Query 034157
Match_columns 102
No_of_seqs 107 out of 575
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 10:24:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034157.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034157hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03246 26S proteasome regula 99.9 8.6E-28 1.9E-32 186.1 9.5 84 19-102 2-92 (303)
2 cd08057 MPN_euk_non_mb Mpr1p, 99.9 1.4E-27 3.1E-32 168.4 8.7 78 25-102 1-81 (157)
3 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.9 1.1E-26 2.4E-31 178.1 9.6 80 23-102 1-87 (280)
4 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.9 1.3E-26 2.9E-31 175.8 8.3 78 25-102 1-81 (265)
5 KOG2975 Translation initiation 99.9 2.7E-27 5.9E-32 179.7 4.0 85 18-102 16-103 (288)
6 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.9 2.9E-26 6.2E-31 175.8 7.3 79 24-102 2-88 (288)
7 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.9 1.4E-24 3E-29 165.1 9.2 80 23-102 1-84 (266)
8 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 3.1E-24 6.7E-29 143.3 7.0 82 21-102 2-86 (114)
9 KOG1556 26S proteasome regulat 99.9 1.4E-23 3.1E-28 158.9 7.3 85 18-102 4-95 (309)
10 cd08069 MPN_RPN11_CSN5 Mov34/M 99.8 5.5E-20 1.2E-24 140.3 9.5 88 15-102 2-92 (268)
11 KOG1560 Translation initiation 99.8 1.5E-18 3.3E-23 133.4 7.1 86 17-102 7-103 (339)
12 KOG3050 COP9 signalosome, subu 99.7 8.2E-19 1.8E-23 132.9 3.6 83 20-102 6-95 (299)
13 smart00232 JAB_MPN JAB/MPN dom 99.7 4.3E-17 9.3E-22 109.9 8.6 79 24-102 1-81 (135)
14 KOG1554 COP9 signalosome, subu 99.7 2.4E-17 5.2E-22 127.1 6.6 98 5-102 35-136 (347)
15 cd08067 MPN_2A_DUB Mov34/MPN/P 99.3 5.3E-12 1.1E-16 92.3 8.2 78 21-102 4-84 (187)
16 cd07767 MPN Mpr1p, Pad1p N-ter 99.2 4.9E-11 1.1E-15 78.6 7.1 67 33-102 2-68 (116)
17 cd08058 MPN_euk_mb Mpr1p, Pad1 99.1 1.5E-10 3.3E-15 78.1 6.5 64 31-102 2-70 (119)
18 KOG1555 26S proteasome regulat 98.4 4.3E-07 9.2E-12 71.2 5.2 83 20-102 28-120 (316)
19 cd08068 MPN_BRCC36 Mov34/MPN/P 98.4 1.6E-06 3.5E-11 66.0 7.4 80 23-102 2-94 (244)
20 cd08070 MPN_like Mpr1p, Pad1p 97.7 0.00017 3.7E-09 49.0 6.6 70 31-102 3-75 (128)
21 PF03665 UPF0172: Uncharacteri 97.6 0.00013 2.9E-09 53.7 4.8 48 24-71 3-52 (196)
22 cd08060 MPN_UPF0172 Mov34/MPN/ 97.5 0.00016 3.5E-09 52.7 4.7 44 28-71 2-46 (182)
23 cd08066 MPN_AMSH_like Mov34/MP 97.4 0.00074 1.6E-08 48.8 7.1 74 24-102 3-80 (173)
24 KOG3289 Uncharacterized conser 97.0 0.00088 1.9E-08 49.3 4.1 47 24-70 3-51 (199)
25 COG1310 Predicted metal-depend 96.8 0.0032 7E-08 43.0 5.0 70 25-102 2-74 (134)
26 cd08072 MPN_archaeal Mov34/MPN 93.1 0.26 5.6E-06 33.2 4.9 36 31-70 5-40 (117)
27 PF14464 Prok-JAB: Prokaryotic 92.6 0.69 1.5E-05 29.4 6.2 37 31-67 4-40 (104)
28 TIGR02256 ICE_VC0181 integrati 89.8 2.1 4.6E-05 29.8 6.7 69 32-101 2-77 (131)
29 cd08059 MPN_prok_mb Mpr1p, Pad 73.6 8.6 0.00019 24.5 4.3 37 32-71 3-39 (101)
30 cd08073 MPN_NLPC_P60 Mpr1p, Pa 72.1 7.1 0.00015 25.8 3.7 33 32-69 3-35 (108)
31 cd08061 MPN_NPL4 Mov34/MPN/PAD 66.3 53 0.0011 25.5 7.9 55 18-72 6-68 (274)
32 PF13824 zf-Mss51: Zinc-finger 65.0 9.6 0.00021 22.9 2.9 33 65-97 14-52 (55)
33 PF07002 Copine: Copine; Inte 57.8 14 0.00031 25.8 3.2 39 31-71 19-57 (146)
34 KOG4445 Uncharacterized conser 51.8 19 0.00042 28.9 3.3 40 31-70 96-141 (368)
35 TIGR03735 PRTRC_A PRTRC system 47.7 32 0.00069 25.5 3.8 41 26-69 74-114 (192)
36 PF07620 SLEI_Leptospira: SLEI 42.3 20 0.00043 16.3 1.3 10 56-65 6-15 (16)
37 PF14232 DUF4334: Domain of un 33.7 15 0.00033 22.3 0.2 23 33-55 26-48 (59)
38 PF14778 ODR4-like: Olfactory 31.6 84 0.0018 25.0 4.1 47 49-95 1-60 (362)
39 COG2957 Peptidylarginine deimi 31.4 86 0.0019 25.3 4.1 69 18-101 255-323 (346)
40 KOG4832 Uncharacterized conser 28.6 25 0.00055 27.1 0.7 29 21-49 217-247 (253)
41 KOG1784 Small Nuclear ribonucl 27.1 32 0.0007 22.8 0.9 26 45-70 21-46 (96)
42 smart00459 Sorb Sorbin homolog 27.1 93 0.002 18.3 2.7 20 79-98 28-47 (50)
43 KOG2550 IMP dehydrogenase/GMP 24.5 59 0.0013 27.3 2.2 23 79-101 275-297 (503)
44 PF10813 DUF2733: Protein of u 21.1 54 0.0012 17.6 0.9 20 48-67 1-30 (32)
45 PF05021 NPL4: NPL4 family; I 20.8 1.6E+02 0.0035 23.2 3.9 25 48-72 2-33 (306)
46 PF07581 Glug: The GLUG motif; 20.6 1.4E+02 0.003 15.1 2.6 21 46-67 3-23 (28)
47 KOG3446 NADH:ubiquinone oxidor 20.3 87 0.0019 20.7 1.9 22 79-100 32-53 (97)
No 1
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.95 E-value=8.6e-28 Score=186.12 Aligned_cols=84 Identities=29% Similarity=0.488 Sum_probs=77.0
Q ss_pred CCCceEEEEeehHHHHHHHHHhhcCC---ceeEEEEeeeEeCCEEEEEeeeecCCCCchh----hhchHHHHHHHHHHHH
Q 034157 19 APPLRVVQIEGLVMLKIIKHCKEFSP---ALVTGQLLGLDVGSVLEVTNCFPFPEEDEEI----EADGANYQLEMMRCLR 91 (102)
Q Consensus 19 ~~~~~~V~ihplVlLkI~dH~~r~~~---~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~----~~~d~~y~~~ml~~~k 91 (102)
++|+.+|+|||+|||+|+|||+|..+ .+|+|+|||.+.++++||||||++|++++++ ..+|.+|+++|+++||
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 57889999999999999999999974 6799999999999999999999999866433 3589999999999999
Q ss_pred hhCCCCCcccC
Q 034157 92 EVNVDNNTVGW 102 (102)
Q Consensus 92 ~v~~~e~iVGW 102 (102)
+|||++.+|||
T Consensus 82 ~V~~~~~vVGW 92 (303)
T PLN03246 82 RINAKEHVVGW 92 (303)
T ss_pred HhCCCCcEEee
Confidence 99999999999
No 2
>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=1.4e-27 Score=168.42 Aligned_cols=78 Identities=33% Similarity=0.459 Sum_probs=72.8
Q ss_pred EEEeehHHHHHHHHHhhcC--CceeEEEEeeeEeCCEEEEEeeeecCCCCch-hhhchHHHHHHHHHHHHhhCCCCCccc
