Query psy9217
Match_columns 90
No_of_seqs 103 out of 202
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 21:53:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9217.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9217hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1560|consensus 99.9 1.8E-22 4E-27 158.6 4.7 78 10-89 6-93 (339)
2 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.8 1.8E-19 3.9E-24 137.0 6.0 68 17-88 1-73 (266)
3 PLN03246 26S proteasome regula 99.7 5.2E-18 1.1E-22 132.3 6.8 57 13-69 2-58 (303)
4 cd08057 MPN_euk_non_mb Mpr1p, 99.7 2.1E-17 4.5E-22 116.2 5.1 50 19-69 1-50 (157)
5 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.7 2.5E-17 5.4E-22 124.9 4.6 50 19-69 1-50 (265)
6 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.7 1.3E-16 2.7E-21 123.0 6.8 53 17-69 1-53 (280)
7 PF01398 JAB: JAB1/Mov34/MPN/P 99.7 1E-16 2.2E-21 106.2 4.2 52 15-69 2-54 (114)
8 KOG2975|consensus 99.6 3.2E-17 6.8E-22 127.7 0.7 71 14-85 18-95 (288)
9 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.6 1.2E-15 2.6E-20 117.0 3.3 52 18-69 2-56 (288)
10 cd08069 MPN_RPN11_CSN5 Mov34/M 99.5 3.2E-14 6.9E-19 108.9 6.3 54 13-69 6-59 (268)
11 KOG1556|consensus 99.1 8.9E-11 1.9E-15 91.8 5.3 75 12-86 4-88 (309)
12 smart00232 JAB_MPN JAB/MPN dom 99.1 4E-10 8.6E-15 74.8 6.3 49 18-69 1-49 (135)
13 cd08067 MPN_2A_DUB Mov34/MPN/P 99.0 4.7E-10 1E-14 82.5 6.1 48 18-69 6-55 (187)
14 KOG1554|consensus 98.9 8E-10 1.7E-14 87.8 4.2 55 14-71 50-104 (347)
15 cd08058 MPN_euk_mb Mpr1p, Pad1 98.8 7.2E-09 1.6E-13 69.8 5.0 43 24-69 1-48 (119)
16 cd07767 MPN Mpr1p, Pad1p N-ter 98.6 6.3E-08 1.4E-12 63.0 4.9 40 27-69 2-41 (116)
17 KOG3050|consensus 97.8 7.2E-06 1.6E-10 64.4 1.2 55 15-69 7-64 (299)
18 cd08060 MPN_UPF0172 Mov34/MPN/ 97.6 9.5E-05 2E-09 54.3 4.3 45 22-69 2-47 (182)
19 cd08068 MPN_BRCC36 Mov34/MPN/P 97.4 0.0005 1.1E-08 53.0 6.0 50 16-68 1-57 (244)
20 PF03665 UPF0172: Uncharacteri 97.2 0.00054 1.2E-08 50.9 4.8 49 18-69 3-53 (196)
21 cd08070 MPN_like Mpr1p, Pad1p 96.6 0.0034 7.3E-08 42.5 4.1 42 25-69 3-44 (128)
22 cd08066 MPN_AMSH_like Mov34/MP 96.6 0.0099 2.2E-07 43.2 6.6 52 17-69 2-53 (173)
23 KOG3289|consensus 96.4 0.0054 1.2E-07 46.4 4.5 49 18-69 3-53 (199)
24 cd08072 MPN_archaeal Mov34/MPN 94.8 0.051 1.1E-06 36.9 4.0 39 24-69 4-42 (117)
25 PF14464 Prok-JAB: Prokaryotic 92.6 0.41 9E-06 30.4 5.1 38 24-64 3-40 (104)
26 TIGR02256 ICE_VC0181 integrati 90.9 0.59 1.3E-05 33.0 4.7 41 25-67 1-41 (131)
27 KOG1555|consensus 88.8 0.37 8.1E-06 38.8 2.6 51 16-69 30-86 (316)
28 COG1310 Predicted metal-depend 80.1 3.4 7.4E-05 28.0 3.9 42 19-68 2-43 (134)
29 cd08073 MPN_NLPC_P60 Mpr1p, Pa 76.6 3.4 7.5E-05 27.6 3.1 24 26-52 3-26 (108)
30 PF07620 SLEI_Leptospira: SLEI 75.5 2.1 4.5E-05 20.6 1.3 10 53-62 6-15 (16)
31 cd08059 MPN_prok_mb Mpr1p, Pad 69.3 7.4 0.00016 24.9 3.2 39 25-69 2-40 (101)
32 TIGR03735 PRTRC_A PRTRC system 59.6 16 0.00034 27.5 3.8 46 17-68 71-116 (192)
33 KOG1784|consensus 49.6 11 0.00024 25.7 1.5 28 41-68 20-47 (96)
34 smart00651 Sm snRNP Sm protein 34.7 48 0.001 19.4 2.5 26 41-66 18-43 (67)
35 KOG4445|consensus 33.9 36 0.00079 28.0 2.4 46 23-68 94-142 (368)
36 PF02237 BPL_C: Biotin protein 33.6 74 0.0016 18.1 3.1 21 41-61 12-32 (48)
37 cd00600 Sm_like The eukaryotic 30.4 58 0.0013 18.7 2.4 25 41-65 16-40 (63)
38 PF07581 Glug: The GLUG motif; 29.8 54 0.0012 17.1 1.9 21 43-64 3-23 (28)
39 PF01423 LSM: LSM domain ; In 29.2 92 0.002 18.2 3.1 28 41-68 18-45 (67)
40 cd01728 LSm1 The eukaryotic Sm 26.4 78 0.0017 20.0 2.6 25 41-65 22-46 (74)
41 cd01726 LSm6 The eukaryotic Sm 23.8 1.2E+02 0.0027 18.2 3.1 25 41-65 20-44 (67)
42 cd01727 LSm8 The eukaryotic Sm 23.4 83 0.0018 19.4 2.3 25 42-66 20-44 (74)
43 PRK04290 30S ribosomal protein 23.4 1.7E+02 0.0036 20.5 3.9 39 15-60 15-53 (115)
44 cd01731 archaeal_Sm1 The archa 22.2 1.4E+02 0.0031 17.9 3.1 25 41-65 20-44 (68)
45 cd01722 Sm_F The eukaryotic Sm 20.5 1.4E+02 0.0031 18.0 2.9 23 41-63 21-43 (68)
No 1
>KOG1560|consensus
Probab=99.86 E-value=1.8e-22 Score=158.55 Aligned_cols=78 Identities=50% Similarity=0.856 Sum_probs=66.6
Q ss_pred ccCCCCeeeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC--CC------Ccccc--cch
Q psy9217 10 QIDESPISYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY--DE------SVDEG--CYE 79 (90)
Q Consensus 10 ~~~~~~v~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~--de------~~~~~--~Yq 79 (90)
...+++|+.|+||+||+|||||||++++ ++...++|+|||++.|++||||||||||... || .++++ +||
T Consensus 6 ~~~~p~vk~v~ldsLvVMkiiKHc~ee~-~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~ 84 (339)
T KOG1560|consen 6 ELESPPVKRVELDSLVVMKIIKHCREEF-PNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQ 84 (339)
T ss_pred CCCCCccceeeehhHHHHHHHHHHHhhc-CCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHH
