Query psy15166
Match_columns 90
No_of_seqs 109 out of 134
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 22:15:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15166.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15166hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06297 PET: PET Domain; Int 100.0 5.8E-31 1.3E-35 181.7 7.0 71 17-87 22-92 (106)
2 PF06297 PET: PET Domain; Int 94.0 0.014 3.1E-07 40.5 -0.1 26 1-26 37-62 (106)
3 cd06536 CIDE_N_ICAD CIDE_N dom 78.1 0.59 1.3E-05 31.2 -0.3 24 28-51 56-79 (80)
4 cd06535 CIDE_N_CAD CIDE_N doma 78.1 0.58 1.2E-05 31.1 -0.4 42 8-51 35-76 (77)
5 cd06539 CIDE_N_A CIDE_N domain 75.3 0.77 1.7E-05 30.6 -0.4 43 8-51 35-77 (78)
6 cd06538 CIDE_N_FSP27 CIDE_N do 73.2 0.93 2E-05 30.2 -0.4 24 29-52 54-77 (79)
7 cd06537 CIDE_N_B CIDE_N domain 73.2 0.96 2.1E-05 30.4 -0.3 24 29-52 54-77 (81)
8 smart00266 CAD Domains present 72.0 1.1 2.5E-05 29.5 -0.2 23 28-50 52-74 (74)
9 cd01615 CIDE_N CIDE_N domain, 71.2 1.1 2.4E-05 29.7 -0.3 23 29-51 55-77 (78)
10 PF11304 DUF3106: Protein of u 56.1 9.5 0.00021 25.9 2.0 26 55-81 73-104 (107)
11 PF04353 Rsd_AlgQ: Regulator o 51.4 14 0.00031 27.1 2.4 14 74-87 48-61 (153)
12 PF02017 CIDE-N: CIDE-N domain 46.7 1.7 3.7E-05 28.7 -2.7 23 29-51 55-77 (78)
13 PF06394 Pepsin-I3: Pepsin inh 39.4 19 0.00041 23.8 1.3 21 67-87 35-55 (76)
14 PF08599 Nbs1_C: DNA damage re 37.6 14 0.00031 24.0 0.5 23 4-26 13-37 (65)
15 PRK11718 anti-RNA polymerase s 36.8 22 0.00047 26.5 1.5 12 76-87 50-61 (161)
16 cd08776 DED_Caspase-like_repea 32.8 29 0.00063 22.4 1.4 18 70-87 10-27 (71)
17 PF02877 PARP_reg: Poly(ADP-ri 26.2 1.1E+02 0.0024 21.1 3.5 38 22-59 66-107 (133)
18 cd02639 R3H_RRM R3H domain of 25.5 78 0.0017 19.7 2.4 23 67-89 21-43 (60)
19 cd04388 RhoGAP_p85 RhoGAP_p85: 24.5 97 0.0021 23.2 3.2 18 25-42 70-87 (200)
20 PF09832 DUF2059: Uncharacteri 24.3 57 0.0012 19.3 1.6 19 66-84 11-29 (64)
21 cd04398 RhoGAP_fRGD1 RhoGAP_fR 22.5 1.8E+02 0.004 20.6 4.2 54 25-88 77-139 (192)
22 cd04393 RhoGAP_FAM13A1a RhoGAP 22.3 1.6E+02 0.0035 21.0 3.8 17 26-42 77-93 (189)
23 PRK15441 peptidyl-prolyl cis-t 22.1 67 0.0014 20.5 1.7 36 12-47 46-83 (93)
24 PF04201 TPD52: Tumour protein 21.9 70 0.0015 23.9 1.9 16 69-84 23-38 (162)
25 PF08278 DnaG_DnaB_bind: DNA p 21.9 63 0.0014 21.3 1.6 13 70-82 113-125 (127)
26 PF13035 DUF3896: Protein of u 20.7 57 0.0012 20.8 1.1 18 71-88 29-46 (61)
27 cd04386 RhoGAP_nadrin RhoGAP_n 20.2 2.3E+02 0.0051 20.4 4.4 19 24-42 77-95 (203)
28 PF12368 DUF3650: Protein of u 20.0 77 0.0017 17.4 1.4 10 70-79 14-23 (28)
No 1
