Query psy12650
Match_columns 90
No_of_seqs 101 out of 240
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 16:03:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12650.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12650hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2880|consensus 99.9 5.3E-24 1.2E-28 172.1 2.5 61 30-90 267-332 (424)
2 KOG2880|consensus 99.8 2E-21 4.4E-26 157.3 4.2 61 1-61 287-351 (424)
3 cd08056 MPN_PRP8 Mpr1p, Pad1p 99.0 9.9E-10 2.1E-14 85.1 5.4 59 29-90 47-113 (252)
4 cd08066 MPN_AMSH_like Mov34/MP 98.8 1.1E-08 2.5E-13 74.4 7.2 63 28-90 12-82 (173)
5 cd08056 MPN_PRP8 Mpr1p, Pad1p 98.7 1.8E-08 3.9E-13 78.1 3.8 43 3-47 72-114 (252)
6 cd08066 MPN_AMSH_like Mov34/MP 98.2 3.6E-06 7.8E-11 61.4 5.0 45 3-47 39-83 (173)
7 cd08067 MPN_2A_DUB Mov34/MPN/P 97.4 0.00045 9.8E-09 51.1 5.8 53 38-90 25-86 (187)
8 cd08061 MPN_NPL4 Mov34/MPN/PAD 97.3 0.00078 1.7E-08 52.7 6.4 58 33-90 28-100 (274)
9 cd07767 MPN Mpr1p, Pad1p N-ter 97.0 0.0029 6.3E-08 40.9 6.1 60 31-90 5-70 (116)
10 cd08058 MPN_euk_mb Mpr1p, Pad1 96.8 0.0055 1.2E-07 41.1 6.3 54 37-90 14-72 (119)
11 cd08061 MPN_NPL4 Mov34/MPN/PAD 96.4 0.0091 2E-07 46.8 5.6 69 3-80 54-125 (274)
12 cd08067 MPN_2A_DUB Mov34/MPN/P 96.0 0.013 2.9E-07 43.3 4.7 45 3-47 41-87 (187)
13 cd08069 MPN_RPN11_CSN5 Mov34/M 95.1 0.087 1.9E-06 40.7 6.4 55 36-90 29-94 (268)
14 cd07767 MPN Mpr1p, Pad1p N-ter 94.8 0.067 1.4E-06 34.4 4.3 45 3-47 27-71 (116)
15 PF05021 NPL4: NPL4 family; I 94.2 0.15 3.3E-06 40.6 5.9 48 42-89 2-64 (306)
16 smart00232 JAB_MPN JAB/MPN dom 93.5 0.33 7.2E-06 31.8 5.8 54 36-90 19-83 (135)
17 PF01398 JAB: JAB1/Mov34/MPN/P 92.5 0.45 9.9E-06 31.1 5.2 51 40-90 27-88 (114)
18 cd08058 MPN_euk_mb Mpr1p, Pad1 89.0 0.77 1.7E-05 30.7 4.0 41 7-47 33-73 (119)
19 cd08070 MPN_like Mpr1p, Pad1p 88.7 2.9 6.4E-05 28.1 6.7 62 29-90 6-77 (128)
20 PF01398 JAB: JAB1/Mov34/MPN/P 87.4 0.34 7.4E-06 31.7 1.4 55 4-58 41-104 (114)
21 cd08068 MPN_BRCC36 Mov34/MPN/P 87.2 2 4.3E-05 33.4 5.7 54 37-90 22-96 (244)
22 cd08069 MPN_RPN11_CSN5 Mov34/M 87.0 1.4 2.9E-05 34.1 4.7 46 2-47 44-95 (268)
23 PF05021 NPL4: NPL4 family; I 85.4 1.7 3.6E-05 34.7 4.6 74 5-80 21-101 (306)
24 smart00232 JAB_MPN JAB/MPN dom 83.0 3.6 7.7E-05 26.8 4.7 44 4-47 36-84 (135)
25 KOG2834|consensus 71.2 2.4 5.3E-05 36.3 1.6 42 6-47 220-264 (510)
26 PF14464 Prok-JAB: Prokaryotic 60.3 25 0.00053 22.1 4.4 57 29-90 7-66 (104)
27 KOG2834|consensus 53.3 34 0.00074 29.6 5.2 61 29-89 187-262 (510)
28 cd08068 MPN_BRCC36 Mov34/MPN/P 49.6 30 0.00065 26.9 4.0 34 14-47 56-97 (244)
29 COG1310 Predicted metal-depend 27.9 1.8E+02 0.0038 19.5 4.7 55 33-90 16-76 (134)
30 TIGR02256 ICE_VC0181 integrati 27.3 2.3E+02 0.0049 20.0 5.7 31 29-59 5-42 (131)
31 cd08065 MPN_eIF3h Mpr1p, Pad1p 26.6 1.4E+02 0.0031 22.8 4.5 55 36-90 20-86 (266)
32 PF03634 TCP: TCP family trans 20.6 26 0.00056 24.2 -0.6 20 28-47 30-53 (138)
No 1
>KOG2880|consensus
Probab=99.88 E-value=5.3e-24 Score=172.14 Aligned_cols=61 Identities=51% Similarity=0.784 Sum_probs=58.0
Q ss_pred hhhhhhhCCceEEeeeee-----eEEEeEEeeeccccCCCCceecchhHHHHhhhcCCceEeeeeC
Q psy12650 30 IFACQDKYNLITLGWIHW-----QLHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIH 90 (90)
Q Consensus 30 ~f~~~~~~~l~tcGwIht-----~~~it~l~iP~Q~~t~dsC~t~~Ee~~f~~~~~~~l~~lGWIH 90 (90)
+..-++++||||||+|+| .|+|||||||||++|||+|.|+||||+|++||+++|++|||||
T Consensus 267 la~~NT~knlETCGiL~g~L~~n~f~IThliiPkQeatsd~C~t~neeelF~vQdq~~L~tlGWIH 332 (424)
T KOG2880|consen 267 LAKSNTKKNLETCGILAGKLERNEFYITHLIIPKQEATSDSCNTMNEEELFEVQDQHELLTLGWIH 332 (424)
T ss_pred HHhhcccccchHHHHhhhHhhcCcEEEEEEEeecccCCCccccccCHHHHheecccccceeeeeee
Confidence 444588999999999999 9999999999999999999999999999999999999999999
No 2
>KOG2880|consensus
Probab=99.83 E-value=2e-21 Score=157.25 Aligned_cols=61 Identities=44% Similarity=0.740 Sum_probs=56.4