Confidence 3456789999999999999999999999 5567899999999999999999999999865 33 24554 788
Q ss_pred hhhhhhcccC
Q psy9217 80 DSETLSRGKH 89 (90)
Q Consensus 80 ~~~~l~~~~~ 89 (90)
++ ++++.|+
T Consensus 85 l~-mlrrlr~ 93 (339)
T KOG1560|consen 85 LA-MLRRLRY 93 (339)
T ss_pred HH-HHHHhhh
Confidence 88 9999885
No 2
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=99.78 E-value=1.8e-19 Score=136.98 Aligned_cols=68 Identities=49% Similarity=0.804 Sum_probs=57.0
Q ss_pred eeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCCCCC-----cccccchhhhhhhccc
Q psy9217 17 SYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNYDES-----VDEGCYEDSETLSRGK 88 (90)
Q Consensus 17 ~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~de~-----~~~~~Yq~~~~l~~~~ 88 (90)
++|+|+++|++||+|||++++ |.+|+|+|||++.++++|||||||||+.++++ .+..+||.+ |++..|
T Consensus 1 ~~V~I~~~vllkIv~H~~~~~---p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~-m~~~~r 73 (266)
T cd08065 1 TSVQIDGLVVLKIIKHCKEEL---PELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLE-MMRLLR 73 (266)
T ss_pred CEEEEeHHHHHHHHHHHhcCC---CcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHH-HHHHHH
Confidence 479999999999999999999 78999999999999999999999999987332 233577776 555544
No 3
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.73 E-value=5.2e-18 Score=132.31 Aligned_cols=57 Identities=26% Similarity=0.412 Sum_probs=51.6
Q ss_pred CCCeeeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 13 ESPISYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 13 ~~~v~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
..|+.+|+|||+|+|+|++||.|+.+..+.+|+|+|||++.++.|||||||++|+.+
T Consensus 2 ~~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e 58 (303)
T PLN03246 2 PRGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEE 58 (303)
T ss_pred CCCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCccc
Confidence 468899999999999999999999843357899999999999999999999999965
No 4
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=99.69 E-value=2.1e-17 Score=116.19 Aligned_cols=50 Identities=32% Similarity=0.549 Sum_probs=46.4
Q ss_pred EEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 19 VQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 19 V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
|+|||+|+|||++||.++. .++.+++|+|||...++.+|||||||+|+.+
T Consensus 1 V~ihplvll~I~dh~~R~~-~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~ 50 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRK-YGIKRVIGVLLGYVDGDKIEVTNSFELPFDE 50 (157)
T ss_pred CEEccHHHhhHHHHHHhcc-CCCCeEEEEEEeEEeCCEEEEEEeEEccccC
Confidence 6899999999999999987 3568999999999999999999999999966
No 5
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=99.68 E-value=2.5e-17 Score=124.90 Aligned_cols=50 Identities=30% Similarity=0.551 Sum_probs=46.4
Q ss_pred EEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 19 VQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 19 V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
|+|||+|+|+|+|||.++. .++.+|+|+|||...++.+|||||||+|+.+
T Consensus 1 v~ihPlVll~I~dH~~R~~-~~~~~V~G~LLG~~~~~~veItnsF~~p~~~ 50 (265)
T cd08064 1 VRVHPVVLFSILDSYERRN-EGQERVIGTLLGTRSEGEVEITNCFAVPHNE 50 (265)
T ss_pred CEEccHHHHhHHHHHhhhc-CCCcEEEEEEEEEEeCCEEEEEeCeecceeC
Confidence 6899999999999999986 4578999999999999999999999999976
No 6
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=99.67 E-value=1.3e-16 Score=123.02 Aligned_cols=53 Identities=25% Similarity=0.374 Sum_probs=48.4
Q ss_pred eeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 17 SYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 17 ~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
++|+|||+|+|+|+|||.++.+..+.+|+|+|||...++.+||||||++|+.+
T Consensus 1 ~~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~ 53 (280)
T cd08062 1 KKVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEE 53 (280)
T ss_pred CeEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccC
Confidence 47999999999999999998744468999999999999999999999999976
No 7
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=99.65 E-value=1e-16 Score=106.21 Aligned_cols=52 Identities=35% Similarity=0.549 Sum_probs=48.8
Q ss_pred CeeeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCC-EEEEEeeccCCCCC
Q psy9217 15 PISYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDN-RLEITNCFPFPKNY 69 (90)
Q Consensus 15 ~v~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~-~lEVTn~Fp~P~~~ 69 (90)
++.+|+|+|+|+++|++||.++. +.+++|.|||...++ ++||||||++|..+
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~---~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~ 54 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSS---PNEVIGLLLGTQDGDNTVEITNSFPVPHSE 54 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHH---CTEEEEEEEEEEETT-EEEEEEEEEESEEE
