Query 034084
Match_columns 104
No_of_seqs 110 out of 587
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 09:36:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034084.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034084hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd08057 MPN_euk_non_mb Mpr1p, 100.0 2.5E-28 5.5E-33 172.5 8.7 79 25-104 1-81 (157)
2 PLN03246 26S proteasome regula 100.0 3.2E-28 6.9E-33 188.7 9.5 86 19-104 2-92 (303)
3 KOG2975 Translation initiation 100.0 3.9E-29 8.5E-34 189.6 4.2 82 22-104 20-103 (288)
4 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.9 1E-27 2.2E-32 182.2 8.6 79 25-104 1-81 (265)
5 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.9 3.5E-27 7.5E-32 181.1 9.8 82 23-104 1-87 (280)
6 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.9 5.6E-27 1.2E-31 180.0 7.7 80 24-104 2-88 (288)
7 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 1.1E-25 2.3E-30 150.6 7.5 84 21-104 2-86 (114)
8 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.9 3.2E-25 6.9E-30 168.8 8.9 82 23-104 1-84 (266)
9 KOG1556 26S proteasome regulat 99.9 7.6E-25 1.6E-29 165.8 7.3 87 18-104 4-95 (309)
10 cd08069 MPN_RPN11_CSN5 Mov34/M 99.8 1E-20 2.2E-25 144.5 9.8 89 15-104 2-92 (268)
11 KOG3050 COP9 signalosome, subu 99.8 1.2E-19 2.5E-24 137.4 3.6 87 16-104 3-95 (299)
12 KOG1560 Translation initiation 99.8 7E-19 1.5E-23 135.2 6.9 88 17-104 7-103 (339)
13 smart00232 JAB_MPN JAB/MPN dom 99.7 2.9E-17 6.2E-22 111.0 8.7 81 24-104 1-81 (135)
14 KOG1554 COP9 signalosome, subu 99.7 9.8E-18 2.1E-22 129.2 5.9 98 7-104 37-136 (347)
15 cd08067 MPN_2A_DUB Mov34/MPN/P 99.4 5.8E-13 1.3E-17 97.4 8.8 81 19-104 2-84 (187)
16 cd07767 MPN Mpr1p, Pad1p N-ter 99.2 1.2E-10 2.7E-15 76.8 7.1 67 33-104 2-68 (116)
17 cd08058 MPN_euk_mb Mpr1p, Pad1 99.1 3.4E-10 7.4E-15 76.5 5.8 64 31-104 2-70 (119)
18 cd08068 MPN_BRCC36 Mov34/MPN/P 98.6 2.8E-07 6E-12 70.2 7.5 82 23-104 2-94 (244)
19 KOG1555 26S proteasome regulat 98.4 4.5E-07 9.7E-12 71.1 4.8 83 22-104 30-120 (316)
20 cd08070 MPN_like Mpr1p, Pad1p 97.7 0.00016 3.4E-09 49.2 6.9 71 31-104 3-75 (128)
21 cd08066 MPN_AMSH_like Mov34/MP 97.7 0.00036 7.8E-09 50.5 8.1 76 24-104 3-80 (173)
22 cd08060 MPN_UPF0172 Mov34/MPN/ 97.5 0.0002 4.3E-09 52.3 4.7 44 28-71 2-46 (182)
23 PF03665 UPF0172: Uncharacteri 97.4 0.00032 6.9E-09 51.8 4.7 49 24-72 3-53 (196)
24 KOG3289 Uncharacterized conser 96.9 0.0016 3.4E-08 48.0 4.1 48 24-71 3-52 (199)
25 COG1310 Predicted metal-depend 96.8 0.0032 6.8E-08 43.1 5.2 72 25-104 2-74 (134)
26 cd08072 MPN_archaeal Mov34/MPN 93.1 0.32 7E-06 32.7 5.3 39 31-73 5-43 (117)
27 PF14464 Prok-JAB: Prokaryotic 92.6 0.78 1.7E-05 29.3 6.4 37 31-67 4-40 (104)
28 TIGR02256 ICE_VC0181 integrati 92.2 0.96 2.1E-05 31.5 6.9 72 31-103 1-77 (131)
29 cd08073 MPN_NLPC_P60 Mpr1p, Pa 83.5 3.2 6.9E-05 27.5 4.7 50 32-86 3-54 (108)
30 cd08061 MPN_NPL4 Mov34/MPN/PAD 76.9 28 0.00061 27.0 8.6 85 18-104 6-98 (274)
31 PF07002 Copine: Copine; Inte 74.6 3.9 8.5E-05 28.7 3.1 41 31-73 19-59 (146)
32 cd08059 MPN_prok_mb Mpr1p, Pad 66.5 8.7 0.00019 24.5 3.2 37 32-71 3-39 (101)
33 KOG4445 Uncharacterized conser 53.0 25 0.00054 28.2 4.1 41 31-71 96-142 (368)
34 TIGR03735 PRTRC_A PRTRC system 49.7 28 0.0006 25.8 3.7 42 26-70 74-115 (192)
35 PF05021 NPL4: NPL4 family; I 47.3 33 0.00072 27.0 4.0 55 48-104 2-63 (306)
36 PF07620 SLEI_Leptospira: SLEI 44.2 18 0.00038 16.5 1.2 10 56-65 6-15 (16)
37 cd08056 MPN_PRP8 Mpr1p, Pad1p 43.3 57 0.0012 25.1 4.7 54 25-79 37-93 (252)
38 PF13824 zf-Mss51: Zinc-finger 41.6 32 0.00069 20.6 2.4 22 79-100 32-53 (55)
39 PF07581 Glug: The GLUG motif; 39.2 55 0.0012 16.6 2.9 22 46-68 3-24 (28)
40 PF14232 DUF4334: Domain of un 31.3 16 0.00035 22.1 0.0 23 33-55 26-48 (59)
41 KOG2550 IMP dehydrogenase/GMP 30.4 40 0.00087 28.3 2.2 23 81-103 275-297 (503)
42 KOG4832 Uncharacterized conser 30.3 24 0.00051 27.2 0.8 29 22-50 218-248 (253)
43 PF10922 DUF2745: Protein of u 27.3 1E+02 0.0022 20.0 3.2 35 56-94 49-83 (85)
44 cd01720 Sm_D2 The eukaryotic S 24.2 2E+02 0.0044 18.4 4.5 28 44-71 24-51 (87)
45 KOG3446 NADH:ubiquinone oxidor 24.2 64 0.0014 21.3 1.9 21 82-102 33-53 (97)
46 cd01727 LSm8 The eukaryotic Sm 21.8 1.3E+02 0.0028 18.3 2.9 27 44-70 19-45 (74)
47 cd01729 LSm7 The eukaryotic Sm 20.6 1.2E+02 0.0027 18.9 2.7 28 44-71 22-49 (81)
No 1
>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=99.95 E-value=2.5e-28 Score=172.53 Aligned_cols=79 Identities=35% Similarity=0.524 Sum_probs=73.8
Q ss_pred EEEeehHHHHHHHHHhhhC--CceeEEEEeeeEeCCEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhCCCCCcc
Q 034084 25 VQIEGLVMLKIIKHCKEFS--PALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVNVDNNTV 102 (104)
Q Consensus 25 V~vhplVll~I~dh~~r~~--~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~~~e~iV 102 (104)
|+|||+|||+|+|||+|+. +.+|+|+|||.+.+++++|+|||++|+.++++...+ +.+|+++|++++|+|+|++.+|
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~~~-d~~y~~~m~~~~~~v~~~~~vV 79 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFI-DTEYLEKRYNLHKKVYPQEKIV 79 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcchhh-hHHHHHHHHHHHHHhCCCCCEE
Confidence 6899999999999999998 799999999999999999999999999887766545 5999999999999999999999
Q ss_pred cC
Q 034084 103 GW 104 (104)
Q Consensus 103 GW 104 (104)
||
T Consensus 80 GW 81 (157)
T cd08057 80 GW 81 (157)
T ss_pred EE
Confidence 99
No 2
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.95 E-value=3.2e-28 Score=188.73 Aligned_cols=86 Identities=30% Similarity=0.538 Sum_probs=76.9
Q ss_pred CCCceeEEEeehHHHHHHHHHhhhCC---ceeEEEEeeeEeCCEEEEEEEeecccccCcch--hhcccHHHHHHHHHHHH
Q 034084 19 APPLRVVQIEGLVMLKIIKHCKEFSP---ALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEE--IEADGANYQLEMMRCLR 93 (104)
Q Consensus 19 ~~~~~~V~vhplVll~I~dh~~r~~~---~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~--~~~~~~~y~~~m~~~~k 93 (104)
+.|+.+|+|||+|||+|+|||+|+.+ .+|+|+|||.+.+++|||||||++|+.++++. ..+.|.+|+++|+++||
T Consensus 2 ~~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~k 81 (303)
T PLN03246 2 PRGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMFK 81 (303)
T ss_pred CCCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHHH
Confidence 46788899999999999999999874 68999999999999999999999999876553 12335999999999999
Q ss_pred hhCCCCCcccC
Q 034084 94 EVNVDNNTVGW 104 (104)
