Query 039881
Match_columns 315
No_of_seqs 196 out of 532
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 02:56:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039881.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039881hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1560 Translation initiation 100.0 9.1E-85 2E-89 592.2 23.3 293 18-314 9-336 (339)
2 cd08065 MPN_eIF3h Mpr1p, Pad1p 100.0 4.5E-64 9.7E-69 468.8 27.5 240 22-264 1-266 (266)
3 cd08069 MPN_RPN11_CSN5 Mov34/M 100.0 2.4E-37 5.2E-42 289.0 17.1 194 18-221 6-228 (268)
4 KOG1554 COP9 signalosome, subu 100.0 2.5E-34 5.4E-39 263.1 9.5 195 18-222 49-270 (347)
5 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.9 5.3E-27 1.2E-31 219.1 17.0 177 24-222 1-198 (265)
6 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.9 3.4E-23 7.4E-28 194.8 18.3 145 22-187 1-170 (280)
7 cd08057 MPN_euk_non_mb Mpr1p, 99.9 2E-23 4.4E-28 180.5 11.2 114 24-140 1-138 (157)
8 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.9 1.1E-22 2.5E-27 192.1 16.6 183 23-234 2-211 (288)
9 PLN03246 26S proteasome regula 99.9 6.7E-22 1.5E-26 187.6 18.3 150 18-187 2-176 (303)
10 cd08067 MPN_2A_DUB Mov34/MPN/P 99.9 2.3E-22 4.9E-27 178.9 12.1 117 21-140 4-148 (187)
11 KOG2975 Translation initiation 99.9 1.6E-21 3.5E-26 177.5 11.7 179 20-222 19-218 (288)
12 KOG1555 26S proteasome regulat 99.9 4.3E-21 9.4E-26 180.3 13.3 229 19-256 28-294 (316)
13 cd08068 MPN_BRCC36 Mov34/MPN/P 99.8 3E-20 6.4E-25 170.9 14.3 194 21-249 1-243 (244)
14 smart00232 JAB_MPN JAB/MPN dom 99.8 7.3E-20 1.6E-24 152.3 12.8 114 23-138 1-134 (135)
15 cd08058 MPN_euk_mb Mpr1p, Pad1 99.8 3.8E-20 8.3E-25 153.0 9.4 104 29-137 1-119 (119)
16 PF01398 JAB: JAB1/Mov34/MPN/P 99.8 1.3E-19 2.9E-24 148.0 5.8 91 20-110 2-113 (114)
17 KOG1556 26S proteasome regulat 99.8 3.3E-18 7.1E-23 154.7 13.3 149 18-187 5-178 (309)
18 cd08066 MPN_AMSH_like Mov34/MP 99.5 7.1E-14 1.5E-18 123.1 11.5 114 22-147 2-138 (173)
19 cd07767 MPN Mpr1p, Pad1p N-ter 99.5 3.3E-14 7.2E-19 115.4 8.4 96 32-134 2-116 (116)
20 cd08070 MPN_like Mpr1p, Pad1p 98.8 1.8E-08 3.8E-13 84.2 9.5 96 30-137 3-119 (128)
21 COG1310 Predicted metal-depend 98.8 4.8E-09 1E-13 88.3 6.1 92 24-119 2-107 (134)
22 KOG2880 SMAD6 interacting prot 98.4 1.6E-07 3.5E-12 89.6 2.2 68 79-153 326-397 (424)
23 cd08056 MPN_PRP8 Mpr1p, Pad1p 98.0 1.9E-05 4.1E-10 73.4 7.9 66 78-148 106-176 (252)
24 cd08072 MPN_archaeal Mov34/MPN 97.6 0.00023 5.1E-09 58.7 7.9 94 28-137 3-108 (117)
25 KOG3050 COP9 signalosome, subu 97.4 0.00025 5.5E-09 65.1 6.0 146 21-188 8-178 (299)
26 cd08061 MPN_NPL4 Mov34/MPN/PAD 97.0 0.0087 1.9E-07 56.6 12.0 72 77-152 92-173 (274)
27 PF14464 Prok-JAB: Prokaryotic 96.8 0.00072 1.6E-08 53.7 2.2 86 29-119 3-96 (104)
28 cd08073 MPN_NLPC_P60 Mpr1p, Pa 96.5 0.014 3.1E-07 47.5 7.7 77 31-119 3-95 (108)
29 cd08059 MPN_prok_mb Mpr1p, Pad 95.8 0.067 1.5E-06 42.4 8.3 77 30-117 2-90 (101)
30 cd08060 MPN_UPF0172 Mov34/MPN/ 95.7 0.15 3.3E-06 45.4 10.9 95 26-122 1-115 (182)
31 PF05021 NPL4: NPL4 family; I 94.2 0.31 6.7E-06 46.9 9.3 71 77-151 57-155 (306)
32 PF03665 UPF0172: Uncharacteri 93.4 1.3 2.9E-05 39.8 11.4 101 22-123 2-122 (196)
33 TIGR03735 PRTRC_A PRTRC system 93.0 0.073 1.6E-06 47.8 2.6 72 25-102 74-158 (192)
34 TIGR02256 ICE_VC0181 integrati 87.7 3.9 8.5E-05 34.6 8.3 56 63-118 58-113 (131)
35 KOG3289 Uncharacterized conser 72.6 20 0.00044 32.0 7.6 99 23-122 3-121 (199)
36 PF08084 PROCT: PROCT (NUC072) 60.5 9.6 0.00021 32.0 3.1 22 127-148 11-32 (125)
37 KOG1795 U5 snRNP spliceosome s 52.7 17 0.00037 41.3 4.2 62 76-142 2163-2225(2321)
38 cd00225 API3 Ascaris pepsin in 43.4 97 0.0021 26.9 6.6 11 267-277 81-91 (159)
39 PF06442 DHFR_2: R67 dihydrofo 35.9 18 0.0004 26.9 0.9 10 79-88 41-50 (78)
40 KOG4538 Predicted coiled-coil 33.1 2.1E+02 0.0046 23.7 6.7 29 228-256 60-92 (130)
41 PF09454 Vps23_core: Vps23 cor 29.5 1.2E+02 0.0027 22.3 4.5 35 205-239 22-56 (65)
42 KOG0923 mRNA splicing factor A 28.8 59 0.0013 34.9 3.5 54 161-215 608-662 (902)
43 PF14198 TnpV: Transposon-enco 28.6 69 0.0015 26.2 3.3 33 275-307 38-70 (111)
44 KOG0848 Transcription factor C 23.6 1.2E+02 0.0025 29.0 4.2 63 220-286 237-303 (317)
45 COG5178 PRP8 U5 snRNP spliceos 21.1 1.1E+02 0.0025 35.0 4.0 59 79-142 2206-2265(2365)
No 1
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.1e-85 Score=592.16 Aligned_cols=293 Identities=34% Similarity=0.601 Sum_probs=270.5
Q ss_pred CCCcceEEEeHhHHHHHHhhhhccCCc--cccC-------------------CCCC--Cccc----hhhhh--hHHHHHH
Q 039881 18 PPALQVVQIEGLVLLKIIKHCKDLSPS--WLRQ-------------------ENDI--DQET----DDIGA--NYQLDMM 68 (315)
Q Consensus 18 ~~~~~~V~I~~lvllKIikH~~~~~~~--~V~G-------------------p~~~--~~~~----~~~~~--~Yq~~Ml 68 (315)
++|++.|++|++|||||||||+++.|. .++| |+.. +|+. ..+.+ .||.+||
T Consensus 9 ~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Glvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~ml 88 (339)
T KOG1560|consen 9 SPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGLVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAML 88 (339)
T ss_pred CCccceeeehhHHHHHHHHHHHhhcCCcchhhheeeeeeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHHH
Confidence 678999999999999999999998874 3444 4422 3332 22333 7999999
Q ss_pred HHHHhcCCCCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCC
Q 039881 69 SCLRDANVDSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGN 148 (315)
Q Consensus 69 ~~l~~vn~d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~ 148 (315)
+.||.||+|+.+||||+|++.|+ |+|..++++||.||++++++|++||||++|++ |.|++|||||+|.+|+++++++
T Consensus 89 rrlr~vnid~~hVGwYqs~~vgs-~lS~~lveSqy~YQ~a~pesVvliYD~~kssq--G~L~lrAyrLTp~am~~~kekd 165 (339)
T KOG1560|consen 89 RRLRYVNIDHLHVGWYQSAYVGS-FLSPALVESQYAYQKAIPESVVLIYDPIKSSQ--GTLSLRAYRLTPEAMAAHKEKD 165 (339)
T ss_pred HHhhhcCccceeeeeeeeehhcc-ccCHHHHHHHHHHHhcCCccEEEEeccccccC--ceEEeehhhcCHHHHHHHhcCC
Confidence 99999999999999999999999 99999999999999999999999999999999 9999999999999999999999
Q ss_pred CCccccccccccccceeEEEeeeEeccHHHHHHHhccCC--CCCCCCCCCCcccCCCchHHHHHHHHHHHHHHHhHHHHH
Q 039881 149 FSGESLRDKNISWADVFEEITIRVSNSALVSAFMSTLEP--DRVTDQSDHDRLQISSKPLLESNVEFLIRCMDDLSTEQK 226 (315)
Q Consensus 149 ~~~e~l~~~~l~~~~if~EIPi~I~ns~L~~~~L~~L~~--~~~~~~~~~d~L~Ls~~~~Lek~l~~L~e~id~l~~e~~ 226 (315)
|++|.++.+++++.++|+||||.|+||+|.+++|++|.. ..+...+.+..++|++...|+|+++.||+.+|++++|++
T Consensus 166 wtpealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDEl~qe~~ 245 (339)
T KOG1560|consen 166 WTPEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDELHQEIV 245 (339)
T ss_pred CCHHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999983 322223347778999999999999999999999999999
Q ss_pred HHHHHHHHHHHHH----HHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHHHHHHHhHH
Q 039881 227 KLKFYFKDVTRQQ----AWVQERRDENEARKAAGEDPLPEGDSSNPFFKPIPEPSRLESLLITNRIADYCNQIHRVAGHS 302 (315)
Q Consensus 227 ~~~~yqr~l~r~q----~~~~kr~~EN~~R~~~g~~~lpe~d~~~~~fk~~~~Psrl~~ll~s~qi~~~~~~i~~~~~~~ 302 (315)
|+++|||+++||| ||++||++||+.|+++|+||||||| |.|+||+|++|.|||++|+|+||+++|++|..||+++
T Consensus 246 ~l~kyqr~~~rqq~~~~q~~aKrqaENa~R~argep~lP~dd-~kr~fk~pq~p~rLdslLiS~qint~aq~ike~tSqn 324 (339)
T KOG1560|consen 246 NLNKYQRQLARQQAKKHQWIAKRQAENANRAARGEPPLPEDD-WKRIFKPPQEPRRLDSLLISGQINTSAQQIKEFTSQN 324 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCCCChHH-HHHHhcCCCchhHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 9999999999999 9999999999999999999999999 9999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcc
Q 039881 303 FSRLSLIKALHD 314 (315)
Q Consensus 303 ~~kl~~~~~~~~ 314 (315)
|+|||+++++|.