T ss_pred CcEEEEECHHHHHHHHHHHhcCC---CCEEEEEEEEEecCceEEEEEEEEEeeEec
Confidence 57899999999999999999988 569999999999999 99999999999976
No 8
>KOG2975|consensus
Probab=99.64 E-value=3.2e-17 Score=127.66 Aligned_cols=71 Identities=27% Similarity=0.448 Sum_probs=60.9
Q ss_pred CCeeeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC-CC------Ccccccchhhhhhh
Q psy9217 14 SPISYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY-DE------SVDEGCYEDSETLS 85 (90)
Q Consensus 14 ~~v~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~-de------~~~~~~Yq~~~~l~ 85 (90)
+....|+|+|+|+|+|++|+.++. ++.++|+|+|||...+|++||||||++||++ +| ++..+||.+.++.+
T Consensus 18 ss~ltv~ihP~Vlf~ivD~~~RR~-~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm~y~~~M~~l~~k~n 95 (288)
T KOG2975|consen 18 SSNLTVRLHPVVLFSIVDAYERRN-KGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDMEYAKNMYELHKKVN 95 (288)
T ss_pred CCCceEEEcceEEeEeehhhhcCC-ccchhhhhheeecccCCeEEEEEeeeccCccccccceeeHHHHHHHHHHhcccC
Confidence 345689999999999999999999 7789999999999999999999999999998 33 24457788776654
No 9
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=99.57 E-value=1.2e-15 Score=117.01 Aligned_cols=52 Identities=25% Similarity=0.376 Sum_probs=46.8
Q ss_pred eEEEehhHHHHHHHHhhhcCCCC---cceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 18 YVQMDGLAVMKIVKHCHEESTNN---IEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 18 ~V~id~lVllKIikH~~~~~~~~---~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
+|+|||+|+|+|++||.+..... +.+|+|+|||.+.++.|||||||++|+.+
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~ 56 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDT 56 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEeccccc
Confidence 69999999999999999975322 57999999999999999999999999976
No 10
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.50 E-value=3.2e-14 Score=108.92 Aligned_cols=54 Identities=24% Similarity=0.367 Sum_probs=50.1
Q ss_pred CCCeeeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 13 ESPISYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 13 ~~~v~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
...+++|+|+++|++||++||++.. |.+|+|.|||.+.+++++||||||+|+.+
T Consensus 6 ~~~~~~V~Is~~allkil~Ha~~~~---p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~ 59 (268)
T cd08069 6 PDYFEKVYISSLALLKMLKHARAGG---PIEVMGLMLGKVDDYTIIVVDVFALPVEG 59 (268)
T ss_pred CCcccEEEECHHHHHHHHHHHhccC---CceEEEEEEeeecCCeEEEEEEEECCcCC
Confidence 3468999999999999999999977 78999999999999999999999999865
No 11
>KOG1556|consensus
Probab=99.12 E-value=8.9e-11 Score=91.85 Aligned_cols=75 Identities=20% Similarity=0.302 Sum_probs=61.5
Q ss_pred CCCCeeeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCCCCC----------cccccchhh
Q psy9217 12 DESPISYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNYDES----------VDEGCYEDS 81 (90)
Q Consensus 12 ~~~~v~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~de~----------~~~~~Yq~~ 81 (90)
..-++.+|-|+|||||.+++||.+....+..+|.|.|||-+.+++|.|||||++|-.+||. +-++||.+-
T Consensus 4 ~~~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mf 83 (309)
T KOG1556|consen 4 SELTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMF 83 (309)
T ss_pred cccccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHH
Confidence 3456889999999999999999998865568999999999999999999999999877442 224677766
Q ss_pred hhhhc
Q psy9217 82 ETLSR 86 (90)
Q Consensus 82 ~~l~~ 86 (90)
++++.
T Consensus 84 kKvNa 88 (309)
T KOG1556|consen 84 KKVNA 88 (309)
T ss_pred HHhcc
Confidence 66553
No 12
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.07 E-value=4e-10 Score=74.76 Aligned_cols=49 Identities=29% Similarity=0.440 Sum_probs=45.6
Q ss_pred eEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 18 YVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 18 ~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
.|+|+++|+++|++||.+.. |.++.|.|+|...+++++|++||++|...
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~---p~e~~G~L~G~~~~~~~~i~~~~~~p~~~ 49 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDG---PEEVCGVLLGKSNKDRPEVKEVFAVPNEP 49 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCC---CcEEEEEEEEEEcCCEEEEEEEEecCcCC
Confidence 37899999999999999987 78999999999999999999999999865
No 13
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=99.04 E-value=4.7e-10 Score=82.52 Aligned_cols=48 Identities=25% Similarity=0.324 Sum_probs=43.1
Q ss_pred eEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEe--CCEEEEEeeccCCCCC
Q psy9217 18 YVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVV--DNRLEITNCFPFPKNY 69 (90)
Q Consensus 18 ~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~--~~~lEVTn~Fp~P~~~ 69 (90)
+|+|+++|+|||++||++.. .++.|.|+|... ++.++||+|||+|...