Q ss_pred CcccEEEEEEEeeCcccCCCcccccchhhhhhhhhhCCceEEeeeee----eEEEeEEeeecccc
Q psy12650 1 VQSELHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIHW----QLHITHLLIPKQAG 61 (90)
Q Consensus 1 ~~~~~~it~liIPkQ~~t~dsC~t~~Ee~~f~~~~~~~l~tcGwIht----~~~it~l~iP~Q~~ 61 (90)
.+|+|+|||||||||++|||||.|+||||+|++||+++|.|+||||| ++|++++.++.-++
T Consensus 287 ~~n~f~IThliiPkQeatsd~C~t~neeelF~vQdq~~L~tlGWIHTHPTQt~FmSSVDlHTHcS 351 (424)
T KOG2880|consen 287 ERNEFYITHLIIPKQEATSDSCNTMNEEELFEVQDQHELLTLGWIHTHPTQTCFMSSVDLHTHCS 351 (424)
T ss_pred hcCcEEEEEEEeecccCCCccccccCHHHHheecccccceeeeeeecCCccchhheeccccccce
Confidence 37999999999999999999999999999999999999999999999 88888888876543
No 3
>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=98.96 E-value=9.9e-10 Score=85.09 Aligned_cols=59 Identities=20% Similarity=0.281 Sum_probs=51.3
Q ss_pred hhhhhhhhCCceEEeeeee--------eEEEeEEeeeccccCCCCceecchhHHHHhhhcCCceEeeeeC
Q psy12650 29 EIFACQDKYNLITLGWIHW--------QLHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIH 90 (90)
Q Consensus 29 ~~f~~~~~~~l~tcGwIht--------~~~it~l~iP~Q~~t~dsC~t~~Ee~~f~~~~~~~l~~lGWIH 90 (90)
.++.++|. +.++||+|+| ...|.++++|.|.|++|+|.+.++. ++.++.+||.+|||||
T Consensus 47 kFi~iaD~-rtQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~--~~~~~l~~Le~LGWIH 113 (252)
T cd08056 47 KFISISDL-RTQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQL--PQHEYLEDLEPLGWIH 113 (252)
T ss_pred HHHHHhhh-cceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccC--ccchhhCCCEeeEEEE
Confidence 44455554 4489999999 6799999999999999999999874 8899999999999999
No 4
>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=98.84 E-value=1.1e-08 Score=74.44 Aligned_cols=63 Identities=51% Similarity=0.831 Sum_probs=55.6
Q ss_pred hhhhhhhhh---CCceEEeeeee-----eEEEeEEeeeccccCCCCceecchhHHHHhhhcCCceEeeeeC
Q psy12650 28 EEIFACQDK---YNLITLGWIHW-----QLHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIH 90 (90)
Q Consensus 28 e~~f~~~~~---~~l~tcGwIht-----~~~it~l~iP~Q~~t~dsC~t~~Ee~~f~~~~~~~l~~lGWIH 90 (90)
+++++.+++ ++.|+||.|.| ...|+.+++|.|.+++++|...++++++++++.+||-.+||+|
T Consensus 12 ~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~~~e~~~~~~~~gle~vGwyH 82 (173)
T cd08066 12 DKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTNEEELFDFQDQHDLITLGWIH 82 (173)
T ss_pred HHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCCHHHHHHHHHhCCCeeEEEEe
Confidence 355666666 46899999999 4578999999999999999999999999999999999999999
No 5
>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=98.67 E-value=1.8e-08 Score=78.10 Aligned_cols=43 Identities=23% Similarity=0.289 Sum_probs=40.7
Q ss_pred ccEEEEEEEeeCcccCCCcccccchhhhhhhhhhCCceEEeeeee
Q psy12650 3 SELHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIHW 47 (90)
Q Consensus 3 ~~~~it~liIPkQ~~t~dsC~t~~Ee~~f~~~~~~~l~tcGwIht 47 (90)
|+..|+++++|.|.|++|+|.+.++. ++.+...||+++|||||
T Consensus 72 ~vkeI~cIvipPQ~gt~~sv~l~~~~--~~~~~l~~Le~LGWIHT 114 (252)
T cd08056 72 QVKEIRCIVLVPQLGTHQTVTLPQQL--PQHEYLEDLEPLGWIHT 114 (252)
T ss_pred CeEEEEEEEECCEeCCcCcEECCccC--ccchhhCCCEeeEEEEc
Confidence 67899999999999999999999884 88999999999999999
No 6
>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=98.16 E-value=3.6e-06 Score=61.35 Aligned_cols=45 Identities=62% Similarity=1.043 Sum_probs=42.5
Q ss_pred ccEEEEEEEeeCcccCCCcccccchhhhhhhhhhCCceEEeeeee
Q psy12650 3 SELHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIHW 47 (90)
Q Consensus 3 ~~~~it~liIPkQ~~t~dsC~t~~Ee~~f~~~~~~~l~tcGwIht 47 (90)
+.+.|+.+++|.|.+++++|...++++++++++.+|++.+||+|+
T Consensus 39 ~~~~I~~i~~~~q~~~~~~~~~~~~~e~~~~~~~~gle~vGwyHS 83 (173)
T cd08066 39 NAFFITHLIIPKQSGTSDSCQTTNEEELFDFQDQHDLITLGWIHT 83 (173)
T ss_pred CeEEEEEEEeccccCCCceecCCCHHHHHHHHHhCCCeeEEEEec
Confidence 467899999999999999999999999999999999999999999
No 7