Q Consensus 94 ~v~~~e~iVGW 104 (104)
+|||++.+|||
T Consensus 82 ~V~~~~~vVGW 92 (303)
T PLN03246 82 RINAKEHVVGW 92 (303)
T ss_pred HhCCCCcEEee
Confidence 99999999999
No 3
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=3.9e-29 Score=189.64 Aligned_cols=82 Identities=30% Similarity=0.533 Sum_probs=78.5
Q ss_pred ceeEEEeehHHHHHHHHHhhhCC--ceeEEEEeeeEeCCEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhCCCC
Q 034084 22 LRVVQIEGLVMLKIIKHCKEFSP--ALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVNVDN 99 (104)
Q Consensus 22 ~~~V~vhplVll~I~dh~~r~~~--~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~~~e 99 (104)
-.+|.|||+|+++|+|+|.|++. .||||+|||+.++++|||||||++||+|++|++++| ++|+.+|+++++|+||+|
T Consensus 20 ~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevd-m~y~~~M~~l~~k~npnE 98 (288)
T KOG2975|consen 20 NLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVD-MEYAKNMYELHKKVNPNE 98 (288)
T ss_pred CceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceee-HHHHHHHHHHhcccCCCc
Confidence 34699999999999999999975 899999999999999999999999999999999997 999999999999999999
Q ss_pred CcccC
Q 034084 100 NTVGW 104 (104)
Q Consensus 100 ~iVGW 104 (104)
.+|||
T Consensus 99 ~vvGW 103 (288)
T KOG2975|consen 99 LVVGW 103 (288)
T ss_pred eeEEE
Confidence 99999
No 4
>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=99.95 E-value=1e-27 Score=182.22 Aligned_cols=79 Identities=29% Similarity=0.577 Sum_probs=73.9
Q ss_pred EEEeehHHHHHHHHHhhh--CCceeEEEEeeeEeCCEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhCCCCCcc
Q 034084 25 VQIEGLVMLKIIKHCKEF--SPALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVNVDNNTV 102 (104)
Q Consensus 25 V~vhplVll~I~dh~~r~--~~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~~~e~iV 102 (104)
|+|||+|+|+|+|||+|+ .+.+|+|+|||.+.++++||||||++|++++++++.+| .+|+++|+++||++||++.+|
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~d-~~y~~~m~~~~kkv~~~~~vV 79 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVD-MEYHRTMYELHQKVNPKEVIV 79 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEEc-HHHHHHHHHHHHHhCCCCcEE
Confidence 689999999999999996 45899999999999999999999999999887766665 999999999999999999999
Q ss_pred cC
Q 034084 103 GW 104 (104)
Q Consensus 103 GW 104 (104)
||
T Consensus 80 GW 81 (265)
T cd08064 80 GW 81 (265)
T ss_pred ee
Confidence 99
No 5
>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=99.94 E-value=3.5e-27 Score=181.11 Aligned_cols=82 Identities=32% Similarity=0.533 Sum_probs=74.4
Q ss_pred eeEEEeehHHHHHHHHHhhhC---CceeEEEEeeeEeCCEEEEEEEeecccccCcchh--hcccHHHHHHHHHHHHhhCC
Q 034084 23 RVVQIEGLVMLKIIKHCKEFS---PALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEI--EADGANYQLEMMRCLREVNV 97 (104)
Q Consensus 23 ~~V~vhplVll~I~dh~~r~~---~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~--~~~~~~y~~~m~~~~k~v~~ 97 (104)
++|+|||+|||+|+|||+|+. +.+|+|+|||.+.++++||||||++|+++++++. .+.|.+|+++|+++||+|||
T Consensus 1 ~~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~ 80 (280)
T cd08062 1 KKVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNA 80 (280)
T ss_pred CeEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCC
Confidence 369999999999999999975 4789999999999999999999999998877653 33459999999999999999
Q ss_pred CCCcccC
Q 034084 98 DNNTVGW 104 (104)
Q Consensus 98 ~e~iVGW 104 (104)
++.+|||
T Consensus 81 ~e~vVGW 87 (280)
T cd08062 81 KEKIVGW 87 (280)
T ss_pred CCCeEEE
Confidence 9999999
No 6
>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=99.94 E-value=5.6e-27 Score=180.02 Aligned_cols=80 Identities=30% Similarity=0.515 Sum_probs=73.3
Q ss_pred eEEEeehHHHHHHHHHhhhC------CceeEEEEeeeEeCCEEEEEEEeecccccCc-chhhcccHHHHHHHHHHHHhhC
Q 034084 24 VVQIEGLVMLKIIKHCKEFS------PALVTGQLLGLDVGSVLEVTNCFPFPIQEED-EEIEADGANYQLEMMRCLREVN 96 (104)
Q Consensus 24 ~V~vhplVll~I~dh~~r~~------~~~viG~LLG~~~~~~veVtnsF~vP~~~~~-~~~~~~~~~y~~~m~~~~k~v~ 96 (104)
+|+|||+|||+|+|||+|.. +.+|+|+|||.++|++|||||||++|+.+++ +...+| .+|+++|+++||+||
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id-~~y~~~m~~~~kkV~ 80 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLD-KEFLETRLEQFKQVF 80 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeC-HHHHHHHHHHHHHhc
Confidence 59999999999999999952 5899999999999999999999999998876 445554 999999999999999
Q ss_pred CCCCcccC
Q 034084 97 VDNNTVGW 104 (104)
Q Consensus 97 ~~e~iVGW 104 (104)
|++.+|||
T Consensus 81 ~~~~vVGW 88 (288)
T cd08063 81 KDLDFVGW 88 (288)
T ss_pred cCCceEEE
Confidence 99999999
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=99.93 E-value=1.1e-25 Score=150.65 Aligned_cols=84 Identities=40% Similarity=0.715 Sum_probs=77.4
Q ss_pred CceeEEEeehHHHHHHHHHhhhCCceeEEEEeeeEeCC-EEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhCCCC
Q 034084 21 PLRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGS-VLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVNVDN 99 (104)
Q Consensus 21 ~~~~V~vhplVll~I~dh~~r~~~~~viG~LLG~~~~~-~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~~~e 99 (104)
++++|+|||+|+++|+||+.|+.+.+|+|+|||..+++ .++|+|||++|+.+++++....+.++.++|++++++++|++
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSSPNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPNL 81 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHHCTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTTS
T ss_pred CcEEEEECHHHHHHHHHHHhcCCCCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhccccccc
Confidence 57899999999999999999999999999999999999 99999999999998777655555677799999999999999
Q ss_pred CcccC
Q 034084 100 NTVGW 104 (104)
Q Consensus 100 ~iVGW 104 (104)
.+|||
T Consensus 82 ~iVGW 86 (114)
T PF01398_consen 82 EIVGW 86 (114)
T ss_dssp EEEEE
T ss_pred eEEEE
Confidence 99999
No 8
>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=99.92 E-value=3.2e-25 Score=168.79 Aligned_cols=82 Identities=73% Similarity=1.161 Sum_probs=75.7
Q ss_pred eeEEEeehHHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccCcch--hhcccHHHHHHHHHHHHhhCCCCC
Q 034084 23 RVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEE--IEADGANYQLEMMRCLREVNVDNN 100 (104)
Q Consensus 23 ~~V~vhplVll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~--~~~~~~~y~~~m~~~~k~v~~~e~ 100 (104)
++|+|||+|+++|+|||.|+.|.+|+|+|||...++++|||||||+|+.+++++ ...++.+|+.+|+++++++|+++.