T Consensus 6 ~V~Is~~all~m~~Ha~~~~----~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~ 55 (187)
T cd08067 6 KVTVSSNALLLMDFHCHLTT----SEVIGYLGGTWDPNTQNLTILQAFPCRSRL 55 (187)
T ss_pred EEEECHHHHHHHHHHhcCCC----cEEEEEEEeEEcCCCCeEEEEEEEecCCCC
Confidence 79999999999999999865 789999999843 5789999999999865
No 14
>KOG1554|consensus
Probab=98.94 E-value=8e-10 Score=87.78 Aligned_cols=55 Identities=22% Similarity=0.332 Sum_probs=51.0
Q ss_pred CCeeeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCCCC
Q psy9217 14 SPISYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNYDE 71 (90)
Q Consensus 14 ~~v~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~de 71 (90)
..++.|+|++++++||+.|++++. +-++||.|+|...++++.|.+||++|+.+.|
T Consensus 50 ~~fk~vkISalAllKm~~hA~~Gg---nlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTE 104 (347)
T KOG1554|consen 50 HYFKHVKISALALLKMVMHARSGG---NLEIMGLMQGKVDGDTIIVMDSFALPVEGTE 104 (347)
T ss_pred chhhhhhhHHHHHHHHHHHHhcCC---CeEEEeeecccccCCeEEEEecccccccccc
Confidence 358899999999999999999987 7899999999999999999999999998844
No 15
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=98.82 E-value=7.2e-09 Score=69.79 Aligned_cols=43 Identities=19% Similarity=0.254 Sum_probs=37.9
Q ss_pred hHHHHHHHHhhhcCCCCcceeeeEEeeeEe-----CCEEEEEeeccCCCCC
Q psy9217 24 LAVMKIVKHCHEESTNNIEVAQGALLGLVV-----DNRLEITNCFPFPKNY 69 (90)
Q Consensus 24 lVllKIikH~~~~~~~~~~~v~G~LLG~~~-----~~~lEVTn~Fp~P~~~ 69 (90)
.|++||++||++.. |.++.|.|+|... +.+++||||||+|...
T Consensus 1 ~~~~~i~~ha~~~~---p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~ 48 (119)
T cd08058 1 DALLKMLQHAESNT---GIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSC 48 (119)
T ss_pred CHHHHHHHHhcCCC---CeEEEEEeeeEEecCccceeEEEEeecCCCCCCc
Confidence 37999999999998 7899999999865 5679999999999754
No 16
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=98.63 E-value=6.3e-08 Score=62.97 Aligned_cols=40 Identities=13% Similarity=0.165 Sum_probs=36.3
Q ss_pred HHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 27 MKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 27 lKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
-+|++||.+.. |.++.|.|+|...+++++|++||++|...
T Consensus 2 k~il~~a~~~~---~~ev~G~L~G~~~~~~~~i~~~~~~~~~~ 41 (116)
T cd07767 2 KMFLDAAKSIN---GKEVIGLLYGSKTKKVLDVDEVIAVPFDE 41 (116)
T ss_pred HhHHHHHhcCC---CcEEEEEeEEEEcCCEEEEEEEEecccCC
Confidence 57999999986 68999999999999999999999999855
No 17
>KOG3050|consensus
Probab=97.81 E-value=7.2e-06 Score=64.44 Aligned_cols=55 Identities=25% Similarity=0.357 Sum_probs=45.3
Q ss_pred CeeeEEEehhHHHHHHHHhhhcCC---CCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 15 PISYVQMDGLAVMKIVKHCHEEST---NNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 15 ~v~~V~id~lVllKIikH~~~~~~---~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
--.+|.++|||+|+|-+|+.+-.. +....|.|.|+|...+..+||.|+|-+-...
T Consensus 7 ~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~ 64 (299)
T KOG3050|consen 7 GSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDT 64 (299)
T ss_pred CceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecc
Confidence 345899999999999999988521 2123799999999999999999999997544
No 18
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=97.59 E-value=9.5e-05 Score=54.28 Aligned_cols=45 Identities=27% Similarity=0.364 Sum_probs=39.6
Q ss_pred ehhHHHHHHHHhhhcCCCCcceeeeEEeeeEe-CCEEEEEeeccCCCCC
Q psy9217 22 DGLAVMKIVKHCHEESTNNIEVAQGALLGLVV-DNRLEITNCFPFPKNY 69 (90)
Q Consensus 22 d~lVllKIikH~~~~~~~~~~~v~G~LLG~~~-~~~lEVTn~Fp~P~~~ 69 (90)
...+..||+.||...+ +..+-|.|+|... ++.+.|++++|++|..
T Consensus 2 s~~ay~ki~~HA~k~p---~~evcGlLlG~~~~~~~~~V~d~vPl~h~~ 47 (182)
T cd08060 2 STLAYVKMLLHAAKYP---HCAVNGLLLGKKSSGGSVEITDAVPLFHSC 47 (182)
T ss_pred CHHHHHHHHHHHHHcC---CchheEEEEeeecCCCCEEEEEEEEcCCCc
Confidence 4678899999999966 6799999999977 8889999999999864
No 19
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=97.37 E-value=0.0005 Score=53.00 Aligned_cols=50 Identities=16% Similarity=0.228 Sum_probs=41.7
Q ss_pred eeeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEe-------CCEEEEEeeccCCCC
Q psy9217 16 ISYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVV-------DNRLEITNCFPFPKN 68 (90)
Q Consensus 16 v~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~-------~~~lEVTn~Fp~P~~ 68 (90)
+++|.|...++++|+.||++.. |.++.|.|+|... ...++|+.-++.+..