>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=97.40 E-value=0.00045 Score=51.07 Aligned_cols=53 Identities=23% Similarity=0.324 Sum_probs=45.7
Q ss_pred CceEEeeeee-------eEEEeEEeeeccccCCCCcee--cchhHHHHhhhcCCceEeeeeC
Q psy12650 38 NLITLGWIHW-------QLHITHLLIPKQAGTADSCIT--HHEEEIFACQDKYNLITLGWIH 90 (90)
Q Consensus 38 ~l~tcGwIht-------~~~it~l~iP~Q~~t~dsC~t--~~Ee~~f~~~~~~~l~~lGWIH 90 (90)
..|.||.|-| .+.|+.+..+.+..+++.|+. ..+.+++++++++|+..+||.|
T Consensus 25 ~~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~gl~vVGwYH 86 (187)
T cd08067 25 TSEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRGLSVVGWYH 86 (187)
T ss_pred CcEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcCCEEEEEEe
Confidence 3789999988 457888888888888999987 4567899999999999999998
No 8
>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=97.30 E-value=0.00078 Score=52.72 Aligned_cols=58 Identities=21% Similarity=0.315 Sum_probs=49.1
Q ss_pred hhhhCCceEEeeeee------------eEEEeEEeeeccccCCCCceecch---hHHHHhhhcCCceEeeeeC
Q psy12650 33 CQDKYNLITLGWIHW------------QLHITHLLIPKQAGTADSCITHHE---EEIFACQDKYNLITLGWIH 90 (90)
Q Consensus 33 ~~~~~~l~tcGwIht------------~~~it~l~iP~Q~~t~dsC~t~~E---e~~f~~~~~~~l~~lGWIH 90 (90)
+..+-+..-+|||.| ...+..+.-|.|.|++|.++...+ +.+-+++...||..+|||+
T Consensus 28 ~w~~~~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA~~lGL~~VG~If 100 (274)
T cd08061 28 FWRKTGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIAAALGLERVGWIF 100 (274)
T ss_pred HHHhhcceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHHHHcCCeEEEEEE
Confidence 445678889999999 357778888999999999999744 6788889999999999995
No 9
>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=97.03 E-value=0.0029 Score=40.90 Aligned_cols=60 Identities=10% Similarity=0.062 Sum_probs=42.9
Q ss_pred hhhhhhC-CceEEeeeee-----eEEEeEEeeeccccCCCCceecchhHHHHhhhcCCceEeeeeC
Q psy12650 31 FACQDKY-NLITLGWIHW-----QLHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIH 90 (90)
Q Consensus 31 f~~~~~~-~l~tcGwIht-----~~~it~l~iP~Q~~t~dsC~t~~Ee~~f~~~~~~~l~~lGWIH 90 (90)
+..+.+. ..+.||+|-| ...|+.+..+.|....+.+.......+...+.+.|+-.+||+|
T Consensus 5 l~~a~~~~~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyh 70 (116)
T cd07767 5 LDAAKSINGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYH 70 (116)
T ss_pred HHHHhcCCCcEEEEEeEEEEcCCEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEE
Confidence 3334443 6789999999 4578888777777766655443333566778889999999998
No 10
>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=96.83 E-value=0.0055 Score=41.14 Aligned_cols=54 Identities=31% Similarity=0.625 Sum_probs=44.5
Q ss_pred CCceEEeeeeeeEE-----EeEEeeeccccCCCCceecchhHHHHhhhcCCceEeeeeC
Q psy12650 37 YNLITLGWIHWQLH-----ITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIH 90 (90)
Q Consensus 37 ~~l~tcGwIht~~~-----it~l~iP~Q~~t~dsC~t~~Ee~~f~~~~~~~l~~lGWIH 90 (90)
...|+||.|-|.+. +..+-|+.+...++++....+.+.+..+.++|+-.+||.|
T Consensus 14 ~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~~~~~~~~~~~~~~g~~~vG~YH 72 (119)
T cd08058 14 TGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTGENVEELFNVQTGRPLLVVGWYH 72 (119)
T ss_pred CCeEEEEEeeeEEecCccceeEEEEeecCCCCCCchhHHHHHHHHHHhCCCCeEEEEEe
Confidence 47889999999543 6677788888888888766666777788999999999998
No 11
>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=96.36 E-value=0.0091 Score=46.76 Aligned_cols=69 Identities=23% Similarity=0.302 Sum_probs=55.6
Q ss_pred ccEEEEEEEeeCcccCCCcccccch---hhhhhhhhhCCceEEeeeeeeEEEeEEeeeccccCCCCceecchhHHHHhhh
Q psy12650 3 SELHITHLLIPKQAGTADSCITHHE---EEIFACQDKYNLITLGWIHWQLHITHLLIPKQAGTADSCITHHEEEIFACQD 79 (90)
Q Consensus 3 ~~~~it~liIPkQ~~t~dsC~t~~E---e~~f~~~~~~~l~tcGwIht~~~it~l~iP~Q~~t~dsC~t~~Ee~~f~~~~ 79 (90)
.+..|..+.-|.|.+++|.++...+ +.+-.++...||+-+|||.|-+.-. ..|++..++.|-+++...