>PF06297 PET: PET Domain; InterPro: IPR010442 The PET domain is a ~110 amino acid motif in the N-terminal part of LIM domain proteins. The domain was described in Drosophila proteins involved in cell differentiation and is named after Prickle, Espinas and Testin. PET domain proteins contain about three zinc-binding LIM domains (see PDOC00382 from INTERPRO, IPR001781 from INTERPRO) and are found among metazoans. The PET domain has been suggested to play a role in protein-protein interactions with proteins involved in planar polarity signalling or organisation of the cytoskeleton []. Some proteins known to contain a PET domain: Mammalian testin protein (Q9UGI8 from SWISSPROT), which may function as a tumour suppressor. Mammalian LIM domain only protein 6 (LMO6/Prickle3, O43900 from SWISSPROT). Fruit fly prickle (A1Z6W3 from SWISSPROT) and espinas (Q9U1I1 from SWISSPROT) proteins encoded by the tissue polarity gene prickle (pk), involved in the control of orientation of bristles and hairs. Mammalian prickle-like proteins 1 (Q96MT3 from SWISSPROT) and 2 (Q7Z3G6 from SWISSPROT). ; GO: 0008270 zinc ion binding
Probab=99.97 E-value=5.8e-31 Score=181.69 Aligned_cols=71 Identities=35% Similarity=0.525 Sum_probs=67.9
Q ss_pred cchhhhhcHHHHHHHHhcCCCCCCCCCCChhHHHHHHHHHHhcCCCCCChhhhcCCCHHHHHHHHHhhhhh
Q psy15166 17 ALYRRQQLEKQAAEYMQQLPAGKLPISGSDGALYRRQQLEKQVPLHDLNANLCHNLTADEIKCEKMECQHM 87 (90)
Q Consensus 17 ~l~~kqQl~e~v~~Ym~~LP~~kvP~~gS~Ge~~R~kQL~~QLP~hD~d~~yC~~LseeE~kel~~~~~~~ 87 (90)
+|+++...+++|++||++||+++||++||+||+||++||++|||+||+|++||++||++|++++++|+...
T Consensus 22 ~WvPpgl~~~~v~~Ym~~LP~~~vP~~gS~Ge~~R~~QL~~QLP~hD~d~~~C~~Lse~E~k~l~~F~~~r 92 (106)
T PF06297_consen 22 AWVPPGLSPELVEQYMSCLPEEKVPVVGSPGEKYRRRQLLYQLPPHDLDPRYCHSLSEEEKKELEDFVKQR 92 (106)
T ss_pred eecCCCCChHHHHHHHHhCCCcCCCCCCCHHHHHHHHHHHHcCCcccCCHHHHhhCCHHHHHHHHHHHHHH
Confidence 67888888999999999999999999999999999999999999999999999999999999999999754
No 2
>PF06297 PET: PET Domain; InterPro: IPR010442 The PET domain is a ~110 amino acid motif in the N-terminal part of LIM domain proteins. The domain was described in Drosophila proteins involved in cell differentiation and is named after Prickle, Espinas and Testin. PET domain proteins contain about three zinc-binding LIM domains (see PDOC00382 from INTERPRO, IPR001781 from INTERPRO) and are found among metazoans. The PET domain has been suggested to play a role in protein-protein interactions with proteins involved in planar polarity signalling or organisation of the cytoskeleton []. Some proteins known to contain a PET domain: Mammalian testin protein (Q9UGI8 from SWISSPROT), which may function as a tumour suppressor. Mammalian LIM domain only protein 6 (LMO6/Prickle3, O43900 from SWISSPROT). Fruit fly prickle (A1Z6W3 from SWISSPROT) and espinas (Q9U1I1 from SWISSPROT) proteins encoded by the tissue polarity gene prickle (pk), involved in the control of orientation of bristles and hairs. Mammalian prickle-like proteins 1 (Q96MT3 from SWISSPROT) and 2 (Q7Z3G6 from SWISSPROT). ; GO: 0008270 zinc ion binding
Probab=94.02 E-value=0.014 Score=40.46 Aligned_cols=26 Identities=50% Similarity=0.778 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCCCCccchhhhhcHH
Q psy15166 1 MQQLPAGKLPISGSDGALYRRQQLEK 26 (90)
Q Consensus 1 ~~~l~~~~~p~~gSD~~l~~kqQl~e 26 (90)
|++|+.-+||+.||+|+..|+.||..
