Query psy9211
Match_columns 226
No_of_seqs 131 out of 246
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 21:45:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9211.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9211hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1560|consensus 100.0 1.9E-78 4.1E-83 532.5 19.9 223 1-223 87-338 (339)
2 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 1E-50 2.2E-55 360.7 18.9 172 1-172 68-266 (266)
3 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 3.5E-28 7.6E-33 216.7 8.6 121 1-122 74-205 (268)
4 KOG1555|consensus 99.8 6.8E-21 1.5E-25 171.9 5.6 120 1-123 104-236 (316)
5 cd08058 MPN_euk_mb Mpr1p, Pad1 99.7 2.9E-17 6.3E-22 129.3 6.4 65 1-68 54-119 (119)
6 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.6 2.7E-14 5.9E-19 127.1 15.1 101 1-120 65-167 (265)
7 KOG1554|consensus 99.5 4.3E-15 9.4E-20 132.3 4.2 114 2-119 121-244 (347)
8 smart00232 JAB_MPN JAB/MPN dom 99.4 4E-13 8.7E-18 105.7 7.4 69 1-69 65-134 (135)
9 cd08057 MPN_euk_non_mb Mpr1p, 99.4 4.7E-13 1E-17 110.2 6.2 70 1-71 65-138 (157)
10 cd08067 MPN_2A_DUB Mov34/MPN/P 99.4 1E-12 2.2E-17 111.9 6.4 69 1-71 70-148 (187)
11 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.3 4.1E-11 8.9E-16 108.0 11.7 100 1-118 72-172 (288)
12 cd08068 MPN_BRCC36 Mov34/MPN/P 99.2 2.1E-11 4.5E-16 107.8 7.0 85 3-105 80-169 (244)
13 cd08066 MPN_AMSH_like Mov34/MP 99.2 5E-11 1.1E-15 100.3 6.0 66 10-80 73-140 (173)
14 cd07767 MPN Mpr1p, Pad1p N-ter 99.1 1.1E-10 2.3E-15 89.8 6.1 64 1-65 52-116 (116)
15 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.1 2.3E-09 5E-14 96.6 14.5 100 1-118 71-170 (280)
16 PF01398 JAB: JAB1/Mov34/MPN/P 98.8 4.5E-09 9.8E-14 81.5 4.6 44 1-44 70-114 (114)
17 PLN03246 26S proteasome regula 98.7 3.3E-07 7E-12 83.6 13.8 101 1-118 76-176 (303)
18 KOG2880|consensus 97.6 2E-05 4.3E-10 72.9 1.6 67 11-82 324-395 (424)
19 cd08056 MPN_PRP8 Mpr1p, Pad1p 97.6 0.00022 4.8E-09 63.6 8.1 87 12-103 106-198 (252)
20 COG1310 Predicted metal-depend 97.3 0.00026 5.7E-09 56.6 3.8 50 5-58 62-113 (134)
21 KOG2975|consensus 97.2 0.0032 7E-08 56.4 9.7 99 1-119 87-186 (288)
22 cd08070 MPN_like Mpr1p, Pad1p 97.2 0.00086 1.9E-08 53.1 5.5 52 11-70 69-121 (128)
23 KOG1556|consensus 95.8 0.014 3.1E-07 52.1 4.6 90 1-108 79-168 (309)
24 cd08061 MPN_NPL4 Mov34/MPN/PAD 95.2 0.064 1.4E-06 48.5 7.0 69 12-82 93-172 (274)
25 PF14464 Prok-JAB: Prokaryotic 90.9 0.25 5.5E-06 36.9 3.2 31 7-37 54-85 (104)
26 cd08072 MPN_archaeal Mov34/MPN 89.9 1.1 2.3E-05 35.2 6.1 51 11-69 58-109 (117)
27 PF05021 NPL4: NPL4 family; I 87.0 3.1 6.6E-05 38.3 7.8 67 13-81 59-154 (306)
28 cd08060 MPN_UPF0172 Mov34/MPN/ 85.8 2.7 5.9E-05 35.7 6.4 47 11-57 69-117 (182)
29 cd08073 MPN_NLPC_P60 Mpr1p, Pa 74.4 5.2 0.00011 30.9 4.1 46 13-68 60-106 (108)
30 cd08059 MPN_prok_mb Mpr1p, Pad 70.5 14 0.0003 27.5 5.6 28 8-35 52-80 (101)
31 PF08084 PROCT: PROCT (NUC072) 70.0 7.2 0.00016 31.5 4.0 48 56-105 9-56 (125)
32 KOG4538|consensus 52.3 23 0.0005 28.2 3.9 36 130-165 58-93 (130)
33 TIGR03735 PRTRC_A PRTRC system 38.1 19 0.0004 31.1 1.5 25 9-33 131-156 (192)
34 PF12794 MscS_TM: Mechanosensi 38.0 99 0.0021 28.6 6.4 30 140-170 254-283 (340)
35 PRK13750 replication protein; 34.4 59 0.0013 29.5 4.0 32 139-176 165-197 (285)
36 TIGR03474 incFII_RepA incFII f 33.5 62 0.0013 29.2 4.0 32 139-176 157-189 (275)
37 PF06903 VirK: VirK protein; 33.4 20 0.00043 27.8 0.8 29 43-71 16-55 (100)
38 PF03665 UPF0172: Uncharacteri 32.3 1.3E+02 0.0028 25.8 5.8 47 12-58 76-124 (196)
39 PF09935 DUF2167: Protein of u 31.8 35 0.00076 30.5 2.2 29 146-174 85-113 (239)
40 PF14198 TnpV: Transposon-enco 30.4 58 0.0013 25.5 3.0 32 182-213 38-69 (111)
41 PF06442 DHFR_2: R67 dihydrofo 22.3 46 0.001 24.1 1.0 9 13-21 41-49 (78)
42 KOG1795|consensus 21.2 1.2E+02 0.0026 33.8 4.1 64 10-76 2163-2228(2321)
43 TIGR02256 ICE_VC0181 integrati 21.1 2.4E+02 0.0052 22.8 5.1 44 6-49 67-111 (131)
44 PF11791 Aconitase_B_N: Aconit 20.5 1.3E+02 0.0027 25.2 3.4 16 156-171 5-20 (154)
No 1
>KOG1560|consensus
Probab=100.00 E-value=1.9e-78 Score=532.50 Aligned_cols=223 Identities=48% Similarity=0.815 Sum_probs=214.4
Q ss_pred ChhHHhhhCCCCceeEEEEeecCCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHHHHHHhhcCCC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSDVANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYKEGEF 80 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~ke~~~ 80 (226)
|||.||.||+|+.+||||||+++|+|+|..++|+||.||+.++++||+||||++|++|.|++|||||||++|++++|++|
T Consensus 87 mlrrlr~vnid~~hVGwYqs~~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp~am~~~kekdw 166 (339)
T KOG1560|consen 87 MLRRLRYVNIDHLHVGWYQSAYVGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTPEAMAAHKEKDW 166 (339)
T ss_pred HHHHhhhcCccceeeeeeeeehhccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCHHHHHHHhcCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHhhcCCCCCCceEEeeeEEeccHHHHHHHhcccCC--CCCC-CCCcccccchH-----------------------
Q psy9211 81 TPEALRAIKVGFENLLLEVPVKIRNSPLTNVLLSEVDGL--VSPA-EGNNFLDLGTA----------------------- 134 (226)
Q Consensus 81 t~~~l~~~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~~--~~~~-~~~~~L~l~~~----------------------- 134 (226)
+++.++++||||+++|+||||.|+||||.|++|++|..+ .+.+ +.+++|||++.