T Consensus 54 ika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA~~lGL~~VG~IfT~l~~~---------~~d~~~LSs~Evi~aA~~ 124 (274)
T cd08061 54 IKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIAAALGLERVGWIFTDLPRE---------DKDGYFLSAEEVILAAKF 124 (274)
T ss_pred eEEEEEEEECCCccCCCCCeEEccchhhhHHHHHHHHcCCeEEEEEEecCCCC---------CCCceeECHHHHHHHHHH
Confidence 3567888999999999999998744 5677889999999999999933211 188999999998887766
Q ss_pred c
Q psy12650 80 K 80 (90)
Q Consensus 80 ~ 80 (90)
+
T Consensus 125 Q 125 (274)
T cd08061 125 Q 125 (274)
T ss_pred h
Confidence 5
No 12
>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=96.01 E-value=0.013 Score=43.27 Aligned_cols=45 Identities=24% Similarity=0.311 Sum_probs=39.3
Q ss_pred ccEEEEEEEeeCcccCCCcccc--cchhhhhhhhhhCCceEEeeeee
Q psy12650 3 SELHITHLLIPKQAGTADSCIT--HHEEEIFACQDKYNLITLGWIHW 47 (90)
Q Consensus 3 ~~~~it~liIPkQ~~t~dsC~t--~~Ee~~f~~~~~~~l~tcGwIht 47 (90)
+.+.|+..+.+.+..+++.|+. ..+.+++++..++|+..+||.|+
T Consensus 41 ~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~gl~vVGwYHS 87 (187)
T cd08067 41 QNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRGLSVVGWYHS 87 (187)
T ss_pred CeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcCCEEEEEEec
Confidence 4678999998899888999986 45678899999999999999999
No 13
>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=95.09 E-value=0.087 Score=40.70 Aligned_cols=55 Identities=15% Similarity=0.184 Sum_probs=42.7
Q ss_pred hCCceEEeeeee-----eEEEeEEeeeccccCCCCceecchh--HHHH--h--hhcCCceEeeeeC
Q psy12650 36 KYNLITLGWIHW-----QLHITHLLIPKQAGTADSCITHHEE--EIFA--C--QDKYNLITLGWIH 90 (90)
Q Consensus 36 ~~~l~tcGwIht-----~~~it~l~iP~Q~~t~dsC~t~~Ee--~~f~--~--~~~~~l~~lGWIH 90 (90)
....+.||.|-| .+.|+...-..+.++++.|....|. ++.+ . +..+++..+||.|
T Consensus 29 ~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~~~~vVGWYH 94 (268)
T cd08069 29 GGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGRPENVVGWYH 94 (268)
T ss_pred cCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCCCceeEeeec
Confidence 356889999999 6788888888899999999987643 3343 2 2348899999998
No 14
>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=94.78 E-value=0.067 Score=34.44 Aligned_cols=45 Identities=11% Similarity=0.033 Sum_probs=31.8
Q ss_pred ccEEEEEEEeeCcccCCCcccccchhhhhhhhhhCCceEEeeeee
Q psy12650 3 SELHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIHW 47 (90)
Q Consensus 3 ~~~~it~liIPkQ~~t~dsC~t~~Ee~~f~~~~~~~l~tcGwIht 47 (90)
+.+.|+....+.+....+.+.......+...+..+|+..+||.|+
T Consensus 27 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGwyhs 71 (116)
T cd07767 27 KVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHT 71 (116)
T ss_pred CEEEEEEEEecccCCCCCccHHHHHHHHHHHHhcCCCeEEEEEEc
Confidence 356788887777777665553322224556678899999999998
No 15
>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=94.16 E-value=0.15 Score=40.58 Aligned_cols=48 Identities=25% Similarity=0.439 Sum_probs=40.4
Q ss_pred Eeeeee------------eEEEeEEeeeccccCCCCceec---chhHHHHhhhcCCceEeeee
Q psy12650 42 LGWIHW------------QLHITHLLIPKQAGTADSCITH---HEEEIFACQDKYNLITLGWI 89 (90)
Q Consensus 42 cGwIht------------~~~it~l~iP~Q~~t~dsC~t~---~Ee~~f~~~~~~~l~~lGWI 89 (90)
+|||.| .-.+.-+.-|.|.|++|+-.-. +|+.+=+++..-||.-+|||
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~lGL~rVG~I 64 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASALGLERVGWI 64 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHCCCEEEEEE
Confidence 688888 3466777889999999997763 67788889999999999999
No 16