Q 034157 25 VQIEGLVMLKIIKHCKEFS--PALVTGQLLGLDVGSVLEVTNCFPFPEEDEE-IEADGANYQLEMMRCLREVNVDNNTVG 101 (102)
Q Consensus 25 V~ihplVlLkI~dH~~r~~--~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~-~~~~d~~y~~~ml~~~k~v~~~e~iVG 101 (102)
|+|||+|||||+|||+|+. +.+++|+|||.+.+++++|+|||++|+++++ ...+|.+|+++|++++|+++|++.+||
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~~~d~~y~~~m~~~~~~v~~~~~vVG 80 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFIDTEYLEKRYNLHKKVYPQEKIVG 80 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcchhhhHHHHHHHHHHHHHhCCCCCEEE
Confidence 6899999999999999998 7999999999999999999999999986643 356799999999999999999999999
Q ss_pred C
Q 034157 102 W 102 (102)
Q Consensus 102 W 102 (102)
|
T Consensus 81 W 81 (157)
T cd08057 81 W 81 (157)
T ss_pred E
Confidence 9
No 3
>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=1.1e-26 Score=178.12 Aligned_cols=80 Identities=34% Similarity=0.519 Sum_probs=73.2
Q ss_pred eEEEEeehHHHHHHHHHhhcC---CceeEEEEeeeEeCCEEEEEeeeecCCCCchh----hhchHHHHHHHHHHHHhhCC
Q 034157 23 RVVQIEGLVMLKIIKHCKEFS---PALVTGQLLGLDVGSVLEVTNCFPFPEEDEEI----EADGANYQLEMMRCLREVNV 95 (102)
Q Consensus 23 ~~V~ihplVlLkI~dH~~r~~---~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~----~~~d~~y~~~ml~~~k~v~~ 95 (102)
++|+|||+|||+|+|||+|.. +.+|+|+|||.+.++++||+|||++|++++++ ..+|.+|+++|+++||++||
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 479999999999999999975 47899999999999999999999999876443 35899999999999999999
Q ss_pred CCCcccC
Q 034157 96 DNNTVGW 102 (102)
Q Consensus 96 ~e~iVGW 102 (102)
++.+|||
T Consensus 81 ~e~vVGW 87 (280)
T cd08062 81 KEKIVGW 87 (280)
T ss_pred CCCeEEE
Confidence 9999999
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=99.94 E-value=1.3e-26 Score=175.81 Aligned_cols=78 Identities=29% Similarity=0.528 Sum_probs=71.9
Q ss_pred EEEeehHHHHHHHHHhhcC--CceeEEEEeeeEeCCEEEEEeeeecCCCCch-hhhchHHHHHHHHHHHHhhCCCCCccc
Q 034157 25 VQIEGLVMLKIIKHCKEFS--PALVTGQLLGLDVGSVLEVTNCFPFPEEDEE-IEADGANYQLEMMRCLREVNVDNNTVG 101 (102)
Q Consensus 25 V~ihplVlLkI~dH~~r~~--~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~-~~~~d~~y~~~ml~~~k~v~~~e~iVG 101 (102)
|+|||+|||+|+|||+|+. +.+|+|+|||.+.++++||||||++|+++++ ...+|.+|+++|+++||++||++.+||
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~d~~y~~~m~~~~kkv~~~~~vVG 80 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVDMEYHRTMYELHQKVNPKEVIVG 80 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEEcHHHHHHHHHHHHHhCCCCcEEe
Confidence 6899999999999999964 5899999999999999999999999986643 457899999999999999999999999
Q ss_pred C
Q 034157 102 W 102 (102)
Q Consensus 102 W 102 (102)
|
T Consensus 81 W 81 (265)
T cd08064 81 W 81 (265)
T ss_pred e
Confidence 9
No 5
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=2.7e-27 Score=179.68 Aligned_cols=85 Identities=26% Similarity=0.430 Sum_probs=78.4
Q ss_pred CCCCceEEEEeehHHHHHHHHHhhcCC--ceeEEEEeeeEeCCEEEEEeeeecCCCC-chhhhchHHHHHHHHHHHHhhC
Q 034157 18 VAPPLRVVQIEGLVMLKIIKHCKEFSP--ALVTGQLLGLDVGSVLEVTNCFPFPEED-EEIEADGANYQLEMMRCLREVN 94 (102)
Q Consensus 18 ~~~~~~~V~ihplVlLkI~dH~~r~~~--~~v~G~LLG~~~~~~veVtnsF~~P~~~-~~~~~~d~~y~~~ml~~~k~v~ 94 (102)
+-+...+|.|||+|+++|+||+.|++. .+|||+|||..++|+|||||||++|+.| +++..+|++|+.+|+++++|+|
T Consensus 16 ~~ss~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm~y~~~M~~l~~k~n 95 (288)
T KOG2975|consen 16 PFSSNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDMEYAKNMYELHKKVN 95 (288)
T ss_pred CCCCCceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceeeHHHHHHHHHHhcccC
Confidence 444566999999999999999999975 8999999999999999999999999866 5667899999999999999999
Q ss_pred CCCCcccC
Q 034157 95 VDNNTVGW 102 (102)
Q Consensus 95 ~~e~iVGW 102 (102)
|+|.+|||
T Consensus 96 pnE~vvGW 103 (288)
T KOG2975|consen 96 PNELVVGW 103 (288)
T ss_pred CCceeEEE
Confidence 99999999
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=99.93 E-value=2.9e-26 Score=175.82 Aligned_cols=79 Identities=28% Similarity=0.451 Sum_probs=73.0
Q ss_pred EEEEeehHHHHHHHHHhhcC------CceeEEEEeeeEeCCEEEEEeeeecCCCCch--hhhchHHHHHHHHHHHHhhCC
Q 034157 24 VVQIEGLVMLKIIKHCKEFS------PALVTGQLLGLDVGSVLEVTNCFPFPEEDEE--IEADGANYQLEMMRCLREVNV 95 (102)
Q Consensus 24 ~V~ihplVlLkI~dH~~r~~------~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~--~~~~d~~y~~~ml~~~k~v~~ 95 (102)
+|+|||+|||+|+|||+|.. +.+|+|+|||.++++++||||||++|+++++ +..+|.+|+++|+++||+|||
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV~~ 81 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQVFK 81 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHhcc
Confidence 69999999999999999963 4799999999999999999999999987643 467899999999999999999
Q ss_pred CCCcccC
Q 034157 96 DNNTVGW 102 (102)
Q Consensus 96 ~e~iVGW 102 (102)
++.+|||
T Consensus 82 ~~~vVGW 88 (288)
T cd08063 82 DLDFVGW 88 (288)
T ss_pred CCceEEE
Confidence 9999999
No 7
>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=99.91 E-value=1.4e-24 Score=165.09 Aligned_cols=80 Identities=73% Similarity=1.167 Sum_probs=73.9
Q ss_pred eEEEEeehHHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCCCchh----hhchHHHHHHHHHHHHhhCCCCC
Q 034157 23 RVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEEDEEI----EADGANYQLEMMRCLREVNVDNN 98 (102)
Q Consensus 23 ~~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~----~~~d~~y~~~ml~~~k~v~~~e~ 98 (102)
++|+|||+|+++|+|||.|+.|.+|+|+|||.+.++++|||||||+|..+++. ..++.+|+.+|+++++++|+++.