T Consensus 1 l~~V~Is~~~l~~il~HA~~~~---P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~ 57 (244)
T cd08068 1 LSKVHLSADVYLVCLTHALSTE---KEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRS 57 (244)
T ss_pred CcEEEECHHHHHHHHHHHHhCC---CcceeEEEEeecccccccccceeEEEeeecccccc
Confidence 3689999999999999999998 7999999999763 556777777776543
No 20
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.24 E-value=0.00054 Score=50.87 Aligned_cols=49 Identities=22% Similarity=0.371 Sum_probs=43.3
Q ss_pred eEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCE--EEEEeeccCCCCC
Q psy9217 18 YVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNR--LEITNCFPFPKNY 69 (90)
Q Consensus 18 ~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~--lEVTn~Fp~P~~~ 69 (90)
+|+|+..+-.||+=||-..+ ...|.|.|||-..++. ++|++|.|+=|..
T Consensus 3 ~v~is~~AY~K~~LHaaKyP---~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~ 53 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYP---HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHW 53 (196)
T ss_pred eEEEcHHHHHHHHHHhccCC---CCceeeEEEeccCCCCceEEEeeceeccccc
Confidence 68999999999999999987 5789999999876444 9999999999853
No 21
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=96.62 E-value=0.0034 Score=42.50 Aligned_cols=42 Identities=24% Similarity=0.234 Sum_probs=36.9
Q ss_pred HHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 25 AVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 25 VllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
++-+|++||++.+ |.++.|.|+|...+....|+..||.|...
T Consensus 3 ~~~~il~ha~~~~---P~E~cGlL~G~~~~~~~~i~~~~p~~n~~ 44 (128)
T cd08070 3 LLEAILAHAEAEY---PEECCGLLLGKGGGVTAIVTEVYPVRNVA 44 (128)
T ss_pred HHHHHHHHHHhCC---CCceEEEEEeecCCCCceEEEEEEccCCC
Confidence 5678999999998 78999999999887777789999999865
No 22
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=96.58 E-value=0.0099 Score=43.20 Aligned_cols=52 Identities=15% Similarity=0.071 Sum_probs=44.0
Q ss_pred eeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 17 SYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 17 ~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
..+.|..-.+-||+.||+.+. +.|.++.|.|+|...+++.+|+++|..|...
T Consensus 2 ~~l~Ipk~il~~~l~~A~~~~-~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~ 53 (173)
T cd08066 2 RQVVVPADLMDKFLQLAEPNT-SRNLETCGILCGKLSNNAFFITHLIIPKQSG 53 (173)
T ss_pred eEEEECHHHHHHHHHHHHhCC-CCCCeEEEEEEeEcCCCeEEEEEEEeccccC
Confidence 357888899999999999996 3368999999999888999999997777655
No 23
>KOG3289|consensus
Probab=96.43 E-value=0.0054 Score=46.37 Aligned_cols=49 Identities=27% Similarity=0.409 Sum_probs=43.3
Q ss_pred eEEEehhHHHHHHHHhhhcCCCCcceeeeEEee--eEeCCEEEEEeeccCCCCC
Q psy9217 18 YVQMDGLAVMKIVKHCHEESTNNIEVAQGALLG--LVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 18 ~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG--~~~~~~lEVTn~Fp~P~~~ 69 (90)
.|+|.+++-.|||=||-+.+ ..-|.|.|+| --.++.+|||+|.|+=|+.
T Consensus 3 ~veis~~aY~kmiLH~akyp---h~aVnGLLla~~~~kg~~v~itdcVPLfH~~ 53 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYP---HAAVNGLLLAPATGKGECVEITDCVPLFHSH 53 (199)
T ss_pred ceeehhhHHHHHHHHhccCc---ccceeeEEEeccCCCCCeEEEEecchhhccc
Confidence 58999999999999999987 4679999999 4568999999999998875
No 24
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=94.82 E-value=0.051 Score=36.87 Aligned_cols=39 Identities=15% Similarity=0.038 Sum_probs=32.8
Q ss_pred hHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 24 LAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 24 lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
-.+-.|++||++.+ |.++-|.|+|... .||+.+++|...
T Consensus 4 ~~~~~i~~ha~~~~---P~E~CGlL~G~~~----~v~~~~~~~n~~ 42 (117)
T cd08072 4 DLLDSILEAAKSSH---PNEFAALLRGKDG----VITELLILPGTE 42 (117)
T ss_pred HHHHHHHHHHhhcC---CceEEEEEEeecc----EEEEEEECCCCC
Confidence 45668999999999 7899999999653 699999999654
No 25
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=92.65 E-value=0.41 Score=30.41 Aligned_cols=38 Identities=24% Similarity=0.254 Sum_probs=31.7
Q ss_pred hHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeecc
Q psy9217 24 LAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFP 64 (90)
Q Consensus 24 lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp 64 (90)
.++-+|+.||++.. |.++-|.|+|...+..+.|+...+
T Consensus 3 ~~~~~i~~~~~~~~---p~E~~G~L~g~~~~~~~~~~~~~~ 40 (104)
T PF14464_consen 3 EVLEQIIAHARAAY---PNEACGLLLGRRDDQRFIVVPNVN 40 (104)
T ss_dssp HHHHHHHHHHHHHT---TS-EEEEEEEEEECCEEEEEEEEE
T ss_pred HHHHHHHHHHhhCC---CCeEEEEEEEEecCCEEEEEeCCC
Confidence 46778999999998 789999999998888888877765
No 26
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=90.87 E-value=0.59 Score=33.03 Aligned_cols=41 Identities=20% Similarity=0.172 Sum_probs=33.0
Q ss_pred HHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCC
Q psy9217 25 AVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPK 67 (90)
Q Consensus 25 VllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~ 67 (90)
+++++++.|+... ..+.++=|.|+|...+..+.|+.+- .|.