T Consensus 325 l~Klfiaea~~~ 336 (339)
T KOG1560|consen 325 LSKLFIAEALQE 336 (339)
T ss_pred HHHHHHHHHHHH
Confidence 999999999985
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=4.5e-64 Score=468.82 Aligned_cols=240 Identities=48% Similarity=0.823 Sum_probs=224.0
Q ss_pred ceEEEeHhHHHHHHhhhhccCCccccC-------------------CCCCCccc---hhhhhhHHHHHHHHHHhcCCCCc
Q 039881 22 QVVQIEGLVLLKIIKHCKDLSPSWLRQ-------------------ENDIDQET---DDIGANYQLDMMSCLRDANVDSN 79 (315)
Q Consensus 22 ~~V~I~~lvllKIikH~~~~~~~~V~G-------------------p~~~~~~~---~~~~~~Yq~~Ml~~l~~vn~d~~ 79 (315)
++|+|+++|+|||+|||.++.|.+|+| |..++++. ..++..||.+|+++++++|+|++
T Consensus 1 ~~V~I~~~vllkIv~H~~~~~p~~v~G~LLG~~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~e~ 80 (266)
T cd08065 1 TSVQIDGLVVLKIIKHCKEELPELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDHN 80 (266)
T ss_pred CEEEEeHHHHHHHHHHHhcCCCcEEEEEEeeeEcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCCCc
Confidence 479999999999999999999999999 44444332 45678999999999999999999
Q ss_pred ceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCCCCccccccccc
Q 039881 80 VVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGNFSGESLRDKNI 159 (315)
Q Consensus 80 ~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~~~~e~l~~~~l 159 (315)
+||||||||+| ||.+..+|++|+.||...+++|+|||||.++.+ |.+++||||++|.||.+|++|+|+.+.++++++
T Consensus 81 iVGWY~S~p~~-~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~--g~l~lkAyrl~~~~~~~~~~~~~~~~~l~~~~~ 157 (266)
T cd08065 81 HVGWYQSTYLG-SFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQ--GSLSLKAYRLSEKFMELYKEGKFSTESLREANL 157 (266)
T ss_pred EEEeEeecCCC-CcCCHHHHHHHHHHhccCCCCEEEEECCCcccc--cceeeEEEEEcHHHHHHhhcCCcCHHHHHHhcC
Confidence 99999999955 599999999999999988999999999999765 999999999999999999999999999999999
Q ss_pred cccceeEEEeeeEeccHHHHHHHhccCCCCCCCCCCCCcccCCCchHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 039881 160 SWADVFEEITIRVSNSALVSAFMSTLEPDRVTDQSDHDRLQISSKPLLESNVEFLIRCMDDLSTEQKKLKFYFKDVTRQQ 239 (315)
Q Consensus 160 ~~~~if~EIPi~I~ns~L~~~~L~~L~~~~~~~~~~~d~L~Ls~~~~Lek~l~~L~e~id~l~~e~~~~~~yqr~l~r~q 239 (315)
++.+||+||||+|+|++|++++|.+|.+..+...++++.|+|+++++|+++|+.|+++||++++|++||++|||+++|||
T Consensus 158 ~~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~~~y~r~~~~~~ 237 (266)
T cd08065 158 TFSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKFNYYQRNLARQQ 237 (266)
T ss_pred chhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999876555347899999999999999999999999999999999999999999999
Q ss_pred ----HHHHHHHHHHHHHHHcCCCCCCCCC
Q 039881 240 ----AWVQERRDENEARKAAGEDPLPEGD 264 (315)
Q Consensus 240 ----~~~~kr~~EN~~R~~~g~~~lpe~d 264 (315)
||++|||+||++|+++|++|||+||
T Consensus 238 ~~~~~~~~kr~~en~~r~~~~~~~lp~~~ 266 (266)
T cd08065 238 AQIQQWLQKRKAENAQREARGEEPLPEED 266 (266)
T ss_pred HHHHHHHHHHHHHhHHHHhcCCCCCCCCC
Confidence 8999999999999999999999986
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=100.00 E-value=2.4e-37 Score=288.99 Aligned_cols=194 Identities=24% Similarity=0.287 Sum_probs=161.5
Q ss_pred CCCcceEEEeHhHHHHHHhhhhccCCccccC-------------------CCCCCccchhhhhhHHHHHHH--HHHhcCC
Q 039881 18 PPALQVVQIEGLVLLKIIKHCKDLSPSWLRQ-------------------ENDIDQETDDIGANYQLDMMS--CLRDANV 76 (315)
Q Consensus 18 ~~~~~~V~I~~lvllKIikH~~~~~~~~V~G-------------------p~~~~~~~~~~~~~Yq~~Ml~--~l~~vn~ 76 (315)
...+++|+|+++|++||++||.++.|.+|+| |.+++++....+..||..|++ +++++|+
T Consensus 6 ~~~~~~V~Is~~allkil~Ha~~~~p~Ev~GlLlG~~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~~~ 85 (268)
T cd08069 6 PDYFEKVYISSLALLKMLKHARAGGPIEVMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGR 85 (268)
T ss_pred CCcccEEEECHHHHHHHHHHHhccCCceEEEEEEeeecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHhCC
Confidence 4678999999999999999999999999999 444433322223489999999 9999999
Q ss_pred CCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCC-ccCCCceeeeEEEechhhHhh--hhc-----CC
Q 039881 77 DSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRS-NIQGGLAGLKALKLSDTFLEL--YRN-----GN 148 (315)
Q Consensus 77 d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s-~~~~g~lslkAfRls~~~~~~--~k~-----g~ 148 (315)
++++||||||||+++||+|..||++|..||...+++|+|||||.++ .+ |+++++|||++|.++.+ +++ |.
T Consensus 86 ~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~--g~~~i~Afr~~~~~~~~~~~~~~~s~~~~ 163 (268)
T cd08069 86 PENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVK--GKVVIGAFRTIPPGYKPLEPRQTTSNIGH 163 (268)
T ss_pred CceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccC--CcceeeEEEEECccccccCcccCccccCc
Confidence 9999999999999999999999999999999999999999999998 55 99999999999999876 555 88
Q ss_pred CCccccccccccccceeEEEeeeEeccHHHHHHHhccCCCCCCCCCCCCcccCCCchHHHHHHHHHHHHHHHh
Q 039881 149 FSGESLRDKNISWADVFEEITIRVSNSALVSAFMSTLEPDRVTDQSDHDRLQISSKPLLESNVEFLIRCMDDL 221 (315)
Q Consensus 149 ~~~e~l~~~~l~~~~if~EIPi~I~ns~L~~~~L~~L~~~~~~~~~~~d~L~Ls~~~~Lek~l~~L~e~id~l 221 (315)
|+.++++ ...++.++|+||||+|++++|++.+|..|++. +|.-.|+.+++.+..-+.....+-++
T Consensus 164 ~~~~~~~-~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~-------~w~~~l~~~~~~~~~~~~~~~~~~~l 228 (268)
T cd08069 164 LPKPKIE-DFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNK-------YWVNTLSLSPLLENSNEYTIKQILDL 228 (268)
T ss_pred cCcHHHH-HhCchhcEEEEeeeEEecCHHHHHHHHHHHHH-------hHHHHhhCCchhhhhhHHHHHHHHHH
Confidence 9999999 78899999999999999999999999999864 33334555444433223333444443
No 4
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=2.5e-34 Score=263.08 Aligned_cols=195 Identities=21% Similarity=0.258 Sum_probs=166.0
Q ss_pred CCCcceEEEeHhHHHHHHhhhhccCCccccC-------------------CCCCCcc-chh--hhhhHHHHHHHHHHhcC
Q 039881 18 PPALQVVQIEGLVLLKIIKHCKDLSPSWLRQ-------------------ENDIDQE-TDD--IGANYQLDMMSCLRDAN 75 (315)
Q Consensus 18 ~~~~~~V~I~~lvllKIikH~~~~~~~~V~G-------------------p~~~~~~-~~~--~~~~Yq~~Ml~~l~~vn 75 (315)
...++.|.|+++++|||+.|++++++.+||| |.+++|+ +++ ...+|+...++..+.+|
T Consensus 49 p~~fk~vkISalAllKm~~hA~~GgnlEiMGlm~Gkv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~g 128 (347)
T KOG1554|consen 49 PHYFKHVKISALALLKMVMHARSGGNLEIMGLMQGKVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKNVG 128 (347)
T ss_pred CchhhhhhhHHHHHHHHHHHHhcCCCeEEEeeecccccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHHhh
Confidence 4568999999999999999999999999999 7788777 554 45678888999999999
Q ss_pred CCCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCCCC-----
Q 039881 76 VDSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGNFS----- 150 (315)
Q Consensus 76 ~d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~~~----- 150 (315)
+.+++||||||||+++||+|+.||+||...|++.+|+|++|+||.||.. .|++.|+|||.+|.+.....++.+.
T Consensus 129 r~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtls-agkv~iGAFRTyp~gyk~~d~~~seyqtip 207 (347)
T KOG1554|consen 129 RLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLS-AGKVNIGAFRTYPKGYKPPDEPPSEYQTIP 207 (347)
T ss_pred hhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccc-cCceeeceeecccCCCCCCCCCchhhhccc
Confidence 9999999999999999999999999999999999999999999999975 7999999999999984443344332
Q ss_pred ccccccccccccceeEEEeeeEeccHHHHHHHhccCCCCCCCCCCCCcccCCCchHHHHHHHHHHHHHHHhH
Q 039881 151 GESLRDKNISWADVFEEITIRVSNSALVSAFMSTLEPDRVTDQSDHDRLQISSKPLLESNVEFLIRCMDDLS 222 (315)
Q Consensus 151 ~e~l~~~~l~~~~if~EIPi~I~ns~L~~~~L~~L~~~~~~~~~~~d~L~Ls~~~~Lek~l~~L~e~id~l~ 222 (315)
..++.++|+ +..+|+.++|.++.|.|+...|+.|++. +|.-+|++++ |-+|.+++.++|-+++
T Consensus 208 l~kied~gv-Hck~yysl~isyfks~ld~kll~~Lwnk-------ywv~Tlsss~-ll~N~dy~~~qi~d~~ 270 (347)
T KOG1554|consen 208 LNKIEDFGV-HCKQYYSLEISYFKSSLDMKLLELLWNK-------YWVRTLSSSP-LLKNIDYLNGQIRDLS 270 (347)
T ss_pred hhhhhhccc-ceEEeeccchhhhhhhhhHHHHHHHHhh-------hhhccccccc-ccccchhhcchhhhHH
Confidence 246677777 6889999999999999999999999875 4444455543 6677888888887775
No 5
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=99.95 E-value=5.3e-27 Score=219.10 Aligned_cols=177 Identities=16% Similarity=0.224 Sum_probs=136.4
Q ss_pred EEEeHhHHHHHHhhhhc--cCCccccC-------------------CCCCCccchhhhhhHHHHHHHHHHhcCCCCccee
Q 039881 24 VQIEGLVLLKIIKHCKD--LSPSWLRQ-------------------ENDIDQETDDIGANYQLDMMSCLRDANVDSNVVG 82 (315)
Q Consensus 24 V~I~~lvllKIikH~~~--~~~~~V~G-------------------p~~~~~~~~~~~~~Yq~~Ml~~l~~vn~d~~~VG 82 (315)
|.|||+|+|+|+|||.+ ..+.+|+| |++++++....+.+|+.+|++++++||+++.+||
T Consensus 1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~d~~y~~~m~~~~kkv~~~~~vVG 80 (265)
T cd08064 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVDMEYHRTMYELHQKVNPKEVIVG 80 (265)
T ss_pred CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEEEeCCEEEEEeCeecceeCCCCeEEEcHHHHHHHHHHHHHhCCCCcEEe
Confidence 68999999999999997 45788999 5555545556789999999999999999999999
Q ss_pred EEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCCCCcccccccccccc
Q 039881 83 WYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGNFSGESLRDKNISWA 162 (315)
Q Consensus 83 WY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~~~~e~l~~~~l~~~ 162 (315)
||+|++..+ .+..+|+.||.++...+++|+|++||..+. |+++++||++++.++. +-+..
T Consensus 81 WY~tg~~~~--~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~---~~l~i~ay~~~~~~~~---------------~~~~~ 140 (265)
T cd08064 81 WYATGSEIT--EHSALIHDYYSRECTSYNPIHLTVDTSLDD---GKMSIKAYVSSPLGVP---------------GKTLG 140 (265)
T ss_pred eeeCCCCCC--ccHHHHHHHHHhhCCCCCCEEEEEeCCCCC---CCcceEEEEEEecccC---------------CCCcc
Confidence 999999543 448899999999987678999999998753 6899999999987631 11567
Q ss_pred ceeEEEeeeEeccHHHHHHHhccCCCCCCCCCCCCcccCCCchHHHHHHHHHHHHHHHhH
Q 039881 163 DVFEEITIRVSNSALVSAFMSTLEPDRVTDQSDHDRLQISSKPLLESNVEFLIRCMDDLS 222 (315)
Q Consensus 163 ~if~EIPi~I~ns~L~~~~L~~L~~~~~~~~~~~d~L~Ls~~~~Lek~l~~L~e~id~l~ 222 (315)
.+|.|||++|.+++.+++.++.|..........- .+ .+.-..+...+..|.+.||.+.
T Consensus 141 ~~F~~ip~~i~~~eaE~i~v~~l~~~~~~~~~~~-~~-~~~l~~~~~al~~L~~~l~~i~ 198 (265)
T cd08064 141 SMFVPIPLELLYSEAERVALDLLAKTLASPSRSA-PL-TSDLEQLEASLEKLQEMLDRVL 198 (265)
T ss_pred eEEEEcceeeecCcHHHHHHHHHHhhccCCcccc-cc-hhhHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999986433311110 00 1122345555556666666553
No 6
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=99.91 E-value=3.4e-23 Score=194.77 Aligned_cols=145 Identities=15% Similarity=0.201 Sum_probs=119.6
Q ss_pred ceEEEeHhHHHHHHhhhhccC---CccccC-------------------CCCCCcc---chhhhhhHHHHHHHHHHhcCC
Q 039881 22 QVVQIEGLVLLKIIKHCKDLS---PSWLRQ-------------------ENDIDQE---TDDIGANYQLDMMSCLRDANV 76 (315)
Q Consensus 22 ~~V~I~~lvllKIikH~~~~~---~~~V~G-------------------p~~~~~~---~~~~~~~Yq~~Ml~~l~~vn~ 76 (315)
++|+|||+|||+|+|||.+.. +.+|+| |.+++++ ..+.+..|+.+|++++++||+
T Consensus 1 ~~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~ 80 (280)
T cd08062 1 KKVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNA 80 (280)
T ss_pred CeEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEEEeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCC
Confidence 479999999999999999753 568999 5554333 246789999999999999999
Q ss_pred CCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCCCCcccccc
Q 039881 77 DSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGNFSGESLRD 156 (315)
Q Consensus 77 d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~~~~e~l~~ 156 (315)
++.+||||||+|..+ ..++..+-.|+..++++|+|++||... ++.+.++||...+....