T Consensus 37 m~~LP~~~vP~~gS~Ge~~R~~QL~~ 62 (106)
T PF06297_consen 37 MSCLPEEKVPVVGSPGEKYRRRQLLY 62 (106)
T ss_pred HHhCCCcCCCCCCCHHHHHHHHHHHH
Confidence 68899999999999999999988754
No 3
>cd06536 CIDE_N_ICAD CIDE_N domain of ICAD. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD (DFF45). 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 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease.
Probab=78.09 E-value=0.59 Score=31.21 Aligned_cols=24 Identities=13% Similarity=0.231 Sum_probs=21.7
Q ss_pred HHHHHhcCCCCCCCCCCChhHHHH
Q psy15166 28 AAEYMQQLPAGKLPISGSDGALYR 51 (90)
Q Consensus 28 v~~Ym~~LP~~kvP~~gS~Ge~~R 51 (90)
=++||.+||.+-+=++=.+|++|+
T Consensus 56 dEeyF~tLp~nT~l~~L~~gq~W~ 79 (80)
T cd06536 56 DEDYFLCLPPNTKFVLLAENEKWA 79 (80)
T ss_pred cHHHHhhCCCCcEEEEECCCCccC
Confidence 379999999999999999999885
No 4
>cd06535 CIDE_N_CAD CIDE_N domain of CAD nuclease. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). 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 CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and the release of active DFF40/CAD nuclease.
Probab=78.09 E-value=0.58 Score=31.12 Aligned_cols=42 Identities=26% Similarity=0.404 Sum_probs=28.7
Q ss_pred CCCCCCCCccchhhhhcHHHHHHHHhcCCCCCCCCCCChhHHHH
Q psy15166 8 KLPISGSDGALYRRQQLEKQAAEYMQQLPAGKLPISGSDGALYR 51 (90)
Q Consensus 8 ~~p~~gSD~~l~~kqQl~e~v~~Ym~~LP~~kvP~~gS~Ge~~R 51 (90)
+||..++-..|.-=+.--+ ++||.+||.+-+=++=.+|++|+
T Consensus 35 ~l~~~~~~l~L~eDGTeVt--EeyF~tLp~nT~lmvL~~gq~W~ 76 (77)
T cd06535 35 QLPCAGSRLCLYEDGTEVT--EEYFPTLPDNTELVLLTPGQSWQ 76 (77)
T ss_pred CCCCCCcEEEEecCCcEeh--HHHHhcCCCCcEEEEEcCCCccC
Confidence 3444444444433333332 79999999999999999999885
No 5
>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=75.25 E-value=0.77 Score=30.59 Aligned_cols=43 Identities=12% Similarity=0.060 Sum_probs=28.7
Q ss_pred CCCCCCCCccchhhhhcHHHHHHHHhcCCCCCCCCCCChhHHHH
Q psy15166 8 KLPISGSDGALYRRQQLEKQAAEYMQQLPAGKLPISGSDGALYR 51 (90)
Q Consensus 8 ~~p~~gSD~~l~~kqQl~e~v~~Ym~~LP~~kvP~~gS~Ge~~R 51 (90)
+||.+++-..|.-=+.--+ =++||.+||.+.+=++=..|++|+
T Consensus 35 ~~~~~~~~lvL~eDGT~Vd-~EeyF~~LpdnT~lm~L~~gq~W~ 77 (78)
T cd06539 35 VITSGLVTLVLEEDGTVVD-TEEFFQTLGDNTHFMVLEKGQKWT 77 (78)
T ss_pred CCCCCCcEEEEeCCCCEEc-cHHHHhhCCCCCEEEEECCCCccC
Confidence 4454444444433322221 379999999999999999999885
No 6
>cd06538 CIDE_N_FSP27 CIDE_N domain of FSP27 proteins. The CIDE-N (cell death-inducing DFF45-like effector, N-terminal) domain is found in the FSP27/CIDE-C protein, which has been identified as a n adipocyte lipid droplet protein that negatively regulates lipolysis and promotes triglyceride accumulation. 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. The CIDE-N domain of FSP27 is sufficient to increase apoptosis in vitro when overexpressed.
