Query psy9511
Match_columns 1301
No_of_seqs 87 out of 89
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 21:24:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9511.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9511hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05217 STOP: STOP protein; 96.5 0.019 4.1E-07 60.8 10.7 100 380-511 103-207 (215)
2 PF05217 STOP: STOP protein; 96.2 0.028 6.1E-07 59.5 10.0 73 251-324 72-145 (215)
3 PF15373 DUF4601: Domain of un 42.7 1.1E+02 0.0025 37.6 9.3 48 265-312 205-255 (440)
4 PF14162 YozD: YozD-like prote 3.3 3.5E+02 0.0076 24.9 -0.3 9 1289-1297 14-22 (57)
5 KOG0629|consensus 2.0 8.3E+02 0.018 30.8 0.5 10 1291-1300 103-112 (510)
6 PF15373 DUF4601: Domain of un 1.8 7.6E+03 0.16 22.6 8.1 61 960-1020 239-314 (440)
7 PF15000 TUSC2: Tumour suppres 1.2 1.5E+03 0.033 23.7 0.6 21 258-278 74-94 (111)
8 PF02189 ITAM: Immunoreceptor 1.2 1.4E+03 0.031 17.5 0.3 8 1294-1301 1-8 (21)
9 PF06773 Bim_N: Bim protein N- 1.0 3.4E+03 0.073 17.8 1.8 16 222-237 13-28 (41)
10 KOG1230|consensus 0.9 1.5E+03 0.032 28.7 -0.8 18 1273-1298 85-102 (521)
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=96.48 E-value=0.019 Score=60.76 Aligned_cols=100 Identities=15% Similarity=0.236 Sum_probs=55.7
Q ss_pred chhhhhcccccchhhhcccCCCccc-CCceEEeccccccccccCCccccccccccccccCCcceeccCccccccccCCcc
Q psy9511 380 SSETFQAHQIIKKEEIRRREDNLVQ-EGEMIFVTSAHEEFTEKTPERVKPQRRRTWTKQDGEIYFQTTSATEFTEHSTTD 458 (1301)
Q Consensus 380 ~~~~y~~~~~~ER~~~~rp~DNLr~-EGef~~~t~~~~df~~~~~e~~~~~~~~~~~k~eg~~~~~~~~k~~~~~~~~~g 458 (1301)
++++|..|. +.+...+++..+..+ .+-|...|+++.+|+....++++..
T Consensus 103 y~~dy~~~~-~~~~~~~kp~~~~~~~~~pF~~~TtYr~~y~~~~~~~~~~~----------------------------- 152 (215)
T PF05217_consen 103 YKSDYPPKP-IPPPPSFKPPNQPTSSDAPFDGETTYRDDYQPWQGQRPKPE----------------------------- 152 (215)
T ss_pred cccccccCC-CCcccccCCCCCCCCCCCCccccccCccccccCcccccCcc-----------------------------
Confidence 455666543 334455555554444 4667778888888886433221111
Q ss_pred ccccccccC-CCcccCCccCCCC-CCCCCccCCCCCCC--CCCCCCCCCCCCccCCC
Q psy9511 459 LRQAQVRHV-DNLKTGGTFEGKP-KDDYMPVTAERPKQ--QKPKDNLRPEGDFERPT 511 (1301)
Q Consensus 459 ERp~~vrp~-DNL~pEG~Fe~~~-k~dy~p~~aERp~~--kkP~DNL~pEGdFe~~~ 511 (1301)
+..+.+. -.+.+.+.|++.| +.+|.+..+++..+ ++...++.+...|.+..
T Consensus 153 --~~~~~~~~~~~p~~~pF~~~T~~~~y~~~~~~~~~~~~~~~~~~~~~~~~F~gq~ 207 (215)
T PF05217_consen 153 --PKFKPPKETYSPPSGPFDGTTYQSDYQPKQGEPAKSPCKPTSQPPQPSPSFQGQF 207 (215)
T ss_pred --ccccccccccCCCCCcccCCccccccCCCCCCcccccccCccCCCCcCcCccccc
Confidence 0011111 1234577888776 88999988888873 33344444555555443
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=96.19 E-value=0.028 Score=59.51 Aligned_cols=73 Identities=19% Similarity=0.289 Sum_probs=40.0
Q ss_pred CCCCCCCccccccccccCCCcccCCcccccccccccccccccCCCCccccCCCccc-cccccccccccccccccC
Q psy9511 251 SQPLVPLKGERAEIKRYEDHKITGGEFTGITTQQVEFTGELTERPPLIRRNTWTKL-EGEFTSETTSQTEFKRFD 324 (1301)
Q Consensus 251 ~k~y~~~p~ERa~~kRp~DNLkpEGeFe~~t~~~~dy~~~~gERp~~iRp~DnLk~-eGeF~~~T~n~~eF~~y~ 324 (1301)
+.||...... ...++......+.+.|.++|+++.+|++....+...+++..+..+ .+-|++.|+.+.+|..+.