>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=93.49 E-value=0.33 Score=31.76 Aligned_cols=54 Identities=15% Similarity=0.155 Sum_probs=33.9
Q ss_pred hCCceEEeeeee-----eEEEeEEeeeccccCCCCceecchhHHHH------hhhcCCceEeeeeC
Q psy12650 36 KYNLITLGWIHW-----QLHITHLLIPKQAGTADSCITHHEEEIFA------CQDKYNLITLGWIH 90 (90)
Q Consensus 36 ~~~l~tcGwIht-----~~~it~l~iP~Q~~t~dsC~t~~Ee~~f~------~~~~~~l~~lGWIH 90 (90)
...-+.||.|-+ ...|+..+...+....++.... +.+.++ .+.+.++-.+||.|
T Consensus 19 ~~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~vGwyh 83 (135)
T smart00232 19 DGPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEY-DEDYSHLMDEELKKVNKDLEIVGWYH 83 (135)
T ss_pred CCCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhh-hhhHHHHHHHHHHhhCCCceEEEEEE
Confidence 356789999998 5677666554455555554222 222222 23468899999998
No 17
>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=92.45 E-value=0.45 Score=31.08 Aligned_cols=51 Identities=24% Similarity=0.391 Sum_probs=40.3
Q ss_pred eEEeeeee------eEEEeEEeeeccccCCCCceecchhH---HHHhhhc--CCceEeeeeC
Q psy12650 40 ITLGWIHW------QLHITHLLIPKQAGTADSCITHHEEE---IFACQDK--YNLITLGWIH 90 (90)
Q Consensus 40 ~tcGwIht------~~~it~l~iP~Q~~t~dsC~t~~Ee~---~f~~~~~--~~l~~lGWIH 90 (90)
+.+|.|-| .+.|+..+.-++.++.+.|....++. .++...+ .++..+||.|
T Consensus 27 ~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGWY~ 88 (114)
T PF01398_consen 27 EVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPNLEIVGWYH 88 (114)
T ss_dssp EEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTTSEEEEEEE
T ss_pred EEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhccccccceEEEEEE
Confidence 89999998 57889999899999999999877753 3444332 5699999987
No 18
>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=89.05 E-value=0.77 Score=30.66 Aligned_cols=41 Identities=37% Similarity=0.713 Sum_probs=32.0
Q ss_pred EEEEEeeCcccCCCcccccchhhhhhhhhhCCceEEeeeee
Q psy12650 7 ITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIHW 47 (90)
Q Consensus 7 it~liIPkQ~~t~dsC~t~~Ee~~f~~~~~~~l~tcGwIht 47 (90)
+..+-|+.+...++++....+.+.+....++|+..+||-|+
T Consensus 33 ~~~~~v~~~~p~~~~~~~~~~~~~~~~~~~~g~~~vG~YHS 73 (119)
T cd08058 33 DKHVIVPKQSAGPDSCTGENVEELFNVQTGRPLLVVGWYHS 73 (119)
T ss_pred eeEEEEeecCCCCCCchhHHHHHHHHHHhCCCCeEEEEEec
Confidence 45566777887888776655556677788999999999998
No 19
>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=88.70 E-value=2.9 Score=28.09 Aligned_cols=62 Identities=16% Similarity=0.143 Sum_probs=36.1
Q ss_pred hhhhhhh-hCCceEEeeeee-----eEEEeEEe-eeccccCCCCceecchhHH---HHhhhcCCceEeeeeC
Q psy12650 29 EIFACQD-KYNLITLGWIHW-----QLHITHLL-IPKQAGTADSCITHHEEEI---FACQDKYNLITLGWIH 90 (90)
Q Consensus 29 ~~f~~~~-~~~l~tcGwIht-----~~~it~l~-iP~Q~~t~dsC~t~~Ee~~---f~~~~~~~l~~lGWIH 90 (90)
.+++.+. ....|.||+|-+ ...++.++ +|.-...+......+.+++ .....++|+-.+||.|
T Consensus 6 ~il~ha~~~~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~g~~~vG~~H 77 (128)
T cd08070 6 AILAHAEAEYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARERGLEVVGIYH 77 (128)
T ss_pred HHHHHHHhCCCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHCCCeEEEEEe
Confidence 3444433 367899999988 22344333 3443444413433444433 4445568999999998
No 20
>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=87.43 E-value=0.34 Score=31.69 Aligned_cols=55 Identities=22% Similarity=0.266 Sum_probs=37.9
Q ss_pred cEEEEEEEeeCcccCCCcccccchhhh---hhhhhh--CCceEEeeeee----eEEEeEEeeec
Q psy12650 4 ELHITHLLIPKQAGTADSCITHHEEEI---FACQDK--YNLITLGWIHW----QLHITHLLIPK 58 (90)
Q Consensus 4 ~~~it~liIPkQ~~t~dsC~t~~Ee~~---f~~~~~--~~l~tcGwIht----~~~it~l~iP~ 58 (90)
.+.|+..+.-++..+.+.|....++.. ++...+ .++..+||.|+ ..+.|...|..