T Consensus 167 tpealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDEl~qe~~~ 246 (339)
T KOG1560|consen 167 TPEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDELHQEIVN 246 (339)
T ss_pred CHHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999843 3333 33788999865
Q ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChhhhhhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHhHHHHH
Q psy9211 135 ---FQQQVVRQAQDKHRYQAKRMQENQARAAKDEPPLPEEDLNKIFRPIPVPPRLSPMLMAAQVSAYADHISQFSSQSLA 211 (226)
Q Consensus 135 ---yqR~l~req~~~~q~~~kR~~EN~~R~~~ge~plpeed~~~~fK~~~~PsrL~~lL~s~qi~~~c~~i~~~~~~~l~ 211 (226)
|||+++||+++++||++||++||+.|.++|+||||||||.++||+|++|.|||++|+|+||+++|++|.+||+++|+
T Consensus 247 l~kyqr~~~rqq~~~~q~~aKrqaENa~R~argep~lP~dd~kr~fk~pq~p~rLdslLiS~qint~aq~ike~tSqnl~ 326 (339)
T KOG1560|consen 247 LNKYQRQLARQQAKKHQWIAKRQAENANRAARGEPPLPEDDWKRIFKPPQEPRRLDSLLISGQINTSAQQIKEFTSQNLS 326 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCCCChHHHHHHhcCCCchhHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccc
Q psy9211 212 KLYMMEAVKSHN 223 (226)
Q Consensus 212 Klf~~~~~~~~~ 223 (226)
|||+++++|..|
T Consensus 327 Klfiaea~~~~k 338 (339)
T KOG1560|consen 327 KLFIAEALQESK 338 (339)
T ss_pred HHHHHHHHHHhc
Confidence 999999999875
No 2
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=100.00 E-value=1e-50 Score=360.68 Aligned_cols=172 Identities=50% Similarity=0.804 Sum_probs=166.3
Q ss_pred ChhHHhhhCCCCceeEEEEeecCCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHHHHHHhhcCCC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSDVANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYKEGEF 80 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~ke~~~ 80 (226)
|++++|++|.|+++|||||||++|+|++.++|+++++||..++++|+|||||.+|.+|++++||||+++.+|.++++|+|
T Consensus 68 m~~~~r~v~~~e~iVGWY~S~p~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~~~~~~~~~~~~ 147 (266)
T cd08065 68 MMRLLREVNVDHNHVGWYQSTYLGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSEKFMELYKEGKF 147 (266)
T ss_pred HHHHHHHhCCCCcEEEeEeecCCCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEcHHHHHHhhcCCc
Confidence 89999999999999999999999999999999999999999999999999999998999999999999999999999999
Q ss_pred CHHHHhhcCCCCCCceEEeeeEEeccHHHHHHHhcccCCCCCC-CCCcccccchH-------------------------
Q psy9211 81 TPEALRAIKVGFENLLLEVPVKIRNSPLTNVLLSEVDGLVSPA-EGNNFLDLGTA------------------------- 134 (226)
Q Consensus 81 t~~~l~~~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~~~~~~-~~~~~L~l~~~------------------------- 134 (226)
+++.++++++++.+||+||||+|+|++|+++||.+|..+.+.+ ++++.|+|+++
T Consensus 148 ~~~~l~~~~~~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~~ 227 (266)
T cd08065 148 STESLREANLTFSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKFN 227 (266)
T ss_pred CHHHHHHhcCchhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999998877776 78899999765
Q ss_pred -HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChhh
Q psy9211 135 -FQQQVVRQAQDKHRYQAKRMQENQARAAKDEPPLPEED 172 (226)
Q Consensus 135 -yqR~l~req~~~~q~~~kR~~EN~~R~~~ge~plpeed 172 (226)
|||+++|||++++||++||++||++|+++|++|||+||
T Consensus 228 ~y~r~~~~~~~~~~~~~~kr~~en~~r~~~~~~~lp~~~ 266 (266)
T cd08065 228 YYQRNLARQQAQIQQWLQKRKAENAQREARGEEPLPEED 266 (266)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHhcCCCCCCCCC
Confidence 99999999999999999999999999999999999986
No 3
>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=99.95 E-value=3.5e-28 Score=216.69 Aligned_cols=121 Identities=19% Similarity=0.268 Sum_probs=112.9
Q ss_pred Chh--HHhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCCcc-CCceeeEEEEecCHHHHHH--
Q psy9211 1 MMR--RLRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQKT-SRGFLTLKAYRLTPQAIQM-- 74 (226)
Q Consensus 1 Mm~--~Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s-~~G~lslkAfRLs~~~~~~-- 74 (226)
|++ +++++|++.++|||||||| +|||+|..+|+||..||...+++|+||+||.+| ++|+++|+|||+++.++.+
T Consensus 74 m~~~~~~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~~~ 153 (268)
T cd08069 74 MVQYEMLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLE 153 (268)
T ss_pred HHHHHHHHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccccccC
Confidence 667 9999999999999999999 999999999999999999999999999999999 8999999999999999876
Q ss_pred hhc-----CCCCHHHHhhcCCCCCCceEEeeeEEeccHHHHHHHhcccCCCCC
Q psy9211 75 YKE-----GEFTPEALRAIKVGFENLLLEVPVKIRNSPLTNVLLSEVDGLVSP 122 (226)
Q Consensus 75 ~ke-----~~~t~~~l~~~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~~~~~ 122 (226)
+++ +.|+.+.++ ..+++.++|+||||.|++|+|++.+|..|.++.+.
T Consensus 154 ~~~~~s~~~~~~~~~~~-~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~~w~ 205 (268)
T cd08069 154 PRQTTSNIGHLPKPKIE-DFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNKYWV 205 (268)
T ss_pred cccCccccCccCcHHHH-HhCchhcEEEEeeeEEecCHHHHHHHHHHHHHhHH
Confidence 555 789999999 88999999999999999999999999999876543
No 4
>KOG1555|consensus
Probab=99.82 E-value=6.8e-21 Score=171.87 Aligned_cols=120 Identities=21% Similarity=0.232 Sum_probs=107.3
Q ss_pred ChhHHhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHHH-HHHhhcC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQA-IQMYKEG 78 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~-~~~~ke~ 78 (226)
||++|+..|++..+|||||||| ||||.|.++|+||.+||...+++|+.++||++|..|+++++|||++..+ +....++
T Consensus 104 ~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In~~~~~~~~ep 183 (316)
T KOG1555|consen 104 MMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINPQWISPGGEP 183 (316)
T ss_pred HHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCcccccCCCCC
Confidence 7899999999999999999999 9999999999999999999999999999999999999999999999877 5566788
Q ss_pred CCCHHHHhh-----------cCCCCCCceEEeeeEEeccHHHHHHHhcccCCCCCC
Q psy9211 79 EFTPEALRA-----------IKVGFENLLLEVPVKIRNSPLTNVLLSEVDGLVSPA 123 (226)
Q Consensus 79 ~~t~~~l~~-----------~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~~~~~~ 123 (226)
+.++++++. ||+ + .|+.+.|.+|..++...++.++...++..