Probab=73.23 E-value=0.93 Score=30.23 Aligned_cols=24 Identities=17% Similarity=0.328 Sum_probs=21.8
Q ss_pred HHHHhcCCCCCCCCCCChhHHHHH
Q psy15166 29 AEYMQQLPAGKLPISGSDGALYRR 52 (90)
Q Consensus 29 ~~Ym~~LP~~kvP~~gS~Ge~~R~ 52 (90)
++||.+||.+.+=++=.+|++|+.
T Consensus 54 EeyF~tLp~nt~l~vL~~gq~W~p 77 (79)
T cd06538 54 EEFFQALADNTVFMVLGKGQKWKP 77 (79)
T ss_pred HHHHhhCCCCcEEEEECCCCccCC
Confidence 789999999999999999999863
No 7
>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=73.20 E-value=0.96 Score=30.37 Aligned_cols=24 Identities=8% Similarity=0.205 Sum_probs=22.0
Q ss_pred HHHHhcCCCCCCCCCCChhHHHHH
Q psy15166 29 AEYMQQLPAGKLPISGSDGALYRR 52 (90)
Q Consensus 29 ~~Ym~~LP~~kvP~~gS~Ge~~R~ 52 (90)
++||.+||.+-+=++=..|++|+.
T Consensus 54 EeyF~tLpdnT~lm~L~~gq~W~p 77 (81)
T cd06537 54 EDFFELLEDDTCLMVLEQGQSWSP 77 (81)
T ss_pred HHHHhhCCCCCEEEEECCCCccCC
Confidence 789999999999999999999874
No 8
>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation.
Probab=72.04 E-value=1.1 Score=29.46 Aligned_cols=23 Identities=26% Similarity=0.445 Sum_probs=19.8
Q ss_pred HHHHHhcCCCCCCCCCCChhHHH
Q psy15166 28 AAEYMQQLPAGKLPISGSDGALY 50 (90)
Q Consensus 28 v~~Ym~~LP~~kvP~~gS~Ge~~ 50 (90)
=++||.+||.+-+=++=.+|++|
T Consensus 52 dEeyF~tLp~nt~l~~L~~gq~W 74 (74)
T smart00266 52 DEEYFQTLPDNTELMALEKGEKW 74 (74)
T ss_pred cHHHHhcCCCCcEEEEEcCCCCC
Confidence 37899999999998888888875
No 9
>cd01615 CIDE_N CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). 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 ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein.
Probab=71.23 E-value=1.1 Score=29.66 Aligned_cols=23 Identities=26% Similarity=0.446 Sum_probs=20.8
Q ss_pred HHHHhcCCCCCCCCCCChhHHHH
Q psy15166 29 AEYMQQLPAGKLPISGSDGALYR 51 (90)
Q Consensus 29 ~~Ym~~LP~~kvP~~gS~Ge~~R 51 (90)
++||.+||.+-+=++-.+|++|.
T Consensus 55 EeYF~tLp~nT~l~~l~~gq~W~ 77 (78)
T cd01615 55 EEYFQTLPDNTVLMLLEPGQKWT 77 (78)
T ss_pred HHHHhcCCCCcEEEEECCCCCcC
Confidence 78999999999999999998874
No 10
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=56.07 E-value=9.5 Score=25.92 Aligned_cols=26 Identities=19% Similarity=0.239 Sum_probs=20.1
Q ss_pred HHHhcCCCCCC------hhhhcCCCHHHHHHHH
Q psy15166 55 LEKQVPLHDLN------ANLCHNLTADEIKCEK 81 (90)
Q Consensus 55 L~~QLP~hD~d------~~yC~~LseeE~kel~ 81 (90)
-+.+||+.+.. -.| ..|+++|++.|+
T Consensus 73 ~~~~Lpp~qR~~lr~~w~~y-q~l~~eeR~~l~ 104 (107)
T PF11304_consen 73 RFKQLPPEQRQALRARWEAY-QQLPPEERQALR 104 (107)
T ss_pred HHHcCCHHHHHHHHHHHHHH-HcCCHHHHHHHH
Confidence 35688888777 344 799999999986
No 11
>PF04353 Rsd_AlgQ: Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; InterPro: IPR007448 This family includes bacterial transcriptional regulators that are thought to act through an interaction with the conserved region 4 of the sigma(70) subunit of RNA polymerase. The Pseudomonas aeruginosa homologue, AlgQ, positively regulates virulence gene expression and is associated with the mucoid phenotype observed in P. aeruginosa isolates from cystic fibrosis patients.; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_A.