T Consensus 41 ~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iVGWY~s~p~~~~~~S~~di~~ 104 (114)
T PF01398_consen 41 TVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPNLEIVGWYHSHPNISCFPSPTDIET 104 (114)
T ss_dssp EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTTSEEEEEEEEESSS-SS--HHHHHH
T ss_pred EEEEEEEEEeeEecCccccccchhhHHHHHHhhhccccccceEEEEEEccCCccccCCHHHHHH
Confidence 688999999999999999988766533 333322 56999999999 33445544443
No 21
>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=87.17 E-value=2 Score=33.39 Aligned_cols=54 Identities=13% Similarity=0.236 Sum_probs=35.1
Q ss_pred CCceEEeeeeeeE----------EE--eEEeee-ccccCCCCceecchhHHH--Hhhhc------CCceEeeeeC
Q psy12650 37 YNLITLGWIHWQL----------HI--THLLIP-KQAGTADSCITHHEEEIF--ACQDK------YNLITLGWIH 90 (90)
Q Consensus 37 ~~l~tcGwIht~~----------~i--t~l~iP-~Q~~t~dsC~t~~Ee~~f--~~~~~------~~l~~lGWIH 90 (90)
.-.|.||.|-|.. .+ +..+.+ .....+|.+++..|+.+- ...++ +|+..+||.|
T Consensus 22 ~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~~~~~~~~rgl~vVGwYH 96 (244)
T cd08068 22 EKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAERLTEETGRPMRVVGWYH 96 (244)
T ss_pred CCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHHHHHhhccCCceEEEEEe
Confidence 5678999999843 22 122222 445677888877766432 23345 9999999998
No 22
>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=87.02 E-value=1.4 Score=34.13 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=35.3
Q ss_pred cccEEEEEEEeeCcccCCCcccccch--hhhhh--h--hhhCCceEEeeeee
Q psy12650 2 QSELHITHLLIPKQAGTADSCITHHE--EEIFA--C--QDKYNLITLGWIHW 47 (90)
Q Consensus 2 ~~~~~it~liIPkQ~~t~dsC~t~~E--e~~f~--~--~~~~~l~tcGwIht 47 (90)
.+.+.|+..+-..+.++++.|....| +.+.+ . ...++...+||.|+
T Consensus 44 ~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~~~~vVGWYHS 95 (268)
T cd08069 44 DYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGRPENVVGWYHS 95 (268)
T ss_pred CCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCCCceeEeeecc
Confidence 35788899988889999999988654 34444 2 34488999999999
No 23
>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=85.44 E-value=1.7 Score=34.73 Aligned_cols=74 Identities=26% Similarity=0.289 Sum_probs=50.5
Q ss_pred EEEEEEEeeCcccCCCccccc---chhhhhhhhhhCCceEEeeeeeeEE----EeEEeeeccccCCCCceecchhHHHHh
Q psy12650 5 LHITHLLIPKQAGTADSCITH---HEEEIFACQDKYNLITLGWIHWQLH----ITHLLIPKQAGTADSCITHHEEEIFAC 77 (90)
Q Consensus 5 ~~it~liIPkQ~~t~dsC~t~---~Ee~~f~~~~~~~l~tcGwIht~~~----it~l~iP~Q~~t~dsC~t~~Ee~~f~~ 77 (90)
-.|--+.-|.|++++|+-... +|+.+=+++...||+-+|||.|-+. =...++-|. ..|+...+++|=+++.