T Consensus 81 ~e~vVGWY~tg~~~~----~~d~~ih~~~~~~~~~pv~l~vd~~~~---~~~lpi~aY~s~~~~~~-------------- 139 (280)
T cd08062 81 KEKIVGWYSTGPKLR----PNDLDINELFRRYCPNPVLVIIDVRPK---DLGLPTEAYIAVEEVHD-------------- 139 (280)
T ss_pred CCCeEEEecCCCCCC----cchHHHHHHHHHhCCCCEEEEEecCCC---CCCCceEEEEEeeeccC--------------
Confidence 999999999999754 566666677788888999999999874 37899999999875431
Q ss_pred ccccccceeEEEeeeEeccHHHHHHHhccCC
Q 039881 157 KNISWADVFEEITIRVSNSALVSAFMSTLEP 187 (315)
Q Consensus 157 ~~l~~~~if~EIPi~I~ns~L~~~~L~~L~~ 187 (315)
.|.+...+|.+||.+|.....+++.++.|..
T Consensus 140 ~g~~~~~~F~~vp~~i~~~eaE~igve~l~r 170 (280)
T cd08062 140 DGTPTSKTFVHVPSEIGAEEAEEVGVEHLLR 170 (280)
T ss_pred CCCcceeEEEEcceEeeccchHHHHHHHHHh
Confidence 1223578999999999999999999999975
No 7
>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=99.90 E-value=2e-23 Score=180.52 Aligned_cols=114 Identities=18% Similarity=0.209 Sum_probs=95.7
Q ss_pred EEEeHhHHHHHHhhhhccC--CccccC-------------------CCCCCccchhhhhhHHHHHHHHHHhcCCCCccee
Q 039881 24 VQIEGLVLLKIIKHCKDLS--PSWLRQ-------------------ENDIDQETDDIGANYQLDMMSCLRDANVDSNVVG 82 (315)
Q Consensus 24 V~I~~lvllKIikH~~~~~--~~~V~G-------------------p~~~~~~~~~~~~~Yq~~Ml~~l~~vn~d~~~VG 82 (315)
|+|||+|+|||+|||.+.. +.+|+| |.+++++....+..|+.+|++++++|++++.+||
T Consensus 1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~~~~~~veV~nsF~lp~~~~~~~~~~d~~y~~~m~~~~~~v~~~~~vVG 80 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFIDTEYLEKRYNLHKKVYPQEKIVG 80 (157)
T ss_pred CEEccHHHhhHHHHHHhccCCCCeEEEEEEeEEeCCEEEEEEeEEccccCCCcchhhhHHHHHHHHHHHHHhCCCCCEEE
Confidence 6899999999999999887 789999 4544444456689999999999999999999999
Q ss_pred EEecCCCCCC--CCCHHHHHHHHhhhhcCCCeEEEEeCCCCC-ccCCCceeeeEEEechhh
Q 039881 83 WYQSTPPGDC--FQSVEFIETFMNYKENIGKCVCIICDPSRS-NIQGGLAGLKALKLSDTF 140 (315)
Q Consensus 83 WY~S~~~g~~--f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s-~~~~g~lslkAfRls~~~ 140 (315)
||++++.+++ +.+...|+.++.++ ..+++|+|++||.++ .. |+++++|||+++.+
T Consensus 81 WY~~~~~~~~~~~~~~~~i~~~~~~~-~~~~~v~L~~D~~~~~~~--~~l~i~ay~~~~~~ 138 (157)
T cd08057 81 WYSIGSNNSNEISKSDNSLHSQFSLI-SEENPLILILDPSLQSDS--EKLEISTFTSAQRE 138 (157)
T ss_pred EEeecCCCCCCCChhHHHHHHHHHhc-cCCCCEEEEEcCCcccCC--CcccEEEEEEecCC
Confidence 9999999753 45566688888877 347789999999884 44 99999999998654
No 8
>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=99.90 E-value=1.1e-22 Score=192.08 Aligned_cols=183 Identities=15% Similarity=0.194 Sum_probs=136.8
Q ss_pred eEEEeHhHHHHHHhhhhcc----C--CccccC-------------------CCCCCc-cchhhhhhHHHHHHHHHHhcCC
Q 039881 23 VVQIEGLVLLKIIKHCKDL----S--PSWLRQ-------------------ENDIDQ-ETDDIGANYQLDMMSCLRDANV 76 (315)
Q Consensus 23 ~V~I~~lvllKIikH~~~~----~--~~~V~G-------------------p~~~~~-~~~~~~~~Yq~~Ml~~l~~vn~ 76 (315)
+|+|||+|||+|++||.+. . +.+|+| |.++++ +....+.+|+.+|++++++||+
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV~~ 81 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQVFK 81 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcCCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHhcc
Confidence 6999999999999999984 2 678998 554443 4456789999999999999999
Q ss_pred CCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCC-ccCCCceeeeEEEechhhHhhhhcCCCCccccc
Q 039881 77 DSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRS-NIQGGLAGLKALKLSDTFLELYRNGNFSGESLR 155 (315)
Q Consensus 77 d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s-~~~~g~lslkAfRls~~~~~~~k~g~~~~e~l~ 155 (315)
++.+||||+|++.|. +.+...|+.|+. ..++++|+|++||..+ .+ |.++++||+..+....
T Consensus 82 ~~~vVGWY~tg~~~~-~~~~~~Ih~~~~--~~~~~pv~L~~D~~~~~~~--~~lpi~ay~s~~~~~~------------- 143 (288)
T cd08063 82 DLDFVGWYTTGPGGP-TESDLPIHKQIL--EINESPVLLLLDPEANASG--KDLPVTIYESVLELVD------------- 143 (288)
T ss_pred CCceEEEEecCCCCC-CHHHHHHHHHHH--hhCCCcEEEEEccccccCC--CCCceeEEEEEEeccC-------------
Confidence 999999999999965 888888998888 3457899999999886 55 8899999999876532
Q ss_pred cccccccceeEEEeeeEeccHHHHHHHhccCCCCCCCCCCCCcccCCCchHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 039881 156 DKNISWADVFEEITIRVSNSALVSAFMSTLEPDRVTDQSDHDRLQISSKPLLESNVEFLIRCMDDLSTEQKKLKFYFKD 234 (315)
Q Consensus 156 ~~~l~~~~if~EIPi~I~ns~L~~~~L~~L~~~~~~~~~~~d~L~Ls~~~~Lek~l~~L~e~id~l~~e~~~~~~yqr~ 234 (315)
+ .....|.+||.+|..+..+++.++.+........ +..+.+...++.+..++..+..-......|-+.
T Consensus 144 --~-~~~~~F~~i~~~i~~~eaErIgv~~l~~~~~~~~--------~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl~~ 211 (288)
T cd08063 144 --G-EATLRFRELPYTIETGEAERIGVDHVARGGASGS--------SEKSTVAAHLQAQHNAIKMLNSRVELILEYLKA 211 (288)
T ss_pred --C-ccccEEEeeeeEEEeccCceeeHHHHHhcCCCCC--------CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 2457899999999999999999999975432111 111234445555555555554333333334333
No 9
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.89 E-value=6.7e-22 Score=187.64 Aligned_cols=150 Identities=19% Similarity=0.229 Sum_probs=119.3
Q ss_pred CCCcceEEEeHhHHHHHHhhhhccCC---ccccC-------------------CCCCCcc---chhhhhhHHHHHHHHHH
Q 039881 18 PPALQVVQIEGLVLLKIIKHCKDLSP---SWLRQ-------------------ENDIDQE---TDDIGANYQLDMMSCLR 72 (315)
Q Consensus 18 ~~~~~~V~I~~lvllKIikH~~~~~~---~~V~G-------------------p~~~~~~---~~~~~~~Yq~~Ml~~l~ 72 (315)
..|+.+|+|||+|+|+|+|||.+..+ .+|+| |.+++++ ..+.+.+|+.+|+++++
T Consensus 2 ~~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~k 81 (303)
T PLN03246 2 PRGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMFK 81 (303)
T ss_pred CCCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEeeecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHHH
Confidence 57899999999999999999998764 56888 5443322 24578999999999999
Q ss_pred hcCCCCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCCCCcc
Q 039881 73 DANVDSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGNFSGE 152 (315)
Q Consensus 73 ~vn~d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~~~~e 152 (315)
+||+++.+||||+|++..+ .+...|+.+| ....+++|+|++|+... ++.++++||.+.+..... |
T Consensus 82 ~V~~~~~vVGWY~tg~~i~--~~d~~IH~~~--~~~~~~Pv~L~vD~~~~---~~~lpi~aY~s~~~~~~~---~----- 146 (303)
T PLN03246 82 RINAKEHVVGWYSTGPKLR--ENDLDIHELF--NDYVPNPVLVIIDVQPK---ELGIPTKAYYAVEEVKEN---A----- 146 (303)
T ss_pred HhCCCCcEEeeecCCCCCC--cchHHHHHHH--HhhCCCCeEEEEecCCC---CCCCceEEEEEEEeccCC---C-----
Confidence 9999999999999999765 4455666544 55667899999998762 377999999987664310 0
Q ss_pred ccccccccccceeEEEeeeEeccHHHHHHHhccCC
Q 039881 153 SLRDKNISWADVFEEITIRVSNSALVSAFMSTLEP 187 (315)
Q Consensus 153 ~l~~~~l~~~~if~EIPi~I~ns~L~~~~L~~L~~ 187 (315)
......+|.+||.+|.....+++.++.+..
T Consensus 147 -----~~~~~~~F~~vp~~i~~~EaE~Igve~l~r 176 (303)
T PLN03246 147 -----TQKSQKVFVHVPSEIGAHEAEEIGVEHLLR 176 (303)
T ss_pred -----CcccccEEEECCeeeeecCHHHHHHHHHHh
Confidence 012467899999999999999999999975
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=99.88 E-value=2.3e-22 Score=178.89 Aligned_cols=117 Identities=20% Similarity=0.265 Sum_probs=96.0
Q ss_pred cceEEEeHhHHHHHHhhhhccCCccccCC---------------------CCCCccchhhhhhHHHHHHHHHHhcCCCCc
Q 039881 21 LQVVQIEGLVLLKIIKHCKDLSPSWLRQE---------------------NDIDQETDDIGANYQLDMMSCLRDANVDSN 79 (315)
Q Consensus 21 ~~~V~I~~lvllKIikH~~~~~~~~V~Gp---------------------~~~~~~~~~~~~~Yq~~Ml~~l~~vn~d~~ 79 (315)
.-+|+|+++|||||++||+++. .+|+|. ...+.+....+..+|.+|++.+++.|. .