T Consensus 184 rqtts~~~~m~~~~s~q~~~~g~--n-~y~~~ei~~~v~~~~~~~~~nv~~~s~~~ 236 (316)
T KOG1555|consen 184 RQTTSNGGHMDMQESLQEDIHGL--N-RYYRIEIPLHVLPYEQLMLLNVPLKSWKS 236 (316)
T ss_pred ccccccccccccchhHHhHhhcc--C-ceEEEEeeEEechhhhhchhccchhhhhh
Confidence 888876552 444 3 79999999999999999999998765543
No 5
>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=99.69 E-value=2.9e-17 Score=129.32 Aligned_cols=65 Identities=23% Similarity=0.315 Sum_probs=61.3
Q ss_pred ChhHHhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLT 68 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs 68 (226)
|+.+++..++|.++|||||||| +|+|.|..+|++|++||...+++|+||+||.++ ++++||||||
T Consensus 54 ~~~~~~~~~~g~~~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~---~~~~~a~rl~ 119 (119)
T cd08058 54 EELFNVQTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR---NKDTGIFRLT 119 (119)
T ss_pred HHHHHHHhCCCCeEEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC---CcccceEEeC
Confidence 4667788999999999999999 999999999999999999999999999999885 8999999997
No 6
>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=99.60 E-value=2.7e-14 Score=127.08 Aligned_cols=101 Identities=22% Similarity=0.367 Sum_probs=85.0
Q ss_pred ChhHHhhhCCCCceeEEEEeecCCCccC--HHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHHHHHHhhcC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSDVANFIS--LPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYKEG 78 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~~G~f~s--~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~ke~ 78 (226)
|++++|+||.|+.+||||++++ +++ ..+|..+++++...+++|+|++||..+. |++++||||+++.++ +. +
T Consensus 65 m~~~~kkv~~~~~vVGWY~tg~---~~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~-~~l~i~ay~~~~~~~--~~-~ 137 (265)
T cd08064 65 MYELHQKVNPKEVIVGWYATGS---EITEHSALIHDYYSRECTSYNPIHLTVDTSLDD-GKMSIKAYVSSPLGV--PG-K 137 (265)
T ss_pred HHHHHHHhCCCCcEEeeeeCCC---CCCccHHHHHHHHHhhCCCCCCEEEEEeCCCCC-CCcceEEEEEEeccc--CC-C
Confidence 8899999999999999999976 555 7789999888876668999999998765 489999999998752 11 1
Q ss_pred CCCHHHHhhcCCCCCCceEEeeeEEeccHHHHHHHhcccCCC
Q psy9211 79 EFTPEALRAIKVGFENLLLEVPVKIRNSPLTNVLLSEVDGLV 120 (226)
Q Consensus 79 ~~t~~~l~~~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~~~ 120 (226)
+...+|.|||++|+++.-+..-+.-+.+..
T Consensus 138 ------------~~~~~F~~ip~~i~~~eaE~i~v~~l~~~~ 167 (265)
T cd08064 138 ------------TLGSMFVPIPLELLYSEAERVALDLLAKTL 167 (265)
T ss_pred ------------CcceEEEEcceeeecCcHHHHHHHHHHhhc
Confidence 567999999999999999888888876543
No 7
>KOG1554|consensus
Probab=99.53 E-value=4.3e-15 Score=132.31 Aligned_cols=114 Identities=22% Similarity=0.282 Sum_probs=91.6
Q ss_pred hhHHhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccC-CceeeEEEEecCHHHHHHhhcCC
Q psy9211 2 MRRLRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQKTS-RGFLTLKAYRLTPQAIQMYKEGE 79 (226)
Q Consensus 2 m~~Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~-~G~lslkAfRLs~~~~~~~ke~~ 79 (226)
++..+.+|+-+|+|||||||| .|||++..+|.||..=|+--+.=|++|+||.+|. -|+|.|-|||--|.= |+.++
T Consensus 121 ~e~~k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~g---yk~~d 197 (347)
T KOG1554|consen 121 IEEAKNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKG---YKPPD 197 (347)
T ss_pred HHHHHHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeecccCC---CCCCC
Confidence 467789999999999999999 9999999999999988888889999999999998 689999999998864 66554
Q ss_pred CCHH---H-----HhhcCCCCCCceEEeeeEEeccHHHHHHHhcccCC
Q psy9211 80 FTPE---A-----LRAIKVGFENLLLEVPVKIRNSPLTNVLLSEVDGL 119 (226)
Q Consensus 80 ~t~~---~-----l~~~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~~ 119 (226)
--+. . +.+.|+ .-.+|+.++|.+-.+.|...+|.-|-.+
T Consensus 198 ~~~seyqtipl~kied~gv-Hck~yysl~isyfks~ld~kll~~Lwnk 244 (347)
T KOG1554|consen 198 EPPSEYQTIPLNKIEDFGV-HCKQYYSLEISYFKSSLDMKLLELLWNK 244 (347)
T ss_pred CCchhhhccchhhhhhccc-ceEEeeccchhhhhhhhhHHHHHHHHhh
Confidence 2222 2 222222 1357899999999998887777776443
No 8
>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=99.42 E-value=4e-13 Score=105.69 Aligned_cols=69 Identities=41% Similarity=0.559 Sum_probs=64.4
Q ss_pred ChhHHhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCH
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTP 69 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~ 69 (226)
|.+.+++++.+...|||||||+ .+++.|..++.++..|+.....+|.+++||.+|..|++.++|||+++
T Consensus 65 ~~~~~~~~~~~~~~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 65 MDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred HHHHHHhhCCCceEEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 4567789999999999999999 57899999999999999999999999999999999999999999985
No 9
>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=99.39 E-value=4.7e-13 Score=110.20 Aligned_cols=70 Identities=21% Similarity=0.286 Sum_probs=61.2
Q ss_pred ChhHHhhhCCCCceeEEEEeecCCC---ccCHHHHHHHHHHhHhcCCeEEEEEeCCc-cCCceeeEEEEecCHHH
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSDVAN---FISLPLIESQFHYQISIEEAVVLIYDTQK-TSRGFLTLKAYRLTPQA 71 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~~G~---f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~-s~~G~lslkAfRLs~~~ 71 (226)
|++++++|+.++.+||||++++.|. +.+...|+.++.++ ..++.|+|++||.+ +.+|++.|+|||+++.+
T Consensus 65 m~~~~~~v~~~~~vVGWY~~~~~~~~~~~~~~~~i~~~~~~~-~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~ 138 (157)
T cd08057 65 RYNLHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLI-SEENPLILILDPSLQSDSEKLEISTFTSAQRE 138 (157)
T ss_pred HHHHHHHhCCCCCEEEEEeecCCCCCCCChhHHHHHHHHHhc-cCCCCEEEEEcCCcccCCCcccEEEEEEecCC
Confidence 7899999999999999999999764 67777888888877 45778999999998 57899999999999653
No 10
>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=99.36 E-value=1e-12 Score=111.88 Aligned_cols=69 Identities=25% Similarity=0.360 Sum_probs=59.5
Q ss_pred ChhHHhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcC-------CeEEEEEeCCccC--CceeeEEEEecCHH
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIE-------EAVVLIYDTQKTS--RGFLTLKAYRLTPQ 70 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~-------~~V~lV~Dp~~s~--~G~lslkAfRLs~~ 70 (226)
|++.|++.|. ++|||||||| .++|.|..+|+||+.||...+ ++|+||+||..+. ...-.|+||+..+.
T Consensus 70 ~~~~l~~~gl--~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~ 147 (187)
T cd08067 70 IRESLESRGL--SVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPP 147 (187)
T ss_pred HHHHHHHcCC--EEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECC
Confidence 5778888886 9999999999 668999999999999999875 6999999999753 34578999999986
Q ss_pred H
Q psy9211 71 A 71 (226)
Q Consensus 71 ~ 71 (226)
.