Probab=51.42 E-value=14 Score=27.12 Aligned_cols=14 Identities=14% Similarity=0.195 Sum_probs=8.6
Q ss_pred HHHHHHHHHhhhhh
Q psy15166 74 ADEIKCEKMECQHM 87 (90)
Q Consensus 74 eeE~kel~~~~~~~ 87 (90)
.-..++|+-|||+.
T Consensus 48 ~~~~~~l~~FCq~L 61 (153)
T PF04353_consen 48 LPSEEALQNFCQQL 61 (153)
T ss_dssp ----HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHH
Confidence 34678899999974
No 12
>PF02017 CIDE-N: CIDE-N domain; InterPro: IPR003508 This domain consists of caspase-activated (CAD) nucleases, which induce DNA fragmentation and chromatin condensation during apoptosis, and the cell death activator proteins CIDE-A and CIDE-B, which are inhibitors of CAD nuclease. The two proteins interact through the region defined by the method signatures.; GO: 0006915 apoptosis, 0005622 intracellular; PDB: 1IBX_A 2EEL_A 1F2R_I 1C9F_A 1D4B_A.
Probab=46.74 E-value=1.7 Score=28.72 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=17.9
Q ss_pred HHHHhcCCCCCCCCCCChhHHHH
Q psy15166 29 AEYMQQLPAGKLPISGSDGALYR 51 (90)
Q Consensus 29 ~~Ym~~LP~~kvP~~gS~Ge~~R 51 (90)
++||.+||.+-+=++=..|++|+
T Consensus 55 EeyF~tLp~nT~lm~L~~ge~W~ 77 (78)
T PF02017_consen 55 EEYFQTLPDNTVLMLLEKGEKWT 77 (78)
T ss_dssp CHHHCCSSSSEEEEEEESSS--S
T ss_pred HHHHhhCCCCCEEEEECCCCccC
Confidence 47999999998888888888774
No 13
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=39.37 E-value=19 Score=23.77 Aligned_cols=21 Identities=24% Similarity=0.227 Sum_probs=15.4
Q ss_pred hhhcCCCHHHHHHHHHhhhhh
Q psy15166 67 NLCHNLTADEIKCEKMECQHM 87 (90)
Q Consensus 67 ~yC~~LseeE~kel~~~~~~~ 87 (90)
.|-+.||++|++||+.|-.-+
T Consensus 35 ~~~R~Lt~~E~~eL~~y~~~v 55 (76)
T PF06394_consen 35 KYARDLTPDEQQELKTYQKKV 55 (76)
T ss_dssp CEEEE--HHHHHHHHHHHHHH
T ss_pred EeeccCCHHHHHHHHHHHHHH
Confidence 456789999999999987654
No 14
>PF08599 Nbs1_C: DNA damage repair protein Nbs1; InterPro: IPR013908 This C-terminal region of the DNA damage repair protein Nbs1 has been identified to be necessary for the binding of Mre11 and Tel1 [].
Probab=37.63 E-value=14 Score=24.00 Aligned_cols=23 Identities=35% Similarity=0.346 Sum_probs=17.5
Q ss_pred CCCCCCC--CCCCCccchhhhhcHH
Q psy15166 4 LPAGKLP--ISGSDGALYRRQQLEK 26 (90)
Q Consensus 4 l~~~~~p--~~gSD~~l~~kqQl~e 26 (90)
-|+..+| ++|||.+-.-+..+.+
T Consensus 13 pGa~~lP~IIGGSDLi~h~~~knse 37 (65)
T PF08599_consen 13 PGAGGLPHIIGGSDLIAHHAGKNSE 37 (65)
T ss_pred CCCCCCCeeecchhhhhcccccccc
Confidence 4777888 8999998776665554
No 15
>PRK11718 anti-RNA polymerase sigma 70 factor; Provisional
Probab=36.77 E-value=22 Score=26.51 Aligned_cols=12 Identities=25% Similarity=0.218 Sum_probs=8.6
Q ss_pred HHHHHHHhhhhh
Q psy15166 76 EIKCEKMECQHM 87 (90)
Q Consensus 76 E~kel~~~~~~~ 87 (90)
..+.|+-|||+.