T Consensus 4 pf~V~Is~~all~m~~Ha~~~~-~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~gl--~ 80 (187)
T cd08067 4 PFKVTVSSNALLLMDFHCHLTT-SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRGL--S 80 (187)
T ss_pred CEEEEECHHHHHHHHHHhcCCC-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcCC--E
Confidence 3489999999999999999987 899991 111111112357899999999998885 9
Q ss_pred ceeEEecCCCCCCCCCHHHHHHHHhhhhcCC-------CeEEEEeCCCCCccCCCceeeeEEEechhh
Q 039881 80 VVGWYQSTPPGDCFQSVEFIETFMNYKENIG-------KCVCIICDPSRSNIQGGLAGLKALKLSDTF 140 (315)
Q Consensus 80 ~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~-------~~V~LV~Dp~~s~~~~g~lslkAfRls~~~ 140 (315)
+||||||||.+.||+|..||+||+.||.... ++|+||+||..+...+....++||+++|+-
T Consensus 81 vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~~ 148 (187)
T cd08067 81 VVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPP 148 (187)
T ss_pred EEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECCC
Confidence 9999999999999999999999999998764 899999999886432356789999998763
No 11
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=1.6e-21 Score=177.49 Aligned_cols=179 Identities=15% Similarity=0.191 Sum_probs=145.0
Q ss_pred CcceEEEeHhHHHHHHhhhhccC--CccccC-------------------CCCCCccchhhhhhHHHHHHHHHHhcCCCC
Q 039881 20 ALQVVQIEGLVLLKIIKHCKDLS--PSWLRQ-------------------ENDIDQETDDIGANYQLDMMSCLRDANVDS 78 (315)
Q Consensus 20 ~~~~V~I~~lvllKIikH~~~~~--~~~V~G-------------------p~~~~~~~~~~~~~Yq~~Ml~~l~~vn~d~ 78 (315)
..-+|.|+|+|+++|++|+.+.. ..+||| |+.+.++....+.+|+.+|+++++++|+.|
T Consensus 19 s~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~~~~g~ieitNCFaVPhnEssdqvevdm~y~~~M~~l~~k~npnE 98 (288)
T KOG2975|consen 19 SNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGTVDKGSVEVTNCFAVPHNESSDQVEVDMEYAKNMYELHKKVNPNE 98 (288)
T ss_pred CCceEEEcceEEeEeehhhhcCCccchhhhhheeecccCCeEEEEEeeeccCccccccceeeHHHHHHHHHHhcccCCCc
Confidence 35689999999999999999764 578999 777777777889999999999999999999
Q ss_pred cceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCCCCcccccccc
Q 039881 79 NVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGNFSGESLRDKN 158 (315)
Q Consensus 79 ~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~~~~e~l~~~~ 158 (315)
.+||||.+++..+ -++.+|++.|.... +++|||.+|+..+ +|.+++|||-.++.++. |
T Consensus 99 ~vvGWyaTg~dvt--~~sslihdyYare~--~~pvhLtVDT~~~---n~rm~ikaYvss~~Gvp---------------g 156 (288)
T KOG2975|consen 99 LVVGWYATGHDVT--EHSSLIHDYYAREA--PNPVHLTVDTSLQ---NGRMSIKAYVSSLMGVP---------------G 156 (288)
T ss_pred eeEEEEecCCCcc--cchhHHHHHhhccC--CCCeEEEEecccc---CCccceeEEEEeccCCC---------------C
Confidence 9999999999886 45899999998776 5699999999884 49999999999987752 2
Q ss_pred ccccceeEEEeeeEeccHHHHHHHhccCCCCCCCCCCCCcccCCCchHHHHHHHHHHHHHHHhH
Q 039881 159 ISWADVFEEITIRVSNSALVSAFMSTLEPDRVTDQSDHDRLQISSKPLLESNVEFLIRCMDDLS 222 (315)
Q Consensus 159 l~~~~if~EIPi~I~ns~L~~~~L~~L~~~~~~~~~~~d~L~Ls~~~~Lek~l~~L~e~id~l~ 222 (315)
.+...+|.+||++|.+-..++..|..+.+.. ..++....| .+.-.-++.....|.+.||...
T Consensus 157 ~~~~~mF~plpvel~~~~~ervgl~li~kt~-~sp~r~~~l-~~dLqQv~~at~~l~~~L~~Vl 218 (288)
T KOG2975|consen 157 RTMGVMFTPLPVELAYYDAERVGLDLIEKTS-FSPSRVAGL-SSDLQQVEGATARLQSLLERVL 218 (288)
T ss_pred cccceeeeeeeeEEeecchhhhHHHHHHHhc-cChhhhccc-cchHHHHHHHHHHHHHHHHHHH
Confidence 3345599999999999999999999997654 212222222 1122446777788888888874
No 12
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=4.3e-21 Score=180.27 Aligned_cols=229 Identities=20% Similarity=0.211 Sum_probs=153.9
Q ss_pred CCcceEEEeHhHHHHHHhhhhccCCcc-ccCC------------------------CCCCcc---chhhhhhHHHHHHHH
Q 039881 19 PALQVVQIEGLVLLKIIKHCKDLSPSW-LRQE------------------------NDIDQE---TDDIGANYQLDMMSC 70 (315)
Q Consensus 19 ~~~~~V~I~~lvllKIikH~~~~~~~~-V~Gp------------------------~~~~~~---~~~~~~~Yq~~Ml~~ 70 (315)
..-.+|.|+++++++|++|.+.+.|.+ |||- .++..- +++.+..||..|+++
T Consensus 28 ~~~e~v~i~slall~m~rh~r~~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~d~V~q~q~~~~ 107 (316)
T KOG1555|consen 28 DEKETVYISSLALLKMLRHDRAGSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQMMDL 107 (316)
T ss_pred cCcceeeeehhhhhhcccccccCCchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHHHHH
Confidence 345789999999999999999999987 8881 111111 345689999999999
Q ss_pred HHhcCCCCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhh-----
Q 039881 71 LRDANVDSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYR----- 145 (315)
Q Consensus 71 l~~vn~d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k----- 145 (315)
++..|+++.+||||||||+.+||+|..||+||.+||...+++++.++||+.|-. |+....|||+.....-.-.
T Consensus 108 l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~--g~vv~d~f~~In~~~~~~~~eprq 185 (316)
T KOG1555|consen 108 LKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPY--GKVVPDAFSSINPQWISPGGEPRQ 185 (316)
T ss_pred HHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCC--CCccCChhhhcCcccccCCCCCcc
Confidence 999999999999999999999999999999999999999999999999999976 9988889999866432211
Q ss_pred ----cCCCCc-cccccccccccceeEEEeeeEeccHHHHHHHhccCCCCCCCCCCCCcccCCCchHHHHHHHHHHHHHHH
Q 039881 146 ----NGNFSG-ESLRDKNISWADVFEEITIRVSNSALVSAFMSTLEPDRVTDQSDHDRLQISSKPLLESNVEFLIRCMDD 220 (315)
Q Consensus 146 ----~g~~~~-e~l~~~~l~~~~if~EIPi~I~ns~L~~~~L~~L~~~~~~~~~~~d~L~Ls~~~~Lek~l~~L~e~id~ 220 (315)
-|.+.. +++++.....+ -|+-+.|.++...+...++..+...+.. + +...+-.-..++-+.-.....+
T Consensus 186 tts~~~~m~~~~s~q~~~~g~n-~y~~~ei~~~v~~~~~~~~~nv~~~s~~-----~-~~~~~y~e~~k~~~~~~~~~~s 258 (316)
T KOG1555|consen 186 TTSNGGHMDMQESLQEDIHGLN-RYYRIEIPLHVLPYEQLMLLNVPLKSWK-----S-LQDVLYEEKLKAYLQSVPSMKS 258 (316)
T ss_pred ccccccccccchhHHhHhhccC-ceEEEEeeEEechhhhhchhccchhhhh-----h-cchhhHHHHHHHhhhhhhHHHh
Confidence 134444 55554444444 5677777777777777776666433221 1 1111111112222222233333
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Q 039881 221 LSTEQKKLKFYFKDVTRQQAWVQERRDENEARKAAG 256 (315)
Q Consensus 221 l~~e~~~~~~yqr~l~r~q~~~~kr~~EN~~R~~~g 256 (315)
++.--|+..--..+..-.+.|+..+-.-|.++..++
T Consensus 259 L~~~~N~~~~~~k~~~~~~~~i~d~~~~~~kq~l~~ 294 (316)
T KOG1555|consen 259 LSKVYNKVCDVCKQMSDFLLMIEDVGEQNPKQHLKE 294 (316)
T ss_pred HHHHHHHHHHHHhhccHHHHHHHHhhhhhHHHHhHH
Confidence 333222222223333333388888877776555544
No 13
>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=99.84 E-value=3e-20 Score=170.86 Aligned_cols=194 Identities=15% Similarity=0.132 Sum_probs=134.1
Q ss_pred cceEEEeHhHHHHHHhhhhccCCccccC----CCCC------Ccc------------------chhhhh---hHHHHHHH
Q 039881 21 LQVVQIEGLVLLKIIKHCKDLSPSWLRQ----ENDI------DQE------------------TDDIGA---NYQLDMMS 69 (315)
Q Consensus 21 ~~~V~I~~lvllKIikH~~~~~~~~V~G----p~~~------~~~------------------~~~~~~---~Yq~~Ml~ 69 (315)
+++|.|+..++++|+.||.++.|.+++| ...+ .+. .+.+.. .-+.+|-+
T Consensus 1 l~~V~Is~~~l~~il~HA~~~~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~~ 80 (244)
T cd08068 1 LSKVHLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAER 80 (244)
T ss_pred CcEEEECHHHHHHHHHHHHhCCCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHHH
Confidence 4689999999999999999999999999 2211 110 111122 22356667
Q ss_pred HHHhcCCCCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCC---CccCCCceeeeEEEechhhHhhhhc
Q 039881 70 CLRDANVDSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSR---SNIQGGLAGLKALKLSDTFLELYRN 146 (315)
Q Consensus 70 ~l~~vn~d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~---s~~~~g~lslkAfRls~~~~~~~k~ 146 (315)
+++.++++..+||||||||.+.||+|..||++|..||...+++|+||+++.. ++. .|++.++|||+.+.-
T Consensus 81 ~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~-~~~~~i~aFr~~~g~------ 153 (244)
T cd08068 81 LTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTK-MGEVQVTCFQSVQGN------ 153 (244)
T ss_pred HHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccc-cCCEEEEEEEecCCC------
Confidence 7888999999999999999999999999999999999888999999997643 232 388999999997541
Q ss_pred CCCCccccccccccccceeEEEeeeEe-ccHHHHHHHhccCCCCCCC-------------CCCCCccc-CCCchHHHHHH
Q 039881 147 GNFSGESLRDKNISWADVFEEITIRVS-NSALVSAFMSTLEPDRVTD-------------QSDHDRLQ-ISSKPLLESNV 211 (315)
Q Consensus 147 g~~~~e~l~~~~l~~~~if~EIPi~I~-ns~L~~~~L~~L~~~~~~~-------------~~~~d~L~-Ls~~~~Lek~l 211 (315)
........|+|+.|. .+.+...+|..+......+ .+..|.|+ +++.+..+++|
T Consensus 154 ------------~~~~~~~~e~pl~i~~~~~~~~~~~~~~~~l~~~l~~e~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (244)
T cd08068 154 ------------KAGQYERIEVPLEIVPTSTISEACLESLVELPEILYQEEEDAYNKALQSCDLDPLTKIHNGSVYTKSL 221 (244)
T ss_pred ------------CCCcceEEEeeeEEecCccccccCHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhhHHHHHHH
Confidence 134567899999997 4445555655554211000 11122233 44444455555
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 039881 212 EFLIRCMDDLSTEQKKLKFYFKDVTRQQAWVQERRDEN 249 (315)
Q Consensus 212 ~~L~e~id~l~~e~~~~~~yqr~l~r~q~~~~kr~~EN 249 (315)
..+++.+-... + +|++.|.++|
T Consensus 222 ~~~~~~~~~p~------------~----~~l~~~~~~~ 243 (244)
T cd08068 222 CHILETISGPL------------L----QLLEARLEQN 243 (244)
T ss_pred HHHHHHHHhhH------------H----HHHHHHHHhc
Confidence 55555443332 2 8999998887
No 14
>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=99.83 E-value=7.3e-20 Score=152.31 Aligned_cols=114 Identities=29% Similarity=0.430 Sum_probs=101.0
Q ss_pred eEEEeHhHHHHHHhhhhccCCccccC-------------------CCCCCcc-chhhhhhHHHHHHHHHHhcCCCCccee
Q 039881 23 VVQIEGLVLLKIIKHCKDLSPSWLRQ-------------------ENDIDQE-TDDIGANYQLDMMSCLRDANVDSNVVG 82 (315)
Q Consensus 23 ~V~I~~lvllKIikH~~~~~~~~V~G-------------------p~~~~~~-~~~~~~~Yq~~Ml~~l~~vn~d~~~VG 82 (315)
.|+|++.|+++|++||.+..|.+++| |...+++ ....+.+|+..|.+.+++++.+..+||
T Consensus 1 ~v~i~~~v~~~i~~h~~~~~p~e~~G~L~G~~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vG 80 (135)
T smart00232 1 EVKVHPLVPLNILKHAIRDGPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLEIVG 80 (135)
T ss_pred CEEEcHHHHHHHHHHHhcCCCcEEEEEEEEEEcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCceEEE
Confidence 48999999999999999999999999 2222222 224577999999999999999999999
Q ss_pred EEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEech
Q 039881 83 WYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSD 138 (315)
Q Consensus 83 WY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~ 138 (315)
||||||.+.+++|..|+.++..|+.....+|++++|+.++.. |.++++|||+++
T Consensus 81 wyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~--g~~~~~af~~~~ 134 (135)
T smart00232 81 WYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQ--GRLSLRAFRLTP 134 (135)
T ss_pred EEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCcccc--CcEEEEEEEecC
Confidence 999999988899999999999999999999999999999887 999999999975
No 15
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.82 E-value=3.8e-20 Score=152.96 Aligned_cols=104 Identities=17% Similarity=0.165 Sum_probs=82.7
Q ss_pred hHHHHHHhhhhccCCccccCCCCC---Cc---c-----chhhh----hhHHHHHHHHHHhcCCCCcceeEEecCCCCCCC
Q 039881 29 LVLLKIIKHCKDLSPSWLRQENDI---DQ---E-----TDDIG----ANYQLDMMSCLRDANVDSNVVGWYQSTPPGDCF 93 (315)
Q Consensus 29 lvllKIikH~~~~~~~~V~Gp~~~---~~---~-----~~~~~----~~Yq~~Ml~~l~~vn~d~~~VGWY~S~~~g~~f 93 (315)
.|++||++||.++.|.+++|..-+ ++ + .+... ..=...|..+++..+.+.++||||||||.+.+|
T Consensus 1 ~~~~~i~~ha~~~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~~~~~~~~~~~~~~g~~~vG~YHSHP~~~~~ 80 (119)
T cd08058 1 DALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTGENVEELFNVQTGRPLLVVGWYHSHPTFTAW 80 (119)
T ss_pred CHHHHHHHHhcCCCCeEEEEEeeeEEecCccceeEEEEeecCCCCCCchhHHHHHHHHHHhCCCCeEEEEEecCCCCCCc
Confidence 489999999999999999993211 10 0 01111 111335777778899999999999999977789
Q ss_pred CCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEec
Q 039881 94 QSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLS 137 (315)
Q Consensus 94 ~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls 137 (315)
+|..||++|+.||...+++|+||+||.++ ++++|||||+
T Consensus 81 pS~~Di~~~~~~q~~~p~~~~lI~s~~~~-----~~~~~a~rl~ 119 (119)
T cd08058 81 LSSVDIHTQASYQLMLPEAIAIVVSPKHR-----NKDTGIFRLT 119 (119)
T ss_pred cCHHHHHHHHHHhccCCCeEEEEECcCCC-----CcccceEEeC
Confidence 99999999999999999999999999772 5789999986
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=99.78 E-value=1.3e-19 Score=148.02 Aligned_cols=91 Identities=35% Similarity=0.516 Sum_probs=74.6
Q ss_pred CcceEEEeHhHHHHHHhhhhccCCccccC--------------------CCCCCcc-chhhhhhHHHHHHHHHHhcCCCC
Q 039881 20 ALQVVQIEGLVLLKIIKHCKDLSPSWLRQ--------------------ENDIDQE-TDDIGANYQLDMMSCLRDANVDS 78 (315)
Q Consensus 20 ~~~~V~I~~lvllKIikH~~~~~~~~V~G--------------------p~~~~~~-~~~~~~~Yq~~Ml~~l~~vn~d~ 78 (315)
++.+|+|+|+|+|+|++||.+..+.+|+| |..++++ ....+..+..+|++++++++++.
