Query psy4369
Match_columns 71
No_of_seqs 101 out of 152
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 23:44:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4369.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4369hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0170|consensus 99.9 3.2E-25 6.9E-30 174.7 1.8 69 1-69 165-234 (621)
2 KOG0942|consensus 83.8 0.84 1.8E-05 39.4 2.3 22 4-25 598-619 (1001)
3 PF07817 GLE1: GLE1-like prote 30.8 21 0.00045 25.7 0.5 13 4-16 128-140 (256)
4 KOG2412|consensus 26.6 30 0.00066 28.7 0.8 16 3-18 428-443 (591)
5 COG4040 Predicted membrane pro 24.0 72 0.0016 20.2 2.0 22 17-38 26-47 (85)
6 KOG0170|consensus 22.9 17 0.00037 30.2 -1.2 42 1-42 157-198 (621)
7 PF12243 CTK3: CTD kinase subu 22.0 60 0.0013 21.9 1.5 11 15-25 3-13 (139)
8 PF09029 Preseq_ALAS: 5-aminol 20.8 32 0.00069 22.4 -0.1 8 6-13 7-14 (107)
9 COG5021 HUL4 Ubiquitin-protein 18.9 5.8 0.00013 34.0 -4.8 35 7-41 442-476 (872)
10 PF02865 STAT_int: STAT protei 16.8 73 0.0016 20.9 1.0 18 5-22 16-33 (124)
No 1
>KOG0170|consensus
Probab=99.90 E-value=3.2e-25 Score=174.69 Aligned_cols=69 Identities=30% Similarity=0.520 Sum_probs=63.4
Q ss_pred CchHHhhhhCCceeeHHHHHHHHHHhhcchhHHHHHHHhhCC-cCCCCCCCCcccCCCcCceeEEeeCCC
Q psy4369 1 MVTEHLATTCPFLLNFEIRQLLLYASSFDRDRALQRLVDSTP-EINNHSDTQERVTPRLDRRKRTVSRQG 69 (71)
Q Consensus 1 ~W~~~L~~~cpFLFPFetR~~~f~~TsFG~~R~i~~~q~~~~-~~~~~~~~~~~~~gRl~R~KvrVsR~~ 69 (71)
+||.+|++.|||||||+||++||||||||++|+||+||+.+. +.+++.++...++|||+|||+||+|++
T Consensus 165 ~w~~~L~~~cpfLfpf~Tr~~~f~~taFg~~R~~~~~k~~s~~~~~~s~~e~~~~~grL~RkK~risR~~ 234 (621)
T KOG0170|consen 165 DWSLFLTRRCPFLFPFDTRMLYFYSTAFGLSRAIQLLKNKSKGSKDGSNDEALQQLGRLTRKKLRISRKT 234 (621)
T ss_pred hhhhhhhhcCCeeccHHHHHHHHHHHHhhhhhHHHHHhhcccCCCCCCchHHhHhhcccchhhhhhhHHH
Confidence 599999999999999999999999999999999999999884 445667778899999999999999974
No 2
>KOG0942|consensus
Probab=83.77 E-value=0.84 Score=39.41 Aligned_cols=22 Identities=27% Similarity=0.404 Sum_probs=19.5
Q ss_pred HHhhhhCCceeeHHHHHHHHHH
Q psy4369 4 EHLATTCPFLLNFEIRQLLLYA 25 (71)
Q Consensus 4 ~~L~~~cpFLFPFetR~~~f~~ 25 (71)
..+...|||+.||+-|-++||.
T Consensus 598 l~IL~e~PF~vPF~~RVklfq~ 619 (1001)
T KOG0942|consen 598 LCILKEIPFFVPFEERVKLFQR 619 (1001)
T ss_pred HHHHHcCCeeechHHHHHHHHH
Confidence 4578899999999999999984
No 3
>PF07817 GLE1: GLE1-like protein; InterPro: IPR012476 The members of this family are sequences that are similar to the human protein GLE1 (O75458 from SWISSPROT). This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm []. ; GO: 0016973 poly(A)+ mRNA export from nucleus, 0005643 nuclear pore; PDB: 3PEV_B 3RRN_B 3PEU_B 3RRM_B.