T Consensus 1 ~~V~I~~~vllkIv~H~~~~~p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e~ 80 (266)
T cd08065 1 TSVQIDGLVVLKIIKHCKEELPELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDHN 80 (266)
T ss_pred CEEEEeHHHHHHHHHHHhcCCCcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCCc
Confidence 369999999999999999999999999999999999999999999999887665 344457999999999999999999
Q ss_pred cccC
Q 034084 101 TVGW 104 (104)
Q Consensus 101 iVGW 104 (104)
+|||
T Consensus 81 iVGW 84 (266)
T cd08065 81 HVGW 84 (266)
T ss_pred EEEe
Confidence 9999
No 9
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=7.6e-25 Score=165.75 Aligned_cols=87 Identities=31% Similarity=0.514 Sum_probs=80.3
Q ss_pred CCCCceeEEEeehHHHHHHHHHhhhCC---ceeEEEEeeeEeCCEEEEEEEeecccccCcc--hhhcccHHHHHHHHHHH
Q 034084 18 VAPPLRVVQIEGLVMLKIIKHCKEFSP---ALVTGQLLGLDVGSVLEVTNCFPFPIQEEDE--EIEADGANYQLEMMRCL 92 (104)
Q Consensus 18 ~~~~~~~V~vhplVll~I~dh~~r~~~---~~viG~LLG~~~~~~veVtnsF~vP~~~~~~--~~~~~~~~y~~~m~~~~ 92 (104)
+..++++|.|||||||+++|||.|... +||.|.|||..+++++.|||||++|++|+++ .++|.|++|++.|+.||
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 345678999999999999999999865 8999999999999999999999999999876 46777899999999999
Q ss_pred HhhCCCCCcccC
Q 034084 93 REVNVDNNTVGW 104 (104)
Q Consensus 93 k~v~~~e~iVGW 104 (104)
+++|.+|.+|||
T Consensus 84 kKvNakekivGW 95 (309)
T KOG1556|consen 84 KKVNAKEKVVGW 95 (309)
T ss_pred HHhcchhheeee
Confidence 999999999999
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=99.84 E-value=1e-20 Score=144.52 Aligned_cols=89 Identities=26% Similarity=0.456 Sum_probs=82.9
Q ss_pred cccCCCCceeEEEeehHHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccCcchhhcccHHHHHHHHH--HH
Q 034084 15 AEEVAPPLRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMR--CL 92 (104)
Q Consensus 15 ~~~~~~~~~~V~vhplVll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~--~~ 92 (104)
|...+..+++|+|+|+|+++|++||.+..|.+|+|+|||..++++++|+|||++|+.+++++++.+ .+|++.|++ ++
T Consensus 2 ~~~~~~~~~~V~Is~~allkil~Ha~~~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~-~e~~~~m~~~~~~ 80 (268)
T cd08069 2 WKPDPDYFEKVYISSLALLKMLKHARAGGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQ-DEFQEYMVQYEML 80 (268)
T ss_pred CCCCCCcccEEEECHHHHHHHHHHHhccCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceecc-HHHHHHHHHHHHH
Confidence 556677899999999999999999999999999999999999999999999999998888777776 599999999 99
Q ss_pred HhhCCCCCcccC
Q 034084 93 REVNVDNNTVGW 104 (104)
Q Consensus 93 k~v~~~e~iVGW 104 (104)
+++++++.+|||
T Consensus 81 ~~~~~~~~vVGW 92 (268)
T cd08069 81 KQTGRPENVVGW 92 (268)
T ss_pred HHhCCCceeEee
Confidence 999999999999
No 11
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.77 E-value=1.2e-19 Score=137.38 Aligned_cols=87 Identities=24% Similarity=0.444 Sum_probs=75.0
Q ss_pred ccCCCCceeEEEeehHHHHHHHHHhhhC-----C-ceeEEEEeeeEeCCEEEEEEEeecccccCcchhhcccHHHHHHHH
Q 034084 16 EEVAPPLRVVQIEGLVMLKIIKHCKEFS-----P-ALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIEADGANYQLEMM 89 (104)
Q Consensus 16 ~~~~~~~~~V~vhplVll~I~dh~~r~~-----~-~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~ 89 (104)
++.+..+ +|.+||||+++|+|||+|.. | .+|.|+|+|.+.|+.|||.|||.+.....++...++ .+|..+.-
T Consensus 3 ps~S~s~-tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~~~~d-ke~l~kk~ 80 (299)
T KOG3050|consen 3 PSSSGSV-TVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDTETID-KEYLEKKE 80 (299)
T ss_pred CCCCCce-eEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecchhhhhhcc-HHHHHHHH
Confidence 3344444 59999999999999999963 3 589999999999999999999999977655544464 99999999
Q ss_pred HHHHhhCCCCCcccC
Q 034084 90 RCLREVNVDNNTVGW 104 (104)
Q Consensus 90 ~~~k~v~~~e~iVGW 104 (104)
++||+|+|+..++||
T Consensus 81 eqykqVFpdl~vlGw 95 (299)
T KOG3050|consen 81 EQYKQVFPDLYVLGW 95 (299)
T ss_pred HHHHHhcccceEEEE
Confidence 999999999999999
No 12
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.77 E-value=7e-19 Score=135.19 Aligned_cols=88 Identities=50% Similarity=0.879 Sum_probs=75.6
Q ss_pred cCCCCceeEEEeehHHHHHHHHHhhhCC--ceeEEEEeeeEeCCEEEEEEEeeccccc--Ccchhh---ccc--HHHHHH
Q 034084 17 EVAPPLRVVQIEGLVMLKIIKHCKEFSP--ALVTGQLLGLDVGSVLEVTNCFPFPIQE--EDEEIE---ADG--ANYQLE 87 (104)
Q Consensus 17 ~~~~~~~~V~vhplVll~I~dh~~r~~~--~~viG~LLG~~~~~~veVtnsF~vP~~~--~~~~~~---~~~--~~y~~~ 87 (104)
..++|++.|.++.||++||+|||.+..+ .-+.|+|+|.+.++.+|||||||.|... +++.++ .+- ..|+..