T Consensus 148 ~ 148 (187)
T cd08067 148 P 148 (187)
T ss_pred C
Confidence 3
No 11
>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=99.27 E-value=4.1e-11 Score=107.96 Aligned_cols=100 Identities=21% Similarity=0.248 Sum_probs=82.3
Q ss_pred ChhHHhhhCCCCceeEEEEeecCCCccCHHHHHHHHHHhHhcCCeEEEEEeCCcc-CCceeeEEEEecCHHHHHHhhcCC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSDVANFISLPLIESQFHYQISIEEAVVLIYDTQKT-SRGFLTLKAYRLTPQAIQMYKEGE 79 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s-~~G~lslkAfRLs~~~~~~~ke~~ 79 (226)
|++++++||.|+.+||||++.+.|.+.+...|..|+. ..++..|+|++||..+ .+|.+.++||+..+.... +
T Consensus 72 m~~~~kkV~~~~~vVGWY~tg~~~~~~~~~~Ih~~~~--~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~----~- 144 (288)
T cd08063 72 RLEQFKQVFKDLDFVGWYTTGPGGPTESDLPIHKQIL--EINESPVLLLLDPEANASGKDLPVTIYESVLELVD----G- 144 (288)
T ss_pred HHHHHHHhccCCceEEEEecCCCCCCHHHHHHHHHHH--hhCCCcEEEEEccccccCCCCCceeEEEEEEeccC----C-
Confidence 7899999999999999999999999999999998886 4467789999999986 789999999997765332 1
Q ss_pred CCHHHHhhcCCCCCCceEEeeeEEeccHHHHHHHhcccC
Q psy9211 80 FTPEALRAIKVGFENLLLEVPVKIRNSPLTNVLLSEVDG 118 (226)
Q Consensus 80 ~t~~~l~~~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~ 118 (226)
....+|.++|.+|..+.-+..-+..+.+
T Consensus 145 -----------~~~~~F~~i~~~i~~~eaErIgv~~l~~ 172 (288)
T cd08063 145 -----------EATLRFRELPYTIETGEAERIGVDHVAR 172 (288)
T ss_pred -----------ccccEEEeeeeEEEeccCceeeHHHHHh
Confidence 2357899999999998766555555543
No 12
>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=99.22 E-value=2.1e-11 Score=107.78 Aligned_cols=85 Identities=22% Similarity=0.263 Sum_probs=71.2
Q ss_pred hHHhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCC----ccCCceeeEEEEecCHHHHHHhhc
Q psy9211 3 RRLRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQ----KTSRGFLTLKAYRLTPQAIQMYKE 77 (226)
Q Consensus 3 ~~Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~----~s~~G~lslkAfRLs~~~~~~~ke 77 (226)
++++.+|++..+|||||||| .++|.|..||++|..||...+..|.||+++. .+..|++.++|||+.+.-=
T Consensus 80 ~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g~~----- 154 (244)
T cd08068 80 RLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQGNK----- 154 (244)
T ss_pred HHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCCCC-----
Confidence 46778999999999999999 9999999999999999988899999998643 5668999999999987411
Q ss_pred CCCCHHHHhhcCCCCCCceEEeeeEEec
Q psy9211 78 GEFTPEALRAIKVGFENLLLEVPVKIRN 105 (226)
Q Consensus 78 ~~~t~~~l~~~~lt~~~i~~EiPI~i~n 105 (226)
...-...|+|+.|-.
T Consensus 155 -------------~~~~~~~e~pl~i~~ 169 (244)
T cd08068 155 -------------AGQYERIEVPLEIVP 169 (244)
T ss_pred -------------CCcceEEEeeeEEec
Confidence 234577899998843
No 13
>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=99.15 E-value=5e-11 Score=100.35 Aligned_cols=66 Identities=20% Similarity=0.402 Sum_probs=58.2
Q ss_pred CCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecC-HHHHHHhhcCCC
Q psy9211 10 VDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLT-PQAIQMYKEGEF 80 (226)
Q Consensus 10 ~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs-~~~~~~~ke~~~ 80 (226)
.+-.+|||||||+ .++|.|..+|+||.+||...++++.||++| |..+++||||+ +.-++..++++-
T Consensus 73 ~gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp-----~~~~l~afrl~~~~g~~~~~~~~~ 140 (173)
T cd08066 73 HDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAP-----KYNEFGIFRLTDPPGLDEILNCKK 140 (173)
T ss_pred CCCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECC-----CCcEEeEEEeecCCcceecccCCc
Confidence 4568999999999 889999999999999999999999999998 47999999999 666766666554
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=99.12 E-value=1.1e-10 Score=89.84 Aligned_cols=64 Identities=23% Similarity=0.366 Sum_probs=55.6
Q ss_pred ChhHHhhhCCCCceeEEEEeecCC-CccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEE
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSDVA-NFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAY 65 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~~G-~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAf 65 (226)
|+...+.++.|..+|||||||+.| +|.+..+++++..||+..+++|+||+|+..... .+.++||
T Consensus 52 ~~~~~~~~~~~~~iVGwyhshp~~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~~-~~~~~~~ 116 (116)
T cd07767 52 MYLDFKKLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDL-GNSWKCY 116 (116)
T ss_pred HHHHHHHhcCCCeEEEEEEcCCCCCCccCHHHHHHHHHHHHhCCCCEEEEEECCCccC-CCCcccC
Confidence 355678899999999999999966 799999999999999999999999999987432 5778886
No 15
>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=99.10 E-value=2.3e-09 Score=96.55 Aligned_cols=100 Identities=18% Similarity=0.260 Sum_probs=80.1
Q ss_pred ChhHHhhhCCCCceeEEEEeecCCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHHHHHHhhcCCC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSDVANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYKEGEF 80 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~ke~~~ 80 (226)
|++++++||.++.+||||+|++- ++..++..+-.|+.-+++.|.|++||... .+.+.++||...+.-. .+|
T Consensus 71 m~~~~kkv~~~e~vVGWY~tg~~---~~~~d~~ih~~~~~~~~~pv~l~vd~~~~-~~~lpi~aY~s~~~~~---~~g-- 141 (280)
T cd08062 71 MYGMFKKVNAKEKIVGWYSTGPK---LRPNDLDINELFRRYCPNPVLVIIDVRPK-DLGLPTEAYIAVEEVH---DDG-- 141 (280)
T ss_pred HHHHHHHhCCCCCeEEEecCCCC---CCcchHHHHHHHHHhCCCCEEEEEecCCC-CCCCceEEEEEeeecc---CCC--
Confidence 78999999999999999999873 45677788888899899999999999875 6679999999877433 111
Q ss_pred CHHHHhhcCCCCCCceEEeeeEEeccHHHHHHHhcccC
Q psy9211 81 TPEALRAIKVGFENLLLEVPVKIRNSPLTNVLLSEVDG 118 (226)
Q Consensus 81 t~~~l~~~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~ 118 (226)
-....+|.+||.+|....-+..-+.-+.+
T Consensus 142 ---------~~~~~~F~~vp~~i~~~eaE~igve~l~r 170 (280)
T cd08062 142 ---------TPTSKTFVHVPSEIGAEEAEEVGVEHLLR 170 (280)
T ss_pred ---------CcceeEEEEcceEeeccchHHHHHHHHHh
Confidence 11467999999999998776666666644
No 16
>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=98.82 E-value=4.5e-09 Score=81.47 Aligned_cols=44 Identities=36% Similarity=0.505 Sum_probs=37.6
Q ss_pred ChhHHhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEE 44 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~ 44 (226)
|+++++.++-+..+||||||++ .++|.|..+|++|..||..+++
T Consensus 70 ~~~~~~~~~~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 70 MIELLKKVNPNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp HHHHHHHCSTTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred HHhhhccccccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 5688999999999999999999 6699999999999999998864
No 17
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=98.71 E-value=3.3e-07 Score=83.59 Aligned_cols=101 Identities=17% Similarity=0.267 Sum_probs=74.9
Q ss_pred ChhHHhhhCCCCceeEEEEeecCCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHHHHHHhhcCCC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSDVANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYKEGEF 80 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~ke~~~ 80 (226)
|++++|+||.|+.+||||++.+ =++..++.-+-.|..-.++.|.|++|+.- ..|.+.++||...+.-.. .+
T Consensus 76 m~~~~k~V~~~~~vVGWY~tg~---~i~~~d~~IH~~~~~~~~~Pv~L~vD~~~-~~~~lpi~aY~s~~~~~~---~~-- 146 (303)
T PLN03246 76 MFGMFKRINAKEHVVGWYSTGP---KLRENDLDIHELFNDYVPNPVLVIIDVQP-KELGIPTKAYYAVEEVKE---NA-- 146 (303)
T ss_pred HHHHHHHhCCCCcEEeeecCCC---CCCcchHHHHHHHHhhCCCCeEEEEecCC-CCCCCceEEEEEEEeccC---CC--
Confidence 8999999999999999999876 23334444455667778889999999865 356799999997764331 01
Q ss_pred CHHHHhhcCCCCCCceEEeeeEEeccHHHHHHHhcccC
Q psy9211 81 TPEALRAIKVGFENLLLEVPVKIRNSPLTNVLLSEVDG 118 (226)
Q Consensus 81 t~~~l~~~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~ 118 (226)
.-+...+|.+||.+|....-+..-+.-+.+
T Consensus 147 --------~~~~~~~F~~vp~~i~~~EaE~Igve~l~r 176 (303)
T PLN03246 147 --------TQKSQKVFVHVPSEIGAHEAEEIGVEHLLR 176 (303)
T ss_pred --------CcccccEEEECCeeeeecCHHHHHHHHHHh
Confidence 012356899999999999877766666654
No 18
>KOG2880|consensus
Probab=97.64 E-value=2e-05 Score=72.92 Aligned_cols=67 Identities=22% Similarity=0.538 Sum_probs=54.8
Q ss_pred CCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHHH-HHH---hhcCCCCH
Q psy9211 11 DHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQA-IQM---YKEGEFTP 82 (226)
Q Consensus 11 D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~-~~~---~ke~~~t~ 82 (226)
+-..+||-|+|| -+||+|++++-|.++||-..|+||++|.-|..-..|- |||++.. |+. +++.-|-+
T Consensus 324 ~L~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~~tGi-----FrLt~~~Gm~~i~~C~~~GFHp 395 (424)
T KOG2880|consen 324 ELLTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSKTTGI-----FRLTDPGGMEVIRGCRKKGFHP 395 (424)
T ss_pred cceeeeeeecCCccchhheeccccccceeeeecchheeEEeccccCCcce-----EEecCCcchHHHhhcccCCCCC
Confidence 346799999999 8999999999999999999999999999998655564 8999654 554 44444655
No 19
>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=97.64 E-value=0.00022 Score=63.62 Aligned_cols=87 Identities=16% Similarity=0.199 Sum_probs=67.1
Q ss_pred CceeEEEEeec-CCCccCHHHHHHHHHHhHhcC-----CeEEEEEeCCccCCceeeEEEEecCHHHHHHhhcCCCCHHHH
Q psy9211 12 HYHVGWYQSSD-VANFISLPLIESQFHYQISIE-----EAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYKEGEFTPEAL 85 (226)
Q Consensus 12 ~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~-----~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~ke~~~t~~~l 85 (226)
=..+||-|+++ =.+|++..+|.++..||..++ ++|+++.-+. .|.++|.||+||++-++..++++-...+.