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~~~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSSPNEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVNPNL 81 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHHCTEEEEEEEEEEETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCSTTS
T ss_pred CcEEEEECHHHHHHHHHHHhcCCCCEEEEEEEEEecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhccccccc
Confidence 57899999999999999999988889999 2222222 23345566689999999999999
Q ss_pred cceeEEecCCCCCCCCCHHHHHHHHhhhhcCC
Q 039881 79 NVVGWYQSTPPGDCFQSVEFIETFMNYKENIG 110 (315)
Q Consensus 79 ~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~ 110 (315)
.+||||||||.+.||+|..||++|..||.+++
T Consensus 82 ~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~ 113 (114)
T PF01398_consen 82 EIVGWYHSHPNISCFPSPTDIETQKQYQRMNP 113 (114)
T ss_dssp EEEEEEEEESSS-SS--HHHHHHHHHHHHHTT
T ss_pred eEEEEEEccCCccccCCHHHHHHHHHHHHhCC
Confidence 99999999999999999999999999999875
No 17
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=99.77 E-value=3.3e-18 Score=154.68 Aligned_cols=149 Identities=17% Similarity=0.208 Sum_probs=124.1
Q ss_pred CCCcceEEEeHhHHHHHHhhhhccCC---ccccC-------------------CCCCCcc---chhhhhhHHHHHHHHHH
Q 039881 18 PPALQVVQIEGLVLLKIIKHCKDLSP---SWLRQ-------------------ENDIDQE---TDDIGANYQLDMMSCLR 72 (315)
Q Consensus 18 ~~~~~~V~I~~lvllKIikH~~~~~~---~~V~G-------------------p~~~~~~---~~~~~~~Yq~~Ml~~l~ 72 (315)
..++..|.|+|+|||++++|+.+... .+|.| |.+++|. +.+-|.+|...|..|++
T Consensus 5 ~~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mfk 84 (309)
T KOG1556|consen 5 ELTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGSWNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMFK 84 (309)
T ss_pred ccccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEecCCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHHH
Confidence 46788999999999999999998754 68888 6655443 46789999999999999
Q ss_pred hcCCCCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCCCCcc
Q 039881 73 DANVDSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGNFSGE 152 (315)
Q Consensus 73 ~vn~d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~~~~e 152 (315)
+||.++.+||||||+|.. ...||+.....-++.+++|.+|+|...- +-.|...|| |..+
T Consensus 85 KvNakekivGWYhTGPkl----~~nDl~In~l~k~y~pnpvLvIIdvkpk---~~gLPT~AY--------------~aVe 143 (309)
T KOG1556|consen 85 KVNAKEKVVGWYHTGPKL----RENDLDINELLKRYVPNPVLVIIDVKPK---ELGLPTEAY--------------IAVE 143 (309)
T ss_pred HhcchhheeeeeccCCcc----ccchhhHHHHHhhcCCCceEEEEecccc---cCCCCchhe--------------eeee
Confidence 999999999999999964 3677777777778889999999999762 234778888 5556
Q ss_pred ccccccccccceeEEEeeeEeccHHHHHHHhccCC
Q 039881 153 SLRDKNISWADVFEEITIRVSNSALVSAFMSTLEP 187 (315)
Q Consensus 153 ~l~~~~l~~~~if~EIPi~I~ns~L~~~~L~~L~~ 187 (315)
.+.+.|......|+.+|.+|-.-..+....+.|-.
T Consensus 144 ev~dDgt~t~ktF~Hvps~I~AeEAEEvGVEHLlR 178 (309)
T KOG1556|consen 144 EVKDDGTPTSKTFVHVPSEIEAEEAEEVGVEHLLR 178 (309)
T ss_pred eeecCCCCccceeEecCcccchhHHHHhhHHHHHH
Confidence 66778888899999999999999999998888754
No 18
>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=99.53 E-value=7.1e-14 Score=123.09 Aligned_cols=114 Identities=15% Similarity=0.263 Sum_probs=87.8
Q ss_pred ceEEEeHhHHHHHHhhhhccC--CccccC-------------------CCCCCcc-chhhhhhHHHHHHHHHHhcCCCCc
Q 039881 22 QVVQIEGLVLLKIIKHCKDLS--PSWLRQ-------------------ENDIDQE-TDDIGANYQLDMMSCLRDANVDSN 79 (315)
Q Consensus 22 ~~V~I~~lvllKIikH~~~~~--~~~V~G-------------------p~~~~~~-~~~~~~~Yq~~Ml~~l~~vn~d~~ 79 (315)
..+.|....+-||+.||..+. |.++.| |..++.. ....+ +.++++.++. .+..
T Consensus 2 ~~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~~~~~~~~I~~i~~~~q~~~~~~~~~~~---~~e~~~~~~~--~gle 76 (173)
T cd08066 2 RQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQTTN---EEELFDFQDQ--HDLI 76 (173)
T ss_pred eEEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeEcCCCeEEEEEEEeccccCCCceecCCC---HHHHHHHHHh--CCCe
Confidence 467899999999999999985 578888 1122111 11111 2335554443 4679
Q ss_pred ceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEec-hhhHhhhhcC
Q 039881 80 VVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLS-DTFLELYRNG 147 (315)
Q Consensus 80 ~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls-~~~~~~~k~g 147 (315)
+||||||||...||+|..||+||..||.+.+++++||++| +..+++|||++ |.+++-.+++
T Consensus 77 ~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp-------~~~~l~afrl~~~~g~~~~~~~ 138 (173)
T cd08066 77 TLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAP-------KYNEFGIFRLTDPPGLDEILNC 138 (173)
T ss_pred eEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECC-------CCcEEeEEEeecCCcceecccC
Confidence 9999999999999999999999999999999999999997 45789999999 7787766543
No 19
>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=99.52 E-value=3.3e-14 Score=115.42 Aligned_cols=96 Identities=20% Similarity=0.263 Sum_probs=75.8
Q ss_pred HHHHhhhhccCCccccC-------------------CCCCCccchhhhhhHHHHHHHHHHhcCCCCcceeEEecCCCCCC
Q 039881 32 LKIIKHCKDLSPSWLRQ-------------------ENDIDQETDDIGANYQLDMMSCLRDANVDSNVVGWYQSTPPGDC 92 (315)
Q Consensus 32 lKIikH~~~~~~~~V~G-------------------p~~~~~~~~~~~~~Yq~~Ml~~l~~vn~d~~~VGWY~S~~~g~~ 92 (315)
.+|++||++..|.+|+| |....+. ....++. |+...+.++.+..+||||||||.+.+
T Consensus 2 k~il~~a~~~~~~ev~G~L~G~~~~~~~~i~~~~~~~~~~~~~---~~~~~~~-~~~~~~~~~~~~~iVGwyhshp~~~~ 77 (116)
T cd07767 2 KMFLDAAKSINGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDK---DDNVWFL-MYLDFKKLNAGLRIVGWYHTHPKPSC 77 (116)
T ss_pred HhHHHHHhcCCCcEEEEEeEEEEcCCEEEEEEEEecccCCCCC---ccHHHHH-HHHHHHHhcCCCeEEEEEEcCCCCCC
Confidence 58999999988999999 1111111 1122332 67777888999999999999999988
Q ss_pred CCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEE
Q 039881 93 FQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKAL 134 (315)
Q Consensus 93 f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAf 134 (315)
|+|..+|.++..||...+++|+||+|+.... ..++++||
T Consensus 78 ~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~---~~~~~~~~ 116 (116)
T cd07767 78 FLSPNDLATHELFQRYFPEKVMIIVDVKPKD---LGNSWKCY 116 (116)
T ss_pred ccCHHHHHHHHHHHHhCCCCEEEEEECCCcc---CCCCcccC
Confidence 9999999999999998889999999998832 35778876
No 20
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=98.85 E-value=1.8e-08 Score=84.18 Aligned_cols=96 Identities=23% Similarity=0.228 Sum_probs=70.9
Q ss_pred HHHHHHhhhhccCCccccCC-------------------CCCCcc-ch-hhhhhHHHHHHHHHHhcCCCCcceeEEecCC
Q 039881 30 VLLKIIKHCKDLSPSWLRQE-------------------NDIDQE-TD-DIGANYQLDMMSCLRDANVDSNVVGWYQSTP 88 (315)
Q Consensus 30 vllKIikH~~~~~~~~V~Gp-------------------~~~~~~-~~-~~~~~Yq~~Ml~~l~~vn~d~~~VGWY~S~~ 88 (315)
++-+|++||+++.|.++.|- ...++. .. ..+...+..+.+..++. +..+||||||||
T Consensus 3 ~~~~il~ha~~~~P~E~cGlL~G~~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~--g~~~vG~~HSHP 80 (128)
T cd08070 3 LLEAILAHAEAEYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARER--GLEVVGIYHSHP 80 (128)
T ss_pred HHHHHHHHHHhCCCCceEEEEEeecCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHC--CCeEEEEEeCCC
Confidence 56799999999999999981 111111 11 12455556666666655 479999999999
Q ss_pred CCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEec
Q 039881 89 PGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLS 137 (315)
Q Consensus 89 ~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls 137 (315)
.+.+++|..|+..+... ..+.||+.+.. +...++||++.