T Consensus 50 ~~~~l~~FC~~L 61 (161)
T PRK11718 50 NEKALDDFCQLL 61 (161)
T ss_pred CHHHHHHHHHHH
Confidence 456788888863
No 16
>cd08776 DED_Caspase-like_repeat1 Death effector domain, repeat 1, of initator caspase-like proteins. Death Effector Domain (DED), first repeat, found in initator caspase-like proteins, like caspase-8 and -10 and c-FLIP. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of DI
Probab=32.82 E-value=29 Score=22.42 Aligned_cols=18 Identities=17% Similarity=0.086 Sum_probs=15.9
Q ss_pred cCCCHHHHHHHHHhhhhh
Q psy15166 70 HNLTADEIKCEKMECQHM 87 (90)
Q Consensus 70 ~~LseeE~kel~~~~~~~ 87 (90)
.+|+++|...++-+|.|.
T Consensus 10 ~~L~~~e~~~lkFLC~d~ 27 (71)
T cd08776 10 EKLGTDEREVLLFLLNVF 27 (71)
T ss_pred HHcCHHHHHHHHHHcccc
Confidence 479999999999999874
No 17
>PF02877 PARP_reg: Poly(ADP-ribose) polymerase, regulatory domain; InterPro: IPR004102 Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The regulatory domain of the polymerase is almost always associated with the C-terminal catalytic domain (see IPR001290 from INTERPRO). This domain consists of a duplication of two helix-loop-helix structural repeats [].; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0006471 protein ADP-ribosylation; PDB: 1GS0_B 3FHB_A 3C49_A 3CE0_A 3C4H_A 3KCZ_B 3KJD_B 3L3M_A 3GJW_A 1UK1_A ....
Probab=26.16 E-value=1.1e+02 Score=21.06 Aligned_cols=38 Identities=13% Similarity=0.378 Sum_probs=26.0
Q ss_pred hhcHHHHHHHHhcCCCC----CCCCCCChhHHHHHHHHHHhc
Q psy15166 22 QQLEKQAAEYMQQLPAG----KLPISGSDGALYRRQQLEKQV 59 (90)
Q Consensus 22 qQl~e~v~~Ym~~LP~~----kvP~~gS~Ge~~R~kQL~~QL 59 (90)
..+.++-.+||+.+|-. ..|+.+|.-.-.++.+|+.-|
T Consensus 66 ~~i~~lsn~fYtlIPh~fg~~~~~~I~~~~~l~~k~~lle~L 107 (133)
T PF02877_consen 66 SKIEDLSNRFYTLIPHNFGRSRPPVIDTEEKLKEKLELLEAL 107 (133)
T ss_dssp HHHHHHHHHHHHHSTB-STTS-S--STSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCcccCCCCCCcCCHHHHHHHHHHHHHH
Confidence 44566788999999976 778888888887777776544
No 18
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=25.46 E-value=78 Score=19.68 Aligned_cols=23 Identities=9% Similarity=0.182 Sum_probs=19.1
Q ss_pred hhhcCCCHHHHHHHHHhhhhhcc
Q psy15166 67 NLCHNLTADEIKCEKMECQHMEM 89 (90)
Q Consensus 67 ~yC~~LseeE~kel~~~~~~~~~ 89 (90)
.+=.+||++|++-+...|+.|-+
T Consensus 21 ~Fp~~ls~~eRriih~la~~lGL 43 (60)
T cd02639 21 AFPSSLSPAERRIVHLLASRLGL 43 (60)
T ss_pred EcCCCCCHHHHHHHHHHHHHcCC
Confidence 34468999999999999998754
No 19
>cd04388 RhoGAP_p85 RhoGAP_p85: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in the p85 isoforms of the regulatory subunit of the class IA PI3K (phosphatidylinositol 3'-kinase). This domain is also called Bcr (breakpoint cluster region protein) homology (BH) domain. Class IA PI3Ks are heterodimers, containing a regulatory subunit (p85) and a catalytic subunit (p110) and are activated by growth factor receptor tyrosine kinases (RTKs); this activation is mediated by the p85 subunit. p85 isoforms, alpha and beta, contain a C-terminal p110-binding domain flanked by two SH2 domains, an N-terminal SH3 domain, and a RhoGAP domain flanked by two proline-rich regions. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell p
Probab=24.48 E-value=97 Score=23.22 Aligned_cols=18 Identities=22% Similarity=0.493 Sum_probs=15.4
Q ss_pred HHHHHHHHhcCCCCCCCC
Q psy15166 25 EKQAAEYMQQLPAGKLPI 42 (90)
Q Consensus 25 ~e~v~~Ym~~LP~~kvP~ 42 (90)
-..+..||..||+--+|.