T Consensus 106 Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~Sft---pGs~sl~ay~LT~~G~~wg~~n~d~~~~~ 182 (252)
T cd08056 106 LEPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFT---PGSCSLTAYKLTPEGYEWGKQNKDLGNNT 182 (252)
T ss_pred CEeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCC---CCceEEEEEecCHHHHHHHHhCccccccC
Confidence 45799999999 446999999999999999997 7999998665 89999999999999998888876543221
Q ss_pred hhcCCCCCCceEEeeeEE
Q psy9211 86 RAIKVGFENLLLEVPVKI 103 (226)
Q Consensus 86 ~~~~lt~~~i~~EiPI~i 103 (226)
-.|.. ...++.+.+-+
T Consensus 183 -p~g~~-~~~~ek~qllL 198 (252)
T cd08056 183 -PKGYS-PSFYEKVQLLL 198 (252)
T ss_pred -CCCCC-ccccceeEEEE
Confidence 12221 34666666654
No 20
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=97.29 E-value=0.00026 Score=56.62 Aligned_cols=50 Identities=16% Similarity=0.175 Sum_probs=34.9
Q ss_pred HhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCC-eEEEEEeCCccCCc
Q psy9211 5 LRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEE-AVVLIYDTQKTSRG 58 (226)
Q Consensus 5 Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~-~V~lV~Dp~~s~~G 58 (226)
+.....+..+|||||||| .++|.|..++. ++...+- -++++.+|.....+
T Consensus 62 ~~~~~~g~~vvg~yHSHP~~~~~pS~~D~~----~~~~~~~~~~iv~~~~~~~~~~ 113 (134)
T COG1310 62 LAAEDAGEVVVGWYHSHPGGPPYPSEADRR----LSKLGPLPWLIVSVPPGRVHKG 113 (134)
T ss_pred HHHhhCCCEEEEEEcCCCCCCCCcCHHHHh----hccccCCCEEEEEcCCCceeEE
Confidence 334445599999999999 67999999997 4554443 46666666444443
No 21
>KOG2975|consensus
Probab=97.17 E-value=0.0032 Score=56.41 Aligned_cols=99 Identities=23% Similarity=0.346 Sum_probs=72.3
Q ss_pred ChhHHhhhCCCCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHHHHHHhhcCC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYKEGE 79 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~ke~~ 79 (226)
|+...+.+|-.+.+||||.+.+ ... +..+|-.. |-.-.+++|.|.+|..-+ .|.++||||--++--+
T Consensus 87 M~~l~~k~npnE~vvGWyaTg~dvt~--~sslihdy--Yare~~~pvhLtVDT~~~-n~rm~ikaYvss~~Gv------- 154 (288)
T KOG2975|consen 87 MYELHKKVNPNELVVGWYATGHDVTE--HSSLIHDY--YAREAPNPVHLTVDTSLQ-NGRMSIKAYVSSLMGV------- 154 (288)
T ss_pred HHHHhcccCCCceeEEEEecCCCccc--chhHHHHH--hhccCCCCeEEEEecccc-CCccceeEEEEeccCC-------
Confidence 7788899999999999998765 332 23455433 444567899999999755 7899999997665311
Q ss_pred CCHHHHhhcCCCCCCceEEeeeEEeccHHHHHHHhcccCC
Q psy9211 80 FTPEALRAIKVGFENLLLEVPVKIRNSPLTNVLLSEVDGL 119 (226)
Q Consensus 80 ~t~~~l~~~~lt~~~i~~EiPI~i~ns~L~~~~L~~L~~~ 119 (226)
-|-+..-+|.+||++|++-.-+..-|.-+.+.
T Consensus 155 --------pg~~~~~mF~plpvel~~~~~ervgl~li~kt 186 (288)
T KOG2975|consen 155 --------PGRTMGVMFTPLPVELAYYDAERVGLDLIEKT 186 (288)
T ss_pred --------CCcccceeeeeeeeEEeecchhhhHHHHHHHh
Confidence 23333459999999999988777766666554
No 22
>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=97.16 E-value=0.00086 Score=53.15 Aligned_cols=52 Identities=21% Similarity=0.109 Sum_probs=41.1
Q ss_pred CCceeEEEEeec-CCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHH
Q psy9211 11 DHYHVGWYQSSD-VANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQ 70 (226)
Q Consensus 11 D~~~VGwYqS~~-~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~ 70 (226)
+..+|||||||| .+++.|..++.++.. ...+-+|+.+... .-.++||++...
T Consensus 69 g~~~vG~~HSHP~~~~~PS~~D~~~~~~-----~~~~~lIv~~~~~---~~~~~~~~~~~~ 121 (128)
T cd08070 69 GLEVVGIYHSHPDGPARPSETDLRLAWP-----PGVSYLIVSLAGG---APELRAWRLEGG 121 (128)
T ss_pred CCeEEEEEeCCCCCCCCCCHHHHHhccC-----CCCeEEEEECCCC---CcEEEEEEEcCC
Confidence 468999999999 569999999987753 2677888876533 578999999753
No 23
>KOG1556|consensus
Probab=95.77 E-value=0.014 Score=52.10 Aligned_cols=90 Identities=20% Similarity=0.328 Sum_probs=59.1
Q ss_pred ChhHHhhhCCCCceeEEEEeecCCCccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCHHHHHHhhcCCC
Q psy9211 1 MMRRLRRVNVDHYHVGWYQSSDVANFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYKEGEF 80 (226)
Q Consensus 1 Mm~~Lr~vn~D~~~VGwYqS~~~G~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~ke~~~ 80 (226)
|-.|.+.||.-+.+|||||+.| -+...+|+---.+-.-.++.|.+|+|.-.-.-| |--+||--.