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 37999999999999999999999999999999999999999999999865433 35677999999999999999999
Q ss_pred cccC
Q 034157 99 TVGW 102 (102)
Q Consensus 99 iVGW 102 (102)
+|||
T Consensus 81 iVGW 84 (266)
T cd08065 81 HVGW 84 (266)
T ss_pred EEEe
Confidence 9999
No 8
>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=99.90 E-value=3.1e-24 Score=143.33 Aligned_cols=82 Identities=41% Similarity=0.710 Sum_probs=73.9
Q ss_pred CceEEEEeehHHHHHHHHHhhcCCceeEEEEeeeEeCC-EEEEEeeeecCCCCchh--hhchHHHHHHHHHHHHhhCCCC
Q 034157 21 PLRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGS-VLEVTNCFPFPEEDEEI--EADGANYQLEMMRCLREVNVDN 97 (102)
Q Consensus 21 ~~~~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~~~-~veVtnsF~~P~~~~~~--~~~d~~y~~~ml~~~k~v~~~e 97 (102)
++.+|+|||+|+++|+||+.|..+.+|+|+|+|..+++ +++|+|||++|..+++. ...+.++..+|++++++++|++
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 99999999999865432 3455666699999999999999
Q ss_pred CcccC
Q 034157 98 NTVGW 102 (102)
Q Consensus 98 ~iVGW 102 (102)
.+|||
T Consensus 82 ~iVGW 86 (114)
T PF01398_consen 82 EIVGW 86 (114)
T ss_dssp EEEEE
T ss_pred eEEEE
Confidence 99999
No 9
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=1.4e-23 Score=158.93 Aligned_cols=85 Identities=31% Similarity=0.477 Sum_probs=78.8
Q ss_pred CCCCceEEEEeehHHHHHHHHHhhcCC---ceeEEEEeeeEeCCEEEEEeeeecCCCCchh----hhchHHHHHHHHHHH
Q 034157 18 VAPPLRVVQIEGLVMLKIIKHCKEFSP---ALVTGQLLGLDVGSVLEVTNCFPFPEEDEEI----EADGANYQLEMMRCL 90 (102)
Q Consensus 18 ~~~~~~~V~ihplVlLkI~dH~~r~~~---~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~----~~~d~~y~~~ml~~~ 90 (102)
+..+..+|.+||||||+++|||.|... .||.|.|||..+++++.|||||++|+++++. .+.|.+|+++|+++|
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 455688999999999999999999975 8999999999999999999999999988764 367999999999999
Q ss_pred HhhCCCCCcccC
Q 034157 91 REVNVDNNTVGW 102 (102)
Q Consensus 91 k~v~~~e~iVGW 102 (102)
+++|.+|.+|||
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=99.82 E-value=5.5e-20 Score=140.29 Aligned_cols=88 Identities=27% Similarity=0.412 Sum_probs=79.3
Q ss_pred hccCCCCceEEEEeehHHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCCCchh-hhchHHHHHHHHH--HHH
Q 034157 15 AEEVAPPLRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEEDEEI-EADGANYQLEMMR--CLR 91 (102)
Q Consensus 15 ~~~~~~~~~~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~-~~~d~~y~~~ml~--~~k 91 (102)
|...+.++++|+|+|+|+++|++||.+..+.+|+|+|||..++++++|+|||++|.++.+. ...+.+|++.|++ +++
T Consensus 2 ~~~~~~~~~~V~Is~~allkil~Ha~~~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~ 81 (268)
T cd08069 2 WKPDPDYFEKVYISSLALLKMLKHARAGGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLK 81 (268)
T ss_pred CCCCCCcccEEEECHHHHHHHHHHHhccCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHH
Confidence 5667888999999999999999999999999999999999999999999999999765433 2335599999999 999
Q ss_pred hhCCCCCcccC
Q 034157 92 EVNVDNNTVGW 102 (102)
Q Consensus 92 ~v~~~e~iVGW 102 (102)
++++++++|||
T Consensus 82 ~~~~~~~vVGW 92 (268)
T cd08069 82 QTGRPENVVGW 92 (268)
T ss_pred HhCCCceeEee
Confidence 99999999999
No 11
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=99.76 E-value=1.5e-18 Score=133.37 Aligned_cols=86 Identities=49% Similarity=0.879 Sum_probs=73.7
Q ss_pred cCCCCceEEEEeehHHHHHHHHHhhcCC--ceeEEEEeeeEeCCEEEEEeeeecCC-C---Cchhh---h--chHHHHHH
Q 034157 17 EVAPPLRVVQIEGLVMLKIIKHCKEFSP--ALVTGQLLGLDVGSVLEVTNCFPFPE-E---DEEIE---A--DGANYQLE 85 (102)
Q Consensus 17 ~~~~~~~~V~ihplVlLkI~dH~~r~~~--~~v~G~LLG~~~~~~veVtnsF~~P~-~---~~~~~---~--~d~~y~~~ 85 (102)
..++|+++|.|++||++||+|||.+..+ .-+.|+|+|.+.++.+|||||||.|. . ++... . .-..|+..