T Consensus 7 ~~~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~ 86 (339)
T KOG1560|consen 7 LESPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLA 86 (339)
T ss_pred CCCCccceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHH
Confidence 4678899999999999999999999876 5799999999999999999999999743 222222 221 489999
Q ss_pred HHHHHHhhCCCCCcccC
Q 034084 88 MMRCLREVNVDNNTVGW 104 (104)
Q Consensus 88 m~~~~k~v~~~e~iVGW 104 (104)
|++.++.+|.++.+|||
T Consensus 87 mlrrlr~vnid~~hVGw 103 (339)
T KOG1560|consen 87 MLRRLRYVNIDHLHVGW 103 (339)
T ss_pred HHHHhhhcCccceeeee
Confidence 99999999999999999
No 13
>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=99.72 E-value=2.9e-17 Score=110.98 Aligned_cols=81 Identities=33% Similarity=0.498 Sum_probs=72.9
Q ss_pred eEEEeehHHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhCCCCCccc
Q 034084 24 VVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVNVDNNTVG 103 (104)
Q Consensus 24 ~V~vhplVll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~~~e~iVG 103 (104)
.|+|+|+++++|++|+.|..+.+++|+|+|...++.++|+++|++|...+.+.....+.+|++.|.++++++++++.+||
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vG 80 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDGPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEIVG 80 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCCCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceEEE
Confidence 37899999999999999999999999999999999999999999998765544423358999999999999999999999
Q ss_pred C
Q 034084 104 W 104 (104)
Q Consensus 104 W 104 (104)
|
T Consensus 81 w 81 (135)
T smart00232 81 W 81 (135)
T ss_pred E
Confidence 9
No 14
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.71 E-value=9.8e-18 Score=129.19 Aligned_cols=98 Identities=20% Similarity=0.395 Sum_probs=88.9
Q ss_pred hhhhhhhhcccCCCCceeEEEeehHHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccCcchhhc--ccHHH
Q 034084 7 RSFLQVAAAEEVAPPLRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIEA--DGANY 84 (104)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~V~vhplVll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~~~--~~~~y 84 (104)
|....+-+|...+..++.|+|+.|++|||..|+.|+.+-.|||.|+|..+|+++.|.+||++|.+++|.++++ ++.+|
T Consensus 37 ~~~~~~kpw~~Dp~~fk~vkISalAllKm~~hA~~GgnlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEY 116 (347)
T KOG1554|consen 37 RKIILEKPWSTDPHYFKHVKISALALLKMVMHARSGGNLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEY 116 (347)
T ss_pred HHHHhcCcccCCCchhhhhhhHHHHHHHHHHHHhcCCCeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHH
Confidence 4444555677777779999999999999999999999999999999999999999999999999999988774 46899
Q ss_pred HHHHHHHHHhhCCCCCcccC
Q 034084 85 QLEMMRCLREVNVDNNTVGW 104 (104)
Q Consensus 85 ~~~m~~~~k~v~~~e~iVGW 104 (104)
+....+..|.+++.|++|||
T Consensus 117 mv~Y~e~~k~~gr~envVGW 136 (347)
T KOG1554|consen 117 MVQYIEEAKNVGRLENVVGW 136 (347)
T ss_pred HHHHHHHHHHhhhhhceeee
Confidence 99999999999999999999
No 15
>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=99.44 E-value=5.8e-13 Score=97.39 Aligned_cols=81 Identities=23% Similarity=0.329 Sum_probs=70.4
Q ss_pred CCCceeEEEeehHHHHHHHHHhhhCCceeEEEEeeeEe--CCEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhC
Q 034084 19 APPLRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDV--GSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVN 96 (104)
Q Consensus 19 ~~~~~~V~vhplVll~I~dh~~r~~~~~viG~LLG~~~--~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~ 96 (104)
..|++ |+|+++|+|+|++||.... ..++|.|+|..+ ++.++|+++|++|...+.++..++ .+++.+|++.+++.+
T Consensus 2 ~~pf~-V~Is~~all~m~~Ha~~~~-~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~d-p~~q~e~~~~l~~~g 78 (187)
T cd08067 2 IQPFK-VTVSSNALLLMDFHCHLTT-SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMD-PVSETEIRESLESRG 78 (187)
T ss_pred CCCEE-EEECHHHHHHHHHHhcCCC-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccC-HHHHHHHHHHHHHcC
Confidence 46786 9999999999999999877 999999999964 579999999999987665566665 899999999999877
Q ss_pred CCCCcccC
Q 034084 97 VDNNTVGW 104 (104)
Q Consensus 97 ~~e~iVGW 104 (104)
..+|||
T Consensus 79 --l~vVGw 84 (187)
T cd08067 79 --LSVVGW 84 (187)
T ss_pred --CEEEEE
Confidence 599999
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=99.17 E-value=1.2e-10 Score=76.81 Aligned_cols=67 Identities=24% Similarity=0.385 Sum_probs=54.2
Q ss_pred HHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhCCCCCcccC
Q 034084 33 LKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVNVDNNTVGW 104 (104)
Q Consensus 33 l~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~~~e~iVGW 104 (104)
.+|++|+.+..+.++.|.|+|...++.++|+++|++|...++... ..++ -|....+....++.+|||
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~----~~~~-~~~~~~~~~~~~~~iVGw 68 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDD----NVWF-LMYLDFKKLNAGLRIVGW 68 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcCCEEEEEEEEecccCCCCCcc----HHHH-HHHHHHHHhcCCCeEEEE
Confidence 478999999889999999999998899999999999986654322 1122 266777788899999999
No 17
>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=99.07 E-value=3.4e-10 Score=76.50 Aligned_cols=64 Identities=19% Similarity=0.122 Sum_probs=52.7
Q ss_pred HHHHHHHHHhhhCCceeEEEEeeeEe-----CCEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhCCCCCcccC
Q 034084 31 VMLKIIKHCKEFSPALVTGQLLGLDV-----GSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVNVDNNTVGW 104 (104)
Q Consensus 31 Vll~I~dh~~r~~~~~viG~LLG~~~-----~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~~~e~iVGW 104 (104)
|+++|++||.+..|..+.|.|+|... ...++|+++|+.|...+. .+.|..+.+..+.++++|||
T Consensus 2 ~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~----------~~~~~~~~~~~~~g~~~vG~ 70 (119)