T Consensus 1 ~v~~~~~~~~Q~~-~~~~EtGGiLiG~~~~~~~ii~~~t-~P~ 41 (131)
T TIGR02256 1 VVVAMLKSYRQWH-DLSTETGGVLIGERRGAHAVITKIS-EPG 41 (131)
T ss_pred CHHHHHHHHHhCc-CCCCccceEEEEEEcCCcEEEEEEE-cCC
Confidence 4788888898887 5578999999998878889999855 443
No 27
>KOG1555|consensus
Probab=88.81 E-value=0.37 Score=38.80 Aligned_cols=51 Identities=27% Similarity=0.473 Sum_probs=44.2
Q ss_pred eeeEEEehhHHHHHHHHhhhcCCCCcce-eeeEE-ee----eEeCCEEEEEeeccCCCCC
Q psy9217 16 ISYVQMDGLAVMKIVKHCHEESTNNIEV-AQGAL-LG----LVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 16 v~~V~id~lVllKIikH~~~~~~~~~~~-v~G~L-LG----~~~~~~lEVTn~Fp~P~~~ 69 (90)
-.+|.|..++++++.+|.+... |.. ++|.| || ++.+-++.|...|+.|..+
T Consensus 30 ~e~v~i~slall~m~rh~r~~~---p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg 86 (316)
T KOG1555|consen 30 KETVYISSLALLKMLRHDRAGS---PEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSG 86 (316)
T ss_pred cceeeeehhhhhhcccccccCC---chhhccceeecccccceeeecceeeeeeecccccc
Confidence 4589999999999999999987 555 99999 99 4668888899999999876
No 28
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=80.07 E-value=3.4 Score=27.98 Aligned_cols=42 Identities=19% Similarity=0.253 Sum_probs=32.9
Q ss_pred EEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCC
Q psy9217 19 VQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKN 68 (90)
Q Consensus 19 V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~ 68 (90)
+.|...++-.|+.|+++.. |.++.|.|+|...+ .-+|+++..
T Consensus 2 ~~i~~~~l~~il~~a~~~~---p~E~~g~l~~~~~~-----~~~~~~~n~ 43 (134)
T COG1310 2 LVIPKEVLGAILEHARREH---PREVCGLLAGTREG-----ERYFPLKNV 43 (134)
T ss_pred ceecHHHHHHHHHHHHhcC---ChheEEEEEeeccc-----ceeeccccc
Confidence 4577889999999999998 68999999998655 444444443
No 29
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=76.62 E-value=3.4 Score=27.61 Aligned_cols=24 Identities=21% Similarity=0.105 Sum_probs=20.6
Q ss_pred HHHHHHHhhhcCCCCcceeeeEEeeeE
Q psy9217 26 VMKIVKHCHEESTNNIEVAQGALLGLV 52 (90)
Q Consensus 26 llKIikH~~~~~~~~~~~v~G~LLG~~ 52 (90)
+-.|+.|+++.+ |.++-|.|+|..
T Consensus 3 ~~~i~~ha~~~~---P~E~CGll~g~~ 26 (108)
T cd08073 3 EDAILAHAKAEY---PREACGLVVRKG 26 (108)
T ss_pred HHHHHHHHhHCC---CCcceEEEEecC
Confidence 447899999999 789999999965
No 30
>PF07620 SLEI_Leptospira: SLEI; InterPro: IPR011512 This entry represents a highly conserved sequence motif found at the C-terminal of some hypothetical proteins from Leptospira interrogans.
Probab=75.52 E-value=2.1 Score=20.61 Aligned_cols=10 Identities=60% Similarity=0.694 Sum_probs=8.7
Q ss_pred eCCEEEEEee
Q psy9217 53 VDNRLEITNC 62 (90)
Q Consensus 53 ~~~~lEVTn~ 62 (90)
.|++|||.|+
T Consensus 6 rdNsLeIsn~ 15 (16)
T PF07620_consen 6 RDNSLEISNQ 15 (16)
T ss_pred cCCeEEEeec
Confidence 3899999997
No 31
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=69.32 E-value=7.4 Score=24.87 Aligned_cols=39 Identities=15% Similarity=0.123 Sum_probs=30.0
Q ss_pred HHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCCC
Q psy9217 25 AVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKNY 69 (90)
Q Consensus 25 VllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~~ 69 (90)
++-.|..|++..+ |.++-|.|+|-..+ .|+|..++|...
T Consensus 2 ~~~~i~~~~~~~~---p~E~~gll~~~~~~---~~~~~~~~~~~~ 40 (101)
T cd08059 2 LLKTILVHAKDAH---PDEFCGFLSGSKDN---VMDELIFLPFVS 40 (101)
T ss_pred HHHHHHHHHHhcC---ChhhheeeecCCCC---eEEEEEeCCCcC
Confidence 3456889999997 68899999996433 788888888644
No 32
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=59.63 E-value=16 Score=27.52 Aligned_cols=46 Identities=2% Similarity=-0.127 Sum_probs=35.1
Q ss_pred eeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEEeeccCCCC
Q psy9217 17 SYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEITNCFPFPKN 68 (90)
Q Consensus 17 ~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVTn~Fp~P~~ 68 (90)
..=+|..-.+-+|+.||++.. |.++-|.|.|-..++.. .++|+.+.