T Consensus 21 a~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~lGL~rVG~IfTdl~~~~~~~g~v~~~r--~~~~~~LSs~Eii~aA 98 (306)
T PF05021_consen 21 AVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASALGLERVGWIFTDLTDDGSGDGTVKCKR--HKDSYFLSSLEIIFAA 98 (306)
T ss_pred EEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHCCCEEEEEEEecCcccccCCCceeecc--ccccccccHHHHHHHH
Confidence 456667789999999997774 6677888899999999999999221 011111111 3567777777766665
Q ss_pred hhc
Q psy12650 78 QDK 80 (90)
Q Consensus 78 ~~~ 80 (90)
..+
T Consensus 99 ~~Q 101 (306)
T PF05021_consen 99 KLQ 101 (306)
T ss_pred HHH
Confidence 444
No 24
>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=82.96 E-value=3.6 Score=26.80 Aligned_cols=44 Identities=16% Similarity=0.197 Sum_probs=26.2
Q ss_pred cEEEEEEEeeCcccCCCcccccch---hhhhh--hhhhCCceEEeeeee
Q psy12650 4 ELHITHLLIPKQAGTADSCITHHE---EEIFA--CQDKYNLITLGWIHW 47 (90)
Q Consensus 4 ~~~it~liIPkQ~~t~dsC~t~~E---e~~f~--~~~~~~l~tcGwIht 47 (90)
.+.|+..+...+....++.....+ +++.+ .+..+|+..+||.|+
T Consensus 36 ~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vGwyhs 84 (135)
T smart00232 36 RPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEIVGWYHS 84 (135)
T ss_pred EEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceEEEEEEc
Confidence 567777666555555555422211 12222 245689999999999
No 25
>KOG2834|consensus
Probab=71.18 E-value=2.4 Score=36.34 Aligned_cols=42 Identities=24% Similarity=0.362 Sum_probs=33.2
Q ss_pred EEEEEEeeCcccCCCccccc--chhh-hhhhhhhCCceEEeeeee
Q psy12650 6 HITHLLIPKQAGTADSCITH--HEEE-IFACQDKYNLITLGWIHW 47 (90)
Q Consensus 6 ~it~liIPkQ~~t~dsC~t~--~Ee~-~f~~~~~~~l~tcGwIht 47 (90)
.|.-+.=|.|.++.|.-+.. +|+. +=+.+...||.-+|||.|
T Consensus 220 ~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~~lGLrRVG~IFT 264 (510)
T KOG2834|consen 220 VVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAEGLGLRRVGWIFT 264 (510)
T ss_pred eEEEEecCCccCCcCCeEEeccchhhhHHHHHHhcCceeeEEEEe
Confidence 45556679999999999886 4444 445688899999999999
No 26
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=60.31 E-value=25 Score=22.12 Aligned_cols=57 Identities=14% Similarity=0.100 Sum_probs=30.5
Q ss_pred hhhhh-hhhCCceEEeeeeeeE-EEeEEeeeccccCCCCceecchhHHHH-hhhcCCceEeeeeC
Q psy12650 29 EIFAC-QDKYNLITLGWIHWQL-HITHLLIPKQAGTADSCITHHEEEIFA-CQDKYNLITLGWIH 90 (90)
Q Consensus 29 ~~f~~-~~~~~l~tcGwIht~~-~it~l~iP~Q~~t~dsC~t~~Ee~~f~-~~~~~~l~~lGWIH 90 (90)
+|.++ +.....|.||+|-+.. .-..+++|.+.. .......... ...+.++..+|..|
T Consensus 7 ~i~~~~~~~~p~E~~G~L~g~~~~~~~~~~~~~~~-----~p~~~~~~~~~~~~~~~~~~vg~~H 66 (104)
T PF14464_consen 7 QIIAHARAAYPNEACGLLLGRRDDQRFIVVPNVNP-----DPRDSFRRERFEARERGLEIVGIWH 66 (104)
T ss_dssp HHHHHHHHHTTS-EEEEEEEEEECCEEEEEEEEE-------HHCHHHHHH-HHHHHT-EEEEEEE
T ss_pred HHHHHHhhCCCCeEEEEEEEEecCCEEEEEeCCCC-----CcHHHHHHHhhhhhcccceeeEEEE
Confidence 34444 4558899999999954 223344443330 0111122222 56678889999887
No 27
>KOG2834|consensus
Probab=53.26 E-value=34 Score=29.61 Aligned_cols=61 Identities=18% Similarity=0.298 Sum_probs=46.3
Q ss_pred hhhhhhhhCCceEEeeeeeeE------------EEeEEeeeccccCCCCceec--chhH-HHHhhhcCCceEeeee
Q psy12650 29 EIFACQDKYNLITLGWIHWQL------------HITHLLIPKQAGTADSCITH--HEEE-IFACQDKYNLITLGWI 89 (90)
Q Consensus 29 ~~f~~~~~~~l~tcGwIht~~------------~it~l~iP~Q~~t~dsC~t~--~Ee~-~f~~~~~~~l~~lGWI 89 (90)
.++++=.+-|..-.|++.|.+ .|.-+.=|.|.|++|.-+.. +|+. +=+.+..-||.-+|||
T Consensus 187 ~Fl~~wr~sg~QR~GflyG~y~e~~~vPLGika~V~aIYEPPQ~~~~dgl~l~~~~e~~~vD~~a~~lGLrRVG~I 262 (510)
T KOG2834|consen 187 HFLNEWRASGVQRFGFLYGRYTEHGNVPLGIKAVVAAIYEPPQHGEEDGLELLEDDEAKRVDAIAEGLGLRRVGWI 262 (510)
T ss_pred HHHHHHHHhhhhhcceEEEeecccccccccceeeEEEEecCCccCCcCCeEEeccchhhhHHHHHHhcCceeeEEE
Confidence 445555567778889988822 56677779999999999886 3443 5567778999999999
No 28
>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=49.56 E-value=30 Score=26.93 Aligned_cols=34 Identities=15% Similarity=0.240 Sum_probs=24.4
Q ss_pred CcccCCCcccccchhhhh--hhhhh------CCceEEeeeee