T cd08058 2 ALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTG----------ENVEELFNVQTGRPLLVVGW 70 (119)
T ss_pred HHHHHHHHhcCCCCeEEEEEeeeEEecCccceeEEEEeecCCCCCCchh----------HHHHHHHHHHhCCCCeEEEE
Confidence 78999999999999999999999865 457899999999864321 22556667778999999999
No 18
>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=98.56 E-value=2.8e-07 Score=70.16 Aligned_cols=82 Identities=18% Similarity=0.262 Sum_probs=62.4
Q ss_pred eeEEEeehHHHHHHHHHhhhCCceeEEEEeeeEe-------CCEEEEEEEeeccccc-CcchhhcccHHH---HHHHHHH
Q 034084 23 RVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDV-------GSVLEVTNCFPFPIQE-EDEEIEADGANY---QLEMMRC 91 (104)
Q Consensus 23 ~~V~vhplVll~I~dh~~r~~~~~viG~LLG~~~-------~~~veVtnsF~vP~~~-~~~~~~~~~~~y---~~~m~~~ 91 (104)
++|+|.+.++.+|+.|+.+..|..++|.|+|..+ ...+.|+..++.+..+ ..+.+.++..++ ++.+-++
T Consensus 2 ~~V~Is~~~l~~il~HA~~~~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~~~ 81 (244)
T cd08068 2 SKVHLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAERL 81 (244)
T ss_pred cEEEECHHHHHHHHHHHHhCCCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999999874 3455565555554332 334555654433 4566677
Q ss_pred HHhhCCCCCcccC
Q 034084 92 LREVNVDNNTVGW 104 (104)
Q Consensus 92 ~k~v~~~e~iVGW 104 (104)
.+..+.++.+|||
T Consensus 82 ~~~~~rgl~vVGw 94 (244)
T cd08068 82 TEETGRPMRVVGW 94 (244)
T ss_pred HhhccCCceEEEE
Confidence 8888999999999
No 19
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=98.39 E-value=4.5e-07 Score=71.13 Aligned_cols=83 Identities=29% Similarity=0.450 Sum_probs=72.0
Q ss_pred ceeEEEeehHHHHHHHHHhhhCCce-eEEEE-ee---e-EeCCEEEEEEEeecccccCcch--hhcccHHHHHHHHHHHH
Q 034084 22 LRVVQIEGLVMLKIIKHCKEFSPAL-VTGQL-LG---L-DVGSVLEVTNCFPFPIQEEDEE--IEADGANYQLEMMRCLR 93 (104)
Q Consensus 22 ~~~V~vhplVll~I~dh~~r~~~~~-viG~L-LG---~-~~~~~veVtnsF~vP~~~~~~~--~~~~~~~y~~~m~~~~k 93 (104)
-.+|.|+.++++++++|-+-..+.. ++|.+ +| . .+..++.|.+.|+.|....+-. +...|..|+.+|+++++
T Consensus 30 ~e~v~i~slall~m~rh~r~~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~d~V~q~q~~~~l~ 109 (316)
T KOG1555|consen 30 KETVYISSLALLKMLRHDRAGSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQMMDLLK 109 (316)
T ss_pred cceeeeehhhhhhcccccccCCchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHHHHHHH
Confidence 3479999999999999998888865 99999 99 3 5677999999999998876544 44446999999999999
Q ss_pred hhCCCCCcccC
Q 034084 94 EVNVDNNTVGW 104 (104)
Q Consensus 94 ~v~~~e~iVGW 104 (104)
..+..+.+|||
T Consensus 110 ~tGrp~~VVGW 120 (316)
T KOG1555|consen 110 QTGRPELVVGW 120 (316)
T ss_pred hcCCcceEEee
Confidence 99999999999
No 20
>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=97.74 E-value=0.00016 Score=49.18 Aligned_cols=71 Identities=30% Similarity=0.340 Sum_probs=52.5
Q ss_pred HHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccCcc--hhhcccHHHHHHHHHHHHhhCCCCCcccC
Q 034084 31 VMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEEDE--EIEADGANYQLEMMRCLREVNVDNNTVGW 104 (104)
Q Consensus 31 Vll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~--~~~~~~~~y~~~m~~~~k~v~~~e~iVGW 104 (104)
++-+|++|+++..|..+.|.|+|..++....|+..|++|....+. ...++ .+.+.++.+..++. +..+|||
T Consensus 3 ~~~~il~ha~~~~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d-~~~~~~~~~~~~~~--g~~~vG~ 75 (128)
T cd08070 3 LLEAILAHAEAEYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEID-PAEQLAAQREARER--GLEVVGI 75 (128)
T ss_pred HHHHHHHHHHhCCCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEEC-HHHHHHHHHHHHHC--CCeEEEE
Confidence 567899999999999999999999877766789999999654432 33454 55555555666544 4777776
No 21
>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=97.66 E-value=0.00036 Score=50.47 Aligned_cols=76 Identities=16% Similarity=0.156 Sum_probs=55.3
Q ss_pred eEEEeehHHHHHHHHHhhhC--CceeEEEEeeeEeCCEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhCCCCCc
Q 034084 24 VVQIEGLVMLKIIKHCKEFS--PALVTGQLLGLDVGSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVNVDNNT 101 (104)
Q Consensus 24 ~V~vhplVll~I~dh~~r~~--~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~~~e~i 101 (104)
.+.|..-.+-+|+.|+.++. |.++.|.|+|...++..+|++.|..|...++..++..+. .++++..+ ..+..+
T Consensus 3 ~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~~---~e~~~~~~--~~gle~ 77 (173)
T cd08066 3 QVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTNE---EELFDFQD--QHDLIT 77 (173)
T ss_pred EEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCCH---HHHHHHHH--hCCCee
Confidence 46667778889999999985 589999999998888899999988887766555443322 12333222 356889
Q ss_pred ccC
Q 034084 102 VGW 104 (104)
Q Consensus 102 VGW 104 (104)
|||
T Consensus 78 vGw 80 (173)
T cd08066 78 LGW 80 (173)
T ss_pred EEE
Confidence 998
No 22
>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=97.48 E-value=0.0002 Score=52.26 Aligned_cols=44 Identities=27% Similarity=0.506 Sum_probs=39.1
Q ss_pred eehHHHHHHHHHhhhCCceeEEEEeeeEe-CCEEEEEEEeecccc
Q 034084 28 EGLVMLKIIKHCKEFSPALVTGQLLGLDV-GSVLEVTNCFPFPIQ 71 (104)
Q Consensus 28 hplVll~I~dh~~r~~~~~viG~LLG~~~-~~~veVtnsF~vP~~ 71 (104)
.+.+..+|+.|+.+..+..|.|.|+|... ++.+.|++++|+.+.
T Consensus 2 s~~ay~ki~~HA~k~p~~evcGlLlG~~~~~~~~~V~d~vPl~h~ 46 (182)
T cd08060 2 STLAYVKMLLHAAKYPHCAVNGLLLGKKSSGGSVEITDAVPLFHS 46 (182)
T ss_pred CHHHHHHHHHHHHHcCCchheEEEEeeecCCCCEEEEEEEEcCCC
Confidence 45678999999999777899999999987 778999999999985
No 23
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.37 E-value=0.00032 Score=51.77 Aligned_cols=49 Identities=27% Similarity=0.381 Sum_probs=43.8
Q ss_pred eEEEeehHHHHHHHHHhhhCCceeEEEEeeeEeCC--EEEEEEEeeccccc
Q 034084 24 VVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGS--VLEVTNCFPFPIQE 72 (104)
Q Consensus 24 ~V~vhplVll~I~dh~~r~~~~~viG~LLG~~~~~--~veVtnsF~vP~~~ 72 (104)
+|++++.+..||+=|+.+-....|.|.|||...++ .|+|++|.|+=|..