T Consensus 71 ~~g~Ip~~l~~~ii~hAr~~~---P~EacG~Iag~~~~~~~---r~~p~~N~ 116 (192)
T TIGR03735 71 LCGPIPASLLEEFAEAARAAL---PNEVAAWIVWNSETGSL---RLAALESI 116 (192)
T ss_pred ecCCCCHHHHHHHHHHHHhcC---CcceEEEEEEcCCCCEE---EEEecccc
Confidence 344778888999999999999 78999999997555554 33666543
No 33
>KOG1784|consensus
Probab=49.59 E-value=11 Score=25.73 Aligned_cols=28 Identities=21% Similarity=0.110 Sum_probs=23.5
Q ss_pred cceeeeEEeeeEeCCEEEEEeeccCCCC
Q psy9217 41 IEVAQGALLGLVVDNRLEITNCFPFPKN 68 (90)
Q Consensus 41 ~~~v~G~LLG~~~~~~lEVTn~Fp~P~~ 68 (90)
...+.|+|=|+|+.-.|-|++||-=-.+
T Consensus 20 Gr~ivgsLkGFDq~tNlii~~~heRi~s 47 (96)
T KOG1784|consen 20 GRVIVGSLKGFDQTTNLIIDESHERIFS 47 (96)
T ss_pred CeEEEEEeccccccceeeehhhHhhhhh
Confidence 3578999999999999999999964443
No 34
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=34.72 E-value=48 Score=19.45 Aligned_cols=26 Identities=15% Similarity=-0.013 Sum_probs=21.5
Q ss_pred cceeeeEEeeeEeCCEEEEEeeccCC
Q psy9217 41 IEVAQGALLGLVVDNRLEITNCFPFP 66 (90)
Q Consensus 41 ~~~v~G~LLG~~~~~~lEVTn~Fp~P 66 (90)
.....|.|.|+|..-.|..+||.-..
T Consensus 18 g~~~~G~L~~~D~~~NlvL~~~~e~~ 43 (67)
T smart00651 18 GREYRGTLKGFDQFMNLVLEDVEETV 43 (67)
T ss_pred CcEEEEEEEEECccccEEEccEEEEe
Confidence 36799999999998889888886544
No 35
>KOG4445|consensus
Probab=33.87 E-value=36 Score=28.02 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=34.2
Q ss_pred hhHHHHHHHHhhhcCCCCc---ceeeeEEeeeEeCCEEEEEeeccCCCC
Q psy9217 23 GLAVMKIVKHCHEESTNNI---EVAQGALLGLVVDNRLEITNCFPFPKN 68 (90)
Q Consensus 23 ~lVllKIikH~~~~~~~~~---~~v~G~LLG~~~~~~lEVTn~Fp~P~~ 68 (90)
--++..||.||++-..++. ....=-|.|+-....+-+|-||-+=|.
T Consensus 94 ~pii~~lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~ 142 (368)
T KOG4445|consen 94 MPIICQLIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHF 142 (368)
T ss_pred CchhHHHHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHH
Confidence 3478999999999764322 123345899998999999999987664
No 36
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=33.57 E-value=74 Score=18.07 Aligned_cols=21 Identities=19% Similarity=0.143 Sum_probs=17.6
Q ss_pred cceeeeEEeeeEeCCEEEEEe
Q psy9217 41 IEVAQGALLGLVVDNRLEITN 61 (90)
Q Consensus 41 ~~~v~G~LLG~~~~~~lEVTn 61 (90)
...+.|...|++.+|.|-|..
T Consensus 12 ~~~~~G~~~gId~~G~L~v~~ 32 (48)
T PF02237_consen 12 DGEIEGIAEGIDDDGALLVRT 32 (48)
T ss_dssp SCEEEEEEEEEETTSEEEEEE
T ss_pred CeEEEEEEEEECCCCEEEEEE
Confidence 356899999999999998853
No 37
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=30.40 E-value=58 Score=18.73 Aligned_cols=25 Identities=16% Similarity=0.082 Sum_probs=20.9
Q ss_pred cceeeeEEeeeEeCCEEEEEeeccC
Q psy9217 41 IEVAQGALLGLVVDNRLEITNCFPF 65 (90)
Q Consensus 41 ~~~v~G~LLG~~~~~~lEVTn~Fp~ 65 (90)
.....|.|.++|....+..+||.-.
T Consensus 16 g~~~~G~L~~~D~~~Ni~L~~~~~~ 40 (63)
T cd00600 16 GRVLEGVLVAFDKYMNLVLDDVEET 40 (63)
T ss_pred CcEEEEEEEEECCCCCEEECCEEEE
Confidence 3679999999998888988888644
No 38
>PF07581 Glug: The GLUG motif; InterPro: IPR011493 This domain is found in the IgA1-specific metalloendopeptidases, which attach to the cell wall peptidoglycan by an amide bond []. IgA1 protease selectively cleaves human IgA1 and is likely to be a pathogenicity factor in some pathogens including Giardia spp []. This domain is also found in various other contexts, including with IPR008638 from INTERPRO. It is named GLUG after the mostly conserved G-L-any-G motif. The IgA1-specific metalloendopeptidases belong to MEROPS peptidase family M26, clan MA(E).
Probab=29.82 E-value=54 Score=17.15 Aligned_cols=21 Identities=33% Similarity=0.559 Sum_probs=15.0
Q ss_pred eeeeEEeeeEeCCEEEEEeecc
Q psy9217 43 VAQGALLGLVVDNRLEITNCFP 64 (90)
Q Consensus 43 ~v~G~LLG~~~~~~lEVTn~Fp 64 (90)
...|-|.|...++ =.|+||++
T Consensus 3 ~~vGGlvG~~~~~-~~I~nc~a 23 (28)
T PF07581_consen 3 YYVGGLVGYNDNG-GSITNCYA 23 (28)
T ss_pred ccEEeEEEECCCC-CEEEEEEE
Confidence 4578888887653 46788875
No 39
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=29.21 E-value=92 Score=18.24 Aligned_cols=28 Identities=18% Similarity=0.096 Sum_probs=23.2
Q ss_pred cceeeeEEeeeEeCCEEEEEeeccCCCC
Q psy9217 41 IEVAQGALLGLVVDNRLEITNCFPFPKN 68 (90)
Q Consensus 41 ~~~v~G~LLG~~~~~~lEVTn~Fp~P~~ 68 (90)
.....|.|.++|..-.|..++|.-....