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 3567899999999999999999999987 57899999999999999999999995 2 22211 1 12479999
Q ss_pred HHHHHHhhCCCCCcccC
Q 034157 86 MMRCLREVNVDNNTVGW 102 (102)
Q Consensus 86 ml~~~k~v~~~e~iVGW 102 (102)
|++.++.+|.+..+|||
T Consensus 87 mlrrlr~vnid~~hVGw 103 (339)
T KOG1560|consen 87 MLRRLRYVNIDHLHVGW 103 (339)
T ss_pred HHHHhhhcCccceeeee
Confidence 99999999999999999
No 12
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.74 E-value=8.2e-19 Score=132.89 Aligned_cols=83 Identities=27% Similarity=0.421 Sum_probs=74.3
Q ss_pred CCceEEEEeehHHHHHHHHHhhcC-----C-ceeEEEEeeeEeCCEEEEEeeeecCCCCch-hhhchHHHHHHHHHHHHh
Q 034157 20 PPLRVVQIEGLVMLKIIKHCKEFS-----P-ALVTGQLLGLDVGSVLEVTNCFPFPEEDEE-IEADGANYQLEMMRCLRE 92 (102)
Q Consensus 20 ~~~~~V~ihplVlLkI~dH~~r~~-----~-~~v~G~LLG~~~~~~veVtnsF~~P~~~~~-~~~~d~~y~~~ml~~~k~ 92 (102)
+...+|.+||||+++|+|||.|.. | .+|.|+|+|.+.|+.|||.|||.+..+..+ ...+|.+|..+.-++||+
T Consensus 6 S~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~~~~dke~l~kk~eqykq 85 (299)
T KOG3050|consen 6 SGSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDTETIDKEYLEKKEEQYKQ 85 (299)
T ss_pred CCceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecchhhhhhccHHHHHHHHHHHHH
Confidence 345689999999999999999985 2 489999999999999999999999976543 346899999999999999
Q ss_pred hCCCCCcccC
Q 034157 93 VNVDNNTVGW 102 (102)
Q Consensus 93 v~~~e~iVGW 102 (102)
|+|+..++||
T Consensus 86 VFpdl~vlGw 95 (299)
T KOG3050|consen 86 VFPDLYVLGW 95 (299)
T ss_pred hcccceEEEE
Confidence 9999999999
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=4.3e-17 Score=109.86 Aligned_cols=79 Identities=34% Similarity=0.477 Sum_probs=72.0
Q ss_pred EEEEeehHHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCCCchhh--hchHHHHHHHHHHHHhhCCCCCccc
Q 034157 24 VVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEEDEEIE--ADGANYQLEMMRCLREVNVDNNTVG 101 (102)
Q Consensus 24 ~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~~--~~d~~y~~~ml~~~k~v~~~e~iVG 101 (102)
.|+|+|+++++|++|+.|..+.++.|.|+|...++.++|+++|++|...+... ..+.+|++.|.++++++++++.+||
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 47999999999999999999999999999999999999999999997553322 5688999999999999999999999
Q ss_pred C
Q 034157 102 W 102 (102)
Q Consensus 102 W 102 (102)
|
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=99.70 E-value=2.4e-17 Score=127.13 Aligned_cols=98 Identities=22% Similarity=0.375 Sum_probs=88.1
Q ss_pred hhhhHHhhhhhccCCCCceEEEEeehHHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCCCchh----hhchH
Q 034157 5 MARSFLQVAAAEEVAPPLRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEEDEEI----EADGA 80 (102)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~----~~~d~ 80 (102)
+-|.+...-+|...+.+++.|+|+.|++|||..|++++.+..|||.|+|..+++++.|.+||++|.++.|. .+...
T Consensus 35 sq~~~~~~kpw~~Dp~~fk~vkISalAllKm~~hA~~GgnlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~Ay 114 (347)
T KOG1554|consen 35 SQRKIILEKPWSTDPHYFKHVKISALALLKMVMHARSGGNLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAY 114 (347)
T ss_pred HHHHHHhcCcccCCCchhhhhhhHHHHHHHHHHHHhcCCCeEEEeeecccccCCeEEEEeccccccccccceechHHHHH
Confidence 34555566677788889999999999999999999999999999999999999999999999999988663 34578
Q ss_pred HHHHHHHHHHHhhCCCCCcccC
Q 034157 81 NYQLEMMRCLREVNVDNNTVGW 102 (102)
Q Consensus 81 ~y~~~ml~~~k~v~~~e~iVGW 102 (102)
+|+....+..+.+++.+++|||
T Consensus 115 EYmv~Y~e~~k~~gr~envVGW 136 (347)
T KOG1554|consen 115 EYMVQYIEEAKNVGRLENVVGW 136 (347)
T ss_pred HHHHHHHHHHHHhhhhhceeee
Confidence 9999999999999999999999
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=99.34 E-value=5.3e-12 Score=92.27 Aligned_cols=78 Identities=22% Similarity=0.245 Sum_probs=66.2
Q ss_pred CceEEEEeehHHHHHHHHHhhcCCceeEEEEeeeEe--CCEEEEEeeeecCCCCc-hhhhchHHHHHHHHHHHHhhCCCC
Q 034157 21 PLRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDV--GSVLEVTNCFPFPEEDE-EIEADGANYQLEMMRCLREVNVDN 97 (102)
Q Consensus 21 ~~~~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~--~~~veVtnsF~~P~~~~-~~~~~d~~y~~~ml~~~k~v~~~e 97 (102)
|+ +|+|+++|+|+|++||.... ..+.|.|+|..+ ++.++|+++|++|.... .....|..++.+|++.+++.+ .
T Consensus 4 pf-~V~Is~~all~m~~Ha~~~~-~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~g--l 79 (187)
T cd08067 4 PF-KVTVSSNALLLMDFHCHLTT-SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRG--L 79 (187)
T ss_pred CE-EEEECHHHHHHHHHHhcCCC-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcC--C
Confidence 44 69999999999999999887 999999999964 47999999999997442 233457899999999999877 5
Q ss_pred CcccC
Q 034157 98 NTVGW 102 (102)
Q Consensus 98 ~iVGW 102 (102)
.+|||
T Consensus 80 ~vVGw 84 (187)
T cd08067 80 SVVGW 84 (187)
T ss_pred EEEEE
Confidence 99999
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=99.22 E-value=4.9e-11 Score=78.58 Aligned_cols=67 Identities=21% Similarity=0.323 Sum_probs=53.6
Q ss_pred HHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCCCchhhhchHHHHHHHHHHHHhhCCCCCcccC
Q 034157 33 LKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEEDEEIEADGANYQLEMMRCLREVNVDNNTVGW 102 (102)
Q Consensus 33 LkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~~~~d~~y~~~ml~~~k~v~~~e~iVGW 102 (102)