T Consensus 3 ~v~is~~AY~K~~LHaaKyP~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~ 53 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYPHCAVNGVLLGKSSKSSSEVEIVDAVPLFHHW 53 (196)
T ss_pred eEEEcHHHHHHHHHHhccCCCCceeeEEEeccCCCCceEEEeeceeccccc
Confidence 68999999999999999998899999999997544 39999999998853
No 24
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=96.86 E-value=0.0016 Score=47.98 Aligned_cols=48 Identities=33% Similarity=0.584 Sum_probs=43.6
Q ss_pred eEEEeehHHHHHHHHHhhhCCceeEEEEee--eEeCCEEEEEEEeecccc
Q 034084 24 VVQIEGLVMLKIIKHCKEFSPALVTGQLLG--LDVGSVLEVTNCFPFPIQ 71 (104)
Q Consensus 24 ~V~vhplVll~I~dh~~r~~~~~viG~LLG--~~~~~~veVtnsF~vP~~ 71 (104)
.|+|+.++..||+=|+.|-...-|.|.|+| .-.|+.+|||+|.|+=|+
T Consensus 3 ~veis~~aY~kmiLH~akyph~aVnGLLla~~~~kg~~v~itdcVPLfH~ 52 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPHAAVNGLLLAPATGKGECVEITDCVPLFHS 52 (199)
T ss_pred ceeehhhHHHHHHHHhccCcccceeeEEEeccCCCCCeEEEEecchhhcc
Confidence 488999999999999999888999999999 457889999999999775
No 25
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=96.83 E-value=0.0032 Score=43.11 Aligned_cols=72 Identities=25% Similarity=0.394 Sum_probs=46.4
Q ss_pred EEEeehHHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccCcc-hhhcccHHHHHHHHHHHHhhCCCCCccc
Q 034084 25 VQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEEDE-EIEADGANYQLEMMRCLREVNVDNNTVG 103 (104)
Q Consensus 25 V~vhplVll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~~~-~~~~~~~~y~~~m~~~~k~v~~~e~iVG 103 (104)
+.|...++-.|+.|+.|..|.++.|.|+|...+ ...|+++....+- .....+.++.. ++...++.+ +.+||
T Consensus 2 ~~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~~g--~~vvg 73 (134)
T COG1310 2 LVIPKEVLGAILEHARREHPREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEIDPEYSL-FYLAAEDAG--EVVVG 73 (134)
T ss_pred ceecHHHHHHHHHHHHhcCChheEEEEEeeccc-----ceeeccccccCCcceeEeeCHHHHH-HHHHHhhCC--CEEEE
Confidence 456677889999999999999999999999876 4445544332221 11122244444 344334333 89999
Q ss_pred C
Q 034084 104 W 104 (104)
Q Consensus 104 W 104 (104)
|
T Consensus 74 ~ 74 (134)
T COG1310 74 W 74 (134)
T ss_pred E
Confidence 8
No 26
>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=93.08 E-value=0.32 Score=32.73 Aligned_cols=39 Identities=23% Similarity=0.275 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccC
Q 034084 31 VMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE 73 (104)
Q Consensus 31 Vll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~ 73 (104)
.+-.|++|+++..|..+-|.|+|... .|++.+++|....
T Consensus 5 ~~~~i~~ha~~~~P~E~CGlL~G~~~----~v~~~~~~~n~~~ 43 (117)
T cd08072 5 LLDSILEAAKSSHPNEFAALLRGKDG----VITELLILPGTES 43 (117)
T ss_pred HHHHHHHHHhhcCCceEEEEEEeecc----EEEEEEECCCCCC
Confidence 45579999999999999999999764 6899999995543
No 27
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=92.55 E-value=0.78 Score=29.26 Aligned_cols=37 Identities=27% Similarity=0.301 Sum_probs=31.3
Q ss_pred HHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEee
Q 034084 31 VMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFP 67 (104)
Q Consensus 31 Vll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~ 67 (104)
++-.|+.|+.+..+.++-|.|+|...+..+.++....
T Consensus 4 ~~~~i~~~~~~~~p~E~~G~L~g~~~~~~~~~~~~~~ 40 (104)
T PF14464_consen 4 VLEQIIAHARAAYPNEACGLLLGRRDDQRFIVVPNVN 40 (104)
T ss_dssp HHHHHHHHHHHHTTS-EEEEEEEEEECCEEEEEEEEE
T ss_pred HHHHHHHHHhhCCCCeEEEEEEEEecCCEEEEEeCCC
Confidence 5668999999999999999999999878888887776
No 28
>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=92.25 E-value=0.96 Score=31.49 Aligned_cols=72 Identities=14% Similarity=0.164 Sum_probs=41.3
Q ss_pred HHHHHHHHHhhhC--CceeEEEEeeeEeCCEEEEEEEeecccccCc-chhhcc-cHHHHH-HHHHHHHhhCCCCCccc
Q 034084 31 VMLKIIKHCKEFS--PALVTGQLLGLDVGSVLEVTNCFPFPIQEED-EEIEAD-GANYQL-EMMRCLREVNVDNNTVG 103 (104)
Q Consensus 31 Vll~I~dh~~r~~--~~~viG~LLG~~~~~~veVtnsF~vP~~~~~-~~~~~~-~~~y~~-~m~~~~k~v~~~e~iVG 103 (104)
++++++..|.... +.+.=|.|+|...+..+.|+++- .|..++- ....+. +..+++ ..-+.+++.+-....||
T Consensus 1 ~v~~~~~~~~Q~~~~~~EtGGiLiG~~~~~~~ii~~~t-~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylG 77 (131)
T TIGR02256 1 VVVAMLKSYRQWHDLSTETGGVLIGERRGAHAVITKIS-EPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLG 77 (131)
T ss_pred CHHHHHHHHHhCcCCCCccceEEEEEEcCCcEEEEEEE-cCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEE
Confidence 3566777776554 47899999999888888888844 4443321 122222 244444 44444555443344444
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=83.48 E-value=3.2 Score=27.54 Aligned_cols=50 Identities=20% Similarity=0.220 Sum_probs=32.2
Q ss_pred HHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccCc--chhhcccHHHHH
Q 034084 32 MLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEED--EEIEADGANYQL 86 (104)
Q Consensus 32 ll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~~--~~~~~~~~~y~~ 86 (104)
+-.|++|+++..|...-|.|+|.. .++..|+++....+ ....++..+|.+
T Consensus 3 ~~~i~~ha~~~~P~E~CGll~g~~-----~~~~~~p~~N~~~~p~~~F~idp~e~~~ 54 (108)
T cd08073 3 EDAILAHAKAEYPREACGLVVRKG-----RKLRYIPCRNIAADPEEHFEISPEDYAA 54 (108)
T ss_pred HHHHHHHHhHCCCCcceEEEEecC-----CceEEEECccCCCCccceEEeCHHHHHH
Confidence 447899999999999999999965 23445666522211 234455455544
No 30
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. 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=76.85 E-value=28 Score=26.98 Aligned_cols=85 Identities=12% Similarity=0.081 Sum_probs=51.3
Q ss_pred CCCCceeEEEeehHHHHHHHH-HhhhCCceeEEEEeeeEeC-------CEEEEEEEeecccccCcchhhcccHHHHHHHH
Q 034084 18 VAPPLRVVQIEGLVMLKIIKH-CKEFSPALVTGQLLGLDVG-------SVLEVTNCFPFPIQEEDEEIEADGANYQLEMM 89 (104)
Q Consensus 18 ~~~~~~~V~vhplVll~I~dh-~~r~~~~~viG~LLG~~~~-------~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~ 89 (104)
..+.+..|...-..+..=.-. +.|.....-+|.|.|+.+. ..+.|.--|.=|...+.+.+.+......++ .