T Consensus 79 M~~mfkKvNakekivGWYhTGP---kl~~nDl~In~l~k~y~pnpvLvIIdvkpk~~g-LPT~AY~aV------------ 142 (309)
T KOG1556|consen 79 MFGMFKKVNAKEKVVGWYHTGP---KLRENDLDINELLKRYVPNPVLVIIDVKPKELG-LPTEAYIAV------------ 142 (309)
T ss_pred HHHHHHHhcchhheeeeeccCC---ccccchhhHHHHHhhcCCCceEEEEecccccCC-CCchheeee------------
Confidence 6789999999999999999965 344455544444455578899999998633222 333343211
Q ss_pred CHHHHhhcCCCCCCceEEeeeEEeccHH
Q psy9211 81 TPEALRAIKVGFENLLLEVPVKIRNSPL 108 (226)
Q Consensus 81 t~~~l~~~~lt~~~i~~EiPI~i~ns~L 108 (226)
+.+...|-..+.-|+-+|-.|.--.-
T Consensus 143 --eev~dDgt~t~ktF~Hvps~I~AeEA 168 (309)
T KOG1556|consen 143 --EEVKDDGTPTSKTFVHVPSEIEAEEA 168 (309)
T ss_pred --eeeecCCCCccceeEecCcccchhHH
Confidence 22333444556788888888876544
No 24
>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=95.19 E-value=0.064 Score=48.52 Aligned_cols=69 Identities=22% Similarity=0.382 Sum_probs=58.1
Q ss_pred CceeEEEEeec-C----CCccCHHHHHHHHHHhH------hcCCeEEEEEeCCccCCceeeEEEEecCHHHHHHhhcCCC
Q psy9211 12 HYHVGWYQSSD-V----ANFISLPLIESQFHYQI------SIEEAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYKEGEF 80 (226)
Q Consensus 12 ~~~VGwYqS~~-~----G~f~s~~~Ietq~~yQ~------~~~~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~ke~~~ 80 (226)
=..|||=.|+. - +.|+|..-|-....||. -..+.|.+|+.|.. .|.+++.||.+|+..|.+.+++=+
T Consensus 93 L~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~--~g~i~~~ayQvSdq~~~lv~~~~i 170 (274)
T cd08061 93 LERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK--DGQIHFEAYQVSDQAMALVRDGLL 170 (274)
T ss_pred CeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC--CCceeeeeeeecHHHHHHHHcCcc
Confidence 36899999998 4 67999999999999996 34578889999964 499999999999999999998755
Q ss_pred CH
Q psy9211 81 TP 82 (226)
Q Consensus 81 t~ 82 (226)
.+
T Consensus 171 ~~ 172 (274)
T cd08061 171 LP 172 (274)
T ss_pred cc
Confidence 44
No 25
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=90.94 E-value=0.25 Score=36.93 Aligned_cols=31 Identities=23% Similarity=0.078 Sum_probs=21.9
Q ss_pred hhCCCCceeEEEEeecCC-CccCHHHHHHHHH
Q psy9211 7 RVNVDHYHVGWYQSSDVA-NFISLPLIESQFH 37 (226)
Q Consensus 7 ~vn~D~~~VGwYqS~~~G-~f~s~~~Ietq~~ 37 (226)
..+.+...||.|||||-| .+.|..|+.+...
T Consensus 54 ~~~~~~~~vg~~HSHP~~~a~pS~~D~~~~~~ 85 (104)
T PF14464_consen 54 ARERGLEIVGIWHSHPSGPAFPSSTDIRSMRD 85 (104)
T ss_dssp HHHHT-EEEEEEEEESSSSSS--HHHHHTHCC
T ss_pred hhcccceeeEEEEcCCCCCCCCCHHHHHhhhc
Confidence 345567899999999955 5999999976653
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=89.95 E-value=1.1 Score=35.23 Aligned_cols=51 Identities=18% Similarity=-0.071 Sum_probs=36.0
Q ss_pred CCceeEEEEeecCC-CccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecCH
Q psy9211 11 DHYHVGWYQSSDVA-NFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLTP 69 (226)
Q Consensus 11 D~~~VGwYqS~~~G-~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs~ 69 (226)
+-..||.|||||.| .+-|..++.... .+..+-+|+.+-. +.=.+|||++.-
T Consensus 58 g~~ivgi~HSHP~~~~~PS~~D~~~~~-----~~~~~~lIvs~~~---~~~~~~a~~~~g 109 (117)
T cd08072 58 DMSIVGSVHSHPSGSPRPSDADLSFFS-----KTGLVHIIVGYPY---DEDDWRAYDSDG 109 (117)
T ss_pred CCeEEEEEEcCCCCCCCCCHHHHHhhh-----cCCCEEEEEECcC---CCCCEEEEecCC
Confidence 45799999999955 888999986332 3667777775431 224588998753
No 27
>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=86.99 E-value=3.1 Score=38.33 Aligned_cols=67 Identities=19% Similarity=0.289 Sum_probs=55.2
Q ss_pred ceeEEEEeecC----------------CCccCHHHHHHHHHHhHhcC-------------CeEEEEEeCCccCCceeeEE
Q psy9211 13 YHVGWYQSSDV----------------ANFISLPLIESQFHYQISIE-------------EAVVLIYDTQKTSRGFLTLK 63 (226)
Q Consensus 13 ~~VGwYqS~~~----------------G~f~s~~~Ietq~~yQ~~~~-------------~~V~lV~Dp~~s~~G~lslk 63 (226)
..|||--++.. +-|+|..-|-....+|...+ +.|.+|+.+- ..|.+.+.
T Consensus 59 ~rVG~IfTdl~~~~~~~g~v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~--~~g~i~~~ 136 (306)
T PF05021_consen 59 ERVGWIFTDLTDDGSGDGTVKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGD--EEGEIHFE 136 (306)
T ss_pred EEEEEEEecCcccccCCCceeeccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCC--CCCceeeE
Confidence 68999888865 37889998999999998652 4688888883 57999999
Q ss_pred EEecCHHHHHHhhcCCCC
Q psy9211 64 AYRLTPQAIQMYKEGEFT 81 (226)
Q Consensus 64 AfRLs~~~~~~~ke~~~t 81 (226)
||.+|++.|.++++|=+.
T Consensus 137 ayQvS~q~~~Lv~~~~l~ 154 (306)
T PF05021_consen 137 AYQVSNQCVALVRAGILE 154 (306)
T ss_pred EeeehHHHHHHHHCCccc
Confidence 999999999999977443
No 28
>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=85.78 E-value=2.7 Score=35.71 Aligned_cols=47 Identities=19% Similarity=0.304 Sum_probs=28.9
Q ss_pred CCceeEEEEeec-CCCccCHHHHH-HHHHHhHhcCCeEEEEEeCCccCC
Q psy9211 11 DHYHVGWYQSSD-VANFISLPLIE-SQFHYQISIEEAVVLIYDTQKTSR 57 (226)
Q Consensus 11 D~~~VGwYqS~~-~G~f~s~~~Ie-tq~~yQ~~~~~~V~lV~Dp~~s~~ 57 (226)
+-..||+||||+ ++.---...-. -.=.-++..++++++++|-.+...
T Consensus 69 gl~IvG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l~~ 117 (182)
T cd08060 69 GLVIVGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKLTL 117 (182)
T ss_pred CCEEEEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccccc
Confidence 347999999999 65322211111 111234455689999999988743
No 29
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=74.37 E-value=5.2 Score=30.93 Aligned_cols=46 Identities=17% Similarity=-0.012 Sum_probs=29.7
Q ss_pred ceeEEEEeecCC-CccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCceeeEEEEecC
Q psy9211 13 YHVGWYQSSDVA-NFISLPLIESQFHYQISIEEAVVLIYDTQKTSRGFLTLKAYRLT 68 (226)
Q Consensus 13 ~~VGwYqS~~~G-~f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G~lslkAfRLs 68 (226)
.+||.||||+.| ..-|..|+..+ ..+..+-+|+--- .|.+ ++||-.