.+|++|+++..+.++.|.|+|...++.++|+++|++|....+......+ -|....+....++.+|||
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~iVGw 68 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWF---LMYLDFKKLNAGLRIVGW 68 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHH---HHHHHHHHhcCCCeEEEE
Confidence 5789999998899999999999998999999999999755432221122 266677788899999999
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=99.13 E-value=1.5e-10 Score=78.08 Aligned_cols=64 Identities=19% Similarity=0.150 Sum_probs=53.3
Q ss_pred HHHHHHHHHhhcCCceeEEEEeeeEe-----CCEEEEEeeeecCCCCchhhhchHHHHHHHHHHHHhhCCCCCcccC
Q 034157 31 VMLKIIKHCKEFSPALVTGQLLGLDV-----GSVLEVTNCFPFPEEDEEIEADGANYQLEMMRCLREVNVDNNTVGW 102 (102)
Q Consensus 31 VlLkI~dH~~r~~~~~v~G~LLG~~~-----~~~veVtnsF~~P~~~~~~~~~d~~y~~~ml~~~k~v~~~e~iVGW 102 (102)
|+++|++||.+..|..+.|.|+|... +..++|+++|+.|...+. .+.|..+.+..+.+.++|||
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 78999999999999999999999875 456899999999974432 12556667788999999999
No 18
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=98.41 E-value=4.3e-07 Score=71.23 Aligned_cols=83 Identities=29% Similarity=0.469 Sum_probs=72.2
Q ss_pred CCceEEEEeehHHHHHHHHHhhcCCce-eEEEE-ee---e-EeCCEEEEEeeeecCCCCch----hhhchHHHHHHHHHH
Q 034157 20 PPLRVVQIEGLVMLKIIKHCKEFSPAL-VTGQL-LG---L-DVGSVLEVTNCFPFPEEDEE----IEADGANYQLEMMRC 89 (102)
Q Consensus 20 ~~~~~V~ihplVlLkI~dH~~r~~~~~-v~G~L-LG---~-~~~~~veVtnsF~~P~~~~~----~~~~d~~y~~~ml~~ 89 (102)
....+|.|+.++++++++|-+-..+.. ++|.+ +| . .+..++.|.+.|+.|..... ..+.|..|+.+|+++
T Consensus 28 ~~~e~v~i~slall~m~rh~r~~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~d~V~q~q~~~~ 107 (316)
T KOG1555|consen 28 DEKETVYISSLALLKMLRHDRAGSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQMMDL 107 (316)
T ss_pred cCcceeeeehhhhhhcccccccCCchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHHHHH
Confidence 346699999999999999999888866 99999 99 3 46679999999999976533 246799999999999
Q ss_pred HHhhCCCCCcccC
Q 034157 90 LREVNVDNNTVGW 102 (102)
Q Consensus 90 ~k~v~~~e~iVGW 102 (102)
++..+..+.+|||
T Consensus 108 l~~tGrp~~VVGW 120 (316)
T KOG1555|consen 108 LKQTGRPELVVGW 120 (316)
T ss_pred HHhcCCcceEEee
Confidence 9999999999999
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=98.37 E-value=1.6e-06 Score=65.97 Aligned_cols=80 Identities=19% Similarity=0.214 Sum_probs=59.6
Q ss_pred eEEEEeehHHHHHHHHHhhcCCceeEEEEeeeEe-------CCEEEEEeeeecCCCC-ch-hhhchH----HHHHHHHHH
Q 034157 23 RVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDV-------GSVLEVTNCFPFPEED-EE-IEADGA----NYQLEMMRC 89 (102)
Q Consensus 23 ~~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~-------~~~veVtnsF~~P~~~-~~-~~~~d~----~y~~~ml~~ 89 (102)
++|+|.+.++.+|+.|+.+..|..++|.|+|..+ +..+.|+..++.+..+ .. ...+|. .-+.++-++
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 5899999999999999999999999999999874 3466666666654322 11 112232 234456677
Q ss_pred HHhhCCCCCcccC
Q 034157 90 LREVNVDNNTVGW 102 (102)
Q Consensus 90 ~k~v~~~e~iVGW 102 (102)
.+..+.+..+|||
T Consensus 82 ~~~~~rgl~vVGw 94 (244)
T cd08068 82 TEETGRPMRVVGW 94 (244)
T ss_pred HhhccCCceEEEE
Confidence 8889999999999
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=97.70 E-value=0.00017 Score=48.96 Aligned_cols=70 Identities=27% Similarity=0.271 Sum_probs=52.2
Q ss_pred HHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCCCch---hhhchHHHHHHHHHHHHhhCCCCCcccC
Q 034157 31 VMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEEDEE---IEADGANYQLEMMRCLREVNVDNNTVGW 102 (102)
Q Consensus 31 VlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~---~~~~d~~y~~~ml~~~k~v~~~e~iVGW 102 (102)
++-+|++|+++..|.++.|.|+|..++....|+..|++|....+ ....|...+..+.+..++. +..+|||
T Consensus 3 ~~~~il~ha~~~~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~--g~~~vG~ 75 (128)
T cd08070 3 LLEAILAHAEAEYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARER--GLEVVGI 75 (128)
T ss_pred HHHHHHHHHHhCCCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHC--CCeEEEE
Confidence 56789999999999999999999998777678999999953322 2235666666666666544 4777776
No 21
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.56 E-value=0.00013 Score=53.70 Aligned_cols=48 Identities=27% Similarity=0.431 Sum_probs=43.6
Q ss_pred EEEEeehHHHHHHHHHhhcCCceeEEEEeeeEeCC--EEEEEeeeecCCC
Q 034157 24 VVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGS--VLEVTNCFPFPEE 71 (102)
Q Consensus 24 ~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~~~--~veVtnsF~~P~~ 71 (102)
+|+|++.+..||+=|+...+...|.|.|||...++ .|+|+||.|+=+.
T Consensus 3 ~v~is~~AY~K~~LHaaKyP~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~ 52 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYPHCAVNGVLLGKSSKSSSEVEIVDAVPLFHH 52 (196)
T ss_pred eEEEcHHHHHHHHHHhccCCCCceeeEEEeccCCCCceEEEeeceecccc
Confidence 68999999999999999999999999999998654 3999999999873
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=97.52 E-value=0.00016 Score=52.67 Aligned_cols=44 Identities=27% Similarity=0.526 Sum_probs=39.3
Q ss_pred eehHHHHHHHHHhhcCCceeEEEEeeeEe-CCEEEEEeeeecCCC
Q 034157 28 EGLVMLKIIKHCKEFSPALVTGQLLGLDV-GSVLEVTNCFPFPEE 71 (102)
Q Consensus 28 hplVlLkI~dH~~r~~~~~v~G~LLG~~~-~~~veVtnsF~~P~~ 71 (102)
.+.++.||+.|+.+.++..|.|.|+|... ++.+.|++++|+.+.