T Consensus 6 ~~r~Vd~vef~~~~~~~~f~~~~w~~~~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~-v 84 (274)
T cd08061 6 KYRHVDHVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADT-V 84 (274)
T ss_pred cCCCcCEEEEecHHHHHHHHHHHHHhhcceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhH-H
Confidence 334456677776666654445 5666667888999999653 478888888877766655555432222222 2
Q ss_pred HHHHhhCCCCCcccC
Q 034084 90 RCLREVNVDNNTVGW 104 (104)
Q Consensus 90 ~~~k~v~~~e~iVGW 104 (104)
+... .......|||
T Consensus 85 d~iA-~~lGL~~VG~ 98 (274)
T cd08061 85 DAIA-AALGLERVGW 98 (274)
T ss_pred HHHH-HHcCCeEEEE
Confidence 2222 2345667777
No 31
>PF07002 Copine: Copine; InterPro: IPR010734 This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca2+-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [].
Probab=74.59 E-value=3.9 Score=28.71 Aligned_cols=41 Identities=17% Similarity=0.327 Sum_probs=25.8
Q ss_pred HHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccccC
Q 034084 31 VMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQEE 73 (104)
Q Consensus 31 Vll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~~~ 73 (104)
.+-+|+.+|.+...-.+.| +|-.....-.+++||++-.+.+
T Consensus 19 ~vg~il~~Yd~dk~~p~~G--FGa~~~~~~~vsh~F~ln~~~~ 59 (146)
T PF07002_consen 19 AVGEILQDYDSDKMIPAYG--FGAKIPPDYSVSHCFPLNGNPQ 59 (146)
T ss_pred HHHHHHHhhccCCccceec--cCCcCCCCcccccceeeecCCC
Confidence 4556777776665556666 3443333456899999976543
No 32
>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=66.54 E-value=8.7 Score=24.47 Aligned_cols=37 Identities=22% Similarity=0.305 Sum_probs=28.3
Q ss_pred HHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeecccc
Q 034084 32 MLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPIQ 71 (104)
Q Consensus 32 ll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~~ 71 (104)
+-.|.+|+....|....|.|+|...+ .+.+...+|..
T Consensus 3 ~~~i~~~~~~~~p~E~~gll~~~~~~---~~~~~~~~~~~ 39 (101)
T cd08059 3 LKTILVHAKDAHPDEFCGFLSGSKDN---VMDELIFLPFV 39 (101)
T ss_pred HHHHHHHHHhcCChhhheeeecCCCC---eEEEEEeCCCc
Confidence 34577888888899999999997543 67788888743
No 33
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=53.01 E-value=25 Score=28.25 Aligned_cols=41 Identities=24% Similarity=0.442 Sum_probs=33.6
Q ss_pred HHHHHHHHHhhhC------CceeEEEEeeeEeCCEEEEEEEeecccc
Q 034084 31 VMLKIIKHCKEFS------PALVTGQLLGLDVGSVLEVTNCFPFPIQ 71 (104)
Q Consensus 31 Vll~I~dh~~r~~------~~~viG~LLG~~~~~~veVtnsF~vP~~ 71 (104)
+|..|+.|+.+.. .....=+|.|+.++..+.+|-||-.=|.
T Consensus 96 ii~~lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~ 142 (368)
T KOG4445|consen 96 IICQLIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHF 142 (368)
T ss_pred hhHHHHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHH
Confidence 5789999998863 2567779999999999999999987653
No 34
>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=49.74 E-value=28 Score=25.81 Aligned_cols=42 Identities=10% Similarity=0.045 Sum_probs=31.8
Q ss_pred EEeehHHHHHHHHHhhhCCceeEEEEeeeEeCCEEEEEEEeeccc
Q 034084 26 QIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPI 70 (104)
Q Consensus 26 ~vhplVll~I~dh~~r~~~~~viG~LLG~~~~~~veVtnsF~vP~ 70 (104)
+|-.-.+=+|+.|+++..|.++-|.|.|...++.. ..+++..
T Consensus 74 ~Ip~~l~~~ii~hAr~~~P~EacG~Iag~~~~~~~---r~~p~~N 115 (192)
T TIGR03735 74 PIPASLLEEFAEAARAALPNEVAAWIVWNSETGSL---RLAALES 115 (192)
T ss_pred CCCHHHHHHHHHHHHhcCCcceEEEEEEcCCCCEE---EEEeccc
Confidence 55566778999999999999999999997544443 3366653
No 35
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=47.28 E-value=33 Score=27.03 Aligned_cols=55 Identities=16% Similarity=0.148 Sum_probs=32.3
Q ss_pred EEEEeeeEeC-------CEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHhhCCCCCcccC
Q 034084 48 TGQLLGLDVG-------SVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLREVNVDNNTVGW 104 (104)
Q Consensus 48 iG~LLG~~~~-------~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~v~~~e~iVGW 104 (104)
+|.|.|.++. -.+.|.--|.=|...+.+.+.+.+.+..+..-+.-+. -....|||
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~--lGL~rVG~ 63 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASA--LGLERVGW 63 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHH--CCCEEEEE
Confidence 6999999642 2688888888887766666555322222222222221 25566776
No 36
>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=44.22 E-value=18 Score=16.48 Aligned_cols=10 Identities=30% Similarity=0.388 Sum_probs=8.0
Q ss_pred eCCEEEEEEE
Q 034084 56 VGSVLEVTNC 65 (104)
Q Consensus 56 ~~~~veVtns 65 (104)
.++++||+|+
T Consensus 6 rdNsLeIsn~ 15 (16)
T PF07620_consen 6 RDNSLEISNQ 15 (16)
T ss_pred cCCeEEEeec
Confidence 4788999886
No 37
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t
Probab=43.28 E-value=57 Score=25.12 Aligned_cols=54 Identities=17% Similarity=0.168 Sum_probs=35.1
Q ss_pred EEEeehHHHHHHHHHhhhCCceeEEEEeeeEe---CCEEEEEEEeecccccCcchhhc
Q 034084 25 VQIEGLVMLKIIKHCKEFSPALVTGQLLGLDV---GSVLEVTNCFPFPIQEEDEEIEA 79 (104)
Q Consensus 25 V~vhplVll~I~dh~~r~~~~~viG~LLG~~~---~~~veVtnsF~vP~~~~~~~~~~ 79 (104)
..|=|--||+-.-...+-. .++.|.|.|... .+.-||+-....|...+.+.+..
T Consensus 37 t~vlPknllkkFi~iaD~r-tQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l 93 (252)
T cd08056 37 TYILPKNLLKKFISISDLR-TQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTL 93 (252)
T ss_pred EEEeCHHHHHHHHHHhhhc-ceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEEC
Confidence 4556665555333333222 479999999953 37789998888887766555554
No 38
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=41.64 E-value=32 Score=20.59 Aligned_cols=22 Identities=27% Similarity=0.366 Sum_probs=18.2
Q ss_pred cccHHHHHHHHHHHHhhCCCCC
Q 034084 79 ADGANYQLEMMRCLREVNVDNN 100 (104)
Q Consensus 79 ~~~~~y~~~m~~~~k~v~~~e~ 100 (104)
.+|.+|+.+....+|+||-++.