T Consensus 70 a~~LK~ylReLPePLip~ 87 (200)
T cd04388 70 ADALKRYLLDLPNPVIPA 87 (200)
T ss_pred HHHHHHHHHhCCCccCCH
Confidence 446889999999999995
No 20
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=24.28 E-value=57 Score=19.30 Aligned_cols=19 Identities=11% Similarity=0.078 Sum_probs=15.3
Q ss_pred hhhhcCCCHHHHHHHHHhh
Q psy15166 66 ANLCHNLTADEIKCEKMEC 84 (90)
Q Consensus 66 ~~yC~~LseeE~kel~~~~ 84 (90)
..|..++|++|.+.+--|=
T Consensus 11 ~~y~~~ft~~El~~i~~FY 29 (64)
T PF09832_consen 11 PIYAEHFTEEELDAILAFY 29 (64)
T ss_dssp HHHHHHS-HHHHHHHHHHH
T ss_pred HHHHHHCCHHHHHHHHHHH
Confidence 5689999999999988773
No 21
>cd04398 RhoGAP_fRGD1 RhoGAP_fRGD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD1-like proteins. Yeast Rgd1 is a GAP protein for Rho3 and Rho4 and plays a role in low-pH response. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=22.46 E-value=1.8e+02 Score=20.55 Aligned_cols=54 Identities=17% Similarity=0.228 Sum_probs=31.5
Q ss_pred HHHHHHHHhcCCCCCCCCC---------CChhHHHHHHHHHHhcCCCCCChhhhcCCCHHHHHHHHHhhhhhc
Q psy15166 25 EKQAAEYMQQLPAGKLPIS---------GSDGALYRRQQLEKQVPLHDLNANLCHNLTADEIKCEKMECQHME 88 (90)
Q Consensus 25 ~e~v~~Ym~~LP~~kvP~~---------gS~Ge~~R~kQL~~QLP~hD~d~~yC~~LseeE~kel~~~~~~~~ 88 (90)
-..+..||..||+.-+|.. ...+...|..++. ..+..|...-+..|+-++.|+.
T Consensus 77 a~~LK~fLreLp~pLi~~~~~~~~~~~~~~~~~~~~~~~l~----------~li~~LP~~n~~~L~~l~~~L~ 139 (192)
T cd04398 77 ASLLKLFFRELPEPLLTKALSREFIEAAKIEDESRRRDALH----------GLINDLPDANYATLRALMFHLA 139 (192)
T ss_pred HHHHHHHHHhCCCccCCHHHHHHHHHHHhCCCHHHHHHHHH----------HHHHHCCHHHHHHHHHHHHHHH
Confidence 3468899999999888852 1111222222111 2355666667777777777653
No 22
>cd04393 RhoGAP_FAM13A1a RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by up several orders of magnitude.
Probab=22.32 E-value=1.6e+02 Score=21.04 Aligned_cols=17 Identities=29% Similarity=0.626 Sum_probs=14.5
Q ss_pred HHHHHHHhcCCCCCCCC
Q psy15166 26 KQAAEYMQQLPAGKLPI 42 (90)
Q Consensus 26 e~v~~Ym~~LP~~kvP~ 42 (90)
..+..||..||+.-+|.