T Consensus 72 ~~Dy~~~~~~-~~~~~~~~~~~~~~~f~~~Tty~~dy~~~~~~~~~~~kp~~~~~~~~~pF~~~TtYr~~y~~~~ 145 (215)
T PF05217_consen 72 RQDYKPWPIP-PPKKPKPQYPPPSGPFDGTTTYKSDYPPKPIPPPPSFKPPNQPTSSDAPFDGETTYRDDYQPWQ 145 (215)
T ss_pred cccCCCCCcc-cccCccccccccCCCCCCCcccccccccCCCCcccccCCCCCCCCCCCCccccccCccccccCc
Confidence 4455555455 222222233444666666666666666666666666666555333 455666666666665544
No 3
>PF15373 DUF4601: Domain of unknown function (DUF4601)
Probab=42.72 E-value=1.1e+02 Score=37.63 Aligned_cols=48 Identities=19% Similarity=0.094 Sum_probs=30.0
Q ss_pred cccCCCccc-CCcccccccccccccccccCCCCccccCCC--ccccccccc
Q psy9511 265 KRYEDHKIT-GGEFTGITTQQVEFTGELTERPPLIRRNTW--TKLEGEFTS 312 (1301)
Q Consensus 265 kRp~DNLkp-EGeFe~~t~~~~dy~~~~gERp~~iRp~Dn--Lk~eGeF~~ 312 (1301)
+-..-|+++ .|-|-..|+.-..|-....|+..+.....+ -+++|+...
T Consensus 205 ~I~~vNi~pGDg~f~~~TT~ae~f~~~~~ep~~l~~~~~~~S~i~~Gd~~P 255 (440)
T PF15373_consen 205 HIHQVNIQPGDGLFHDRTTMAEHFYAREPEPFVLHHDQTPESHIPKGDWDP 255 (440)
T ss_pred hheeeecccCCccccccccchhhccCCCCCCceeccCCCcccccccCCCCC
Confidence 334567777 777877777666666555576666665443 455666544
No 4
>PF14162 YozD: YozD-like protein
Probab=3.35 E-value=3.5e+02 Score=24.94 Aligned_cols=9 Identities=56% Similarity=1.069 Sum_probs=7.4
Q ss_pred eeehHHhhh
Q psy9511 1289 FEFFYNQLY 1297 (1301)
Q Consensus 1289 ~~~~~~~~~ 1297 (1301)
++|||++|.
T Consensus 14 AefFy~eL~ 22 (57)
T PF14162_consen 14 AEFFYHELV 22 (57)
T ss_pred HHHHHHHHH
Confidence 689999885
No 5
>KOG0629|consensus
Probab=2.00 E-value=8.3e+02 Score=30.82 Aligned_cols=10 Identities=70% Similarity=1.009 Sum_probs=6.5
Q ss_pred ehHHhhhccC
Q psy9511 1291 FFYNQLYSGL 1300 (1301)
Q Consensus 1291 ~~~~~~~~~~ 1300 (1301)
-|+|||++||
T Consensus 103 rffNQl~~gl 112 (510)
T KOG0629|consen 103 RFFNQLSSGL 112 (510)
T ss_pred cchhhhccCC
Confidence 4667777765
No 6
>PF15373 DUF4601: Domain of unknown function (DUF4601)
Probab=1.80 E-value=7.6e+03 Score=22.58 Aligned_cols=61 Identities=18% Similarity=0.389 Sum_probs=30.7
Q ss_pred CcCcCCCCCCCCCCCCCC-CCccCcccC--------CCCcccccCCccCCCCCCC-----CCCccCCC-CCCCCCC
Q psy9511 960 QKAERPKAFKPHDNLKPE-GDFERPIKE--------KPKQAERVEPFKLRDNLKP-----EGEFEGRP-KDDYGPK 1020 (1301)
Q Consensus 960 ~paERp~~vr~~DNLkpE-GeF~~~~k~--------~~~~aeRp~~~kp~DNLkp-----EGeF~~~~-k~~~~p~ 1020 (1301)
..-.++....++-|+-|+ |.+.+.... +.-+...-.-++..+|..+ -|.|++++ ..+|.|.
