK 502 (511)
Q Consensus 481 eG~f~~~-~k~~~~paer~~~~~ 502 (511)
-|.|+.+ -...|.|.+.+..++
T Consensus 299 ~~~ff~TT~~sdy~p~~~~~~~~ 321 (440)
T PF15373_consen 299 LGRFFSTTMGSDYCPPEKPRPQK 321 (440)
T ss_pred ccccccccCCCCcCCCCCcccCc
Confidence 4566554 344667766554333
No 4
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=3.13 E-value=8.7e+02 Score=20.70 Aligned_cols=23 Identities=22% Similarity=0.209 Sum_probs=19.1
Q ss_pred CceeeccceeeeeeCCccccccc
Q psy9508 1 MIFVTSAHEEFTEKTPERVKPQR 23 (511)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~ 23 (511)
.||++.++..-|++.|.++.|.-
T Consensus 37 ~tF~t~es~s~tis~p~~~~~~~ 59 (72)
T PRK09678 37 ATFITYESVQRYIVKPGEVHAVR 59 (72)
T ss_pred CEEEEEEEEEEEEcCCCCCCCCC
Confidence 37999999999999998876653
No 5
>PF06773 Bim_N: Bim protein N-terminus; InterPro: IPR014771 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. This entry represents the N-terminal region of several mammal specific Bim proteins. The Bim protein is one of the BH3-only proteins, members of the Bcl-2 family that have only one of the Bcl-2 homology regions, BH3.
Probab=2.34 E-value=1.2e+03 Score=18.03 Aligned_cols=16 Identities=31% Similarity=0.600 Sum_probs=9.9
Q ss_pred CcccccCCCCCCCCCC
Q psy9508 192 EHQEYKKGERPTAYKP 207 (511)
Q Consensus 192 ek~~y~p~eRp~~vr~ 207 (511)
|--..+|+|||.+.++
T Consensus 13 EGgqLqp~er~~q~r~ 28 (41)
T PF06773_consen 13 EGGQLQPTERPPQLRP 28 (41)
T ss_pred cccccccccCCcccCc
Confidence 3345567777777665
No 6
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=1.94 E-value=8.9e+02 Score=22.10 Aligned_cols=11 Identities=55% Similarity=0.534 Sum_probs=8.6
Q ss_pred cccCCCcCCCC
Q psy9508 234 FKVRDNLKTEG 244 (511)
Q Consensus 234 ~Kp~DNLkpEG 244 (511)
-+-.|||+++|
T Consensus 78 ~~VFDNl~p~G 88 (100)
T PF15643_consen 78 EIVFDNLHPEG 88 (100)
T ss_pred eEEecccCccc
Confidence 45678888888
No 7
>PF15000 TUSC2: Tumour suppressor candidate 2
Probab=1.81 E-value=9.1e+02 Score=22.46 Aligned_cols=42 Identities=26% Similarity=0.362 Sum_probs=25.7
Q ss_pred cccCCceeeccc--CccccccC---CCcccccCccccCCCCcCCCcc
Q psy9508 28 TKQDGEIYFQTT--SATEFTEH---STTDLRQAQVRHVDNLKTGGTF 69 (511)
Q Consensus 28 ~~~~~~~~~~~~--~~~ef~~~---~~~~eRp~~vr~~DNLkpEG~F 69 (511)
+.--|+.|+.+. -+-||-+. -.++.|..-.|-..||.|.|..
T Consensus 47 ~tr~sS~y~DeDGdlAhEFYeE~v~~~g~~~~~l~rv~knL~PqG~v 93 (111)
T PF15000_consen 47 FTRRSSMYFDEDGDLAHEFYEEVVTKNGRKRAKLRRVQKNLRPQGIV 93 (111)
T ss_pred EecCCceeEcCCcchhhhhhhhhhccCCccchhhhhhhhcCCcccee
Confidence 344556666552 22255443 1246677888888999998876
No 8
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=1.57 E-value=9.5e+02 Score=20.65 Aligned_cols=31 Identities=29% Similarity=0.560 Sum_probs=10.5
Q ss_pred CCCcccCCcccccCCCCCCCCCC-----------CCCCCCCC
Q psy9508 185 EGDFERPEHQEYKKGERPTAYKP-----------HDNLKPEG 215 (511)
Q Consensus 185 EG~F~~~ek~~y~p~eRp~~vr~-----------~DNL~pEG 215 (511)
.|.|..|+.+.|+-+.|=--++- +.+|+|||
T Consensus 13 ag~fa~ps~atf~~gdrvrkksgaawqg~vvgwy~t~ltpeg 54 (78)
T PF06442_consen 13 AGQFAFPSNATFGMGDRVRKKSGAAWQGQVVGWYCTKLTPEG 54 (78)
T ss_dssp --------S-SS-TT-EEEESSSS--EEEEEEEE--SS-SSE
T ss_pred ccceecccccccccchhhhhcccccccceEeEEEeccccccc
Confidence 68888888888887765433332 66777777
No 9
>PF07193 DUF1408: Protein of unknown function (DUF1408); InterPro: IPR009848 This entry is represented by Bacteriophage bIL285, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Lactococcus lactis and related phage proteins of around 75 residues in length. The function of this family is unknown.
Probab=1.42 E-value=1.5e+03 Score=19.39 Aligned_cols=18 Identities=28% Similarity=0.822 Sum_probs=14.1
Q ss_pred ccccccCCceeecccCcc
Q psy9508 25 RTWTKQDGEIYFQTTSAT 42 (511)
Q Consensus 25 ~~~~~~~~~~~~~~~~~~ 42 (511)
++|-+++|++|+-..+.+
T Consensus 37 ~t~~r~dgs~y~~~r~~~ 54 (75)
T PF07193_consen 37 ETWERPDGSMYMTSRKKN 54 (75)
T ss_pred EEEEcCCCeEEEEEcccc
Confidence 568899999998776543
No 10
>cd00389 microbial_RNases microbial_RNases. Ribonucleases (RNAses) cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. The alignment contains fungal RNases (U2, T1, F1, Th, Pb, N1, and Ms) and bacterial RNases (barnase, binase, RNase Sa) , the majority of which are guanyl specific and fungal ribotoxins.
Probab=1.12 E-value=3.1e+03 Score=17.08 Aligned_cols=28 Identities=29% Similarity=0.323 Sum_probs=15.9
Q ss_pred eeeeeeCCccccccccccccccCCceee
Q psy9508 9 EEFTEKTPERVKPQRRRTWTKQDGEIYF 36 (511)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 (511)
++|+|.+|.--.+--++-+.-.+|++|.
T Consensus 39 ~E~~v~~~g~~~rGa~RIV~~~~g~~y~ 66 (71)
T cd00389 39 HEYPVNTPGGGSRGADRVVYGGDGEFYG 66 (71)
T ss_pred EEeecCCCCCCCCCCCEEEECCCCcEEE
Confidence 5677777763344434445555566664
Done!