T Consensus 32 ~~D~e~H~~~c~~LRqvNedeH 53 (55)
T PF13824_consen 32 EDDYEEHRQLCERLRQVNEDEH 53 (55)
T ss_pred HHhHHHHHHHHHHHHHhccccc
Confidence 3457999999999999998763
No 39
>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=39.22 E-value=55 Score=16.57 Aligned_cols=22 Identities=27% Similarity=0.560 Sum_probs=15.4
Q ss_pred eeEEEEeeeEeCCEEEEEEEeec
Q 034084 46 LVTGQLLGLDVGSVLEVTNCFPF 68 (104)
Q Consensus 46 ~viG~LLG~~~~~~veVtnsF~v 68 (104)
..+|-|.|.-... =.|+||++-
T Consensus 3 ~~vGGlvG~~~~~-~~I~nc~at 24 (28)
T PF07581_consen 3 YYVGGLVGYNDNG-GSITNCYAT 24 (28)
T ss_pred ccEEeEEEECCCC-CEEEEEEEE
Confidence 3578889986552 358899873
No 40
>PF14232 DUF4334: Domain of unknown function (DUF4334)
Probab=31.26 E-value=16 Score=22.13 Aligned_cols=23 Identities=26% Similarity=0.372 Sum_probs=18.4
Q ss_pred HHHHHHHhhhCCceeEEEEeeeE
Q 034084 33 LKIIKHCKEFSPALVTGQLLGLD 55 (104)
Q Consensus 33 l~I~dh~~r~~~~~viG~LLG~~ 55 (104)
+-|+||+++.....++|.+=+..
T Consensus 26 ~PI~D~FR~Vd~~tv~G~Md~k~ 48 (59)
T PF14232_consen 26 QPIIDHFRKVDDDTVLGAMDGKG 48 (59)
T ss_pred CcccceEEEEcCCEEEEEeccCC
Confidence 35789999999999999876554
No 41
>KOG2550 consensus IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism]
Probab=30.44 E-value=40 Score=28.28 Aligned_cols=23 Identities=30% Similarity=0.538 Sum_probs=21.0
Q ss_pred cHHHHHHHHHHHHhhCCCCCccc
Q 034084 81 GANYQLEMMRCLREVNVDNNTVG 103 (104)
Q Consensus 81 ~~~y~~~m~~~~k~v~~~e~iVG 103 (104)
+..||-+|++..|+.+|+..++|
T Consensus 275 nS~~qiemik~iK~~yP~l~Via 297 (503)
T KOG2550|consen 275 NSIYQLEMIKYIKETYPDLQIIA 297 (503)
T ss_pred cchhHHHHHHHHHhhCCCceeec
Confidence 46899999999999999999876
No 42
>KOG4832 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.28 E-value=24 Score=27.21 Aligned_cols=29 Identities=24% Similarity=0.574 Sum_probs=20.6
Q ss_pred ceeEEEee--hHHHHHHHHHhhhCCceeEEE
Q 034084 22 LRVVQIEG--LVMLKIIKHCKEFSPALVTGQ 50 (104)
Q Consensus 22 ~~~V~vhp--lVll~I~dh~~r~~~~~viG~ 50 (104)
+.+-+++| -|+|+|+.||.|.+..|..|+
T Consensus 218 ~~~lkld~~f~~~l~~LRH~rRisE~R~ggl 248 (253)
T KOG4832|consen 218 FTTLKLDKKFHVLLNILRHCRRISEVRGGGL 248 (253)
T ss_pred hhhhhcchhhhHHHHHHHHHHHHhhhhcCCc
Confidence 33445555 389999999999877666553
No 43
>PF10922 DUF2745: Protein of unknown function (DUF2745); InterPro: IPR020147 The T7-like bacteriophage gene 1.2 protein is an inhibitor of the Escherichia coli dGTP triphosphohydrolase (dGTPase) and is implicated in DNA replication.
Probab=27.32 E-value=1e+02 Score=20.04 Aligned_cols=35 Identities=17% Similarity=0.302 Sum_probs=22.4
Q ss_pred eCCEEEEEEEeecccccCcchhhcccHHHHHHHHHHHHh
Q 034084 56 VGSVLEVTNCFPFPIQEEDEEIEADGANYQLEMMRCLRE 94 (104)
Q Consensus 56 ~~~~veVtnsF~vP~~~~~~~~~~~~~~y~~~m~~~~k~ 94 (104)
.|+.| .+.+|. +.+.+...+. ..++..+|++.+|.
T Consensus 49 ~G~~v-~~~tf~--h~DeDV~~n~-~T~WLnk~~~qLk~ 83 (85)
T PF10922_consen 49 SGNSV-FSKTFE--HHDEDVLYNM-CTEWLNKMYDQLKD 83 (85)
T ss_pred CCCEe-eeeeEE--eeCCceeehH-HHHHHHHHHHHhcc
Confidence 34444 888998 2322223334 38999999999873
No 44
>cd01720 Sm_D2 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 D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=24.19 E-value=2e+02 Score=18.36 Aligned_cols=28 Identities=11% Similarity=0.084 Sum_probs=22.9
Q ss_pred CceeEEEEeeeEeCCEEEEEEEeecccc
Q 034084 44 PALVTGQLLGLDVGSVLEVTNCFPFPIQ 71 (104)
Q Consensus 44 ~~~viG~LLG~~~~~~veVtnsF~vP~~ 71 (104)
...+.|.|.|++.--.+-..||..+...
T Consensus 24 ~r~~~G~L~~fD~hmNlvL~d~~E~~~~ 51 (87)
T cd01720 24 NKKLLGRVKAFDRHCNMVLENVKEMWTE 51 (87)
T ss_pred CCEEEEEEEEecCccEEEEcceEEEeec
Confidence 3679999999998888888888887543
No 45
>KOG3446 consensus NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion]
Probab=24.18 E-value=64 Score=21.27 Aligned_cols=21 Identities=14% Similarity=0.191 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHhhCCCCCcc
Q 034084 82 ANYQLEMMRCLREVNVDNNTV 102 (104)
Q Consensus 82 ~~y~~~m~~~~k~v~~~e~iV 102 (104)
.+|.++.|--+|+.||+.-|+
T Consensus 33 R~fvEk~Y~~lKkaNP~lPIL 53 (97)
T KOG3446|consen 33 REFVEKFYVNLKKANPDLPIL 53 (97)
T ss_pred HHHHHHhhhhhhhcCCCCcEe
Confidence 789999999999999998664
No 46
>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=21.80 E-value=1.3e+02 Score=18.30 Aligned_cols=27 Identities=19% Similarity=0.272 Sum_probs=22.9
Q ss_pred CceeEEEEeeeEeCCEEEEEEEeeccc
Q 034084 44 PALVTGQLLGLDVGSVLEVTNCFPFPI 70 (104)
Q Consensus 44 ~~~viG~LLG~~~~~~veVtnsF~vP~ 70 (104)
.....|+|.|++.-..+...+|+....
T Consensus 19 gr~~~G~L~~~D~~~NlvL~~~~E~~~ 45 (74)
T cd01727 19 GRVIVGTLKGFDQATNLILDDSHERVY 45 (74)
T ss_pred CcEEEEEEEEEccccCEEccceEEEEe
Confidence 367899999999888899999988754
No 47
>cd01729 LSm7 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. LSm7 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=20.55 E-value=1.2e+02 Score=18.88 Aligned_cols=28 Identities=25% Similarity=0.182 Sum_probs=23.3
Q ss_pred CceeEEEEeeeEeCCEEEEEEEeecccc
Q 034084 44 PALVTGQLLGLDVGSVLEVTNCFPFPIQ 71 (104)
Q Consensus 44 ~~~viG~LLG~~~~~~veVtnsF~vP~~ 71 (104)
...+.|+|.|++.-..+-..+|......
T Consensus 22 gr~~~G~L~~~D~~mNlvL~~~~E~~~~ 49 (81)
T cd01729 22 GREVTGILKGYDQLLNLVLDDTVEYLRD 49 (81)
T ss_pred CcEEEEEEEEEcCcccEEecCEEEEEcc
Confidence 3679999999998888889999887643
Done!