T Consensus 239 ~~~~~~~S~i~~Gd~~Pgp~sl~Tt~~~fy~q~~~~~~pp~~~~~~~~~~ShV~LGep~l~~~ff~TT~~sdy~p~ 314 (440)
T PF15373_consen 239 HHDQTPESHIPKGDWDPGPGSLSTTMQFFYGQPPPPTQPPSRHVSHERLQSHVTLGEPKLLGRFFSTTMGSDYCPP 314 (440)
T ss_pred ccCCCcccccccCCCCCCccccccccceeeeccCcCCCCCCcccccccccCceEecCCccccccccccCCCCcCCC
Confidence 334566666666666665 554443222 1112222233445555543 35566655 7888883
No 7
>PF15000 TUSC2: Tumour suppressor candidate 2
Probab=1.25 E-value=1.5e+03 Score=23.74 Aligned_cols=21 Identities=19% Similarity=0.297 Sum_probs=16.9
Q ss_pred ccccccccccCCCcccCCccc
Q psy9511 258 KGERAEIKRYEDHKITGGEFT 278 (1301)
Q Consensus 258 p~ERa~~kRp~DNLkpEGeFe 278 (1301)
-+.|+.++|-..||+|+|...
T Consensus 74 g~~~~~l~rv~knL~PqG~v~ 94 (111)
T PF15000_consen 74 GRKRAKLRRVQKNLRPQGIVK 94 (111)
T ss_pred CccchhhhhhhhcCCccceee
Confidence 457788999999999998743
No 8
>PF02189 ITAM: Immunoreceptor tyrosine-based activation motif; InterPro: IPR003110 Phosphorylated immunoreceptor signalling motifs (ITAMs) exhibit unique abilities to bind and activate Lyn and Syk tyrosine kinases []. Motif may be dually phosphorylated on tyrosine that links antigen receptors to downstream signalling machinery. ; GO: 0004888 transmembrane signaling receptor activity, 0007166 cell surface receptor linked signaling pathway, 0016020 membrane; PDB: 2K4F_A 1TCE_B 3IOZ_B 3IK5_B 1YGR_D 2OQ1_B 1A81_F 2ROL_B.
Probab=1.23 E-value=1.4e+03 Score=17.53 Aligned_cols=8 Identities=50% Similarity=0.829 Sum_probs=5.3
Q ss_pred HhhhccCC
Q psy9511 1294 NQLYSGLH 1301 (1301)
Q Consensus 1294 ~~~~~~~~ 1301 (1301)
||||.+|.
T Consensus 1 d~lYq~L~ 8 (21)
T PF02189_consen 1 DQLYQPLR 8 (21)
T ss_dssp SHHCCTTT
T ss_pred Cccccccc
Confidence 57777763
No 9
>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=0.97 E-value=3.4e+03 Score=17.83 Aligned_cols=16 Identities=44% Similarity=0.916 Sum_probs=11.6
Q ss_pred CCCCCCCCCCCCCCCC
Q psy9511 222 EVGKYSPAERPKAVKP 237 (1301)
Q Consensus 222 e~~~~~PaERp~~vrp 237 (1301)
|-.+..|+|||.+.++
T Consensus 13 EGgqLqp~er~~q~r~ 28 (41)
T PF06773_consen 13 EGGQLQPTERPPQLRP 28 (41)
T ss_pred cccccccccCCcccCc
Confidence 4556778888887776
No 10
>KOG1230|consensus
Probab=0.90 E-value=1.5e+03 Score=28.71 Aligned_cols=18 Identities=44% Similarity=0.772 Sum_probs=0.0
Q ss_pred CCccccCCCCCCCCCceeehHHhhhc
Q psy9511 1273 EGDFEGRPKDDYGPKTFEFFYNQLYS 1298 (1301)
Q Consensus 1273 eG~f~~~~k~~~~p~~~~~~~~~~~~ 1298 (1301)
.|+|+...|. +|||.||+
T Consensus 85 GGEf~ngqkT--------~vYndLy~ 102 (521)
T KOG1230|consen 85 GGEFYNGQKT--------HVYNDLYS 102 (521)
T ss_pred cceeecceeE--------EEeeeeeE
Done!