T Consensus 81 ~~~~~PS~~D~~~~~~~-----~~~~lIv~~~~-----~~~~~~~~~~~ 119 (128)
T cd08070 81 DGPARPSETDLRLAWPP-----GVSYLIVSLAG-----GAPELRAWRLE 119 (128)
T ss_pred CCCCCCCHHHHHhccCC-----CCeEEEEECCC-----CCcEEEEEEEc
Confidence 99999999999887643 67899998754 45679999985
No 21
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=98.85 E-value=4.8e-09 Score=88.34 Aligned_cols=92 Identities=18% Similarity=0.173 Sum_probs=58.9
Q ss_pred EEEeHhHHHHHHhhhhccCCccccC----CCCC----Ccc---chhhhhhHHHHHH--HHHHhcCCCCcceeEEecCCCC
Q 039881 24 VQIEGLVLLKIIKHCKDLSPSWLRQ----ENDI----DQE---TDDIGANYQLDMM--SCLRDANVDSNVVGWYQSTPPG 90 (315)
Q Consensus 24 V~I~~lvllKIikH~~~~~~~~V~G----p~~~----~~~---~~~~~~~Yq~~Ml--~~l~~vn~d~~~VGWY~S~~~g 90 (315)
+.|...++-.|+.|+.+..|.+++| +..+ ... .+.....++..|+ ..+.....++.+||||||||++
T Consensus 2 ~~i~~~~l~~il~~a~~~~p~E~~g~l~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~g~~vvg~yHSHP~~ 81 (134)
T COG1310 2 LVIPKEVLGAILEHARREHPREVCGLLAGTREGERYFPLKNVSVEPVEYFEIDPEYSLFYLAAEDAGEVVVGWYHSHPGG 81 (134)
T ss_pred ceecHHHHHHHHHHHHhcCChheEEEEEeecccceeeccccccCCcceeEeeCHHHHHHHHHHhhCCCEEEEEEcCCCCC
Confidence 4678899999999999999999998 3222 000 1111112222222 2222333449999999999999
Q ss_pred CCCCCHHHHHHHHhhhhcCCC-eEEEEeCC
Q 039881 91 DCFQSVEFIETFMNYKENIGK-CVCIICDP 119 (315)
Q Consensus 91 ~~f~s~~~Ietq~~yQ~~~~~-~V~LV~Dp 119 (315)
.||+|..|+. .+...+. ++.++.++
T Consensus 82 ~~~pS~~D~~----~~~~~~~~~~iv~~~~ 107 (134)
T COG1310 82 PPYPSEADRR----LSKLGPLPWLIVSVPP 107 (134)
T ss_pred CCCcCHHHHh----hccccCCCEEEEEcCC
Confidence 9999999998 4444333 45555555
No 22
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=98.36 E-value=1.6e-07 Score=89.64 Aligned_cols=68 Identities=24% Similarity=0.507 Sum_probs=56.7
Q ss_pred cceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEec-hhhHhhhh---cCCCCccc
Q 039881 79 NVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLS-DTFLELYR---NGNFSGES 153 (315)
Q Consensus 79 ~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls-~~~~~~~k---~g~~~~e~ 153 (315)
..+||-|+||.-+||+|+.|++|+++||.+.+++|+||..|..-+ .+-|||+ |.+|+.+. +..|.+..
T Consensus 326 ~tlGWIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~~-------tGiFrLt~~~Gm~~i~~C~~~GFHpH~ 397 (424)
T KOG2880|consen 326 LTLGWIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSKT-------TGIFRLTDPGGMEVIRGCRKKGFHPHS 397 (424)
T ss_pred eeeeeeecCCccchhheeccccccceeeeecchheeEEeccccCC-------cceEEecCCcchHHHhhcccCCCCCCC
Confidence 589999999999999999999999999999999999999997533 3459999 55777664 33377754
No 23
>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=98.00 E-value=1.9e-05 Score=73.42 Aligned_cols=66 Identities=21% Similarity=0.246 Sum_probs=58.4
Q ss_pred CcceeEEecCCCCCCCCCHHHHHHHHhhhhcCC-----CeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCC
Q 039881 78 SNVVGWYQSTPPGDCFQSVEFIETFMNYKENIG-----KCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGN 148 (315)
Q Consensus 78 ~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~-----~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~ 148 (315)
-..+||-||+|.-.||+++.||.++..||...+ ++|++++.... |.+++.||+|++.+++-.++++
T Consensus 106 Le~LGWIHTqp~e~~~Lss~Dv~tha~~~~~~~~w~~~~~V~it~Sftp-----Gs~sl~ay~LT~~G~~wg~~n~ 176 (252)
T cd08056 106 LEPLGWIHTQPNELPQLSPQDVTTHAKILADNPSWDGEKTVILTCSFTP-----GSCSLTAYKLTPEGYEWGKQNK 176 (252)
T ss_pred CEeeEEEEcCCCCccccCHHHHHHHHHHHHhccccCCCcEEEEEEcCCC-----CceEEEEEecCHHHHHHHHhCc
Confidence 358999999999999999999999999999886 78999988754 9999999999999988766544
No 24
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=97.64 E-value=0.00023 Score=58.74 Aligned_cols=94 Identities=20% Similarity=0.151 Sum_probs=60.5
Q ss_pred HhHHHHHHhhhhccCCccccCCCCCCcc----------chhhhhh--HHHHHHHHHHhcCCCCcceeEEecCCCCCCCCC
Q 039881 28 GLVLLKIIKHCKDLSPSWLRQENDIDQE----------TDDIGAN--YQLDMMSCLRDANVDSNVVGWYQSTPPGDCFQS 95 (315)
Q Consensus 28 ~lvllKIikH~~~~~~~~V~Gp~~~~~~----------~~~~~~~--Yq~~Ml~~l~~vn~d~~~VGWY~S~~~g~~f~s 95 (315)
.-++-.|++||.++.|.++.|-..+..+ ....+.. |-.+|. + .+..+||-|||||.+..++|
T Consensus 3 ~~~~~~i~~ha~~~~P~E~CGlL~G~~~~v~~~~~~~n~~~~~~~~~f~~~~~----~--~g~~ivgi~HSHP~~~~~PS 76 (117)
T cd08072 3 RDLLDSILEAAKSSHPNEFAALLRGKDGVITELLILPGTESGEVSAVFPLLML----P--LDMSIVGSVHSHPSGSPRPS 76 (117)
T ss_pred HHHHHHHHHHHhhcCCceEEEEEEeeccEEEEEEECCCCCCCCcceeechHHh----c--CCCeEEEEEEcCCCCCCCCC
Confidence 4466789999999999988881111000 0111111 112222 2 36789999999999999999
Q ss_pred HHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEec
Q 039881 96 VEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLS 137 (315)
Q Consensus 96 ~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls 137 (315)
..|+.... .++.+.||+.+-. +.=.++||+..
T Consensus 77 ~~D~~~~~-----~~~~~~lIvs~~~-----~~~~~~a~~~~ 108 (117)
T cd08072 77 DADLSFFS-----KTGLVHIIVGYPY-----DEDDWRAYDSD 108 (117)
T ss_pred HHHHHhhh-----cCCCEEEEEECcC-----CCCCEEEEecC
Confidence 99986332 2567889988543 22348899773
No 25
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.44 E-value=0.00025 Score=65.06 Aligned_cols=146 Identities=13% Similarity=0.170 Sum_probs=99.9
Q ss_pred cceEEEeHhHHHHHHhhhhcc-----CCc-cccCC----C---------------CCCccchhhhhhHHHHHHHHHHhcC
Q 039881 21 LQVVQIEGLVLLKIIKHCKDL-----SPS-WLRQE----N---------------DIDQETDDIGANYQLDMMSCLRDAN 75 (315)
Q Consensus 21 ~~~V~I~~lvllKIikH~~~~-----~~~-~V~Gp----~---------------~~~~~~~~~~~~Yq~~Ml~~l~~vn 75 (315)
--+|.+||+|+|.|-+|+.+. .|. .|.|. + +..++....+..|-..=-+..++|-
T Consensus 8 s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR~vEi~NSFeL~~d~~~~~~~~dke~l~kk~eqykqVF 87 (299)
T KOG3050|consen 8 SVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGRNVEIMNSFELKMDTEEDTETIDKEYLEKKEEQYKQVF 87 (299)
T ss_pred ceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCceEEEeeeeEEEecchhhhhhccHHHHHHHHHHHHHhc
Confidence 347899999999999999864 343 56661 1 1112233456677666677889999
Q ss_pred CCCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhcCCCCccccc
Q 039881 76 VDSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRNGNFSGESLR 155 (315)
Q Consensus 76 ~d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~g~~~~e~l~ 155 (315)
+|-.++|||.++..- +.++|+.+..--..++-++.|-..|..... ....+.-|-.--. +.
T Consensus 88 pdl~vlGwYttG~d~----t~sd~~i~k~l~~i~esplflkLNp~t~~t--~~~pv~lfese~d--------------vi 147 (299)
T KOG3050|consen 88 PDLYVLGWYTTGSDP----TPSDIHIHKQLMDINESPLFLKLNPATNHT--DKDPVTLFESEID--------------VI 147 (299)
T ss_pred ccceEEEEeecCCCC----ChhhhHHHHHHHhhhcCceEEEecchhccc--cCCCceeeeeehe--------------ee
Confidence 999999999998854 488888777666666889999999976432 2223333322100 01
Q ss_pred cccccccceeEEEeeeEeccHHHHHHHhccCCC
Q 039881 156 DKNISWADVFEEITIRVSNSALVSAFMSTLEPD 188 (315)
Q Consensus 156 ~~~l~~~~if~EIPi~I~ns~L~~~~L~~L~~~ 188 (315)
.|. ..-+|.++.-++..-..++...+.....
T Consensus 148 -dg~-~q~~f~~~tytl~teEaERIgVdHVA~l 178 (299)
T KOG3050|consen 148 -DGE-AQMLFVPLTYTLATEEAERIGVDHVARL 178 (299)
T ss_pred -cCc-ceeeeeeeEEEEeehhhhhccchhheee
Confidence 111 2457999999999999999998887654
No 26
>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=97.05 E-value=0.0087 Score=56.58 Aligned_cols=72 Identities=22% Similarity=0.298 Sum_probs=62.8
Q ss_pred CCcceeEEecCCCC----CCCCCHHHHHHHHhhhh------cCCCeEEEEeCCCCCccCCCceeeeEEEechhhHhhhhc
Q 039881 77 DSNVVGWYQSTPPG----DCFQSVEFIETFMNYKE------NIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLELYRN 146 (315)
Q Consensus 77 d~~~VGWY~S~~~g----~~f~s~~~Ietq~~yQ~------~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~~~k~ 146 (315)
.-..|||-.|++.. ++|+|+..|..-..+|. ...++|.+|+.+.. . |.+.+.||++|+.+|..+++
T Consensus 92 GL~~VG~IfT~l~~~~~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~--~--g~i~~~ayQvSdq~~~lv~~ 167 (274)
T cd08061 92 GLERVGWIFTDLPREDKDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK--D--GQIHFEAYQVSDQAMALVRD 167 (274)
T ss_pred CCeEEEEEEecCCCCCCCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC--C--CceeeeeeeecHHHHHHHHc
Confidence 35899999999966 88999999999999994 55899999999965 2 88999999999999999999
Q ss_pred CCCCcc
Q 039881 147 GNFSGE 152 (315)
Q Consensus 147 g~~~~e 152 (315)
|-+.+.
T Consensus 168 ~~i~~s 173 (274)
T cd08061 168 GLLLPT 173 (274)
T ss_pred CccccC
Confidence 877653
No 27
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=96.81 E-value=0.00072 Score=53.67 Aligned_cols=86 Identities=20% Similarity=0.210 Sum_probs=50.1
Q ss_pred hHHHHHHhhhhccCCccccC----CCCCCcc--ch--hhhhhHHHHHHHHHHhcCCCCcceeEEecCCCCCCCCCHHHHH
Q 039881 29 LVLLKIIKHCKDLSPSWLRQ----ENDIDQE--TD--DIGANYQLDMMSCLRDANVDSNVVGWYQSTPPGDCFQSVEFIE 100 (315)
Q Consensus 29 lvllKIikH~~~~~~~~V~G----p~~~~~~--~~--~~~~~Yq~~Ml~~l~~vn~d~~~VGWY~S~~~g~~f~s~~~Ie 100 (315)
.++-.|+.||.+..|.+..| ....... .. ..+..-+..+... ...+.+..+||+|||||.+..++|..|+.
T Consensus 3 ~~~~~i~~~~~~~~p~E~~G~L~g~~~~~~~~~~~~~~~~p~~~~~~~~~-~~~~~~~~~vg~~HSHP~~~a~pS~~D~~ 81 (104)
T PF14464_consen 3 EVLEQIIAHARAAYPNEACGLLLGRRDDQRFIVVPNVNPDPRDSFRRERF-EARERGLEIVGIWHSHPSGPAFPSSTDIR 81 (104)
T ss_dssp HHHHHHHHHHHHHTTS-EEEEEEEEEECCEEEEEEEEE--HHCHHHHHH--HHHHHT-EEEEEEEEESSSSSS--HHHHH
T ss_pred HHHHHHHHHHhhCCCCeEEEEEEEEecCCEEEEEeCCCCCcHHHHHHHhh-hhhcccceeeEEEEcCCCCCCCCCHHHHH
Confidence 46778999999999988888 1111000 00 0111111111110 34456779999999999999999999998
Q ss_pred HHHhhhhcCCCeEEEEeCC
Q 039881 101 TFMNYKENIGKCVCIICDP 119 (315)
Q Consensus 101 tq~~yQ~~~~~~V~LV~Dp 119 (315)
+....- ..+.||+-.