T Consensus 77 ~~lK~flr~Lp~pLi~~ 93 (189)
T cd04393 77 SLLRLFLQELPEGLIPA 93 (189)
T ss_pred HHHHHHHHhCCCccCCH
Confidence 47889999999988875
No 23
>PRK15441 peptidyl-prolyl cis-trans isomerase C; Provisional
Probab=22.09 E-value=67 Score=20.47 Aligned_cols=36 Identities=19% Similarity=0.249 Sum_probs=26.6
Q ss_pred CCCCccchhhhhcHHHHHHHHhcCCCCCC--CCCCChh
Q psy15166 12 SGSDGALYRRQQLEKQAAEYMQQLPAGKL--PISGSDG 47 (90)
Q Consensus 12 ~gSD~~l~~kqQl~e~v~~Ym~~LP~~kv--P~~gS~G 47 (90)
.|-|.-|....+++..+.+....||...+ |+...-|
T Consensus 46 ~gG~lg~~~~~~l~~~f~~a~~~l~~G~vs~Pi~t~~G 83 (93)
T PRK15441 46 RGGDLGEFRQGQMVPAFDKVVFSCPVLEPTGPLHTQFG 83 (93)
T ss_pred cCccceeecccccCHHHHHHHHhCCCCCcCCcEEcCCE
Confidence 34466777788888888888888998887 6654433
No 24
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=21.94 E-value=70 Score=23.93 Aligned_cols=16 Identities=19% Similarity=0.127 Sum_probs=13.4
Q ss_pred hcCCCHHHHHHHHHhh
Q psy15166 69 CHNLTADEIKCEKMEC 84 (90)
Q Consensus 69 C~~LseeE~kel~~~~ 84 (90)
+..|||+|+.|||.+-
T Consensus 23 ~~~LsEeE~eeLr~EL 38 (162)
T PF04201_consen 23 EEGLSEEEREELRSEL 38 (162)
T ss_pred cccCCHHHHHHHHHHH
Confidence 4689999999998764
No 25
>PF08278 DnaG_DnaB_bind: DNA primase DnaG DnaB-binding ; InterPro: IPR013173 Eubacterial DnaG primases interact with several factors to form the replisome. One of these factors is DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB []. This domain has a multi-helical structure that forms an orthogonal bundle [].; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 2HAJ_A 1T3W_B.
Probab=21.91 E-value=63 Score=21.28 Aligned_cols=13 Identities=23% Similarity=0.158 Sum_probs=8.6
Q ss_pred cCCCHHHHHHHHH
Q psy15166 70 HNLTADEIKCEKM 82 (90)
Q Consensus 70 ~~LseeE~kel~~ 82 (90)
..||++|+++|+.
T Consensus 113 ~~Lt~eEk~el~~ 125 (127)
T PF08278_consen 113 GGLTDEEKQELRR 125 (127)
T ss_dssp T---HHHHHHHHH
T ss_pred CCcCHHHHHHHHH
Confidence 6799999999875
No 26
>PF13035 DUF3896: Protein of unknown function (DUF3896)
Probab=20.65 E-value=57 Score=20.80 Aligned_cols=18 Identities=28% Similarity=0.344 Sum_probs=14.7
Q ss_pred CCCHHHHHHHHHhhhhhc
Q psy15166 71 NLTADEIKCEKMECQHME 88 (90)
Q Consensus 71 ~LseeE~kel~~~~~~~~ 88 (90)
.||++|+..++++-...|
T Consensus 29 ~ls~~er~qi~~eidnye 46 (61)
T PF13035_consen 29 HLSEKEREQIKLEIDNYE 46 (61)
T ss_pred ccCHHHHHHHHhhhhhHH
Confidence 688999999999876554
No 27
>cd04386 RhoGAP_nadrin RhoGAP_nadrin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Nadrin-like proteins. Nadrin, also named Rich-1, has been shown to be involved in the regulation of Ca2+-dependent exocytosis in neurons and recently has been implicated in tight junction maintenance in mammalian epithelium. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=20.23 E-value=2.3e+02 Score=20.42 Aligned_cols=19 Identities=21% Similarity=0.441 Sum_probs=15.3
Q ss_pred cHHHHHHHHhcCCCCCCCC
Q psy15166 24 LEKQAAEYMQQLPAGKLPI 42 (90)
Q Consensus 24 l~e~v~~Ym~~LP~~kvP~ 42 (90)
.-..+..|+..||+.-+|.
T Consensus 77 va~~lK~fLreLp~pli~~ 95 (203)
T cd04386 77 VASALKSYLRELPDPLLTY 95 (203)
T ss_pred HHHHHHHHHHhCCCccCCH
Confidence 3457889999999988876
No 28
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=20.05 E-value=77 Score=17.42 Aligned_cols=10 Identities=30% Similarity=0.597 Sum_probs=7.8
Q ss_pred cCCCHHHHHH
Q psy15166 70 HNLTADEIKC 79 (90)
Q Consensus 70 ~~LseeE~ke 79 (90)
|+||++|..+
T Consensus 14 h~ls~ee~~~ 23 (28)
T PF12368_consen 14 HGLSEEEVAE 23 (28)
T ss_pred cCCCHHHHHH
Confidence 6799988764
Done!