T Consensus 60 ~ivgi~HSHP~~~a~PS~~D~~~~-----~~~~~~~iIvs~~---~~~~--~~~~p~ 106 (108)
T cd08073 60 EIVAVVHSHPDGSPAPSEADRAQQ-----EATGLPWIIVSWP---EGDL--RVFRPV 106 (108)
T ss_pred CEEEEEEcCCCCCCCCCHHHHHHh-----hcCCCcEEEEEcC---CCCE--EEEecC
Confidence 799999999955 88999998532 2345555555321 4443 456643
No 30
>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=70.50 E-value=14 Score=27.52 Aligned_cols=28 Identities=14% Similarity=-0.032 Sum_probs=21.7
Q ss_pred hCCCCceeEEEEeecCC-CccCHHHHHHH
Q psy9211 8 VNVDHYHVGWYQSSDVA-NFISLPLIESQ 35 (226)
Q Consensus 8 vn~D~~~VGwYqS~~~G-~f~s~~~Ietq 35 (226)
...+...||.|||||.| ..-|..++...
T Consensus 52 ~~~~~~~v~i~HsHP~g~~~PS~~D~~~~ 80 (101)
T cd08059 52 LEIGMKVVGLVHSHPSGSCRPSEADLSLF 80 (101)
T ss_pred hhCCCcEEEEEecCcCCCCCCCHHHHHHH
Confidence 34456789999999966 78888998643
No 31
>PF08084 PROCT: PROCT (NUC072) domain; InterPro: IPR012984 The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family [].; PDB: 2P87_A 2P8R_A 3SBG_A 2OG4_A.
Probab=69.97 E-value=7.2 Score=31.46 Aligned_cols=48 Identities=17% Similarity=0.256 Sum_probs=29.8
Q ss_pred CCceeeEEEEecCHHHHHHhhcCCCCHHHHhhcCCCCCCceEEeeeEEec
Q psy9211 56 SRGFLTLKAYRLTPQAIQMYKEGEFTPEALRAIKVGFENLLLEVPVKIRN 105 (226)
Q Consensus 56 ~~G~lslkAfRLs~~~~~~~ke~~~t~~~l~~~~lt~~~i~~EiPI~i~n 105 (226)
+.|+++|.||+||++=.+-.++++-.....- .|.. .++++.+.+-+..
T Consensus 9 tpGSvsL~Ay~LT~~G~eWg~~nkD~~~~~p-~g~~-p~~~ek~QllLSd 56 (125)
T PF08084_consen 9 TPGSVSLSAYKLTPEGYEWGRQNKDLISDNP-QGFS-PSFYEKVQLLLSD 56 (125)
T ss_dssp ETTEEEEEEEEE-HHHHHHHHCTTT--SS---TT---GGGEEEEEEEEET
T ss_pred cCCceEEEEEecCHHHHHHHhhcccccccCC-CCCC-cchhheeeeeeec
Confidence 4899999999999999888887764221111 2232 3577777766543
No 32
>KOG4538|consensus
Probab=52.30 E-value=23 Score=28.23 Aligned_cols=36 Identities=19% Similarity=0.313 Sum_probs=26.5
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q psy9211 130 DLGTAFQQQVVRQAQDKHRYQAKRMQENQARAAKDE 165 (226)
Q Consensus 130 ~l~~~yqR~l~req~~~~q~~~kR~~EN~~R~~~ge 165 (226)
++.-..++++...+-+-.|-...|+.||+.|+..+|
T Consensus 58 ~~vK~~~~~i~ek~~~~rqeKkqRrvEn~kRRLeNE 93 (130)
T KOG4538|consen 58 DMVKRVQDNIREKQVQERQEKKQRRVENEKRRLENE 93 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 333447888877776666777889999999988764
No 33
>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=38.07 E-value=19 Score=31.14 Aligned_cols=25 Identities=16% Similarity=-0.116 Sum_probs=22.4
Q ss_pred CCCCceeEEEEeec-CCCccCHHHHH
Q psy9211 9 NVDHYHVGWYQSSD-VANFISLPLIE 33 (226)
Q Consensus 9 n~D~~~VGwYqS~~-~G~f~s~~~Ie 33 (226)
..+...|+-||||+ ...|.|.+|+.
T Consensus 131 ~~ge~lV~iyHSH~~spA~PS~tD~~ 156 (192)
T TIGR03735 131 DDGEHLVVDLHSHGTGSAFFSETDDA 156 (192)
T ss_pred hCCCeEEEEEcCCCCCCCCCCcccch
Confidence 67789999999999 77999999984
No 34
>PF12794 MscS_TM: Mechanosensitive ion channel inner membrane domain 1
Probab=37.99 E-value=99 Score=28.57 Aligned_cols=30 Identities=23% Similarity=0.258 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCCCh
Q psy9211 140 VRQAQDKHRYQAKRMQENQARAAKDEPPLPE 170 (226)
Q Consensus 140 ~req~~~~q~~~kR~~EN~~R~~~ge~plpe 170 (226)
++.+-..++-++||++..++|. +.|+..++
T Consensus 254 ~~RRLA~~Ra~~kR~~~~aqr~-~~e~~~~~ 283 (340)
T PF12794_consen 254 ARRRLAYERAKEKRAEALAQRE-AEEEESSE 283 (340)
T ss_pred HHHHHHHHHHHHHHHHHHHhhh-cccccCCc
Confidence 3444555666788888888887 44443333
No 35
>PRK13750 replication protein; Provisional
Probab=34.39 E-value=59 Score=29.50 Aligned_cols=32 Identities=19% Similarity=0.322 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChhh-hhhh
Q psy9211 139 VVRQAQDKHRYQAKRMQENQARAAKDEPPLPEED-LNKI 176 (226)
Q Consensus 139 l~req~~~~q~~~kR~~EN~~R~~~ge~plpeed-~~~~ 176 (226)
+..-+.++-.| ||.++.++|++||..+| +.+.
T Consensus 165 l~~A~~qql~W------~Nk~l~kkGl~pltl~Eai~~a 197 (285)
T PRK13750 165 VAAARRSRVEW------ENRQRKKQGLDTLGMDELIAKA 197 (285)
T ss_pred HHHHHHHHHHH------HHHHHHhcCCCCccHHHHHHHH
Confidence 44444455567 68999999999999987 4433
No 36
>TIGR03474 incFII_RepA incFII family plasmid replication initiator RepA. Members of this protein are the plasmid replication initiator RepA of incFII (plasmid incompatibility group F-II) plasmids. R1 and R100 are plasmids in this group. Immediately upstream of repA is found tap, a leader peptide of about 24 amino acids, often not assigned as a gene in annotated plasmid sequences. Note that other, non-homologous plasmid replication proteins share the gene symbol (repA) and similar names (plasmid replication protein RepA).
Probab=33.49 E-value=62 Score=29.17 Aligned_cols=32 Identities=19% Similarity=0.334 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChhh-hhhh
Q psy9211 139 VVRQAQDKHRYQAKRMQENQARAAKDEPPLPEED-LNKI 176 (226)
Q Consensus 139 l~req~~~~q~~~kR~~EN~~R~~~ge~plpeed-~~~~ 176 (226)
+..-+.++-.| ||.++.++|++||..+| +.+.
T Consensus 157 l~~A~~qql~W------~Nk~l~kkGl~pltl~Eai~~a 189 (275)
T TIGR03474 157 VAAARRSRVEW------ENKQRKKQGLDTLEMDELIAKA 189 (275)
T ss_pred HHHHHHHHHHH------HHHHHHhcCCCcccHHHHHHHH
Confidence 44444555567 68899999999999987 4433
No 37
>PF06903 VirK: VirK protein; InterPro: IPR010694 This family consists of several bacterial VirK proteins of around 145 residues in length. The function of this family is unknown [].