T Consensus 82 ~~~~~~----~~~~iI~~~ 96 (104)
T PF14464_consen 82 SMRDLA----PPSYIIVGN 96 (104)
T ss_dssp THCCS-----SCEEEEEEE
T ss_pred hhhccC----CeEEEEEeC
Confidence 766433 566666654
No 28
>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=96.48 E-value=0.014 Score=47.50 Aligned_cols=77 Identities=17% Similarity=0.074 Sum_probs=48.8
Q ss_pred HHHHHhhhhccCCccccCCC-------------CCCccchhhhhhHH---HHHHHHHHhcCCCCcceeEEecCCCCCCCC
Q 039881 31 LLKIIKHCKDLSPSWLRQEN-------------DIDQETDDIGANYQ---LDMMSCLRDANVDSNVVGWYQSTPPGDCFQ 94 (315)
Q Consensus 31 llKIikH~~~~~~~~V~Gp~-------------~~~~~~~~~~~~Yq---~~Ml~~l~~vn~d~~~VGWY~S~~~g~~f~ 94 (315)
+=.|+.|+++..|.+.-|-. +..++. ...|. .++++..+ ...+||-|||||.+.+.+
T Consensus 3 ~~~i~~ha~~~~P~E~CGll~g~~~~~~~~p~~N~~~~p---~~~F~idp~e~~~a~~----~~~ivgi~HSHP~~~a~P 75 (108)
T cd08073 3 EDAILAHAKAEYPREACGLVVRKGRKLRYIPCRNIAADP---EEHFEISPEDYAAAED----EGEIVAVVHSHPDGSPAP 75 (108)
T ss_pred HHHHHHHHhHCCCCcceEEEEecCCceEEEECccCCCCc---cceEEeCHHHHHHHhc----CCCEEEEEEcCCCCCCCC
Confidence 44799999999998888811 001110 01121 22333332 227999999999999999
Q ss_pred CHHHHHHHHhhhhcCCCeEEEEeCC
Q 039881 95 SVEFIETFMNYKENIGKCVCIICDP 119 (315)
Q Consensus 95 s~~~Ietq~~yQ~~~~~~V~LV~Dp 119 (315)
|..|+.-+. .++.+.||+..
T Consensus 76 S~~D~~~~~-----~~~~~~iIvs~ 95 (108)
T cd08073 76 SEADRAQQE-----ATGLPWIIVSW 95 (108)
T ss_pred CHHHHHHhh-----cCCCcEEEEEc
Confidence 999985322 24667788775
No 29
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=95.78 E-value=0.067 Score=42.41 Aligned_cols=77 Identities=22% Similarity=0.268 Sum_probs=47.7
Q ss_pred HHHHHHhhhhccCCccccCCCCCC--ccc----------hhhhhhHHHHHHHHHHhcCCCCcceeEEecCCCCCCCCCHH
Q 039881 30 VLLKIIKHCKDLSPSWLRQENDID--QET----------DDIGANYQLDMMSCLRDANVDSNVVGWYQSTPPGDCFQSVE 97 (315)
Q Consensus 30 vllKIikH~~~~~~~~V~Gp~~~~--~~~----------~~~~~~Yq~~Ml~~l~~vn~d~~~VGWY~S~~~g~~f~s~~ 97 (315)
++-.|+.|+....|.+..|-.-++ ... ...+..+ ++ ........+||-|||||.|.+.+|..
T Consensus 2 ~~~~i~~~~~~~~p~E~~gll~~~~~~~~~~~~~~~~~~~~~~~~~----~~--~a~~~~~~~v~i~HsHP~g~~~PS~~ 75 (101)
T cd08059 2 LLKTILVHAKDAHPDEFCGFLSGSKDNVMDELIFLPFVSGSVSAVI----DL--AALEIGMKVVGLVHSHPSGSCRPSEA 75 (101)
T ss_pred HHHHHHHHHHhcCChhhheeeecCCCCeEEEEEeCCCcCCccChHH----HH--HHhhCCCcEEEEEecCcCCCCCCCHH
Confidence 445688999998898888721100 000 0001111 22 23344567999999999999999999
Q ss_pred HHHHHHhhhhcCCCeEEEEe
Q 039881 98 FIETFMNYKENIGKCVCIIC 117 (315)
Q Consensus 98 ~Ietq~~yQ~~~~~~V~LV~ 117 (315)
|+...... ...++|+
T Consensus 76 D~~~~~~~-----~~~~iIv 90 (101)
T cd08059 76 DLSLFTRF-----GLYHVIV 90 (101)
T ss_pred HHHHHHhc-----CCeEEEE
Confidence 99744321 4566666
No 30
>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=95.66 E-value=0.15 Score=45.39 Aligned_cols=95 Identities=14% Similarity=0.138 Sum_probs=52.6
Q ss_pred EeHhHHHHHHhhhhccCCccccC----CCC-CCcc-c-hhh---hhhHH---------HHHHHHHHhcCCCCcceeEEec
Q 039881 26 IEGLVLLKIIKHCKDLSPSWLRQ----END-IDQE-T-DDI---GANYQ---------LDMMSCLRDANVDSNVVGWYQS 86 (315)
Q Consensus 26 I~~lvllKIikH~~~~~~~~V~G----p~~-~~~~-~-~~~---~~~Yq---------~~Ml~~l~~vn~d~~~VGWY~S 86 (315)
|+..++.||+.||....|.+|.| ... ++.. + +.. ...|. ...-+..++ .+-.+||+|||
T Consensus 1 is~~ay~ki~~HA~k~p~~evcGlLlG~~~~~~~~~V~d~vPl~h~~~~l~P~~Eval~~ve~~~~~--~gl~IvG~Yhs 78 (182)
T cd08060 1 LSTLAYVKMLLHAAKYPHCAVNGLLLGKKSSGGSVEITDAVPLFHSCLALAPMLEVALALVDAYCKS--SGLVIVGYYQA 78 (182)
T ss_pred CCHHHHHHHHHHHHHcCCchheEEEEeeecCCCCEEEEEEEEcCCCccccCHHHHHHHHHHHHHHHH--CCCEEEEEEec
Confidence 46788999999999977778888 222 1111 1 110 11111 111222233 35689999999
Q ss_pred CCCCCC-CCCHHHHHHHHhhhhcCCCeEEEEeCCCCC
Q 039881 87 TPPGDC-FQSVEFIETFMNYKENIGKCVCIICDPSRS 122 (315)
Q Consensus 87 ~~~g~~-f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s 122 (315)
||.... -++..--..--.-+...++++.+++|-.+.
T Consensus 79 h~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l 115 (182)
T cd08060 79 NERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKL 115 (182)
T ss_pred CCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccc
Confidence 997531 122111111111233446899999998775
No 31
>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=94.18 E-value=0.31 Score=46.89 Aligned_cols=71 Identities=20% Similarity=0.224 Sum_probs=59.1
Q ss_pred CCcceeEEecCCC---------------CCCCCCHHHHHHHHhhhhcC-------------CCeEEEEeCCCCCccCCCc
Q 039881 77 DSNVVGWYQSTPP---------------GDCFQSVEFIETFMNYKENI-------------GKCVCIICDPSRSNIQGGL 128 (315)
Q Consensus 77 d~~~VGWY~S~~~---------------g~~f~s~~~Ietq~~yQ~~~-------------~~~V~LV~Dp~~s~~~~g~ 128 (315)
+-..|||-=|+.. .+.|+|+.-|-.-..+|... .++|.+|+.+.. . |.
T Consensus 57 GL~rVG~IfTdl~~~~~~~g~v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~~--~--g~ 132 (306)
T PF05021_consen 57 GLERVGWIFTDLTDDGSGDGTVKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGDE--E--GE 132 (306)
T ss_pred CCEEEEEEEecCcccccCCCceeeccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCCC--C--Cc
Confidence 4579999888876 66799999999999998632 478999998843 3 99
Q ss_pred eeeeEEEechhhHhhhhcCCCCc
Q 039881 129 AGLKALKLSDTFLELYRNGNFSG 151 (315)
Q Consensus 129 lslkAfRls~~~~~~~k~g~~~~ 151 (315)
+.+.||.+|+..|..+++|-+.+
T Consensus 133 i~~~ayQvS~q~~~Lv~~~~l~~ 155 (306)
T PF05021_consen 133 IHFEAYQVSNQCVALVRAGILEP 155 (306)
T ss_pred eeeEEeeehHHHHHHHHCCcccc
Confidence 99999999999999999886654
No 32
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=93.36 E-value=1.3 Score=39.83 Aligned_cols=101 Identities=16% Similarity=0.167 Sum_probs=57.3
Q ss_pred ceEEEeHhHHHHHHhhhhccCCccccC----CCCCCcc-c---hhh-----------hhhHHHHHHHHHHhcCCCCccee
Q 039881 22 QVVQIEGLVLLKIIKHCKDLSPSWLRQ----ENDIDQE-T---DDI-----------GANYQLDMMSCLRDANVDSNVVG 82 (315)
Q Consensus 22 ~~V~I~~lvllKIikH~~~~~~~~V~G----p~~~~~~-~---~~~-----------~~~Yq~~Ml~~l~~vn~d~~~VG 82 (315)
.+|.|+..|..||+-||.......|.| ....++. + +++ -.+--..+++..-+ ..+..+||
T Consensus 2 ~~v~is~~AY~K~~LHaaKyP~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L~PmlEvAL~qvd~~~~-~~gl~IvG 80 (196)
T PF03665_consen 2 SSVEISSRAYAKMILHAAKYPHCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSLSPMLEVALAQVDAYAK-SNGLVIVG 80 (196)
T ss_pred ceEEEcHHHHHHHHHHhccCCCCceeeEEEeccCCCCceEEEeeceeccccccCcchHHHHHHHHHHHHHh-hCCCEEEE
Confidence 368999999999999999866567887 2222221 1 111 01111222333222 24578999
Q ss_pred EEecCCCCC-CCCCHHHHHHHHhhhhcCCCeEEEEeCCCCCc
Q 039881 83 WYQSTPPGD-CFQSVEFIETFMNYKENIGKCVCIICDPSRSN 123 (315)
Q Consensus 83 WY~S~~~g~-~f~s~~~Ietq~~yQ~~~~~~V~LV~Dp~~s~ 123 (315)
|||...... .-++..-...--.-....+.++.|++|-.+-.
T Consensus 81 yY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~ 122 (196)
T PF03665_consen 81 YYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLS 122 (196)
T ss_pred EEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccc
Confidence 999977321 12333221111112234578999999987744
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=92.98 E-value=0.073 Score=47.79 Aligned_cols=72 Identities=14% Similarity=0.090 Sum_probs=51.0
Q ss_pred EEeHhHHHHHHhhhhccCCccccC----CCCCC---------ccchhhhhhHHHHHHHHHHhcCCCCcceeEEecCCCCC
Q 039881 25 QIEGLVLLKIIKHCKDLSPSWLRQ----ENDID---------QETDDIGANYQLDMMSCLRDANVDSNVVGWYQSTPPGD 91 (315)
Q Consensus 25 ~I~~lvllKIikH~~~~~~~~V~G----p~~~~---------~~~~~~~~~Yq~~Ml~~l~~vn~d~~~VGWY~S~~~g~ 91 (315)
+|....+=+|+.||++..|.++.| +.++. -+....--.|...|+ ..++..|+-||||+...