T Consensus 18 g~~~~G~L~~~D~~~Nl~L~~~~~~~~~ 45 (67)
T PF01423_consen 18 GRTYRGTLVSFDQFMNLVLSDVTETIKN 45 (67)
T ss_dssp SEEEEEEEEEEETTEEEEEEEEEEEETT
T ss_pred CEEEEEEEEEeechheEEeeeEEEEECC
Confidence 3679999999999888999998776543
No 40
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=26.42 E-value=78 Score=19.96 Aligned_cols=25 Identities=12% Similarity=-0.061 Sum_probs=20.9
Q ss_pred cceeeeEEeeeEeCCEEEEEeeccC
Q psy9217 41 IEVAQGALLGLVVDNRLEITNCFPF 65 (90)
Q Consensus 41 ~~~v~G~LLG~~~~~~lEVTn~Fp~ 65 (90)
.....|.|.|+|.-..|-..||+-.
T Consensus 22 gr~~~G~L~~fD~~~NlvL~d~~E~ 46 (74)
T cd01728 22 GRKLIGILRSFDQFANLVLQDTVER 46 (74)
T ss_pred CeEEEEEEEEECCcccEEecceEEE
Confidence 3579999999999888888888644
No 41
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=23.83 E-value=1.2e+02 Score=18.23 Aligned_cols=25 Identities=12% Similarity=-0.049 Sum_probs=19.9
Q ss_pred cceeeeEEeeeEeCCEEEEEeeccC
Q psy9217 41 IEVAQGALLGLVVDNRLEITNCFPF 65 (90)
Q Consensus 41 ~~~v~G~LLG~~~~~~lEVTn~Fp~ 65 (90)
.....|+|.|+|.-=-|-.+||.-+
T Consensus 20 g~~~~G~L~~~D~~mNlvL~~~~~~ 44 (67)
T cd01726 20 GVDYRGILACLDGYMNIALEQTEEY 44 (67)
T ss_pred CCEEEEEEEEEccceeeEEeeEEEE
Confidence 4679999999998777777887543
No 42
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=23.43 E-value=83 Score=19.43 Aligned_cols=25 Identities=20% Similarity=0.216 Sum_probs=20.6
Q ss_pred ceeeeEEeeeEeCCEEEEEeeccCC
Q psy9217 42 EVAQGALLGLVVDNRLEITNCFPFP 66 (90)
Q Consensus 42 ~~v~G~LLG~~~~~~lEVTn~Fp~P 66 (90)
....|+|.|+|.-..|.+.+|+-..
T Consensus 20 r~~~G~L~~~D~~~NlvL~~~~E~~ 44 (74)
T cd01727 20 RVIVGTLKGFDQATNLILDDSHERV 44 (74)
T ss_pred cEEEEEEEEEccccCEEccceEEEE
Confidence 5689999999998888888886544
No 43
>PRK04290 30S ribosomal protein S6e; Validated
Probab=23.38 E-value=1.7e+02 Score=20.46 Aligned_cols=39 Identities=21% Similarity=0.332 Sum_probs=28.8
Q ss_pred CeeeEEEehhHHHHHHHHhhhcCCCCcceeeeEEeeeEeCCEEEEE
Q psy9217 15 PISYVQMDGLAVMKIVKHCHEESTNNIEVAQGALLGLVVDNRLEIT 60 (90)
Q Consensus 15 ~v~~V~id~lVllKIikH~~~~~~~~~~~v~G~LLG~~~~~~lEVT 60 (90)
....++|+.....+ .+-.+- .+++-|.+||+ .+=.|+||
T Consensus 15 ~~~~~ei~~~~~~~---f~gkri---G~evdg~~lG~-~Gy~l~It 53 (115)
T PRK04290 15 KAYQIEIDGAEANR---LIGKKI---GDEIDGSIVGL-DGYKLKIT 53 (115)
T ss_pred eEEEEEeCcHHHhh---hhcccc---ccEEccceeCC-CCeEEEEe
Confidence 45578888777665 445555 47899999998 56689998
No 44
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=22.23 E-value=1.4e+02 Score=17.91 Aligned_cols=25 Identities=12% Similarity=0.041 Sum_probs=20.7
Q ss_pred cceeeeEEeeeEeCCEEEEEeeccC
Q psy9217 41 IEVAQGALLGLVVDNRLEITNCFPF 65 (90)
Q Consensus 41 ~~~v~G~LLG~~~~~~lEVTn~Fp~ 65 (90)
.....|+|.|+|.---|...||.-.
T Consensus 20 g~~~~G~L~~~D~~mNlvL~~~~e~ 44 (68)
T cd01731 20 GKEVRGRLKSYDQHMNLVLEDAEEI 44 (68)
T ss_pred CCEEEEEEEEECCcceEEEeeEEEE
Confidence 3679999999999888888888644
No 45
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=20.50 E-value=1.4e+02 Score=18.01 Aligned_cols=23 Identities=17% Similarity=0.089 Sum_probs=18.9
Q ss_pred cceeeeEEeeeEeCCEEEEEeec
Q psy9217 41 IEVAQGALLGLVVDNRLEITNCF 63 (90)
Q Consensus 41 ~~~v~G~LLG~~~~~~lEVTn~F 63 (90)
.....|+|.|+|.-=.|-..||.
T Consensus 21 g~~~~G~L~~~D~~mNi~L~~~~ 43 (68)
T cd01722 21 GMEYKGTLVSVDSYMNLQLANTE 43 (68)
T ss_pred CcEEEEEEEEECCCEEEEEeeEE
Confidence 36799999999987777778874
Done!