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 45788999999999878899999999987 778999999999974
No 23
>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=97.43 E-value=0.00074 Score=48.79 Aligned_cols=74 Identities=16% Similarity=0.148 Sum_probs=52.3
Q ss_pred EEEEeehHHHHHHHHHhhcC--CceeEEEEeeeEeCCEEEEEeeeecCCCCchhh--hchHHHHHHHHHHHHhhCCCCCc
Q 034157 24 VVQIEGLVMLKIIKHCKEFS--PALVTGQLLGLDVGSVLEVTNCFPFPEEDEEIE--ADGANYQLEMMRCLREVNVDNNT 99 (102)
Q Consensus 24 ~V~ihplVlLkI~dH~~r~~--~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~~--~~d~~y~~~ml~~~k~v~~~e~i 99 (102)
.+.|..-.+-+|+.|+.++. +..+.|.|+|...++..+|+++|..|....... ..+. .++++..+ ..+..+
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 46677778899999999995 589999999998888999999977775443321 1221 12333222 456799
Q ss_pred ccC
Q 034157 100 VGW 102 (102)
Q Consensus 100 VGW 102 (102)
|||
T Consensus 78 vGw 80 (173)
T cd08066 78 LGW 80 (173)
T ss_pred EEE
Confidence 998
No 24
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=97.04 E-value=0.00088 Score=49.29 Aligned_cols=47 Identities=34% Similarity=0.606 Sum_probs=42.6
Q ss_pred EEEEeehHHHHHHHHHhhcCCceeEEEEeee--EeCCEEEEEeeeecCC
Q 034157 24 VVQIEGLVMLKIIKHCKEFSPALVTGQLLGL--DVGSVLEVTNCFPFPE 70 (102)
Q Consensus 24 ~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~--~~~~~veVtnsF~~P~ 70 (102)
.|+|+.++..||+=|+.+.+..-|.|.|+|. -.|+.++|++|.|+=+
T Consensus 3 ~veis~~aY~kmiLH~akyph~aVnGLLla~~~~kg~~v~itdcVPLfH 51 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPHAAVNGLLLAPATGKGECVEITDCVPLFH 51 (199)
T ss_pred ceeehhhHHHHHHHHhccCcccceeeEEEeccCCCCCeEEEEecchhhc
Confidence 5899999999999999999999999999995 4678999999999865
No 25
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=96.78 E-value=0.0032 Score=43.00 Aligned_cols=70 Identities=26% Similarity=0.410 Sum_probs=46.9
Q ss_pred EEEeehHHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCCCch---hhhchHHHHHHHHHHHHhhCCCCCccc
Q 034157 25 VQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEEDEE---IEADGANYQLEMMRCLREVNVDNNTVG 101 (102)
Q Consensus 25 V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~---~~~~d~~y~~~ml~~~k~v~~~e~iVG 101 (102)
+.|...++-.|+.|+.|..|.++.|.|+|...+ ...|+++..+.+ ....+.++.. ++...++. ++.+||
T Consensus 2 ~~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~~--g~~vvg 73 (134)
T COG1310 2 LVIPKEVLGAILEHARREHPREVCGLLAGTREG-----ERYFPLKNVSVEPVEYFEIDPEYSL-FYLAAEDA--GEVVVG 73 (134)
T ss_pred ceecHHHHHHHHHHHHhcCChheEEEEEeeccc-----ceeeccccccCCcceeEeeCHHHHH-HHHHHhhC--CCEEEE
Confidence 356677889999999999999999999999866 455555532211 1234444444 33333333 389999
Q ss_pred C
Q 034157 102 W 102 (102)
Q Consensus 102 W 102 (102)
|
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=93.12 E-value=0.26 Score=33.19 Aligned_cols=36 Identities=22% Similarity=0.297 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCC
Q 034157 31 VMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPE 70 (102)
Q Consensus 31 VlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~ 70 (102)
.+-.|++|+++..|..+-|.|+|... .|++.+++|.
T Consensus 5 ~~~~i~~ha~~~~P~E~CGlL~G~~~----~v~~~~~~~n 40 (117)
T cd08072 5 LLDSILEAAKSSHPNEFAALLRGKDG----VITELLILPG 40 (117)
T ss_pred HHHHHHHHHhhcCCceEEEEEEeecc----EEEEEEECCC
Confidence 45589999999999999999999764 6899999994
No 27
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=92.56 E-value=0.69 Score=29.44 Aligned_cols=37 Identities=27% Similarity=0.301 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeee
Q 034157 31 VMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFP 67 (102)
Q Consensus 31 VlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~ 67 (102)
++-.|+.|+++..+.++-|.|+|...+..+.++....
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 5668999999999999999999999777777777765
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=89.80 E-value=2.1 Score=29.78 Aligned_cols=69 Identities=12% Similarity=0.178 Sum_probs=39.9
Q ss_pred HHHHHHHHhhcC--CceeEEEEeeeEeCCEEEEEeeeecCCCCch---hh-hchHHHHHHHHH-HHHhhCCCCCccc
Q 034157 32 MLKIIKHCKEFS--PALVTGQLLGLDVGSVLEVTNCFPFPEEDEE---IE-ADGANYQLEMMR-CLREVNVDNNTVG 101 (102)
Q Consensus 32 lLkI~dH~~r~~--~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~---~~-~~d~~y~~~ml~-~~k~v~~~e~iVG 101 (102)
+++++..|+... +.+.=|.|+|.+.+..+.|+++- .|..++- .. .-+..++++.++ .+++.+-....||
T Consensus 2 v~~~~~~~~Q~~~~~~EtGGiLiG~~~~~~~ii~~~t-~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylG 77 (131)
T TIGR02256 2 VVAMLKSYRQWHDLSTETGGVLIGERRGAHAVITKIS-EPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLG 77 (131)
T ss_pred HHHHHHHHHhCcCCCCccceEEEEEEcCCcEEEEEEE-cCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEE
Confidence 566676665554 47899999999988888888855 4432221 11 124555555554 4444333334443
No 29
>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=73.63 E-value=8.6 Score=24.49 Aligned_cols=37 Identities=22% Similarity=0.257 Sum_probs=28.6
Q ss_pred HHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCC
Q 034157 32 MLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEE 71 (102)
Q Consensus 32 lLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~ 71 (102)
+-.|.+|+....|.+..|.|+|...+ .+.+..++|..