Probab=33.35 E-value=20 Score=27.85 Aligned_cols=29 Identities=34% Similarity=0.653 Sum_probs=24.1
Q ss_pred CCeEEEEEeCCc-----------cCCceeeEEEEecCHHH
Q psy9211 43 EEAVVLIYDTQK-----------TSRGFLTLKAYRLTPQA 71 (226)
Q Consensus 43 ~~~V~lV~Dp~~-----------s~~G~lslkAfRLs~~~ 71 (226)
.+.|.+++|.++ .++|.+.|+|||+++.-
T Consensus 16 Gk~V~v~iDls~Ct~~~~~~~~s~t~Gg~~i~ayrI~~D~ 55 (100)
T PF06903_consen 16 GKNVTVVIDLSQCTPEGEGTPPSKTRGGLRIDAYRITPDG 55 (100)
T ss_pred CCeEEEEEEHHHCccCCCCCCCcccCcccceeeEEEeCCC
Confidence 689999999643 45899999999999873
No 38
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=32.32 E-value=1.3e+02 Score=25.77 Aligned_cols=47 Identities=21% Similarity=0.241 Sum_probs=27.9
Q ss_pred CceeEEEEeec-CCC-ccCHHHHHHHHHHhHhcCCeEEEEEeCCccCCc
Q psy9211 12 HYHVGWYQSSD-VAN-FISLPLIESQFHYQISIEEAVVLIYDTQKTSRG 58 (226)
Q Consensus 12 ~~~VGwYqS~~-~G~-f~s~~~Ietq~~yQ~~~~~~V~lV~Dp~~s~~G 58 (226)
--.||+||+.- ++. =.+..-..---.-.+..+.+++|++|-.+-..+
T Consensus 76 l~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~ 124 (196)
T PF03665_consen 76 LVIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSD 124 (196)
T ss_pred CEEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccc
Confidence 57899999765 432 122221111112233567899999998876543
No 39
>PF09935 DUF2167: Protein of unknown function (DUF2167); InterPro: IPR018682 This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Probab=31.76 E-value=35 Score=30.46 Aligned_cols=29 Identities=17% Similarity=0.232 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCChhhhh
Q psy9211 146 KHRYQAKRMQENQARAAKDEPPLPEEDLN 174 (226)
Q Consensus 146 ~~q~~~kR~~EN~~R~~~ge~plpeed~~ 174 (226)
.++.++--++.|++|+++|-|++....|.
T Consensus 85 L~~~k~~t~e~N~eR~~~G~~~l~l~GW~ 113 (239)
T PF09935_consen 85 LKSMKEGTEESNKERKKRGYPPLHLVGWA 113 (239)
T ss_pred HHHHHHhHHhhhHHHHhcCCCceEEeccc
Confidence 34555666778999999999998777775
No 40
>PF14198 TnpV: Transposon-encoded protein TnpV
Probab=30.40 E-value=58 Score=25.49 Aligned_cols=32 Identities=13% Similarity=0.296 Sum_probs=28.0
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q psy9211 182 VPPRLSPMLMAAQVSAYADHISQFSSQSLAKL 213 (226)
Q Consensus 182 ~PsrL~~lL~s~qi~~~c~~i~~~~~~~l~Kl 213 (226)
-|.+...||++|.+..||.+|++-|-+=+-.+
T Consensus 38 ~p~~Y~~ll~~g~L~~~l~eid~~A~e~~e~l 69 (111)
T PF14198_consen 38 KPILYNNLLLSGKLNEHLAEIDEQAQERFERL 69 (111)
T ss_pred HHHHHHHHHHcchHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999988776654
No 41
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=22.29 E-value=46 Score=24.09 Aligned_cols=9 Identities=44% Similarity=1.018 Sum_probs=5.6
Q ss_pred ceeEEEEee
Q psy9211 13 YHVGWYQSS 21 (226)
Q Consensus 13 ~~VGwYqS~ 21 (226)
.+||||.+.
T Consensus 41 ~vvgwy~t~ 49 (78)
T PF06442_consen 41 QVVGWYCTK 49 (78)
T ss_dssp EEEEEE--S
T ss_pred eEeEEEecc
Confidence 479999764
No 42
>KOG1795|consensus
Probab=21.21 E-value=1.2e+02 Score=33.76 Aligned_cols=64 Identities=19% Similarity=0.321 Sum_probs=46.8
Q ss_pred CCCceeEEEEeecCC-CccCHHHHHHHHHHhHhc-CCeEEEEEeCCccCCceeeEEEEecCHHHHHHhh
Q psy9211 10 VDHYHVGWYQSSDVA-NFISLPLIESQFHYQISI-EEAVVLIYDTQKTSRGFLTLKAYRLTPQAIQMYK 76 (226)
Q Consensus 10 ~D~~~VGwYqS~~~G-~f~s~~~Ietq~~yQ~~~-~~~V~lV~Dp~~s~~G~lslkAfRLs~~~~~~~k 76 (226)
.|-...||-|+-+-- .+++..+|-|....-..+ ++||.+..- .+-|++|+-||.||+.-.+-.+
T Consensus 2163 ~d~e~Lgw~hTq~~el~~lsp~dV~th~ki~~~~k~k~i~~t~~---~tpgs~sl~ay~lt~~G~eWg~ 2228 (2321)
T KOG1795|consen 2163 EDLEPLGWIHTQPNELPQLSPQDVTTHAKILVDNKEKCIIITCS---FTPGSCSLTAYKLTPSGYEWGE 2228 (2321)
T ss_pred cCCcccchhhcCccccccCCHHHhhhhhhhhhcCccceEEEEee---ccCCcceeeeeccCccccccch
Confidence 456778999988833 789999888766544333 578877653 4589999999999987554443
No 43
>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=21.08 E-value=2.4e+02 Score=22.76 Aligned_cols=44 Identities=16% Similarity=-0.080 Sum_probs=28.3
Q ss_pred hhhCCCCceeEEEEeecCC-CccCHHHHHHHHHHhHhcCCeEEEE
Q psy9211 6 RRVNVDHYHVGWYQSSDVA-NFISLPLIESQFHYQISIEEAVVLI 49 (226)
Q Consensus 6 r~vn~D~~~VGwYqS~~~G-~f~s~~~Ietq~~yQ~~~~~~V~lV 49 (226)
++-|-...-||-+||||-+ .--|..++.+....-.....-++||
T Consensus 67 ~~s~g~~~ylGeWHtHP~~~p~PS~~D~~~~~~~~~~~~~~l~iI 111 (131)
T TIGR02256 67 EVSGGVDTYLGEWHTHPEDQPEPSWTDRRSWRTIIRSPEAMLLLI 111 (131)
T ss_pred HHhCCceEEEEecCcCCCCCCCCCHHHHHHHHHHHhCCCeeEEEE
Confidence 3444446789999999955 4678888877665544333333343
No 44
>PF11791 Aconitase_B_N: Aconitate B N-terminal domain; InterPro: IPR015933 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [, ]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) []. Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway []. The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [, ]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated []. IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis []. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [, ]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents the N-terminal HEAT-like domain, which is present in bacterial aconitase (AcnB), but not in AcnA or eukaryotic cAcn/IRP2 or mAcn. This domain is multi-helical, forming two curved layers in a right-handed alpha-alpha superhelix. HEAT-like domains are usually implicated in protein-protein interactions. The HEAT-like domain and the 'swivel' domain that follows it were shown to be sufficient for dimerisation and for AcnB binding to mRNA. An iron-mediated dimerisation mechanism may be responsible for switching AcnB between its catalytic and regulatory roles, as dimerisation requires iron while mRNA binding is inhibited by iron. More information about these proteins can be found at Protein of the Month: Aconitase [].; GO: 0003994 aconitate hydratase activity, 0006099 tricarboxylic acid cycle; PDB: 1L5J_B.
Probab=20.55 E-value=1.3e+02 Score=25.25 Aligned_cols=16 Identities=44% Similarity=0.578 Sum_probs=7.0
Q ss_pred HHHHHHhCCCCCCChh
Q psy9211 156 ENQARAAKDEPPLPEE 171 (226)
Q Consensus 156 EN~~R~~~ge~plpee 171 (226)
.-++|.+.|-||+|.+
T Consensus 5 hv~eRa~~GipPlPL~ 20 (154)
T PF11791_consen 5 HVAERAALGIPPLPLN 20 (154)
T ss_dssp HHHHHHCTT-------
T ss_pred HHHHHHHCCCCCCCCC
Confidence 4567899999999985
Done!