Probab=30.80 E-value=21 Score=25.75 Aligned_cols=13 Identities=31% Similarity=0.764 Sum_probs=8.3
Q ss_pred HHhhhhCCceeeH
Q psy4369 4 EHLATTCPFLLNF 16 (71)
Q Consensus 4 ~~L~~~cpFLFPF 16 (71)
..|.+.|||++|+
T Consensus 128 A~l~k~Cp~~vP~ 140 (256)
T PF07817_consen 128 ARLHKKCPYLVPK 140 (256)
T ss_dssp HHHHHH-GGGG--
T ss_pred HHHHHcCceeEee
Confidence 3677899999974
No 4
>KOG2412|consensus
Probab=26.55 E-value=30 Score=28.70 Aligned_cols=16 Identities=31% Similarity=0.854 Sum_probs=12.9
Q ss_pred hHHhhhhCCceeeHHH
Q psy4369 3 TEHLATTCPFLLNFEI 18 (71)
Q Consensus 3 ~~~L~~~cpFLFPFet 18 (71)
+..|-+.|||+.||-.
T Consensus 428 lA~l~KkCP~~VPf~~ 443 (591)
T KOG2412|consen 428 LARLHKKCPYVVPFHI 443 (591)
T ss_pred HHHHHhcCCccccccc
Confidence 3568899999999854
No 5
>COG4040 Predicted membrane protein [Function unknown]
Probab=24.04 E-value=72 Score=20.20 Aligned_cols=22 Identities=23% Similarity=0.217 Sum_probs=17.8
Q ss_pred HHHHHHHHHhhcchhHHHHHHH
Q psy4369 17 EIRQLLLYASSFDRDRALQRLV 38 (71)
Q Consensus 17 etR~~~f~~TsFG~~R~i~~~q 38 (71)
..+.+|+.+.|||.+=+|....
T Consensus 26 a~~lLYLn~~sFgisaliAlyv 47 (85)
T COG4040 26 AAQLLYLNVVSFGISALIALYV 47 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3578899999999998887643
No 6
>KOG0170|consensus
Probab=22.95 E-value=17 Score=30.15 Aligned_cols=42 Identities=7% Similarity=-0.045 Sum_probs=36.1
Q ss_pred CchHHhhhhCCceeeHHHHHHHHHHhhcchhHHHHHHHhhCC
Q psy4369 1 MVTEHLATTCPFLLNFEIRQLLLYASSFDRDRALQRLVDSTP 42 (71)
Q Consensus 1 ~W~~~L~~~cpFLFPFetR~~~f~~TsFG~~R~i~~~q~~~~ 42 (71)
.||.-..-..++..+++++.+|-+.|.++|.|....-.++..
T Consensus 157 ~v~sg~lp~w~~~L~~~cpfLfpf~Tr~~~f~~taFg~~R~~ 198 (621)
T KOG0170|consen 157 VVASGALPDWSLFLTRRCPFLFPFDTRMLYFYSTAFGLSRAI 198 (621)
T ss_pred eeecCCCChhhhhhhhcCCeeccHHHHHHHHHHHHhhhhhHH
Confidence 377778888999999999999999999999998887665554
No 7
>PF12243 CTK3: CTD kinase subunit gamma CTK3
Probab=22.03 E-value=60 Score=21.88 Aligned_cols=11 Identities=27% Similarity=0.386 Sum_probs=9.0
Q ss_pred eHHHHHHHHHH
Q psy4369 15 NFEIRQLLLYA 25 (71)
Q Consensus 15 PFetR~~~f~~ 25 (71)
|||+|..|-+.
T Consensus 3 pFE~r~~F~~~ 13 (139)
T PF12243_consen 3 PFEVRMQFTQL 13 (139)
T ss_pred hHHHHHHHHHH
Confidence 89999988654
No 8
>PF09029 Preseq_ALAS: 5-aminolevulinate synthase presequence; InterPro: IPR015118 The N-terminal presequence domain found in 5-aminolevulinate synthase exists as an amphipathic helix, with a positively charged surface provided by lysine residues and no stable helix at the N terminus. The domain is essential for the import process by which ALAS is transported into the mitochondria: translocase of the outer membrane (Tom) and translocase of the inner membrane protein complexes appear responsible for recognition and import through the mitochondrial membrane. The protein Tom20 is anchored to the mitochondrial outer membrane, and its interaction with presequences is thought to be the recognition step which allows subsequent import []. ; GO: 0003870 5-aminolevulinate synthase activity, 0030170 pyridoxal phosphate binding, 0006778 porphyrin-containing compound metabolic process, 0005759 mitochondrial matrix; PDB: 1H7J_A 1H7D_A.