T Consensus 3 ~~~i~~~~~~~~p~E~~gll~~~~~~---~~~~~~~~~~~ 39 (101)
T cd08059 3 LKTILVHAKDAHPDEFCGFLSGSKDN---VMDELIFLPFV 39 (101)
T ss_pred HHHHHHHHHhcCChhhheeeecCCCC---eEEEEEeCCCc
Confidence 34578888888899999999997543 67788888753
No 30
>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=72.09 E-value=7.1 Score=25.81 Aligned_cols=33 Identities=18% Similarity=0.178 Sum_probs=25.1
Q ss_pred HHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecC
Q 034157 32 MLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFP 69 (102)
Q Consensus 32 lLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P 69 (102)
+-.|++|+++..|.+.-|.|+|.. .++..|+++
T Consensus 3 ~~~i~~ha~~~~P~E~CGll~g~~-----~~~~~~p~~ 35 (108)
T cd08073 3 EDAILAHAKAEYPREACGLVVRKG-----RKLRYIPCR 35 (108)
T ss_pred HHHHHHHHhHCCCCcceEEEEecC-----CceEEEECc
Confidence 447899999999999999999965 234445555
No 31
>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=66.31 E-value=53 Score=25.46 Aligned_cols=55 Identities=13% Similarity=0.053 Sum_probs=39.1
Q ss_pred CCCCceEEEEeehHHHHHHHH-HhhcCCceeEEEEeeeEeCC-------EEEEEeeeecCCCC
Q 034157 18 VAPPLRVVQIEGLVMLKIIKH-CKEFSPALVTGQLLGLDVGS-------VLEVTNCFPFPEED 72 (102)
Q Consensus 18 ~~~~~~~V~ihplVlLkI~dH-~~r~~~~~v~G~LLG~~~~~-------~veVtnsF~~P~~~ 72 (102)
..+-+.+|...-..+..=.-+ +.|......+|.|.|..+.. .+.|.--|+=|.++
T Consensus 6 ~~r~Vd~vef~~~~~~~~f~~~~w~~~~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~ 68 (274)
T cd08061 6 KYRHVDHVEFDNPSIVEFFLYVFWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEG 68 (274)
T ss_pred cCCCcCEEEEecHHHHHHHHHHHHHhhcceeEEEEEEEeecccCCCCceEEEEEEEECCCccC
Confidence 344566777777776655555 66666678889999998543 78888888877544
No 32
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=65.03 E-value=9.6 Score=22.86 Aligned_cols=33 Identities=30% Similarity=0.358 Sum_probs=24.2
Q ss_pred eeecCCC------CchhhhchHHHHHHHHHHHHhhCCCC
Q 034157 65 CFPFPEE------DEEIEADGANYQLEMMRCLREVNVDN 97 (102)
Q Consensus 65 sF~~P~~------~~~~~~~d~~y~~~ml~~~k~v~~~e 97 (102)
.|+.|.. +.+....|.+|+.+....+|+||-++
T Consensus 14 ~~~Cp~cGipthcS~ehw~~D~e~H~~~c~~LRqvNede 52 (55)
T PF13824_consen 14 NFECPDCGIPTHCSEEHWEDDYEEHRQLCERLRQVNEDE 52 (55)
T ss_pred CCcCCCCCCcCccCHHHHHHhHHHHHHHHHHHHHhcccc
Confidence 4666632 23335678899999999999999876
No 33
>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=57.77 E-value=14 Score=25.80 Aligned_cols=39 Identities=18% Similarity=0.367 Sum_probs=24.7
Q ss_pred HHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCC
Q 034157 31 VMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEE 71 (102)
Q Consensus 31 VlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~ 71 (102)
.+-+|+.+|.+...-.+.| +|-.....-.+++||++-.+
T Consensus 19 ~vg~il~~Yd~dk~~p~~G--FGa~~~~~~~vsh~F~ln~~ 57 (146)
T PF07002_consen 19 AVGEILQDYDSDKMIPAYG--FGAKIPPDYSVSHCFPLNGN 57 (146)
T ss_pred HHHHHHHhhccCCccceec--cCCcCCCCcccccceeeecC
Confidence 4566777776665555655 24333335568999999754
No 34
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=51.76 E-value=19 Score=28.87 Aligned_cols=40 Identities=25% Similarity=0.505 Sum_probs=33.3
Q ss_pred HHHHHHHHHhhcCC------ceeEEEEeeeEeCCEEEEEeeeecCC
Q 034157 31 VMLKIIKHCKEFSP------ALVTGQLLGLDVGSVLEVTNCFPFPE 70 (102)
Q Consensus 31 VlLkI~dH~~r~~~------~~v~G~LLG~~~~~~veVtnsF~~P~ 70 (102)
++..|+.||++... ...+=+|.|+.++..+.+|-||-+=+
T Consensus 96 ii~~lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H 141 (368)
T KOG4445|consen 96 IICQLIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMH 141 (368)
T ss_pred hhHHHHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHH
Confidence 57899999988742 56778999999999999999997653
No 35
>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=47.67 E-value=32 Score=25.50 Aligned_cols=41 Identities=10% Similarity=0.061 Sum_probs=30.7
Q ss_pred EEeehHHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecC
Q 034157 26 QIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFP 69 (102)
Q Consensus 26 ~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P 69 (102)
+|-.-.+=+|+.|+++..|.++-|.+.|...++.. ..+++.
T Consensus 74 ~Ip~~l~~~ii~hAr~~~P~EacG~Iag~~~~~~~---r~~p~~ 114 (192)
T TIGR03735 74 PIPASLLEEFAEAARAALPNEVAAWIVWNSETGSL---RLAALE 114 (192)
T ss_pred CCCHHHHHHHHHHHHhcCCcceEEEEEEcCCCCEE---EEEecc
Confidence 55556778999999999999999999997444443 335554
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=42.28 E-value=20 Score=16.34 Aligned_cols=10 Identities=30% Similarity=0.388 Sum_probs=8.1
Q ss_pred eCCEEEEEee
Q 034157 56 VGSVLEVTNC 65 (102)
Q Consensus 56 ~~~~veVtns 65 (102)
.++++||.|+
T Consensus 6 rdNsLeIsn~ 15 (16)
T PF07620_consen 6 RDNSLEISNQ 15 (16)
T ss_pred cCCeEEEeec
Confidence 4789999886
No 37
>PF14232 DUF4334: Domain of unknown function (DUF4334)
Probab=33.73 E-value=15 Score=22.29 Aligned_cols=23 Identities=26% Similarity=0.372 Sum_probs=18.4
Q ss_pred HHHHHHHhhcCCceeEEEEeeeE
Q 034157 33 LKIIKHCKEFSPALVTGQLLGLD 55 (102)
Q Consensus 33 LkI~dH~~r~~~~~v~G~LLG~~ 55 (102)
+-|+||+++.....++|.+=+..
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 34789999999999999876554
No 38
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=31.57 E-value=84 Score=24.99 Aligned_cols=47 Identities=21% Similarity=0.179 Sum_probs=30.3
Q ss_pred EEEeeeE-eCCEEEEEeeeecCCCCchhh------------hchHHHHHHHHHHHHhhCC
Q 034157 49 GQLLGLD-VGSVLEVTNCFPFPEEDEEIE------------ADGANYQLEMMRCLREVNV 95 (102)
Q Consensus 49 G~LLG~~-~~~~veVtnsF~~P~~~~~~~------------~~d~~y~~~ml~~~k~v~~ 95 (102)
|.|+|.. ..+.--|-+..+.|.++++.. .+|.+|..+--.+.-+.-|
T Consensus 1 GLlIGq~~s~~kd~Vv~l~~tP~~d~~~~~~~~~~~~~~~~~id~~WVaeHA~qVsRMLP 60 (362)
T PF14778_consen 1 GLLIGQSSSSQKDYVVHLARTPPEDTDDEESDVRTSDSSIKDIDEEWVAEHARQVSRMLP 60 (362)
T ss_pred CeEeccccCCCcceEEEecCCCCccccccccccccccccccccCHHHHHHHHHHHHhhCC
Confidence 7899998 666778999999996542222 3577776554444333333
No 39
>COG2957 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]
Probab=31.35 E-value=86 Score=25.30 Aligned_cols=69 Identities=14% Similarity=0.190 Sum_probs=41.4
Q ss_pred CCCCceEEEEeehHHHHHHHHHhhcCCceeEEEEeeeEeCCEEEEEeeeecCCCCchhhhchHHHHHHHHHHHHhhCCCC
Q 034157 18 VAPPLRVVQIEGLVMLKIIKHCKEFSPALVTGQLLGLDVGSVLEVTNCFPFPEEDEEIEADGANYQLEMMRCLREVNVDN 97 (102)
Q Consensus 18 ~~~~~~~V~ihplVlLkI~dH~~r~~~~~v~G~LLG~~~~~~veVtnsF~~P~~~~~~~~~d~~y~~~ml~~~k~v~~~e 97 (102)
.+......+||+|.+- ++.......|..++..-+ +.+-++.-+|.-++...++ -++.+++.+|+.