Q psy12650 14 KQAGTADSCITHHEEEIF--ACQDK------YNLITLGWIHW 47 (90)
Q Consensus 14 kQ~~t~dsC~t~~Ee~~f--~~~~~------~~l~tcGwIht 47 (90)
....++|.++...|+.+- ...++ +|+..+||.|+
T Consensus 56 ~~~~s~~r~eidPee~~~a~~ea~~~~~~~~rgl~vVGwYHS 97 (244)
T cd08068 56 RSDKRKDRVEISPEQLSAASTEAERLTEETGRPMRVVGWYHS 97 (244)
T ss_pred ccCCCCceEEeCHHHHHHHHHHHHHHHhhccCCceEEEEEec
Confidence 446677888877776432 22445 99999999998
No 29
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=27.88 E-value=1.8e+02 Score=19.52 Aligned_cols=55 Identities=11% Similarity=0.120 Sum_probs=28.6
Q ss_pred hhhhCCceEEeeeeeeEEE---eEEeeeccccCCCCceecchhH---HHHhhhcCCceEeeeeC
Q psy12650 33 CQDKYNLITLGWIHWQLHI---THLLIPKQAGTADSCITHHEEE---IFACQDKYNLITLGWIH 90 (90)
Q Consensus 33 ~~~~~~l~tcGwIht~~~i---t~l~iP~Q~~t~dsC~t~~Ee~---~f~~~~~~~l~~lGWIH 90 (90)
.++..-.+.||.+-+...- .-+..+...- .+. ...+++ ........|+..+||.|
T Consensus 16 a~~~~p~E~~g~l~~~~~~~~~~~~~n~~~~~-~~~--~~~~~~~~~~~~~~~~~g~~vvg~yH 76 (134)
T COG1310 16 ARREHPREVCGLLAGTREGERYFPLKNVSVEP-VEY--FEIDPEYSLFYLAAEDAGEVVVGWYH 76 (134)
T ss_pred HHhcCChheEEEEEeecccceeeccccccCCc-cee--EeeCHHHHHHHHHHhhCCCEEEEEEc
Confidence 3455568999998884211 0111111111 111 122333 44555567799999988
No 30
>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=27.29 E-value=2.3e+02 Score=20.02 Aligned_cols=31 Identities=19% Similarity=0.081 Sum_probs=22.6
Q ss_pred hhhhhhhhCCc--eEEeeeeee-----EEEeEEeeecc
Q psy12650 29 EIFACQDKYNL--ITLGWIHWQ-----LHITHLLIPKQ 59 (90)
Q Consensus 29 ~~f~~~~~~~l--~tcGwIht~-----~~it~l~iP~Q 59 (90)
-+..|.+...+ |++|+|-+. +.|+.+..|.-
T Consensus 5 ~~~~~~Q~~~~~~EtGGiLiG~~~~~~~ii~~~t~P~p 42 (131)
T TIGR02256 5 MLKSYRQWHDLSTETGGVLIGERRGAHAVITKISEPGS 42 (131)
T ss_pred HHHHHHhCcCCCCccceEEEEEEcCCcEEEEEEEcCCC
Confidence 34567777777 999999993 47777777653
No 31
>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=26.65 E-value=1.4e+02 Score=22.75 Aligned_cols=55 Identities=16% Similarity=0.204 Sum_probs=33.3
Q ss_pred hCCceEEeeeee-----eEEEeEEeeeccccCCCCce-e----cchhHHHHhhhcCCc--eEeeeeC
Q psy12650 36 KYNLITLGWIHW-----QLHITHLLIPKQAGTADSCI-T----HHEEEIFACQDKYNL--ITLGWIH 90 (90)
Q Consensus 36 ~~~l~tcGwIht-----~~~it~l~iP~Q~~t~dsC~-t----~~Ee~~f~~~~~~~l--~~lGWIH 90 (90)
...-+.||.|-| .+-||...--....+.+... . .--.++++...+.|. -.+||-|
T Consensus 20 ~~p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e~iVGWY~ 86 (266)
T cd08065 20 ELPELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDHNHVGWYQ 86 (266)
T ss_pred CCCcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCCcEEEeEe
Confidence 345679999988 55666553322333333221 1 122467777888888 8999976
No 32
>PF03634 TCP: TCP family transcription factor; InterPro: IPR005333 The TCP transcription factor family was named after: teosinte branched 1 (tb1, Zea mays (Maize)) [], cycloidea (cyc) (Antirrhinum majus) (Garden snapdragon) [] and PCF in rice (Oryza sativa) [, ]. The TCP proteins code for structurally related proteins implicated in the evolution of key morphological traits []. However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLP) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization. This family of transcription factors are exclusive to higher plants. They can be divided into two groups, TCP-C and TCP-P, that appear to have separated following an early gene duplication event []. This duplication event may have led to functional divergence and it has been proposed that that the TCP-P subfamily are transcriptional repressors, while the TPC-C subfamily are transcription activators [].
Probab=20.60 E-value=26 Score=24.16 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=17.6
Q ss_pred hhhhhhhhhCCce----EEeeeee
Q psy12650 28 EEIFACQDKYNLI----TLGWIHW 47 (90)
Q Consensus 28 e~~f~~~~~~~l~----tcGwIht 47 (90)
..||++||..|.- |+.||-+
T Consensus 30 r~FFdLQDmLGfDKaSKTveWLL~ 53 (138)
T PF03634_consen 30 RKFFDLQDMLGFDKASKTVEWLLT 53 (138)
T ss_pred HHHHHHHHHhcCCCCCchHHHHHH
Confidence 3799999998876 9999988
Done!