T Consensus 74 ~Ip~~l~~~ii~hAr~~~P~EacG~Iag~~~~~~~r~~p~~N~~~Sp~~~~~d~~~~------~~ge~lV~iyHSH~~sp 147 (192)
T TIGR03735 74 PIPASLLEEFAEAARAALPNEVAAWIVWNSETGSLRLAALESIEASPGHIDYRRPRL------DDGEHLVVDLHSHGTGS 147 (192)
T ss_pred CCCHHHHHHHHHHHHhcCCcceEEEEEEcCCCCEEEEEeccccccCCceEEEcchHH------hCCCeEEEEEcCCCCCC
Confidence 788889999999999999998887 31110 001111122323333 68889999999999998
Q ss_pred CCCCHHHHHHH
Q 039881 92 CFQSVEFIETF 102 (315)
Q Consensus 92 ~f~s~~~Ietq 102 (315)
.|+|.+|+..-
T Consensus 148 A~PS~tD~~Dd 158 (192)
T TIGR03735 148 AFFSETDDADD 158 (192)
T ss_pred CCCCcccchhh
Confidence 89999998643
No 34
>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=87.71 E-value=3.9 Score=34.57 Aligned_cols=56 Identities=9% Similarity=0.019 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhcCCCCcceeEEecCCCCCCCCCHHHHHHHHhhhhcCCCeEEEEeC
Q 039881 63 YQLDMMSCLRDANVDSNVVGWYQSTPPGDCFQSVEFIETFMNYKENIGKCVCIICD 118 (315)
Q Consensus 63 Yq~~Ml~~l~~vn~d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~~~~V~LV~D 118 (315)
.|...-+..++-+-....||=+||||.+..-+|..|+.+....=......++||+=
T Consensus 58 ~q~~i~~~~~~s~g~~~ylGeWHtHP~~~p~PS~~D~~~~~~~~~~~~~~l~iIvG 113 (131)
T TIGR02256 58 HQSEVDEHFEVSGGVDTYLGEWHTHPEDQPEPSWTDRRSWRTIIRSPEAMLLLIVG 113 (131)
T ss_pred HHHHHHHHHHHhCCceEEEEecCcCCCCCCCCCHHHHHHHHHHHhCCCeeEEEEEc
Confidence 34445555566666688999999999987678999988877655544555555553
No 35
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]
Probab=72.60 E-value=20 Score=31.99 Aligned_cols=99 Identities=16% Similarity=0.213 Sum_probs=56.1
Q ss_pred eEEEeHhHHHHHHhhhhccCCccccC----CCCCCcc-chhhh--hhHH-----HHHHHH---HH---hcCCCCcceeEE
Q 039881 23 VVQIEGLVLLKIIKHCKDLSPSWLRQ----ENDIDQE-TDDIG--ANYQ-----LDMMSC---LR---DANVDSNVVGWY 84 (315)
Q Consensus 23 ~V~I~~lvllKIikH~~~~~~~~V~G----p~~~~~~-~~~~~--~~Yq-----~~Ml~~---l~---~vn~d~~~VGWY 84 (315)
.|+|+.++..|||-||.+-.-.-|.| |.++.++ +...+ .-|+ .-|++. |- -+...-.++|+|
T Consensus 3 ~veis~~aY~kmiLH~akyph~aVnGLLla~~~~kg~~v~itdcVPLfH~~laLaPmlEvAl~lId~~~~~~GlviaGyy 82 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYPHAAVNGLLLAPATGKGECVEITDCVPLFHSHLALAPMLEVALNLIDVWGAQAGLVIAGYY 82 (199)
T ss_pred ceeehhhHHHHHHHHhccCcccceeeEEEeccCCCCCeEEEEecchhhccccccccHHHHHHHHHHHHHHhcCeEEEEEe
Confidence 58999999999999999854445555 6555444 22111 1111 223321 11 124556899999
Q ss_pred ecCCCCCCCCCHHHHHHHH--hhhhcCCCeEEEEeCCCCC
Q 039881 85 QSTPPGDCFQSVEFIETFM--NYKENIGKCVCIICDPSRS 122 (315)
Q Consensus 85 ~S~~~g~~f~s~~~Ietq~--~yQ~~~~~~V~LV~Dp~~s 122 (315)
|+.--.+ -.+..-+..-. ..+..-+.+..|++|-.+-
T Consensus 83 ~Ane~~~-D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l 121 (199)
T KOG3289|consen 83 HANERVN-DQSLNPVALKIADRISEFFPDAAILVLDNKKL 121 (199)
T ss_pred ecCCCcc-ccCccHHHHHHHHHHHhhCCCCeEEEEecccc
Confidence 9987543 23322222221 2344557788888887553
No 36
>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=60.51 E-value=9.6 Score=32.01 Aligned_cols=22 Identities=32% Similarity=0.300 Sum_probs=17.8
Q ss_pred CceeeeEEEechhhHhhhhcCC
Q 039881 127 GLAGLKALKLSDTFLELYRNGN 148 (315)
Q Consensus 127 g~lslkAfRls~~~~~~~k~g~ 148 (315)
|.++|.||.|+|++.+=.++++
T Consensus 11 GSvsL~Ay~LT~~G~eWg~~nk 32 (125)
T PF08084_consen 11 GSVSLSAYKLTPEGYEWGRQNK 32 (125)
T ss_dssp TEEEEEEEEE-HHHHHHHHCTT
T ss_pred CceEEEEEecCHHHHHHHhhcc
Confidence 9999999999999887666543
No 37
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=52.70 E-value=17 Score=41.29 Aligned_cols=62 Identities=27% Similarity=0.386 Sum_probs=48.0
Q ss_pred CCCcceeEEecCCCCCCCCCHHHHHHHHhhh-hcCCCeEEEEeCCCCCccCCCceeeeEEEechhhHh
Q 039881 76 VDSNVVGWYQSTPPGDCFQSVEFIETFMNYK-ENIGKCVCIICDPSRSNIQGGLAGLKALKLSDTFLE 142 (315)
Q Consensus 76 ~d~~~VGWY~S~~~g~~f~s~~~Ietq~~yQ-~~~~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~ 142 (315)
.|-..+||-|+-+.---++++.+|-+..--- ....+||.|.+.-.. |.+++.||.++|.+.+
T Consensus 2163 ~d~e~Lgw~hTq~~el~~lsp~dV~th~ki~~~~k~k~i~~t~~~tp-----gs~sl~ay~lt~~G~e 2225 (2321)
T KOG1795|consen 2163 EDLEPLGWIHTQPNELPQLSPQDVTTHAKILVDNKEKCIIITCSFTP-----GSCSLTAYKLTPSGYE 2225 (2321)
T ss_pred cCCcccchhhcCccccccCCHHHhhhhhhhhhcCccceEEEEeeccC-----CcceeeeeccCccccc
Confidence 4556799999999765599999998877643 333678888776433 9999999999998764
No 38
>cd00225 API3 Ascaris pepsin inhibitor-3 (API3); protein inhibitor that reversibly inhibits aspartic proteinase cathepsin E, and gastric enzymes pepsin and gastricsin.
Probab=43.44 E-value=97 Score=26.88 Aligned_cols=11 Identities=27% Similarity=0.298 Sum_probs=8.1
Q ss_pred CCCCCCCCCCc
Q 039881 267 NPFFKPIPEPS 277 (315)
Q Consensus 267 ~~~fk~~~~Ps 277 (315)
..+-|+|..||
T Consensus 81 ~~~Pk~PkkPs 91 (159)
T cd00225 81 EKLPKAPKKPS 91 (159)
T ss_pred ccCCCCCCCCC
Confidence 44668888887
No 39
>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=35.89 E-value=18 Score=26.90 Aligned_cols=10 Identities=50% Similarity=1.099 Sum_probs=6.4
Q ss_pred cceeEEecCC
Q 039881 79 NVVGWYQSTP 88 (315)
Q Consensus 79 ~~VGWY~S~~ 88 (315)
.+||||.+.-
T Consensus 41 ~vvgwy~t~l 50 (78)
T PF06442_consen 41 QVVGWYCTKL 50 (78)
T ss_dssp EEEEEE--SS
T ss_pred eEeEEEeccc
Confidence 6999998743
No 40
>KOG4538 consensus Predicted coiled-coil protein [General function prediction only]
Probab=33.09 E-value=2.1e+02 Score=23.66 Aligned_cols=29 Identities=28% Similarity=0.335 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHH----HHHHHHHHHHHHHHHcC
Q 039881 228 LKFYFKDVTRQQ----AWVQERRDENEARKAAG 256 (315)
Q Consensus 228 ~~~yqr~l~r~q----~~~~kr~~EN~~R~~~g 256 (315)
...+++.+.-.+ |-...|+.||+.|+..+
T Consensus 60 vK~~~~~i~ek~~~~rqeKkqRrvEn~kRRLeN 92 (130)
T KOG4538|consen 60 VKRVQDNIREKQVQERQEKKQRRVENEKRRLEN 92 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 334445554333 55667888888887765
No 41
>PF09454 Vps23_core: Vps23 core domain; InterPro: IPR017916 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ]. This entry represents the Steadiness box domain.; PDB: 2CAZ_A 2F66_D 2F6M_A 2P22_A.
Probab=29.45 E-value=1.2e+02 Score=22.30 Aligned_cols=35 Identities=17% Similarity=0.268 Sum_probs=27.5
Q ss_pred hHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 039881 205 PLLESNVEFLIRCMDDLSTEQKKLKFYFKDVTRQQ 239 (315)
Q Consensus 205 ~~Lek~l~~L~e~id~l~~e~~~~~~yqr~l~r~q 239 (315)
..++..+..|-+.+..=.-....|-..-|.|+|||
T Consensus 22 ~AieDtiy~L~~al~~g~I~~d~~lK~vR~LaReQ 56 (65)
T PF09454_consen 22 HAIEDTIYYLDRALQRGSIDLDTFLKQVRSLAREQ 56 (65)
T ss_dssp HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 45777777777777776677778999999999997
No 42
>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=28.80 E-value=59 Score=34.95 Aligned_cols=54 Identities=17% Similarity=0.119 Sum_probs=37.2
Q ss_pred ccceeEEEe-eeEeccHHHHHHHhccCCCCCCCCCCCCcccCCCchHHHHHHHHHH
Q 039881 161 WADVFEEIT-IRVSNSALVSAFMSTLEPDRVTDQSDHDRLQISSKPLLESNVEFLI 215 (315)
Q Consensus 161 ~~~if~EIP-i~I~ns~L~~~~L~~L~~~~~~~~~~~d~L~Ls~~~~Lek~l~~L~ 215 (315)
|.+-+++.| =+|....|.++.|.-+.--... --+||.|+-.....|-+.|++|.
T Consensus 608 Y~~eLE~~t~PEIqRtnL~nvVL~LkSLGI~D-l~~FdFmDpPp~etL~~aLE~Ly 662 (902)
T KOG0923|consen 608 YEHELEEMTVPEIQRTNLGNVVLLLKSLGIHD-LIHFDFLDPPPTETLLKALEQLY 662 (902)
T ss_pred hhhhhccCCCcceeeccchhHHHHHHhcCcch-hcccccCCCCChHHHHHHHHHHH
Confidence 566677777 4788888999887766422111 23578887666677888888875
No 43
>PF14198 TnpV: Transposon-encoded protein TnpV
Probab=28.63 E-value=69 Score=26.19 Aligned_cols=33 Identities=24% Similarity=0.452 Sum_probs=28.8
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 039881 275 EPSRLESLLITNRIADYCNQIHRVAGHSFSRLS 307 (315)
Q Consensus 275 ~Psrl~~ll~s~qi~~~~~~i~~~~~~~~~kl~ 307 (315)
-|.+...||.+|.+..||.+|+.-|-+-+-.+.
T Consensus 38 ~p~~Y~~ll~~g~L~~~l~eid~~A~e~~e~l~ 70 (111)
T PF14198_consen 38 KPILYNNLLLSGKLNEHLAEIDEQAQERFERLV 70 (111)
T ss_pred HHHHHHHHHHcchHHHHHHHHHHHHHHHHHHHH
Confidence 477899999999999999999999988776653
No 44
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=23.59 E-value=1.2e+02 Score=29.02 Aligned_cols=63 Identities=24% Similarity=0.266 Sum_probs=34.4
Q ss_pred HhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHcCCCCCCCCCCCCC---CCCCCCCCcchHHHHHHH
Q 039881 220 DLSTEQKKLKFYFKDVTRQQ-AWVQERRDENEARKAAGEDPLPEGDSSNP---FFKPIPEPSRLESLLITN 286 (315)
Q Consensus 220 ~l~~e~~~~~~yqr~l~r~q-~~~~kr~~EN~~R~~~g~~~lpe~d~~~~---~fk~~~~Psrl~~ll~s~ 286 (315)
.|+.-|.|..|..|. +||+ +-+.||. .+-.+.++++++.++.... +--.+.+-+||-++|.+.
T Consensus 237 gLsERQVKIWFQNRR-AKERK~nKKk~~---~q~q~~~~p~~~~s~s~~p~~p~~~~~~P~~~~ts~~A~~ 303 (317)
T KOG0848|consen 237 GLSERQVKIWFQNRR-AKERKDNKKKRL---QQQQQPPQPPLHLSHSLAPMGPMAAMNIPAMRLTSLLAAH 303 (317)
T ss_pred CccHhhhhHhhhhhh-HHHHHHHHHHHH---HHhhcCCCCCCCCccccCCCCccccccCccccccchhhhc
Confidence 455667777766665 4555 3333331 2334457888887764333 222233456677766543
No 45
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=21.10 E-value=1.1e+02 Score=34.96 Aligned_cols=59 Identities=14% Similarity=0.121 Sum_probs=39.5
Q ss_pred cceeEEecCCCCCCCCCHHHHHHHHhhhhcC-CCeEEEEeCCCCCccCCCceeeeEEEechhhHh
Q 039881 79 NVVGWYQSTPPGDCFQSVEFIETFMNYKENI-GKCVCIICDPSRSNIQGGLAGLKALKLSDTFLE 142 (315)
Q Consensus 79 ~~VGWY~S~~~g~~f~s~~~Ietq~~yQ~~~-~~~V~LV~Dp~~s~~~~g~lslkAfRls~~~~~ 142 (315)
.++||-|+...---|+..+.+-|..--=... -.||-|.+.... |.++++||.++.++.+
T Consensus 2206 e~lGwihtq~~el~~l~~~~v~th~k~~~d~~~d~v~ltv~~~p-----gsiSl~ay~v~keG~~ 2265 (2365)
T COG5178 2206 EILGWIHTQDDELPYLEVAGVLTHRKKIVDPEWDAVTLTVSYLP-----GSISLRAYVVKKEGCN 2265 (2365)
T ss_pred eeeEEEecCCcccchhhhhhhhhhhhcccCccccceeeeeeecc-----ceeeeeeeeehhcccc
Confidence 4999999998754577777776654321111 135555554432 9999999999887653
Done!