T Consensus 255 ~d~~G~~~~l~~Lp~P---~~~~~e~~~rL~aSY~NF-----lI~N~avIvP~y~D~~D~~-------a~~~L~~~fP~r 319 (346)
T COG2957 255 RDAKGRPLKLHKLPIP---KPVTDEDGERLPASYVNF-----LIINGAVIVPQYDDPNDAL-------ALDVLQQAFPGR 319 (346)
T ss_pred cccCCCeeEEEEcCCC---cccccccCCCCcccceeE-----EEecCeEEeeccCCcchHH-------HHHHHHHhCCCC
Confidence 4445667888888765 455555444444443333 3444555677544332222 267789999999
Q ss_pred Cccc
Q 034157 98 NTVG 101 (102)
Q Consensus 98 ~iVG 101 (102)
.|||
T Consensus 320 eVVG 323 (346)
T COG2957 320 EVVG 323 (346)
T ss_pred eEec
Confidence 9998
No 40
>KOG4832 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.62 E-value=25 Score=27.06 Aligned_cols=29 Identities=24% Similarity=0.587 Sum_probs=21.3
Q ss_pred CceEEEEee--hHHHHHHHHHhhcCCceeEE
Q 034157 21 PLRVVQIEG--LVMLKIIKHCKEFSPALVTG 49 (102)
Q Consensus 21 ~~~~V~ihp--lVlLkI~dH~~r~~~~~v~G 49 (102)
++.+-+++| -|+|+|+.||+|-+..|..|
T Consensus 217 ~~~~lkld~~f~~~l~~LRH~rRisE~R~gg 247 (253)
T KOG4832|consen 217 EFTTLKLDKKFHVLLNILRHCRRISEVRGGG 247 (253)
T ss_pred chhhhhcchhhhHHHHHHHHHHHHhhhhcCC
Confidence 344455555 48999999999988766655
No 41
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=27.13 E-value=32 Score=22.76 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=22.5
Q ss_pred ceeEEEEeeeEeCCEEEEEeeeecCC
Q 034157 45 ALVTGQLLGLDVGSVLEVTNCFPFPE 70 (102)
Q Consensus 45 ~~v~G~LLG~~~~~~veVtnsF~~P~ 70 (102)
..++|.|=|++..-.+-+++||.=-+
T Consensus 21 r~ivgsLkGFDq~tNlii~~~heRi~ 46 (96)
T KOG1784|consen 21 RVIVGSLKGFDQTTNLIIDESHERIF 46 (96)
T ss_pred eEEEEEeccccccceeeehhhHhhhh
Confidence 45789999999888999999998664
No 42
>smart00459 Sorb Sorbin homologous domain. First found in the peptide hormone sorbin and later in the ponsin/ArgBP2/vinexin family of proteins.
Probab=27.11 E-value=93 Score=18.30 Aligned_cols=20 Identities=10% Similarity=0.243 Sum_probs=16.3
Q ss_pred hHHHHHHHHHHHHhhCCCCC
Q 034157 79 GANYQLEMMRCLREVNVDNN 98 (102)
Q Consensus 79 d~~y~~~ml~~~k~v~~~e~ 98 (102)
..+|.++|++.++++..+..
T Consensus 28 ~~dWYk~MfkqiHk~~~d~~ 47 (50)
T smart00459 28 PKDWYRTMFKQIHRKGPDGD 47 (50)
T ss_pred HHHHHHHHHHHHHccCCCcc
Confidence 34599999999998887764
No 43
>KOG2550 consensus IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism]
Probab=24.51 E-value=59 Score=27.31 Aligned_cols=23 Identities=30% Similarity=0.538 Sum_probs=21.1
Q ss_pred hHHHHHHHHHHHHhhCCCCCccc
Q 034157 79 GANYQLEMMRCLREVNVDNNTVG 101 (102)
Q Consensus 79 d~~y~~~ml~~~k~v~~~e~iVG 101 (102)
+..||-+|++..|+.+|+..++|
T Consensus 275 nS~~qiemik~iK~~yP~l~Via 297 (503)
T KOG2550|consen 275 NSIYQLEMIKYIKETYPDLQIIA 297 (503)
T ss_pred cchhHHHHHHHHHhhCCCceeec
Confidence 56899999999999999999876
No 44
>PF10813 DUF2733: Protein of unknown function (DUF2733); InterPro: IPR024360 The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment []. UL11 is acylated, which is crucial for lipid raft association [].
Probab=21.12 E-value=54 Score=17.56 Aligned_cols=20 Identities=25% Similarity=0.433 Sum_probs=11.1
Q ss_pred EEEEeeeE----------eCCEEEEEeeee
Q 034157 48 TGQLLGLD----------VGSVLEVTNCFP 67 (102)
Q Consensus 48 ~G~LLG~~----------~~~~veVtnsF~ 67 (102)
||.|+|.+ +|+.|.+++-|+
T Consensus 1 MG~~~s~Ckrr~n~l~Dv~G~~Inl~~dFe 30 (32)
T PF10813_consen 1 MGSLLSMCKRRHNPLKDVKGNPINLYKDFE 30 (32)
T ss_pred CcceeeeeeccCCcccccCCCEEechhccc
Confidence 46666654 345566655554
No 45
>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=20.82 E-value=1.6e+02 Score=23.20 Aligned_cols=25 Identities=24% Similarity=0.217 Sum_probs=19.1
Q ss_pred EEEEeeeEeC-C------EEEEEeeeecCCCC
Q 034157 48 TGQLLGLDVG-S------VLEVTNCFPFPEED 72 (102)
Q Consensus 48 ~G~LLG~~~~-~------~veVtnsF~~P~~~ 72 (102)
+|.|.|.++. . ...|.--|+=|.++
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~ 33 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEG 33 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCC
Confidence 6999999843 2 68888888888644
No 46
>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=20.58 E-value=1.4e+02 Score=15.07 Aligned_cols=21 Identities=29% Similarity=0.621 Sum_probs=14.3
Q ss_pred eeEEEEeeeEeCCEEEEEeeee
Q 034157 46 LVTGQLLGLDVGSVLEVTNCFP 67 (102)
Q Consensus 46 ~v~G~LLG~~~~~~veVtnsF~ 67 (102)
..+|-|.|.-.++ =.|+||++
T Consensus 3 ~~vGGlvG~~~~~-~~I~nc~a 23 (28)
T PF07581_consen 3 YYVGGLVGYNDNG-GSITNCYA 23 (28)
T ss_pred ccEEeEEEECCCC-CEEEEEEE
Confidence 3568888886542 45788876
No 47
>KOG3446 consensus NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion]
Probab=20.26 E-value=87 Score=20.68 Aligned_cols=22 Identities=14% Similarity=0.132 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHHhhCCCCCcc
Q 034157 79 GANYQLEMMRCLREVNVDNNTV 100 (102)
Q Consensus 79 d~~y~~~ml~~~k~v~~~e~iV 100 (102)
-.+|.++.+-.+|+.||+.-|+
T Consensus 32 vR~fvEk~Y~~lKkaNP~lPIL 53 (97)
T KOG3446|consen 32 VREFVEKFYVNLKKANPDLPIL 53 (97)
T ss_pred HHHHHHHhhhhhhhcCCCCcEe
Confidence 4589999999999999998654
Done!