Probab=20.84 E-value=32 Score=22.39 Aligned_cols=8 Identities=50% Similarity=1.269 Sum_probs=2.5
Q ss_pred hhhhCCce
Q psy4369 6 LATTCPFL 13 (71)
Q Consensus 6 L~~~cpFL 13 (71)
+.+.||||
T Consensus 7 ~l~rCPFL 14 (107)
T PF09029_consen 7 FLRRCPFL 14 (107)
T ss_dssp TTSS---S
T ss_pred HHhhCCce
Confidence 34556665
No 9
>COG5021 HUL4 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=18.93 E-value=5.8 Score=34.00 Aligned_cols=35 Identities=20% Similarity=0.236 Sum_probs=28.9
Q ss_pred hhhCCceeeHHHHHHHHHHhhcchhHHHHHHHhhC
Q psy4369 7 ATTCPFLLNFEIRQLLLYASSFDRDRALQRLVDST 41 (71)
Q Consensus 7 ~~~cpFLFPFetR~~~f~~TsFG~~R~i~~~q~~~ 41 (71)
...-|+++|+++|...++...|+..+...-+....
T Consensus 442 ~~~~~l~~~~~~r~~~~~~~~~~~h~k~~~~~~~~ 476 (872)
T COG5021 442 SREGPLLSGWKTRLNNLYRFYFVEHRKKTLTKNDS 476 (872)
T ss_pred cccccccchHHHHhhhhheeeehhcccceeeecCC
Confidence 45679999999999999999999988776654443
No 10
>PF02865 STAT_int: STAT protein, protein interaction domain; InterPro: IPR013799 The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus []. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT proteins play a critical role in regulating innate and acquired host immune responses. Dysregulation of at least two STAT signalling cascades (i.e. Stat3 and Stat5) is associated with cellular transformation. Signalling through the JAK/STAT pathway is initiated when a cytokine binds to its corresponding receptor. This leads to conformational changes in the cytoplasmic portion of the receptor, initiating activation of receptor associated members of the JAK family of kinases. The JAKs, in turn, mediate phosphorylation at the specific receptor tyrosine residues, which then serve as docking sites for STATs and other signalling molecules. Once recruited to the receptor, STATs also become phosphorylated by JAKs, on a single tyrosine residue. Activated STATs dissociate from the receptor, dimerise, translocate to the nucleus and bind to members of the GAS (gamma activated site) family of enhancers. The seven STAT proteins identified in mammals range in size from 750 and 850 amino acids. The chromosomal distribution of these STATs, as well as the identification of STATs in more primitive eukaryotes, suggest that this family arose from a single primordial gene. STATs share structurally and functionally conserved domains including: an N-terminal domain that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain that is implicated in protein-protein interactions; a DNA-binding domain with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain (IPR000980 from INTERPRO) that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain []. The crystal structure of the N terminus of Stat4 reveals a dimer. The interface of this dimer is formed by a ring-shaped element consisting of five short helices. Several studies suggest that this N-terminal dimerisation promotes cooperativity of binding to tandem GAS elements and with the transcriptional coactivator CBP/p300. This entry represents the N-terminal domain, which is responsible for protein interactions. This domain has a multi-helical structure that can be subdivided into two structural sub-domains.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0004871 signal transducer activity, 0006355 regulation of transcription, DNA-dependent, 0007165 signal transduction; PDB: 1BGF_A 1YVL_A.
Probab=16.79 E-value=73 Score=20.89 Aligned_cols=18 Identities=17% Similarity=0.218 Sum_probs=10.2
Q ss_pred HhhhhCCceeeHHHHHHH
Q psy4369 5 HLATTCPFLLNFEIRQLL 22 (71)
Q Consensus 5 ~L~~~cpFLFPFetR~~~ 22 (71)
++-..|+==||.|.|+.+
T Consensus 16 qv~~lY~~~FPiEvRh~L 33 (124)
T PF02865_consen 16 QVQQLYGDHFPIEVRHYL 33 (124)
T ss_dssp HHHCC-BTTC-HHHHHHT
T ss_pred HHHHHhcccCCHHHHHHH
Confidence 344444434799999875
Done!